[Met_help] [rt.rap.ucar.edu #88502] History for met install help
Julie Prestopnik via RT
met_help at ucar.edu
Thu Feb 21 13:46:15 MST 2019
----------------------------------------------------------------
Initial Request
----------------------------------------------------------------
Hey all,
I'm presently trying to compile MET 8.0 on our HPC; when I configure it,
I'm getting a few warnings on .h files:
configure: WARNING: errno.h: present but cannot be compiled
configure: WARNING: errno.h: check for missing prerequisite headers?
configure: WARNING: errno.h: see the Autoconf documentation
configure: WARNING: errno.h: section "Present But Cannot Be Compiled"
configure: WARNING: errno.h: proceeding with the compiler's result
configure: WARNING: ## -------------------------------- ##
configure: WARNING: ## Report this to met_help at ucar.edu ##
configure: WARNING: ## -------------------------------- ##
and the same for fcntl.h, limits.h, stddef.h, file.h and param.h.
When I try to make install, I get this error on the tail of the log:
config_scanner.cc: In function ‘void* configalloc(yy_size_t)’:
config_scanner.cc:2179:31: error: ‘rpl_malloc’ was not declared in this
scope
config_scanner.cc: In function ‘void* configrealloc(void*, yy_size_t)’:
config_scanner.cc:2191:46: error: ‘rpl_realloc’ was not declared in this
scope
/* The cast to (char *) in the following accommodates both
^
make[3]: *** [libvx_config_a-config_scanner.o] Error 1
make[3]: Leaving directory
`/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/E1/taylorm/MET8/met-8.0_bugfix/src'
make: *** [install-recursive] Error 1
Not sure how to address either of these, hopefully you guys can provide
some insight.
Thanks!
--
*Taylor Mandelbaum*
Research Technician
SoMAS | Stony Brook University
678.468.5789
----------------------------------------------------------------
Complete Ticket History
----------------------------------------------------------------
Subject: met install help
From: Julie Prestopnik
Time: Mon Jan 14 15:13:30 2019
Hi Taylor. It is difficult to tell what is going without more
context.
Could you please send me your config.log file and your make.log file?
We could also consider doing a hangouts session where you can share
your
screen, and I can directly help that way. Either way though, if you
could
please send those files, I would appreciate it.
Thanks,
Julie
Thanks!
Julie
On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum via RT
<met_help at ucar.edu>
wrote:
>
> Mon Jan 14 15:05:33 2019: Request 88502 was acted upon.
> Transaction: Ticket created by taylor.mandelbaum at stonybrook.edu
> Queue: met_help
> Subject: met install help
> Owner: Nobody
> Requestors: taylor.mandelbaum at stonybrook.edu
> Status: new
> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
>
> Hey all,
>
> I'm presently trying to compile MET 8.0 on our HPC; when I configure
it,
> I'm getting a few warnings on .h files:
>
> configure: WARNING: errno.h: present but cannot be compiled
> configure: WARNING: errno.h: check for missing prerequisite
headers?
> configure: WARNING: errno.h: see the Autoconf documentation
> configure: WARNING: errno.h: section "Present But Cannot Be
Compiled"
> configure: WARNING: errno.h: proceeding with the compiler's result
> configure: WARNING: ## -------------------------------- ##
> configure: WARNING: ## Report this to met_help at ucar.edu ##
> configure: WARNING: ## -------------------------------- ##
>
> and the same for fcntl.h, limits.h, stddef.h, file.h and param.h.
>
> When I try to make install, I get this error on the tail of the log:
>
> config_scanner.cc: In function ‘void* configalloc(yy_size_t)’:
> config_scanner.cc:2179:31: error: ‘rpl_malloc’ was not declared in
this
> scope
> config_scanner.cc: In function ‘void* configrealloc(void*,
yy_size_t)’:
> config_scanner.cc:2191:46: error: ‘rpl_realloc’ was not declared in
this
> scope
> /* The cast to (char *) in the following accommodates both
> ^
> make[3]: *** [libvx_config_a-config_scanner.o] Error 1
> make[3]: Leaving directory
> `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> make[2]: *** [install-recursive] Error 1
> make[2]: Leaving directory `/E1/taylorm/MET8/met-
8.0_bugfix/src/basic'
> make[1]: *** [install-recursive] Error 1
> make[1]: Leaving directory `/E1/taylorm/MET8/met-8.0_bugfix/src'
> make: *** [install-recursive] Error 1
>
> Not sure how to address either of these, hopefully you guys can
provide
> some insight.
>
> Thanks!
> --
> *Taylor Mandelbaum*
> Research Technician
> SoMAS | Stony Brook University
> 678.468.5789
>
>
------------------------------------------------
Subject: met install help
From: Taylor Mandelbaum
Time: Mon Jan 14 16:41:20 2019
Hey Julie,
I attached the config and make_install logs here. We could do a
hangouts
session as well if you can't pinpoint the issue; I'm remoting in from
my
home windows computer so it will be a bit hacky.
On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via RT
<met_help at ucar.edu>
wrote:
> Hi Taylor. It is difficult to tell what is going without more
context.
> Could you please send me your config.log file and your make.log
file?
>
> We could also consider doing a hangouts session where you can share
your
> screen, and I can directly help that way. Either way though, if you
could
> please send those files, I would appreciate it.
>
> Thanks,
> Julie
>
> Thanks!
>
> Julie
>
> On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum via RT <
> met_help at ucar.edu>
> wrote:
>
> >
> > Mon Jan 14 15:05:33 2019: Request 88502 was acted upon.
> > Transaction: Ticket created by taylor.mandelbaum at stonybrook.edu
> > Queue: met_help
> > Subject: met install help
> > Owner: Nobody
> > Requestors: taylor.mandelbaum at stonybrook.edu
> > Status: new
> > Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> >
> >
> > Hey all,
> >
> > I'm presently trying to compile MET 8.0 on our HPC; when I
configure it,
> > I'm getting a few warnings on .h files:
> >
> > configure: WARNING: errno.h: present but cannot be compiled
> > configure: WARNING: errno.h: check for missing prerequisite
headers?
> > configure: WARNING: errno.h: see the Autoconf documentation
> > configure: WARNING: errno.h: section "Present But Cannot Be
Compiled"
> > configure: WARNING: errno.h: proceeding with the compiler's result
> > configure: WARNING: ## -------------------------------- ##
> > configure: WARNING: ## Report this to met_help at ucar.edu ##
> > configure: WARNING: ## -------------------------------- ##
> >
> > and the same for fcntl.h, limits.h, stddef.h, file.h and param.h.
> >
> > When I try to make install, I get this error on the tail of the
log:
> >
> > config_scanner.cc: In function ‘void* configalloc(yy_size_t)’:
> > config_scanner.cc:2179:31: error: ‘rpl_malloc’ was not declared in
this
> > scope
> > config_scanner.cc: In function ‘void* configrealloc(void*,
yy_size_t)’:
> > config_scanner.cc:2191:46: error: ‘rpl_realloc’ was not declared
in this
> > scope
> > /* The cast to (char *) in the following accommodates both
> > ^
> > make[3]: *** [libvx_config_a-config_scanner.o] Error 1
> > make[3]: Leaving directory
> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > make[2]: *** [install-recursive] Error 1
> > make[2]: Leaving directory `/E1/taylorm/MET8/met-
8.0_bugfix/src/basic'
> > make[1]: *** [install-recursive] Error 1
> > make[1]: Leaving directory `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > make: *** [install-recursive] Error 1
> >
> > Not sure how to address either of these, hopefully you guys can
provide
> > some insight.
> >
> > Thanks!
> > --
> > *Taylor Mandelbaum*
> > Research Technician
> > SoMAS | Stony Brook University
> > 678.468.5789
> >
> >
>
>
--
*Taylor Mandelbaum*
Research Technician
SoMAS | Stony Brook University
678.468.5789
------------------------------------------------
Subject: met install help
From: Julie Prestopnik
Time: Tue Jan 15 09:35:02 2019
Hi Taylor. Thank you for passing along your files. I have a few
questions
for you.
1) Are you installing the external libraries yourself or were they
previously installed?
2) Can you please verify that the external libraries and MET are being
built with the same family of compilers (e.g. all are built with GNU,
or
all are build with Intel, etc.)? Which compiler are you using?
3) Are you following the directions on this page as your instructions
for
installation?
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
Thank you!
Julie
On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> Hey Julie,
>
> I attached the config and make_install logs here. We could do a
hangouts
> session as well if you can't pinpoint the issue; I'm remoting in
from my
> home windows computer so it will be a bit hacky.
>
> On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via RT
<met_help at ucar.edu
> >
> wrote:
>
> > Hi Taylor. It is difficult to tell what is going without more
context.
> > Could you please send me your config.log file and your make.log
file?
> >
> > We could also consider doing a hangouts session where you can
share your
> > screen, and I can directly help that way. Either way though, if
you
> could
> > please send those files, I would appreciate it.
> >
> > Thanks,
> > Julie
> >
> > Thanks!
> >
> > Julie
> >
> > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum via RT <
> > met_help at ucar.edu>
> > wrote:
> >
> > >
> > > Mon Jan 14 15:05:33 2019: Request 88502 was acted upon.
> > > Transaction: Ticket created by taylor.mandelbaum at stonybrook.edu
> > > Queue: met_help
> > > Subject: met install help
> > > Owner: Nobody
> > > Requestors: taylor.mandelbaum at stonybrook.edu
> > > Status: new
> > > Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> >
> > >
> > >
> > > Hey all,
> > >
> > > I'm presently trying to compile MET 8.0 on our HPC; when I
configure
> it,
> > > I'm getting a few warnings on .h files:
> > >
> > > configure: WARNING: errno.h: present but cannot be compiled
> > > configure: WARNING: errno.h: check for missing prerequisite
> headers?
> > > configure: WARNING: errno.h: see the Autoconf documentation
> > > configure: WARNING: errno.h: section "Present But Cannot Be
> Compiled"
> > > configure: WARNING: errno.h: proceeding with the compiler's
result
> > > configure: WARNING: ## -------------------------------- ##
> > > configure: WARNING: ## Report this to met_help at ucar.edu ##
> > > configure: WARNING: ## -------------------------------- ##
> > >
> > > and the same for fcntl.h, limits.h, stddef.h, file.h and
param.h.
> > >
> > > When I try to make install, I get this error on the tail of the
log:
> > >
> > > config_scanner.cc: In function ‘void* configalloc(yy_size_t)’:
> > > config_scanner.cc:2179:31: error: ‘rpl_malloc’ was not declared
in this
> > > scope
> > > config_scanner.cc: In function ‘void* configrealloc(void*,
yy_size_t)’:
> > > config_scanner.cc:2191:46: error: ‘rpl_realloc’ was not declared
in
> this
> > > scope
> > > /* The cast to (char *) in the following accommodates both
> > > ^
> > > make[3]: *** [libvx_config_a-config_scanner.o] Error 1
> > > make[3]: Leaving directory
> > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > make[2]: *** [install-recursive] Error 1
> > > make[2]: Leaving directory `/E1/taylorm/MET8/met-
8.0_bugfix/src/basic'
> > > make[1]: *** [install-recursive] Error 1
> > > make[1]: Leaving directory `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > make: *** [install-recursive] Error 1
> > >
> > > Not sure how to address either of these, hopefully you guys can
provide
> > > some insight.
> > >
> > > Thanks!
> > > --
> > > *Taylor Mandelbaum*
> > > Research Technician
> > > SoMAS | Stony Brook University
> > > 678.468.5789
> > >
> > >
> >
> >
>
> --
> *Taylor Mandelbaum*
> Research Technician
> SoMAS | Stony Brook University
> 678.468.5789
>
>
------------------------------------------------
Subject: met install help
From: Taylor Mandelbaum
Time: Tue Jan 15 17:53:50 2019
Hey Julie,
1) They were previously installed, but I just tried running it with
some of
my own installed versions and they're not working properly (e.g. the
make
install fails due to gsl/gsl_cdf.h missing... though I set MET_GSL to
my
gsl-2.5 directory).
2) Not sure how I can verify that one, though I think they're not as
I've
seen GNU and Intel prompts in the config output. My CC var in my
bashrc
links to an Intel compiler.
3) I followed those for the packages, though for the compilers
section, I
do not know my CXX or F77 paths on the hpc that I'm using. I also
think the
icc is not working properly as I could not run icc without a license
prompt
coming up.
I'm not sure if any of that helps, but let me know. Maybe some of
these
issues are still on our end. The fact that met needs to only use one
compiler might be the issue...
On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via RT
<met_help at ucar.edu>
wrote:
> Hi Taylor. Thank you for passing along your files. I have a few
questions
> for you.
>
> 1) Are you installing the external libraries yourself or were they
> previously installed?
> 2) Can you please verify that the external libraries and MET are
being
> built with the same family of compilers (e.g. all are built with
GNU, or
> all are build with Intel, etc.)? Which compiler are you using?
> 3) Are you following the directions on this page as your
instructions for
> installation?
>
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
>
> Thank you!
>
> Julie
>
> On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via RT <
> met_help at ucar.edu>
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> >
> > Hey Julie,
> >
> > I attached the config and make_install logs here. We could do a
hangouts
> > session as well if you can't pinpoint the issue; I'm remoting in
from my
> > home windows computer so it will be a bit hacky.
> >
> > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via RT <
> met_help at ucar.edu
> > >
> > wrote:
> >
> > > Hi Taylor. It is difficult to tell what is going without more
context.
> > > Could you please send me your config.log file and your make.log
file?
> > >
> > > We could also consider doing a hangouts session where you can
share
> your
> > > screen, and I can directly help that way. Either way though, if
you
> > could
> > > please send those files, I would appreciate it.
> > >
> > > Thanks,
> > > Julie
> > >
> > > Thanks!
> > >
> > > Julie
> > >
> > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum via RT <
> > > met_help at ucar.edu>
> > > wrote:
> > >
> > > >
> > > > Mon Jan 14 15:05:33 2019: Request 88502 was acted upon.
> > > > Transaction: Ticket created by
taylor.mandelbaum at stonybrook.edu
> > > > Queue: met_help
> > > > Subject: met install help
> > > > Owner: Nobody
> > > > Requestors: taylor.mandelbaum at stonybrook.edu
> > > > Status: new
> > > > Ticket <URL:
> https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > >
> > > >
> > > >
> > > > Hey all,
> > > >
> > > > I'm presently trying to compile MET 8.0 on our HPC; when I
configure
> > it,
> > > > I'm getting a few warnings on .h files:
> > > >
> > > > configure: WARNING: errno.h: present but cannot be compiled
> > > > configure: WARNING: errno.h: check for missing
prerequisite
> > headers?
> > > > configure: WARNING: errno.h: see the Autoconf documentation
> > > > configure: WARNING: errno.h: section "Present But Cannot
Be
> > Compiled"
> > > > configure: WARNING: errno.h: proceeding with the compiler's
result
> > > > configure: WARNING: ## -------------------------------- ##
> > > > configure: WARNING: ## Report this to met_help at ucar.edu ##
> > > > configure: WARNING: ## -------------------------------- ##
> > > >
> > > > and the same for fcntl.h, limits.h, stddef.h, file.h and
param.h.
> > > >
> > > > When I try to make install, I get this error on the tail of
the log:
> > > >
> > > > config_scanner.cc: In function ‘void* configalloc(yy_size_t)’:
> > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’ was not
declared in
> this
> > > > scope
> > > > config_scanner.cc: In function ‘void* configrealloc(void*,
> yy_size_t)’:
> > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’ was not
declared in
> > this
> > > > scope
> > > > /* The cast to (char *) in the following accommodates both
> > > > ^
> > > > make[3]: *** [libvx_config_a-config_scanner.o] Error 1
> > > > make[3]: Leaving directory
> > > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > > make[2]: *** [install-recursive] Error 1
> > > > make[2]: Leaving directory
> `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > make[1]: *** [install-recursive] Error 1
> > > > make[1]: Leaving directory `/E1/taylorm/MET8/met-
8.0_bugfix/src'
> > > > make: *** [install-recursive] Error 1
> > > >
> > > > Not sure how to address either of these, hopefully you guys
can
> provide
> > > > some insight.
> > > >
> > > > Thanks!
> > > > --
> > > > *Taylor Mandelbaum*
> > > > Research Technician
> > > > SoMAS | Stony Brook University
> > > > 678.468.5789
> > > >
> > > >
> > >
> > >
> >
> > --
> > *Taylor Mandelbaum*
> > Research Technician
> > SoMAS | Stony Brook University
> > 678.468.5789
> >
> >
>
>
--
*Taylor Mandelbaum*
Research Technician
SoMAS | Stony Brook University
678.468.5789
------------------------------------------------
Subject: met install help
From: Julie Prestopnik
Time: Wed Jan 16 10:06:49 2019
Hi Taylor. Thank you for all of this information.
Since the libraries were previously installed and we cannot be certain
which compiler was used, are you able and would you be comfortable
installing each of the dependent libraries and not using the
previously
installed versions? If so, we have an install script that I can point
you
to, which would install all of the packages and MET as well. I can
walk
through this with you via google hangouts and you can share your
screen so
we can make sure it is going smoothly. I could do a hangouts session
with
you tomorrow at 1:15pm (Mountain time) or on Friday at 9:00am
(Mountain
time). If those times don't work. I can get you started with very
specific instructions via email and we can continue to work through
any
problems. We can also set up a different time for next week, however,
I
didn't want you to have to wait that long. Please let me know your
preference.
If you think that icc may not be working properly, then you should
probably
use the GNU set of compilers, unless there is some reason not to, in
which
case you may need to get a system administrator correct the problems
with
the intel compiler.
Running "which g++" and running "which gfortran" can tell you what the
CXX
and F77 paths should be set to. Please let me know if you have any
issues
with that.
Julie
On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> Hey Julie,
>
> 1) They were previously installed, but I just tried running it with
some of
> my own installed versions and they're not working properly (e.g. the
make
> install fails due to gsl/gsl_cdf.h missing... though I set MET_GSL
to my
> gsl-2.5 directory).
>
> 2) Not sure how I can verify that one, though I think they're not as
I've
> seen GNU and Intel prompts in the config output. My CC var in my
bashrc
> links to an Intel compiler.
>
> 3) I followed those for the packages, though for the compilers
section, I
> do not know my CXX or F77 paths on the hpc that I'm using. I also
think the
> icc is not working properly as I could not run icc without a license
prompt
> coming up.
>
> I'm not sure if any of that helps, but let me know. Maybe some of
these
> issues are still on our end. The fact that met needs to only use one
> compiler might be the issue...
>
> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via RT <
> met_help at ucar.edu>
> wrote:
>
> > Hi Taylor. Thank you for passing along your files. I have a few
> questions
> > for you.
> >
> > 1) Are you installing the external libraries yourself or were they
> > previously installed?
> > 2) Can you please verify that the external libraries and MET are
being
> > built with the same family of compilers (e.g. all are built with
GNU, or
> > all are build with Intel, etc.)? Which compiler are you using?
> > 3) Are you following the directions on this page as your
instructions for
> > installation?
> >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> >
> > Thank you!
> >
> > Julie
> >
> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via RT <
> > met_help at ucar.edu>
> > wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > >
> > > Hey Julie,
> > >
> > > I attached the config and make_install logs here. We could do a
> hangouts
> > > session as well if you can't pinpoint the issue; I'm remoting in
from
> my
> > > home windows computer so it will be a bit hacky.
> > >
> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via RT <
> > met_help at ucar.edu
> > > >
> > > wrote:
> > >
> > > > Hi Taylor. It is difficult to tell what is going without more
> context.
> > > > Could you please send me your config.log file and your
make.log file?
> > > >
> > > > We could also consider doing a hangouts session where you can
share
> > your
> > > > screen, and I can directly help that way. Either way though,
if you
> > > could
> > > > please send those files, I would appreciate it.
> > > >
> > > > Thanks,
> > > > Julie
> > > >
> > > > Thanks!
> > > >
> > > > Julie
> > > >
> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum via RT <
> > > > met_help at ucar.edu>
> > > > wrote:
> > > >
> > > > >
> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was acted upon.
> > > > > Transaction: Ticket created by
taylor.mandelbaum at stonybrook.edu
> > > > > Queue: met_help
> > > > > Subject: met install help
> > > > > Owner: Nobody
> > > > > Requestors: taylor.mandelbaum at stonybrook.edu
> > > > > Status: new
> > > > > Ticket <URL:
> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > >
> > > > >
> > > > >
> > > > > Hey all,
> > > > >
> > > > > I'm presently trying to compile MET 8.0 on our HPC; when I
> configure
> > > it,
> > > > > I'm getting a few warnings on .h files:
> > > > >
> > > > > configure: WARNING: errno.h: present but cannot be compiled
> > > > > configure: WARNING: errno.h: check for missing
prerequisite
> > > headers?
> > > > > configure: WARNING: errno.h: see the Autoconf documentation
> > > > > configure: WARNING: errno.h: section "Present But Cannot
Be
> > > Compiled"
> > > > > configure: WARNING: errno.h: proceeding with the compiler's
result
> > > > > configure: WARNING: ## --------------------------------
##
> > > > > configure: WARNING: ## Report this to met_help at ucar.edu
##
> > > > > configure: WARNING: ## --------------------------------
##
> > > > >
> > > > > and the same for fcntl.h, limits.h, stddef.h, file.h and
param.h.
> > > > >
> > > > > When I try to make install, I get this error on the tail of
the
> log:
> > > > >
> > > > > config_scanner.cc: In function ‘void*
configalloc(yy_size_t)’:
> > > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’ was not
declared in
> > this
> > > > > scope
> > > > > config_scanner.cc: In function ‘void* configrealloc(void*,
> > yy_size_t)’:
> > > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’ was not
declared in
> > > this
> > > > > scope
> > > > > /* The cast to (char *) in the following accommodates both
> > > > > ^
> > > > > make[3]: *** [libvx_config_a-config_scanner.o] Error 1
> > > > > make[3]: Leaving directory
> > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > > > make[2]: *** [install-recursive] Error 1
> > > > > make[2]: Leaving directory
> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > > make[1]: *** [install-recursive] Error 1
> > > > > make[1]: Leaving directory `/E1/taylorm/MET8/met-
8.0_bugfix/src'
> > > > > make: *** [install-recursive] Error 1
> > > > >
> > > > > Not sure how to address either of these, hopefully you guys
can
> > provide
> > > > > some insight.
> > > > >
> > > > > Thanks!
> > > > > --
> > > > > *Taylor Mandelbaum*
> > > > > Research Technician
> > > > > SoMAS | Stony Brook University
> > > > > 678.468.5789
> > > > >
> > > > >
> > > >
> > > >
> > >
> > > --
> > > *Taylor Mandelbaum*
> > > Research Technician
> > > SoMAS | Stony Brook University
> > > 678.468.5789
> > >
> > >
> >
> >
>
> --
> *Taylor Mandelbaum*
> Research Technician
> SoMAS | Stony Brook University
> 678.468.5789
>
>
------------------------------------------------
Subject: met install help
From: Julie Prestopnik
Time: Wed Jan 16 10:23:25 2019
Hi Taylor. In talking with more with John about your config.log file
we
see that CC is set to use icc (intel), but CXX and F77 are set to use
g++
and gfortran (GNU).
CC='/home/taylorm/MET8/met-8.0_bugfix/compile
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
CXX='g++'
F77='gfortran'
Let's see if we can solve the immediate problem before worrying about
any
potential problems with the external libraries. For now, please
choose
either the GNU compilers or the Intel compilers and set the following
variables accordingly. You can chose one and then simply run the
commands
below.
*For GNU:*
export CC=`which gcc`
export CXX=`which g++`
export F77=`which gfortran`
*For Intel:*
export CC=`which icc`
export CXX=`which icc`
export F77=`which ifort`
Then run "make clean", rerun the configure command, and then try to
make
MET again.
Let's go from there and see how it works out. Please let me know.
Julie
On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik <jpresto at ucar.edu>
wrote:
> Hi Taylor. Thank you for all of this information.
>
> Since the libraries were previously installed and we cannot be
certain
> which compiler was used, are you able and would you be comfortable
> installing each of the dependent libraries and not using the
previously
> installed versions? If so, we have an install script that I can
point you
> to, which would install all of the packages and MET as well. I can
walk
> through this with you via google hangouts and you can share your
screen so
> we can make sure it is going smoothly. I could do a hangouts
session with
> you tomorrow at 1:15pm (Mountain time) or on Friday at 9:00am
(Mountain
> time). If those times don't work. I can get you started with very
> specific instructions via email and we can continue to work through
any
> problems. We can also set up a different time for next week,
however, I
> didn't want you to have to wait that long. Please let me know your
> preference.
>
> If you think that icc may not be working properly, then you should
> probably use the GNU set of compilers, unless there is some reason
not to,
> in which case you may need to get a system administrator correct the
> problems with the intel compiler.
>
> Running "which g++" and running "which gfortran" can tell you what
the CXX
> and F77 paths should be set to. Please let me know if you have any
issues
> with that.
>
> Julie
>
> On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via RT <
> met_help at ucar.edu> wrote:
>
>>
>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>>
>> Hey Julie,
>>
>> 1) They were previously installed, but I just tried running it with
some
>> of
>> my own installed versions and they're not working properly (e.g.
the make
>> install fails due to gsl/gsl_cdf.h missing... though I set MET_GSL
to my
>> gsl-2.5 directory).
>>
>> 2) Not sure how I can verify that one, though I think they're not
as I've
>> seen GNU and Intel prompts in the config output. My CC var in my
bashrc
>> links to an Intel compiler.
>>
>> 3) I followed those for the packages, though for the compilers
section, I
>> do not know my CXX or F77 paths on the hpc that I'm using. I also
think
>> the
>> icc is not working properly as I could not run icc without a
license
>> prompt
>> coming up.
>>
>> I'm not sure if any of that helps, but let me know. Maybe some of
these
>> issues are still on our end. The fact that met needs to only use
one
>> compiler might be the issue...
>>
>> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via RT <
>> met_help at ucar.edu>
>> wrote:
>>
>> > Hi Taylor. Thank you for passing along your files. I have a few
>> questions
>> > for you.
>> >
>> > 1) Are you installing the external libraries yourself or were
they
>> > previously installed?
>> > 2) Can you please verify that the external libraries and MET are
being
>> > built with the same family of compilers (e.g. all are built with
GNU, or
>> > all are build with Intel, etc.)? Which compiler are you using?
>> > 3) Are you following the directions on this page as your
instructions
>> for
>> > installation?
>> >
>> >
>>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
>> >
>> > Thank you!
>> >
>> > Julie
>> >
>> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via RT <
>> > met_help at ucar.edu>
>> > wrote:
>> >
>> > >
>> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>> > >
>> > > Hey Julie,
>> > >
>> > > I attached the config and make_install logs here. We could do a
>> hangouts
>> > > session as well if you can't pinpoint the issue; I'm remoting
in from
>> my
>> > > home windows computer so it will be a bit hacky.
>> > >
>> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via RT <
>> > met_help at ucar.edu
>> > > >
>> > > wrote:
>> > >
>> > > > Hi Taylor. It is difficult to tell what is going without
more
>> context.
>> > > > Could you please send me your config.log file and your
make.log
>> file?
>> > > >
>> > > > We could also consider doing a hangouts session where you can
share
>> > your
>> > > > screen, and I can directly help that way. Either way though,
if you
>> > > could
>> > > > please send those files, I would appreciate it.
>> > > >
>> > > > Thanks,
>> > > > Julie
>> > > >
>> > > > Thanks!
>> > > >
>> > > > Julie
>> > > >
>> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum via RT <
>> > > > met_help at ucar.edu>
>> > > > wrote:
>> > > >
>> > > > >
>> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was acted upon.
>> > > > > Transaction: Ticket created by
taylor.mandelbaum at stonybrook.edu
>> > > > > Queue: met_help
>> > > > > Subject: met install help
>> > > > > Owner: Nobody
>> > > > > Requestors: taylor.mandelbaum at stonybrook.edu
>> > > > > Status: new
>> > > > > Ticket <URL:
>> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
>> > > >
>> > > > >
>> > > > >
>> > > > > Hey all,
>> > > > >
>> > > > > I'm presently trying to compile MET 8.0 on our HPC; when I
>> configure
>> > > it,
>> > > > > I'm getting a few warnings on .h files:
>> > > > >
>> > > > > configure: WARNING: errno.h: present but cannot be compiled
>> > > > > configure: WARNING: errno.h: check for missing
prerequisite
>> > > headers?
>> > > > > configure: WARNING: errno.h: see the Autoconf documentation
>> > > > > configure: WARNING: errno.h: section "Present But
Cannot Be
>> > > Compiled"
>> > > > > configure: WARNING: errno.h: proceeding with the compiler's
result
>> > > > > configure: WARNING: ## --------------------------------
##
>> > > > > configure: WARNING: ## Report this to met_help at ucar.edu
##
>> > > > > configure: WARNING: ## --------------------------------
##
>> > > > >
>> > > > > and the same for fcntl.h, limits.h, stddef.h, file.h and
param.h.
>> > > > >
>> > > > > When I try to make install, I get this error on the tail of
the
>> log:
>> > > > >
>> > > > > config_scanner.cc: In function ‘void*
configalloc(yy_size_t)’:
>> > > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’ was not
declared in
>> > this
>> > > > > scope
>> > > > > config_scanner.cc: In function ‘void* configrealloc(void*,
>> > yy_size_t)’:
>> > > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’ was not
declared
>> in
>> > > this
>> > > > > scope
>> > > > > /* The cast to (char *) in the following accommodates
both
>> > > > > ^
>> > > > > make[3]: *** [libvx_config_a-config_scanner.o] Error 1
>> > > > > make[3]: Leaving directory
>> > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
>> > > > > make[2]: *** [install-recursive] Error 1
>> > > > > make[2]: Leaving directory
>> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
>> > > > > make[1]: *** [install-recursive] Error 1
>> > > > > make[1]: Leaving directory `/E1/taylorm/MET8/met-
8.0_bugfix/src'
>> > > > > make: *** [install-recursive] Error 1
>> > > > >
>> > > > > Not sure how to address either of these, hopefully you guys
can
>> > provide
>> > > > > some insight.
>> > > > >
>> > > > > Thanks!
>> > > > > --
>> > > > > *Taylor Mandelbaum*
>> > > > > Research Technician
>> > > > > SoMAS | Stony Brook University
>> > > > > 678.468.5789
>> > > > >
>> > > > >
>> > > >
>> > > >
>> > >
>> > > --
>> > > *Taylor Mandelbaum*
>> > > Research Technician
>> > > SoMAS | Stony Brook University
>> > > 678.468.5789
>> > >
>> > >
>> >
>> >
>>
>> --
>> *Taylor Mandelbaum*
>> Research Technician
>> SoMAS | Stony Brook University
>> 678.468.5789
>>
>>
------------------------------------------------
Subject: met install help
From: Taylor Mandelbaum
Time: Wed Jan 16 17:43:40 2019
Hey Julie,
Thanks for all the help on this, it's really appreciated. I ran the
install
with CC, CXX, and F77 set to the appropriate locations and came across
the
same error with gsl_cdf.h. I reconfigured and re-make/make install'd
the
gsl-2.5 package in my directory prior to running the install for MET
again
(MET_GSL is set to the directory I made it in) and still came across
this
error:
../../../src/libcode/vx_gsl_prob/gsl_cdf.h:17:25: fatal error:
gsl/gsl_cdf.h: No such file or directory
compilation terminated.
On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT
<met_help at ucar.edu>
wrote:
> Hi Taylor. In talking with more with John about your config.log
file we
> see that CC is set to use icc (intel), but CXX and F77 are set to
use g++
> and gfortran (GNU).
>
> CC='/home/taylorm/MET8/met-8.0_bugfix/compile
>
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> CXX='g++'
> F77='gfortran'
>
> Let's see if we can solve the immediate problem before worrying
about any
> potential problems with the external libraries. For now, please
choose
> either the GNU compilers or the Intel compilers and set the
following
> variables accordingly. You can chose one and then simply run the
commands
> below.
>
> *For GNU:*
> export CC=`which gcc`
> export CXX=`which g++`
> export F77=`which gfortran`
>
> *For Intel:*
>
> export CC=`which icc`
> export CXX=`which icc`
> export F77=`which ifort`
>
> Then run "make clean", rerun the configure command, and then try to
make
> MET again.
>
> Let's go from there and see how it works out. Please let me know.
>
> Julie
>
>
> On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik <jpresto at ucar.edu>
> wrote:
>
> > Hi Taylor. Thank you for all of this information.
> >
> > Since the libraries were previously installed and we cannot be
certain
> > which compiler was used, are you able and would you be comfortable
> > installing each of the dependent libraries and not using the
previously
> > installed versions? If so, we have an install script that I can
point
> you
> > to, which would install all of the packages and MET as well. I
can walk
> > through this with you via google hangouts and you can share your
screen
> so
> > we can make sure it is going smoothly. I could do a hangouts
session
> with
> > you tomorrow at 1:15pm (Mountain time) or on Friday at 9:00am
(Mountain
> > time). If those times don't work. I can get you started with
very
> > specific instructions via email and we can continue to work
through any
> > problems. We can also set up a different time for next week,
however, I
> > didn't want you to have to wait that long. Please let me know
your
> > preference.
> >
> > If you think that icc may not be working properly, then you should
> > probably use the GNU set of compilers, unless there is some reason
not
> to,
> > in which case you may need to get a system administrator correct
the
> > problems with the intel compiler.
> >
> > Running "which g++" and running "which gfortran" can tell you what
the
> CXX
> > and F77 paths should be set to. Please let me know if you have
any
> issues
> > with that.
> >
> > Julie
> >
> > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via RT <
> > met_help at ucar.edu> wrote:
> >
> >>
> >> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> >>
> >> Hey Julie,
> >>
> >> 1) They were previously installed, but I just tried running it
with some
> >> of
> >> my own installed versions and they're not working properly (e.g.
the
> make
> >> install fails due to gsl/gsl_cdf.h missing... though I set
MET_GSL to my
> >> gsl-2.5 directory).
> >>
> >> 2) Not sure how I can verify that one, though I think they're not
as
> I've
> >> seen GNU and Intel prompts in the config output. My CC var in my
bashrc
> >> links to an Intel compiler.
> >>
> >> 3) I followed those for the packages, though for the compilers
section,
> I
> >> do not know my CXX or F77 paths on the hpc that I'm using. I also
think
> >> the
> >> icc is not working properly as I could not run icc without a
license
> >> prompt
> >> coming up.
> >>
> >> I'm not sure if any of that helps, but let me know. Maybe some of
these
> >> issues are still on our end. The fact that met needs to only use
one
> >> compiler might be the issue...
> >>
> >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via RT <
> >> met_help at ucar.edu>
> >> wrote:
> >>
> >> > Hi Taylor. Thank you for passing along your files. I have a
few
> >> questions
> >> > for you.
> >> >
> >> > 1) Are you installing the external libraries yourself or were
they
> >> > previously installed?
> >> > 2) Can you please verify that the external libraries and MET
are being
> >> > built with the same family of compilers (e.g. all are built
with GNU,
> or
> >> > all are build with Intel, etc.)? Which compiler are you using?
> >> > 3) Are you following the directions on this page as your
instructions
> >> for
> >> > installation?
> >> >
> >> >
> >>
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> >> >
> >> > Thank you!
> >> >
> >> > Julie
> >> >
> >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via RT <
> >> > met_help at ucar.edu>
> >> > wrote:
> >> >
> >> > >
> >> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
>
> >> > >
> >> > > Hey Julie,
> >> > >
> >> > > I attached the config and make_install logs here. We could do
a
> >> hangouts
> >> > > session as well if you can't pinpoint the issue; I'm remoting
in
> from
> >> my
> >> > > home windows computer so it will be a bit hacky.
> >> > >
> >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via RT <
> >> > met_help at ucar.edu
> >> > > >
> >> > > wrote:
> >> > >
> >> > > > Hi Taylor. It is difficult to tell what is going without
more
> >> context.
> >> > > > Could you please send me your config.log file and your
make.log
> >> file?
> >> > > >
> >> > > > We could also consider doing a hangouts session where you
can
> share
> >> > your
> >> > > > screen, and I can directly help that way. Either way
though, if
> you
> >> > > could
> >> > > > please send those files, I would appreciate it.
> >> > > >
> >> > > > Thanks,
> >> > > > Julie
> >> > > >
> >> > > > Thanks!
> >> > > >
> >> > > > Julie
> >> > > >
> >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum via RT <
> >> > > > met_help at ucar.edu>
> >> > > > wrote:
> >> > > >
> >> > > > >
> >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was acted upon.
> >> > > > > Transaction: Ticket created by
taylor.mandelbaum at stonybrook.edu
> >> > > > > Queue: met_help
> >> > > > > Subject: met install help
> >> > > > > Owner: Nobody
> >> > > > > Requestors: taylor.mandelbaum at stonybrook.edu
> >> > > > > Status: new
> >> > > > > Ticket <URL:
> >> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> >> > > >
> >> > > > >
> >> > > > >
> >> > > > > Hey all,
> >> > > > >
> >> > > > > I'm presently trying to compile MET 8.0 on our HPC; when
I
> >> configure
> >> > > it,
> >> > > > > I'm getting a few warnings on .h files:
> >> > > > >
> >> > > > > configure: WARNING: errno.h: present but cannot be
compiled
> >> > > > > configure: WARNING: errno.h: check for missing
prerequisite
> >> > > headers?
> >> > > > > configure: WARNING: errno.h: see the Autoconf
documentation
> >> > > > > configure: WARNING: errno.h: section "Present But
Cannot Be
> >> > > Compiled"
> >> > > > > configure: WARNING: errno.h: proceeding with the
compiler's
> result
> >> > > > > configure: WARNING: ##
-------------------------------- ##
> >> > > > > configure: WARNING: ## Report this to
met_help at ucar.edu ##
> >> > > > > configure: WARNING: ##
-------------------------------- ##
> >> > > > >
> >> > > > > and the same for fcntl.h, limits.h, stddef.h, file.h and
> param.h.
> >> > > > >
> >> > > > > When I try to make install, I get this error on the tail
of the
> >> log:
> >> > > > >
> >> > > > > config_scanner.cc: In function ‘void*
configalloc(yy_size_t)’:
> >> > > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’ was not
declared
> in
> >> > this
> >> > > > > scope
> >> > > > > config_scanner.cc: In function ‘void*
configrealloc(void*,
> >> > yy_size_t)’:
> >> > > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’ was not
declared
> >> in
> >> > > this
> >> > > > > scope
> >> > > > > /* The cast to (char *) in the following accommodates
both
> >> > > > > ^
> >> > > > > make[3]: *** [libvx_config_a-config_scanner.o] Error 1
> >> > > > > make[3]: Leaving directory
> >> > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> >> > > > > make[2]: *** [install-recursive] Error 1
> >> > > > > make[2]: Leaving directory
> >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> >> > > > > make[1]: *** [install-recursive] Error 1
> >> > > > > make[1]: Leaving directory `/E1/taylorm/MET8/met-
8.0_bugfix/src'
> >> > > > > make: *** [install-recursive] Error 1
> >> > > > >
> >> > > > > Not sure how to address either of these, hopefully you
guys can
> >> > provide
> >> > > > > some insight.
> >> > > > >
> >> > > > > Thanks!
> >> > > > > --
> >> > > > > *Taylor Mandelbaum*
> >> > > > > Research Technician
> >> > > > > SoMAS | Stony Brook University
> >> > > > > 678.468.5789
> >> > > > >
> >> > > > >
> >> > > >
> >> > > >
> >> > >
> >> > > --
> >> > > *Taylor Mandelbaum*
> >> > > Research Technician
> >> > > SoMAS | Stony Brook University
> >> > > 678.468.5789
> >> > >
> >> > >
> >> >
> >> >
> >>
> >> --
> >> *Taylor Mandelbaum*
> >> Research Technician
> >> SoMAS | Stony Brook University
> >> 678.468.5789
> >>
> >>
>
>
--
*Taylor Mandelbaum*
Research Technician
SoMAS | Stony Brook University
678.468.5789
------------------------------------------------
Subject: met install help
From: Julie Prestopnik
Time: Wed Jan 16 17:55:21 2019
Hi Taylor. Thanks! Could you please send the new config.log file and
the
new make.log file?
Thanks!
On Wed, Jan 16, 2019, 5:43 PM Taylor Mandelbaum via RT
<met_help at ucar.edu
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> Hey Julie,
>
> Thanks for all the help on this, it's really appreciated. I ran the
install
> with CC, CXX, and F77 set to the appropriate locations and came
across the
> same error with gsl_cdf.h. I reconfigured and re-make/make install'd
the
> gsl-2.5 package in my directory prior to running the install for MET
again
> (MET_GSL is set to the directory I made it in) and still came across
this
> error:
> ../../../src/libcode/vx_gsl_prob/gsl_cdf.h:17:25: fatal error:
> gsl/gsl_cdf.h: No such file or directory
> compilation terminated.
>
> On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT <
> met_help at ucar.edu>
> wrote:
>
> > Hi Taylor. In talking with more with John about your config.log
file we
> > see that CC is set to use icc (intel), but CXX and F77 are set to
use g++
> > and gfortran (GNU).
> >
> > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> >
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > CXX='g++'
> > F77='gfortran'
> >
> > Let's see if we can solve the immediate problem before worrying
about any
> > potential problems with the external libraries. For now, please
choose
> > either the GNU compilers or the Intel compilers and set the
following
> > variables accordingly. You can chose one and then simply run the
> commands
> > below.
> >
> > *For GNU:*
> > export CC=`which gcc`
> > export CXX=`which g++`
> > export F77=`which gfortran`
> >
> > *For Intel:*
> >
> > export CC=`which icc`
> > export CXX=`which icc`
> > export F77=`which ifort`
> >
> > Then run "make clean", rerun the configure command, and then try
to make
> > MET again.
> >
> > Let's go from there and see how it works out. Please let me know.
> >
> > Julie
> >
> >
> > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik
<jpresto at ucar.edu>
> > wrote:
> >
> > > Hi Taylor. Thank you for all of this information.
> > >
> > > Since the libraries were previously installed and we cannot be
certain
> > > which compiler was used, are you able and would you be
comfortable
> > > installing each of the dependent libraries and not using the
previously
> > > installed versions? If so, we have an install script that I can
point
> > you
> > > to, which would install all of the packages and MET as well. I
can
> walk
> > > through this with you via google hangouts and you can share your
screen
> > so
> > > we can make sure it is going smoothly. I could do a hangouts
session
> > with
> > > you tomorrow at 1:15pm (Mountain time) or on Friday at 9:00am
(Mountain
> > > time). If those times don't work. I can get you started with
very
> > > specific instructions via email and we can continue to work
through any
> > > problems. We can also set up a different time for next week,
however,
> I
> > > didn't want you to have to wait that long. Please let me know
your
> > > preference.
> > >
> > > If you think that icc may not be working properly, then you
should
> > > probably use the GNU set of compilers, unless there is some
reason not
> > to,
> > > in which case you may need to get a system administrator correct
the
> > > problems with the intel compiler.
> > >
> > > Running "which g++" and running "which gfortran" can tell you
what the
> > CXX
> > > and F77 paths should be set to. Please let me know if you have
any
> > issues
> > > with that.
> > >
> > > Julie
> > >
> > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via RT <
> > > met_help at ucar.edu> wrote:
> > >
> > >>
> > >> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > >>
> > >> Hey Julie,
> > >>
> > >> 1) They were previously installed, but I just tried running it
with
> some
> > >> of
> > >> my own installed versions and they're not working properly
(e.g. the
> > make
> > >> install fails due to gsl/gsl_cdf.h missing... though I set
MET_GSL to
> my
> > >> gsl-2.5 directory).
> > >>
> > >> 2) Not sure how I can verify that one, though I think they're
not as
> > I've
> > >> seen GNU and Intel prompts in the config output. My CC var in
my
> bashrc
> > >> links to an Intel compiler.
> > >>
> > >> 3) I followed those for the packages, though for the compilers
> section,
> > I
> > >> do not know my CXX or F77 paths on the hpc that I'm using. I
also
> think
> > >> the
> > >> icc is not working properly as I could not run icc without a
license
> > >> prompt
> > >> coming up.
> > >>
> > >> I'm not sure if any of that helps, but let me know. Maybe some
of
> these
> > >> issues are still on our end. The fact that met needs to only
use one
> > >> compiler might be the issue...
> > >>
> > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via RT <
> > >> met_help at ucar.edu>
> > >> wrote:
> > >>
> > >> > Hi Taylor. Thank you for passing along your files. I have a
few
> > >> questions
> > >> > for you.
> > >> >
> > >> > 1) Are you installing the external libraries yourself or were
they
> > >> > previously installed?
> > >> > 2) Can you please verify that the external libraries and MET
are
> being
> > >> > built with the same family of compilers (e.g. all are built
with
> GNU,
> > or
> > >> > all are build with Intel, etc.)? Which compiler are you
using?
> > >> > 3) Are you following the directions on this page as your
> instructions
> > >> for
> > >> > installation?
> > >> >
> > >> >
> > >>
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > >> >
> > >> > Thank you!
> > >> >
> > >> > Julie
> > >> >
> > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via RT <
> > >> > met_help at ucar.edu>
> > >> > wrote:
> > >> >
> > >> > >
> > >> > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > >> > >
> > >> > > Hey Julie,
> > >> > >
> > >> > > I attached the config and make_install logs here. We could
do a
> > >> hangouts
> > >> > > session as well if you can't pinpoint the issue; I'm
remoting in
> > from
> > >> my
> > >> > > home windows computer so it will be a bit hacky.
> > >> > >
> > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via RT <
> > >> > met_help at ucar.edu
> > >> > > >
> > >> > > wrote:
> > >> > >
> > >> > > > Hi Taylor. It is difficult to tell what is going without
more
> > >> context.
> > >> > > > Could you please send me your config.log file and your
make.log
> > >> file?
> > >> > > >
> > >> > > > We could also consider doing a hangouts session where you
can
> > share
> > >> > your
> > >> > > > screen, and I can directly help that way. Either way
though, if
> > you
> > >> > > could
> > >> > > > please send those files, I would appreciate it.
> > >> > > >
> > >> > > > Thanks,
> > >> > > > Julie
> > >> > > >
> > >> > > > Thanks!
> > >> > > >
> > >> > > > Julie
> > >> > > >
> > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum via RT
<
> > >> > > > met_help at ucar.edu>
> > >> > > > wrote:
> > >> > > >
> > >> > > > >
> > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was acted upon.
> > >> > > > > Transaction: Ticket created by
> taylor.mandelbaum at stonybrook.edu
> > >> > > > > Queue: met_help
> > >> > > > > Subject: met install help
> > >> > > > > Owner: Nobody
> > >> > > > > Requestors: taylor.mandelbaum at stonybrook.edu
> > >> > > > > Status: new
> > >> > > > > Ticket <URL:
> > >> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > >> > > >
> > >> > > > >
> > >> > > > >
> > >> > > > > Hey all,
> > >> > > > >
> > >> > > > > I'm presently trying to compile MET 8.0 on our HPC;
when I
> > >> configure
> > >> > > it,
> > >> > > > > I'm getting a few warnings on .h files:
> > >> > > > >
> > >> > > > > configure: WARNING: errno.h: present but cannot be
compiled
> > >> > > > > configure: WARNING: errno.h: check for missing
> prerequisite
> > >> > > headers?
> > >> > > > > configure: WARNING: errno.h: see the Autoconf
documentation
> > >> > > > > configure: WARNING: errno.h: section "Present But
Cannot
> Be
> > >> > > Compiled"
> > >> > > > > configure: WARNING: errno.h: proceeding with the
compiler's
> > result
> > >> > > > > configure: WARNING: ##
-------------------------------- ##
> > >> > > > > configure: WARNING: ## Report this to
met_help at ucar.edu
> ##
> > >> > > > > configure: WARNING: ##
-------------------------------- ##
> > >> > > > >
> > >> > > > > and the same for fcntl.h, limits.h, stddef.h, file.h
and
> > param.h.
> > >> > > > >
> > >> > > > > When I try to make install, I get this error on the
tail of
> the
> > >> log:
> > >> > > > >
> > >> > > > > config_scanner.cc: In function ‘void*
configalloc(yy_size_t)’:
> > >> > > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’ was not
> declared
> > in
> > >> > this
> > >> > > > > scope
> > >> > > > > config_scanner.cc: In function ‘void*
configrealloc(void*,
> > >> > yy_size_t)’:
> > >> > > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’ was not
> declared
> > >> in
> > >> > > this
> > >> > > > > scope
> > >> > > > > /* The cast to (char *) in the following accommodates
both
> > >> > > > > ^
> > >> > > > > make[3]: *** [libvx_config_a-config_scanner.o] Error 1
> > >> > > > > make[3]: Leaving directory
> > >> > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > >> > > > > make[2]: *** [install-recursive] Error 1
> > >> > > > > make[2]: Leaving directory
> > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > >> > > > > make[1]: *** [install-recursive] Error 1
> > >> > > > > make[1]: Leaving directory
> `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > >> > > > > make: *** [install-recursive] Error 1
> > >> > > > >
> > >> > > > > Not sure how to address either of these, hopefully you
guys
> can
> > >> > provide
> > >> > > > > some insight.
> > >> > > > >
> > >> > > > > Thanks!
> > >> > > > > --
> > >> > > > > *Taylor Mandelbaum*
> > >> > > > > Research Technician
> > >> > > > > SoMAS | Stony Brook University
> > >> > > > > 678.468.5789
> > >> > > > >
> > >> > > > >
> > >> > > >
> > >> > > >
> > >> > >
> > >> > > --
> > >> > > *Taylor Mandelbaum*
> > >> > > Research Technician
> > >> > > SoMAS | Stony Brook University
> > >> > > 678.468.5789
> > >> > >
> > >> > >
> > >> >
> > >> >
> > >>
> > >> --
> > >> *Taylor Mandelbaum*
> > >> Research Technician
> > >> SoMAS | Stony Brook University
> > >> 678.468.5789
> > >>
> > >>
> >
> >
>
> --
> *Taylor Mandelbaum*
> Research Technician
> SoMAS | Stony Brook University
> 678.468.5789
>
>
------------------------------------------------
Subject: met install help
From: Taylor Mandelbaum
Time: Wed Jan 16 17:58:25 2019
Sure!
On Wed, Jan 16, 2019 at 7:55 PM Julie Prestopnik via RT
<met_help at ucar.edu>
wrote:
> Hi Taylor. Thanks! Could you please send the new config.log file and
the
> new make.log file?
>
> Thanks!
>
> On Wed, Jan 16, 2019, 5:43 PM Taylor Mandelbaum via RT
<met_help at ucar.edu
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> >
> > Hey Julie,
> >
> > Thanks for all the help on this, it's really appreciated. I ran
the
> install
> > with CC, CXX, and F77 set to the appropriate locations and came
across
> the
> > same error with gsl_cdf.h. I reconfigured and re-make/make
install'd the
> > gsl-2.5 package in my directory prior to running the install for
MET
> again
> > (MET_GSL is set to the directory I made it in) and still came
across this
> > error:
> > ../../../src/libcode/vx_gsl_prob/gsl_cdf.h:17:25: fatal error:
> > gsl/gsl_cdf.h: No such file or directory
> > compilation terminated.
> >
> > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT <
> > met_help at ucar.edu>
> > wrote:
> >
> > > Hi Taylor. In talking with more with John about your config.log
file
> we
> > > see that CC is set to use icc (intel), but CXX and F77 are set
to use
> g++
> > > and gfortran (GNU).
> > >
> > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > >
>
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > CXX='g++'
> > > F77='gfortran'
> > >
> > > Let's see if we can solve the immediate problem before worrying
about
> any
> > > potential problems with the external libraries. For now, please
choose
> > > either the GNU compilers or the Intel compilers and set the
following
> > > variables accordingly. You can chose one and then simply run
the
> > commands
> > > below.
> > >
> > > *For GNU:*
> > > export CC=`which gcc`
> > > export CXX=`which g++`
> > > export F77=`which gfortran`
> > >
> > > *For Intel:*
> > >
> > > export CC=`which icc`
> > > export CXX=`which icc`
> > > export F77=`which ifort`
> > >
> > > Then run "make clean", rerun the configure command, and then try
to
> make
> > > MET again.
> > >
> > > Let's go from there and see how it works out. Please let me
know.
> > >
> > > Julie
> > >
> > >
> > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik
<jpresto at ucar.edu>
> > > wrote:
> > >
> > > > Hi Taylor. Thank you for all of this information.
> > > >
> > > > Since the libraries were previously installed and we cannot be
> certain
> > > > which compiler was used, are you able and would you be
comfortable
> > > > installing each of the dependent libraries and not using the
> previously
> > > > installed versions? If so, we have an install script that I
can
> point
> > > you
> > > > to, which would install all of the packages and MET as well.
I can
> > walk
> > > > through this with you via google hangouts and you can share
your
> screen
> > > so
> > > > we can make sure it is going smoothly. I could do a hangouts
> session
> > > with
> > > > you tomorrow at 1:15pm (Mountain time) or on Friday at 9:00am
> (Mountain
> > > > time). If those times don't work. I can get you started with
very
> > > > specific instructions via email and we can continue to work
through
> any
> > > > problems. We can also set up a different time for next week,
> however,
> > I
> > > > didn't want you to have to wait that long. Please let me know
your
> > > > preference.
> > > >
> > > > If you think that icc may not be working properly, then you
should
> > > > probably use the GNU set of compilers, unless there is some
reason
> not
> > > to,
> > > > in which case you may need to get a system administrator
correct the
> > > > problems with the intel compiler.
> > > >
> > > > Running "which g++" and running "which gfortran" can tell you
what
> the
> > > CXX
> > > > and F77 paths should be set to. Please let me know if you
have any
> > > issues
> > > > with that.
> > > >
> > > > Julie
> > > >
> > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via RT <
> > > > met_help at ucar.edu> wrote:
> > > >
> > > >>
> > > >> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
>
> > > >>
> > > >> Hey Julie,
> > > >>
> > > >> 1) They were previously installed, but I just tried running
it with
> > some
> > > >> of
> > > >> my own installed versions and they're not working properly
(e.g. the
> > > make
> > > >> install fails due to gsl/gsl_cdf.h missing... though I set
MET_GSL
> to
> > my
> > > >> gsl-2.5 directory).
> > > >>
> > > >> 2) Not sure how I can verify that one, though I think they're
not as
> > > I've
> > > >> seen GNU and Intel prompts in the config output. My CC var in
my
> > bashrc
> > > >> links to an Intel compiler.
> > > >>
> > > >> 3) I followed those for the packages, though for the
compilers
> > section,
> > > I
> > > >> do not know my CXX or F77 paths on the hpc that I'm using. I
also
> > think
> > > >> the
> > > >> icc is not working properly as I could not run icc without a
license
> > > >> prompt
> > > >> coming up.
> > > >>
> > > >> I'm not sure if any of that helps, but let me know. Maybe
some of
> > these
> > > >> issues are still on our end. The fact that met needs to only
use one
> > > >> compiler might be the issue...
> > > >>
> > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via RT <
> > > >> met_help at ucar.edu>
> > > >> wrote:
> > > >>
> > > >> > Hi Taylor. Thank you for passing along your files. I have
a few
> > > >> questions
> > > >> > for you.
> > > >> >
> > > >> > 1) Are you installing the external libraries yourself or
were they
> > > >> > previously installed?
> > > >> > 2) Can you please verify that the external libraries and
MET are
> > being
> > > >> > built with the same family of compilers (e.g. all are built
with
> > GNU,
> > > or
> > > >> > all are build with Intel, etc.)? Which compiler are you
using?
> > > >> > 3) Are you following the directions on this page as your
> > instructions
> > > >> for
> > > >> > installation?
> > > >> >
> > > >> >
> > > >>
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > >> >
> > > >> > Thank you!
> > > >> >
> > > >> > Julie
> > > >> >
> > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via RT <
> > > >> > met_help at ucar.edu>
> > > >> > wrote:
> > > >> >
> > > >> > >
> > > >> > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > >> > >
> > > >> > > Hey Julie,
> > > >> > >
> > > >> > > I attached the config and make_install logs here. We
could do a
> > > >> hangouts
> > > >> > > session as well if you can't pinpoint the issue; I'm
remoting in
> > > from
> > > >> my
> > > >> > > home windows computer so it will be a bit hacky.
> > > >> > >
> > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via RT <
> > > >> > met_help at ucar.edu
> > > >> > > >
> > > >> > > wrote:
> > > >> > >
> > > >> > > > Hi Taylor. It is difficult to tell what is going
without more
> > > >> context.
> > > >> > > > Could you please send me your config.log file and your
> make.log
> > > >> file?
> > > >> > > >
> > > >> > > > We could also consider doing a hangouts session where
you can
> > > share
> > > >> > your
> > > >> > > > screen, and I can directly help that way. Either way
though,
> if
> > > you
> > > >> > > could
> > > >> > > > please send those files, I would appreciate it.
> > > >> > > >
> > > >> > > > Thanks,
> > > >> > > > Julie
> > > >> > > >
> > > >> > > > Thanks!
> > > >> > > >
> > > >> > > > Julie
> > > >> > > >
> > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum via
RT <
> > > >> > > > met_help at ucar.edu>
> > > >> > > > wrote:
> > > >> > > >
> > > >> > > > >
> > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was acted
upon.
> > > >> > > > > Transaction: Ticket created by
> > taylor.mandelbaum at stonybrook.edu
> > > >> > > > > Queue: met_help
> > > >> > > > > Subject: met install help
> > > >> > > > > Owner: Nobody
> > > >> > > > > Requestors: taylor.mandelbaum at stonybrook.edu
> > > >> > > > > Status: new
> > > >> > > > > Ticket <URL:
> > > >> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > >> > > >
> > > >> > > > >
> > > >> > > > >
> > > >> > > > > Hey all,
> > > >> > > > >
> > > >> > > > > I'm presently trying to compile MET 8.0 on our HPC;
when I
> > > >> configure
> > > >> > > it,
> > > >> > > > > I'm getting a few warnings on .h files:
> > > >> > > > >
> > > >> > > > > configure: WARNING: errno.h: present but cannot be
compiled
> > > >> > > > > configure: WARNING: errno.h: check for missing
> > prerequisite
> > > >> > > headers?
> > > >> > > > > configure: WARNING: errno.h: see the Autoconf
documentation
> > > >> > > > > configure: WARNING: errno.h: section "Present But
Cannot
> > Be
> > > >> > > Compiled"
> > > >> > > > > configure: WARNING: errno.h: proceeding with the
compiler's
> > > result
> > > >> > > > > configure: WARNING: ##
--------------------------------
> ##
> > > >> > > > > configure: WARNING: ## Report this to
met_help at ucar.edu
> > ##
> > > >> > > > > configure: WARNING: ##
--------------------------------
> ##
> > > >> > > > >
> > > >> > > > > and the same for fcntl.h, limits.h, stddef.h, file.h
and
> > > param.h.
> > > >> > > > >
> > > >> > > > > When I try to make install, I get this error on the
tail of
> > the
> > > >> log:
> > > >> > > > >
> > > >> > > > > config_scanner.cc: In function ‘void*
> configalloc(yy_size_t)’:
> > > >> > > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’ was
not
> > declared
> > > in
> > > >> > this
> > > >> > > > > scope
> > > >> > > > > config_scanner.cc: In function ‘void*
configrealloc(void*,
> > > >> > yy_size_t)’:
> > > >> > > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’ was
not
> > declared
> > > >> in
> > > >> > > this
> > > >> > > > > scope
> > > >> > > > > /* The cast to (char *) in the following
accommodates both
> > > >> > > > > ^
> > > >> > > > > make[3]: *** [libvx_config_a-config_scanner.o] Error
1
> > > >> > > > > make[3]: Leaving directory
> > > >> > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > >> > > > > make[2]: *** [install-recursive] Error 1
> > > >> > > > > make[2]: Leaving directory
> > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > >> > > > > make[1]: *** [install-recursive] Error 1
> > > >> > > > > make[1]: Leaving directory
> > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > >> > > > > make: *** [install-recursive] Error 1
> > > >> > > > >
> > > >> > > > > Not sure how to address either of these, hopefully
you guys
> > can
> > > >> > provide
> > > >> > > > > some insight.
> > > >> > > > >
> > > >> > > > > Thanks!
> > > >> > > > > --
> > > >> > > > > *Taylor Mandelbaum*
> > > >> > > > > Research Technician
> > > >> > > > > SoMAS | Stony Brook University
> > > >> > > > > 678.468.5789
> > > >> > > > >
> > > >> > > > >
> > > >> > > >
> > > >> > > >
> > > >> > >
> > > >> > > --
> > > >> > > *Taylor Mandelbaum*
> > > >> > > Research Technician
> > > >> > > SoMAS | Stony Brook University
> > > >> > > 678.468.5789
> > > >> > >
> > > >> > >
> > > >> >
> > > >> >
> > > >>
> > > >> --
> > > >> *Taylor Mandelbaum*
> > > >> Research Technician
> > > >> SoMAS | Stony Brook University
> > > >> 678.468.5789
> > > >>
> > > >>
> > >
> > >
> >
> > --
> > *Taylor Mandelbaum*
> > Research Technician
> > SoMAS | Stony Brook University
> > 678.468.5789
> >
> >
>
>
--
*Taylor Mandelbaum*
Research Technician
SoMAS | Stony Brook University
678.468.5789
------------------------------------------------
Subject: met install help
From: Julie Prestopnik
Time: Thu Jan 17 08:59:41 2019
Hi Taylor. Thank you.
It looks like you may be missing a leading slash in front of E1 in the
environment variables below:
MET_GSL='E1/taylorm/MET8/gsl-2.5'
MET_BUFRLIB='E1/taylorm/MET8/BUFRLIB'
Also, can you please confirm that gsl_cdf.h exists at the following
location?
${MET_GSL}/include
If gsl_cdf.h exists in that location and you are missing a leading
slash,
please modify the value of the environment variables above, try
running
"make clean", rerun the configure command, and then try to make MET
again.
Please let me know how it goes. If you encounter other problems,
please
include your new config.log and make.log files.
Thanks!
Julie
On Wed, Jan 16, 2019 at 5:58 PM Taylor Mandelbaum via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> Sure!
>
> On Wed, Jan 16, 2019 at 7:55 PM Julie Prestopnik via RT
<met_help at ucar.edu
> >
> wrote:
>
> > Hi Taylor. Thanks! Could you please send the new config.log file
and the
> > new make.log file?
> >
> > Thanks!
> >
> > On Wed, Jan 16, 2019, 5:43 PM Taylor Mandelbaum via RT <
> met_help at ucar.edu
> > wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > >
> > > Hey Julie,
> > >
> > > Thanks for all the help on this, it's really appreciated. I ran
the
> > install
> > > with CC, CXX, and F77 set to the appropriate locations and came
across
> > the
> > > same error with gsl_cdf.h. I reconfigured and re-make/make
install'd
> the
> > > gsl-2.5 package in my directory prior to running the install for
MET
> > again
> > > (MET_GSL is set to the directory I made it in) and still came
across
> this
> > > error:
> > > ../../../src/libcode/vx_gsl_prob/gsl_cdf.h:17:25: fatal error:
> > > gsl/gsl_cdf.h: No such file or directory
> > > compilation terminated.
> > >
> > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT <
> > > met_help at ucar.edu>
> > > wrote:
> > >
> > > > Hi Taylor. In talking with more with John about your
config.log file
> > we
> > > > see that CC is set to use icc (intel), but CXX and F77 are set
to use
> > g++
> > > > and gfortran (GNU).
> > > >
> > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > >
> >
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > CXX='g++'
> > > > F77='gfortran'
> > > >
> > > > Let's see if we can solve the immediate problem before
worrying about
> > any
> > > > potential problems with the external libraries. For now,
please
> choose
> > > > either the GNU compilers or the Intel compilers and set the
following
> > > > variables accordingly. You can chose one and then simply run
the
> > > commands
> > > > below.
> > > >
> > > > *For GNU:*
> > > > export CC=`which gcc`
> > > > export CXX=`which g++`
> > > > export F77=`which gfortran`
> > > >
> > > > *For Intel:*
> > > >
> > > > export CC=`which icc`
> > > > export CXX=`which icc`
> > > > export F77=`which ifort`
> > > >
> > > > Then run "make clean", rerun the configure command, and then
try to
> > make
> > > > MET again.
> > > >
> > > > Let's go from there and see how it works out. Please let me
know.
> > > >
> > > > Julie
> > > >
> > > >
> > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik
<jpresto at ucar.edu>
> > > > wrote:
> > > >
> > > > > Hi Taylor. Thank you for all of this information.
> > > > >
> > > > > Since the libraries were previously installed and we cannot
be
> > certain
> > > > > which compiler was used, are you able and would you be
comfortable
> > > > > installing each of the dependent libraries and not using the
> > previously
> > > > > installed versions? If so, we have an install script that I
can
> > point
> > > > you
> > > > > to, which would install all of the packages and MET as well.
I can
> > > walk
> > > > > through this with you via google hangouts and you can share
your
> > screen
> > > > so
> > > > > we can make sure it is going smoothly. I could do a
hangouts
> > session
> > > > with
> > > > > you tomorrow at 1:15pm (Mountain time) or on Friday at
9:00am
> > (Mountain
> > > > > time). If those times don't work. I can get you started
with very
> > > > > specific instructions via email and we can continue to work
through
> > any
> > > > > problems. We can also set up a different time for next
week,
> > however,
> > > I
> > > > > didn't want you to have to wait that long. Please let me
know your
> > > > > preference.
> > > > >
> > > > > If you think that icc may not be working properly, then you
should
> > > > > probably use the GNU set of compilers, unless there is some
reason
> > not
> > > > to,
> > > > > in which case you may need to get a system administrator
correct
> the
> > > > > problems with the intel compiler.
> > > > >
> > > > > Running "which g++" and running "which gfortran" can tell
you what
> > the
> > > > CXX
> > > > > and F77 paths should be set to. Please let me know if you
have any
> > > > issues
> > > > > with that.
> > > > >
> > > > > Julie
> > > > >
> > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via RT <
> > > > > met_help at ucar.edu> wrote:
> > > > >
> > > > >>
> > > > >> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > >>
> > > > >> Hey Julie,
> > > > >>
> > > > >> 1) They were previously installed, but I just tried running
it
> with
> > > some
> > > > >> of
> > > > >> my own installed versions and they're not working properly
(e.g.
> the
> > > > make
> > > > >> install fails due to gsl/gsl_cdf.h missing... though I set
MET_GSL
> > to
> > > my
> > > > >> gsl-2.5 directory).
> > > > >>
> > > > >> 2) Not sure how I can verify that one, though I think
they're not
> as
> > > > I've
> > > > >> seen GNU and Intel prompts in the config output. My CC var
in my
> > > bashrc
> > > > >> links to an Intel compiler.
> > > > >>
> > > > >> 3) I followed those for the packages, though for the
compilers
> > > section,
> > > > I
> > > > >> do not know my CXX or F77 paths on the hpc that I'm using.
I also
> > > think
> > > > >> the
> > > > >> icc is not working properly as I could not run icc without
a
> license
> > > > >> prompt
> > > > >> coming up.
> > > > >>
> > > > >> I'm not sure if any of that helps, but let me know. Maybe
some of
> > > these
> > > > >> issues are still on our end. The fact that met needs to
only use
> one
> > > > >> compiler might be the issue...
> > > > >>
> > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via RT <
> > > > >> met_help at ucar.edu>
> > > > >> wrote:
> > > > >>
> > > > >> > Hi Taylor. Thank you for passing along your files. I
have a
> few
> > > > >> questions
> > > > >> > for you.
> > > > >> >
> > > > >> > 1) Are you installing the external libraries yourself or
were
> they
> > > > >> > previously installed?
> > > > >> > 2) Can you please verify that the external libraries and
MET are
> > > being
> > > > >> > built with the same family of compilers (e.g. all are
built with
> > > GNU,
> > > > or
> > > > >> > all are build with Intel, etc.)? Which compiler are you
using?
> > > > >> > 3) Are you following the directions on this page as your
> > > instructions
> > > > >> for
> > > > >> > installation?
> > > > >> >
> > > > >> >
> > > > >>
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > >> >
> > > > >> > Thank you!
> > > > >> >
> > > > >> > Julie
> > > > >> >
> > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via RT
<
> > > > >> > met_help at ucar.edu>
> > > > >> > wrote:
> > > > >> >
> > > > >> > >
> > > > >> > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> >
> > > > >> > >
> > > > >> > > Hey Julie,
> > > > >> > >
> > > > >> > > I attached the config and make_install logs here. We
could do
> a
> > > > >> hangouts
> > > > >> > > session as well if you can't pinpoint the issue; I'm
remoting
> in
> > > > from
> > > > >> my
> > > > >> > > home windows computer so it will be a bit hacky.
> > > > >> > >
> > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via RT
<
> > > > >> > met_help at ucar.edu
> > > > >> > > >
> > > > >> > > wrote:
> > > > >> > >
> > > > >> > > > Hi Taylor. It is difficult to tell what is going
without
> more
> > > > >> context.
> > > > >> > > > Could you please send me your config.log file and
your
> > make.log
> > > > >> file?
> > > > >> > > >
> > > > >> > > > We could also consider doing a hangouts session where
you
> can
> > > > share
> > > > >> > your
> > > > >> > > > screen, and I can directly help that way. Either way
> though,
> > if
> > > > you
> > > > >> > > could
> > > > >> > > > please send those files, I would appreciate it.
> > > > >> > > >
> > > > >> > > > Thanks,
> > > > >> > > > Julie
> > > > >> > > >
> > > > >> > > > Thanks!
> > > > >> > > >
> > > > >> > > > Julie
> > > > >> > > >
> > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum via
RT <
> > > > >> > > > met_help at ucar.edu>
> > > > >> > > > wrote:
> > > > >> > > >
> > > > >> > > > >
> > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was acted
upon.
> > > > >> > > > > Transaction: Ticket created by
> > > taylor.mandelbaum at stonybrook.edu
> > > > >> > > > > Queue: met_help
> > > > >> > > > > Subject: met install help
> > > > >> > > > > Owner: Nobody
> > > > >> > > > > Requestors: taylor.mandelbaum at stonybrook.edu
> > > > >> > > > > Status: new
> > > > >> > > > > Ticket <URL:
> > > > >> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > >> > > >
> > > > >> > > > >
> > > > >> > > > >
> > > > >> > > > > Hey all,
> > > > >> > > > >
> > > > >> > > > > I'm presently trying to compile MET 8.0 on our HPC;
when I
> > > > >> configure
> > > > >> > > it,
> > > > >> > > > > I'm getting a few warnings on .h files:
> > > > >> > > > >
> > > > >> > > > > configure: WARNING: errno.h: present but cannot be
> compiled
> > > > >> > > > > configure: WARNING: errno.h: check for missing
> > > prerequisite
> > > > >> > > headers?
> > > > >> > > > > configure: WARNING: errno.h: see the Autoconf
> documentation
> > > > >> > > > > configure: WARNING: errno.h: section "Present
But
> Cannot
> > > Be
> > > > >> > > Compiled"
> > > > >> > > > > configure: WARNING: errno.h: proceeding with the
> compiler's
> > > > result
> > > > >> > > > > configure: WARNING: ##
> --------------------------------
> > ##
> > > > >> > > > > configure: WARNING: ## Report this to
> met_help at ucar.edu
> > > ##
> > > > >> > > > > configure: WARNING: ##
> --------------------------------
> > ##
> > > > >> > > > >
> > > > >> > > > > and the same for fcntl.h, limits.h, stddef.h,
file.h and
> > > > param.h.
> > > > >> > > > >
> > > > >> > > > > When I try to make install, I get this error on the
tail
> of
> > > the
> > > > >> log:
> > > > >> > > > >
> > > > >> > > > > config_scanner.cc: In function ‘void*
> > configalloc(yy_size_t)’:
> > > > >> > > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’ was
not
> > > declared
> > > > in
> > > > >> > this
> > > > >> > > > > scope
> > > > >> > > > > config_scanner.cc: In function ‘void*
configrealloc(void*,
> > > > >> > yy_size_t)’:
> > > > >> > > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’ was
not
> > > declared
> > > > >> in
> > > > >> > > this
> > > > >> > > > > scope
> > > > >> > > > > /* The cast to (char *) in the following
accommodates
> both
> > > > >> > > > > ^
> > > > >> > > > > make[3]: *** [libvx_config_a-config_scanner.o]
Error 1
> > > > >> > > > > make[3]: Leaving directory
> > > > >> > > > > `/E1/taylorm/MET8/met-
8.0_bugfix/src/basic/vx_config'
> > > > >> > > > > make[2]: *** [install-recursive] Error 1
> > > > >> > > > > make[2]: Leaving directory
> > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > >> > > > > make[1]: *** [install-recursive] Error 1
> > > > >> > > > > make[1]: Leaving directory
> > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > >> > > > > make: *** [install-recursive] Error 1
> > > > >> > > > >
> > > > >> > > > > Not sure how to address either of these, hopefully
you
> guys
> > > can
> > > > >> > provide
> > > > >> > > > > some insight.
> > > > >> > > > >
> > > > >> > > > > Thanks!
> > > > >> > > > > --
> > > > >> > > > > *Taylor Mandelbaum*
> > > > >> > > > > Research Technician
> > > > >> > > > > SoMAS | Stony Brook University
> > > > >> > > > > 678.468.5789
> > > > >> > > > >
> > > > >> > > > >
> > > > >> > > >
> > > > >> > > >
> > > > >> > >
> > > > >> > > --
> > > > >> > > *Taylor Mandelbaum*
> > > > >> > > Research Technician
> > > > >> > > SoMAS | Stony Brook University
> > > > >> > > 678.468.5789
> > > > >> > >
> > > > >> > >
> > > > >> >
> > > > >> >
> > > > >>
> > > > >> --
> > > > >> *Taylor Mandelbaum*
> > > > >> Research Technician
> > > > >> SoMAS | Stony Brook University
> > > > >> 678.468.5789
> > > > >>
> > > > >>
> > > >
> > > >
> > >
> > > --
> > > *Taylor Mandelbaum*
> > > Research Technician
> > > SoMAS | Stony Brook University
> > > 678.468.5789
> > >
> > >
> >
> >
>
> --
> *Taylor Mandelbaum*
> Research Technician
> SoMAS | Stony Brook University
> 678.468.5789
>
>
------------------------------------------------
Subject: met install help
From: John Halley Gotway
Time: Thu Jan 17 09:19:27 2019
Hi Julie and Taylor,
I have one pesky little detail to mention about GSL that may be a
point of
confusion here.
Typically when your run "make install" on a software package and tell
it to
install to "/install_dir", it installs header files into
"/install_dir/include" and library files into "/install_dir/lib".
However,
the GSL package installs header files into "/install_dir/include/gsl".
And
because of this, the MET code uses that gsl prefix:
include "gsl/gsl_cdf.h"
So Taylor, after you fix the typo in your MET_GSL setting, please
check if
this file exists:
MET_GSL='/E1/taylorm/MET8/gsl-2.5'
*ls /E1/taylorm/MET8/gsl-2**.5/include/gsl/gsl_cdf.h*
There is a second potential point of confusion. The vx_gsl_prob
library *inside
of MET* contains code which wraps functions from the GSL library. I
think
we chose filenames poorly in that library. For example,
vx_gsl_prob/gsl_cdf.h is a header file in the *MET* code tree while
$MET_GSL/include/gsl/gsl_cdf.h is a file from the GSL library. This
doesn't cause a problem in the compilation or running of MET but can
cause
confusion if you go hunting around for a file named gsl_cdf.h.
Thanks,
John
On Thu, Jan 17, 2019 at 9:00 AM Julie Prestopnik via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> Hi Taylor. Thank you.
>
> It looks like you may be missing a leading slash in front of E1 in
the
> environment variables below:
>
> MET_GSL='E1/taylorm/MET8/gsl-2.5'
> MET_BUFRLIB='E1/taylorm/MET8/BUFRLIB'
>
> Also, can you please confirm that gsl_cdf.h exists at the following
> location?
> ${MET_GSL}/include
>
> If gsl_cdf.h exists in that location and you are missing a leading
slash,
> please modify the value of the environment variables above, try
running
> "make clean", rerun the configure command, and then try to make MET
again.
>
> Please let me know how it goes. If you encounter other problems,
please
> include your new config.log and make.log files.
>
> Thanks!
>
> Julie
>
>
>
> On Wed, Jan 16, 2019 at 5:58 PM Taylor Mandelbaum via RT <
> met_help at ucar.edu>
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> >
> > Sure!
> >
> > On Wed, Jan 16, 2019 at 7:55 PM Julie Prestopnik via RT <
> met_help at ucar.edu
> > >
> > wrote:
> >
> > > Hi Taylor. Thanks! Could you please send the new config.log file
and
> the
> > > new make.log file?
> > >
> > > Thanks!
> > >
> > > On Wed, Jan 16, 2019, 5:43 PM Taylor Mandelbaum via RT <
> > met_help at ucar.edu
> > > wrote:
> > >
> > > >
> > > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
>
> > > >
> > > > Hey Julie,
> > > >
> > > > Thanks for all the help on this, it's really appreciated. I
ran the
> > > install
> > > > with CC, CXX, and F77 set to the appropriate locations and
came
> across
> > > the
> > > > same error with gsl_cdf.h. I reconfigured and re-make/make
install'd
> > the
> > > > gsl-2.5 package in my directory prior to running the install
for MET
> > > again
> > > > (MET_GSL is set to the directory I made it in) and still came
across
> > this
> > > > error:
> > > > ../../../src/libcode/vx_gsl_prob/gsl_cdf.h:17:25: fatal error:
> > > > gsl/gsl_cdf.h: No such file or directory
> > > > compilation terminated.
> > > >
> > > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT <
> > > > met_help at ucar.edu>
> > > > wrote:
> > > >
> > > > > Hi Taylor. In talking with more with John about your
config.log
> file
> > > we
> > > > > see that CC is set to use icc (intel), but CXX and F77 are
set to
> use
> > > g++
> > > > > and gfortran (GNU).
> > > > >
> > > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > > >
> > >
>
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > > CXX='g++'
> > > > > F77='gfortran'
> > > > >
> > > > > Let's see if we can solve the immediate problem before
worrying
> about
> > > any
> > > > > potential problems with the external libraries. For now,
please
> > choose
> > > > > either the GNU compilers or the Intel compilers and set the
> following
> > > > > variables accordingly. You can chose one and then simply
run the
> > > > commands
> > > > > below.
> > > > >
> > > > > *For GNU:*
> > > > > export CC=`which gcc`
> > > > > export CXX=`which g++`
> > > > > export F77=`which gfortran`
> > > > >
> > > > > *For Intel:*
> > > > >
> > > > > export CC=`which icc`
> > > > > export CXX=`which icc`
> > > > > export F77=`which ifort`
> > > > >
> > > > > Then run "make clean", rerun the configure command, and then
try to
> > > make
> > > > > MET again.
> > > > >
> > > > > Let's go from there and see how it works out. Please let me
know.
> > > > >
> > > > > Julie
> > > > >
> > > > >
> > > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik <
> jpresto at ucar.edu>
> > > > > wrote:
> > > > >
> > > > > > Hi Taylor. Thank you for all of this information.
> > > > > >
> > > > > > Since the libraries were previously installed and we
cannot be
> > > certain
> > > > > > which compiler was used, are you able and would you be
> comfortable
> > > > > > installing each of the dependent libraries and not using
the
> > > previously
> > > > > > installed versions? If so, we have an install script that
I can
> > > point
> > > > > you
> > > > > > to, which would install all of the packages and MET as
well. I
> can
> > > > walk
> > > > > > through this with you via google hangouts and you can
share your
> > > screen
> > > > > so
> > > > > > we can make sure it is going smoothly. I could do a
hangouts
> > > session
> > > > > with
> > > > > > you tomorrow at 1:15pm (Mountain time) or on Friday at
9:00am
> > > (Mountain
> > > > > > time). If those times don't work. I can get you started
with
> very
> > > > > > specific instructions via email and we can continue to
work
> through
> > > any
> > > > > > problems. We can also set up a different time for next
week,
> > > however,
> > > > I
> > > > > > didn't want you to have to wait that long. Please let me
know
> your
> > > > > > preference.
> > > > > >
> > > > > > If you think that icc may not be working properly, then
you
> should
> > > > > > probably use the GNU set of compilers, unless there is
some
> reason
> > > not
> > > > > to,
> > > > > > in which case you may need to get a system administrator
correct
> > the
> > > > > > problems with the intel compiler.
> > > > > >
> > > > > > Running "which g++" and running "which gfortran" can tell
you
> what
> > > the
> > > > > CXX
> > > > > > and F77 paths should be set to. Please let me know if you
have
> any
> > > > > issues
> > > > > > with that.
> > > > > >
> > > > > > Julie
> > > > > >
> > > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via RT <
> > > > > > met_help at ucar.edu> wrote:
> > > > > >
> > > > > >>
> > > > > >> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > > >>
> > > > > >> Hey Julie,
> > > > > >>
> > > > > >> 1) They were previously installed, but I just tried
running it
> > with
> > > > some
> > > > > >> of
> > > > > >> my own installed versions and they're not working
properly (e.g.
> > the
> > > > > make
> > > > > >> install fails due to gsl/gsl_cdf.h missing... though I
set
> MET_GSL
> > > to
> > > > my
> > > > > >> gsl-2.5 directory).
> > > > > >>
> > > > > >> 2) Not sure how I can verify that one, though I think
they're
> not
> > as
> > > > > I've
> > > > > >> seen GNU and Intel prompts in the config output. My CC
var in my
> > > > bashrc
> > > > > >> links to an Intel compiler.
> > > > > >>
> > > > > >> 3) I followed those for the packages, though for the
compilers
> > > > section,
> > > > > I
> > > > > >> do not know my CXX or F77 paths on the hpc that I'm
using. I
> also
> > > > think
> > > > > >> the
> > > > > >> icc is not working properly as I could not run icc
without a
> > license
> > > > > >> prompt
> > > > > >> coming up.
> > > > > >>
> > > > > >> I'm not sure if any of that helps, but let me know. Maybe
some
> of
> > > > these
> > > > > >> issues are still on our end. The fact that met needs to
only use
> > one
> > > > > >> compiler might be the issue...
> > > > > >>
> > > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via RT
<
> > > > > >> met_help at ucar.edu>
> > > > > >> wrote:
> > > > > >>
> > > > > >> > Hi Taylor. Thank you for passing along your files. I
have a
> > few
> > > > > >> questions
> > > > > >> > for you.
> > > > > >> >
> > > > > >> > 1) Are you installing the external libraries yourself
or were
> > they
> > > > > >> > previously installed?
> > > > > >> > 2) Can you please verify that the external libraries
and MET
> are
> > > > being
> > > > > >> > built with the same family of compilers (e.g. all are
built
> with
> > > > GNU,
> > > > > or
> > > > > >> > all are build with Intel, etc.)? Which compiler are
you
> using?
> > > > > >> > 3) Are you following the directions on this page as
your
> > > > instructions
> > > > > >> for
> > > > > >> > installation?
> > > > > >> >
> > > > > >> >
> > > > > >>
> > > > >
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > > >> >
> > > > > >> > Thank you!
> > > > > >> >
> > > > > >> > Julie
> > > > > >> >
> > > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via
RT <
> > > > > >> > met_help at ucar.edu>
> > > > > >> > wrote:
> > > > > >> >
> > > > > >> > >
> > > > > >> > > <URL:
> https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > >
> > > > > >> > >
> > > > > >> > > Hey Julie,
> > > > > >> > >
> > > > > >> > > I attached the config and make_install logs here. We
could
> do
> > a
> > > > > >> hangouts
> > > > > >> > > session as well if you can't pinpoint the issue; I'm
> remoting
> > in
> > > > > from
> > > > > >> my
> > > > > >> > > home windows computer so it will be a bit hacky.
> > > > > >> > >
> > > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via
RT <
> > > > > >> > met_help at ucar.edu
> > > > > >> > > >
> > > > > >> > > wrote:
> > > > > >> > >
> > > > > >> > > > Hi Taylor. It is difficult to tell what is going
without
> > more
> > > > > >> context.
> > > > > >> > > > Could you please send me your config.log file and
your
> > > make.log
> > > > > >> file?
> > > > > >> > > >
> > > > > >> > > > We could also consider doing a hangouts session
where you
> > can
> > > > > share
> > > > > >> > your
> > > > > >> > > > screen, and I can directly help that way. Either
way
> > though,
> > > if
> > > > > you
> > > > > >> > > could
> > > > > >> > > > please send those files, I would appreciate it.
> > > > > >> > > >
> > > > > >> > > > Thanks,
> > > > > >> > > > Julie
> > > > > >> > > >
> > > > > >> > > > Thanks!
> > > > > >> > > >
> > > > > >> > > > Julie
> > > > > >> > > >
> > > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum
via RT <
> > > > > >> > > > met_help at ucar.edu>
> > > > > >> > > > wrote:
> > > > > >> > > >
> > > > > >> > > > >
> > > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was acted
upon.
> > > > > >> > > > > Transaction: Ticket created by
> > > > taylor.mandelbaum at stonybrook.edu
> > > > > >> > > > > Queue: met_help
> > > > > >> > > > > Subject: met install help
> > > > > >> > > > > Owner: Nobody
> > > > > >> > > > > Requestors: taylor.mandelbaum at stonybrook.edu
> > > > > >> > > > > Status: new
> > > > > >> > > > > Ticket <URL:
> > > > > >> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > >> > > >
> > > > > >> > > > >
> > > > > >> > > > >
> > > > > >> > > > > Hey all,
> > > > > >> > > > >
> > > > > >> > > > > I'm presently trying to compile MET 8.0 on our
HPC;
> when I
> > > > > >> configure
> > > > > >> > > it,
> > > > > >> > > > > I'm getting a few warnings on .h files:
> > > > > >> > > > >
> > > > > >> > > > > configure: WARNING: errno.h: present but cannot
be
> > compiled
> > > > > >> > > > > configure: WARNING: errno.h: check for
missing
> > > > prerequisite
> > > > > >> > > headers?
> > > > > >> > > > > configure: WARNING: errno.h: see the Autoconf
> > documentation
> > > > > >> > > > > configure: WARNING: errno.h: section "Present
But
> > Cannot
> > > > Be
> > > > > >> > > Compiled"
> > > > > >> > > > > configure: WARNING: errno.h: proceeding with the
> > compiler's
> > > > > result
> > > > > >> > > > > configure: WARNING: ##
> > --------------------------------
> > > ##
> > > > > >> > > > > configure: WARNING: ## Report this to
> > met_help at ucar.edu
> > > > ##
> > > > > >> > > > > configure: WARNING: ##
> > --------------------------------
> > > ##
> > > > > >> > > > >
> > > > > >> > > > > and the same for fcntl.h, limits.h, stddef.h,
file.h and
> > > > > param.h.
> > > > > >> > > > >
> > > > > >> > > > > When I try to make install, I get this error on
the tail
> > of
> > > > the
> > > > > >> log:
> > > > > >> > > > >
> > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > configalloc(yy_size_t)’:
> > > > > >> > > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’
was not
> > > > declared
> > > > > in
> > > > > >> > this
> > > > > >> > > > > scope
> > > > > >> > > > > config_scanner.cc: In function ‘void*
> configrealloc(void*,
> > > > > >> > yy_size_t)’:
> > > > > >> > > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’
was not
> > > > declared
> > > > > >> in
> > > > > >> > > this
> > > > > >> > > > > scope
> > > > > >> > > > > /* The cast to (char *) in the following
accommodates
> > both
> > > > > >> > > > > ^
> > > > > >> > > > > make[3]: *** [libvx_config_a-config_scanner.o]
Error 1
> > > > > >> > > > > make[3]: Leaving directory
> > > > > >> > > > > `/E1/taylorm/MET8/met-
8.0_bugfix/src/basic/vx_config'
> > > > > >> > > > > make[2]: *** [install-recursive] Error 1
> > > > > >> > > > > make[2]: Leaving directory
> > > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > > >> > > > > make[1]: *** [install-recursive] Error 1
> > > > > >> > > > > make[1]: Leaving directory
> > > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > > >> > > > > make: *** [install-recursive] Error 1
> > > > > >> > > > >
> > > > > >> > > > > Not sure how to address either of these,
hopefully you
> > guys
> > > > can
> > > > > >> > provide
> > > > > >> > > > > some insight.
> > > > > >> > > > >
> > > > > >> > > > > Thanks!
> > > > > >> > > > > --
> > > > > >> > > > > *Taylor Mandelbaum*
> > > > > >> > > > > Research Technician
> > > > > >> > > > > SoMAS | Stony Brook University
> > > > > >> > > > > 678.468.5789
> > > > > >> > > > >
> > > > > >> > > > >
> > > > > >> > > >
> > > > > >> > > >
> > > > > >> > >
> > > > > >> > > --
> > > > > >> > > *Taylor Mandelbaum*
> > > > > >> > > Research Technician
> > > > > >> > > SoMAS | Stony Brook University
> > > > > >> > > 678.468.5789
> > > > > >> > >
> > > > > >> > >
> > > > > >> >
> > > > > >> >
> > > > > >>
> > > > > >> --
> > > > > >> *Taylor Mandelbaum*
> > > > > >> Research Technician
> > > > > >> SoMAS | Stony Brook University
> > > > > >> 678.468.5789
> > > > > >>
> > > > > >>
> > > > >
> > > > >
> > > >
> > > > --
> > > > *Taylor Mandelbaum*
> > > > Research Technician
> > > > SoMAS | Stony Brook University
> > > > 678.468.5789
> > > >
> > > >
> > >
> > >
> >
> > --
> > *Taylor Mandelbaum*
> > Research Technician
> > SoMAS | Stony Brook University
> > 678.468.5789
> >
> >
>
>
------------------------------------------------
Subject: met install help
From: Taylor Mandelbaum
Time: Thu Jan 17 15:44:20 2019
Thanks all. I fixed the typos, checked to see if the file is in
gsl2.5/include/gsl (it is), and reran it with the same error. Attached
the
logs. I also attached my bashrc for brevity.
On Thu, Jan 17, 2019 at 11:19 AM John Halley Gotway via RT <
met_help at ucar.edu> wrote:
> Hi Julie and Taylor,
>
> I have one pesky little detail to mention about GSL that may be a
point of
> confusion here.
>
> Typically when your run "make install" on a software package and
tell it to
> install to "/install_dir", it installs header files into
> "/install_dir/include" and library files into "/install_dir/lib".
However,
> the GSL package installs header files into
"/install_dir/include/gsl". And
> because of this, the MET code uses that gsl prefix:
> include "gsl/gsl_cdf.h"
>
> So Taylor, after you fix the typo in your MET_GSL setting, please
check if
> this file exists:
>
> MET_GSL='/E1/taylorm/MET8/gsl-2.5'
>
> *ls /E1/taylorm/MET8/gsl-2**.5/include/gsl/gsl_cdf.h*
>
> There is a second potential point of confusion. The vx_gsl_prob
> library *inside
> of MET* contains code which wraps functions from the GSL library. I
think
> we chose filenames poorly in that library. For example,
> vx_gsl_prob/gsl_cdf.h is a header file in the *MET* code tree while
> $MET_GSL/include/gsl/gsl_cdf.h is a file from the GSL library. This
> doesn't cause a problem in the compilation or running of MET but can
cause
> confusion if you go hunting around for a file named gsl_cdf.h.
>
> Thanks,
> John
>
>
>
>
>
> On Thu, Jan 17, 2019 at 9:00 AM Julie Prestopnik via RT
<met_help at ucar.edu
> >
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> >
> > Hi Taylor. Thank you.
> >
> > It looks like you may be missing a leading slash in front of E1 in
the
> > environment variables below:
> >
> > MET_GSL='E1/taylorm/MET8/gsl-2.5'
> > MET_BUFRLIB='E1/taylorm/MET8/BUFRLIB'
> >
> > Also, can you please confirm that gsl_cdf.h exists at the
following
> > location?
> > ${MET_GSL}/include
> >
> > If gsl_cdf.h exists in that location and you are missing a leading
slash,
> > please modify the value of the environment variables above, try
running
> > "make clean", rerun the configure command, and then try to make
MET
> again.
> >
> > Please let me know how it goes. If you encounter other problems,
please
> > include your new config.log and make.log files.
> >
> > Thanks!
> >
> > Julie
> >
> >
> >
> > On Wed, Jan 16, 2019 at 5:58 PM Taylor Mandelbaum via RT <
> > met_help at ucar.edu>
> > wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > >
> > > Sure!
> > >
> > > On Wed, Jan 16, 2019 at 7:55 PM Julie Prestopnik via RT <
> > met_help at ucar.edu
> > > >
> > > wrote:
> > >
> > > > Hi Taylor. Thanks! Could you please send the new config.log
file and
> > the
> > > > new make.log file?
> > > >
> > > > Thanks!
> > > >
> > > > On Wed, Jan 16, 2019, 5:43 PM Taylor Mandelbaum via RT <
> > > met_help at ucar.edu
> > > > wrote:
> > > >
> > > > >
> > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > >
> > > > > Hey Julie,
> > > > >
> > > > > Thanks for all the help on this, it's really appreciated. I
ran the
> > > > install
> > > > > with CC, CXX, and F77 set to the appropriate locations and
came
> > across
> > > > the
> > > > > same error with gsl_cdf.h. I reconfigured and re-make/make
> install'd
> > > the
> > > > > gsl-2.5 package in my directory prior to running the install
for
> MET
> > > > again
> > > > > (MET_GSL is set to the directory I made it in) and still
came
> across
> > > this
> > > > > error:
> > > > > ../../../src/libcode/vx_gsl_prob/gsl_cdf.h:17:25: fatal
error:
> > > > > gsl/gsl_cdf.h: No such file or directory
> > > > > compilation terminated.
> > > > >
> > > > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT <
> > > > > met_help at ucar.edu>
> > > > > wrote:
> > > > >
> > > > > > Hi Taylor. In talking with more with John about your
config.log
> > file
> > > > we
> > > > > > see that CC is set to use icc (intel), but CXX and F77 are
set to
> > use
> > > > g++
> > > > > > and gfortran (GNU).
> > > > > >
> > > > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > > > >
> > > >
> >
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > > > CXX='g++'
> > > > > > F77='gfortran'
> > > > > >
> > > > > > Let's see if we can solve the immediate problem before
worrying
> > about
> > > > any
> > > > > > potential problems with the external libraries. For now,
please
> > > choose
> > > > > > either the GNU compilers or the Intel compilers and set
the
> > following
> > > > > > variables accordingly. You can chose one and then simply
run the
> > > > > commands
> > > > > > below.
> > > > > >
> > > > > > *For GNU:*
> > > > > > export CC=`which gcc`
> > > > > > export CXX=`which g++`
> > > > > > export F77=`which gfortran`
> > > > > >
> > > > > > *For Intel:*
> > > > > >
> > > > > > export CC=`which icc`
> > > > > > export CXX=`which icc`
> > > > > > export F77=`which ifort`
> > > > > >
> > > > > > Then run "make clean", rerun the configure command, and
then try
> to
> > > > make
> > > > > > MET again.
> > > > > >
> > > > > > Let's go from there and see how it works out. Please let
me
> know.
> > > > > >
> > > > > > Julie
> > > > > >
> > > > > >
> > > > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik <
> > jpresto at ucar.edu>
> > > > > > wrote:
> > > > > >
> > > > > > > Hi Taylor. Thank you for all of this information.
> > > > > > >
> > > > > > > Since the libraries were previously installed and we
cannot be
> > > > certain
> > > > > > > which compiler was used, are you able and would you be
> > comfortable
> > > > > > > installing each of the dependent libraries and not using
the
> > > > previously
> > > > > > > installed versions? If so, we have an install script
that I
> can
> > > > point
> > > > > > you
> > > > > > > to, which would install all of the packages and MET as
well. I
> > can
> > > > > walk
> > > > > > > through this with you via google hangouts and you can
share
> your
> > > > screen
> > > > > > so
> > > > > > > we can make sure it is going smoothly. I could do a
hangouts
> > > > session
> > > > > > with
> > > > > > > you tomorrow at 1:15pm (Mountain time) or on Friday at
9:00am
> > > > (Mountain
> > > > > > > time). If those times don't work. I can get you
started with
> > very
> > > > > > > specific instructions via email and we can continue to
work
> > through
> > > > any
> > > > > > > problems. We can also set up a different time for next
week,
> > > > however,
> > > > > I
> > > > > > > didn't want you to have to wait that long. Please let
me know
> > your
> > > > > > > preference.
> > > > > > >
> > > > > > > If you think that icc may not be working properly, then
you
> > should
> > > > > > > probably use the GNU set of compilers, unless there is
some
> > reason
> > > > not
> > > > > > to,
> > > > > > > in which case you may need to get a system administrator
> correct
> > > the
> > > > > > > problems with the intel compiler.
> > > > > > >
> > > > > > > Running "which g++" and running "which gfortran" can
tell you
> > what
> > > > the
> > > > > > CXX
> > > > > > > and F77 paths should be set to. Please let me know if
you have
> > any
> > > > > > issues
> > > > > > > with that.
> > > > > > >
> > > > > > > Julie
> > > > > > >
> > > > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via RT
<
> > > > > > > met_help at ucar.edu> wrote:
> > > > > > >
> > > > > > >>
> > > > > > >> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> >
> > > > > > >>
> > > > > > >> Hey Julie,
> > > > > > >>
> > > > > > >> 1) They were previously installed, but I just tried
running it
> > > with
> > > > > some
> > > > > > >> of
> > > > > > >> my own installed versions and they're not working
properly
> (e.g.
> > > the
> > > > > > make
> > > > > > >> install fails due to gsl/gsl_cdf.h missing... though I
set
> > MET_GSL
> > > > to
> > > > > my
> > > > > > >> gsl-2.5 directory).
> > > > > > >>
> > > > > > >> 2) Not sure how I can verify that one, though I think
they're
> > not
> > > as
> > > > > > I've
> > > > > > >> seen GNU and Intel prompts in the config output. My CC
var in
> my
> > > > > bashrc
> > > > > > >> links to an Intel compiler.
> > > > > > >>
> > > > > > >> 3) I followed those for the packages, though for the
compilers
> > > > > section,
> > > > > > I
> > > > > > >> do not know my CXX or F77 paths on the hpc that I'm
using. I
> > also
> > > > > think
> > > > > > >> the
> > > > > > >> icc is not working properly as I could not run icc
without a
> > > license
> > > > > > >> prompt
> > > > > > >> coming up.
> > > > > > >>
> > > > > > >> I'm not sure if any of that helps, but let me know.
Maybe some
> > of
> > > > > these
> > > > > > >> issues are still on our end. The fact that met needs to
only
> use
> > > one
> > > > > > >> compiler might be the issue...
> > > > > > >>
> > > > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via
RT <
> > > > > > >> met_help at ucar.edu>
> > > > > > >> wrote:
> > > > > > >>
> > > > > > >> > Hi Taylor. Thank you for passing along your files.
I have
> a
> > > few
> > > > > > >> questions
> > > > > > >> > for you.
> > > > > > >> >
> > > > > > >> > 1) Are you installing the external libraries yourself
or
> were
> > > they
> > > > > > >> > previously installed?
> > > > > > >> > 2) Can you please verify that the external libraries
and MET
> > are
> > > > > being
> > > > > > >> > built with the same family of compilers (e.g. all are
built
> > with
> > > > > GNU,
> > > > > > or
> > > > > > >> > all are build with Intel, etc.)? Which compiler are
you
> > using?
> > > > > > >> > 3) Are you following the directions on this page as
your
> > > > > instructions
> > > > > > >> for
> > > > > > >> > installation?
> > > > > > >> >
> > > > > > >> >
> > > > > > >>
> > > > > >
> > > > >
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > > > >> >
> > > > > > >> > Thank you!
> > > > > > >> >
> > > > > > >> > Julie
> > > > > > >> >
> > > > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via
RT <
> > > > > > >> > met_help at ucar.edu>
> > > > > > >> > wrote:
> > > > > > >> >
> > > > > > >> > >
> > > > > > >> > > <URL:
> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > >
> > > > > > >> > >
> > > > > > >> > > Hey Julie,
> > > > > > >> > >
> > > > > > >> > > I attached the config and make_install logs here.
We could
> > do
> > > a
> > > > > > >> hangouts
> > > > > > >> > > session as well if you can't pinpoint the issue;
I'm
> > remoting
> > > in
> > > > > > from
> > > > > > >> my
> > > > > > >> > > home windows computer so it will be a bit hacky.
> > > > > > >> > >
> > > > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik
via RT <
> > > > > > >> > met_help at ucar.edu
> > > > > > >> > > >
> > > > > > >> > > wrote:
> > > > > > >> > >
> > > > > > >> > > > Hi Taylor. It is difficult to tell what is going
> without
> > > more
> > > > > > >> context.
> > > > > > >> > > > Could you please send me your config.log file and
your
> > > > make.log
> > > > > > >> file?
> > > > > > >> > > >
> > > > > > >> > > > We could also consider doing a hangouts session
where
> you
> > > can
> > > > > > share
> > > > > > >> > your
> > > > > > >> > > > screen, and I can directly help that way. Either
way
> > > though,
> > > > if
> > > > > > you
> > > > > > >> > > could
> > > > > > >> > > > please send those files, I would appreciate it.
> > > > > > >> > > >
> > > > > > >> > > > Thanks,
> > > > > > >> > > > Julie
> > > > > > >> > > >
> > > > > > >> > > > Thanks!
> > > > > > >> > > >
> > > > > > >> > > > Julie
> > > > > > >> > > >
> > > > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum
via
> RT <
> > > > > > >> > > > met_help at ucar.edu>
> > > > > > >> > > > wrote:
> > > > > > >> > > >
> > > > > > >> > > > >
> > > > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was
acted
> upon.
> > > > > > >> > > > > Transaction: Ticket created by
> > > > > taylor.mandelbaum at stonybrook.edu
> > > > > > >> > > > > Queue: met_help
> > > > > > >> > > > > Subject: met install help
> > > > > > >> > > > > Owner: Nobody
> > > > > > >> > > > > Requestors: taylor.mandelbaum at stonybrook.edu
> > > > > > >> > > > > Status: new
> > > > > > >> > > > > Ticket <URL:
> > > > > > >> >
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > >> > > >
> > > > > > >> > > > >
> > > > > > >> > > > >
> > > > > > >> > > > > Hey all,
> > > > > > >> > > > >
> > > > > > >> > > > > I'm presently trying to compile MET 8.0 on our
HPC;
> > when I
> > > > > > >> configure
> > > > > > >> > > it,
> > > > > > >> > > > > I'm getting a few warnings on .h files:
> > > > > > >> > > > >
> > > > > > >> > > > > configure: WARNING: errno.h: present but cannot
be
> > > compiled
> > > > > > >> > > > > configure: WARNING: errno.h: check for
missing
> > > > > prerequisite
> > > > > > >> > > headers?
> > > > > > >> > > > > configure: WARNING: errno.h: see the Autoconf
> > > documentation
> > > > > > >> > > > > configure: WARNING: errno.h: section
"Present But
> > > Cannot
> > > > > Be
> > > > > > >> > > Compiled"
> > > > > > >> > > > > configure: WARNING: errno.h: proceeding with
the
> > > compiler's
> > > > > > result
> > > > > > >> > > > > configure: WARNING: ##
> > > --------------------------------
> > > > ##
> > > > > > >> > > > > configure: WARNING: ## Report this to
> > > met_help at ucar.edu
> > > > > ##
> > > > > > >> > > > > configure: WARNING: ##
> > > --------------------------------
> > > > ##
> > > > > > >> > > > >
> > > > > > >> > > > > and the same for fcntl.h, limits.h, stddef.h,
file.h
> and
> > > > > > param.h.
> > > > > > >> > > > >
> > > > > > >> > > > > When I try to make install, I get this error on
the
> tail
> > > of
> > > > > the
> > > > > > >> log:
> > > > > > >> > > > >
> > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > configalloc(yy_size_t)’:
> > > > > > >> > > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’
was not
> > > > > declared
> > > > > > in
> > > > > > >> > this
> > > > > > >> > > > > scope
> > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > configrealloc(void*,
> > > > > > >> > yy_size_t)’:
> > > > > > >> > > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’
was
> not
> > > > > declared
> > > > > > >> in
> > > > > > >> > > this
> > > > > > >> > > > > scope
> > > > > > >> > > > > /* The cast to (char *) in the following
> accommodates
> > > both
> > > > > > >> > > > > ^
> > > > > > >> > > > > make[3]: *** [libvx_config_a-config_scanner.o]
Error 1
> > > > > > >> > > > > make[3]: Leaving directory
> > > > > > >> > > > > `/E1/taylorm/MET8/met-
8.0_bugfix/src/basic/vx_config'
> > > > > > >> > > > > make[2]: *** [install-recursive] Error 1
> > > > > > >> > > > > make[2]: Leaving directory
> > > > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > > > >> > > > > make[1]: *** [install-recursive] Error 1
> > > > > > >> > > > > make[1]: Leaving directory
> > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > > > >> > > > > make: *** [install-recursive] Error 1
> > > > > > >> > > > >
> > > > > > >> > > > > Not sure how to address either of these,
hopefully you
> > > guys
> > > > > can
> > > > > > >> > provide
> > > > > > >> > > > > some insight.
> > > > > > >> > > > >
> > > > > > >> > > > > Thanks!
> > > > > > >> > > > > --
> > > > > > >> > > > > *Taylor Mandelbaum*
> > > > > > >> > > > > Research Technician
> > > > > > >> > > > > SoMAS | Stony Brook University
> > > > > > >> > > > > 678.468.5789
> > > > > > >> > > > >
> > > > > > >> > > > >
> > > > > > >> > > >
> > > > > > >> > > >
> > > > > > >> > >
> > > > > > >> > > --
> > > > > > >> > > *Taylor Mandelbaum*
> > > > > > >> > > Research Technician
> > > > > > >> > > SoMAS | Stony Brook University
> > > > > > >> > > 678.468.5789
> > > > > > >> > >
> > > > > > >> > >
> > > > > > >> >
> > > > > > >> >
> > > > > > >>
> > > > > > >> --
> > > > > > >> *Taylor Mandelbaum*
> > > > > > >> Research Technician
> > > > > > >> SoMAS | Stony Brook University
> > > > > > >> 678.468.5789
> > > > > > >>
> > > > > > >>
> > > > > >
> > > > > >
> > > > >
> > > > > --
> > > > > *Taylor Mandelbaum*
> > > > > Research Technician
> > > > > SoMAS | Stony Brook University
> > > > > 678.468.5789
> > > > >
> > > > >
> > > >
> > > >
> > >
> > > --
> > > *Taylor Mandelbaum*
> > > Research Technician
> > > SoMAS | Stony Brook University
> > > 678.468.5789
> > >
> > >
> >
> >
>
>
--
*Taylor Mandelbaum*
Research Technician
SoMAS | Stony Brook University
678.468.5789
------------------------------------------------
Subject: met install help
From: Taylor Mandelbaum
Time: Thu Jan 17 15:44:20 2019
# .bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
source
/cm/shared/apps/intel/composer_xe/2013_sp1.3.174/bin/ifortvars.sh
intel64
module load python/3.5.2
module load shared
module load gcc/5.1.0
module load torque/5.1.0
module load netcdf
export CC=/cm/local/apps/gcc/5.1.0/bin/gcc
export CXX=/cm/local/apps/gcc/5.1.0/bin/g++
export F77=/cm/local/apps/gcc/5.1.0/bin/gfortran
export NETCDF=/opt/netcdf-gfortan/
export WRFIO_NCD_LARGE_FILE_SUPPORT=1
export JASPERLIB=/opt-soft/lib
export JASPERINC=/opt-soft/include
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel-soft/lib
export MET_BUFRLIB=/E1/taylorm/MET8/BUFRLIB
export MET_GRIB2CINC=/D2/ryan/g2clib-1.6.0
export MET_GRIB2CLIB=/D2/ryan/g2clib-1.6.0
export MET_GSL=/E1/taylorm/MET8/gsl-2.5
export MET_CAIROINC=/D2/ryan/cairo-1.12.0/include/cairo
export MET_CAIROLIB=/D2/ryan/cairo-1.12.0/lib/cairo
export MET_FREETYPE=/D2/ryan/freetype-2.6.4
export MET_FONT_DIR=/D2/ryan/fonts
export MET_NETCDF=/opt/netcdf-gfortan/
------------------------------------------------
Subject: met install help
From: Julie Prestopnik
Time: Thu Jan 17 16:35:53 2019
Hi Taylor.
Unfortunately the change, which I see in your bashrc.txt file, was not
picked up. I still see the following in config.log:
MET_BUFRLIB='E1/taylorm/MET8/BUFRLIB'
MET_GSL='E1/taylorm/MET8/gsl-2.5'
Please note that there is no leading slash before "E1". After you
changed
your .bashrc file, did you either run "source ~/.bashrc" or open a new
shell? If not, that would explain what is happening. Please either
run
"source ~/.bashrc" or open a new shell. You can run "echo $MET_GSL"
afterward to verify that you see a leading slash in front of "E1".
Please give that a try and let us know how it goes.
Thanks,
Julie
On Thu, Jan 17, 2019 at 3:44 PM Taylor Mandelbaum via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> Thanks all. I fixed the typos, checked to see if the file is in
> gsl2.5/include/gsl (it is), and reran it with the same error.
Attached the
> logs. I also attached my bashrc for brevity.
>
> On Thu, Jan 17, 2019 at 11:19 AM John Halley Gotway via RT <
> met_help at ucar.edu> wrote:
>
> > Hi Julie and Taylor,
> >
> > I have one pesky little detail to mention about GSL that may be a
point
> of
> > confusion here.
> >
> > Typically when your run "make install" on a software package and
tell it
> to
> > install to "/install_dir", it installs header files into
> > "/install_dir/include" and library files into "/install_dir/lib".
> However,
> > the GSL package installs header files into
"/install_dir/include/gsl".
> And
> > because of this, the MET code uses that gsl prefix:
> > include "gsl/gsl_cdf.h"
> >
> > So Taylor, after you fix the typo in your MET_GSL setting, please
check
> if
> > this file exists:
> >
> > MET_GSL='/E1/taylorm/MET8/gsl-2.5'
> >
> > *ls /E1/taylorm/MET8/gsl-2**.5/include/gsl/gsl_cdf.h*
> >
> > There is a second potential point of confusion. The vx_gsl_prob
> > library *inside
> > of MET* contains code which wraps functions from the GSL library.
I
> think
> > we chose filenames poorly in that library. For example,
> > vx_gsl_prob/gsl_cdf.h is a header file in the *MET* code tree
while
> > $MET_GSL/include/gsl/gsl_cdf.h is a file from the GSL library.
This
> > doesn't cause a problem in the compilation or running of MET but
can
> cause
> > confusion if you go hunting around for a file named gsl_cdf.h.
> >
> > Thanks,
> > John
> >
> >
> >
> >
> >
> > On Thu, Jan 17, 2019 at 9:00 AM Julie Prestopnik via RT <
> met_help at ucar.edu
> > >
> > wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > >
> > > Hi Taylor. Thank you.
> > >
> > > It looks like you may be missing a leading slash in front of E1
in the
> > > environment variables below:
> > >
> > > MET_GSL='E1/taylorm/MET8/gsl-2.5'
> > > MET_BUFRLIB='E1/taylorm/MET8/BUFRLIB'
> > >
> > > Also, can you please confirm that gsl_cdf.h exists at the
following
> > > location?
> > > ${MET_GSL}/include
> > >
> > > If gsl_cdf.h exists in that location and you are missing a
leading
> slash,
> > > please modify the value of the environment variables above, try
running
> > > "make clean", rerun the configure command, and then try to make
MET
> > again.
> > >
> > > Please let me know how it goes. If you encounter other
problems,
> please
> > > include your new config.log and make.log files.
> > >
> > > Thanks!
> > >
> > > Julie
> > >
> > >
> > >
> > > On Wed, Jan 16, 2019 at 5:58 PM Taylor Mandelbaum via RT <
> > > met_help at ucar.edu>
> > > wrote:
> > >
> > > >
> > > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
>
> > > >
> > > > Sure!
> > > >
> > > > On Wed, Jan 16, 2019 at 7:55 PM Julie Prestopnik via RT <
> > > met_help at ucar.edu
> > > > >
> > > > wrote:
> > > >
> > > > > Hi Taylor. Thanks! Could you please send the new config.log
file
> and
> > > the
> > > > > new make.log file?
> > > > >
> > > > > Thanks!
> > > > >
> > > > > On Wed, Jan 16, 2019, 5:43 PM Taylor Mandelbaum via RT <
> > > > met_help at ucar.edu
> > > > > wrote:
> > > > >
> > > > > >
> > > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > > >
> > > > > > Hey Julie,
> > > > > >
> > > > > > Thanks for all the help on this, it's really appreciated.
I ran
> the
> > > > > install
> > > > > > with CC, CXX, and F77 set to the appropriate locations and
came
> > > across
> > > > > the
> > > > > > same error with gsl_cdf.h. I reconfigured and re-make/make
> > install'd
> > > > the
> > > > > > gsl-2.5 package in my directory prior to running the
install for
> > MET
> > > > > again
> > > > > > (MET_GSL is set to the directory I made it in) and still
came
> > across
> > > > this
> > > > > > error:
> > > > > > ../../../src/libcode/vx_gsl_prob/gsl_cdf.h:17:25: fatal
error:
> > > > > > gsl/gsl_cdf.h: No such file or directory
> > > > > > compilation terminated.
> > > > > >
> > > > > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT <
> > > > > > met_help at ucar.edu>
> > > > > > wrote:
> > > > > >
> > > > > > > Hi Taylor. In talking with more with John about your
> config.log
> > > file
> > > > > we
> > > > > > > see that CC is set to use icc (intel), but CXX and F77
are set
> to
> > > use
> > > > > g++
> > > > > > > and gfortran (GNU).
> > > > > > >
> > > > > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > > > > >
> > > > >
> > >
>
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > > > > CXX='g++'
> > > > > > > F77='gfortran'
> > > > > > >
> > > > > > > Let's see if we can solve the immediate problem before
worrying
> > > about
> > > > > any
> > > > > > > potential problems with the external libraries. For
now,
> please
> > > > choose
> > > > > > > either the GNU compilers or the Intel compilers and set
the
> > > following
> > > > > > > variables accordingly. You can chose one and then
simply run
> the
> > > > > > commands
> > > > > > > below.
> > > > > > >
> > > > > > > *For GNU:*
> > > > > > > export CC=`which gcc`
> > > > > > > export CXX=`which g++`
> > > > > > > export F77=`which gfortran`
> > > > > > >
> > > > > > > *For Intel:*
> > > > > > >
> > > > > > > export CC=`which icc`
> > > > > > > export CXX=`which icc`
> > > > > > > export F77=`which ifort`
> > > > > > >
> > > > > > > Then run "make clean", rerun the configure command, and
then
> try
> > to
> > > > > make
> > > > > > > MET again.
> > > > > > >
> > > > > > > Let's go from there and see how it works out. Please
let me
> > know.
> > > > > > >
> > > > > > > Julie
> > > > > > >
> > > > > > >
> > > > > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik <
> > > jpresto at ucar.edu>
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi Taylor. Thank you for all of this information.
> > > > > > > >
> > > > > > > > Since the libraries were previously installed and we
cannot
> be
> > > > > certain
> > > > > > > > which compiler was used, are you able and would you be
> > > comfortable
> > > > > > > > installing each of the dependent libraries and not
using the
> > > > > previously
> > > > > > > > installed versions? If so, we have an install script
that I
> > can
> > > > > point
> > > > > > > you
> > > > > > > > to, which would install all of the packages and MET as
> well. I
> > > can
> > > > > > walk
> > > > > > > > through this with you via google hangouts and you can
share
> > your
> > > > > screen
> > > > > > > so
> > > > > > > > we can make sure it is going smoothly. I could do a
> hangouts
> > > > > session
> > > > > > > with
> > > > > > > > you tomorrow at 1:15pm (Mountain time) or on Friday at
9:00am
> > > > > (Mountain
> > > > > > > > time). If those times don't work. I can get you
started
> with
> > > very
> > > > > > > > specific instructions via email and we can continue to
work
> > > through
> > > > > any
> > > > > > > > problems. We can also set up a different time for
next week,
> > > > > however,
> > > > > > I
> > > > > > > > didn't want you to have to wait that long. Please let
me
> know
> > > your
> > > > > > > > preference.
> > > > > > > >
> > > > > > > > If you think that icc may not be working properly,
then you
> > > should
> > > > > > > > probably use the GNU set of compilers, unless there is
some
> > > reason
> > > > > not
> > > > > > > to,
> > > > > > > > in which case you may need to get a system
administrator
> > correct
> > > > the
> > > > > > > > problems with the intel compiler.
> > > > > > > >
> > > > > > > > Running "which g++" and running "which gfortran" can
tell you
> > > what
> > > > > the
> > > > > > > CXX
> > > > > > > > and F77 paths should be set to. Please let me know if
you
> have
> > > any
> > > > > > > issues
> > > > > > > > with that.
> > > > > > > >
> > > > > > > > Julie
> > > > > > > >
> > > > > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via
RT <
> > > > > > > > met_help at ucar.edu> wrote:
> > > > > > > >
> > > > > > > >>
> > > > > > > >> <URL:
> https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > >
> > > > > > > >>
> > > > > > > >> Hey Julie,
> > > > > > > >>
> > > > > > > >> 1) They were previously installed, but I just tried
running
> it
> > > > with
> > > > > > some
> > > > > > > >> of
> > > > > > > >> my own installed versions and they're not working
properly
> > (e.g.
> > > > the
> > > > > > > make
> > > > > > > >> install fails due to gsl/gsl_cdf.h missing... though
I set
> > > MET_GSL
> > > > > to
> > > > > > my
> > > > > > > >> gsl-2.5 directory).
> > > > > > > >>
> > > > > > > >> 2) Not sure how I can verify that one, though I think
> they're
> > > not
> > > > as
> > > > > > > I've
> > > > > > > >> seen GNU and Intel prompts in the config output. My
CC var
> in
> > my
> > > > > > bashrc
> > > > > > > >> links to an Intel compiler.
> > > > > > > >>
> > > > > > > >> 3) I followed those for the packages, though for the
> compilers
> > > > > > section,
> > > > > > > I
> > > > > > > >> do not know my CXX or F77 paths on the hpc that I'm
using. I
> > > also
> > > > > > think
> > > > > > > >> the
> > > > > > > >> icc is not working properly as I could not run icc
without a
> > > > license
> > > > > > > >> prompt
> > > > > > > >> coming up.
> > > > > > > >>
> > > > > > > >> I'm not sure if any of that helps, but let me know.
Maybe
> some
> > > of
> > > > > > these
> > > > > > > >> issues are still on our end. The fact that met needs
to only
> > use
> > > > one
> > > > > > > >> compiler might be the issue...
> > > > > > > >>
> > > > > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via
RT <
> > > > > > > >> met_help at ucar.edu>
> > > > > > > >> wrote:
> > > > > > > >>
> > > > > > > >> > Hi Taylor. Thank you for passing along your files.
I
> have
> > a
> > > > few
> > > > > > > >> questions
> > > > > > > >> > for you.
> > > > > > > >> >
> > > > > > > >> > 1) Are you installing the external libraries
yourself or
> > were
> > > > they
> > > > > > > >> > previously installed?
> > > > > > > >> > 2) Can you please verify that the external
libraries and
> MET
> > > are
> > > > > > being
> > > > > > > >> > built with the same family of compilers (e.g. all
are
> built
> > > with
> > > > > > GNU,
> > > > > > > or
> > > > > > > >> > all are build with Intel, etc.)? Which compiler
are you
> > > using?
> > > > > > > >> > 3) Are you following the directions on this page as
your
> > > > > > instructions
> > > > > > > >> for
> > > > > > > >> > installation?
> > > > > > > >> >
> > > > > > > >> >
> > > > > > > >>
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > > > > >> >
> > > > > > > >> > Thank you!
> > > > > > > >> >
> > > > > > > >> > Julie
> > > > > > > >> >
> > > > > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum
via RT <
> > > > > > > >> > met_help at ucar.edu>
> > > > > > > >> > wrote:
> > > > > > > >> >
> > > > > > > >> > >
> > > > > > > >> > > <URL:
> > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > >
> > > > > > > >> > >
> > > > > > > >> > > Hey Julie,
> > > > > > > >> > >
> > > > > > > >> > > I attached the config and make_install logs here.
We
> could
> > > do
> > > > a
> > > > > > > >> hangouts
> > > > > > > >> > > session as well if you can't pinpoint the issue;
I'm
> > > remoting
> > > > in
> > > > > > > from
> > > > > > > >> my
> > > > > > > >> > > home windows computer so it will be a bit hacky.
> > > > > > > >> > >
> > > > > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik
via RT
> <
> > > > > > > >> > met_help at ucar.edu
> > > > > > > >> > > >
> > > > > > > >> > > wrote:
> > > > > > > >> > >
> > > > > > > >> > > > Hi Taylor. It is difficult to tell what is
going
> > without
> > > > more
> > > > > > > >> context.
> > > > > > > >> > > > Could you please send me your config.log file
and your
> > > > > make.log
> > > > > > > >> file?
> > > > > > > >> > > >
> > > > > > > >> > > > We could also consider doing a hangouts session
where
> > you
> > > > can
> > > > > > > share
> > > > > > > >> > your
> > > > > > > >> > > > screen, and I can directly help that way.
Either way
> > > > though,
> > > > > if
> > > > > > > you
> > > > > > > >> > > could
> > > > > > > >> > > > please send those files, I would appreciate it.
> > > > > > > >> > > >
> > > > > > > >> > > > Thanks,
> > > > > > > >> > > > Julie
> > > > > > > >> > > >
> > > > > > > >> > > > Thanks!
> > > > > > > >> > > >
> > > > > > > >> > > > Julie
> > > > > > > >> > > >
> > > > > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor
Mandelbaum via
> > RT <
> > > > > > > >> > > > met_help at ucar.edu>
> > > > > > > >> > > > wrote:
> > > > > > > >> > > >
> > > > > > > >> > > > >
> > > > > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was
acted
> > upon.
> > > > > > > >> > > > > Transaction: Ticket created by
> > > > > > taylor.mandelbaum at stonybrook.edu
> > > > > > > >> > > > > Queue: met_help
> > > > > > > >> > > > > Subject: met install help
> > > > > > > >> > > > > Owner: Nobody
> > > > > > > >> > > > > Requestors:
taylor.mandelbaum at stonybrook.edu
> > > > > > > >> > > > > Status: new
> > > > > > > >> > > > > Ticket <URL:
> > > > > > > >> >
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > >> > > >
> > > > > > > >> > > > >
> > > > > > > >> > > > >
> > > > > > > >> > > > > Hey all,
> > > > > > > >> > > > >
> > > > > > > >> > > > > I'm presently trying to compile MET 8.0 on
our HPC;
> > > when I
> > > > > > > >> configure
> > > > > > > >> > > it,
> > > > > > > >> > > > > I'm getting a few warnings on .h files:
> > > > > > > >> > > > >
> > > > > > > >> > > > > configure: WARNING: errno.h: present but
cannot be
> > > > compiled
> > > > > > > >> > > > > configure: WARNING: errno.h: check for
missing
> > > > > > prerequisite
> > > > > > > >> > > headers?
> > > > > > > >> > > > > configure: WARNING: errno.h: see the Autoconf
> > > > documentation
> > > > > > > >> > > > > configure: WARNING: errno.h: section
"Present
> But
> > > > Cannot
> > > > > > Be
> > > > > > > >> > > Compiled"
> > > > > > > >> > > > > configure: WARNING: errno.h: proceeding with
the
> > > > compiler's
> > > > > > > result
> > > > > > > >> > > > > configure: WARNING: ##
> > > > --------------------------------
> > > > > ##
> > > > > > > >> > > > > configure: WARNING: ## Report this to
> > > > met_help at ucar.edu
> > > > > > ##
> > > > > > > >> > > > > configure: WARNING: ##
> > > > --------------------------------
> > > > > ##
> > > > > > > >> > > > >
> > > > > > > >> > > > > and the same for fcntl.h, limits.h, stddef.h,
file.h
> > and
> > > > > > > param.h.
> > > > > > > >> > > > >
> > > > > > > >> > > > > When I try to make install, I get this error
on the
> > tail
> > > > of
> > > > > > the
> > > > > > > >> log:
> > > > > > > >> > > > >
> > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > configalloc(yy_size_t)’:
> > > > > > > >> > > > > config_scanner.cc:2179:31: error:
‘rpl_malloc’ was
> not
> > > > > > declared
> > > > > > > in
> > > > > > > >> > this
> > > > > > > >> > > > > scope
> > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > configrealloc(void*,
> > > > > > > >> > yy_size_t)’:
> > > > > > > >> > > > > config_scanner.cc:2191:46: error:
‘rpl_realloc’ was
> > not
> > > > > > declared
> > > > > > > >> in
> > > > > > > >> > > this
> > > > > > > >> > > > > scope
> > > > > > > >> > > > > /* The cast to (char *) in the following
> > accommodates
> > > > both
> > > > > > > >> > > > >
^
> > > > > > > >> > > > > make[3]: *** [libvx_config_a-
config_scanner.o]
> Error 1
> > > > > > > >> > > > > make[3]: Leaving directory
> > > > > > > >> > > > >
> `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > > > > > >> > > > > make[2]: *** [install-recursive] Error 1
> > > > > > > >> > > > > make[2]: Leaving directory
> > > > > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > > > > >> > > > > make[1]: *** [install-recursive] Error 1
> > > > > > > >> > > > > make[1]: Leaving directory
> > > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > > > > >> > > > > make: *** [install-recursive] Error 1
> > > > > > > >> > > > >
> > > > > > > >> > > > > Not sure how to address either of these,
hopefully
> you
> > > > guys
> > > > > > can
> > > > > > > >> > provide
> > > > > > > >> > > > > some insight.
> > > > > > > >> > > > >
> > > > > > > >> > > > > Thanks!
> > > > > > > >> > > > > --
> > > > > > > >> > > > > *Taylor Mandelbaum*
> > > > > > > >> > > > > Research Technician
> > > > > > > >> > > > > SoMAS | Stony Brook University
> > > > > > > >> > > > > 678.468.5789
> > > > > > > >> > > > >
> > > > > > > >> > > > >
> > > > > > > >> > > >
> > > > > > > >> > > >
> > > > > > > >> > >
> > > > > > > >> > > --
> > > > > > > >> > > *Taylor Mandelbaum*
> > > > > > > >> > > Research Technician
> > > > > > > >> > > SoMAS | Stony Brook University
> > > > > > > >> > > 678.468.5789
> > > > > > > >> > >
> > > > > > > >> > >
> > > > > > > >> >
> > > > > > > >> >
> > > > > > > >>
> > > > > > > >> --
> > > > > > > >> *Taylor Mandelbaum*
> > > > > > > >> Research Technician
> > > > > > > >> SoMAS | Stony Brook University
> > > > > > > >> 678.468.5789
> > > > > > > >>
> > > > > > > >>
> > > > > > >
> > > > > > >
> > > > > >
> > > > > > --
> > > > > > *Taylor Mandelbaum*
> > > > > > Research Technician
> > > > > > SoMAS | Stony Brook University
> > > > > > 678.468.5789
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > > > --
> > > > *Taylor Mandelbaum*
> > > > Research Technician
> > > > SoMAS | Stony Brook University
> > > > 678.468.5789
> > > >
> > > >
> > >
> > >
> >
> >
>
> --
> *Taylor Mandelbaum*
> Research Technician
> SoMAS | Stony Brook University
> 678.468.5789
>
>
------------------------------------------------
Subject: met install help
From: Taylor Mandelbaum
Time: Thu Jan 17 17:10:46 2019
Good catch, that's what happens when you have been working on Windows
for a
while.
Now I'm getting an error with respect to netcdf.
In file included from nc_var_info.cc:24:0:
nc_utils.h:22:18: fatal error: netcdf: No such file or directory
I would guess netcdf-gfortran is properly installed, what do you
think?
On Thu, Jan 17, 2019 at 6:36 PM Julie Prestopnik via RT
<met_help at ucar.edu>
wrote:
> Hi Taylor.
>
> Unfortunately the change, which I see in your bashrc.txt file, was
not
> picked up. I still see the following in config.log:
>
> MET_BUFRLIB='E1/taylorm/MET8/BUFRLIB'
> MET_GSL='E1/taylorm/MET8/gsl-2.5'
>
> Please note that there is no leading slash before "E1". After you
changed
> your .bashrc file, did you either run "source ~/.bashrc" or open a
new
> shell? If not, that would explain what is happening. Please either
run
> "source ~/.bashrc" or open a new shell. You can run "echo $MET_GSL"
> afterward to verify that you see a leading slash in front of "E1".
>
> Please give that a try and let us know how it goes.
>
> Thanks,
> Julie
>
> On Thu, Jan 17, 2019 at 3:44 PM Taylor Mandelbaum via RT <
> met_help at ucar.edu>
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> >
> > Thanks all. I fixed the typos, checked to see if the file is in
> > gsl2.5/include/gsl (it is), and reran it with the same error.
Attached
> the
> > logs. I also attached my bashrc for brevity.
> >
> > On Thu, Jan 17, 2019 at 11:19 AM John Halley Gotway via RT <
> > met_help at ucar.edu> wrote:
> >
> > > Hi Julie and Taylor,
> > >
> > > I have one pesky little detail to mention about GSL that may be
a point
> > of
> > > confusion here.
> > >
> > > Typically when your run "make install" on a software package and
tell
> it
> > to
> > > install to "/install_dir", it installs header files into
> > > "/install_dir/include" and library files into
"/install_dir/lib".
> > However,
> > > the GSL package installs header files into
"/install_dir/include/gsl".
> > And
> > > because of this, the MET code uses that gsl prefix:
> > > include "gsl/gsl_cdf.h"
> > >
> > > So Taylor, after you fix the typo in your MET_GSL setting,
please check
> > if
> > > this file exists:
> > >
> > > MET_GSL='/E1/taylorm/MET8/gsl-2.5'
> > >
> > > *ls /E1/taylorm/MET8/gsl-2**.5/include/gsl/gsl_cdf.h*
> > >
> > > There is a second potential point of confusion. The vx_gsl_prob
> > > library *inside
> > > of MET* contains code which wraps functions from the GSL
library. I
> > think
> > > we chose filenames poorly in that library. For example,
> > > vx_gsl_prob/gsl_cdf.h is a header file in the *MET* code tree
while
> > > $MET_GSL/include/gsl/gsl_cdf.h is a file from the GSL library.
This
> > > doesn't cause a problem in the compilation or running of MET but
can
> > cause
> > > confusion if you go hunting around for a file named gsl_cdf.h.
> > >
> > > Thanks,
> > > John
> > >
> > >
> > >
> > >
> > >
> > > On Thu, Jan 17, 2019 at 9:00 AM Julie Prestopnik via RT <
> > met_help at ucar.edu
> > > >
> > > wrote:
> > >
> > > >
> > > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
>
> > > >
> > > > Hi Taylor. Thank you.
> > > >
> > > > It looks like you may be missing a leading slash in front of
E1 in
> the
> > > > environment variables below:
> > > >
> > > > MET_GSL='E1/taylorm/MET8/gsl-2.5'
> > > > MET_BUFRLIB='E1/taylorm/MET8/BUFRLIB'
> > > >
> > > > Also, can you please confirm that gsl_cdf.h exists at the
following
> > > > location?
> > > > ${MET_GSL}/include
> > > >
> > > > If gsl_cdf.h exists in that location and you are missing a
leading
> > slash,
> > > > please modify the value of the environment variables above,
try
> running
> > > > "make clean", rerun the configure command, and then try to
make MET
> > > again.
> > > >
> > > > Please let me know how it goes. If you encounter other
problems,
> > please
> > > > include your new config.log and make.log files.
> > > >
> > > > Thanks!
> > > >
> > > > Julie
> > > >
> > > >
> > > >
> > > > On Wed, Jan 16, 2019 at 5:58 PM Taylor Mandelbaum via RT <
> > > > met_help at ucar.edu>
> > > > wrote:
> > > >
> > > > >
> > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > >
> > > > > Sure!
> > > > >
> > > > > On Wed, Jan 16, 2019 at 7:55 PM Julie Prestopnik via RT <
> > > > met_help at ucar.edu
> > > > > >
> > > > > wrote:
> > > > >
> > > > > > Hi Taylor. Thanks! Could you please send the new
config.log file
> > and
> > > > the
> > > > > > new make.log file?
> > > > > >
> > > > > > Thanks!
> > > > > >
> > > > > > On Wed, Jan 16, 2019, 5:43 PM Taylor Mandelbaum via RT <
> > > > > met_help at ucar.edu
> > > > > > wrote:
> > > > > >
> > > > > > >
> > > > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> >
> > > > > > >
> > > > > > > Hey Julie,
> > > > > > >
> > > > > > > Thanks for all the help on this, it's really
appreciated. I ran
> > the
> > > > > > install
> > > > > > > with CC, CXX, and F77 set to the appropriate locations
and came
> > > > across
> > > > > > the
> > > > > > > same error with gsl_cdf.h. I reconfigured and re-
make/make
> > > install'd
> > > > > the
> > > > > > > gsl-2.5 package in my directory prior to running the
install
> for
> > > MET
> > > > > > again
> > > > > > > (MET_GSL is set to the directory I made it in) and still
came
> > > across
> > > > > this
> > > > > > > error:
> > > > > > > ../../../src/libcode/vx_gsl_prob/gsl_cdf.h:17:25: fatal
error:
> > > > > > > gsl/gsl_cdf.h: No such file or directory
> > > > > > > compilation terminated.
> > > > > > >
> > > > > > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT
<
> > > > > > > met_help at ucar.edu>
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi Taylor. In talking with more with John about your
> > config.log
> > > > file
> > > > > > we
> > > > > > > > see that CC is set to use icc (intel), but CXX and F77
are
> set
> > to
> > > > use
> > > > > > g++
> > > > > > > > and gfortran (GNU).
> > > > > > > >
> > > > > > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > > > > > >
> > > > > >
> > > >
> >
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > > > > > CXX='g++'
> > > > > > > > F77='gfortran'
> > > > > > > >
> > > > > > > > Let's see if we can solve the immediate problem before
> worrying
> > > > about
> > > > > > any
> > > > > > > > potential problems with the external libraries. For
now,
> > please
> > > > > choose
> > > > > > > > either the GNU compilers or the Intel compilers and
set the
> > > > following
> > > > > > > > variables accordingly. You can chose one and then
simply run
> > the
> > > > > > > commands
> > > > > > > > below.
> > > > > > > >
> > > > > > > > *For GNU:*
> > > > > > > > export CC=`which gcc`
> > > > > > > > export CXX=`which g++`
> > > > > > > > export F77=`which gfortran`
> > > > > > > >
> > > > > > > > *For Intel:*
> > > > > > > >
> > > > > > > > export CC=`which icc`
> > > > > > > > export CXX=`which icc`
> > > > > > > > export F77=`which ifort`
> > > > > > > >
> > > > > > > > Then run "make clean", rerun the configure command,
and then
> > try
> > > to
> > > > > > make
> > > > > > > > MET again.
> > > > > > > >
> > > > > > > > Let's go from there and see how it works out. Please
let me
> > > know.
> > > > > > > >
> > > > > > > > Julie
> > > > > > > >
> > > > > > > >
> > > > > > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik <
> > > > jpresto at ucar.edu>
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > > Hi Taylor. Thank you for all of this information.
> > > > > > > > >
> > > > > > > > > Since the libraries were previously installed and we
cannot
> > be
> > > > > > certain
> > > > > > > > > which compiler was used, are you able and would you
be
> > > > comfortable
> > > > > > > > > installing each of the dependent libraries and not
using
> the
> > > > > > previously
> > > > > > > > > installed versions? If so, we have an install
script that
> I
> > > can
> > > > > > point
> > > > > > > > you
> > > > > > > > > to, which would install all of the packages and MET
as
> > well. I
> > > > can
> > > > > > > walk
> > > > > > > > > through this with you via google hangouts and you
can share
> > > your
> > > > > > screen
> > > > > > > > so
> > > > > > > > > we can make sure it is going smoothly. I could do
a
> > hangouts
> > > > > > session
> > > > > > > > with
> > > > > > > > > you tomorrow at 1:15pm (Mountain time) or on Friday
at
> 9:00am
> > > > > > (Mountain
> > > > > > > > > time). If those times don't work. I can get you
started
> > with
> > > > very
> > > > > > > > > specific instructions via email and we can continue
to work
> > > > through
> > > > > > any
> > > > > > > > > problems. We can also set up a different time for
next
> week,
> > > > > > however,
> > > > > > > I
> > > > > > > > > didn't want you to have to wait that long. Please
let me
> > know
> > > > your
> > > > > > > > > preference.
> > > > > > > > >
> > > > > > > > > If you think that icc may not be working properly,
then you
> > > > should
> > > > > > > > > probably use the GNU set of compilers, unless there
is some
> > > > reason
> > > > > > not
> > > > > > > > to,
> > > > > > > > > in which case you may need to get a system
administrator
> > > correct
> > > > > the
> > > > > > > > > problems with the intel compiler.
> > > > > > > > >
> > > > > > > > > Running "which g++" and running "which gfortran" can
tell
> you
> > > > what
> > > > > > the
> > > > > > > > CXX
> > > > > > > > > and F77 paths should be set to. Please let me know
if you
> > have
> > > > any
> > > > > > > > issues
> > > > > > > > > with that.
> > > > > > > > >
> > > > > > > > > Julie
> > > > > > > > >
> > > > > > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum
via RT <
> > > > > > > > > met_help at ucar.edu> wrote:
> > > > > > > > >
> > > > > > > > >>
> > > > > > > > >> <URL:
> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > >
> > > > > > > > >>
> > > > > > > > >> Hey Julie,
> > > > > > > > >>
> > > > > > > > >> 1) They were previously installed, but I just tried
> running
> > it
> > > > > with
> > > > > > > some
> > > > > > > > >> of
> > > > > > > > >> my own installed versions and they're not working
properly
> > > (e.g.
> > > > > the
> > > > > > > > make
> > > > > > > > >> install fails due to gsl/gsl_cdf.h missing...
though I set
> > > > MET_GSL
> > > > > > to
> > > > > > > my
> > > > > > > > >> gsl-2.5 directory).
> > > > > > > > >>
> > > > > > > > >> 2) Not sure how I can verify that one, though I
think
> > they're
> > > > not
> > > > > as
> > > > > > > > I've
> > > > > > > > >> seen GNU and Intel prompts in the config output. My
CC var
> > in
> > > my
> > > > > > > bashrc
> > > > > > > > >> links to an Intel compiler.
> > > > > > > > >>
> > > > > > > > >> 3) I followed those for the packages, though for
the
> > compilers
> > > > > > > section,
> > > > > > > > I
> > > > > > > > >> do not know my CXX or F77 paths on the hpc that I'm
> using. I
> > > > also
> > > > > > > think
> > > > > > > > >> the
> > > > > > > > >> icc is not working properly as I could not run icc
> without a
> > > > > license
> > > > > > > > >> prompt
> > > > > > > > >> coming up.
> > > > > > > > >>
> > > > > > > > >> I'm not sure if any of that helps, but let me know.
Maybe
> > some
> > > > of
> > > > > > > these
> > > > > > > > >> issues are still on our end. The fact that met
needs to
> only
> > > use
> > > > > one
> > > > > > > > >> compiler might be the issue...
> > > > > > > > >>
> > > > > > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik
via RT <
> > > > > > > > >> met_help at ucar.edu>
> > > > > > > > >> wrote:
> > > > > > > > >>
> > > > > > > > >> > Hi Taylor. Thank you for passing along your
files. I
> > have
> > > a
> > > > > few
> > > > > > > > >> questions
> > > > > > > > >> > for you.
> > > > > > > > >> >
> > > > > > > > >> > 1) Are you installing the external libraries
yourself or
> > > were
> > > > > they
> > > > > > > > >> > previously installed?
> > > > > > > > >> > 2) Can you please verify that the external
libraries and
> > MET
> > > > are
> > > > > > > being
> > > > > > > > >> > built with the same family of compilers (e.g. all
are
> > built
> > > > with
> > > > > > > GNU,
> > > > > > > > or
> > > > > > > > >> > all are build with Intel, etc.)? Which compiler
are you
> > > > using?
> > > > > > > > >> > 3) Are you following the directions on this page
as your
> > > > > > > instructions
> > > > > > > > >> for
> > > > > > > > >> > installation?
> > > > > > > > >> >
> > > > > > > > >> >
> > > > > > > > >>
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > > > > > >> >
> > > > > > > > >> > Thank you!
> > > > > > > > >> >
> > > > > > > > >> > Julie
> > > > > > > > >> >
> > > > > > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum
via
> RT <
> > > > > > > > >> > met_help at ucar.edu>
> > > > > > > > >> > wrote:
> > > > > > > > >> >
> > > > > > > > >> > >
> > > > > > > > >> > > <URL:
> > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > >
> > > > > > > > >> > >
> > > > > > > > >> > > Hey Julie,
> > > > > > > > >> > >
> > > > > > > > >> > > I attached the config and make_install logs
here. We
> > could
> > > > do
> > > > > a
> > > > > > > > >> hangouts
> > > > > > > > >> > > session as well if you can't pinpoint the
issue; I'm
> > > > remoting
> > > > > in
> > > > > > > > from
> > > > > > > > >> my
> > > > > > > > >> > > home windows computer so it will be a bit
hacky.
> > > > > > > > >> > >
> > > > > > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie
Prestopnik via
> RT
> > <
> > > > > > > > >> > met_help at ucar.edu
> > > > > > > > >> > > >
> > > > > > > > >> > > wrote:
> > > > > > > > >> > >
> > > > > > > > >> > > > Hi Taylor. It is difficult to tell what is
going
> > > without
> > > > > more
> > > > > > > > >> context.
> > > > > > > > >> > > > Could you please send me your config.log file
and
> your
> > > > > > make.log
> > > > > > > > >> file?
> > > > > > > > >> > > >
> > > > > > > > >> > > > We could also consider doing a hangouts
session
> where
> > > you
> > > > > can
> > > > > > > > share
> > > > > > > > >> > your
> > > > > > > > >> > > > screen, and I can directly help that way.
Either
> way
> > > > > though,
> > > > > > if
> > > > > > > > you
> > > > > > > > >> > > could
> > > > > > > > >> > > > please send those files, I would appreciate
it.
> > > > > > > > >> > > >
> > > > > > > > >> > > > Thanks,
> > > > > > > > >> > > > Julie
> > > > > > > > >> > > >
> > > > > > > > >> > > > Thanks!
> > > > > > > > >> > > >
> > > > > > > > >> > > > Julie
> > > > > > > > >> > > >
> > > > > > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor
Mandelbaum
> via
> > > RT <
> > > > > > > > >> > > > met_help at ucar.edu>
> > > > > > > > >> > > > wrote:
> > > > > > > > >> > > >
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was
acted
> > > upon.
> > > > > > > > >> > > > > Transaction: Ticket created by
> > > > > > > taylor.mandelbaum at stonybrook.edu
> > > > > > > > >> > > > > Queue: met_help
> > > > > > > > >> > > > > Subject: met install help
> > > > > > > > >> > > > > Owner: Nobody
> > > > > > > > >> > > > > Requestors:
taylor.mandelbaum at stonybrook.edu
> > > > > > > > >> > > > > Status: new
> > > > > > > > >> > > > > Ticket <URL:
> > > > > > > > >> >
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > > >> > > >
> > > > > > > > >> > > > >
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > Hey all,
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > I'm presently trying to compile MET 8.0 on
our
> HPC;
> > > > when I
> > > > > > > > >> configure
> > > > > > > > >> > > it,
> > > > > > > > >> > > > > I'm getting a few warnings on .h files:
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > configure: WARNING: errno.h: present but
cannot be
> > > > > compiled
> > > > > > > > >> > > > > configure: WARNING: errno.h: check for
missing
> > > > > > > prerequisite
> > > > > > > > >> > > headers?
> > > > > > > > >> > > > > configure: WARNING: errno.h: see the
Autoconf
> > > > > documentation
> > > > > > > > >> > > > > configure: WARNING: errno.h: section
"Present
> > But
> > > > > Cannot
> > > > > > > Be
> > > > > > > > >> > > Compiled"
> > > > > > > > >> > > > > configure: WARNING: errno.h: proceeding
with the
> > > > > compiler's
> > > > > > > > result
> > > > > > > > >> > > > > configure: WARNING: ##
> > > > > --------------------------------
> > > > > > ##
> > > > > > > > >> > > > > configure: WARNING: ## Report this to
> > > > > met_help at ucar.edu
> > > > > > > ##
> > > > > > > > >> > > > > configure: WARNING: ##
> > > > > --------------------------------
> > > > > > ##
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > and the same for fcntl.h, limits.h,
stddef.h,
> file.h
> > > and
> > > > > > > > param.h.
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > When I try to make install, I get this
error on
> the
> > > tail
> > > > > of
> > > > > > > the
> > > > > > > > >> log:
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > > configalloc(yy_size_t)’:
> > > > > > > > >> > > > > config_scanner.cc:2179:31: error:
‘rpl_malloc’ was
> > not
> > > > > > > declared
> > > > > > > > in
> > > > > > > > >> > this
> > > > > > > > >> > > > > scope
> > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > configrealloc(void*,
> > > > > > > > >> > yy_size_t)’:
> > > > > > > > >> > > > > config_scanner.cc:2191:46: error:
‘rpl_realloc’
> was
> > > not
> > > > > > > declared
> > > > > > > > >> in
> > > > > > > > >> > > this
> > > > > > > > >> > > > > scope
> > > > > > > > >> > > > > /* The cast to (char *) in the following
> > > accommodates
> > > > > both
> > > > > > > > >> > > > >
^
> > > > > > > > >> > > > > make[3]: *** [libvx_config_a-
config_scanner.o]
> > Error 1
> > > > > > > > >> > > > > make[3]: Leaving directory
> > > > > > > > >> > > > >
> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > > > > > > >> > > > > make[2]: *** [install-recursive] Error 1
> > > > > > > > >> > > > > make[2]: Leaving directory
> > > > > > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > > > > > >> > > > > make[1]: *** [install-recursive] Error 1
> > > > > > > > >> > > > > make[1]: Leaving directory
> > > > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > > > > > >> > > > > make: *** [install-recursive] Error 1
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > Not sure how to address either of these,
hopefully
> > you
> > > > > guys
> > > > > > > can
> > > > > > > > >> > provide
> > > > > > > > >> > > > > some insight.
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > Thanks!
> > > > > > > > >> > > > > --
> > > > > > > > >> > > > > *Taylor Mandelbaum*
> > > > > > > > >> > > > > Research Technician
> > > > > > > > >> > > > > SoMAS | Stony Brook University
> > > > > > > > >> > > > > 678.468.5789
> > > > > > > > >> > > > >
> > > > > > > > >> > > > >
> > > > > > > > >> > > >
> > > > > > > > >> > > >
> > > > > > > > >> > >
> > > > > > > > >> > > --
> > > > > > > > >> > > *Taylor Mandelbaum*
> > > > > > > > >> > > Research Technician
> > > > > > > > >> > > SoMAS | Stony Brook University
> > > > > > > > >> > > 678.468.5789
> > > > > > > > >> > >
> > > > > > > > >> > >
> > > > > > > > >> >
> > > > > > > > >> >
> > > > > > > > >>
> > > > > > > > >> --
> > > > > > > > >> *Taylor Mandelbaum*
> > > > > > > > >> Research Technician
> > > > > > > > >> SoMAS | Stony Brook University
> > > > > > > > >> 678.468.5789
> > > > > > > > >>
> > > > > > > > >>
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > *Taylor Mandelbaum*
> > > > > > > Research Technician
> > > > > > > SoMAS | Stony Brook University
> > > > > > > 678.468.5789
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > > --
> > > > > *Taylor Mandelbaum*
> > > > > Research Technician
> > > > > SoMAS | Stony Brook University
> > > > > 678.468.5789
> > > > >
> > > > >
> > > >
> > > >
> > >
> > >
> >
> > --
> > *Taylor Mandelbaum*
> > Research Technician
> > SoMAS | Stony Brook University
> > 678.468.5789
> >
> >
>
>
--
*Taylor Mandelbaum*
Research Technician
SoMAS | Stony Brook University
678.468.5789
------------------------------------------------
Subject: met install help
From: Julie Prestopnik
Time: Thu Jan 17 17:27:15 2019
Hi Taylor. It's good to see that we are making progress!
I see that you have
MET_NETCDF='/opt/netcdf-gfortan/'
MET requires the C and C++ interface to NetCDF. Here is a checklist of
files that are necessary:
Files for NetCDF4 C:
- $MET_NETCDF/include/netcdf.h
- $MET_NETCDF/lib/libnetcdf.a
- $MET_NETCDF/lib/libnetcdf.so
Files for NetCDF4 C++:
- $MET_NETCDF/include/netcdf
- $MET_NETCDF/lib/libnetcdf_c++4.a
- $MET_NETCDF/lib/libnetcdf_c++4.so
If you will need to compile these, please take a look at the
"Compiling
NetCDF" section of this webpage in our online tutorial (for met-6.1,
but
the instructions are the same for met-8.0):
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
In config.log, I see that MET_HDF5 is not set:
MET_HDF5=''
The HDF5 library is required to support NetCDF4. If you need to
compile
HDF5, you will need to do it prior to compiling NetCDF4. Please see
the
instructions on "Compiling HDF5" on the same webpage listed above.
Please let us know if you have any questions.
Thanks,
Julie
On Thu, Jan 17, 2019 at 5:11 PM Taylor Mandelbaum via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> Good catch, that's what happens when you have been working on
Windows for a
> while.
>
> Now I'm getting an error with respect to netcdf.
>
> In file included from nc_var_info.cc:24:0:
> nc_utils.h:22:18: fatal error: netcdf: No such file or directory
>
> I would guess netcdf-gfortran is properly installed, what do you
think?
>
> On Thu, Jan 17, 2019 at 6:36 PM Julie Prestopnik via RT
<met_help at ucar.edu
> >
> wrote:
>
> > Hi Taylor.
> >
> > Unfortunately the change, which I see in your bashrc.txt file, was
not
> > picked up. I still see the following in config.log:
> >
> > MET_BUFRLIB='E1/taylorm/MET8/BUFRLIB'
> > MET_GSL='E1/taylorm/MET8/gsl-2.5'
> >
> > Please note that there is no leading slash before "E1". After you
> changed
> > your .bashrc file, did you either run "source ~/.bashrc" or open a
new
> > shell? If not, that would explain what is happening. Please
either run
> > "source ~/.bashrc" or open a new shell. You can run "echo
$MET_GSL"
> > afterward to verify that you see a leading slash in front of "E1".
> >
> > Please give that a try and let us know how it goes.
> >
> > Thanks,
> > Julie
> >
> > On Thu, Jan 17, 2019 at 3:44 PM Taylor Mandelbaum via RT <
> > met_help at ucar.edu>
> > wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > >
> > > Thanks all. I fixed the typos, checked to see if the file is in
> > > gsl2.5/include/gsl (it is), and reran it with the same error.
Attached
> > the
> > > logs. I also attached my bashrc for brevity.
> > >
> > > On Thu, Jan 17, 2019 at 11:19 AM John Halley Gotway via RT <
> > > met_help at ucar.edu> wrote:
> > >
> > > > Hi Julie and Taylor,
> > > >
> > > > I have one pesky little detail to mention about GSL that may
be a
> point
> > > of
> > > > confusion here.
> > > >
> > > > Typically when your run "make install" on a software package
and tell
> > it
> > > to
> > > > install to "/install_dir", it installs header files into
> > > > "/install_dir/include" and library files into
"/install_dir/lib".
> > > However,
> > > > the GSL package installs header files into
> "/install_dir/include/gsl".
> > > And
> > > > because of this, the MET code uses that gsl prefix:
> > > > include "gsl/gsl_cdf.h"
> > > >
> > > > So Taylor, after you fix the typo in your MET_GSL setting,
please
> check
> > > if
> > > > this file exists:
> > > >
> > > > MET_GSL='/E1/taylorm/MET8/gsl-2.5'
> > > >
> > > > *ls /E1/taylorm/MET8/gsl-2**.5/include/gsl/gsl_cdf.h*
> > > >
> > > > There is a second potential point of confusion. The
vx_gsl_prob
> > > > library *inside
> > > > of MET* contains code which wraps functions from the GSL
library. I
> > > think
> > > > we chose filenames poorly in that library. For example,
> > > > vx_gsl_prob/gsl_cdf.h is a header file in the *MET* code tree
while
> > > > $MET_GSL/include/gsl/gsl_cdf.h is a file from the GSL library.
This
> > > > doesn't cause a problem in the compilation or running of MET
but can
> > > cause
> > > > confusion if you go hunting around for a file named gsl_cdf.h.
> > > >
> > > > Thanks,
> > > > John
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On Thu, Jan 17, 2019 at 9:00 AM Julie Prestopnik via RT <
> > > met_help at ucar.edu
> > > > >
> > > > wrote:
> > > >
> > > > >
> > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > >
> > > > > Hi Taylor. Thank you.
> > > > >
> > > > > It looks like you may be missing a leading slash in front of
E1 in
> > the
> > > > > environment variables below:
> > > > >
> > > > > MET_GSL='E1/taylorm/MET8/gsl-2.5'
> > > > > MET_BUFRLIB='E1/taylorm/MET8/BUFRLIB'
> > > > >
> > > > > Also, can you please confirm that gsl_cdf.h exists at the
following
> > > > > location?
> > > > > ${MET_GSL}/include
> > > > >
> > > > > If gsl_cdf.h exists in that location and you are missing a
leading
> > > slash,
> > > > > please modify the value of the environment variables above,
try
> > running
> > > > > "make clean", rerun the configure command, and then try to
make MET
> > > > again.
> > > > >
> > > > > Please let me know how it goes. If you encounter other
problems,
> > > please
> > > > > include your new config.log and make.log files.
> > > > >
> > > > > Thanks!
> > > > >
> > > > > Julie
> > > > >
> > > > >
> > > > >
> > > > > On Wed, Jan 16, 2019 at 5:58 PM Taylor Mandelbaum via RT <
> > > > > met_help at ucar.edu>
> > > > > wrote:
> > > > >
> > > > > >
> > > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > > >
> > > > > > Sure!
> > > > > >
> > > > > > On Wed, Jan 16, 2019 at 7:55 PM Julie Prestopnik via RT <
> > > > > met_help at ucar.edu
> > > > > > >
> > > > > > wrote:
> > > > > >
> > > > > > > Hi Taylor. Thanks! Could you please send the new
config.log
> file
> > > and
> > > > > the
> > > > > > > new make.log file?
> > > > > > >
> > > > > > > Thanks!
> > > > > > >
> > > > > > > On Wed, Jan 16, 2019, 5:43 PM Taylor Mandelbaum via RT <
> > > > > > met_help at ucar.edu
> > > > > > > wrote:
> > > > > > >
> > > > > > > >
> > > > > > > > <URL:
> https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > >
> > > > > > > >
> > > > > > > > Hey Julie,
> > > > > > > >
> > > > > > > > Thanks for all the help on this, it's really
appreciated. I
> ran
> > > the
> > > > > > > install
> > > > > > > > with CC, CXX, and F77 set to the appropriate locations
and
> came
> > > > > across
> > > > > > > the
> > > > > > > > same error with gsl_cdf.h. I reconfigured and re-
make/make
> > > > install'd
> > > > > > the
> > > > > > > > gsl-2.5 package in my directory prior to running the
install
> > for
> > > > MET
> > > > > > > again
> > > > > > > > (MET_GSL is set to the directory I made it in) and
still came
> > > > across
> > > > > > this
> > > > > > > > error:
> > > > > > > > ../../../src/libcode/vx_gsl_prob/gsl_cdf.h:17:25:
fatal
> error:
> > > > > > > > gsl/gsl_cdf.h: No such file or directory
> > > > > > > > compilation terminated.
> > > > > > > >
> > > > > > > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via
RT <
> > > > > > > > met_help at ucar.edu>
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > > Hi Taylor. In talking with more with John about
your
> > > config.log
> > > > > file
> > > > > > > we
> > > > > > > > > see that CC is set to use icc (intel), but CXX and
F77 are
> > set
> > > to
> > > > > use
> > > > > > > g++
> > > > > > > > > and gfortran (GNU).
> > > > > > > > >
> > > > > > > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > > > > > > >
> > > > > > >
> > > > >
> > >
>
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > > > > > > CXX='g++'
> > > > > > > > > F77='gfortran'
> > > > > > > > >
> > > > > > > > > Let's see if we can solve the immediate problem
before
> > worrying
> > > > > about
> > > > > > > any
> > > > > > > > > potential problems with the external libraries. For
now,
> > > please
> > > > > > choose
> > > > > > > > > either the GNU compilers or the Intel compilers and
set the
> > > > > following
> > > > > > > > > variables accordingly. You can chose one and then
simply
> run
> > > the
> > > > > > > > commands
> > > > > > > > > below.
> > > > > > > > >
> > > > > > > > > *For GNU:*
> > > > > > > > > export CC=`which gcc`
> > > > > > > > > export CXX=`which g++`
> > > > > > > > > export F77=`which gfortran`
> > > > > > > > >
> > > > > > > > > *For Intel:*
> > > > > > > > >
> > > > > > > > > export CC=`which icc`
> > > > > > > > > export CXX=`which icc`
> > > > > > > > > export F77=`which ifort`
> > > > > > > > >
> > > > > > > > > Then run "make clean", rerun the configure command,
and
> then
> > > try
> > > > to
> > > > > > > make
> > > > > > > > > MET again.
> > > > > > > > >
> > > > > > > > > Let's go from there and see how it works out.
Please let
> me
> > > > know.
> > > > > > > > >
> > > > > > > > > Julie
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik <
> > > > > jpresto at ucar.edu>
> > > > > > > > > wrote:
> > > > > > > > >
> > > > > > > > > > Hi Taylor. Thank you for all of this information.
> > > > > > > > > >
> > > > > > > > > > Since the libraries were previously installed and
we
> cannot
> > > be
> > > > > > > certain
> > > > > > > > > > which compiler was used, are you able and would
you be
> > > > > comfortable
> > > > > > > > > > installing each of the dependent libraries and not
using
> > the
> > > > > > > previously
> > > > > > > > > > installed versions? If so, we have an install
script
> that
> > I
> > > > can
> > > > > > > point
> > > > > > > > > you
> > > > > > > > > > to, which would install all of the packages and
MET as
> > > well. I
> > > > > can
> > > > > > > > walk
> > > > > > > > > > through this with you via google hangouts and you
can
> share
> > > > your
> > > > > > > screen
> > > > > > > > > so
> > > > > > > > > > we can make sure it is going smoothly. I could
do a
> > > hangouts
> > > > > > > session
> > > > > > > > > with
> > > > > > > > > > you tomorrow at 1:15pm (Mountain time) or on
Friday at
> > 9:00am
> > > > > > > (Mountain
> > > > > > > > > > time). If those times don't work. I can get you
started
> > > with
> > > > > very
> > > > > > > > > > specific instructions via email and we can
continue to
> work
> > > > > through
> > > > > > > any
> > > > > > > > > > problems. We can also set up a different time for
next
> > week,
> > > > > > > however,
> > > > > > > > I
> > > > > > > > > > didn't want you to have to wait that long. Please
let me
> > > know
> > > > > your
> > > > > > > > > > preference.
> > > > > > > > > >
> > > > > > > > > > If you think that icc may not be working properly,
then
> you
> > > > > should
> > > > > > > > > > probably use the GNU set of compilers, unless
there is
> some
> > > > > reason
> > > > > > > not
> > > > > > > > > to,
> > > > > > > > > > in which case you may need to get a system
administrator
> > > > correct
> > > > > > the
> > > > > > > > > > problems with the intel compiler.
> > > > > > > > > >
> > > > > > > > > > Running "which g++" and running "which gfortran"
can tell
> > you
> > > > > what
> > > > > > > the
> > > > > > > > > CXX
> > > > > > > > > > and F77 paths should be set to. Please let me
know if
> you
> > > have
> > > > > any
> > > > > > > > > issues
> > > > > > > > > > with that.
> > > > > > > > > >
> > > > > > > > > > Julie
> > > > > > > > > >
> > > > > > > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum
via RT
> <
> > > > > > > > > > met_help at ucar.edu> wrote:
> > > > > > > > > >
> > > > > > > > > >>
> > > > > > > > > >> <URL:
> > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > >
> > > > > > > > > >>
> > > > > > > > > >> Hey Julie,
> > > > > > > > > >>
> > > > > > > > > >> 1) They were previously installed, but I just
tried
> > running
> > > it
> > > > > > with
> > > > > > > > some
> > > > > > > > > >> of
> > > > > > > > > >> my own installed versions and they're not working
> properly
> > > > (e.g.
> > > > > > the
> > > > > > > > > make
> > > > > > > > > >> install fails due to gsl/gsl_cdf.h missing...
though I
> set
> > > > > MET_GSL
> > > > > > > to
> > > > > > > > my
> > > > > > > > > >> gsl-2.5 directory).
> > > > > > > > > >>
> > > > > > > > > >> 2) Not sure how I can verify that one, though I
think
> > > they're
> > > > > not
> > > > > > as
> > > > > > > > > I've
> > > > > > > > > >> seen GNU and Intel prompts in the config output.
My CC
> var
> > > in
> > > > my
> > > > > > > > bashrc
> > > > > > > > > >> links to an Intel compiler.
> > > > > > > > > >>
> > > > > > > > > >> 3) I followed those for the packages, though for
the
> > > compilers
> > > > > > > > section,
> > > > > > > > > I
> > > > > > > > > >> do not know my CXX or F77 paths on the hpc that
I'm
> > using. I
> > > > > also
> > > > > > > > think
> > > > > > > > > >> the
> > > > > > > > > >> icc is not working properly as I could not run
icc
> > without a
> > > > > > license
> > > > > > > > > >> prompt
> > > > > > > > > >> coming up.
> > > > > > > > > >>
> > > > > > > > > >> I'm not sure if any of that helps, but let me
know.
> Maybe
> > > some
> > > > > of
> > > > > > > > these
> > > > > > > > > >> issues are still on our end. The fact that met
needs to
> > only
> > > > use
> > > > > > one
> > > > > > > > > >> compiler might be the issue...
> > > > > > > > > >>
> > > > > > > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik
via
> RT <
> > > > > > > > > >> met_help at ucar.edu>
> > > > > > > > > >> wrote:
> > > > > > > > > >>
> > > > > > > > > >> > Hi Taylor. Thank you for passing along your
files. I
> > > have
> > > > a
> > > > > > few
> > > > > > > > > >> questions
> > > > > > > > > >> > for you.
> > > > > > > > > >> >
> > > > > > > > > >> > 1) Are you installing the external libraries
yourself
> or
> > > > were
> > > > > > they
> > > > > > > > > >> > previously installed?
> > > > > > > > > >> > 2) Can you please verify that the external
libraries
> and
> > > MET
> > > > > are
> > > > > > > > being
> > > > > > > > > >> > built with the same family of compilers (e.g.
all are
> > > built
> > > > > with
> > > > > > > > GNU,
> > > > > > > > > or
> > > > > > > > > >> > all are build with Intel, etc.)? Which
compiler are
> you
> > > > > using?
> > > > > > > > > >> > 3) Are you following the directions on this
page as
> your
> > > > > > > > instructions
> > > > > > > > > >> for
> > > > > > > > > >> > installation?
> > > > > > > > > >> >
> > > > > > > > > >> >
> > > > > > > > > >>
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > > > > > > >> >
> > > > > > > > > >> > Thank you!
> > > > > > > > > >> >
> > > > > > > > > >> > Julie
> > > > > > > > > >> >
> > > > > > > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor
Mandelbaum via
> > RT <
> > > > > > > > > >> > met_help at ucar.edu>
> > > > > > > > > >> > wrote:
> > > > > > > > > >> >
> > > > > > > > > >> > >
> > > > > > > > > >> > > <URL:
> > > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > >
> > > > > > > > > >> > >
> > > > > > > > > >> > > Hey Julie,
> > > > > > > > > >> > >
> > > > > > > > > >> > > I attached the config and make_install logs
here. We
> > > could
> > > > > do
> > > > > > a
> > > > > > > > > >> hangouts
> > > > > > > > > >> > > session as well if you can't pinpoint the
issue; I'm
> > > > > remoting
> > > > > > in
> > > > > > > > > from
> > > > > > > > > >> my
> > > > > > > > > >> > > home windows computer so it will be a bit
hacky.
> > > > > > > > > >> > >
> > > > > > > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie
Prestopnik via
> > RT
> > > <
> > > > > > > > > >> > met_help at ucar.edu
> > > > > > > > > >> > > >
> > > > > > > > > >> > > wrote:
> > > > > > > > > >> > >
> > > > > > > > > >> > > > Hi Taylor. It is difficult to tell what is
going
> > > > without
> > > > > > more
> > > > > > > > > >> context.
> > > > > > > > > >> > > > Could you please send me your config.log
file and
> > your
> > > > > > > make.log
> > > > > > > > > >> file?
> > > > > > > > > >> > > >
> > > > > > > > > >> > > > We could also consider doing a hangouts
session
> > where
> > > > you
> > > > > > can
> > > > > > > > > share
> > > > > > > > > >> > your
> > > > > > > > > >> > > > screen, and I can directly help that way.
Either
> > way
> > > > > > though,
> > > > > > > if
> > > > > > > > > you
> > > > > > > > > >> > > could
> > > > > > > > > >> > > > please send those files, I would appreciate
it.
> > > > > > > > > >> > > >
> > > > > > > > > >> > > > Thanks,
> > > > > > > > > >> > > > Julie
> > > > > > > > > >> > > >
> > > > > > > > > >> > > > Thanks!
> > > > > > > > > >> > > >
> > > > > > > > > >> > > > Julie
> > > > > > > > > >> > > >
> > > > > > > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor
Mandelbaum
> > via
> > > > RT <
> > > > > > > > > >> > > > met_help at ucar.edu>
> > > > > > > > > >> > > > wrote:
> > > > > > > > > >> > > >
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502
was
> acted
> > > > upon.
> > > > > > > > > >> > > > > Transaction: Ticket created by
> > > > > > > > taylor.mandelbaum at stonybrook.edu
> > > > > > > > > >> > > > > Queue: met_help
> > > > > > > > > >> > > > > Subject: met install help
> > > > > > > > > >> > > > > Owner: Nobody
> > > > > > > > > >> > > > > Requestors:
taylor.mandelbaum at stonybrook.edu
> > > > > > > > > >> > > > > Status: new
> > > > > > > > > >> > > > > Ticket <URL:
> > > > > > > > > >> >
> https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > > > >> > > >
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > Hey all,
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > I'm presently trying to compile MET 8.0
on our
> > HPC;
> > > > > when I
> > > > > > > > > >> configure
> > > > > > > > > >> > > it,
> > > > > > > > > >> > > > > I'm getting a few warnings on .h files:
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > configure: WARNING: errno.h: present but
cannot
> be
> > > > > > compiled
> > > > > > > > > >> > > > > configure: WARNING: errno.h: check
for
> missing
> > > > > > > > prerequisite
> > > > > > > > > >> > > headers?
> > > > > > > > > >> > > > > configure: WARNING: errno.h: see the
Autoconf
> > > > > > documentation
> > > > > > > > > >> > > > > configure: WARNING: errno.h: section
> "Present
> > > But
> > > > > > Cannot
> > > > > > > > Be
> > > > > > > > > >> > > Compiled"
> > > > > > > > > >> > > > > configure: WARNING: errno.h: proceeding
with the
> > > > > > compiler's
> > > > > > > > > result
> > > > > > > > > >> > > > > configure: WARNING: ##
> > > > > > --------------------------------
> > > > > > > ##
> > > > > > > > > >> > > > > configure: WARNING: ## Report this to
> > > > > > met_help at ucar.edu
> > > > > > > > ##
> > > > > > > > > >> > > > > configure: WARNING: ##
> > > > > > --------------------------------
> > > > > > > ##
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > and the same for fcntl.h, limits.h,
stddef.h,
> > file.h
> > > > and
> > > > > > > > > param.h.
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > When I try to make install, I get this
error on
> > the
> > > > tail
> > > > > > of
> > > > > > > > the
> > > > > > > > > >> log:
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > > > configalloc(yy_size_t)’:
> > > > > > > > > >> > > > > config_scanner.cc:2179:31: error:
‘rpl_malloc’
> was
> > > not
> > > > > > > > declared
> > > > > > > > > in
> > > > > > > > > >> > this
> > > > > > > > > >> > > > > scope
> > > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > configrealloc(void*,
> > > > > > > > > >> > yy_size_t)’:
> > > > > > > > > >> > > > > config_scanner.cc:2191:46: error:
‘rpl_realloc’
> > was
> > > > not
> > > > > > > > declared
> > > > > > > > > >> in
> > > > > > > > > >> > > this
> > > > > > > > > >> > > > > scope
> > > > > > > > > >> > > > > /* The cast to (char *) in the
following
> > > > accommodates
> > > > > > both
> > > > > > > > > >> > > > >
^
> > > > > > > > > >> > > > > make[3]: *** [libvx_config_a-
config_scanner.o]
> > > Error 1
> > > > > > > > > >> > > > > make[3]: Leaving directory
> > > > > > > > > >> > > > >
> > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > > > > > > > >> > > > > make[2]: *** [install-recursive] Error 1
> > > > > > > > > >> > > > > make[2]: Leaving directory
> > > > > > > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > > > > > > >> > > > > make[1]: *** [install-recursive] Error 1
> > > > > > > > > >> > > > > make[1]: Leaving directory
> > > > > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > > > > > > >> > > > > make: *** [install-recursive] Error 1
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > Not sure how to address either of these,
> hopefully
> > > you
> > > > > > guys
> > > > > > > > can
> > > > > > > > > >> > provide
> > > > > > > > > >> > > > > some insight.
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > Thanks!
> > > > > > > > > >> > > > > --
> > > > > > > > > >> > > > > *Taylor Mandelbaum*
> > > > > > > > > >> > > > > Research Technician
> > > > > > > > > >> > > > > SoMAS | Stony Brook University
> > > > > > > > > >> > > > > 678.468.5789
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > >
> > > > > > > > > >> > > >
> > > > > > > > > >> > >
> > > > > > > > > >> > > --
> > > > > > > > > >> > > *Taylor Mandelbaum*
> > > > > > > > > >> > > Research Technician
> > > > > > > > > >> > > SoMAS | Stony Brook University
> > > > > > > > > >> > > 678.468.5789
> > > > > > > > > >> > >
> > > > > > > > > >> > >
> > > > > > > > > >> >
> > > > > > > > > >> >
> > > > > > > > > >>
> > > > > > > > > >> --
> > > > > > > > > >> *Taylor Mandelbaum*
> > > > > > > > > >> Research Technician
> > > > > > > > > >> SoMAS | Stony Brook University
> > > > > > > > > >> 678.468.5789
> > > > > > > > > >>
> > > > > > > > > >>
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > > *Taylor Mandelbaum*
> > > > > > > > Research Technician
> > > > > > > > SoMAS | Stony Brook University
> > > > > > > > 678.468.5789
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > > > --
> > > > > > *Taylor Mandelbaum*
> > > > > > Research Technician
> > > > > > SoMAS | Stony Brook University
> > > > > > 678.468.5789
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > > >
> > >
> > > --
> > > *Taylor Mandelbaum*
> > > Research Technician
> > > SoMAS | Stony Brook University
> > > 678.468.5789
> > >
> > >
> >
> >
>
> --
> *Taylor Mandelbaum*
> Research Technician
> SoMAS | Stony Brook University
> 678.468.5789
>
>
------------------------------------------------
Subject: met install help
From: John Halley Gotway
Time: Fri Jan 18 09:40:37 2019
Taylor (and Julie),
I see that NetCDF setting mentioned:
MET_NETCDF='/opt/netcdf-gfortan/'
That likely indicates that you have the NetCDF FORTRAN interface
installed. MET requires the C and C++ NetCDF interface. That may or
may
not already be installed on your machine.
Please take a look at this page:
On Thu, Jan 17, 2019 at 5:27 PM Julie Prestopnik via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> Hi Taylor. It's good to see that we are making progress!
>
> I see that you have
> MET_NETCDF='/opt/netcdf-gfortan/'
>
> MET requires the C and C++ interface to NetCDF. Here is a checklist
of
> files that are necessary:
>
> Files for NetCDF4 C:
>
> - $MET_NETCDF/include/netcdf.h
> - $MET_NETCDF/lib/libnetcdf.a
> - $MET_NETCDF/lib/libnetcdf.so
>
> Files for NetCDF4 C++:
>
> - $MET_NETCDF/include/netcdf
> - $MET_NETCDF/lib/libnetcdf_c++4.a
> - $MET_NETCDF/lib/libnetcdf_c++4.so
>
> If you will need to compile these, please take a look at the
"Compiling
> NetCDF" section of this webpage in our online tutorial (for met-6.1,
but
> the instructions are the same for met-8.0):
>
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
>
> In config.log, I see that MET_HDF5 is not set:
> MET_HDF5=''
>
> The HDF5 library is required to support NetCDF4. If you need to
compile
> HDF5, you will need to do it prior to compiling NetCDF4. Please see
the
> instructions on "Compiling HDF5" on the same webpage listed above.
>
> Please let us know if you have any questions.
>
> Thanks,
> Julie
>
> On Thu, Jan 17, 2019 at 5:11 PM Taylor Mandelbaum via RT <
> met_help at ucar.edu>
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> >
> > Good catch, that's what happens when you have been working on
Windows
> for a
> > while.
> >
> > Now I'm getting an error with respect to netcdf.
> >
> > In file included from nc_var_info.cc:24:0:
> > nc_utils.h:22:18: fatal error: netcdf: No such file or directory
> >
> > I would guess netcdf-gfortran is properly installed, what do you
think?
> >
> > On Thu, Jan 17, 2019 at 6:36 PM Julie Prestopnik via RT <
> met_help at ucar.edu
> > >
> > wrote:
> >
> > > Hi Taylor.
> > >
> > > Unfortunately the change, which I see in your bashrc.txt file,
was not
> > > picked up. I still see the following in config.log:
> > >
> > > MET_BUFRLIB='E1/taylorm/MET8/BUFRLIB'
> > > MET_GSL='E1/taylorm/MET8/gsl-2.5'
> > >
> > > Please note that there is no leading slash before "E1". After
you
> > changed
> > > your .bashrc file, did you either run "source ~/.bashrc" or open
a new
> > > shell? If not, that would explain what is happening. Please
either
> run
> > > "source ~/.bashrc" or open a new shell. You can run "echo
$MET_GSL"
> > > afterward to verify that you see a leading slash in front of
"E1".
> > >
> > > Please give that a try and let us know how it goes.
> > >
> > > Thanks,
> > > Julie
> > >
> > > On Thu, Jan 17, 2019 at 3:44 PM Taylor Mandelbaum via RT <
> > > met_help at ucar.edu>
> > > wrote:
> > >
> > > >
> > > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
>
> > > >
> > > > Thanks all. I fixed the typos, checked to see if the file is
in
> > > > gsl2.5/include/gsl (it is), and reran it with the same error.
> Attached
> > > the
> > > > logs. I also attached my bashrc for brevity.
> > > >
> > > > On Thu, Jan 17, 2019 at 11:19 AM John Halley Gotway via RT <
> > > > met_help at ucar.edu> wrote:
> > > >
> > > > > Hi Julie and Taylor,
> > > > >
> > > > > I have one pesky little detail to mention about GSL that may
be a
> > point
> > > > of
> > > > > confusion here.
> > > > >
> > > > > Typically when your run "make install" on a software package
and
> tell
> > > it
> > > > to
> > > > > install to "/install_dir", it installs header files into
> > > > > "/install_dir/include" and library files into
"/install_dir/lib".
> > > > However,
> > > > > the GSL package installs header files into
> > "/install_dir/include/gsl".
> > > > And
> > > > > because of this, the MET code uses that gsl prefix:
> > > > > include "gsl/gsl_cdf.h"
> > > > >
> > > > > So Taylor, after you fix the typo in your MET_GSL setting,
please
> > check
> > > > if
> > > > > this file exists:
> > > > >
> > > > > MET_GSL='/E1/taylorm/MET8/gsl-2.5'
> > > > >
> > > > > *ls /E1/taylorm/MET8/gsl-2**.5/include/gsl/gsl_cdf.h*
> > > > >
> > > > > There is a second potential point of confusion. The
vx_gsl_prob
> > > > > library *inside
> > > > > of MET* contains code which wraps functions from the GSL
library.
> I
> > > > think
> > > > > we chose filenames poorly in that library. For example,
> > > > > vx_gsl_prob/gsl_cdf.h is a header file in the *MET* code
tree while
> > > > > $MET_GSL/include/gsl/gsl_cdf.h is a file from the GSL
library.
> This
> > > > > doesn't cause a problem in the compilation or running of MET
but
> can
> > > > cause
> > > > > confusion if you go hunting around for a file named
gsl_cdf.h.
> > > > >
> > > > > Thanks,
> > > > > John
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Thu, Jan 17, 2019 at 9:00 AM Julie Prestopnik via RT <
> > > > met_help at ucar.edu
> > > > > >
> > > > > wrote:
> > > > >
> > > > > >
> > > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > > >
> > > > > > Hi Taylor. Thank you.
> > > > > >
> > > > > > It looks like you may be missing a leading slash in front
of E1
> in
> > > the
> > > > > > environment variables below:
> > > > > >
> > > > > > MET_GSL='E1/taylorm/MET8/gsl-2.5'
> > > > > > MET_BUFRLIB='E1/taylorm/MET8/BUFRLIB'
> > > > > >
> > > > > > Also, can you please confirm that gsl_cdf.h exists at the
> following
> > > > > > location?
> > > > > > ${MET_GSL}/include
> > > > > >
> > > > > > If gsl_cdf.h exists in that location and you are missing a
> leading
> > > > slash,
> > > > > > please modify the value of the environment variables
above, try
> > > running
> > > > > > "make clean", rerun the configure command, and then try to
make
> MET
> > > > > again.
> > > > > >
> > > > > > Please let me know how it goes. If you encounter other
problems,
> > > > please
> > > > > > include your new config.log and make.log files.
> > > > > >
> > > > > > Thanks!
> > > > > >
> > > > > > Julie
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Wed, Jan 16, 2019 at 5:58 PM Taylor Mandelbaum via RT <
> > > > > > met_help at ucar.edu>
> > > > > > wrote:
> > > > > >
> > > > > > >
> > > > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> >
> > > > > > >
> > > > > > > Sure!
> > > > > > >
> > > > > > > On Wed, Jan 16, 2019 at 7:55 PM Julie Prestopnik via RT
<
> > > > > > met_help at ucar.edu
> > > > > > > >
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi Taylor. Thanks! Could you please send the new
config.log
> > file
> > > > and
> > > > > > the
> > > > > > > > new make.log file?
> > > > > > > >
> > > > > > > > Thanks!
> > > > > > > >
> > > > > > > > On Wed, Jan 16, 2019, 5:43 PM Taylor Mandelbaum via RT
<
> > > > > > > met_help at ucar.edu
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > >
> > > > > > > > > <URL:
> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > >
> > > > > > > > >
> > > > > > > > > Hey Julie,
> > > > > > > > >
> > > > > > > > > Thanks for all the help on this, it's really
appreciated. I
> > ran
> > > > the
> > > > > > > > install
> > > > > > > > > with CC, CXX, and F77 set to the appropriate
locations and
> > came
> > > > > > across
> > > > > > > > the
> > > > > > > > > same error with gsl_cdf.h. I reconfigured and re-
make/make
> > > > > install'd
> > > > > > > the
> > > > > > > > > gsl-2.5 package in my directory prior to running the
> install
> > > for
> > > > > MET
> > > > > > > > again
> > > > > > > > > (MET_GSL is set to the directory I made it in) and
still
> came
> > > > > across
> > > > > > > this
> > > > > > > > > error:
> > > > > > > > > ../../../src/libcode/vx_gsl_prob/gsl_cdf.h:17:25:
fatal
> > error:
> > > > > > > > > gsl/gsl_cdf.h: No such file or directory
> > > > > > > > > compilation terminated.
> > > > > > > > >
> > > > > > > > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik
via RT <
> > > > > > > > > met_help at ucar.edu>
> > > > > > > > > wrote:
> > > > > > > > >
> > > > > > > > > > Hi Taylor. In talking with more with John about
your
> > > > config.log
> > > > > > file
> > > > > > > > we
> > > > > > > > > > see that CC is set to use icc (intel), but CXX and
F77
> are
> > > set
> > > > to
> > > > > > use
> > > > > > > > g++
> > > > > > > > > > and gfortran (GNU).
> > > > > > > > > >
> > > > > > > > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > > > > > > > >
> > > > > > > >
> > > > > >
> > > >
> >
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > > > > > > > CXX='g++'
> > > > > > > > > > F77='gfortran'
> > > > > > > > > >
> > > > > > > > > > Let's see if we can solve the immediate problem
before
> > > worrying
> > > > > > about
> > > > > > > > any
> > > > > > > > > > potential problems with the external libraries.
For now,
> > > > please
> > > > > > > choose
> > > > > > > > > > either the GNU compilers or the Intel compilers
and set
> the
> > > > > > following
> > > > > > > > > > variables accordingly. You can chose one and then
simply
> > run
> > > > the
> > > > > > > > > commands
> > > > > > > > > > below.
> > > > > > > > > >
> > > > > > > > > > *For GNU:*
> > > > > > > > > > export CC=`which gcc`
> > > > > > > > > > export CXX=`which g++`
> > > > > > > > > > export F77=`which gfortran`
> > > > > > > > > >
> > > > > > > > > > *For Intel:*
> > > > > > > > > >
> > > > > > > > > > export CC=`which icc`
> > > > > > > > > > export CXX=`which icc`
> > > > > > > > > > export F77=`which ifort`
> > > > > > > > > >
> > > > > > > > > > Then run "make clean", rerun the configure
command, and
> > then
> > > > try
> > > > > to
> > > > > > > > make
> > > > > > > > > > MET again.
> > > > > > > > > >
> > > > > > > > > > Let's go from there and see how it works out.
Please let
> > me
> > > > > know.
> > > > > > > > > >
> > > > > > > > > > Julie
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik
<
> > > > > > jpresto at ucar.edu>
> > > > > > > > > > wrote:
> > > > > > > > > >
> > > > > > > > > > > Hi Taylor. Thank you for all of this
information.
> > > > > > > > > > >
> > > > > > > > > > > Since the libraries were previously installed
and we
> > cannot
> > > > be
> > > > > > > > certain
> > > > > > > > > > > which compiler was used, are you able and would
you be
> > > > > > comfortable
> > > > > > > > > > > installing each of the dependent libraries and
not
> using
> > > the
> > > > > > > > previously
> > > > > > > > > > > installed versions? If so, we have an install
script
> > that
> > > I
> > > > > can
> > > > > > > > point
> > > > > > > > > > you
> > > > > > > > > > > to, which would install all of the packages and
MET as
> > > > well. I
> > > > > > can
> > > > > > > > > walk
> > > > > > > > > > > through this with you via google hangouts and
you can
> > share
> > > > > your
> > > > > > > > screen
> > > > > > > > > > so
> > > > > > > > > > > we can make sure it is going smoothly. I could
do a
> > > > hangouts
> > > > > > > > session
> > > > > > > > > > with
> > > > > > > > > > > you tomorrow at 1:15pm (Mountain time) or on
Friday at
> > > 9:00am
> > > > > > > > (Mountain
> > > > > > > > > > > time). If those times don't work. I can get
you
> started
> > > > with
> > > > > > very
> > > > > > > > > > > specific instructions via email and we can
continue to
> > work
> > > > > > through
> > > > > > > > any
> > > > > > > > > > > problems. We can also set up a different time
for next
> > > week,
> > > > > > > > however,
> > > > > > > > > I
> > > > > > > > > > > didn't want you to have to wait that long.
Please let
> me
> > > > know
> > > > > > your
> > > > > > > > > > > preference.
> > > > > > > > > > >
> > > > > > > > > > > If you think that icc may not be working
properly, then
> > you
> > > > > > should
> > > > > > > > > > > probably use the GNU set of compilers, unless
there is
> > some
> > > > > > reason
> > > > > > > > not
> > > > > > > > > > to,
> > > > > > > > > > > in which case you may need to get a system
> administrator
> > > > > correct
> > > > > > > the
> > > > > > > > > > > problems with the intel compiler.
> > > > > > > > > > >
> > > > > > > > > > > Running "which g++" and running "which gfortran"
can
> tell
> > > you
> > > > > > what
> > > > > > > > the
> > > > > > > > > > CXX
> > > > > > > > > > > and F77 paths should be set to. Please let me
know if
> > you
> > > > have
> > > > > > any
> > > > > > > > > > issues
> > > > > > > > > > > with that.
> > > > > > > > > > >
> > > > > > > > > > > Julie
> > > > > > > > > > >
> > > > > > > > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor
Mandelbaum via
> RT
> > <
> > > > > > > > > > > met_help at ucar.edu> wrote:
> > > > > > > > > > >
> > > > > > > > > > >>
> > > > > > > > > > >> <URL:
> > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > >
> > > > > > > > > > >>
> > > > > > > > > > >> Hey Julie,
> > > > > > > > > > >>
> > > > > > > > > > >> 1) They were previously installed, but I just
tried
> > > running
> > > > it
> > > > > > > with
> > > > > > > > > some
> > > > > > > > > > >> of
> > > > > > > > > > >> my own installed versions and they're not
working
> > properly
> > > > > (e.g.
> > > > > > > the
> > > > > > > > > > make
> > > > > > > > > > >> install fails due to gsl/gsl_cdf.h missing...
though I
> > set
> > > > > > MET_GSL
> > > > > > > > to
> > > > > > > > > my
> > > > > > > > > > >> gsl-2.5 directory).
> > > > > > > > > > >>
> > > > > > > > > > >> 2) Not sure how I can verify that one, though I
think
> > > > they're
> > > > > > not
> > > > > > > as
> > > > > > > > > > I've
> > > > > > > > > > >> seen GNU and Intel prompts in the config
output. My CC
> > var
> > > > in
> > > > > my
> > > > > > > > > bashrc
> > > > > > > > > > >> links to an Intel compiler.
> > > > > > > > > > >>
> > > > > > > > > > >> 3) I followed those for the packages, though
for the
> > > > compilers
> > > > > > > > > section,
> > > > > > > > > > I
> > > > > > > > > > >> do not know my CXX or F77 paths on the hpc that
I'm
> > > using. I
> > > > > > also
> > > > > > > > > think
> > > > > > > > > > >> the
> > > > > > > > > > >> icc is not working properly as I could not run
icc
> > > without a
> > > > > > > license
> > > > > > > > > > >> prompt
> > > > > > > > > > >> coming up.
> > > > > > > > > > >>
> > > > > > > > > > >> I'm not sure if any of that helps, but let me
know.
> > Maybe
> > > > some
> > > > > > of
> > > > > > > > > these
> > > > > > > > > > >> issues are still on our end. The fact that met
needs
> to
> > > only
> > > > > use
> > > > > > > one
> > > > > > > > > > >> compiler might be the issue...
> > > > > > > > > > >>
> > > > > > > > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie
Prestopnik via
> > RT <
> > > > > > > > > > >> met_help at ucar.edu>
> > > > > > > > > > >> wrote:
> > > > > > > > > > >>
> > > > > > > > > > >> > Hi Taylor. Thank you for passing along your
> files. I
> > > > have
> > > > > a
> > > > > > > few
> > > > > > > > > > >> questions
> > > > > > > > > > >> > for you.
> > > > > > > > > > >> >
> > > > > > > > > > >> > 1) Are you installing the external libraries
> yourself
> > or
> > > > > were
> > > > > > > they
> > > > > > > > > > >> > previously installed?
> > > > > > > > > > >> > 2) Can you please verify that the external
libraries
> > and
> > > > MET
> > > > > > are
> > > > > > > > > being
> > > > > > > > > > >> > built with the same family of compilers (e.g.
all
> are
> > > > built
> > > > > > with
> > > > > > > > > GNU,
> > > > > > > > > > or
> > > > > > > > > > >> > all are build with Intel, etc.)? Which
compiler are
> > you
> > > > > > using?
> > > > > > > > > > >> > 3) Are you following the directions on this
page as
> > your
> > > > > > > > > instructions
> > > > > > > > > > >> for
> > > > > > > > > > >> > installation?
> > > > > > > > > > >> >
> > > > > > > > > > >> >
> > > > > > > > > > >>
> > > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > > > > > > > >> >
> > > > > > > > > > >> > Thank you!
> > > > > > > > > > >> >
> > > > > > > > > > >> > Julie
> > > > > > > > > > >> >
> > > > > > > > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor
Mandelbaum
> via
> > > RT <
> > > > > > > > > > >> > met_help at ucar.edu>
> > > > > > > > > > >> > wrote:
> > > > > > > > > > >> >
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > <URL:
> > > > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > >
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > Hey Julie,
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > I attached the config and make_install logs
here.
> We
> > > > could
> > > > > > do
> > > > > > > a
> > > > > > > > > > >> hangouts
> > > > > > > > > > >> > > session as well if you can't pinpoint the
issue;
> I'm
> > > > > > remoting
> > > > > > > in
> > > > > > > > > > from
> > > > > > > > > > >> my
> > > > > > > > > > >> > > home windows computer so it will be a bit
hacky.
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie
Prestopnik
> via
> > > RT
> > > > <
> > > > > > > > > > >> > met_help at ucar.edu
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > wrote:
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > > Hi Taylor. It is difficult to tell what
is
> going
> > > > > without
> > > > > > > more
> > > > > > > > > > >> context.
> > > > > > > > > > >> > > > Could you please send me your config.log
file
> and
> > > your
> > > > > > > > make.log
> > > > > > > > > > >> file?
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > We could also consider doing a hangouts
session
> > > where
> > > > > you
> > > > > > > can
> > > > > > > > > > share
> > > > > > > > > > >> > your
> > > > > > > > > > >> > > > screen, and I can directly help that way.
> Either
> > > way
> > > > > > > though,
> > > > > > > > if
> > > > > > > > > > you
> > > > > > > > > > >> > > could
> > > > > > > > > > >> > > > please send those files, I would
appreciate it.
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > Thanks,
> > > > > > > > > > >> > > > Julie
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > Thanks!
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > Julie
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor
> Mandelbaum
> > > via
> > > > > RT <
> > > > > > > > > > >> > > > met_help at ucar.edu>
> > > > > > > > > > >> > > > wrote:
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502
was
> > acted
> > > > > upon.
> > > > > > > > > > >> > > > > Transaction: Ticket created by
> > > > > > > > > taylor.mandelbaum at stonybrook.edu
> > > > > > > > > > >> > > > > Queue: met_help
> > > > > > > > > > >> > > > > Subject: met install help
> > > > > > > > > > >> > > > > Owner: Nobody
> > > > > > > > > > >> > > > > Requestors:
> taylor.mandelbaum at stonybrook.edu
> > > > > > > > > > >> > > > > Status: new
> > > > > > > > > > >> > > > > Ticket <URL:
> > > > > > > > > > >> >
> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > Hey all,
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > I'm presently trying to compile MET 8.0
on our
> > > HPC;
> > > > > > when I
> > > > > > > > > > >> configure
> > > > > > > > > > >> > > it,
> > > > > > > > > > >> > > > > I'm getting a few warnings on .h files:
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > configure: WARNING: errno.h: present
but
> cannot
> > be
> > > > > > > compiled
> > > > > > > > > > >> > > > > configure: WARNING: errno.h: check
for
> > missing
> > > > > > > > > prerequisite
> > > > > > > > > > >> > > headers?
> > > > > > > > > > >> > > > > configure: WARNING: errno.h: see the
Autoconf
> > > > > > > documentation
> > > > > > > > > > >> > > > > configure: WARNING: errno.h:
section
> > "Present
> > > > But
> > > > > > > Cannot
> > > > > > > > > Be
> > > > > > > > > > >> > > Compiled"
> > > > > > > > > > >> > > > > configure: WARNING: errno.h: proceeding
with
> the
> > > > > > > compiler's
> > > > > > > > > > result
> > > > > > > > > > >> > > > > configure: WARNING: ##
> > > > > > > --------------------------------
> > > > > > > > ##
> > > > > > > > > > >> > > > > configure: WARNING: ## Report this
to
> > > > > > > met_help at ucar.edu
> > > > > > > > > ##
> > > > > > > > > > >> > > > > configure: WARNING: ##
> > > > > > > --------------------------------
> > > > > > > > ##
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > and the same for fcntl.h, limits.h,
stddef.h,
> > > file.h
> > > > > and
> > > > > > > > > > param.h.
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > When I try to make install, I get this
error
> on
> > > the
> > > > > tail
> > > > > > > of
> > > > > > > > > the
> > > > > > > > > > >> log:
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > > > > configalloc(yy_size_t)’:
> > > > > > > > > > >> > > > > config_scanner.cc:2179:31: error:
‘rpl_malloc’
> > was
> > > > not
> > > > > > > > > declared
> > > > > > > > > > in
> > > > > > > > > > >> > this
> > > > > > > > > > >> > > > > scope
> > > > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > > configrealloc(void*,
> > > > > > > > > > >> > yy_size_t)’:
> > > > > > > > > > >> > > > > config_scanner.cc:2191:46: error:
> ‘rpl_realloc’
> > > was
> > > > > not
> > > > > > > > > declared
> > > > > > > > > > >> in
> > > > > > > > > > >> > > this
> > > > > > > > > > >> > > > > scope
> > > > > > > > > > >> > > > > /* The cast to (char *) in the
following
> > > > > accommodates
> > > > > > > both
> > > > > > > > > > >> > > > >
> ^
> > > > > > > > > > >> > > > > make[3]: *** [libvx_config_a-
config_scanner.o]
> > > > Error 1
> > > > > > > > > > >> > > > > make[3]: Leaving directory
> > > > > > > > > > >> > > > >
> > > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > > > > > > > > >> > > > > make[2]: *** [install-recursive] Error
1
> > > > > > > > > > >> > > > > make[2]: Leaving directory
> > > > > > > > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > > > > > > > >> > > > > make[1]: *** [install-recursive] Error
1
> > > > > > > > > > >> > > > > make[1]: Leaving directory
> > > > > > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > > > > > > > >> > > > > make: *** [install-recursive] Error 1
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > Not sure how to address either of
these,
> > hopefully
> > > > you
> > > > > > > guys
> > > > > > > > > can
> > > > > > > > > > >> > provide
> > > > > > > > > > >> > > > > some insight.
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > Thanks!
> > > > > > > > > > >> > > > > --
> > > > > > > > > > >> > > > > *Taylor Mandelbaum*
> > > > > > > > > > >> > > > > Research Technician
> > > > > > > > > > >> > > > > SoMAS | Stony Brook University
> > > > > > > > > > >> > > > > 678.468.5789
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > --
> > > > > > > > > > >> > > *Taylor Mandelbaum*
> > > > > > > > > > >> > > Research Technician
> > > > > > > > > > >> > > SoMAS | Stony Brook University
> > > > > > > > > > >> > > 678.468.5789
> > > > > > > > > > >> > >
> > > > > > > > > > >> > >
> > > > > > > > > > >> >
> > > > > > > > > > >> >
> > > > > > > > > > >>
> > > > > > > > > > >> --
> > > > > > > > > > >> *Taylor Mandelbaum*
> > > > > > > > > > >> Research Technician
> > > > > > > > > > >> SoMAS | Stony Brook University
> > > > > > > > > > >> 678.468.5789
> > > > > > > > > > >>
> > > > > > > > > > >>
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > > --
> > > > > > > > > *Taylor Mandelbaum*
> > > > > > > > > Research Technician
> > > > > > > > > SoMAS | Stony Brook University
> > > > > > > > > 678.468.5789
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > *Taylor Mandelbaum*
> > > > > > > Research Technician
> > > > > > > SoMAS | Stony Brook University
> > > > > > > 678.468.5789
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > > > --
> > > > *Taylor Mandelbaum*
> > > > Research Technician
> > > > SoMAS | Stony Brook University
> > > > 678.468.5789
> > > >
> > > >
> > >
> > >
> >
> > --
> > *Taylor Mandelbaum*
> > Research Technician
> > SoMAS | Stony Brook University
> > 678.468.5789
> >
> >
>
>
------------------------------------------------
Subject: met install help
From: John Halley Gotway
Time: Fri Jan 18 09:42:09 2019
Taylor (and Julie),
I see that NetCDF setting mentioned:
MET_NETCDF='/opt/netcdf-gfortan/'
That likely indicates that you have the NetCDF FORTRAN interface
installed. MET requires the C and C++ NetCDF interface. That may or
may
not already be installed on your machine.
Please take a look at this page:
https://dtcenter.org/met/users/downloads/index.php
At the bottom, the compile_MET_all.sh script is what Julie uses to
install
MET and all its dependent libraries. Scroll down to the section on
NetCDF
and you could use those commands to build it.
Thanks,
John
On Thu, Jan 17, 2019 at 5:27 PM Julie Prestopnik via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> Hi Taylor. It's good to see that we are making progress!
>
> I see that you have
> MET_NETCDF='/opt/netcdf-gfortan/'
>
> MET requires the C and C++ interface to NetCDF. Here is a checklist
of
> files that are necessary:
>
> Files for NetCDF4 C:
>
> - $MET_NETCDF/include/netcdf.h
> - $MET_NETCDF/lib/libnetcdf.a
> - $MET_NETCDF/lib/libnetcdf.so
>
> Files for NetCDF4 C++:
>
> - $MET_NETCDF/include/netcdf
> - $MET_NETCDF/lib/libnetcdf_c++4.a
> - $MET_NETCDF/lib/libnetcdf_c++4.so
>
> If you will need to compile these, please take a look at the
"Compiling
> NetCDF" section of this webpage in our online tutorial (for met-6.1,
but
> the instructions are the same for met-8.0):
>
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
>
> In config.log, I see that MET_HDF5 is not set:
> MET_HDF5=''
>
> The HDF5 library is required to support NetCDF4. If you need to
compile
> HDF5, you will need to do it prior to compiling NetCDF4. Please see
the
> instructions on "Compiling HDF5" on the same webpage listed above.
>
> Please let us know if you have any questions.
>
> Thanks,
> Julie
>
> On Thu, Jan 17, 2019 at 5:11 PM Taylor Mandelbaum via RT <
> met_help at ucar.edu>
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> >
> > Good catch, that's what happens when you have been working on
Windows
> for a
> > while.
> >
> > Now I'm getting an error with respect to netcdf.
> >
> > In file included from nc_var_info.cc:24:0:
> > nc_utils.h:22:18: fatal error: netcdf: No such file or directory
> >
> > I would guess netcdf-gfortran is properly installed, what do you
think?
> >
> > On Thu, Jan 17, 2019 at 6:36 PM Julie Prestopnik via RT <
> met_help at ucar.edu
> > >
> > wrote:
> >
> > > Hi Taylor.
> > >
> > > Unfortunately the change, which I see in your bashrc.txt file,
was not
> > > picked up. I still see the following in config.log:
> > >
> > > MET_BUFRLIB='E1/taylorm/MET8/BUFRLIB'
> > > MET_GSL='E1/taylorm/MET8/gsl-2.5'
> > >
> > > Please note that there is no leading slash before "E1". After
you
> > changed
> > > your .bashrc file, did you either run "source ~/.bashrc" or open
a new
> > > shell? If not, that would explain what is happening. Please
either
> run
> > > "source ~/.bashrc" or open a new shell. You can run "echo
$MET_GSL"
> > > afterward to verify that you see a leading slash in front of
"E1".
> > >
> > > Please give that a try and let us know how it goes.
> > >
> > > Thanks,
> > > Julie
> > >
> > > On Thu, Jan 17, 2019 at 3:44 PM Taylor Mandelbaum via RT <
> > > met_help at ucar.edu>
> > > wrote:
> > >
> > > >
> > > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
>
> > > >
> > > > Thanks all. I fixed the typos, checked to see if the file is
in
> > > > gsl2.5/include/gsl (it is), and reran it with the same error.
> Attached
> > > the
> > > > logs. I also attached my bashrc for brevity.
> > > >
> > > > On Thu, Jan 17, 2019 at 11:19 AM John Halley Gotway via RT <
> > > > met_help at ucar.edu> wrote:
> > > >
> > > > > Hi Julie and Taylor,
> > > > >
> > > > > I have one pesky little detail to mention about GSL that may
be a
> > point
> > > > of
> > > > > confusion here.
> > > > >
> > > > > Typically when your run "make install" on a software package
and
> tell
> > > it
> > > > to
> > > > > install to "/install_dir", it installs header files into
> > > > > "/install_dir/include" and library files into
"/install_dir/lib".
> > > > However,
> > > > > the GSL package installs header files into
> > "/install_dir/include/gsl".
> > > > And
> > > > > because of this, the MET code uses that gsl prefix:
> > > > > include "gsl/gsl_cdf.h"
> > > > >
> > > > > So Taylor, after you fix the typo in your MET_GSL setting,
please
> > check
> > > > if
> > > > > this file exists:
> > > > >
> > > > > MET_GSL='/E1/taylorm/MET8/gsl-2.5'
> > > > >
> > > > > *ls /E1/taylorm/MET8/gsl-2**.5/include/gsl/gsl_cdf.h*
> > > > >
> > > > > There is a second potential point of confusion. The
vx_gsl_prob
> > > > > library *inside
> > > > > of MET* contains code which wraps functions from the GSL
library.
> I
> > > > think
> > > > > we chose filenames poorly in that library. For example,
> > > > > vx_gsl_prob/gsl_cdf.h is a header file in the *MET* code
tree while
> > > > > $MET_GSL/include/gsl/gsl_cdf.h is a file from the GSL
library.
> This
> > > > > doesn't cause a problem in the compilation or running of MET
but
> can
> > > > cause
> > > > > confusion if you go hunting around for a file named
gsl_cdf.h.
> > > > >
> > > > > Thanks,
> > > > > John
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Thu, Jan 17, 2019 at 9:00 AM Julie Prestopnik via RT <
> > > > met_help at ucar.edu
> > > > > >
> > > > > wrote:
> > > > >
> > > > > >
> > > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > > >
> > > > > > Hi Taylor. Thank you.
> > > > > >
> > > > > > It looks like you may be missing a leading slash in front
of E1
> in
> > > the
> > > > > > environment variables below:
> > > > > >
> > > > > > MET_GSL='E1/taylorm/MET8/gsl-2.5'
> > > > > > MET_BUFRLIB='E1/taylorm/MET8/BUFRLIB'
> > > > > >
> > > > > > Also, can you please confirm that gsl_cdf.h exists at the
> following
> > > > > > location?
> > > > > > ${MET_GSL}/include
> > > > > >
> > > > > > If gsl_cdf.h exists in that location and you are missing a
> leading
> > > > slash,
> > > > > > please modify the value of the environment variables
above, try
> > > running
> > > > > > "make clean", rerun the configure command, and then try to
make
> MET
> > > > > again.
> > > > > >
> > > > > > Please let me know how it goes. If you encounter other
problems,
> > > > please
> > > > > > include your new config.log and make.log files.
> > > > > >
> > > > > > Thanks!
> > > > > >
> > > > > > Julie
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Wed, Jan 16, 2019 at 5:58 PM Taylor Mandelbaum via RT <
> > > > > > met_help at ucar.edu>
> > > > > > wrote:
> > > > > >
> > > > > > >
> > > > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> >
> > > > > > >
> > > > > > > Sure!
> > > > > > >
> > > > > > > On Wed, Jan 16, 2019 at 7:55 PM Julie Prestopnik via RT
<
> > > > > > met_help at ucar.edu
> > > > > > > >
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi Taylor. Thanks! Could you please send the new
config.log
> > file
> > > > and
> > > > > > the
> > > > > > > > new make.log file?
> > > > > > > >
> > > > > > > > Thanks!
> > > > > > > >
> > > > > > > > On Wed, Jan 16, 2019, 5:43 PM Taylor Mandelbaum via RT
<
> > > > > > > met_help at ucar.edu
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > >
> > > > > > > > > <URL:
> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > >
> > > > > > > > >
> > > > > > > > > Hey Julie,
> > > > > > > > >
> > > > > > > > > Thanks for all the help on this, it's really
appreciated. I
> > ran
> > > > the
> > > > > > > > install
> > > > > > > > > with CC, CXX, and F77 set to the appropriate
locations and
> > came
> > > > > > across
> > > > > > > > the
> > > > > > > > > same error with gsl_cdf.h. I reconfigured and re-
make/make
> > > > > install'd
> > > > > > > the
> > > > > > > > > gsl-2.5 package in my directory prior to running the
> install
> > > for
> > > > > MET
> > > > > > > > again
> > > > > > > > > (MET_GSL is set to the directory I made it in) and
still
> came
> > > > > across
> > > > > > > this
> > > > > > > > > error:
> > > > > > > > > ../../../src/libcode/vx_gsl_prob/gsl_cdf.h:17:25:
fatal
> > error:
> > > > > > > > > gsl/gsl_cdf.h: No such file or directory
> > > > > > > > > compilation terminated.
> > > > > > > > >
> > > > > > > > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik
via RT <
> > > > > > > > > met_help at ucar.edu>
> > > > > > > > > wrote:
> > > > > > > > >
> > > > > > > > > > Hi Taylor. In talking with more with John about
your
> > > > config.log
> > > > > > file
> > > > > > > > we
> > > > > > > > > > see that CC is set to use icc (intel), but CXX and
F77
> are
> > > set
> > > > to
> > > > > > use
> > > > > > > > g++
> > > > > > > > > > and gfortran (GNU).
> > > > > > > > > >
> > > > > > > > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > > > > > > > >
> > > > > > > >
> > > > > >
> > > >
> >
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > > > > > > > CXX='g++'
> > > > > > > > > > F77='gfortran'
> > > > > > > > > >
> > > > > > > > > > Let's see if we can solve the immediate problem
before
> > > worrying
> > > > > > about
> > > > > > > > any
> > > > > > > > > > potential problems with the external libraries.
For now,
> > > > please
> > > > > > > choose
> > > > > > > > > > either the GNU compilers or the Intel compilers
and set
> the
> > > > > > following
> > > > > > > > > > variables accordingly. You can chose one and then
simply
> > run
> > > > the
> > > > > > > > > commands
> > > > > > > > > > below.
> > > > > > > > > >
> > > > > > > > > > *For GNU:*
> > > > > > > > > > export CC=`which gcc`
> > > > > > > > > > export CXX=`which g++`
> > > > > > > > > > export F77=`which gfortran`
> > > > > > > > > >
> > > > > > > > > > *For Intel:*
> > > > > > > > > >
> > > > > > > > > > export CC=`which icc`
> > > > > > > > > > export CXX=`which icc`
> > > > > > > > > > export F77=`which ifort`
> > > > > > > > > >
> > > > > > > > > > Then run "make clean", rerun the configure
command, and
> > then
> > > > try
> > > > > to
> > > > > > > > make
> > > > > > > > > > MET again.
> > > > > > > > > >
> > > > > > > > > > Let's go from there and see how it works out.
Please let
> > me
> > > > > know.
> > > > > > > > > >
> > > > > > > > > > Julie
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik
<
> > > > > > jpresto at ucar.edu>
> > > > > > > > > > wrote:
> > > > > > > > > >
> > > > > > > > > > > Hi Taylor. Thank you for all of this
information.
> > > > > > > > > > >
> > > > > > > > > > > Since the libraries were previously installed
and we
> > cannot
> > > > be
> > > > > > > > certain
> > > > > > > > > > > which compiler was used, are you able and would
you be
> > > > > > comfortable
> > > > > > > > > > > installing each of the dependent libraries and
not
> using
> > > the
> > > > > > > > previously
> > > > > > > > > > > installed versions? If so, we have an install
script
> > that
> > > I
> > > > > can
> > > > > > > > point
> > > > > > > > > > you
> > > > > > > > > > > to, which would install all of the packages and
MET as
> > > > well. I
> > > > > > can
> > > > > > > > > walk
> > > > > > > > > > > through this with you via google hangouts and
you can
> > share
> > > > > your
> > > > > > > > screen
> > > > > > > > > > so
> > > > > > > > > > > we can make sure it is going smoothly. I could
do a
> > > > hangouts
> > > > > > > > session
> > > > > > > > > > with
> > > > > > > > > > > you tomorrow at 1:15pm (Mountain time) or on
Friday at
> > > 9:00am
> > > > > > > > (Mountain
> > > > > > > > > > > time). If those times don't work. I can get
you
> started
> > > > with
> > > > > > very
> > > > > > > > > > > specific instructions via email and we can
continue to
> > work
> > > > > > through
> > > > > > > > any
> > > > > > > > > > > problems. We can also set up a different time
for next
> > > week,
> > > > > > > > however,
> > > > > > > > > I
> > > > > > > > > > > didn't want you to have to wait that long.
Please let
> me
> > > > know
> > > > > > your
> > > > > > > > > > > preference.
> > > > > > > > > > >
> > > > > > > > > > > If you think that icc may not be working
properly, then
> > you
> > > > > > should
> > > > > > > > > > > probably use the GNU set of compilers, unless
there is
> > some
> > > > > > reason
> > > > > > > > not
> > > > > > > > > > to,
> > > > > > > > > > > in which case you may need to get a system
> administrator
> > > > > correct
> > > > > > > the
> > > > > > > > > > > problems with the intel compiler.
> > > > > > > > > > >
> > > > > > > > > > > Running "which g++" and running "which gfortran"
can
> tell
> > > you
> > > > > > what
> > > > > > > > the
> > > > > > > > > > CXX
> > > > > > > > > > > and F77 paths should be set to. Please let me
know if
> > you
> > > > have
> > > > > > any
> > > > > > > > > > issues
> > > > > > > > > > > with that.
> > > > > > > > > > >
> > > > > > > > > > > Julie
> > > > > > > > > > >
> > > > > > > > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor
Mandelbaum via
> RT
> > <
> > > > > > > > > > > met_help at ucar.edu> wrote:
> > > > > > > > > > >
> > > > > > > > > > >>
> > > > > > > > > > >> <URL:
> > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > >
> > > > > > > > > > >>
> > > > > > > > > > >> Hey Julie,
> > > > > > > > > > >>
> > > > > > > > > > >> 1) They were previously installed, but I just
tried
> > > running
> > > > it
> > > > > > > with
> > > > > > > > > some
> > > > > > > > > > >> of
> > > > > > > > > > >> my own installed versions and they're not
working
> > properly
> > > > > (e.g.
> > > > > > > the
> > > > > > > > > > make
> > > > > > > > > > >> install fails due to gsl/gsl_cdf.h missing...
though I
> > set
> > > > > > MET_GSL
> > > > > > > > to
> > > > > > > > > my
> > > > > > > > > > >> gsl-2.5 directory).
> > > > > > > > > > >>
> > > > > > > > > > >> 2) Not sure how I can verify that one, though I
think
> > > > they're
> > > > > > not
> > > > > > > as
> > > > > > > > > > I've
> > > > > > > > > > >> seen GNU and Intel prompts in the config
output. My CC
> > var
> > > > in
> > > > > my
> > > > > > > > > bashrc
> > > > > > > > > > >> links to an Intel compiler.
> > > > > > > > > > >>
> > > > > > > > > > >> 3) I followed those for the packages, though
for the
> > > > compilers
> > > > > > > > > section,
> > > > > > > > > > I
> > > > > > > > > > >> do not know my CXX or F77 paths on the hpc that
I'm
> > > using. I
> > > > > > also
> > > > > > > > > think
> > > > > > > > > > >> the
> > > > > > > > > > >> icc is not working properly as I could not run
icc
> > > without a
> > > > > > > license
> > > > > > > > > > >> prompt
> > > > > > > > > > >> coming up.
> > > > > > > > > > >>
> > > > > > > > > > >> I'm not sure if any of that helps, but let me
know.
> > Maybe
> > > > some
> > > > > > of
> > > > > > > > > these
> > > > > > > > > > >> issues are still on our end. The fact that met
needs
> to
> > > only
> > > > > use
> > > > > > > one
> > > > > > > > > > >> compiler might be the issue...
> > > > > > > > > > >>
> > > > > > > > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie
Prestopnik via
> > RT <
> > > > > > > > > > >> met_help at ucar.edu>
> > > > > > > > > > >> wrote:
> > > > > > > > > > >>
> > > > > > > > > > >> > Hi Taylor. Thank you for passing along your
> files. I
> > > > have
> > > > > a
> > > > > > > few
> > > > > > > > > > >> questions
> > > > > > > > > > >> > for you.
> > > > > > > > > > >> >
> > > > > > > > > > >> > 1) Are you installing the external libraries
> yourself
> > or
> > > > > were
> > > > > > > they
> > > > > > > > > > >> > previously installed?
> > > > > > > > > > >> > 2) Can you please verify that the external
libraries
> > and
> > > > MET
> > > > > > are
> > > > > > > > > being
> > > > > > > > > > >> > built with the same family of compilers (e.g.
all
> are
> > > > built
> > > > > > with
> > > > > > > > > GNU,
> > > > > > > > > > or
> > > > > > > > > > >> > all are build with Intel, etc.)? Which
compiler are
> > you
> > > > > > using?
> > > > > > > > > > >> > 3) Are you following the directions on this
page as
> > your
> > > > > > > > > instructions
> > > > > > > > > > >> for
> > > > > > > > > > >> > installation?
> > > > > > > > > > >> >
> > > > > > > > > > >> >
> > > > > > > > > > >>
> > > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > > > > > > > >> >
> > > > > > > > > > >> > Thank you!
> > > > > > > > > > >> >
> > > > > > > > > > >> > Julie
> > > > > > > > > > >> >
> > > > > > > > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor
Mandelbaum
> via
> > > RT <
> > > > > > > > > > >> > met_help at ucar.edu>
> > > > > > > > > > >> > wrote:
> > > > > > > > > > >> >
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > <URL:
> > > > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > >
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > Hey Julie,
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > I attached the config and make_install logs
here.
> We
> > > > could
> > > > > > do
> > > > > > > a
> > > > > > > > > > >> hangouts
> > > > > > > > > > >> > > session as well if you can't pinpoint the
issue;
> I'm
> > > > > > remoting
> > > > > > > in
> > > > > > > > > > from
> > > > > > > > > > >> my
> > > > > > > > > > >> > > home windows computer so it will be a bit
hacky.
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie
Prestopnik
> via
> > > RT
> > > > <
> > > > > > > > > > >> > met_help at ucar.edu
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > wrote:
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > > Hi Taylor. It is difficult to tell what
is
> going
> > > > > without
> > > > > > > more
> > > > > > > > > > >> context.
> > > > > > > > > > >> > > > Could you please send me your config.log
file
> and
> > > your
> > > > > > > > make.log
> > > > > > > > > > >> file?
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > We could also consider doing a hangouts
session
> > > where
> > > > > you
> > > > > > > can
> > > > > > > > > > share
> > > > > > > > > > >> > your
> > > > > > > > > > >> > > > screen, and I can directly help that way.
> Either
> > > way
> > > > > > > though,
> > > > > > > > if
> > > > > > > > > > you
> > > > > > > > > > >> > > could
> > > > > > > > > > >> > > > please send those files, I would
appreciate it.
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > Thanks,
> > > > > > > > > > >> > > > Julie
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > Thanks!
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > Julie
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor
> Mandelbaum
> > > via
> > > > > RT <
> > > > > > > > > > >> > > > met_help at ucar.edu>
> > > > > > > > > > >> > > > wrote:
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502
was
> > acted
> > > > > upon.
> > > > > > > > > > >> > > > > Transaction: Ticket created by
> > > > > > > > > taylor.mandelbaum at stonybrook.edu
> > > > > > > > > > >> > > > > Queue: met_help
> > > > > > > > > > >> > > > > Subject: met install help
> > > > > > > > > > >> > > > > Owner: Nobody
> > > > > > > > > > >> > > > > Requestors:
> taylor.mandelbaum at stonybrook.edu
> > > > > > > > > > >> > > > > Status: new
> > > > > > > > > > >> > > > > Ticket <URL:
> > > > > > > > > > >> >
> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > Hey all,
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > I'm presently trying to compile MET 8.0
on our
> > > HPC;
> > > > > > when I
> > > > > > > > > > >> configure
> > > > > > > > > > >> > > it,
> > > > > > > > > > >> > > > > I'm getting a few warnings on .h files:
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > configure: WARNING: errno.h: present
but
> cannot
> > be
> > > > > > > compiled
> > > > > > > > > > >> > > > > configure: WARNING: errno.h: check
for
> > missing
> > > > > > > > > prerequisite
> > > > > > > > > > >> > > headers?
> > > > > > > > > > >> > > > > configure: WARNING: errno.h: see the
Autoconf
> > > > > > > documentation
> > > > > > > > > > >> > > > > configure: WARNING: errno.h:
section
> > "Present
> > > > But
> > > > > > > Cannot
> > > > > > > > > Be
> > > > > > > > > > >> > > Compiled"
> > > > > > > > > > >> > > > > configure: WARNING: errno.h: proceeding
with
> the
> > > > > > > compiler's
> > > > > > > > > > result
> > > > > > > > > > >> > > > > configure: WARNING: ##
> > > > > > > --------------------------------
> > > > > > > > ##
> > > > > > > > > > >> > > > > configure: WARNING: ## Report this
to
> > > > > > > met_help at ucar.edu
> > > > > > > > > ##
> > > > > > > > > > >> > > > > configure: WARNING: ##
> > > > > > > --------------------------------
> > > > > > > > ##
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > and the same for fcntl.h, limits.h,
stddef.h,
> > > file.h
> > > > > and
> > > > > > > > > > param.h.
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > When I try to make install, I get this
error
> on
> > > the
> > > > > tail
> > > > > > > of
> > > > > > > > > the
> > > > > > > > > > >> log:
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > > > > configalloc(yy_size_t)’:
> > > > > > > > > > >> > > > > config_scanner.cc:2179:31: error:
‘rpl_malloc’
> > was
> > > > not
> > > > > > > > > declared
> > > > > > > > > > in
> > > > > > > > > > >> > this
> > > > > > > > > > >> > > > > scope
> > > > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > > configrealloc(void*,
> > > > > > > > > > >> > yy_size_t)’:
> > > > > > > > > > >> > > > > config_scanner.cc:2191:46: error:
> ‘rpl_realloc’
> > > was
> > > > > not
> > > > > > > > > declared
> > > > > > > > > > >> in
> > > > > > > > > > >> > > this
> > > > > > > > > > >> > > > > scope
> > > > > > > > > > >> > > > > /* The cast to (char *) in the
following
> > > > > accommodates
> > > > > > > both
> > > > > > > > > > >> > > > >
> ^
> > > > > > > > > > >> > > > > make[3]: *** [libvx_config_a-
config_scanner.o]
> > > > Error 1
> > > > > > > > > > >> > > > > make[3]: Leaving directory
> > > > > > > > > > >> > > > >
> > > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > > > > > > > > >> > > > > make[2]: *** [install-recursive] Error
1
> > > > > > > > > > >> > > > > make[2]: Leaving directory
> > > > > > > > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > > > > > > > >> > > > > make[1]: *** [install-recursive] Error
1
> > > > > > > > > > >> > > > > make[1]: Leaving directory
> > > > > > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > > > > > > > >> > > > > make: *** [install-recursive] Error 1
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > Not sure how to address either of
these,
> > hopefully
> > > > you
> > > > > > > guys
> > > > > > > > > can
> > > > > > > > > > >> > provide
> > > > > > > > > > >> > > > > some insight.
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > Thanks!
> > > > > > > > > > >> > > > > --
> > > > > > > > > > >> > > > > *Taylor Mandelbaum*
> > > > > > > > > > >> > > > > Research Technician
> > > > > > > > > > >> > > > > SoMAS | Stony Brook University
> > > > > > > > > > >> > > > > 678.468.5789
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > --
> > > > > > > > > > >> > > *Taylor Mandelbaum*
> > > > > > > > > > >> > > Research Technician
> > > > > > > > > > >> > > SoMAS | Stony Brook University
> > > > > > > > > > >> > > 678.468.5789
> > > > > > > > > > >> > >
> > > > > > > > > > >> > >
> > > > > > > > > > >> >
> > > > > > > > > > >> >
> > > > > > > > > > >>
> > > > > > > > > > >> --
> > > > > > > > > > >> *Taylor Mandelbaum*
> > > > > > > > > > >> Research Technician
> > > > > > > > > > >> SoMAS | Stony Brook University
> > > > > > > > > > >> 678.468.5789
> > > > > > > > > > >>
> > > > > > > > > > >>
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > > --
> > > > > > > > > *Taylor Mandelbaum*
> > > > > > > > > Research Technician
> > > > > > > > > SoMAS | Stony Brook University
> > > > > > > > > 678.468.5789
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > *Taylor Mandelbaum*
> > > > > > > Research Technician
> > > > > > > SoMAS | Stony Brook University
> > > > > > > 678.468.5789
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > > > --
> > > > *Taylor Mandelbaum*
> > > > Research Technician
> > > > SoMAS | Stony Brook University
> > > > 678.468.5789
> > > >
> > > >
> > >
> > >
> >
> > --
> > *Taylor Mandelbaum*
> > Research Technician
> > SoMAS | Stony Brook University
> > 678.468.5789
> >
> >
>
>
------------------------------------------------
Subject: met install help
From: Taylor Mandelbaum
Time: Sun Jan 27 09:11:38 2019
Hey all,
I got netcdf4 c and c++ installed; I'm running into an issue now on
configuring MET which says error: C++ compiler cannot create
executables.
It looks like in the config log that g++ is getting imported but
erroring
out when trying to use -V as a command option. Attached the newest
config
log here.
When I configure it, this is the command I'm using:
./configure --prefix=/E1/taylorm/MET8 --enable-grib2 --enable-python
On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT
<met_help at ucar.edu>
wrote:
> Hi Taylor. In talking with more with John about your config.log
file we
> see that CC is set to use icc (intel), but CXX and F77 are set to
use g++
> and gfortran (GNU).
>
> CC='/home/taylorm/MET8/met-8.0_bugfix/compile
>
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> CXX='g++'
> F77='gfortran'
>
> Let's see if we can solve the immediate problem before worrying
about any
> potential problems with the external libraries. For now, please
choose
> either the GNU compilers or the Intel compilers and set the
following
> variables accordingly. You can chose one and then simply run the
commands
> below.
>
> *For GNU:*
> export CC=`which gcc`
> export CXX=`which g++`
> export F77=`which gfortran`
>
> *For Intel:*
>
> export CC=`which icc`
> export CXX=`which icc`
> export F77=`which ifort`
>
> Then run "make clean", rerun the configure command, and then try to
make
> MET again.
>
> Let's go from there and see how it works out. Please let me know.
>
> Julie
>
>
> On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik <jpresto at ucar.edu>
> wrote:
>
> > Hi Taylor. Thank you for all of this information.
> >
> > Since the libraries were previously installed and we cannot be
certain
> > which compiler was used, are you able and would you be comfortable
> > installing each of the dependent libraries and not using the
previously
> > installed versions? If so, we have an install script that I can
point
> you
> > to, which would install all of the packages and MET as well. I
can walk
> > through this with you via google hangouts and you can share your
screen
> so
> > we can make sure it is going smoothly. I could do a hangouts
session
> with
> > you tomorrow at 1:15pm (Mountain time) or on Friday at 9:00am
(Mountain
> > time). If those times don't work. I can get you started with
very
> > specific instructions via email and we can continue to work
through any
> > problems. We can also set up a different time for next week,
however, I
> > didn't want you to have to wait that long. Please let me know
your
> > preference.
> >
> > If you think that icc may not be working properly, then you should
> > probably use the GNU set of compilers, unless there is some reason
not
> to,
> > in which case you may need to get a system administrator correct
the
> > problems with the intel compiler.
> >
> > Running "which g++" and running "which gfortran" can tell you what
the
> CXX
> > and F77 paths should be set to. Please let me know if you have
any
> issues
> > with that.
> >
> > Julie
> >
> > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via RT <
> > met_help at ucar.edu> wrote:
> >
> >>
> >> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> >>
> >> Hey Julie,
> >>
> >> 1) They were previously installed, but I just tried running it
with some
> >> of
> >> my own installed versions and they're not working properly (e.g.
the
> make
> >> install fails due to gsl/gsl_cdf.h missing... though I set
MET_GSL to my
> >> gsl-2.5 directory).
> >>
> >> 2) Not sure how I can verify that one, though I think they're not
as
> I've
> >> seen GNU and Intel prompts in the config output. My CC var in my
bashrc
> >> links to an Intel compiler.
> >>
> >> 3) I followed those for the packages, though for the compilers
section,
> I
> >> do not know my CXX or F77 paths on the hpc that I'm using. I also
think
> >> the
> >> icc is not working properly as I could not run icc without a
license
> >> prompt
> >> coming up.
> >>
> >> I'm not sure if any of that helps, but let me know. Maybe some of
these
> >> issues are still on our end. The fact that met needs to only use
one
> >> compiler might be the issue...
> >>
> >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via RT <
> >> met_help at ucar.edu>
> >> wrote:
> >>
> >> > Hi Taylor. Thank you for passing along your files. I have a
few
> >> questions
> >> > for you.
> >> >
> >> > 1) Are you installing the external libraries yourself or were
they
> >> > previously installed?
> >> > 2) Can you please verify that the external libraries and MET
are being
> >> > built with the same family of compilers (e.g. all are built
with GNU,
> or
> >> > all are build with Intel, etc.)? Which compiler are you using?
> >> > 3) Are you following the directions on this page as your
instructions
> >> for
> >> > installation?
> >> >
> >> >
> >>
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> >> >
> >> > Thank you!
> >> >
> >> > Julie
> >> >
> >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via RT <
> >> > met_help at ucar.edu>
> >> > wrote:
> >> >
> >> > >
> >> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
>
> >> > >
> >> > > Hey Julie,
> >> > >
> >> > > I attached the config and make_install logs here. We could do
a
> >> hangouts
> >> > > session as well if you can't pinpoint the issue; I'm remoting
in
> from
> >> my
> >> > > home windows computer so it will be a bit hacky.
> >> > >
> >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via RT <
> >> > met_help at ucar.edu
> >> > > >
> >> > > wrote:
> >> > >
> >> > > > Hi Taylor. It is difficult to tell what is going without
more
> >> context.
> >> > > > Could you please send me your config.log file and your
make.log
> >> file?
> >> > > >
> >> > > > We could also consider doing a hangouts session where you
can
> share
> >> > your
> >> > > > screen, and I can directly help that way. Either way
though, if
> you
> >> > > could
> >> > > > please send those files, I would appreciate it.
> >> > > >
> >> > > > Thanks,
> >> > > > Julie
> >> > > >
> >> > > > Thanks!
> >> > > >
> >> > > > Julie
> >> > > >
> >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum via RT <
> >> > > > met_help at ucar.edu>
> >> > > > wrote:
> >> > > >
> >> > > > >
> >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was acted upon.
> >> > > > > Transaction: Ticket created by
taylor.mandelbaum at stonybrook.edu
> >> > > > > Queue: met_help
> >> > > > > Subject: met install help
> >> > > > > Owner: Nobody
> >> > > > > Requestors: taylor.mandelbaum at stonybrook.edu
> >> > > > > Status: new
> >> > > > > Ticket <URL:
> >> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> >> > > >
> >> > > > >
> >> > > > >
> >> > > > > Hey all,
> >> > > > >
> >> > > > > I'm presently trying to compile MET 8.0 on our HPC; when
I
> >> configure
> >> > > it,
> >> > > > > I'm getting a few warnings on .h files:
> >> > > > >
> >> > > > > configure: WARNING: errno.h: present but cannot be
compiled
> >> > > > > configure: WARNING: errno.h: check for missing
prerequisite
> >> > > headers?
> >> > > > > configure: WARNING: errno.h: see the Autoconf
documentation
> >> > > > > configure: WARNING: errno.h: section "Present But
Cannot Be
> >> > > Compiled"
> >> > > > > configure: WARNING: errno.h: proceeding with the
compiler's
> result
> >> > > > > configure: WARNING: ##
-------------------------------- ##
> >> > > > > configure: WARNING: ## Report this to
met_help at ucar.edu ##
> >> > > > > configure: WARNING: ##
-------------------------------- ##
> >> > > > >
> >> > > > > and the same for fcntl.h, limits.h, stddef.h, file.h and
> param.h.
> >> > > > >
> >> > > > > When I try to make install, I get this error on the tail
of the
> >> log:
> >> > > > >
> >> > > > > config_scanner.cc: In function ‘void*
configalloc(yy_size_t)’:
> >> > > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’ was not
declared
> in
> >> > this
> >> > > > > scope
> >> > > > > config_scanner.cc: In function ‘void*
configrealloc(void*,
> >> > yy_size_t)’:
> >> > > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’ was not
declared
> >> in
> >> > > this
> >> > > > > scope
> >> > > > > /* The cast to (char *) in the following accommodates
both
> >> > > > > ^
> >> > > > > make[3]: *** [libvx_config_a-config_scanner.o] Error 1
> >> > > > > make[3]: Leaving directory
> >> > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> >> > > > > make[2]: *** [install-recursive] Error 1
> >> > > > > make[2]: Leaving directory
> >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> >> > > > > make[1]: *** [install-recursive] Error 1
> >> > > > > make[1]: Leaving directory `/E1/taylorm/MET8/met-
8.0_bugfix/src'
> >> > > > > make: *** [install-recursive] Error 1
> >> > > > >
> >> > > > > Not sure how to address either of these, hopefully you
guys can
> >> > provide
> >> > > > > some insight.
> >> > > > >
> >> > > > > Thanks!
> >> > > > > --
> >> > > > > *Taylor Mandelbaum*
> >> > > > > Research Technician
> >> > > > > SoMAS | Stony Brook University
> >> > > > > 678.468.5789
> >> > > > >
> >> > > > >
> >> > > >
> >> > > >
> >> > >
> >> > > --
> >> > > *Taylor Mandelbaum*
> >> > > Research Technician
> >> > > SoMAS | Stony Brook University
> >> > > 678.468.5789
> >> > >
> >> > >
> >> >
> >> >
> >>
> >> --
> >> *Taylor Mandelbaum*
> >> Research Technician
> >> SoMAS | Stony Brook University
> >> 678.468.5789
> >>
> >>
>
>
--
*Taylor Mandelbaum*
Research Technician
SoMAS | Stony Brook University
678.468.5789
------------------------------------------------
Subject: met install help
From: Julie Prestopnik
Time: Mon Jan 28 11:43:11 2019
Hi Taylor.
Thanks for getting HDF5 and NetCDF4 C and C++ installed.
Thank you also for attaching your config.log file. I see in your
config.log file:
> /cm/shared/apps/python/3.5.2/include/python3.5m: file not
recognized: Is a
> directory
>
collect2: error: ld returned 1 exit status
>
It looks like there is a problem with the linker in that it is finding
a
directory instead of a file. However, before we proceed, I should
tell you
that the Python functionality with met-8.0 requires Python 2.7 to be
used.
Is Python 2.7 available on your system? If so, please let me know.
I can help you set up the necessary environment variables that are
required
to use the python embedding functionality. You'll need to set
MET_PYTHON_CC and MET_PYTHON_LD prior to configuring MET. Usually the
following is sufficient for csh:
setenv MET_PYTHON_CC `python-config --cflags`
setenv MET_PYTHON_LD `python-config --ldflags`
for bash:
export MET_PYTHON_CC=`python-config --cflags`
export MET_PYTHON_LD=`python-config --ldflags`
However, it may not be. Please run the following commands (using
Python
2.7) and send me the output:
python-config --cflags
python-config --ldflags
Thanks!
Julie
On Sun, Jan 27, 2019 at 9:11 AM Taylor Mandelbaum via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> Hey all,
>
> I got netcdf4 c and c++ installed; I'm running into an issue now on
> configuring MET which says error: C++ compiler cannot create
executables.
> It looks like in the config log that g++ is getting imported but
erroring
> out when trying to use -V as a command option. Attached the newest
config
> log here.
>
> When I configure it, this is the command I'm using:
>
> ./configure --prefix=/E1/taylorm/MET8 --enable-grib2 --enable-
python
>
>
>
> On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT <
> met_help at ucar.edu>
> wrote:
>
> > Hi Taylor. In talking with more with John about your config.log
file we
> > see that CC is set to use icc (intel), but CXX and F77 are set to
use g++
> > and gfortran (GNU).
> >
> > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> >
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > CXX='g++'
> > F77='gfortran'
> >
> > Let's see if we can solve the immediate problem before worrying
about any
> > potential problems with the external libraries. For now, please
choose
> > either the GNU compilers or the Intel compilers and set the
following
> > variables accordingly. You can chose one and then simply run the
> commands
> > below.
> >
> > *For GNU:*
> > export CC=`which gcc`
> > export CXX=`which g++`
> > export F77=`which gfortran`
> >
> > *For Intel:*
> >
> > export CC=`which icc`
> > export CXX=`which icc`
> > export F77=`which ifort`
> >
> > Then run "make clean", rerun the configure command, and then try
to make
> > MET again.
> >
> > Let's go from there and see how it works out. Please let me know.
> >
> > Julie
> >
> >
> > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik
<jpresto at ucar.edu>
> > wrote:
> >
> > > Hi Taylor. Thank you for all of this information.
> > >
> > > Since the libraries were previously installed and we cannot be
certain
> > > which compiler was used, are you able and would you be
comfortable
> > > installing each of the dependent libraries and not using the
previously
> > > installed versions? If so, we have an install script that I can
point
> > you
> > > to, which would install all of the packages and MET as well. I
can
> walk
> > > through this with you via google hangouts and you can share your
screen
> > so
> > > we can make sure it is going smoothly. I could do a hangouts
session
> > with
> > > you tomorrow at 1:15pm (Mountain time) or on Friday at 9:00am
(Mountain
> > > time). If those times don't work. I can get you started with
very
> > > specific instructions via email and we can continue to work
through any
> > > problems. We can also set up a different time for next week,
however,
> I
> > > didn't want you to have to wait that long. Please let me know
your
> > > preference.
> > >
> > > If you think that icc may not be working properly, then you
should
> > > probably use the GNU set of compilers, unless there is some
reason not
> > to,
> > > in which case you may need to get a system administrator correct
the
> > > problems with the intel compiler.
> > >
> > > Running "which g++" and running "which gfortran" can tell you
what the
> > CXX
> > > and F77 paths should be set to. Please let me know if you have
any
> > issues
> > > with that.
> > >
> > > Julie
> > >
> > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via RT <
> > > met_help at ucar.edu> wrote:
> > >
> > >>
> > >> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > >>
> > >> Hey Julie,
> > >>
> > >> 1) They were previously installed, but I just tried running it
with
> some
> > >> of
> > >> my own installed versions and they're not working properly
(e.g. the
> > make
> > >> install fails due to gsl/gsl_cdf.h missing... though I set
MET_GSL to
> my
> > >> gsl-2.5 directory).
> > >>
> > >> 2) Not sure how I can verify that one, though I think they're
not as
> > I've
> > >> seen GNU and Intel prompts in the config output. My CC var in
my
> bashrc
> > >> links to an Intel compiler.
> > >>
> > >> 3) I followed those for the packages, though for the compilers
> section,
> > I
> > >> do not know my CXX or F77 paths on the hpc that I'm using. I
also
> think
> > >> the
> > >> icc is not working properly as I could not run icc without a
license
> > >> prompt
> > >> coming up.
> > >>
> > >> I'm not sure if any of that helps, but let me know. Maybe some
of
> these
> > >> issues are still on our end. The fact that met needs to only
use one
> > >> compiler might be the issue...
> > >>
> > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via RT <
> > >> met_help at ucar.edu>
> > >> wrote:
> > >>
> > >> > Hi Taylor. Thank you for passing along your files. I have a
few
> > >> questions
> > >> > for you.
> > >> >
> > >> > 1) Are you installing the external libraries yourself or were
they
> > >> > previously installed?
> > >> > 2) Can you please verify that the external libraries and MET
are
> being
> > >> > built with the same family of compilers (e.g. all are built
with
> GNU,
> > or
> > >> > all are build with Intel, etc.)? Which compiler are you
using?
> > >> > 3) Are you following the directions on this page as your
> instructions
> > >> for
> > >> > installation?
> > >> >
> > >> >
> > >>
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > >> >
> > >> > Thank you!
> > >> >
> > >> > Julie
> > >> >
> > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via RT <
> > >> > met_help at ucar.edu>
> > >> > wrote:
> > >> >
> > >> > >
> > >> > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > >> > >
> > >> > > Hey Julie,
> > >> > >
> > >> > > I attached the config and make_install logs here. We could
do a
> > >> hangouts
> > >> > > session as well if you can't pinpoint the issue; I'm
remoting in
> > from
> > >> my
> > >> > > home windows computer so it will be a bit hacky.
> > >> > >
> > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via RT <
> > >> > met_help at ucar.edu
> > >> > > >
> > >> > > wrote:
> > >> > >
> > >> > > > Hi Taylor. It is difficult to tell what is going without
more
> > >> context.
> > >> > > > Could you please send me your config.log file and your
make.log
> > >> file?
> > >> > > >
> > >> > > > We could also consider doing a hangouts session where you
can
> > share
> > >> > your
> > >> > > > screen, and I can directly help that way. Either way
though, if
> > you
> > >> > > could
> > >> > > > please send those files, I would appreciate it.
> > >> > > >
> > >> > > > Thanks,
> > >> > > > Julie
> > >> > > >
> > >> > > > Thanks!
> > >> > > >
> > >> > > > Julie
> > >> > > >
> > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum via RT
<
> > >> > > > met_help at ucar.edu>
> > >> > > > wrote:
> > >> > > >
> > >> > > > >
> > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was acted upon.
> > >> > > > > Transaction: Ticket created by
> taylor.mandelbaum at stonybrook.edu
> > >> > > > > Queue: met_help
> > >> > > > > Subject: met install help
> > >> > > > > Owner: Nobody
> > >> > > > > Requestors: taylor.mandelbaum at stonybrook.edu
> > >> > > > > Status: new
> > >> > > > > Ticket <URL:
> > >> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > >> > > >
> > >> > > > >
> > >> > > > >
> > >> > > > > Hey all,
> > >> > > > >
> > >> > > > > I'm presently trying to compile MET 8.0 on our HPC;
when I
> > >> configure
> > >> > > it,
> > >> > > > > I'm getting a few warnings on .h files:
> > >> > > > >
> > >> > > > > configure: WARNING: errno.h: present but cannot be
compiled
> > >> > > > > configure: WARNING: errno.h: check for missing
> prerequisite
> > >> > > headers?
> > >> > > > > configure: WARNING: errno.h: see the Autoconf
documentation
> > >> > > > > configure: WARNING: errno.h: section "Present But
Cannot
> Be
> > >> > > Compiled"
> > >> > > > > configure: WARNING: errno.h: proceeding with the
compiler's
> > result
> > >> > > > > configure: WARNING: ##
-------------------------------- ##
> > >> > > > > configure: WARNING: ## Report this to
met_help at ucar.edu
> ##
> > >> > > > > configure: WARNING: ##
-------------------------------- ##
> > >> > > > >
> > >> > > > > and the same for fcntl.h, limits.h, stddef.h, file.h
and
> > param.h.
> > >> > > > >
> > >> > > > > When I try to make install, I get this error on the
tail of
> the
> > >> log:
> > >> > > > >
> > >> > > > > config_scanner.cc: In function ‘void*
configalloc(yy_size_t)’:
> > >> > > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’ was not
> declared
> > in
> > >> > this
> > >> > > > > scope
> > >> > > > > config_scanner.cc: In function ‘void*
configrealloc(void*,
> > >> > yy_size_t)’:
> > >> > > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’ was not
> declared
> > >> in
> > >> > > this
> > >> > > > > scope
> > >> > > > > /* The cast to (char *) in the following accommodates
both
> > >> > > > > ^
> > >> > > > > make[3]: *** [libvx_config_a-config_scanner.o] Error 1
> > >> > > > > make[3]: Leaving directory
> > >> > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > >> > > > > make[2]: *** [install-recursive] Error 1
> > >> > > > > make[2]: Leaving directory
> > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > >> > > > > make[1]: *** [install-recursive] Error 1
> > >> > > > > make[1]: Leaving directory
> `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > >> > > > > make: *** [install-recursive] Error 1
> > >> > > > >
> > >> > > > > Not sure how to address either of these, hopefully you
guys
> can
> > >> > provide
> > >> > > > > some insight.
> > >> > > > >
> > >> > > > > Thanks!
> > >> > > > > --
> > >> > > > > *Taylor Mandelbaum*
> > >> > > > > Research Technician
> > >> > > > > SoMAS | Stony Brook University
> > >> > > > > 678.468.5789
> > >> > > > >
> > >> > > > >
> > >> > > >
> > >> > > >
> > >> > >
> > >> > > --
> > >> > > *Taylor Mandelbaum*
> > >> > > Research Technician
> > >> > > SoMAS | Stony Brook University
> > >> > > 678.468.5789
> > >> > >
> > >> > >
> > >> >
> > >> >
> > >>
> > >> --
> > >> *Taylor Mandelbaum*
> > >> Research Technician
> > >> SoMAS | Stony Brook University
> > >> 678.468.5789
> > >>
> > >>
> >
> >
>
> --
> *Taylor Mandelbaum*
> Research Technician
> SoMAS | Stony Brook University
> 678.468.5789
>
>
------------------------------------------------
Subject: met install help
From: Taylor Mandelbaum
Time: Tue Feb 05 19:16:17 2019
Hey Julie,
Sorry for the delayed response. We got python 2.7.15 set up as a
module. I
ran python2.7-config --cflags and ..--ldflags:
-I/cm/shared/apps/python/2.7.15/include/python2.7
-I/cm/shared/apps/python/2.7.15/include/python2.7 -fno-strict-aliasing
-g
-O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
-lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic
Those are the returned outputs. I updated my bashrc with module load
python/2.7; same issue is occurring with c++. Attached the config log.
Thanks again for your help.
On Mon, Jan 28, 2019 at 1:43 PM Julie Prestopnik via RT
<met_help at ucar.edu>
wrote:
> Hi Taylor.
>
> Thanks for getting HDF5 and NetCDF4 C and C++ installed.
>
> Thank you also for attaching your config.log file. I see in your
> config.log file:
>
> > /cm/shared/apps/python/3.5.2/include/python3.5m: file not
recognized: Is
> a
> > directory
> >
> collect2: error: ld returned 1 exit status
> >
>
> It looks like there is a problem with the linker in that it is
finding a
> directory instead of a file. However, before we proceed, I should
tell you
> that the Python functionality with met-8.0 requires Python 2.7 to be
used.
> Is Python 2.7 available on your system? If so, please let me know.
>
> I can help you set up the necessary environment variables that are
required
> to use the python embedding functionality. You'll need to set
> MET_PYTHON_CC and MET_PYTHON_LD prior to configuring MET. Usually
the
> following is sufficient for csh:
>
> setenv MET_PYTHON_CC `python-config --cflags`
>
> setenv MET_PYTHON_LD `python-config --ldflags`
>
> for bash:
>
> export MET_PYTHON_CC=`python-config --cflags`
>
> export MET_PYTHON_LD=`python-config --ldflags`
>
> However, it may not be. Please run the following commands (using
Python
> 2.7) and send me the output:
>
> python-config --cflags
> python-config --ldflags
>
> Thanks!
>
> Julie
>
> On Sun, Jan 27, 2019 at 9:11 AM Taylor Mandelbaum via RT <
> met_help at ucar.edu>
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> >
> > Hey all,
> >
> > I got netcdf4 c and c++ installed; I'm running into an issue now
on
> > configuring MET which says error: C++ compiler cannot create
executables.
> > It looks like in the config log that g++ is getting imported but
erroring
> > out when trying to use -V as a command option. Attached the newest
config
> > log here.
> >
> > When I configure it, this is the command I'm using:
> >
> > ./configure --prefix=/E1/taylorm/MET8 --enable-grib2 --enable-
python
> >
> >
> >
> > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT <
> > met_help at ucar.edu>
> > wrote:
> >
> > > Hi Taylor. In talking with more with John about your config.log
file
> we
> > > see that CC is set to use icc (intel), but CXX and F77 are set
to use
> g++
> > > and gfortran (GNU).
> > >
> > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > >
>
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > CXX='g++'
> > > F77='gfortran'
> > >
> > > Let's see if we can solve the immediate problem before worrying
about
> any
> > > potential problems with the external libraries. For now, please
choose
> > > either the GNU compilers or the Intel compilers and set the
following
> > > variables accordingly. You can chose one and then simply run
the
> > commands
> > > below.
> > >
> > > *For GNU:*
> > > export CC=`which gcc`
> > > export CXX=`which g++`
> > > export F77=`which gfortran`
> > >
> > > *For Intel:*
> > >
> > > export CC=`which icc`
> > > export CXX=`which icc`
> > > export F77=`which ifort`
> > >
> > > Then run "make clean", rerun the configure command, and then try
to
> make
> > > MET again.
> > >
> > > Let's go from there and see how it works out. Please let me
know.
> > >
> > > Julie
> > >
> > >
> > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik
<jpresto at ucar.edu>
> > > wrote:
> > >
> > > > Hi Taylor. Thank you for all of this information.
> > > >
> > > > Since the libraries were previously installed and we cannot be
> certain
> > > > which compiler was used, are you able and would you be
comfortable
> > > > installing each of the dependent libraries and not using the
> previously
> > > > installed versions? If so, we have an install script that I
can
> point
> > > you
> > > > to, which would install all of the packages and MET as well.
I can
> > walk
> > > > through this with you via google hangouts and you can share
your
> screen
> > > so
> > > > we can make sure it is going smoothly. I could do a hangouts
> session
> > > with
> > > > you tomorrow at 1:15pm (Mountain time) or on Friday at 9:00am
> (Mountain
> > > > time). If those times don't work. I can get you started with
very
> > > > specific instructions via email and we can continue to work
through
> any
> > > > problems. We can also set up a different time for next week,
> however,
> > I
> > > > didn't want you to have to wait that long. Please let me know
your
> > > > preference.
> > > >
> > > > If you think that icc may not be working properly, then you
should
> > > > probably use the GNU set of compilers, unless there is some
reason
> not
> > > to,
> > > > in which case you may need to get a system administrator
correct the
> > > > problems with the intel compiler.
> > > >
> > > > Running "which g++" and running "which gfortran" can tell you
what
> the
> > > CXX
> > > > and F77 paths should be set to. Please let me know if you
have any
> > > issues
> > > > with that.
> > > >
> > > > Julie
> > > >
> > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via RT <
> > > > met_help at ucar.edu> wrote:
> > > >
> > > >>
> > > >> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
>
> > > >>
> > > >> Hey Julie,
> > > >>
> > > >> 1) They were previously installed, but I just tried running
it with
> > some
> > > >> of
> > > >> my own installed versions and they're not working properly
(e.g. the
> > > make
> > > >> install fails due to gsl/gsl_cdf.h missing... though I set
MET_GSL
> to
> > my
> > > >> gsl-2.5 directory).
> > > >>
> > > >> 2) Not sure how I can verify that one, though I think they're
not as
> > > I've
> > > >> seen GNU and Intel prompts in the config output. My CC var in
my
> > bashrc
> > > >> links to an Intel compiler.
> > > >>
> > > >> 3) I followed those for the packages, though for the
compilers
> > section,
> > > I
> > > >> do not know my CXX or F77 paths on the hpc that I'm using. I
also
> > think
> > > >> the
> > > >> icc is not working properly as I could not run icc without a
license
> > > >> prompt
> > > >> coming up.
> > > >>
> > > >> I'm not sure if any of that helps, but let me know. Maybe
some of
> > these
> > > >> issues are still on our end. The fact that met needs to only
use one
> > > >> compiler might be the issue...
> > > >>
> > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via RT <
> > > >> met_help at ucar.edu>
> > > >> wrote:
> > > >>
> > > >> > Hi Taylor. Thank you for passing along your files. I have
a few
> > > >> questions
> > > >> > for you.
> > > >> >
> > > >> > 1) Are you installing the external libraries yourself or
were they
> > > >> > previously installed?
> > > >> > 2) Can you please verify that the external libraries and
MET are
> > being
> > > >> > built with the same family of compilers (e.g. all are built
with
> > GNU,
> > > or
> > > >> > all are build with Intel, etc.)? Which compiler are you
using?
> > > >> > 3) Are you following the directions on this page as your
> > instructions
> > > >> for
> > > >> > installation?
> > > >> >
> > > >> >
> > > >>
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > >> >
> > > >> > Thank you!
> > > >> >
> > > >> > Julie
> > > >> >
> > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via RT <
> > > >> > met_help at ucar.edu>
> > > >> > wrote:
> > > >> >
> > > >> > >
> > > >> > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > >> > >
> > > >> > > Hey Julie,
> > > >> > >
> > > >> > > I attached the config and make_install logs here. We
could do a
> > > >> hangouts
> > > >> > > session as well if you can't pinpoint the issue; I'm
remoting in
> > > from
> > > >> my
> > > >> > > home windows computer so it will be a bit hacky.
> > > >> > >
> > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via RT <
> > > >> > met_help at ucar.edu
> > > >> > > >
> > > >> > > wrote:
> > > >> > >
> > > >> > > > Hi Taylor. It is difficult to tell what is going
without more
> > > >> context.
> > > >> > > > Could you please send me your config.log file and your
> make.log
> > > >> file?
> > > >> > > >
> > > >> > > > We could also consider doing a hangouts session where
you can
> > > share
> > > >> > your
> > > >> > > > screen, and I can directly help that way. Either way
though,
> if
> > > you
> > > >> > > could
> > > >> > > > please send those files, I would appreciate it.
> > > >> > > >
> > > >> > > > Thanks,
> > > >> > > > Julie
> > > >> > > >
> > > >> > > > Thanks!
> > > >> > > >
> > > >> > > > Julie
> > > >> > > >
> > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum via
RT <
> > > >> > > > met_help at ucar.edu>
> > > >> > > > wrote:
> > > >> > > >
> > > >> > > > >
> > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was acted
upon.
> > > >> > > > > Transaction: Ticket created by
> > taylor.mandelbaum at stonybrook.edu
> > > >> > > > > Queue: met_help
> > > >> > > > > Subject: met install help
> > > >> > > > > Owner: Nobody
> > > >> > > > > Requestors: taylor.mandelbaum at stonybrook.edu
> > > >> > > > > Status: new
> > > >> > > > > Ticket <URL:
> > > >> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > >> > > >
> > > >> > > > >
> > > >> > > > >
> > > >> > > > > Hey all,
> > > >> > > > >
> > > >> > > > > I'm presently trying to compile MET 8.0 on our HPC;
when I
> > > >> configure
> > > >> > > it,
> > > >> > > > > I'm getting a few warnings on .h files:
> > > >> > > > >
> > > >> > > > > configure: WARNING: errno.h: present but cannot be
compiled
> > > >> > > > > configure: WARNING: errno.h: check for missing
> > prerequisite
> > > >> > > headers?
> > > >> > > > > configure: WARNING: errno.h: see the Autoconf
documentation
> > > >> > > > > configure: WARNING: errno.h: section "Present But
Cannot
> > Be
> > > >> > > Compiled"
> > > >> > > > > configure: WARNING: errno.h: proceeding with the
compiler's
> > > result
> > > >> > > > > configure: WARNING: ##
--------------------------------
> ##
> > > >> > > > > configure: WARNING: ## Report this to
met_help at ucar.edu
> > ##
> > > >> > > > > configure: WARNING: ##
--------------------------------
> ##
> > > >> > > > >
> > > >> > > > > and the same for fcntl.h, limits.h, stddef.h, file.h
and
> > > param.h.
> > > >> > > > >
> > > >> > > > > When I try to make install, I get this error on the
tail of
> > the
> > > >> log:
> > > >> > > > >
> > > >> > > > > config_scanner.cc: In function ‘void*
> configalloc(yy_size_t)’:
> > > >> > > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’ was
not
> > declared
> > > in
> > > >> > this
> > > >> > > > > scope
> > > >> > > > > config_scanner.cc: In function ‘void*
configrealloc(void*,
> > > >> > yy_size_t)’:
> > > >> > > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’ was
not
> > declared
> > > >> in
> > > >> > > this
> > > >> > > > > scope
> > > >> > > > > /* The cast to (char *) in the following
accommodates both
> > > >> > > > > ^
> > > >> > > > > make[3]: *** [libvx_config_a-config_scanner.o] Error
1
> > > >> > > > > make[3]: Leaving directory
> > > >> > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > >> > > > > make[2]: *** [install-recursive] Error 1
> > > >> > > > > make[2]: Leaving directory
> > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > >> > > > > make[1]: *** [install-recursive] Error 1
> > > >> > > > > make[1]: Leaving directory
> > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > >> > > > > make: *** [install-recursive] Error 1
> > > >> > > > >
> > > >> > > > > Not sure how to address either of these, hopefully
you guys
> > can
> > > >> > provide
> > > >> > > > > some insight.
> > > >> > > > >
> > > >> > > > > Thanks!
> > > >> > > > > --
> > > >> > > > > *Taylor Mandelbaum*
> > > >> > > > > Research Technician
> > > >> > > > > SoMAS | Stony Brook University
> > > >> > > > > 678.468.5789
> > > >> > > > >
> > > >> > > > >
> > > >> > > >
> > > >> > > >
> > > >> > >
> > > >> > > --
> > > >> > > *Taylor Mandelbaum*
> > > >> > > Research Technician
> > > >> > > SoMAS | Stony Brook University
> > > >> > > 678.468.5789
> > > >> > >
> > > >> > >
> > > >> >
> > > >> >
> > > >>
> > > >> --
> > > >> *Taylor Mandelbaum*
> > > >> Research Technician
> > > >> SoMAS | Stony Brook University
> > > >> 678.468.5789
> > > >>
> > > >>
> > >
> > >
> >
> > --
> > *Taylor Mandelbaum*
> > Research Technician
> > SoMAS | Stony Brook University
> > 678.468.5789
> >
> >
>
>
--
*Taylor Mandelbaum*
Research Technician
SoMAS | Stony Brook University
678.468.5789
------------------------------------------------
Subject: met install help
From: Julie Prestopnik
Time: Fri Feb 08 10:06:48 2019
Hi Taylor.
My apologies for the delay in responding. We had an in-house MET
Tutorial
this week, and I am out of the office today. I will follow up early
next
week on these issues.
Julie
On Tue, Feb 5, 2019 at 7:16 PM Taylor Mandelbaum via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> Hey Julie,
>
> Sorry for the delayed response. We got python 2.7.15 set up as a
module. I
> ran python2.7-config --cflags and ..--ldflags:
>
> -I/cm/shared/apps/python/2.7.15/include/python2.7
> -I/cm/shared/apps/python/2.7.15/include/python2.7 -fno-strict-
aliasing -g
> -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
>
> -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic
>
> Those are the returned outputs. I updated my bashrc with module load
> python/2.7; same issue is occurring with c++. Attached the config
log.
>
> Thanks again for your help.
>
> On Mon, Jan 28, 2019 at 1:43 PM Julie Prestopnik via RT
<met_help at ucar.edu
> >
> wrote:
>
> > Hi Taylor.
> >
> > Thanks for getting HDF5 and NetCDF4 C and C++ installed.
> >
> > Thank you also for attaching your config.log file. I see in your
> > config.log file:
> >
> > > /cm/shared/apps/python/3.5.2/include/python3.5m: file not
recognized:
> Is
> > a
> > > directory
> > >
> > collect2: error: ld returned 1 exit status
> > >
> >
> > It looks like there is a problem with the linker in that it is
finding a
> > directory instead of a file. However, before we proceed, I should
tell
> you
> > that the Python functionality with met-8.0 requires Python 2.7 to
be
> used.
> > Is Python 2.7 available on your system? If so, please let me
know.
> >
> > I can help you set up the necessary environment variables that are
> required
> > to use the python embedding functionality. You'll need to set
> > MET_PYTHON_CC and MET_PYTHON_LD prior to configuring MET. Usually
the
> > following is sufficient for csh:
> >
> > setenv MET_PYTHON_CC `python-config --cflags`
> >
> > setenv MET_PYTHON_LD `python-config --ldflags`
> >
> > for bash:
> >
> > export MET_PYTHON_CC=`python-config --cflags`
> >
> > export MET_PYTHON_LD=`python-config --ldflags`
> >
> > However, it may not be. Please run the following commands (using
Python
> > 2.7) and send me the output:
> >
> > python-config --cflags
> > python-config --ldflags
> >
> > Thanks!
> >
> > Julie
> >
> > On Sun, Jan 27, 2019 at 9:11 AM Taylor Mandelbaum via RT <
> > met_help at ucar.edu>
> > wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > >
> > > Hey all,
> > >
> > > I got netcdf4 c and c++ installed; I'm running into an issue now
on
> > > configuring MET which says error: C++ compiler cannot create
> executables.
> > > It looks like in the config log that g++ is getting imported but
> erroring
> > > out when trying to use -V as a command option. Attached the
newest
> config
> > > log here.
> > >
> > > When I configure it, this is the command I'm using:
> > >
> > > ./configure --prefix=/E1/taylorm/MET8 --enable-grib2 --enable-
python
> > >
> > >
> > >
> > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT <
> > > met_help at ucar.edu>
> > > wrote:
> > >
> > > > Hi Taylor. In talking with more with John about your
config.log file
> > we
> > > > see that CC is set to use icc (intel), but CXX and F77 are set
to use
> > g++
> > > > and gfortran (GNU).
> > > >
> > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > >
> >
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > CXX='g++'
> > > > F77='gfortran'
> > > >
> > > > Let's see if we can solve the immediate problem before
worrying about
> > any
> > > > potential problems with the external libraries. For now,
please
> choose
> > > > either the GNU compilers or the Intel compilers and set the
following
> > > > variables accordingly. You can chose one and then simply run
the
> > > commands
> > > > below.
> > > >
> > > > *For GNU:*
> > > > export CC=`which gcc`
> > > > export CXX=`which g++`
> > > > export F77=`which gfortran`
> > > >
> > > > *For Intel:*
> > > >
> > > > export CC=`which icc`
> > > > export CXX=`which icc`
> > > > export F77=`which ifort`
> > > >
> > > > Then run "make clean", rerun the configure command, and then
try to
> > make
> > > > MET again.
> > > >
> > > > Let's go from there and see how it works out. Please let me
know.
> > > >
> > > > Julie
> > > >
> > > >
> > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik
<jpresto at ucar.edu>
> > > > wrote:
> > > >
> > > > > Hi Taylor. Thank you for all of this information.
> > > > >
> > > > > Since the libraries were previously installed and we cannot
be
> > certain
> > > > > which compiler was used, are you able and would you be
comfortable
> > > > > installing each of the dependent libraries and not using the
> > previously
> > > > > installed versions? If so, we have an install script that I
can
> > point
> > > > you
> > > > > to, which would install all of the packages and MET as well.
I can
> > > walk
> > > > > through this with you via google hangouts and you can share
your
> > screen
> > > > so
> > > > > we can make sure it is going smoothly. I could do a
hangouts
> > session
> > > > with
> > > > > you tomorrow at 1:15pm (Mountain time) or on Friday at
9:00am
> > (Mountain
> > > > > time). If those times don't work. I can get you started
with very
> > > > > specific instructions via email and we can continue to work
through
> > any
> > > > > problems. We can also set up a different time for next
week,
> > however,
> > > I
> > > > > didn't want you to have to wait that long. Please let me
know your
> > > > > preference.
> > > > >
> > > > > If you think that icc may not be working properly, then you
should
> > > > > probably use the GNU set of compilers, unless there is some
reason
> > not
> > > > to,
> > > > > in which case you may need to get a system administrator
correct
> the
> > > > > problems with the intel compiler.
> > > > >
> > > > > Running "which g++" and running "which gfortran" can tell
you what
> > the
> > > > CXX
> > > > > and F77 paths should be set to. Please let me know if you
have any
> > > > issues
> > > > > with that.
> > > > >
> > > > > Julie
> > > > >
> > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via RT <
> > > > > met_help at ucar.edu> wrote:
> > > > >
> > > > >>
> > > > >> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > >>
> > > > >> Hey Julie,
> > > > >>
> > > > >> 1) They were previously installed, but I just tried running
it
> with
> > > some
> > > > >> of
> > > > >> my own installed versions and they're not working properly
(e.g.
> the
> > > > make
> > > > >> install fails due to gsl/gsl_cdf.h missing... though I set
MET_GSL
> > to
> > > my
> > > > >> gsl-2.5 directory).
> > > > >>
> > > > >> 2) Not sure how I can verify that one, though I think
they're not
> as
> > > > I've
> > > > >> seen GNU and Intel prompts in the config output. My CC var
in my
> > > bashrc
> > > > >> links to an Intel compiler.
> > > > >>
> > > > >> 3) I followed those for the packages, though for the
compilers
> > > section,
> > > > I
> > > > >> do not know my CXX or F77 paths on the hpc that I'm using.
I also
> > > think
> > > > >> the
> > > > >> icc is not working properly as I could not run icc without
a
> license
> > > > >> prompt
> > > > >> coming up.
> > > > >>
> > > > >> I'm not sure if any of that helps, but let me know. Maybe
some of
> > > these
> > > > >> issues are still on our end. The fact that met needs to
only use
> one
> > > > >> compiler might be the issue...
> > > > >>
> > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via RT <
> > > > >> met_help at ucar.edu>
> > > > >> wrote:
> > > > >>
> > > > >> > Hi Taylor. Thank you for passing along your files. I
have a
> few
> > > > >> questions
> > > > >> > for you.
> > > > >> >
> > > > >> > 1) Are you installing the external libraries yourself or
were
> they
> > > > >> > previously installed?
> > > > >> > 2) Can you please verify that the external libraries and
MET are
> > > being
> > > > >> > built with the same family of compilers (e.g. all are
built with
> > > GNU,
> > > > or
> > > > >> > all are build with Intel, etc.)? Which compiler are you
using?
> > > > >> > 3) Are you following the directions on this page as your
> > > instructions
> > > > >> for
> > > > >> > installation?
> > > > >> >
> > > > >> >
> > > > >>
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > >> >
> > > > >> > Thank you!
> > > > >> >
> > > > >> > Julie
> > > > >> >
> > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via RT
<
> > > > >> > met_help at ucar.edu>
> > > > >> > wrote:
> > > > >> >
> > > > >> > >
> > > > >> > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> >
> > > > >> > >
> > > > >> > > Hey Julie,
> > > > >> > >
> > > > >> > > I attached the config and make_install logs here. We
could do
> a
> > > > >> hangouts
> > > > >> > > session as well if you can't pinpoint the issue; I'm
remoting
> in
> > > > from
> > > > >> my
> > > > >> > > home windows computer so it will be a bit hacky.
> > > > >> > >
> > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via RT
<
> > > > >> > met_help at ucar.edu
> > > > >> > > >
> > > > >> > > wrote:
> > > > >> > >
> > > > >> > > > Hi Taylor. It is difficult to tell what is going
without
> more
> > > > >> context.
> > > > >> > > > Could you please send me your config.log file and
your
> > make.log
> > > > >> file?
> > > > >> > > >
> > > > >> > > > We could also consider doing a hangouts session where
you
> can
> > > > share
> > > > >> > your
> > > > >> > > > screen, and I can directly help that way. Either way
> though,
> > if
> > > > you
> > > > >> > > could
> > > > >> > > > please send those files, I would appreciate it.
> > > > >> > > >
> > > > >> > > > Thanks,
> > > > >> > > > Julie
> > > > >> > > >
> > > > >> > > > Thanks!
> > > > >> > > >
> > > > >> > > > Julie
> > > > >> > > >
> > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum via
RT <
> > > > >> > > > met_help at ucar.edu>
> > > > >> > > > wrote:
> > > > >> > > >
> > > > >> > > > >
> > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was acted
upon.
> > > > >> > > > > Transaction: Ticket created by
> > > taylor.mandelbaum at stonybrook.edu
> > > > >> > > > > Queue: met_help
> > > > >> > > > > Subject: met install help
> > > > >> > > > > Owner: Nobody
> > > > >> > > > > Requestors: taylor.mandelbaum at stonybrook.edu
> > > > >> > > > > Status: new
> > > > >> > > > > Ticket <URL:
> > > > >> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > >> > > >
> > > > >> > > > >
> > > > >> > > > >
> > > > >> > > > > Hey all,
> > > > >> > > > >
> > > > >> > > > > I'm presently trying to compile MET 8.0 on our HPC;
when I
> > > > >> configure
> > > > >> > > it,
> > > > >> > > > > I'm getting a few warnings on .h files:
> > > > >> > > > >
> > > > >> > > > > configure: WARNING: errno.h: present but cannot be
> compiled
> > > > >> > > > > configure: WARNING: errno.h: check for missing
> > > prerequisite
> > > > >> > > headers?
> > > > >> > > > > configure: WARNING: errno.h: see the Autoconf
> documentation
> > > > >> > > > > configure: WARNING: errno.h: section "Present
But
> Cannot
> > > Be
> > > > >> > > Compiled"
> > > > >> > > > > configure: WARNING: errno.h: proceeding with the
> compiler's
> > > > result
> > > > >> > > > > configure: WARNING: ##
> --------------------------------
> > ##
> > > > >> > > > > configure: WARNING: ## Report this to
> met_help at ucar.edu
> > > ##
> > > > >> > > > > configure: WARNING: ##
> --------------------------------
> > ##
> > > > >> > > > >
> > > > >> > > > > and the same for fcntl.h, limits.h, stddef.h,
file.h and
> > > > param.h.
> > > > >> > > > >
> > > > >> > > > > When I try to make install, I get this error on the
tail
> of
> > > the
> > > > >> log:
> > > > >> > > > >
> > > > >> > > > > config_scanner.cc: In function ‘void*
> > configalloc(yy_size_t)’:
> > > > >> > > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’ was
not
> > > declared
> > > > in
> > > > >> > this
> > > > >> > > > > scope
> > > > >> > > > > config_scanner.cc: In function ‘void*
configrealloc(void*,
> > > > >> > yy_size_t)’:
> > > > >> > > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’ was
not
> > > declared
> > > > >> in
> > > > >> > > this
> > > > >> > > > > scope
> > > > >> > > > > /* The cast to (char *) in the following
accommodates
> both
> > > > >> > > > > ^
> > > > >> > > > > make[3]: *** [libvx_config_a-config_scanner.o]
Error 1
> > > > >> > > > > make[3]: Leaving directory
> > > > >> > > > > `/E1/taylorm/MET8/met-
8.0_bugfix/src/basic/vx_config'
> > > > >> > > > > make[2]: *** [install-recursive] Error 1
> > > > >> > > > > make[2]: Leaving directory
> > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > >> > > > > make[1]: *** [install-recursive] Error 1
> > > > >> > > > > make[1]: Leaving directory
> > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > >> > > > > make: *** [install-recursive] Error 1
> > > > >> > > > >
> > > > >> > > > > Not sure how to address either of these, hopefully
you
> guys
> > > can
> > > > >> > provide
> > > > >> > > > > some insight.
> > > > >> > > > >
> > > > >> > > > > Thanks!
> > > > >> > > > > --
> > > > >> > > > > *Taylor Mandelbaum*
> > > > >> > > > > Research Technician
> > > > >> > > > > SoMAS | Stony Brook University
> > > > >> > > > > 678.468.5789
> > > > >> > > > >
> > > > >> > > > >
> > > > >> > > >
> > > > >> > > >
> > > > >> > >
> > > > >> > > --
> > > > >> > > *Taylor Mandelbaum*
> > > > >> > > Research Technician
> > > > >> > > SoMAS | Stony Brook University
> > > > >> > > 678.468.5789
> > > > >> > >
> > > > >> > >
> > > > >> >
> > > > >> >
> > > > >>
> > > > >> --
> > > > >> *Taylor Mandelbaum*
> > > > >> Research Technician
> > > > >> SoMAS | Stony Brook University
> > > > >> 678.468.5789
> > > > >>
> > > > >>
> > > >
> > > >
> > >
> > > --
> > > *Taylor Mandelbaum*
> > > Research Technician
> > > SoMAS | Stony Brook University
> > > 678.468.5789
> > >
> > >
> >
> >
>
> --
> *Taylor Mandelbaum*
> Research Technician
> SoMAS | Stony Brook University
> 678.468.5789
>
>
------------------------------------------------
Subject: met install help
From: Julie Prestopnik
Time: Mon Feb 11 11:27:50 2019
Hi Taylor. Thanks for the update. I'm glad we are making some
progress.
>From your config.log file:
> /usr/bin/ld: cannot find -lpython2.7
> collect2: error: ld returned 1 exit status
>
and from the output you provided from running "python-config
--ldflags", I
can see what the problem is.
It looks like the output "python-config --ldflags" unfortunately does
not
contain all of the information that the environment variable
MET_PYTHON_LD
needs to have.
In order to proceed, we need to find the location of the libpython.a
file
or the libpython.so file. Based on the information from the output
from
running "python-config --cflags", I am going to guess that the
libpython
file lives in /cm/shared/apps/python/2.7.15/lib or in
/cm/shared/apps/python/2.7.15/lib/python2.7. Could you please check
those
directories and see if you can find a libpython.a file or libpython.so
file? If so, please send me an email with the path to the file. You
could
just run "ls <path>" replacing <path> with the full path and send me
the
output. Then, I will send you a command that you can run to set the
value
of the environment variable MET_PYTHON_LD.
Thanks!
Julie
On Tue, Feb 5, 2019 at 7:16 PM Taylor Mandelbaum via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> Hey Julie,
>
> Sorry for the delayed response. We got python 2.7.15 set up as a
module. I
> ran python2.7-config --cflags and ..--ldflags:
>
> -I/cm/shared/apps/python/2.7.15/include/python2.7
> -I/cm/shared/apps/python/2.7.15/include/python2.7 -fno-strict-
aliasing -g
> -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
>
> -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic
>
> Those are the returned outputs. I updated my bashrc with module load
> python/2.7; same issue is occurring with c++. Attached the config
log.
>
> Thanks again for your help.
>
> On Mon, Jan 28, 2019 at 1:43 PM Julie Prestopnik via RT
<met_help at ucar.edu
> >
> wrote:
>
> > Hi Taylor.
> >
> > Thanks for getting HDF5 and NetCDF4 C and C++ installed.
> >
> > Thank you also for attaching your config.log file. I see in your
> > config.log file:
> >
> > > /cm/shared/apps/python/3.5.2/include/python3.5m: file not
recognized:
> Is
> > a
> > > directory
> > >
> > collect2: error: ld returned 1 exit status
> > >
> >
> > It looks like there is a problem with the linker in that it is
finding a
> > directory instead of a file. However, before we proceed, I should
tell
> you
> > that the Python functionality with met-8.0 requires Python 2.7 to
be
> used.
> > Is Python 2.7 available on your system? If so, please let me
know.
> >
> > I can help you set up the necessary environment variables that are
> required
> > to use the python embedding functionality. You'll need to set
> > MET_PYTHON_CC and MET_PYTHON_LD prior to configuring MET. Usually
the
> > following is sufficient for csh:
> >
> > setenv MET_PYTHON_CC `python-config --cflags`
> >
> > setenv MET_PYTHON_LD `python-config --ldflags`
> >
> > for bash:
> >
> > export MET_PYTHON_CC=`python-config --cflags`
> >
> > export MET_PYTHON_LD=`python-config --ldflags`
> >
> > However, it may not be. Please run the following commands (using
Python
> > 2.7) and send me the output:
> >
> > python-config --cflags
> > python-config --ldflags
> >
> > Thanks!
> >
> > Julie
> >
> > On Sun, Jan 27, 2019 at 9:11 AM Taylor Mandelbaum via RT <
> > met_help at ucar.edu>
> > wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > >
> > > Hey all,
> > >
> > > I got netcdf4 c and c++ installed; I'm running into an issue now
on
> > > configuring MET which says error: C++ compiler cannot create
> executables.
> > > It looks like in the config log that g++ is getting imported but
> erroring
> > > out when trying to use -V as a command option. Attached the
newest
> config
> > > log here.
> > >
> > > When I configure it, this is the command I'm using:
> > >
> > > ./configure --prefix=/E1/taylorm/MET8 --enable-grib2 --enable-
python
> > >
> > >
> > >
> > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT <
> > > met_help at ucar.edu>
> > > wrote:
> > >
> > > > Hi Taylor. In talking with more with John about your
config.log file
> > we
> > > > see that CC is set to use icc (intel), but CXX and F77 are set
to use
> > g++
> > > > and gfortran (GNU).
> > > >
> > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > >
> >
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > CXX='g++'
> > > > F77='gfortran'
> > > >
> > > > Let's see if we can solve the immediate problem before
worrying about
> > any
> > > > potential problems with the external libraries. For now,
please
> choose
> > > > either the GNU compilers or the Intel compilers and set the
following
> > > > variables accordingly. You can chose one and then simply run
the
> > > commands
> > > > below.
> > > >
> > > > *For GNU:*
> > > > export CC=`which gcc`
> > > > export CXX=`which g++`
> > > > export F77=`which gfortran`
> > > >
> > > > *For Intel:*
> > > >
> > > > export CC=`which icc`
> > > > export CXX=`which icc`
> > > > export F77=`which ifort`
> > > >
> > > > Then run "make clean", rerun the configure command, and then
try to
> > make
> > > > MET again.
> > > >
> > > > Let's go from there and see how it works out. Please let me
know.
> > > >
> > > > Julie
> > > >
> > > >
> > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik
<jpresto at ucar.edu>
> > > > wrote:
> > > >
> > > > > Hi Taylor. Thank you for all of this information.
> > > > >
> > > > > Since the libraries were previously installed and we cannot
be
> > certain
> > > > > which compiler was used, are you able and would you be
comfortable
> > > > > installing each of the dependent libraries and not using the
> > previously
> > > > > installed versions? If so, we have an install script that I
can
> > point
> > > > you
> > > > > to, which would install all of the packages and MET as well.
I can
> > > walk
> > > > > through this with you via google hangouts and you can share
your
> > screen
> > > > so
> > > > > we can make sure it is going smoothly. I could do a
hangouts
> > session
> > > > with
> > > > > you tomorrow at 1:15pm (Mountain time) or on Friday at
9:00am
> > (Mountain
> > > > > time). If those times don't work. I can get you started
with very
> > > > > specific instructions via email and we can continue to work
through
> > any
> > > > > problems. We can also set up a different time for next
week,
> > however,
> > > I
> > > > > didn't want you to have to wait that long. Please let me
know your
> > > > > preference.
> > > > >
> > > > > If you think that icc may not be working properly, then you
should
> > > > > probably use the GNU set of compilers, unless there is some
reason
> > not
> > > > to,
> > > > > in which case you may need to get a system administrator
correct
> the
> > > > > problems with the intel compiler.
> > > > >
> > > > > Running "which g++" and running "which gfortran" can tell
you what
> > the
> > > > CXX
> > > > > and F77 paths should be set to. Please let me know if you
have any
> > > > issues
> > > > > with that.
> > > > >
> > > > > Julie
> > > > >
> > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via RT <
> > > > > met_help at ucar.edu> wrote:
> > > > >
> > > > >>
> > > > >> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > >>
> > > > >> Hey Julie,
> > > > >>
> > > > >> 1) They were previously installed, but I just tried running
it
> with
> > > some
> > > > >> of
> > > > >> my own installed versions and they're not working properly
(e.g.
> the
> > > > make
> > > > >> install fails due to gsl/gsl_cdf.h missing... though I set
MET_GSL
> > to
> > > my
> > > > >> gsl-2.5 directory).
> > > > >>
> > > > >> 2) Not sure how I can verify that one, though I think
they're not
> as
> > > > I've
> > > > >> seen GNU and Intel prompts in the config output. My CC var
in my
> > > bashrc
> > > > >> links to an Intel compiler.
> > > > >>
> > > > >> 3) I followed those for the packages, though for the
compilers
> > > section,
> > > > I
> > > > >> do not know my CXX or F77 paths on the hpc that I'm using.
I also
> > > think
> > > > >> the
> > > > >> icc is not working properly as I could not run icc without
a
> license
> > > > >> prompt
> > > > >> coming up.
> > > > >>
> > > > >> I'm not sure if any of that helps, but let me know. Maybe
some of
> > > these
> > > > >> issues are still on our end. The fact that met needs to
only use
> one
> > > > >> compiler might be the issue...
> > > > >>
> > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via RT <
> > > > >> met_help at ucar.edu>
> > > > >> wrote:
> > > > >>
> > > > >> > Hi Taylor. Thank you for passing along your files. I
have a
> few
> > > > >> questions
> > > > >> > for you.
> > > > >> >
> > > > >> > 1) Are you installing the external libraries yourself or
were
> they
> > > > >> > previously installed?
> > > > >> > 2) Can you please verify that the external libraries and
MET are
> > > being
> > > > >> > built with the same family of compilers (e.g. all are
built with
> > > GNU,
> > > > or
> > > > >> > all are build with Intel, etc.)? Which compiler are you
using?
> > > > >> > 3) Are you following the directions on this page as your
> > > instructions
> > > > >> for
> > > > >> > installation?
> > > > >> >
> > > > >> >
> > > > >>
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > >> >
> > > > >> > Thank you!
> > > > >> >
> > > > >> > Julie
> > > > >> >
> > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via RT
<
> > > > >> > met_help at ucar.edu>
> > > > >> > wrote:
> > > > >> >
> > > > >> > >
> > > > >> > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> >
> > > > >> > >
> > > > >> > > Hey Julie,
> > > > >> > >
> > > > >> > > I attached the config and make_install logs here. We
could do
> a
> > > > >> hangouts
> > > > >> > > session as well if you can't pinpoint the issue; I'm
remoting
> in
> > > > from
> > > > >> my
> > > > >> > > home windows computer so it will be a bit hacky.
> > > > >> > >
> > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via RT
<
> > > > >> > met_help at ucar.edu
> > > > >> > > >
> > > > >> > > wrote:
> > > > >> > >
> > > > >> > > > Hi Taylor. It is difficult to tell what is going
without
> more
> > > > >> context.
> > > > >> > > > Could you please send me your config.log file and
your
> > make.log
> > > > >> file?
> > > > >> > > >
> > > > >> > > > We could also consider doing a hangouts session where
you
> can
> > > > share
> > > > >> > your
> > > > >> > > > screen, and I can directly help that way. Either way
> though,
> > if
> > > > you
> > > > >> > > could
> > > > >> > > > please send those files, I would appreciate it.
> > > > >> > > >
> > > > >> > > > Thanks,
> > > > >> > > > Julie
> > > > >> > > >
> > > > >> > > > Thanks!
> > > > >> > > >
> > > > >> > > > Julie
> > > > >> > > >
> > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum via
RT <
> > > > >> > > > met_help at ucar.edu>
> > > > >> > > > wrote:
> > > > >> > > >
> > > > >> > > > >
> > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was acted
upon.
> > > > >> > > > > Transaction: Ticket created by
> > > taylor.mandelbaum at stonybrook.edu
> > > > >> > > > > Queue: met_help
> > > > >> > > > > Subject: met install help
> > > > >> > > > > Owner: Nobody
> > > > >> > > > > Requestors: taylor.mandelbaum at stonybrook.edu
> > > > >> > > > > Status: new
> > > > >> > > > > Ticket <URL:
> > > > >> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > >> > > >
> > > > >> > > > >
> > > > >> > > > >
> > > > >> > > > > Hey all,
> > > > >> > > > >
> > > > >> > > > > I'm presently trying to compile MET 8.0 on our HPC;
when I
> > > > >> configure
> > > > >> > > it,
> > > > >> > > > > I'm getting a few warnings on .h files:
> > > > >> > > > >
> > > > >> > > > > configure: WARNING: errno.h: present but cannot be
> compiled
> > > > >> > > > > configure: WARNING: errno.h: check for missing
> > > prerequisite
> > > > >> > > headers?
> > > > >> > > > > configure: WARNING: errno.h: see the Autoconf
> documentation
> > > > >> > > > > configure: WARNING: errno.h: section "Present
But
> Cannot
> > > Be
> > > > >> > > Compiled"
> > > > >> > > > > configure: WARNING: errno.h: proceeding with the
> compiler's
> > > > result
> > > > >> > > > > configure: WARNING: ##
> --------------------------------
> > ##
> > > > >> > > > > configure: WARNING: ## Report this to
> met_help at ucar.edu
> > > ##
> > > > >> > > > > configure: WARNING: ##
> --------------------------------
> > ##
> > > > >> > > > >
> > > > >> > > > > and the same for fcntl.h, limits.h, stddef.h,
file.h and
> > > > param.h.
> > > > >> > > > >
> > > > >> > > > > When I try to make install, I get this error on the
tail
> of
> > > the
> > > > >> log:
> > > > >> > > > >
> > > > >> > > > > config_scanner.cc: In function ‘void*
> > configalloc(yy_size_t)’:
> > > > >> > > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’ was
not
> > > declared
> > > > in
> > > > >> > this
> > > > >> > > > > scope
> > > > >> > > > > config_scanner.cc: In function ‘void*
configrealloc(void*,
> > > > >> > yy_size_t)’:
> > > > >> > > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’ was
not
> > > declared
> > > > >> in
> > > > >> > > this
> > > > >> > > > > scope
> > > > >> > > > > /* The cast to (char *) in the following
accommodates
> both
> > > > >> > > > > ^
> > > > >> > > > > make[3]: *** [libvx_config_a-config_scanner.o]
Error 1
> > > > >> > > > > make[3]: Leaving directory
> > > > >> > > > > `/E1/taylorm/MET8/met-
8.0_bugfix/src/basic/vx_config'
> > > > >> > > > > make[2]: *** [install-recursive] Error 1
> > > > >> > > > > make[2]: Leaving directory
> > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > >> > > > > make[1]: *** [install-recursive] Error 1
> > > > >> > > > > make[1]: Leaving directory
> > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > >> > > > > make: *** [install-recursive] Error 1
> > > > >> > > > >
> > > > >> > > > > Not sure how to address either of these, hopefully
you
> guys
> > > can
> > > > >> > provide
> > > > >> > > > > some insight.
> > > > >> > > > >
> > > > >> > > > > Thanks!
> > > > >> > > > > --
> > > > >> > > > > *Taylor Mandelbaum*
> > > > >> > > > > Research Technician
> > > > >> > > > > SoMAS | Stony Brook University
> > > > >> > > > > 678.468.5789
> > > > >> > > > >
> > > > >> > > > >
> > > > >> > > >
> > > > >> > > >
> > > > >> > >
> > > > >> > > --
> > > > >> > > *Taylor Mandelbaum*
> > > > >> > > Research Technician
> > > > >> > > SoMAS | Stony Brook University
> > > > >> > > 678.468.5789
> > > > >> > >
> > > > >> > >
> > > > >> >
> > > > >> >
> > > > >>
> > > > >> --
> > > > >> *Taylor Mandelbaum*
> > > > >> Research Technician
> > > > >> SoMAS | Stony Brook University
> > > > >> 678.468.5789
> > > > >>
> > > > >>
> > > >
> > > >
> > >
> > > --
> > > *Taylor Mandelbaum*
> > > Research Technician
> > > SoMAS | Stony Brook University
> > > 678.468.5789
> > >
> > >
> >
> >
>
> --
> *Taylor Mandelbaum*
> Research Technician
> SoMAS | Stony Brook University
> 678.468.5789
>
>
------------------------------------------------
Subject: met install help
From: Taylor Mandelbaum
Time: Sat Feb 16 14:36:14 2019
Hey Julie,
The libpython2.7.so file is in the first directory you
mentioned, /cm/shared/apps/python/2.7.15/lib.
Sorry for the delay, busy week this week.
On Mon, Feb 11, 2019 at 1:28 PM Julie Prestopnik via RT
<met_help at ucar.edu>
wrote:
> Hi Taylor. Thanks for the update. I'm glad we are making some
progress.
>
> From your config.log file:
>
> > /usr/bin/ld: cannot find -lpython2.7
> > collect2: error: ld returned 1 exit status
> >
> and from the output you provided from running "python-config
--ldflags", I
> can see what the problem is.
>
> It looks like the output "python-config --ldflags" unfortunately
does not
> contain all of the information that the environment variable
MET_PYTHON_LD
> needs to have.
>
> In order to proceed, we need to find the location of the libpython.a
file
> or the libpython.so file. Based on the information from the output
from
> running "python-config --cflags", I am going to guess that the
libpython
> file lives in /cm/shared/apps/python/2.7.15/lib or in
> /cm/shared/apps/python/2.7.15/lib/python2.7. Could you please check
those
> directories and see if you can find a libpython.a file or
libpython.so
> file? If so, please send me an email with the path to the file.
You could
> just run "ls <path>" replacing <path> with the full path and send me
the
> output. Then, I will send you a command that you can run to set the
value
> of the environment variable MET_PYTHON_LD.
>
> Thanks!
>
> Julie
>
> On Tue, Feb 5, 2019 at 7:16 PM Taylor Mandelbaum via RT
<met_help at ucar.edu
> >
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> >
> > Hey Julie,
> >
> > Sorry for the delayed response. We got python 2.7.15 set up as a
module.
> I
> > ran python2.7-config --cflags and ..--ldflags:
> >
> > -I/cm/shared/apps/python/2.7.15/include/python2.7
> > -I/cm/shared/apps/python/2.7.15/include/python2.7 -fno-strict-
aliasing -g
> > -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
> >
> > -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic
> >
> > Those are the returned outputs. I updated my bashrc with module
load
> > python/2.7; same issue is occurring with c++. Attached the config
log.
> >
> > Thanks again for your help.
> >
> > On Mon, Jan 28, 2019 at 1:43 PM Julie Prestopnik via RT <
> met_help at ucar.edu
> > >
> > wrote:
> >
> > > Hi Taylor.
> > >
> > > Thanks for getting HDF5 and NetCDF4 C and C++ installed.
> > >
> > > Thank you also for attaching your config.log file. I see in
your
> > > config.log file:
> > >
> > > > /cm/shared/apps/python/3.5.2/include/python3.5m: file not
recognized:
> > Is
> > > a
> > > > directory
> > > >
> > > collect2: error: ld returned 1 exit status
> > > >
> > >
> > > It looks like there is a problem with the linker in that it is
finding
> a
> > > directory instead of a file. However, before we proceed, I
should tell
> > you
> > > that the Python functionality with met-8.0 requires Python 2.7
to be
> > used.
> > > Is Python 2.7 available on your system? If so, please let me
know.
> > >
> > > I can help you set up the necessary environment variables that
are
> > required
> > > to use the python embedding functionality. You'll need to set
> > > MET_PYTHON_CC and MET_PYTHON_LD prior to configuring MET.
Usually the
> > > following is sufficient for csh:
> > >
> > > setenv MET_PYTHON_CC `python-config --cflags`
> > >
> > > setenv MET_PYTHON_LD `python-config --ldflags`
> > >
> > > for bash:
> > >
> > > export MET_PYTHON_CC=`python-config --cflags`
> > >
> > > export MET_PYTHON_LD=`python-config --ldflags`
> > >
> > > However, it may not be. Please run the following commands
(using
> Python
> > > 2.7) and send me the output:
> > >
> > > python-config --cflags
> > > python-config --ldflags
> > >
> > > Thanks!
> > >
> > > Julie
> > >
> > > On Sun, Jan 27, 2019 at 9:11 AM Taylor Mandelbaum via RT <
> > > met_help at ucar.edu>
> > > wrote:
> > >
> > > >
> > > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
>
> > > >
> > > > Hey all,
> > > >
> > > > I got netcdf4 c and c++ installed; I'm running into an issue
now on
> > > > configuring MET which says error: C++ compiler cannot create
> > executables.
> > > > It looks like in the config log that g++ is getting imported
but
> > erroring
> > > > out when trying to use -V as a command option. Attached the
newest
> > config
> > > > log here.
> > > >
> > > > When I configure it, this is the command I'm using:
> > > >
> > > > ./configure --prefix=/E1/taylorm/MET8 --enable-grib2
--enable-python
> > > >
> > > >
> > > >
> > > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT <
> > > > met_help at ucar.edu>
> > > > wrote:
> > > >
> > > > > Hi Taylor. In talking with more with John about your
config.log
> file
> > > we
> > > > > see that CC is set to use icc (intel), but CXX and F77 are
set to
> use
> > > g++
> > > > > and gfortran (GNU).
> > > > >
> > > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > > >
> > >
>
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > > CXX='g++'
> > > > > F77='gfortran'
> > > > >
> > > > > Let's see if we can solve the immediate problem before
worrying
> about
> > > any
> > > > > potential problems with the external libraries. For now,
please
> > choose
> > > > > either the GNU compilers or the Intel compilers and set the
> following
> > > > > variables accordingly. You can chose one and then simply
run the
> > > > commands
> > > > > below.
> > > > >
> > > > > *For GNU:*
> > > > > export CC=`which gcc`
> > > > > export CXX=`which g++`
> > > > > export F77=`which gfortran`
> > > > >
> > > > > *For Intel:*
> > > > >
> > > > > export CC=`which icc`
> > > > > export CXX=`which icc`
> > > > > export F77=`which ifort`
> > > > >
> > > > > Then run "make clean", rerun the configure command, and then
try to
> > > make
> > > > > MET again.
> > > > >
> > > > > Let's go from there and see how it works out. Please let me
know.
> > > > >
> > > > > Julie
> > > > >
> > > > >
> > > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik <
> jpresto at ucar.edu>
> > > > > wrote:
> > > > >
> > > > > > Hi Taylor. Thank you for all of this information.
> > > > > >
> > > > > > Since the libraries were previously installed and we
cannot be
> > > certain
> > > > > > which compiler was used, are you able and would you be
> comfortable
> > > > > > installing each of the dependent libraries and not using
the
> > > previously
> > > > > > installed versions? If so, we have an install script that
I can
> > > point
> > > > > you
> > > > > > to, which would install all of the packages and MET as
well. I
> can
> > > > walk
> > > > > > through this with you via google hangouts and you can
share your
> > > screen
> > > > > so
> > > > > > we can make sure it is going smoothly. I could do a
hangouts
> > > session
> > > > > with
> > > > > > you tomorrow at 1:15pm (Mountain time) or on Friday at
9:00am
> > > (Mountain
> > > > > > time). If those times don't work. I can get you started
with
> very
> > > > > > specific instructions via email and we can continue to
work
> through
> > > any
> > > > > > problems. We can also set up a different time for next
week,
> > > however,
> > > > I
> > > > > > didn't want you to have to wait that long. Please let me
know
> your
> > > > > > preference.
> > > > > >
> > > > > > If you think that icc may not be working properly, then
you
> should
> > > > > > probably use the GNU set of compilers, unless there is
some
> reason
> > > not
> > > > > to,
> > > > > > in which case you may need to get a system administrator
correct
> > the
> > > > > > problems with the intel compiler.
> > > > > >
> > > > > > Running "which g++" and running "which gfortran" can tell
you
> what
> > > the
> > > > > CXX
> > > > > > and F77 paths should be set to. Please let me know if you
have
> any
> > > > > issues
> > > > > > with that.
> > > > > >
> > > > > > Julie
> > > > > >
> > > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via RT <
> > > > > > met_help at ucar.edu> wrote:
> > > > > >
> > > > > >>
> > > > > >> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > > >>
> > > > > >> Hey Julie,
> > > > > >>
> > > > > >> 1) They were previously installed, but I just tried
running it
> > with
> > > > some
> > > > > >> of
> > > > > >> my own installed versions and they're not working
properly (e.g.
> > the
> > > > > make
> > > > > >> install fails due to gsl/gsl_cdf.h missing... though I
set
> MET_GSL
> > > to
> > > > my
> > > > > >> gsl-2.5 directory).
> > > > > >>
> > > > > >> 2) Not sure how I can verify that one, though I think
they're
> not
> > as
> > > > > I've
> > > > > >> seen GNU and Intel prompts in the config output. My CC
var in my
> > > > bashrc
> > > > > >> links to an Intel compiler.
> > > > > >>
> > > > > >> 3) I followed those for the packages, though for the
compilers
> > > > section,
> > > > > I
> > > > > >> do not know my CXX or F77 paths on the hpc that I'm
using. I
> also
> > > > think
> > > > > >> the
> > > > > >> icc is not working properly as I could not run icc
without a
> > license
> > > > > >> prompt
> > > > > >> coming up.
> > > > > >>
> > > > > >> I'm not sure if any of that helps, but let me know. Maybe
some
> of
> > > > these
> > > > > >> issues are still on our end. The fact that met needs to
only use
> > one
> > > > > >> compiler might be the issue...
> > > > > >>
> > > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via RT
<
> > > > > >> met_help at ucar.edu>
> > > > > >> wrote:
> > > > > >>
> > > > > >> > Hi Taylor. Thank you for passing along your files. I
have a
> > few
> > > > > >> questions
> > > > > >> > for you.
> > > > > >> >
> > > > > >> > 1) Are you installing the external libraries yourself
or were
> > they
> > > > > >> > previously installed?
> > > > > >> > 2) Can you please verify that the external libraries
and MET
> are
> > > > being
> > > > > >> > built with the same family of compilers (e.g. all are
built
> with
> > > > GNU,
> > > > > or
> > > > > >> > all are build with Intel, etc.)? Which compiler are
you
> using?
> > > > > >> > 3) Are you following the directions on this page as
your
> > > > instructions
> > > > > >> for
> > > > > >> > installation?
> > > > > >> >
> > > > > >> >
> > > > > >>
> > > > >
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > > >> >
> > > > > >> > Thank you!
> > > > > >> >
> > > > > >> > Julie
> > > > > >> >
> > > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via
RT <
> > > > > >> > met_help at ucar.edu>
> > > > > >> > wrote:
> > > > > >> >
> > > > > >> > >
> > > > > >> > > <URL:
> https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > >
> > > > > >> > >
> > > > > >> > > Hey Julie,
> > > > > >> > >
> > > > > >> > > I attached the config and make_install logs here. We
could
> do
> > a
> > > > > >> hangouts
> > > > > >> > > session as well if you can't pinpoint the issue; I'm
> remoting
> > in
> > > > > from
> > > > > >> my
> > > > > >> > > home windows computer so it will be a bit hacky.
> > > > > >> > >
> > > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik via
RT <
> > > > > >> > met_help at ucar.edu
> > > > > >> > > >
> > > > > >> > > wrote:
> > > > > >> > >
> > > > > >> > > > Hi Taylor. It is difficult to tell what is going
without
> > more
> > > > > >> context.
> > > > > >> > > > Could you please send me your config.log file and
your
> > > make.log
> > > > > >> file?
> > > > > >> > > >
> > > > > >> > > > We could also consider doing a hangouts session
where you
> > can
> > > > > share
> > > > > >> > your
> > > > > >> > > > screen, and I can directly help that way. Either
way
> > though,
> > > if
> > > > > you
> > > > > >> > > could
> > > > > >> > > > please send those files, I would appreciate it.
> > > > > >> > > >
> > > > > >> > > > Thanks,
> > > > > >> > > > Julie
> > > > > >> > > >
> > > > > >> > > > Thanks!
> > > > > >> > > >
> > > > > >> > > > Julie
> > > > > >> > > >
> > > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum
via RT <
> > > > > >> > > > met_help at ucar.edu>
> > > > > >> > > > wrote:
> > > > > >> > > >
> > > > > >> > > > >
> > > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was acted
upon.
> > > > > >> > > > > Transaction: Ticket created by
> > > > taylor.mandelbaum at stonybrook.edu
> > > > > >> > > > > Queue: met_help
> > > > > >> > > > > Subject: met install help
> > > > > >> > > > > Owner: Nobody
> > > > > >> > > > > Requestors: taylor.mandelbaum at stonybrook.edu
> > > > > >> > > > > Status: new
> > > > > >> > > > > Ticket <URL:
> > > > > >> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > >> > > >
> > > > > >> > > > >
> > > > > >> > > > >
> > > > > >> > > > > Hey all,
> > > > > >> > > > >
> > > > > >> > > > > I'm presently trying to compile MET 8.0 on our
HPC;
> when I
> > > > > >> configure
> > > > > >> > > it,
> > > > > >> > > > > I'm getting a few warnings on .h files:
> > > > > >> > > > >
> > > > > >> > > > > configure: WARNING: errno.h: present but cannot
be
> > compiled
> > > > > >> > > > > configure: WARNING: errno.h: check for
missing
> > > > prerequisite
> > > > > >> > > headers?
> > > > > >> > > > > configure: WARNING: errno.h: see the Autoconf
> > documentation
> > > > > >> > > > > configure: WARNING: errno.h: section "Present
But
> > Cannot
> > > > Be
> > > > > >> > > Compiled"
> > > > > >> > > > > configure: WARNING: errno.h: proceeding with the
> > compiler's
> > > > > result
> > > > > >> > > > > configure: WARNING: ##
> > --------------------------------
> > > ##
> > > > > >> > > > > configure: WARNING: ## Report this to
> > met_help at ucar.edu
> > > > ##
> > > > > >> > > > > configure: WARNING: ##
> > --------------------------------
> > > ##
> > > > > >> > > > >
> > > > > >> > > > > and the same for fcntl.h, limits.h, stddef.h,
file.h and
> > > > > param.h.
> > > > > >> > > > >
> > > > > >> > > > > When I try to make install, I get this error on
the tail
> > of
> > > > the
> > > > > >> log:
> > > > > >> > > > >
> > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > configalloc(yy_size_t)’:
> > > > > >> > > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’
was not
> > > > declared
> > > > > in
> > > > > >> > this
> > > > > >> > > > > scope
> > > > > >> > > > > config_scanner.cc: In function ‘void*
> configrealloc(void*,
> > > > > >> > yy_size_t)’:
> > > > > >> > > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’
was not
> > > > declared
> > > > > >> in
> > > > > >> > > this
> > > > > >> > > > > scope
> > > > > >> > > > > /* The cast to (char *) in the following
accommodates
> > both
> > > > > >> > > > > ^
> > > > > >> > > > > make[3]: *** [libvx_config_a-config_scanner.o]
Error 1
> > > > > >> > > > > make[3]: Leaving directory
> > > > > >> > > > > `/E1/taylorm/MET8/met-
8.0_bugfix/src/basic/vx_config'
> > > > > >> > > > > make[2]: *** [install-recursive] Error 1
> > > > > >> > > > > make[2]: Leaving directory
> > > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > > >> > > > > make[1]: *** [install-recursive] Error 1
> > > > > >> > > > > make[1]: Leaving directory
> > > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > > >> > > > > make: *** [install-recursive] Error 1
> > > > > >> > > > >
> > > > > >> > > > > Not sure how to address either of these,
hopefully you
> > guys
> > > > can
> > > > > >> > provide
> > > > > >> > > > > some insight.
> > > > > >> > > > >
> > > > > >> > > > > Thanks!
> > > > > >> > > > > --
> > > > > >> > > > > *Taylor Mandelbaum*
> > > > > >> > > > > Research Technician
> > > > > >> > > > > SoMAS | Stony Brook University
> > > > > >> > > > > 678.468.5789
> > > > > >> > > > >
> > > > > >> > > > >
> > > > > >> > > >
> > > > > >> > > >
> > > > > >> > >
> > > > > >> > > --
> > > > > >> > > *Taylor Mandelbaum*
> > > > > >> > > Research Technician
> > > > > >> > > SoMAS | Stony Brook University
> > > > > >> > > 678.468.5789
> > > > > >> > >
> > > > > >> > >
> > > > > >> >
> > > > > >> >
> > > > > >>
> > > > > >> --
> > > > > >> *Taylor Mandelbaum*
> > > > > >> Research Technician
> > > > > >> SoMAS | Stony Brook University
> > > > > >> 678.468.5789
> > > > > >>
> > > > > >>
> > > > >
> > > > >
> > > >
> > > > --
> > > > *Taylor Mandelbaum*
> > > > Research Technician
> > > > SoMAS | Stony Brook University
> > > > 678.468.5789
> > > >
> > > >
> > >
> > >
> >
> > --
> > *Taylor Mandelbaum*
> > Research Technician
> > SoMAS | Stony Brook University
> > 678.468.5789
> >
> >
>
>
--
*Taylor Mandelbaum*
Research Technician
SoMAS | Stony Brook University
678.468.5789
------------------------------------------------
Subject: met install help
From: Julie Prestopnik
Time: Tue Feb 19 10:40:30 2019
Hi Taylor,
Great! Thanks for the update. Please try setting the following:
or csh:
setenv MET_PYTHON_CC `python-config --cflags`
setenv MET_PYTHON_LD -L/cm/shared/apps/python/2.7.15/lib\ -lpython2.7\
-lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
for bash:
export MET_PYTHON_CC=`python-config --cflags`
export MET_PYTHON_LD=-L/cm/shared/apps/python/2.7.15/lib\ -lpython2.7\
-lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
Please set up your other environment variables and then try
reconfiguring
and reinstalling MET. Please let me know how it goes.
Thanks,
Julie
On Sat, Feb 16, 2019 at 2:36 PM Taylor Mandelbaum via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> Hey Julie,
>
> The libpython2.7.so file is in the first directory you
> mentioned, /cm/shared/apps/python/2.7.15/lib.
>
> Sorry for the delay, busy week this week.
>
> On Mon, Feb 11, 2019 at 1:28 PM Julie Prestopnik via RT
<met_help at ucar.edu
> >
> wrote:
>
> > Hi Taylor. Thanks for the update. I'm glad we are making some
progress.
> >
> > From your config.log file:
> >
> > > /usr/bin/ld: cannot find -lpython2.7
> > > collect2: error: ld returned 1 exit status
> > >
> > and from the output you provided from running "python-config
--ldflags",
> I
> > can see what the problem is.
> >
> > It looks like the output "python-config --ldflags" unfortunately
does not
> > contain all of the information that the environment variable
> MET_PYTHON_LD
> > needs to have.
> >
> > In order to proceed, we need to find the location of the
libpython.a file
> > or the libpython.so file. Based on the information from the
output from
> > running "python-config --cflags", I am going to guess that the
libpython
> > file lives in /cm/shared/apps/python/2.7.15/lib or in
> > /cm/shared/apps/python/2.7.15/lib/python2.7. Could you please
check
> those
> > directories and see if you can find a libpython.a file or
libpython.so
> > file? If so, please send me an email with the path to the file.
You
> could
> > just run "ls <path>" replacing <path> with the full path and send
me the
> > output. Then, I will send you a command that you can run to set
the
> value
> > of the environment variable MET_PYTHON_LD.
> >
> > Thanks!
> >
> > Julie
> >
> > On Tue, Feb 5, 2019 at 7:16 PM Taylor Mandelbaum via RT <
> met_help at ucar.edu
> > >
> > wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > >
> > > Hey Julie,
> > >
> > > Sorry for the delayed response. We got python 2.7.15 set up as a
> module.
> > I
> > > ran python2.7-config --cflags and ..--ldflags:
> > >
> > > -I/cm/shared/apps/python/2.7.15/include/python2.7
> > > -I/cm/shared/apps/python/2.7.15/include/python2.7 -fno-strict-
aliasing
> -g
> > > -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
> > >
> > > -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic
> > >
> > > Those are the returned outputs. I updated my bashrc with module
load
> > > python/2.7; same issue is occurring with c++. Attached the
config log.
> > >
> > > Thanks again for your help.
> > >
> > > On Mon, Jan 28, 2019 at 1:43 PM Julie Prestopnik via RT <
> > met_help at ucar.edu
> > > >
> > > wrote:
> > >
> > > > Hi Taylor.
> > > >
> > > > Thanks for getting HDF5 and NetCDF4 C and C++ installed.
> > > >
> > > > Thank you also for attaching your config.log file. I see in
your
> > > > config.log file:
> > > >
> > > > > /cm/shared/apps/python/3.5.2/include/python3.5m: file not
> recognized:
> > > Is
> > > > a
> > > > > directory
> > > > >
> > > > collect2: error: ld returned 1 exit status
> > > > >
> > > >
> > > > It looks like there is a problem with the linker in that it is
> finding
> > a
> > > > directory instead of a file. However, before we proceed, I
should
> tell
> > > you
> > > > that the Python functionality with met-8.0 requires Python 2.7
to be
> > > used.
> > > > Is Python 2.7 available on your system? If so, please let me
know.
> > > >
> > > > I can help you set up the necessary environment variables that
are
> > > required
> > > > to use the python embedding functionality. You'll need to set
> > > > MET_PYTHON_CC and MET_PYTHON_LD prior to configuring MET.
Usually
> the
> > > > following is sufficient for csh:
> > > >
> > > > setenv MET_PYTHON_CC `python-config --cflags`
> > > >
> > > > setenv MET_PYTHON_LD `python-config --ldflags`
> > > >
> > > > for bash:
> > > >
> > > > export MET_PYTHON_CC=`python-config --cflags`
> > > >
> > > > export MET_PYTHON_LD=`python-config --ldflags`
> > > >
> > > > However, it may not be. Please run the following commands
(using
> > Python
> > > > 2.7) and send me the output:
> > > >
> > > > python-config --cflags
> > > > python-config --ldflags
> > > >
> > > > Thanks!
> > > >
> > > > Julie
> > > >
> > > > On Sun, Jan 27, 2019 at 9:11 AM Taylor Mandelbaum via RT <
> > > > met_help at ucar.edu>
> > > > wrote:
> > > >
> > > > >
> > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > >
> > > > > Hey all,
> > > > >
> > > > > I got netcdf4 c and c++ installed; I'm running into an issue
now on
> > > > > configuring MET which says error: C++ compiler cannot create
> > > executables.
> > > > > It looks like in the config log that g++ is getting imported
but
> > > erroring
> > > > > out when trying to use -V as a command option. Attached the
newest
> > > config
> > > > > log here.
> > > > >
> > > > > When I configure it, this is the command I'm using:
> > > > >
> > > > > ./configure --prefix=/E1/taylorm/MET8 --enable-grib2
> --enable-python
> > > > >
> > > > >
> > > > >
> > > > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT <
> > > > > met_help at ucar.edu>
> > > > > wrote:
> > > > >
> > > > > > Hi Taylor. In talking with more with John about your
config.log
> > file
> > > > we
> > > > > > see that CC is set to use icc (intel), but CXX and F77 are
set to
> > use
> > > > g++
> > > > > > and gfortran (GNU).
> > > > > >
> > > > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > > > >
> > > >
> >
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > > > CXX='g++'
> > > > > > F77='gfortran'
> > > > > >
> > > > > > Let's see if we can solve the immediate problem before
worrying
> > about
> > > > any
> > > > > > potential problems with the external libraries. For now,
please
> > > choose
> > > > > > either the GNU compilers or the Intel compilers and set
the
> > following
> > > > > > variables accordingly. You can chose one and then simply
run the
> > > > > commands
> > > > > > below.
> > > > > >
> > > > > > *For GNU:*
> > > > > > export CC=`which gcc`
> > > > > > export CXX=`which g++`
> > > > > > export F77=`which gfortran`
> > > > > >
> > > > > > *For Intel:*
> > > > > >
> > > > > > export CC=`which icc`
> > > > > > export CXX=`which icc`
> > > > > > export F77=`which ifort`
> > > > > >
> > > > > > Then run "make clean", rerun the configure command, and
then try
> to
> > > > make
> > > > > > MET again.
> > > > > >
> > > > > > Let's go from there and see how it works out. Please let
me
> know.
> > > > > >
> > > > > > Julie
> > > > > >
> > > > > >
> > > > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik <
> > jpresto at ucar.edu>
> > > > > > wrote:
> > > > > >
> > > > > > > Hi Taylor. Thank you for all of this information.
> > > > > > >
> > > > > > > Since the libraries were previously installed and we
cannot be
> > > > certain
> > > > > > > which compiler was used, are you able and would you be
> > comfortable
> > > > > > > installing each of the dependent libraries and not using
the
> > > > previously
> > > > > > > installed versions? If so, we have an install script
that I
> can
> > > > point
> > > > > > you
> > > > > > > to, which would install all of the packages and MET as
well. I
> > can
> > > > > walk
> > > > > > > through this with you via google hangouts and you can
share
> your
> > > > screen
> > > > > > so
> > > > > > > we can make sure it is going smoothly. I could do a
hangouts
> > > > session
> > > > > > with
> > > > > > > you tomorrow at 1:15pm (Mountain time) or on Friday at
9:00am
> > > > (Mountain
> > > > > > > time). If those times don't work. I can get you
started with
> > very
> > > > > > > specific instructions via email and we can continue to
work
> > through
> > > > any
> > > > > > > problems. We can also set up a different time for next
week,
> > > > however,
> > > > > I
> > > > > > > didn't want you to have to wait that long. Please let
me know
> > your
> > > > > > > preference.
> > > > > > >
> > > > > > > If you think that icc may not be working properly, then
you
> > should
> > > > > > > probably use the GNU set of compilers, unless there is
some
> > reason
> > > > not
> > > > > > to,
> > > > > > > in which case you may need to get a system administrator
> correct
> > > the
> > > > > > > problems with the intel compiler.
> > > > > > >
> > > > > > > Running "which g++" and running "which gfortran" can
tell you
> > what
> > > > the
> > > > > > CXX
> > > > > > > and F77 paths should be set to. Please let me know if
you have
> > any
> > > > > > issues
> > > > > > > with that.
> > > > > > >
> > > > > > > Julie
> > > > > > >
> > > > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via RT
<
> > > > > > > met_help at ucar.edu> wrote:
> > > > > > >
> > > > > > >>
> > > > > > >> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> >
> > > > > > >>
> > > > > > >> Hey Julie,
> > > > > > >>
> > > > > > >> 1) They were previously installed, but I just tried
running it
> > > with
> > > > > some
> > > > > > >> of
> > > > > > >> my own installed versions and they're not working
properly
> (e.g.
> > > the
> > > > > > make
> > > > > > >> install fails due to gsl/gsl_cdf.h missing... though I
set
> > MET_GSL
> > > > to
> > > > > my
> > > > > > >> gsl-2.5 directory).
> > > > > > >>
> > > > > > >> 2) Not sure how I can verify that one, though I think
they're
> > not
> > > as
> > > > > > I've
> > > > > > >> seen GNU and Intel prompts in the config output. My CC
var in
> my
> > > > > bashrc
> > > > > > >> links to an Intel compiler.
> > > > > > >>
> > > > > > >> 3) I followed those for the packages, though for the
compilers
> > > > > section,
> > > > > > I
> > > > > > >> do not know my CXX or F77 paths on the hpc that I'm
using. I
> > also
> > > > > think
> > > > > > >> the
> > > > > > >> icc is not working properly as I could not run icc
without a
> > > license
> > > > > > >> prompt
> > > > > > >> coming up.
> > > > > > >>
> > > > > > >> I'm not sure if any of that helps, but let me know.
Maybe some
> > of
> > > > > these
> > > > > > >> issues are still on our end. The fact that met needs to
only
> use
> > > one
> > > > > > >> compiler might be the issue...
> > > > > > >>
> > > > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via
RT <
> > > > > > >> met_help at ucar.edu>
> > > > > > >> wrote:
> > > > > > >>
> > > > > > >> > Hi Taylor. Thank you for passing along your files.
I have
> a
> > > few
> > > > > > >> questions
> > > > > > >> > for you.
> > > > > > >> >
> > > > > > >> > 1) Are you installing the external libraries yourself
or
> were
> > > they
> > > > > > >> > previously installed?
> > > > > > >> > 2) Can you please verify that the external libraries
and MET
> > are
> > > > > being
> > > > > > >> > built with the same family of compilers (e.g. all are
built
> > with
> > > > > GNU,
> > > > > > or
> > > > > > >> > all are build with Intel, etc.)? Which compiler are
you
> > using?
> > > > > > >> > 3) Are you following the directions on this page as
your
> > > > > instructions
> > > > > > >> for
> > > > > > >> > installation?
> > > > > > >> >
> > > > > > >> >
> > > > > > >>
> > > > > >
> > > > >
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > > > >> >
> > > > > > >> > Thank you!
> > > > > > >> >
> > > > > > >> > Julie
> > > > > > >> >
> > > > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum via
RT <
> > > > > > >> > met_help at ucar.edu>
> > > > > > >> > wrote:
> > > > > > >> >
> > > > > > >> > >
> > > > > > >> > > <URL:
> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > >
> > > > > > >> > >
> > > > > > >> > > Hey Julie,
> > > > > > >> > >
> > > > > > >> > > I attached the config and make_install logs here.
We could
> > do
> > > a
> > > > > > >> hangouts
> > > > > > >> > > session as well if you can't pinpoint the issue;
I'm
> > remoting
> > > in
> > > > > > from
> > > > > > >> my
> > > > > > >> > > home windows computer so it will be a bit hacky.
> > > > > > >> > >
> > > > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik
via RT <
> > > > > > >> > met_help at ucar.edu
> > > > > > >> > > >
> > > > > > >> > > wrote:
> > > > > > >> > >
> > > > > > >> > > > Hi Taylor. It is difficult to tell what is going
> without
> > > more
> > > > > > >> context.
> > > > > > >> > > > Could you please send me your config.log file and
your
> > > > make.log
> > > > > > >> file?
> > > > > > >> > > >
> > > > > > >> > > > We could also consider doing a hangouts session
where
> you
> > > can
> > > > > > share
> > > > > > >> > your
> > > > > > >> > > > screen, and I can directly help that way. Either
way
> > > though,
> > > > if
> > > > > > you
> > > > > > >> > > could
> > > > > > >> > > > please send those files, I would appreciate it.
> > > > > > >> > > >
> > > > > > >> > > > Thanks,
> > > > > > >> > > > Julie
> > > > > > >> > > >
> > > > > > >> > > > Thanks!
> > > > > > >> > > >
> > > > > > >> > > > Julie
> > > > > > >> > > >
> > > > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor Mandelbaum
via
> RT <
> > > > > > >> > > > met_help at ucar.edu>
> > > > > > >> > > > wrote:
> > > > > > >> > > >
> > > > > > >> > > > >
> > > > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was
acted
> upon.
> > > > > > >> > > > > Transaction: Ticket created by
> > > > > taylor.mandelbaum at stonybrook.edu
> > > > > > >> > > > > Queue: met_help
> > > > > > >> > > > > Subject: met install help
> > > > > > >> > > > > Owner: Nobody
> > > > > > >> > > > > Requestors: taylor.mandelbaum at stonybrook.edu
> > > > > > >> > > > > Status: new
> > > > > > >> > > > > Ticket <URL:
> > > > > > >> >
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > >> > > >
> > > > > > >> > > > >
> > > > > > >> > > > >
> > > > > > >> > > > > Hey all,
> > > > > > >> > > > >
> > > > > > >> > > > > I'm presently trying to compile MET 8.0 on our
HPC;
> > when I
> > > > > > >> configure
> > > > > > >> > > it,
> > > > > > >> > > > > I'm getting a few warnings on .h files:
> > > > > > >> > > > >
> > > > > > >> > > > > configure: WARNING: errno.h: present but cannot
be
> > > compiled
> > > > > > >> > > > > configure: WARNING: errno.h: check for
missing
> > > > > prerequisite
> > > > > > >> > > headers?
> > > > > > >> > > > > configure: WARNING: errno.h: see the Autoconf
> > > documentation
> > > > > > >> > > > > configure: WARNING: errno.h: section
"Present But
> > > Cannot
> > > > > Be
> > > > > > >> > > Compiled"
> > > > > > >> > > > > configure: WARNING: errno.h: proceeding with
the
> > > compiler's
> > > > > > result
> > > > > > >> > > > > configure: WARNING: ##
> > > --------------------------------
> > > > ##
> > > > > > >> > > > > configure: WARNING: ## Report this to
> > > met_help at ucar.edu
> > > > > ##
> > > > > > >> > > > > configure: WARNING: ##
> > > --------------------------------
> > > > ##
> > > > > > >> > > > >
> > > > > > >> > > > > and the same for fcntl.h, limits.h, stddef.h,
file.h
> and
> > > > > > param.h.
> > > > > > >> > > > >
> > > > > > >> > > > > When I try to make install, I get this error on
the
> tail
> > > of
> > > > > the
> > > > > > >> log:
> > > > > > >> > > > >
> > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > configalloc(yy_size_t)’:
> > > > > > >> > > > > config_scanner.cc:2179:31: error: ‘rpl_malloc’
was not
> > > > > declared
> > > > > > in
> > > > > > >> > this
> > > > > > >> > > > > scope
> > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > configrealloc(void*,
> > > > > > >> > yy_size_t)’:
> > > > > > >> > > > > config_scanner.cc:2191:46: error: ‘rpl_realloc’
was
> not
> > > > > declared
> > > > > > >> in
> > > > > > >> > > this
> > > > > > >> > > > > scope
> > > > > > >> > > > > /* The cast to (char *) in the following
> accommodates
> > > both
> > > > > > >> > > > > ^
> > > > > > >> > > > > make[3]: *** [libvx_config_a-config_scanner.o]
Error 1
> > > > > > >> > > > > make[3]: Leaving directory
> > > > > > >> > > > > `/E1/taylorm/MET8/met-
8.0_bugfix/src/basic/vx_config'
> > > > > > >> > > > > make[2]: *** [install-recursive] Error 1
> > > > > > >> > > > > make[2]: Leaving directory
> > > > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > > > >> > > > > make[1]: *** [install-recursive] Error 1
> > > > > > >> > > > > make[1]: Leaving directory
> > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > > > >> > > > > make: *** [install-recursive] Error 1
> > > > > > >> > > > >
> > > > > > >> > > > > Not sure how to address either of these,
hopefully you
> > > guys
> > > > > can
> > > > > > >> > provide
> > > > > > >> > > > > some insight.
> > > > > > >> > > > >
> > > > > > >> > > > > Thanks!
> > > > > > >> > > > > --
> > > > > > >> > > > > *Taylor Mandelbaum*
> > > > > > >> > > > > Research Technician
> > > > > > >> > > > > SoMAS | Stony Brook University
> > > > > > >> > > > > 678.468.5789
> > > > > > >> > > > >
> > > > > > >> > > > >
> > > > > > >> > > >
> > > > > > >> > > >
> > > > > > >> > >
> > > > > > >> > > --
> > > > > > >> > > *Taylor Mandelbaum*
> > > > > > >> > > Research Technician
> > > > > > >> > > SoMAS | Stony Brook University
> > > > > > >> > > 678.468.5789
> > > > > > >> > >
> > > > > > >> > >
> > > > > > >> >
> > > > > > >> >
> > > > > > >>
> > > > > > >> --
> > > > > > >> *Taylor Mandelbaum*
> > > > > > >> Research Technician
> > > > > > >> SoMAS | Stony Brook University
> > > > > > >> 678.468.5789
> > > > > > >>
> > > > > > >>
> > > > > >
> > > > > >
> > > > >
> > > > > --
> > > > > *Taylor Mandelbaum*
> > > > > Research Technician
> > > > > SoMAS | Stony Brook University
> > > > > 678.468.5789
> > > > >
> > > > >
> > > >
> > > >
> > >
> > > --
> > > *Taylor Mandelbaum*
> > > Research Technician
> > > SoMAS | Stony Brook University
> > > 678.468.5789
> > >
> > >
> >
> >
>
> --
> *Taylor Mandelbaum*
> Research Technician
> SoMAS | Stony Brook University
> 678.468.5789
>
>
------------------------------------------------
Subject: met install help
From: Taylor Mandelbaum
Time: Tue Feb 19 18:10:58 2019
Hey Julie,
I set those up in my bashrc but am still having an issue with the
config
not proceeding due to the c++ compiler:
"checking whether the C++ compiler works... no
configure: error: in `/home/taylorm/MET8/met-8.0_bugfix':
configure: error: C++ compiler cannot create executables"
attached the most recent config log.
Thanks again!
On Tue, Feb 19, 2019 at 12:47 PM Julie Prestopnik via RT
<met_help at ucar.edu>
wrote:
> Hi Taylor,
>
> Great! Thanks for the update. Please try setting the following:
>
> or csh:
>
> setenv MET_PYTHON_CC `python-config --cflags`
> setenv MET_PYTHON_LD -L/cm/shared/apps/python/2.7.15/lib\
-lpython2.7\
> -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
>
> for bash:
>
> export MET_PYTHON_CC=`python-config --cflags`
> export MET_PYTHON_LD=-L/cm/shared/apps/python/2.7.15/lib\
-lpython2.7\
> -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
>
> Please set up your other environment variables and then try
reconfiguring
> and reinstalling MET. Please let me know how it goes.
>
> Thanks,
> Julie
>
> On Sat, Feb 16, 2019 at 2:36 PM Taylor Mandelbaum via RT <
> met_help at ucar.edu>
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> >
> > Hey Julie,
> >
> > The libpython2.7.so file is in the first directory you
> > mentioned, /cm/shared/apps/python/2.7.15/lib.
> >
> > Sorry for the delay, busy week this week.
> >
> > On Mon, Feb 11, 2019 at 1:28 PM Julie Prestopnik via RT <
> met_help at ucar.edu
> > >
> > wrote:
> >
> > > Hi Taylor. Thanks for the update. I'm glad we are making some
> progress.
> > >
> > > From your config.log file:
> > >
> > > > /usr/bin/ld: cannot find -lpython2.7
> > > > collect2: error: ld returned 1 exit status
> > > >
> > > and from the output you provided from running "python-config
> --ldflags",
> > I
> > > can see what the problem is.
> > >
> > > It looks like the output "python-config --ldflags" unfortunately
does
> not
> > > contain all of the information that the environment variable
> > MET_PYTHON_LD
> > > needs to have.
> > >
> > > In order to proceed, we need to find the location of the
libpython.a
> file
> > > or the libpython.so file. Based on the information from the
output
> from
> > > running "python-config --cflags", I am going to guess that the
> libpython
> > > file lives in /cm/shared/apps/python/2.7.15/lib or in
> > > /cm/shared/apps/python/2.7.15/lib/python2.7. Could you please
check
> > those
> > > directories and see if you can find a libpython.a file or
libpython.so
> > > file? If so, please send me an email with the path to the file.
You
> > could
> > > just run "ls <path>" replacing <path> with the full path and
send me
> the
> > > output. Then, I will send you a command that you can run to set
the
> > value
> > > of the environment variable MET_PYTHON_LD.
> > >
> > > Thanks!
> > >
> > > Julie
> > >
> > > On Tue, Feb 5, 2019 at 7:16 PM Taylor Mandelbaum via RT <
> > met_help at ucar.edu
> > > >
> > > wrote:
> > >
> > > >
> > > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
>
> > > >
> > > > Hey Julie,
> > > >
> > > > Sorry for the delayed response. We got python 2.7.15 set up as
a
> > module.
> > > I
> > > > ran python2.7-config --cflags and ..--ldflags:
> > > >
> > > > -I/cm/shared/apps/python/2.7.15/include/python2.7
> > > > -I/cm/shared/apps/python/2.7.15/include/python2.7
> -fno-strict-aliasing
> > -g
> > > > -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
> > > >
> > > > -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic
> > > >
> > > > Those are the returned outputs. I updated my bashrc with
module load
> > > > python/2.7; same issue is occurring with c++. Attached the
config
> log.
> > > >
> > > > Thanks again for your help.
> > > >
> > > > On Mon, Jan 28, 2019 at 1:43 PM Julie Prestopnik via RT <
> > > met_help at ucar.edu
> > > > >
> > > > wrote:
> > > >
> > > > > Hi Taylor.
> > > > >
> > > > > Thanks for getting HDF5 and NetCDF4 C and C++ installed.
> > > > >
> > > > > Thank you also for attaching your config.log file. I see in
your
> > > > > config.log file:
> > > > >
> > > > > > /cm/shared/apps/python/3.5.2/include/python3.5m: file not
> > recognized:
> > > > Is
> > > > > a
> > > > > > directory
> > > > > >
> > > > > collect2: error: ld returned 1 exit status
> > > > > >
> > > > >
> > > > > It looks like there is a problem with the linker in that it
is
> > finding
> > > a
> > > > > directory instead of a file. However, before we proceed, I
should
> > tell
> > > > you
> > > > > that the Python functionality with met-8.0 requires Python
2.7 to
> be
> > > > used.
> > > > > Is Python 2.7 available on your system? If so, please let
me know.
> > > > >
> > > > > I can help you set up the necessary environment variables
that are
> > > > required
> > > > > to use the python embedding functionality. You'll need to
set
> > > > > MET_PYTHON_CC and MET_PYTHON_LD prior to configuring MET.
Usually
> > the
> > > > > following is sufficient for csh:
> > > > >
> > > > > setenv MET_PYTHON_CC `python-config --cflags`
> > > > >
> > > > > setenv MET_PYTHON_LD `python-config --ldflags`
> > > > >
> > > > > for bash:
> > > > >
> > > > > export MET_PYTHON_CC=`python-config --cflags`
> > > > >
> > > > > export MET_PYTHON_LD=`python-config --ldflags`
> > > > >
> > > > > However, it may not be. Please run the following commands
(using
> > > Python
> > > > > 2.7) and send me the output:
> > > > >
> > > > > python-config --cflags
> > > > > python-config --ldflags
> > > > >
> > > > > Thanks!
> > > > >
> > > > > Julie
> > > > >
> > > > > On Sun, Jan 27, 2019 at 9:11 AM Taylor Mandelbaum via RT <
> > > > > met_help at ucar.edu>
> > > > > wrote:
> > > > >
> > > > > >
> > > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > > >
> > > > > > Hey all,
> > > > > >
> > > > > > I got netcdf4 c and c++ installed; I'm running into an
issue now
> on
> > > > > > configuring MET which says error: C++ compiler cannot
create
> > > > executables.
> > > > > > It looks like in the config log that g++ is getting
imported but
> > > > erroring
> > > > > > out when trying to use -V as a command option. Attached
the
> newest
> > > > config
> > > > > > log here.
> > > > > >
> > > > > > When I configure it, this is the command I'm using:
> > > > > >
> > > > > > ./configure --prefix=/E1/taylorm/MET8 --enable-grib2
> > --enable-python
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT <
> > > > > > met_help at ucar.edu>
> > > > > > wrote:
> > > > > >
> > > > > > > Hi Taylor. In talking with more with John about your
> config.log
> > > file
> > > > > we
> > > > > > > see that CC is set to use icc (intel), but CXX and F77
are set
> to
> > > use
> > > > > g++
> > > > > > > and gfortran (GNU).
> > > > > > >
> > > > > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > > > > >
> > > > >
> > >
>
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > > > > CXX='g++'
> > > > > > > F77='gfortran'
> > > > > > >
> > > > > > > Let's see if we can solve the immediate problem before
worrying
> > > about
> > > > > any
> > > > > > > potential problems with the external libraries. For
now,
> please
> > > > choose
> > > > > > > either the GNU compilers or the Intel compilers and set
the
> > > following
> > > > > > > variables accordingly. You can chose one and then
simply run
> the
> > > > > > commands
> > > > > > > below.
> > > > > > >
> > > > > > > *For GNU:*
> > > > > > > export CC=`which gcc`
> > > > > > > export CXX=`which g++`
> > > > > > > export F77=`which gfortran`
> > > > > > >
> > > > > > > *For Intel:*
> > > > > > >
> > > > > > > export CC=`which icc`
> > > > > > > export CXX=`which icc`
> > > > > > > export F77=`which ifort`
> > > > > > >
> > > > > > > Then run "make clean", rerun the configure command, and
then
> try
> > to
> > > > > make
> > > > > > > MET again.
> > > > > > >
> > > > > > > Let's go from there and see how it works out. Please
let me
> > know.
> > > > > > >
> > > > > > > Julie
> > > > > > >
> > > > > > >
> > > > > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik <
> > > jpresto at ucar.edu>
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi Taylor. Thank you for all of this information.
> > > > > > > >
> > > > > > > > Since the libraries were previously installed and we
cannot
> be
> > > > > certain
> > > > > > > > which compiler was used, are you able and would you be
> > > comfortable
> > > > > > > > installing each of the dependent libraries and not
using the
> > > > > previously
> > > > > > > > installed versions? If so, we have an install script
that I
> > can
> > > > > point
> > > > > > > you
> > > > > > > > to, which would install all of the packages and MET as
> well. I
> > > can
> > > > > > walk
> > > > > > > > through this with you via google hangouts and you can
share
> > your
> > > > > screen
> > > > > > > so
> > > > > > > > we can make sure it is going smoothly. I could do a
> hangouts
> > > > > session
> > > > > > > with
> > > > > > > > you tomorrow at 1:15pm (Mountain time) or on Friday at
9:00am
> > > > > (Mountain
> > > > > > > > time). If those times don't work. I can get you
started
> with
> > > very
> > > > > > > > specific instructions via email and we can continue to
work
> > > through
> > > > > any
> > > > > > > > problems. We can also set up a different time for
next week,
> > > > > however,
> > > > > > I
> > > > > > > > didn't want you to have to wait that long. Please let
me
> know
> > > your
> > > > > > > > preference.
> > > > > > > >
> > > > > > > > If you think that icc may not be working properly,
then you
> > > should
> > > > > > > > probably use the GNU set of compilers, unless there is
some
> > > reason
> > > > > not
> > > > > > > to,
> > > > > > > > in which case you may need to get a system
administrator
> > correct
> > > > the
> > > > > > > > problems with the intel compiler.
> > > > > > > >
> > > > > > > > Running "which g++" and running "which gfortran" can
tell you
> > > what
> > > > > the
> > > > > > > CXX
> > > > > > > > and F77 paths should be set to. Please let me know if
you
> have
> > > any
> > > > > > > issues
> > > > > > > > with that.
> > > > > > > >
> > > > > > > > Julie
> > > > > > > >
> > > > > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum via
RT <
> > > > > > > > met_help at ucar.edu> wrote:
> > > > > > > >
> > > > > > > >>
> > > > > > > >> <URL:
> https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > >
> > > > > > > >>
> > > > > > > >> Hey Julie,
> > > > > > > >>
> > > > > > > >> 1) They were previously installed, but I just tried
running
> it
> > > > with
> > > > > > some
> > > > > > > >> of
> > > > > > > >> my own installed versions and they're not working
properly
> > (e.g.
> > > > the
> > > > > > > make
> > > > > > > >> install fails due to gsl/gsl_cdf.h missing... though
I set
> > > MET_GSL
> > > > > to
> > > > > > my
> > > > > > > >> gsl-2.5 directory).
> > > > > > > >>
> > > > > > > >> 2) Not sure how I can verify that one, though I think
> they're
> > > not
> > > > as
> > > > > > > I've
> > > > > > > >> seen GNU and Intel prompts in the config output. My
CC var
> in
> > my
> > > > > > bashrc
> > > > > > > >> links to an Intel compiler.
> > > > > > > >>
> > > > > > > >> 3) I followed those for the packages, though for the
> compilers
> > > > > > section,
> > > > > > > I
> > > > > > > >> do not know my CXX or F77 paths on the hpc that I'm
using. I
> > > also
> > > > > > think
> > > > > > > >> the
> > > > > > > >> icc is not working properly as I could not run icc
without a
> > > > license
> > > > > > > >> prompt
> > > > > > > >> coming up.
> > > > > > > >>
> > > > > > > >> I'm not sure if any of that helps, but let me know.
Maybe
> some
> > > of
> > > > > > these
> > > > > > > >> issues are still on our end. The fact that met needs
to only
> > use
> > > > one
> > > > > > > >> compiler might be the issue...
> > > > > > > >>
> > > > > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik via
RT <
> > > > > > > >> met_help at ucar.edu>
> > > > > > > >> wrote:
> > > > > > > >>
> > > > > > > >> > Hi Taylor. Thank you for passing along your files.
I
> have
> > a
> > > > few
> > > > > > > >> questions
> > > > > > > >> > for you.
> > > > > > > >> >
> > > > > > > >> > 1) Are you installing the external libraries
yourself or
> > were
> > > > they
> > > > > > > >> > previously installed?
> > > > > > > >> > 2) Can you please verify that the external
libraries and
> MET
> > > are
> > > > > > being
> > > > > > > >> > built with the same family of compilers (e.g. all
are
> built
> > > with
> > > > > > GNU,
> > > > > > > or
> > > > > > > >> > all are build with Intel, etc.)? Which compiler
are you
> > > using?
> > > > > > > >> > 3) Are you following the directions on this page as
your
> > > > > > instructions
> > > > > > > >> for
> > > > > > > >> > installation?
> > > > > > > >> >
> > > > > > > >> >
> > > > > > > >>
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > > > > >> >
> > > > > > > >> > Thank you!
> > > > > > > >> >
> > > > > > > >> > Julie
> > > > > > > >> >
> > > > > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum
via RT <
> > > > > > > >> > met_help at ucar.edu>
> > > > > > > >> > wrote:
> > > > > > > >> >
> > > > > > > >> > >
> > > > > > > >> > > <URL:
> > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > >
> > > > > > > >> > >
> > > > > > > >> > > Hey Julie,
> > > > > > > >> > >
> > > > > > > >> > > I attached the config and make_install logs here.
We
> could
> > > do
> > > > a
> > > > > > > >> hangouts
> > > > > > > >> > > session as well if you can't pinpoint the issue;
I'm
> > > remoting
> > > > in
> > > > > > > from
> > > > > > > >> my
> > > > > > > >> > > home windows computer so it will be a bit hacky.
> > > > > > > >> > >
> > > > > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie Prestopnik
via RT
> <
> > > > > > > >> > met_help at ucar.edu
> > > > > > > >> > > >
> > > > > > > >> > > wrote:
> > > > > > > >> > >
> > > > > > > >> > > > Hi Taylor. It is difficult to tell what is
going
> > without
> > > > more
> > > > > > > >> context.
> > > > > > > >> > > > Could you please send me your config.log file
and your
> > > > > make.log
> > > > > > > >> file?
> > > > > > > >> > > >
> > > > > > > >> > > > We could also consider doing a hangouts session
where
> > you
> > > > can
> > > > > > > share
> > > > > > > >> > your
> > > > > > > >> > > > screen, and I can directly help that way.
Either way
> > > > though,
> > > > > if
> > > > > > > you
> > > > > > > >> > > could
> > > > > > > >> > > > please send those files, I would appreciate it.
> > > > > > > >> > > >
> > > > > > > >> > > > Thanks,
> > > > > > > >> > > > Julie
> > > > > > > >> > > >
> > > > > > > >> > > > Thanks!
> > > > > > > >> > > >
> > > > > > > >> > > > Julie
> > > > > > > >> > > >
> > > > > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor
Mandelbaum via
> > RT <
> > > > > > > >> > > > met_help at ucar.edu>
> > > > > > > >> > > > wrote:
> > > > > > > >> > > >
> > > > > > > >> > > > >
> > > > > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was
acted
> > upon.
> > > > > > > >> > > > > Transaction: Ticket created by
> > > > > > taylor.mandelbaum at stonybrook.edu
> > > > > > > >> > > > > Queue: met_help
> > > > > > > >> > > > > Subject: met install help
> > > > > > > >> > > > > Owner: Nobody
> > > > > > > >> > > > > Requestors:
taylor.mandelbaum at stonybrook.edu
> > > > > > > >> > > > > Status: new
> > > > > > > >> > > > > Ticket <URL:
> > > > > > > >> >
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > >> > > >
> > > > > > > >> > > > >
> > > > > > > >> > > > >
> > > > > > > >> > > > > Hey all,
> > > > > > > >> > > > >
> > > > > > > >> > > > > I'm presently trying to compile MET 8.0 on
our HPC;
> > > when I
> > > > > > > >> configure
> > > > > > > >> > > it,
> > > > > > > >> > > > > I'm getting a few warnings on .h files:
> > > > > > > >> > > > >
> > > > > > > >> > > > > configure: WARNING: errno.h: present but
cannot be
> > > > compiled
> > > > > > > >> > > > > configure: WARNING: errno.h: check for
missing
> > > > > > prerequisite
> > > > > > > >> > > headers?
> > > > > > > >> > > > > configure: WARNING: errno.h: see the Autoconf
> > > > documentation
> > > > > > > >> > > > > configure: WARNING: errno.h: section
"Present
> But
> > > > Cannot
> > > > > > Be
> > > > > > > >> > > Compiled"
> > > > > > > >> > > > > configure: WARNING: errno.h: proceeding with
the
> > > > compiler's
> > > > > > > result
> > > > > > > >> > > > > configure: WARNING: ##
> > > > --------------------------------
> > > > > ##
> > > > > > > >> > > > > configure: WARNING: ## Report this to
> > > > met_help at ucar.edu
> > > > > > ##
> > > > > > > >> > > > > configure: WARNING: ##
> > > > --------------------------------
> > > > > ##
> > > > > > > >> > > > >
> > > > > > > >> > > > > and the same for fcntl.h, limits.h, stddef.h,
file.h
> > and
> > > > > > > param.h.
> > > > > > > >> > > > >
> > > > > > > >> > > > > When I try to make install, I get this error
on the
> > tail
> > > > of
> > > > > > the
> > > > > > > >> log:
> > > > > > > >> > > > >
> > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > configalloc(yy_size_t)’:
> > > > > > > >> > > > > config_scanner.cc:2179:31: error:
‘rpl_malloc’ was
> not
> > > > > > declared
> > > > > > > in
> > > > > > > >> > this
> > > > > > > >> > > > > scope
> > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > configrealloc(void*,
> > > > > > > >> > yy_size_t)’:
> > > > > > > >> > > > > config_scanner.cc:2191:46: error:
‘rpl_realloc’ was
> > not
> > > > > > declared
> > > > > > > >> in
> > > > > > > >> > > this
> > > > > > > >> > > > > scope
> > > > > > > >> > > > > /* The cast to (char *) in the following
> > accommodates
> > > > both
> > > > > > > >> > > > >
^
> > > > > > > >> > > > > make[3]: *** [libvx_config_a-
config_scanner.o]
> Error 1
> > > > > > > >> > > > > make[3]: Leaving directory
> > > > > > > >> > > > >
> `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > > > > > >> > > > > make[2]: *** [install-recursive] Error 1
> > > > > > > >> > > > > make[2]: Leaving directory
> > > > > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > > > > >> > > > > make[1]: *** [install-recursive] Error 1
> > > > > > > >> > > > > make[1]: Leaving directory
> > > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > > > > >> > > > > make: *** [install-recursive] Error 1
> > > > > > > >> > > > >
> > > > > > > >> > > > > Not sure how to address either of these,
hopefully
> you
> > > > guys
> > > > > > can
> > > > > > > >> > provide
> > > > > > > >> > > > > some insight.
> > > > > > > >> > > > >
> > > > > > > >> > > > > Thanks!
> > > > > > > >> > > > > --
> > > > > > > >> > > > > *Taylor Mandelbaum*
> > > > > > > >> > > > > Research Technician
> > > > > > > >> > > > > SoMAS | Stony Brook University
> > > > > > > >> > > > > 678.468.5789
> > > > > > > >> > > > >
> > > > > > > >> > > > >
> > > > > > > >> > > >
> > > > > > > >> > > >
> > > > > > > >> > >
> > > > > > > >> > > --
> > > > > > > >> > > *Taylor Mandelbaum*
> > > > > > > >> > > Research Technician
> > > > > > > >> > > SoMAS | Stony Brook University
> > > > > > > >> > > 678.468.5789
> > > > > > > >> > >
> > > > > > > >> > >
> > > > > > > >> >
> > > > > > > >> >
> > > > > > > >>
> > > > > > > >> --
> > > > > > > >> *Taylor Mandelbaum*
> > > > > > > >> Research Technician
> > > > > > > >> SoMAS | Stony Brook University
> > > > > > > >> 678.468.5789
> > > > > > > >>
> > > > > > > >>
> > > > > > >
> > > > > > >
> > > > > >
> > > > > > --
> > > > > > *Taylor Mandelbaum*
> > > > > > Research Technician
> > > > > > SoMAS | Stony Brook University
> > > > > > 678.468.5789
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > > > --
> > > > *Taylor Mandelbaum*
> > > > Research Technician
> > > > SoMAS | Stony Brook University
> > > > 678.468.5789
> > > >
> > > >
> > >
> > >
> >
> > --
> > *Taylor Mandelbaum*
> > Research Technician
> > SoMAS | Stony Brook University
> > 678.468.5789
> >
> >
>
>
--
*Taylor Mandelbaum*
Research Technician
SoMAS | Stony Brook University
678.468.5789
------------------------------------------------
Subject: met install help
From: Julie Prestopnik
Time: Wed Feb 20 12:12:04 2019
Hi Taylor.
I see the following in your config.log file:
/usr/bin/ld: cannot find -lpython2.7-lpthread
It looks like MET_PYTHON_LD was set in the following way:
MET_PYTHON_LD='-L/cm/shared/apps/python/2.7.15/lib -lpython2.7-
lpthread
> -ldl -lutil -lm -Xlinker -export-dynamic'
>
Note, the lack of space between "-lpython2.7" and "-lpthread" in
both the
error message and the setting of MET_PYTHON_LD.
Please copy and paste the following:
for csh:
>
> setenv MET_PYTHON_LD -L/cm/shared/apps/python/2.7.15/lib\
-lpython2.7\
> -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
>
> for bash:
>
> export MET_PYTHON_LD=-L/cm/shared/apps/python/2.7.15/lib\
-lpython2.7\
> -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
Those lines should capture the proper spaces.
Give that a try and reconfigure MET. Please let me know how it goes.
Thanks!
Julie
On Tue, Feb 19, 2019 at 6:11 PM Taylor Mandelbaum via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> Hey Julie,
>
> I set those up in my bashrc but am still having an issue with the
config
> not proceeding due to the c++ compiler:
>
> "checking whether the C++ compiler works... no
> configure: error: in `/home/taylorm/MET8/met-8.0_bugfix':
> configure: error: C++ compiler cannot create executables"
>
> attached the most recent config log.
>
> Thanks again!
>
> On Tue, Feb 19, 2019 at 12:47 PM Julie Prestopnik via RT <
> met_help at ucar.edu>
> wrote:
>
> > Hi Taylor,
> >
> > Great! Thanks for the update. Please try setting the following:
> >
> > or csh:
> >
> > setenv MET_PYTHON_CC `python-config --cflags`
> > setenv MET_PYTHON_LD -L/cm/shared/apps/python/2.7.15/lib\
-lpython2.7\
> > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> >
> > for bash:
> >
> > export MET_PYTHON_CC=`python-config --cflags`
> > export MET_PYTHON_LD=-L/cm/shared/apps/python/2.7.15/lib\
-lpython2.7\
> > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> >
> > Please set up your other environment variables and then try
reconfiguring
> > and reinstalling MET. Please let me know how it goes.
> >
> > Thanks,
> > Julie
> >
> > On Sat, Feb 16, 2019 at 2:36 PM Taylor Mandelbaum via RT <
> > met_help at ucar.edu>
> > wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > >
> > > Hey Julie,
> > >
> > > The libpython2.7.so file is in the first directory you
> > > mentioned, /cm/shared/apps/python/2.7.15/lib.
> > >
> > > Sorry for the delay, busy week this week.
> > >
> > > On Mon, Feb 11, 2019 at 1:28 PM Julie Prestopnik via RT <
> > met_help at ucar.edu
> > > >
> > > wrote:
> > >
> > > > Hi Taylor. Thanks for the update. I'm glad we are making
some
> > progress.
> > > >
> > > > From your config.log file:
> > > >
> > > > > /usr/bin/ld: cannot find -lpython2.7
> > > > > collect2: error: ld returned 1 exit status
> > > > >
> > > > and from the output you provided from running "python-config
> > --ldflags",
> > > I
> > > > can see what the problem is.
> > > >
> > > > It looks like the output "python-config --ldflags"
unfortunately does
> > not
> > > > contain all of the information that the environment variable
> > > MET_PYTHON_LD
> > > > needs to have.
> > > >
> > > > In order to proceed, we need to find the location of the
libpython.a
> > file
> > > > or the libpython.so file. Based on the information from the
output
> > from
> > > > running "python-config --cflags", I am going to guess that the
> > libpython
> > > > file lives in /cm/shared/apps/python/2.7.15/lib or in
> > > > /cm/shared/apps/python/2.7.15/lib/python2.7. Could you please
check
> > > those
> > > > directories and see if you can find a libpython.a file or
> libpython.so
> > > > file? If so, please send me an email with the path to the
file. You
> > > could
> > > > just run "ls <path>" replacing <path> with the full path and
send me
> > the
> > > > output. Then, I will send you a command that you can run to
set the
> > > value
> > > > of the environment variable MET_PYTHON_LD.
> > > >
> > > > Thanks!
> > > >
> > > > Julie
> > > >
> > > > On Tue, Feb 5, 2019 at 7:16 PM Taylor Mandelbaum via RT <
> > > met_help at ucar.edu
> > > > >
> > > > wrote:
> > > >
> > > > >
> > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > >
> > > > > Hey Julie,
> > > > >
> > > > > Sorry for the delayed response. We got python 2.7.15 set up
as a
> > > module.
> > > > I
> > > > > ran python2.7-config --cflags and ..--ldflags:
> > > > >
> > > > > -I/cm/shared/apps/python/2.7.15/include/python2.7
> > > > > -I/cm/shared/apps/python/2.7.15/include/python2.7
> > -fno-strict-aliasing
> > > -g
> > > > > -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
> > > > >
> > > > > -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-
dynamic
> > > > >
> > > > > Those are the returned outputs. I updated my bashrc with
module
> load
> > > > > python/2.7; same issue is occurring with c++. Attached the
config
> > log.
> > > > >
> > > > > Thanks again for your help.
> > > > >
> > > > > On Mon, Jan 28, 2019 at 1:43 PM Julie Prestopnik via RT <
> > > > met_help at ucar.edu
> > > > > >
> > > > > wrote:
> > > > >
> > > > > > Hi Taylor.
> > > > > >
> > > > > > Thanks for getting HDF5 and NetCDF4 C and C++ installed.
> > > > > >
> > > > > > Thank you also for attaching your config.log file. I see
in your
> > > > > > config.log file:
> > > > > >
> > > > > > > /cm/shared/apps/python/3.5.2/include/python3.5m: file
not
> > > recognized:
> > > > > Is
> > > > > > a
> > > > > > > directory
> > > > > > >
> > > > > > collect2: error: ld returned 1 exit status
> > > > > > >
> > > > > >
> > > > > > It looks like there is a problem with the linker in that
it is
> > > finding
> > > > a
> > > > > > directory instead of a file. However, before we proceed,
I
> should
> > > tell
> > > > > you
> > > > > > that the Python functionality with met-8.0 requires Python
2.7 to
> > be
> > > > > used.
> > > > > > Is Python 2.7 available on your system? If so, please let
me
> know.
> > > > > >
> > > > > > I can help you set up the necessary environment variables
that
> are
> > > > > required
> > > > > > to use the python embedding functionality. You'll need to
set
> > > > > > MET_PYTHON_CC and MET_PYTHON_LD prior to configuring MET.
> Usually
> > > the
> > > > > > following is sufficient for csh:
> > > > > >
> > > > > > setenv MET_PYTHON_CC `python-config --cflags`
> > > > > >
> > > > > > setenv MET_PYTHON_LD `python-config --ldflags`
> > > > > >
> > > > > > for bash:
> > > > > >
> > > > > > export MET_PYTHON_CC=`python-config --cflags`
> > > > > >
> > > > > > export MET_PYTHON_LD=`python-config --ldflags`
> > > > > >
> > > > > > However, it may not be. Please run the following commands
(using
> > > > Python
> > > > > > 2.7) and send me the output:
> > > > > >
> > > > > > python-config --cflags
> > > > > > python-config --ldflags
> > > > > >
> > > > > > Thanks!
> > > > > >
> > > > > > Julie
> > > > > >
> > > > > > On Sun, Jan 27, 2019 at 9:11 AM Taylor Mandelbaum via RT <
> > > > > > met_help at ucar.edu>
> > > > > > wrote:
> > > > > >
> > > > > > >
> > > > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> >
> > > > > > >
> > > > > > > Hey all,
> > > > > > >
> > > > > > > I got netcdf4 c and c++ installed; I'm running into an
issue
> now
> > on
> > > > > > > configuring MET which says error: C++ compiler cannot
create
> > > > > executables.
> > > > > > > It looks like in the config log that g++ is getting
imported
> but
> > > > > erroring
> > > > > > > out when trying to use -V as a command option. Attached
the
> > newest
> > > > > config
> > > > > > > log here.
> > > > > > >
> > > > > > > When I configure it, this is the command I'm using:
> > > > > > >
> > > > > > > ./configure --prefix=/E1/taylorm/MET8 --enable-grib2
> > > --enable-python
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via RT
<
> > > > > > > met_help at ucar.edu>
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi Taylor. In talking with more with John about your
> > config.log
> > > > file
> > > > > > we
> > > > > > > > see that CC is set to use icc (intel), but CXX and F77
are
> set
> > to
> > > > use
> > > > > > g++
> > > > > > > > and gfortran (GNU).
> > > > > > > >
> > > > > > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > > > > > >
> > > > > >
> > > >
> >
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > > > > > CXX='g++'
> > > > > > > > F77='gfortran'
> > > > > > > >
> > > > > > > > Let's see if we can solve the immediate problem before
> worrying
> > > > about
> > > > > > any
> > > > > > > > potential problems with the external libraries. For
now,
> > please
> > > > > choose
> > > > > > > > either the GNU compilers or the Intel compilers and
set the
> > > > following
> > > > > > > > variables accordingly. You can chose one and then
simply run
> > the
> > > > > > > commands
> > > > > > > > below.
> > > > > > > >
> > > > > > > > *For GNU:*
> > > > > > > > export CC=`which gcc`
> > > > > > > > export CXX=`which g++`
> > > > > > > > export F77=`which gfortran`
> > > > > > > >
> > > > > > > > *For Intel:*
> > > > > > > >
> > > > > > > > export CC=`which icc`
> > > > > > > > export CXX=`which icc`
> > > > > > > > export F77=`which ifort`
> > > > > > > >
> > > > > > > > Then run "make clean", rerun the configure command,
and then
> > try
> > > to
> > > > > > make
> > > > > > > > MET again.
> > > > > > > >
> > > > > > > > Let's go from there and see how it works out. Please
let me
> > > know.
> > > > > > > >
> > > > > > > > Julie
> > > > > > > >
> > > > > > > >
> > > > > > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik <
> > > > jpresto at ucar.edu>
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > > Hi Taylor. Thank you for all of this information.
> > > > > > > > >
> > > > > > > > > Since the libraries were previously installed and we
cannot
> > be
> > > > > > certain
> > > > > > > > > which compiler was used, are you able and would you
be
> > > > comfortable
> > > > > > > > > installing each of the dependent libraries and not
using
> the
> > > > > > previously
> > > > > > > > > installed versions? If so, we have an install
script that
> I
> > > can
> > > > > > point
> > > > > > > > you
> > > > > > > > > to, which would install all of the packages and MET
as
> > well. I
> > > > can
> > > > > > > walk
> > > > > > > > > through this with you via google hangouts and you
can share
> > > your
> > > > > > screen
> > > > > > > > so
> > > > > > > > > we can make sure it is going smoothly. I could do
a
> > hangouts
> > > > > > session
> > > > > > > > with
> > > > > > > > > you tomorrow at 1:15pm (Mountain time) or on Friday
at
> 9:00am
> > > > > > (Mountain
> > > > > > > > > time). If those times don't work. I can get you
started
> > with
> > > > very
> > > > > > > > > specific instructions via email and we can continue
to work
> > > > through
> > > > > > any
> > > > > > > > > problems. We can also set up a different time for
next
> week,
> > > > > > however,
> > > > > > > I
> > > > > > > > > didn't want you to have to wait that long. Please
let me
> > know
> > > > your
> > > > > > > > > preference.
> > > > > > > > >
> > > > > > > > > If you think that icc may not be working properly,
then you
> > > > should
> > > > > > > > > probably use the GNU set of compilers, unless there
is some
> > > > reason
> > > > > > not
> > > > > > > > to,
> > > > > > > > > in which case you may need to get a system
administrator
> > > correct
> > > > > the
> > > > > > > > > problems with the intel compiler.
> > > > > > > > >
> > > > > > > > > Running "which g++" and running "which gfortran" can
tell
> you
> > > > what
> > > > > > the
> > > > > > > > CXX
> > > > > > > > > and F77 paths should be set to. Please let me know
if you
> > have
> > > > any
> > > > > > > > issues
> > > > > > > > > with that.
> > > > > > > > >
> > > > > > > > > Julie
> > > > > > > > >
> > > > > > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum
via RT <
> > > > > > > > > met_help at ucar.edu> wrote:
> > > > > > > > >
> > > > > > > > >>
> > > > > > > > >> <URL:
> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > >
> > > > > > > > >>
> > > > > > > > >> Hey Julie,
> > > > > > > > >>
> > > > > > > > >> 1) They were previously installed, but I just tried
> running
> > it
> > > > > with
> > > > > > > some
> > > > > > > > >> of
> > > > > > > > >> my own installed versions and they're not working
properly
> > > (e.g.
> > > > > the
> > > > > > > > make
> > > > > > > > >> install fails due to gsl/gsl_cdf.h missing...
though I set
> > > > MET_GSL
> > > > > > to
> > > > > > > my
> > > > > > > > >> gsl-2.5 directory).
> > > > > > > > >>
> > > > > > > > >> 2) Not sure how I can verify that one, though I
think
> > they're
> > > > not
> > > > > as
> > > > > > > > I've
> > > > > > > > >> seen GNU and Intel prompts in the config output. My
CC var
> > in
> > > my
> > > > > > > bashrc
> > > > > > > > >> links to an Intel compiler.
> > > > > > > > >>
> > > > > > > > >> 3) I followed those for the packages, though for
the
> > compilers
> > > > > > > section,
> > > > > > > > I
> > > > > > > > >> do not know my CXX or F77 paths on the hpc that I'm
> using. I
> > > > also
> > > > > > > think
> > > > > > > > >> the
> > > > > > > > >> icc is not working properly as I could not run icc
> without a
> > > > > license
> > > > > > > > >> prompt
> > > > > > > > >> coming up.
> > > > > > > > >>
> > > > > > > > >> I'm not sure if any of that helps, but let me know.
Maybe
> > some
> > > > of
> > > > > > > these
> > > > > > > > >> issues are still on our end. The fact that met
needs to
> only
> > > use
> > > > > one
> > > > > > > > >> compiler might be the issue...
> > > > > > > > >>
> > > > > > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik
via RT <
> > > > > > > > >> met_help at ucar.edu>
> > > > > > > > >> wrote:
> > > > > > > > >>
> > > > > > > > >> > Hi Taylor. Thank you for passing along your
files. I
> > have
> > > a
> > > > > few
> > > > > > > > >> questions
> > > > > > > > >> > for you.
> > > > > > > > >> >
> > > > > > > > >> > 1) Are you installing the external libraries
yourself or
> > > were
> > > > > they
> > > > > > > > >> > previously installed?
> > > > > > > > >> > 2) Can you please verify that the external
libraries and
> > MET
> > > > are
> > > > > > > being
> > > > > > > > >> > built with the same family of compilers (e.g. all
are
> > built
> > > > with
> > > > > > > GNU,
> > > > > > > > or
> > > > > > > > >> > all are build with Intel, etc.)? Which compiler
are you
> > > > using?
> > > > > > > > >> > 3) Are you following the directions on this page
as your
> > > > > > > instructions
> > > > > > > > >> for
> > > > > > > > >> > installation?
> > > > > > > > >> >
> > > > > > > > >> >
> > > > > > > > >>
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > > > > > >> >
> > > > > > > > >> > Thank you!
> > > > > > > > >> >
> > > > > > > > >> > Julie
> > > > > > > > >> >
> > > > > > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor Mandelbaum
via
> RT <
> > > > > > > > >> > met_help at ucar.edu>
> > > > > > > > >> > wrote:
> > > > > > > > >> >
> > > > > > > > >> > >
> > > > > > > > >> > > <URL:
> > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > >
> > > > > > > > >> > >
> > > > > > > > >> > > Hey Julie,
> > > > > > > > >> > >
> > > > > > > > >> > > I attached the config and make_install logs
here. We
> > could
> > > > do
> > > > > a
> > > > > > > > >> hangouts
> > > > > > > > >> > > session as well if you can't pinpoint the
issue; I'm
> > > > remoting
> > > > > in
> > > > > > > > from
> > > > > > > > >> my
> > > > > > > > >> > > home windows computer so it will be a bit
hacky.
> > > > > > > > >> > >
> > > > > > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie
Prestopnik via
> RT
> > <
> > > > > > > > >> > met_help at ucar.edu
> > > > > > > > >> > > >
> > > > > > > > >> > > wrote:
> > > > > > > > >> > >
> > > > > > > > >> > > > Hi Taylor. It is difficult to tell what is
going
> > > without
> > > > > more
> > > > > > > > >> context.
> > > > > > > > >> > > > Could you please send me your config.log file
and
> your
> > > > > > make.log
> > > > > > > > >> file?
> > > > > > > > >> > > >
> > > > > > > > >> > > > We could also consider doing a hangouts
session
> where
> > > you
> > > > > can
> > > > > > > > share
> > > > > > > > >> > your
> > > > > > > > >> > > > screen, and I can directly help that way.
Either
> way
> > > > > though,
> > > > > > if
> > > > > > > > you
> > > > > > > > >> > > could
> > > > > > > > >> > > > please send those files, I would appreciate
it.
> > > > > > > > >> > > >
> > > > > > > > >> > > > Thanks,
> > > > > > > > >> > > > Julie
> > > > > > > > >> > > >
> > > > > > > > >> > > > Thanks!
> > > > > > > > >> > > >
> > > > > > > > >> > > > Julie
> > > > > > > > >> > > >
> > > > > > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor
Mandelbaum
> via
> > > RT <
> > > > > > > > >> > > > met_help at ucar.edu>
> > > > > > > > >> > > > wrote:
> > > > > > > > >> > > >
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502 was
acted
> > > upon.
> > > > > > > > >> > > > > Transaction: Ticket created by
> > > > > > > taylor.mandelbaum at stonybrook.edu
> > > > > > > > >> > > > > Queue: met_help
> > > > > > > > >> > > > > Subject: met install help
> > > > > > > > >> > > > > Owner: Nobody
> > > > > > > > >> > > > > Requestors:
taylor.mandelbaum at stonybrook.edu
> > > > > > > > >> > > > > Status: new
> > > > > > > > >> > > > > Ticket <URL:
> > > > > > > > >> >
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > > >> > > >
> > > > > > > > >> > > > >
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > Hey all,
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > I'm presently trying to compile MET 8.0 on
our
> HPC;
> > > > when I
> > > > > > > > >> configure
> > > > > > > > >> > > it,
> > > > > > > > >> > > > > I'm getting a few warnings on .h files:
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > configure: WARNING: errno.h: present but
cannot be
> > > > > compiled
> > > > > > > > >> > > > > configure: WARNING: errno.h: check for
missing
> > > > > > > prerequisite
> > > > > > > > >> > > headers?
> > > > > > > > >> > > > > configure: WARNING: errno.h: see the
Autoconf
> > > > > documentation
> > > > > > > > >> > > > > configure: WARNING: errno.h: section
"Present
> > But
> > > > > Cannot
> > > > > > > Be
> > > > > > > > >> > > Compiled"
> > > > > > > > >> > > > > configure: WARNING: errno.h: proceeding
with the
> > > > > compiler's
> > > > > > > > result
> > > > > > > > >> > > > > configure: WARNING: ##
> > > > > --------------------------------
> > > > > > ##
> > > > > > > > >> > > > > configure: WARNING: ## Report this to
> > > > > met_help at ucar.edu
> > > > > > > ##
> > > > > > > > >> > > > > configure: WARNING: ##
> > > > > --------------------------------
> > > > > > ##
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > and the same for fcntl.h, limits.h,
stddef.h,
> file.h
> > > and
> > > > > > > > param.h.
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > When I try to make install, I get this
error on
> the
> > > tail
> > > > > of
> > > > > > > the
> > > > > > > > >> log:
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > > configalloc(yy_size_t)’:
> > > > > > > > >> > > > > config_scanner.cc:2179:31: error:
‘rpl_malloc’ was
> > not
> > > > > > > declared
> > > > > > > > in
> > > > > > > > >> > this
> > > > > > > > >> > > > > scope
> > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > configrealloc(void*,
> > > > > > > > >> > yy_size_t)’:
> > > > > > > > >> > > > > config_scanner.cc:2191:46: error:
‘rpl_realloc’
> was
> > > not
> > > > > > > declared
> > > > > > > > >> in
> > > > > > > > >> > > this
> > > > > > > > >> > > > > scope
> > > > > > > > >> > > > > /* The cast to (char *) in the following
> > > accommodates
> > > > > both
> > > > > > > > >> > > > >
^
> > > > > > > > >> > > > > make[3]: *** [libvx_config_a-
config_scanner.o]
> > Error 1
> > > > > > > > >> > > > > make[3]: Leaving directory
> > > > > > > > >> > > > >
> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > > > > > > >> > > > > make[2]: *** [install-recursive] Error 1
> > > > > > > > >> > > > > make[2]: Leaving directory
> > > > > > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > > > > > >> > > > > make[1]: *** [install-recursive] Error 1
> > > > > > > > >> > > > > make[1]: Leaving directory
> > > > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > > > > > >> > > > > make: *** [install-recursive] Error 1
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > Not sure how to address either of these,
hopefully
> > you
> > > > > guys
> > > > > > > can
> > > > > > > > >> > provide
> > > > > > > > >> > > > > some insight.
> > > > > > > > >> > > > >
> > > > > > > > >> > > > > Thanks!
> > > > > > > > >> > > > > --
> > > > > > > > >> > > > > *Taylor Mandelbaum*
> > > > > > > > >> > > > > Research Technician
> > > > > > > > >> > > > > SoMAS | Stony Brook University
> > > > > > > > >> > > > > 678.468.5789
> > > > > > > > >> > > > >
> > > > > > > > >> > > > >
> > > > > > > > >> > > >
> > > > > > > > >> > > >
> > > > > > > > >> > >
> > > > > > > > >> > > --
> > > > > > > > >> > > *Taylor Mandelbaum*
> > > > > > > > >> > > Research Technician
> > > > > > > > >> > > SoMAS | Stony Brook University
> > > > > > > > >> > > 678.468.5789
> > > > > > > > >> > >
> > > > > > > > >> > >
> > > > > > > > >> >
> > > > > > > > >> >
> > > > > > > > >>
> > > > > > > > >> --
> > > > > > > > >> *Taylor Mandelbaum*
> > > > > > > > >> Research Technician
> > > > > > > > >> SoMAS | Stony Brook University
> > > > > > > > >> 678.468.5789
> > > > > > > > >>
> > > > > > > > >>
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > *Taylor Mandelbaum*
> > > > > > > Research Technician
> > > > > > > SoMAS | Stony Brook University
> > > > > > > 678.468.5789
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > > --
> > > > > *Taylor Mandelbaum*
> > > > > Research Technician
> > > > > SoMAS | Stony Brook University
> > > > > 678.468.5789
> > > > >
> > > > >
> > > >
> > > >
> > >
> > > --
> > > *Taylor Mandelbaum*
> > > Research Technician
> > > SoMAS | Stony Brook University
> > > 678.468.5789
> > >
> > >
> >
> >
>
> --
> *Taylor Mandelbaum*
> Research Technician
> SoMAS | Stony Brook University
> 678.468.5789
>
>
------------------------------------------------
Subject: met install help
From: Taylor Mandelbaum
Time: Wed Feb 20 12:37:10 2019
That solved that problem, onto the next one:
nc_utils.h:22:18: fatal error: netcdf: No such file or directory
I had installed netcdf 4.6.2 most recently and netcdfcxx 4.3.0, so I'm
not
sure what this is about.
On Wed, Feb 20, 2019 at 2:12 PM Julie Prestopnik via RT
<met_help at ucar.edu>
wrote:
> Hi Taylor.
>
> I see the following in your config.log file:
>
> /usr/bin/ld: cannot find -lpython2.7-lpthread
>
> It looks like MET_PYTHON_LD was set in the following way:
>
> MET_PYTHON_LD='-L/cm/shared/apps/python/2.7.15/lib -lpython2.7-
lpthread
> > -ldl -lutil -lm -Xlinker -export-dynamic'
> >
>
> Note, the lack of space between "-lpython2.7" and "-lpthread" in
both the
> error message and the setting of MET_PYTHON_LD.
>
> Please copy and paste the following:
>
> for csh:
> >
> > setenv MET_PYTHON_LD -L/cm/shared/apps/python/2.7.15/lib\
-lpython2.7\
> > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> >
> > for bash:
> >
> > export MET_PYTHON_LD=-L/cm/shared/apps/python/2.7.15/lib\
-lpython2.7\
> > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
>
>
> Those lines should capture the proper spaces.
>
> Give that a try and reconfigure MET. Please let me know how it goes.
> Thanks!
>
> Julie
>
> On Tue, Feb 19, 2019 at 6:11 PM Taylor Mandelbaum via RT <
> met_help at ucar.edu>
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> >
> > Hey Julie,
> >
> > I set those up in my bashrc but am still having an issue with the
config
> > not proceeding due to the c++ compiler:
> >
> > "checking whether the C++ compiler works... no
> > configure: error: in `/home/taylorm/MET8/met-8.0_bugfix':
> > configure: error: C++ compiler cannot create executables"
> >
> > attached the most recent config log.
> >
> > Thanks again!
> >
> > On Tue, Feb 19, 2019 at 12:47 PM Julie Prestopnik via RT <
> > met_help at ucar.edu>
> > wrote:
> >
> > > Hi Taylor,
> > >
> > > Great! Thanks for the update. Please try setting the
following:
> > >
> > > or csh:
> > >
> > > setenv MET_PYTHON_CC `python-config --cflags`
> > > setenv MET_PYTHON_LD -L/cm/shared/apps/python/2.7.15/lib\
-lpython2.7\
> > > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> > >
> > > for bash:
> > >
> > > export MET_PYTHON_CC=`python-config --cflags`
> > > export MET_PYTHON_LD=-L/cm/shared/apps/python/2.7.15/lib\
-lpython2.7\
> > > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> > >
> > > Please set up your other environment variables and then try
> reconfiguring
> > > and reinstalling MET. Please let me know how it goes.
> > >
> > > Thanks,
> > > Julie
> > >
> > > On Sat, Feb 16, 2019 at 2:36 PM Taylor Mandelbaum via RT <
> > > met_help at ucar.edu>
> > > wrote:
> > >
> > > >
> > > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
>
> > > >
> > > > Hey Julie,
> > > >
> > > > The libpython2.7.so file is in the first directory you
> > > > mentioned, /cm/shared/apps/python/2.7.15/lib.
> > > >
> > > > Sorry for the delay, busy week this week.
> > > >
> > > > On Mon, Feb 11, 2019 at 1:28 PM Julie Prestopnik via RT <
> > > met_help at ucar.edu
> > > > >
> > > > wrote:
> > > >
> > > > > Hi Taylor. Thanks for the update. I'm glad we are making
some
> > > progress.
> > > > >
> > > > > From your config.log file:
> > > > >
> > > > > > /usr/bin/ld: cannot find -lpython2.7
> > > > > > collect2: error: ld returned 1 exit status
> > > > > >
> > > > > and from the output you provided from running "python-config
> > > --ldflags",
> > > > I
> > > > > can see what the problem is.
> > > > >
> > > > > It looks like the output "python-config --ldflags"
unfortunately
> does
> > > not
> > > > > contain all of the information that the environment variable
> > > > MET_PYTHON_LD
> > > > > needs to have.
> > > > >
> > > > > In order to proceed, we need to find the location of the
> libpython.a
> > > file
> > > > > or the libpython.so file. Based on the information from the
output
> > > from
> > > > > running "python-config --cflags", I am going to guess that
the
> > > libpython
> > > > > file lives in /cm/shared/apps/python/2.7.15/lib or in
> > > > > /cm/shared/apps/python/2.7.15/lib/python2.7. Could you
please
> check
> > > > those
> > > > > directories and see if you can find a libpython.a file or
> > libpython.so
> > > > > file? If so, please send me an email with the path to the
file.
> You
> > > > could
> > > > > just run "ls <path>" replacing <path> with the full path and
send
> me
> > > the
> > > > > output. Then, I will send you a command that you can run to
set
> the
> > > > value
> > > > > of the environment variable MET_PYTHON_LD.
> > > > >
> > > > > Thanks!
> > > > >
> > > > > Julie
> > > > >
> > > > > On Tue, Feb 5, 2019 at 7:16 PM Taylor Mandelbaum via RT <
> > > > met_help at ucar.edu
> > > > > >
> > > > > wrote:
> > > > >
> > > > > >
> > > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > > >
> > > > > > Hey Julie,
> > > > > >
> > > > > > Sorry for the delayed response. We got python 2.7.15 set
up as a
> > > > module.
> > > > > I
> > > > > > ran python2.7-config --cflags and ..--ldflags:
> > > > > >
> > > > > > -I/cm/shared/apps/python/2.7.15/include/python2.7
> > > > > > -I/cm/shared/apps/python/2.7.15/include/python2.7
> > > -fno-strict-aliasing
> > > > -g
> > > > > > -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
> > > > > >
> > > > > > -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-
dynamic
> > > > > >
> > > > > > Those are the returned outputs. I updated my bashrc with
module
> > load
> > > > > > python/2.7; same issue is occurring with c++. Attached the
config
> > > log.
> > > > > >
> > > > > > Thanks again for your help.
> > > > > >
> > > > > > On Mon, Jan 28, 2019 at 1:43 PM Julie Prestopnik via RT <
> > > > > met_help at ucar.edu
> > > > > > >
> > > > > > wrote:
> > > > > >
> > > > > > > Hi Taylor.
> > > > > > >
> > > > > > > Thanks for getting HDF5 and NetCDF4 C and C++ installed.
> > > > > > >
> > > > > > > Thank you also for attaching your config.log file. I
see in
> your
> > > > > > > config.log file:
> > > > > > >
> > > > > > > > /cm/shared/apps/python/3.5.2/include/python3.5m: file
not
> > > > recognized:
> > > > > > Is
> > > > > > > a
> > > > > > > > directory
> > > > > > > >
> > > > > > > collect2: error: ld returned 1 exit status
> > > > > > > >
> > > > > > >
> > > > > > > It looks like there is a problem with the linker in that
it is
> > > > finding
> > > > > a
> > > > > > > directory instead of a file. However, before we
proceed, I
> > should
> > > > tell
> > > > > > you
> > > > > > > that the Python functionality with met-8.0 requires
Python 2.7
> to
> > > be
> > > > > > used.
> > > > > > > Is Python 2.7 available on your system? If so, please
let me
> > know.
> > > > > > >
> > > > > > > I can help you set up the necessary environment
variables that
> > are
> > > > > > required
> > > > > > > to use the python embedding functionality. You'll need
to set
> > > > > > > MET_PYTHON_CC and MET_PYTHON_LD prior to configuring
MET.
> > Usually
> > > > the
> > > > > > > following is sufficient for csh:
> > > > > > >
> > > > > > > setenv MET_PYTHON_CC `python-config --cflags`
> > > > > > >
> > > > > > > setenv MET_PYTHON_LD `python-config --ldflags`
> > > > > > >
> > > > > > > for bash:
> > > > > > >
> > > > > > > export MET_PYTHON_CC=`python-config --cflags`
> > > > > > >
> > > > > > > export MET_PYTHON_LD=`python-config --ldflags`
> > > > > > >
> > > > > > > However, it may not be. Please run the following
commands
> (using
> > > > > Python
> > > > > > > 2.7) and send me the output:
> > > > > > >
> > > > > > > python-config --cflags
> > > > > > > python-config --ldflags
> > > > > > >
> > > > > > > Thanks!
> > > > > > >
> > > > > > > Julie
> > > > > > >
> > > > > > > On Sun, Jan 27, 2019 at 9:11 AM Taylor Mandelbaum via RT
<
> > > > > > > met_help at ucar.edu>
> > > > > > > wrote:
> > > > > > >
> > > > > > > >
> > > > > > > > <URL:
> https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > >
> > > > > > > >
> > > > > > > > Hey all,
> > > > > > > >
> > > > > > > > I got netcdf4 c and c++ installed; I'm running into an
issue
> > now
> > > on
> > > > > > > > configuring MET which says error: C++ compiler cannot
create
> > > > > > executables.
> > > > > > > > It looks like in the config log that g++ is getting
imported
> > but
> > > > > > erroring
> > > > > > > > out when trying to use -V as a command option.
Attached the
> > > newest
> > > > > > config
> > > > > > > > log here.
> > > > > > > >
> > > > > > > > When I configure it, this is the command I'm using:
> > > > > > > >
> > > > > > > > ./configure --prefix=/E1/taylorm/MET8 --enable-grib2
> > > > --enable-python
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik via
RT <
> > > > > > > > met_help at ucar.edu>
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > > Hi Taylor. In talking with more with John about
your
> > > config.log
> > > > > file
> > > > > > > we
> > > > > > > > > see that CC is set to use icc (intel), but CXX and
F77 are
> > set
> > > to
> > > > > use
> > > > > > > g++
> > > > > > > > > and gfortran (GNU).
> > > > > > > > >
> > > > > > > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > > > > > > >
> > > > > > >
> > > > >
> > >
>
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > > > > > > CXX='g++'
> > > > > > > > > F77='gfortran'
> > > > > > > > >
> > > > > > > > > Let's see if we can solve the immediate problem
before
> > worrying
> > > > > about
> > > > > > > any
> > > > > > > > > potential problems with the external libraries. For
now,
> > > please
> > > > > > choose
> > > > > > > > > either the GNU compilers or the Intel compilers and
set the
> > > > > following
> > > > > > > > > variables accordingly. You can chose one and then
simply
> run
> > > the
> > > > > > > > commands
> > > > > > > > > below.
> > > > > > > > >
> > > > > > > > > *For GNU:*
> > > > > > > > > export CC=`which gcc`
> > > > > > > > > export CXX=`which g++`
> > > > > > > > > export F77=`which gfortran`
> > > > > > > > >
> > > > > > > > > *For Intel:*
> > > > > > > > >
> > > > > > > > > export CC=`which icc`
> > > > > > > > > export CXX=`which icc`
> > > > > > > > > export F77=`which ifort`
> > > > > > > > >
> > > > > > > > > Then run "make clean", rerun the configure command,
and
> then
> > > try
> > > > to
> > > > > > > make
> > > > > > > > > MET again.
> > > > > > > > >
> > > > > > > > > Let's go from there and see how it works out.
Please let
> me
> > > > know.
> > > > > > > > >
> > > > > > > > > Julie
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik <
> > > > > jpresto at ucar.edu>
> > > > > > > > > wrote:
> > > > > > > > >
> > > > > > > > > > Hi Taylor. Thank you for all of this information.
> > > > > > > > > >
> > > > > > > > > > Since the libraries were previously installed and
we
> cannot
> > > be
> > > > > > > certain
> > > > > > > > > > which compiler was used, are you able and would
you be
> > > > > comfortable
> > > > > > > > > > installing each of the dependent libraries and not
using
> > the
> > > > > > > previously
> > > > > > > > > > installed versions? If so, we have an install
script
> that
> > I
> > > > can
> > > > > > > point
> > > > > > > > > you
> > > > > > > > > > to, which would install all of the packages and
MET as
> > > well. I
> > > > > can
> > > > > > > > walk
> > > > > > > > > > through this with you via google hangouts and you
can
> share
> > > > your
> > > > > > > screen
> > > > > > > > > so
> > > > > > > > > > we can make sure it is going smoothly. I could
do a
> > > hangouts
> > > > > > > session
> > > > > > > > > with
> > > > > > > > > > you tomorrow at 1:15pm (Mountain time) or on
Friday at
> > 9:00am
> > > > > > > (Mountain
> > > > > > > > > > time). If those times don't work. I can get you
started
> > > with
> > > > > very
> > > > > > > > > > specific instructions via email and we can
continue to
> work
> > > > > through
> > > > > > > any
> > > > > > > > > > problems. We can also set up a different time for
next
> > week,
> > > > > > > however,
> > > > > > > > I
> > > > > > > > > > didn't want you to have to wait that long. Please
let me
> > > know
> > > > > your
> > > > > > > > > > preference.
> > > > > > > > > >
> > > > > > > > > > If you think that icc may not be working properly,
then
> you
> > > > > should
> > > > > > > > > > probably use the GNU set of compilers, unless
there is
> some
> > > > > reason
> > > > > > > not
> > > > > > > > > to,
> > > > > > > > > > in which case you may need to get a system
administrator
> > > > correct
> > > > > > the
> > > > > > > > > > problems with the intel compiler.
> > > > > > > > > >
> > > > > > > > > > Running "which g++" and running "which gfortran"
can tell
> > you
> > > > > what
> > > > > > > the
> > > > > > > > > CXX
> > > > > > > > > > and F77 paths should be set to. Please let me
know if
> you
> > > have
> > > > > any
> > > > > > > > > issues
> > > > > > > > > > with that.
> > > > > > > > > >
> > > > > > > > > > Julie
> > > > > > > > > >
> > > > > > > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor Mandelbaum
via RT
> <
> > > > > > > > > > met_help at ucar.edu> wrote:
> > > > > > > > > >
> > > > > > > > > >>
> > > > > > > > > >> <URL:
> > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > >
> > > > > > > > > >>
> > > > > > > > > >> Hey Julie,
> > > > > > > > > >>
> > > > > > > > > >> 1) They were previously installed, but I just
tried
> > running
> > > it
> > > > > > with
> > > > > > > > some
> > > > > > > > > >> of
> > > > > > > > > >> my own installed versions and they're not working
> properly
> > > > (e.g.
> > > > > > the
> > > > > > > > > make
> > > > > > > > > >> install fails due to gsl/gsl_cdf.h missing...
though I
> set
> > > > > MET_GSL
> > > > > > > to
> > > > > > > > my
> > > > > > > > > >> gsl-2.5 directory).
> > > > > > > > > >>
> > > > > > > > > >> 2) Not sure how I can verify that one, though I
think
> > > they're
> > > > > not
> > > > > > as
> > > > > > > > > I've
> > > > > > > > > >> seen GNU and Intel prompts in the config output.
My CC
> var
> > > in
> > > > my
> > > > > > > > bashrc
> > > > > > > > > >> links to an Intel compiler.
> > > > > > > > > >>
> > > > > > > > > >> 3) I followed those for the packages, though for
the
> > > compilers
> > > > > > > > section,
> > > > > > > > > I
> > > > > > > > > >> do not know my CXX or F77 paths on the hpc that
I'm
> > using. I
> > > > > also
> > > > > > > > think
> > > > > > > > > >> the
> > > > > > > > > >> icc is not working properly as I could not run
icc
> > without a
> > > > > > license
> > > > > > > > > >> prompt
> > > > > > > > > >> coming up.
> > > > > > > > > >>
> > > > > > > > > >> I'm not sure if any of that helps, but let me
know.
> Maybe
> > > some
> > > > > of
> > > > > > > > these
> > > > > > > > > >> issues are still on our end. The fact that met
needs to
> > only
> > > > use
> > > > > > one
> > > > > > > > > >> compiler might be the issue...
> > > > > > > > > >>
> > > > > > > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie Prestopnik
via
> RT <
> > > > > > > > > >> met_help at ucar.edu>
> > > > > > > > > >> wrote:
> > > > > > > > > >>
> > > > > > > > > >> > Hi Taylor. Thank you for passing along your
files. I
> > > have
> > > > a
> > > > > > few
> > > > > > > > > >> questions
> > > > > > > > > >> > for you.
> > > > > > > > > >> >
> > > > > > > > > >> > 1) Are you installing the external libraries
yourself
> or
> > > > were
> > > > > > they
> > > > > > > > > >> > previously installed?
> > > > > > > > > >> > 2) Can you please verify that the external
libraries
> and
> > > MET
> > > > > are
> > > > > > > > being
> > > > > > > > > >> > built with the same family of compilers (e.g.
all are
> > > built
> > > > > with
> > > > > > > > GNU,
> > > > > > > > > or
> > > > > > > > > >> > all are build with Intel, etc.)? Which
compiler are
> you
> > > > > using?
> > > > > > > > > >> > 3) Are you following the directions on this
page as
> your
> > > > > > > > instructions
> > > > > > > > > >> for
> > > > > > > > > >> > installation?
> > > > > > > > > >> >
> > > > > > > > > >> >
> > > > > > > > > >>
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > > > > > > >> >
> > > > > > > > > >> > Thank you!
> > > > > > > > > >> >
> > > > > > > > > >> > Julie
> > > > > > > > > >> >
> > > > > > > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor
Mandelbaum via
> > RT <
> > > > > > > > > >> > met_help at ucar.edu>
> > > > > > > > > >> > wrote:
> > > > > > > > > >> >
> > > > > > > > > >> > >
> > > > > > > > > >> > > <URL:
> > > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > >
> > > > > > > > > >> > >
> > > > > > > > > >> > > Hey Julie,
> > > > > > > > > >> > >
> > > > > > > > > >> > > I attached the config and make_install logs
here. We
> > > could
> > > > > do
> > > > > > a
> > > > > > > > > >> hangouts
> > > > > > > > > >> > > session as well if you can't pinpoint the
issue; I'm
> > > > > remoting
> > > > > > in
> > > > > > > > > from
> > > > > > > > > >> my
> > > > > > > > > >> > > home windows computer so it will be a bit
hacky.
> > > > > > > > > >> > >
> > > > > > > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie
Prestopnik via
> > RT
> > > <
> > > > > > > > > >> > met_help at ucar.edu
> > > > > > > > > >> > > >
> > > > > > > > > >> > > wrote:
> > > > > > > > > >> > >
> > > > > > > > > >> > > > Hi Taylor. It is difficult to tell what is
going
> > > > without
> > > > > > more
> > > > > > > > > >> context.
> > > > > > > > > >> > > > Could you please send me your config.log
file and
> > your
> > > > > > > make.log
> > > > > > > > > >> file?
> > > > > > > > > >> > > >
> > > > > > > > > >> > > > We could also consider doing a hangouts
session
> > where
> > > > you
> > > > > > can
> > > > > > > > > share
> > > > > > > > > >> > your
> > > > > > > > > >> > > > screen, and I can directly help that way.
Either
> > way
> > > > > > though,
> > > > > > > if
> > > > > > > > > you
> > > > > > > > > >> > > could
> > > > > > > > > >> > > > please send those files, I would appreciate
it.
> > > > > > > > > >> > > >
> > > > > > > > > >> > > > Thanks,
> > > > > > > > > >> > > > Julie
> > > > > > > > > >> > > >
> > > > > > > > > >> > > > Thanks!
> > > > > > > > > >> > > >
> > > > > > > > > >> > > > Julie
> > > > > > > > > >> > > >
> > > > > > > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor
Mandelbaum
> > via
> > > > RT <
> > > > > > > > > >> > > > met_help at ucar.edu>
> > > > > > > > > >> > > > wrote:
> > > > > > > > > >> > > >
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502
was
> acted
> > > > upon.
> > > > > > > > > >> > > > > Transaction: Ticket created by
> > > > > > > > taylor.mandelbaum at stonybrook.edu
> > > > > > > > > >> > > > > Queue: met_help
> > > > > > > > > >> > > > > Subject: met install help
> > > > > > > > > >> > > > > Owner: Nobody
> > > > > > > > > >> > > > > Requestors:
taylor.mandelbaum at stonybrook.edu
> > > > > > > > > >> > > > > Status: new
> > > > > > > > > >> > > > > Ticket <URL:
> > > > > > > > > >> >
> https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > > > >> > > >
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > Hey all,
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > I'm presently trying to compile MET 8.0
on our
> > HPC;
> > > > > when I
> > > > > > > > > >> configure
> > > > > > > > > >> > > it,
> > > > > > > > > >> > > > > I'm getting a few warnings on .h files:
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > configure: WARNING: errno.h: present but
cannot
> be
> > > > > > compiled
> > > > > > > > > >> > > > > configure: WARNING: errno.h: check
for
> missing
> > > > > > > > prerequisite
> > > > > > > > > >> > > headers?
> > > > > > > > > >> > > > > configure: WARNING: errno.h: see the
Autoconf
> > > > > > documentation
> > > > > > > > > >> > > > > configure: WARNING: errno.h: section
> "Present
> > > But
> > > > > > Cannot
> > > > > > > > Be
> > > > > > > > > >> > > Compiled"
> > > > > > > > > >> > > > > configure: WARNING: errno.h: proceeding
with the
> > > > > > compiler's
> > > > > > > > > result
> > > > > > > > > >> > > > > configure: WARNING: ##
> > > > > > --------------------------------
> > > > > > > ##
> > > > > > > > > >> > > > > configure: WARNING: ## Report this to
> > > > > > met_help at ucar.edu
> > > > > > > > ##
> > > > > > > > > >> > > > > configure: WARNING: ##
> > > > > > --------------------------------
> > > > > > > ##
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > and the same for fcntl.h, limits.h,
stddef.h,
> > file.h
> > > > and
> > > > > > > > > param.h.
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > When I try to make install, I get this
error on
> > the
> > > > tail
> > > > > > of
> > > > > > > > the
> > > > > > > > > >> log:
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > > > configalloc(yy_size_t)’:
> > > > > > > > > >> > > > > config_scanner.cc:2179:31: error:
‘rpl_malloc’
> was
> > > not
> > > > > > > > declared
> > > > > > > > > in
> > > > > > > > > >> > this
> > > > > > > > > >> > > > > scope
> > > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > configrealloc(void*,
> > > > > > > > > >> > yy_size_t)’:
> > > > > > > > > >> > > > > config_scanner.cc:2191:46: error:
‘rpl_realloc’
> > was
> > > > not
> > > > > > > > declared
> > > > > > > > > >> in
> > > > > > > > > >> > > this
> > > > > > > > > >> > > > > scope
> > > > > > > > > >> > > > > /* The cast to (char *) in the
following
> > > > accommodates
> > > > > > both
> > > > > > > > > >> > > > >
^
> > > > > > > > > >> > > > > make[3]: *** [libvx_config_a-
config_scanner.o]
> > > Error 1
> > > > > > > > > >> > > > > make[3]: Leaving directory
> > > > > > > > > >> > > > >
> > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > > > > > > > >> > > > > make[2]: *** [install-recursive] Error 1
> > > > > > > > > >> > > > > make[2]: Leaving directory
> > > > > > > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > > > > > > >> > > > > make[1]: *** [install-recursive] Error 1
> > > > > > > > > >> > > > > make[1]: Leaving directory
> > > > > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > > > > > > >> > > > > make: *** [install-recursive] Error 1
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > Not sure how to address either of these,
> hopefully
> > > you
> > > > > > guys
> > > > > > > > can
> > > > > > > > > >> > provide
> > > > > > > > > >> > > > > some insight.
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > > Thanks!
> > > > > > > > > >> > > > > --
> > > > > > > > > >> > > > > *Taylor Mandelbaum*
> > > > > > > > > >> > > > > Research Technician
> > > > > > > > > >> > > > > SoMAS | Stony Brook University
> > > > > > > > > >> > > > > 678.468.5789
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > > >
> > > > > > > > > >> > > >
> > > > > > > > > >> > > >
> > > > > > > > > >> > >
> > > > > > > > > >> > > --
> > > > > > > > > >> > > *Taylor Mandelbaum*
> > > > > > > > > >> > > Research Technician
> > > > > > > > > >> > > SoMAS | Stony Brook University
> > > > > > > > > >> > > 678.468.5789
> > > > > > > > > >> > >
> > > > > > > > > >> > >
> > > > > > > > > >> >
> > > > > > > > > >> >
> > > > > > > > > >>
> > > > > > > > > >> --
> > > > > > > > > >> *Taylor Mandelbaum*
> > > > > > > > > >> Research Technician
> > > > > > > > > >> SoMAS | Stony Brook University
> > > > > > > > > >> 678.468.5789
> > > > > > > > > >>
> > > > > > > > > >>
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > > *Taylor Mandelbaum*
> > > > > > > > Research Technician
> > > > > > > > SoMAS | Stony Brook University
> > > > > > > > 678.468.5789
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > > > --
> > > > > > *Taylor Mandelbaum*
> > > > > > Research Technician
> > > > > > SoMAS | Stony Brook University
> > > > > > 678.468.5789
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > > > --
> > > > *Taylor Mandelbaum*
> > > > Research Technician
> > > > SoMAS | Stony Brook University
> > > > 678.468.5789
> > > >
> > > >
> > >
> > >
> >
> > --
> > *Taylor Mandelbaum*
> > Research Technician
> > SoMAS | Stony Brook University
> > 678.468.5789
> >
> >
>
>
--
*Taylor Mandelbaum*
Research Technician
SoMAS | Stony Brook University
678.468.5789
------------------------------------------------
Subject: met install help
From: Julie Prestopnik
Time: Wed Feb 20 14:59:04 2019
Hi Taylor, for met-8.0 both the NetCDF-C package and the NetCDF-CXX
package
are required. I see you said that you have installed version 4.6.2
for
NetCDF-C and version 4.3.0 for NetCDF-CXX. I usually install netcdf
-c-4.4.1.1and netcdf-cxx4-4.3.0, but don't think that other versions
should
be a problem.
The error you received:
nc_utils.h:22:18: error: netcdf: No such file or directory
>
indicates that MET is having a difficult time finding the file
"netcdf",
which is included in the NetCDF-CXX installation.
I see that you have MET_NETCDF set to /E1/taylorm/netcdf462. It is
important to note that there is only one MET_NETCDF environment
variable,
so both NetCDF packages are expected to be installed at the same
location.
Is the file "netcdf" located at $MET_NETCDF/include/
(/E1/taylorm/netcdf462/include)?
Here is a quick reference checklist for NetCDF4 installation that you
can
use to see if you have the necessary files:
Files for NetCDF4 C:
$MET_NETCDF/include/netcdf.h
$MET_NETCDF/lib/libnetcdf.a
$MET_NETCDF/lib/libnetcdf.so
Files for NetCDF4 C++:
$MET_NETCDF/include/netcdf
$MET_NETCDF/lib/libnetcdf_c++4.a
$MET_NETCDF/lib/libnetcdf_c++4.so
I hope that helps. Please let me know if you have any questions.
Thanks,
Julie
On Wed, Feb 20, 2019 at 12:37 PM Taylor Mandelbaum via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> That solved that problem, onto the next one:
>
> nc_utils.h:22:18: fatal error: netcdf: No such file or directory
>
> I had installed netcdf 4.6.2 most recently and netcdfcxx 4.3.0, so
I'm not
> sure what this is about.
>
>
> On Wed, Feb 20, 2019 at 2:12 PM Julie Prestopnik via RT
<met_help at ucar.edu
> >
> wrote:
>
> > Hi Taylor.
> >
> > I see the following in your config.log file:
> >
> > /usr/bin/ld: cannot find -lpython2.7-lpthread
> >
> > It looks like MET_PYTHON_LD was set in the following way:
> >
> > MET_PYTHON_LD='-L/cm/shared/apps/python/2.7.15/lib -lpython2.7-
lpthread
> > > -ldl -lutil -lm -Xlinker -export-dynamic'
> > >
> >
> > Note, the lack of space between "-lpython2.7" and "-lpthread" in
both
> the
> > error message and the setting of MET_PYTHON_LD.
> >
> > Please copy and paste the following:
> >
> > for csh:
> > >
> > > setenv MET_PYTHON_LD -L/cm/shared/apps/python/2.7.15/lib\
-lpython2.7\
> > > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> > >
> > > for bash:
> > >
> > > export MET_PYTHON_LD=-L/cm/shared/apps/python/2.7.15/lib\
-lpython2.7\
> > > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> >
> >
> > Those lines should capture the proper spaces.
> >
> > Give that a try and reconfigure MET. Please let me know how it
goes.
> > Thanks!
> >
> > Julie
> >
> > On Tue, Feb 19, 2019 at 6:11 PM Taylor Mandelbaum via RT <
> > met_help at ucar.edu>
> > wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > >
> > > Hey Julie,
> > >
> > > I set those up in my bashrc but am still having an issue with
the
> config
> > > not proceeding due to the c++ compiler:
> > >
> > > "checking whether the C++ compiler works... no
> > > configure: error: in `/home/taylorm/MET8/met-8.0_bugfix':
> > > configure: error: C++ compiler cannot create executables"
> > >
> > > attached the most recent config log.
> > >
> > > Thanks again!
> > >
> > > On Tue, Feb 19, 2019 at 12:47 PM Julie Prestopnik via RT <
> > > met_help at ucar.edu>
> > > wrote:
> > >
> > > > Hi Taylor,
> > > >
> > > > Great! Thanks for the update. Please try setting the
following:
> > > >
> > > > or csh:
> > > >
> > > > setenv MET_PYTHON_CC `python-config --cflags`
> > > > setenv MET_PYTHON_LD -L/cm/shared/apps/python/2.7.15/lib\
> -lpython2.7\
> > > > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> > > >
> > > > for bash:
> > > >
> > > > export MET_PYTHON_CC=`python-config --cflags`
> > > > export MET_PYTHON_LD=-L/cm/shared/apps/python/2.7.15/lib\
> -lpython2.7\
> > > > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> > > >
> > > > Please set up your other environment variables and then try
> > reconfiguring
> > > > and reinstalling MET. Please let me know how it goes.
> > > >
> > > > Thanks,
> > > > Julie
> > > >
> > > > On Sat, Feb 16, 2019 at 2:36 PM Taylor Mandelbaum via RT <
> > > > met_help at ucar.edu>
> > > > wrote:
> > > >
> > > > >
> > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > >
> > > > > Hey Julie,
> > > > >
> > > > > The libpython2.7.so file is in the first directory you
> > > > > mentioned, /cm/shared/apps/python/2.7.15/lib.
> > > > >
> > > > > Sorry for the delay, busy week this week.
> > > > >
> > > > > On Mon, Feb 11, 2019 at 1:28 PM Julie Prestopnik via RT <
> > > > met_help at ucar.edu
> > > > > >
> > > > > wrote:
> > > > >
> > > > > > Hi Taylor. Thanks for the update. I'm glad we are making
some
> > > > progress.
> > > > > >
> > > > > > From your config.log file:
> > > > > >
> > > > > > > /usr/bin/ld: cannot find -lpython2.7
> > > > > > > collect2: error: ld returned 1 exit status
> > > > > > >
> > > > > > and from the output you provided from running "python-
config
> > > > --ldflags",
> > > > > I
> > > > > > can see what the problem is.
> > > > > >
> > > > > > It looks like the output "python-config --ldflags"
unfortunately
> > does
> > > > not
> > > > > > contain all of the information that the environment
variable
> > > > > MET_PYTHON_LD
> > > > > > needs to have.
> > > > > >
> > > > > > In order to proceed, we need to find the location of the
> > libpython.a
> > > > file
> > > > > > or the libpython.so file. Based on the information from
the
> output
> > > > from
> > > > > > running "python-config --cflags", I am going to guess that
the
> > > > libpython
> > > > > > file lives in /cm/shared/apps/python/2.7.15/lib or in
> > > > > > /cm/shared/apps/python/2.7.15/lib/python2.7. Could you
please
> > check
> > > > > those
> > > > > > directories and see if you can find a libpython.a file or
> > > libpython.so
> > > > > > file? If so, please send me an email with the path to the
file.
> > You
> > > > > could
> > > > > > just run "ls <path>" replacing <path> with the full path
and send
> > me
> > > > the
> > > > > > output. Then, I will send you a command that you can run
to set
> > the
> > > > > value
> > > > > > of the environment variable MET_PYTHON_LD.
> > > > > >
> > > > > > Thanks!
> > > > > >
> > > > > > Julie
> > > > > >
> > > > > > On Tue, Feb 5, 2019 at 7:16 PM Taylor Mandelbaum via RT <
> > > > > met_help at ucar.edu
> > > > > > >
> > > > > > wrote:
> > > > > >
> > > > > > >
> > > > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> >
> > > > > > >
> > > > > > > Hey Julie,
> > > > > > >
> > > > > > > Sorry for the delayed response. We got python 2.7.15 set
up as
> a
> > > > > module.
> > > > > > I
> > > > > > > ran python2.7-config --cflags and ..--ldflags:
> > > > > > >
> > > > > > > -I/cm/shared/apps/python/2.7.15/include/python2.7
> > > > > > > -I/cm/shared/apps/python/2.7.15/include/python2.7
> > > > -fno-strict-aliasing
> > > > > -g
> > > > > > > -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
> > > > > > >
> > > > > > > -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-
dynamic
> > > > > > >
> > > > > > > Those are the returned outputs. I updated my bashrc with
module
> > > load
> > > > > > > python/2.7; same issue is occurring with c++. Attached
the
> config
> > > > log.
> > > > > > >
> > > > > > > Thanks again for your help.
> > > > > > >
> > > > > > > On Mon, Jan 28, 2019 at 1:43 PM Julie Prestopnik via RT
<
> > > > > > met_help at ucar.edu
> > > > > > > >
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi Taylor.
> > > > > > > >
> > > > > > > > Thanks for getting HDF5 and NetCDF4 C and C++
installed.
> > > > > > > >
> > > > > > > > Thank you also for attaching your config.log file. I
see in
> > your
> > > > > > > > config.log file:
> > > > > > > >
> > > > > > > > > /cm/shared/apps/python/3.5.2/include/python3.5m:
file not
> > > > > recognized:
> > > > > > > Is
> > > > > > > > a
> > > > > > > > > directory
> > > > > > > > >
> > > > > > > > collect2: error: ld returned 1 exit status
> > > > > > > > >
> > > > > > > >
> > > > > > > > It looks like there is a problem with the linker in
that it
> is
> > > > > finding
> > > > > > a
> > > > > > > > directory instead of a file. However, before we
proceed, I
> > > should
> > > > > tell
> > > > > > > you
> > > > > > > > that the Python functionality with met-8.0 requires
Python
> 2.7
> > to
> > > > be
> > > > > > > used.
> > > > > > > > Is Python 2.7 available on your system? If so, please
let me
> > > know.
> > > > > > > >
> > > > > > > > I can help you set up the necessary environment
variables
> that
> > > are
> > > > > > > required
> > > > > > > > to use the python embedding functionality. You'll
need to
> set
> > > > > > > > MET_PYTHON_CC and MET_PYTHON_LD prior to configuring
MET.
> > > Usually
> > > > > the
> > > > > > > > following is sufficient for csh:
> > > > > > > >
> > > > > > > > setenv MET_PYTHON_CC `python-config --cflags`
> > > > > > > >
> > > > > > > > setenv MET_PYTHON_LD `python-config --ldflags`
> > > > > > > >
> > > > > > > > for bash:
> > > > > > > >
> > > > > > > > export MET_PYTHON_CC=`python-config --cflags`
> > > > > > > >
> > > > > > > > export MET_PYTHON_LD=`python-config --ldflags`
> > > > > > > >
> > > > > > > > However, it may not be. Please run the following
commands
> > (using
> > > > > > Python
> > > > > > > > 2.7) and send me the output:
> > > > > > > >
> > > > > > > > python-config --cflags
> > > > > > > > python-config --ldflags
> > > > > > > >
> > > > > > > > Thanks!
> > > > > > > >
> > > > > > > > Julie
> > > > > > > >
> > > > > > > > On Sun, Jan 27, 2019 at 9:11 AM Taylor Mandelbaum via
RT <
> > > > > > > > met_help at ucar.edu>
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > >
> > > > > > > > > <URL:
> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > >
> > > > > > > > >
> > > > > > > > > Hey all,
> > > > > > > > >
> > > > > > > > > I got netcdf4 c and c++ installed; I'm running into
an
> issue
> > > now
> > > > on
> > > > > > > > > configuring MET which says error: C++ compiler
cannot
> create
> > > > > > > executables.
> > > > > > > > > It looks like in the config log that g++ is getting
> imported
> > > but
> > > > > > > erroring
> > > > > > > > > out when trying to use -V as a command option.
Attached the
> > > > newest
> > > > > > > config
> > > > > > > > > log here.
> > > > > > > > >
> > > > > > > > > When I configure it, this is the command I'm using:
> > > > > > > > >
> > > > > > > > > ./configure --prefix=/E1/taylorm/MET8 --enable-grib2
> > > > > --enable-python
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik
via RT <
> > > > > > > > > met_help at ucar.edu>
> > > > > > > > > wrote:
> > > > > > > > >
> > > > > > > > > > Hi Taylor. In talking with more with John about
your
> > > > config.log
> > > > > > file
> > > > > > > > we
> > > > > > > > > > see that CC is set to use icc (intel), but CXX and
F77
> are
> > > set
> > > > to
> > > > > > use
> > > > > > > > g++
> > > > > > > > > > and gfortran (GNU).
> > > > > > > > > >
> > > > > > > > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > > > > > > > >
> > > > > > > >
> > > > > >
> > > >
> >
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > > > > > > > CXX='g++'
> > > > > > > > > > F77='gfortran'
> > > > > > > > > >
> > > > > > > > > > Let's see if we can solve the immediate problem
before
> > > worrying
> > > > > > about
> > > > > > > > any
> > > > > > > > > > potential problems with the external libraries.
For now,
> > > > please
> > > > > > > choose
> > > > > > > > > > either the GNU compilers or the Intel compilers
and set
> the
> > > > > > following
> > > > > > > > > > variables accordingly. You can chose one and then
simply
> > run
> > > > the
> > > > > > > > > commands
> > > > > > > > > > below.
> > > > > > > > > >
> > > > > > > > > > *For GNU:*
> > > > > > > > > > export CC=`which gcc`
> > > > > > > > > > export CXX=`which g++`
> > > > > > > > > > export F77=`which gfortran`
> > > > > > > > > >
> > > > > > > > > > *For Intel:*
> > > > > > > > > >
> > > > > > > > > > export CC=`which icc`
> > > > > > > > > > export CXX=`which icc`
> > > > > > > > > > export F77=`which ifort`
> > > > > > > > > >
> > > > > > > > > > Then run "make clean", rerun the configure
command, and
> > then
> > > > try
> > > > > to
> > > > > > > > make
> > > > > > > > > > MET again.
> > > > > > > > > >
> > > > > > > > > > Let's go from there and see how it works out.
Please let
> > me
> > > > > know.
> > > > > > > > > >
> > > > > > > > > > Julie
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > On Wed, Jan 16, 2019 at 10:06 AM Julie Prestopnik
<
> > > > > > jpresto at ucar.edu>
> > > > > > > > > > wrote:
> > > > > > > > > >
> > > > > > > > > > > Hi Taylor. Thank you for all of this
information.
> > > > > > > > > > >
> > > > > > > > > > > Since the libraries were previously installed
and we
> > cannot
> > > > be
> > > > > > > > certain
> > > > > > > > > > > which compiler was used, are you able and would
you be
> > > > > > comfortable
> > > > > > > > > > > installing each of the dependent libraries and
not
> using
> > > the
> > > > > > > > previously
> > > > > > > > > > > installed versions? If so, we have an install
script
> > that
> > > I
> > > > > can
> > > > > > > > point
> > > > > > > > > > you
> > > > > > > > > > > to, which would install all of the packages and
MET as
> > > > well. I
> > > > > > can
> > > > > > > > > walk
> > > > > > > > > > > through this with you via google hangouts and
you can
> > share
> > > > > your
> > > > > > > > screen
> > > > > > > > > > so
> > > > > > > > > > > we can make sure it is going smoothly. I could
do a
> > > > hangouts
> > > > > > > > session
> > > > > > > > > > with
> > > > > > > > > > > you tomorrow at 1:15pm (Mountain time) or on
Friday at
> > > 9:00am
> > > > > > > > (Mountain
> > > > > > > > > > > time). If those times don't work. I can get
you
> started
> > > > with
> > > > > > very
> > > > > > > > > > > specific instructions via email and we can
continue to
> > work
> > > > > > through
> > > > > > > > any
> > > > > > > > > > > problems. We can also set up a different time
for next
> > > week,
> > > > > > > > however,
> > > > > > > > > I
> > > > > > > > > > > didn't want you to have to wait that long.
Please let
> me
> > > > know
> > > > > > your
> > > > > > > > > > > preference.
> > > > > > > > > > >
> > > > > > > > > > > If you think that icc may not be working
properly, then
> > you
> > > > > > should
> > > > > > > > > > > probably use the GNU set of compilers, unless
there is
> > some
> > > > > > reason
> > > > > > > > not
> > > > > > > > > > to,
> > > > > > > > > > > in which case you may need to get a system
> administrator
> > > > > correct
> > > > > > > the
> > > > > > > > > > > problems with the intel compiler.
> > > > > > > > > > >
> > > > > > > > > > > Running "which g++" and running "which gfortran"
can
> tell
> > > you
> > > > > > what
> > > > > > > > the
> > > > > > > > > > CXX
> > > > > > > > > > > and F77 paths should be set to. Please let me
know if
> > you
> > > > have
> > > > > > any
> > > > > > > > > > issues
> > > > > > > > > > > with that.
> > > > > > > > > > >
> > > > > > > > > > > Julie
> > > > > > > > > > >
> > > > > > > > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor
Mandelbaum via
> RT
> > <
> > > > > > > > > > > met_help at ucar.edu> wrote:
> > > > > > > > > > >
> > > > > > > > > > >>
> > > > > > > > > > >> <URL:
> > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > >
> > > > > > > > > > >>
> > > > > > > > > > >> Hey Julie,
> > > > > > > > > > >>
> > > > > > > > > > >> 1) They were previously installed, but I just
tried
> > > running
> > > > it
> > > > > > > with
> > > > > > > > > some
> > > > > > > > > > >> of
> > > > > > > > > > >> my own installed versions and they're not
working
> > properly
> > > > > (e.g.
> > > > > > > the
> > > > > > > > > > make
> > > > > > > > > > >> install fails due to gsl/gsl_cdf.h missing...
though I
> > set
> > > > > > MET_GSL
> > > > > > > > to
> > > > > > > > > my
> > > > > > > > > > >> gsl-2.5 directory).
> > > > > > > > > > >>
> > > > > > > > > > >> 2) Not sure how I can verify that one, though I
think
> > > > they're
> > > > > > not
> > > > > > > as
> > > > > > > > > > I've
> > > > > > > > > > >> seen GNU and Intel prompts in the config
output. My CC
> > var
> > > > in
> > > > > my
> > > > > > > > > bashrc
> > > > > > > > > > >> links to an Intel compiler.
> > > > > > > > > > >>
> > > > > > > > > > >> 3) I followed those for the packages, though
for the
> > > > compilers
> > > > > > > > > section,
> > > > > > > > > > I
> > > > > > > > > > >> do not know my CXX or F77 paths on the hpc that
I'm
> > > using. I
> > > > > > also
> > > > > > > > > think
> > > > > > > > > > >> the
> > > > > > > > > > >> icc is not working properly as I could not run
icc
> > > without a
> > > > > > > license
> > > > > > > > > > >> prompt
> > > > > > > > > > >> coming up.
> > > > > > > > > > >>
> > > > > > > > > > >> I'm not sure if any of that helps, but let me
know.
> > Maybe
> > > > some
> > > > > > of
> > > > > > > > > these
> > > > > > > > > > >> issues are still on our end. The fact that met
needs
> to
> > > only
> > > > > use
> > > > > > > one
> > > > > > > > > > >> compiler might be the issue...
> > > > > > > > > > >>
> > > > > > > > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie
Prestopnik via
> > RT <
> > > > > > > > > > >> met_help at ucar.edu>
> > > > > > > > > > >> wrote:
> > > > > > > > > > >>
> > > > > > > > > > >> > Hi Taylor. Thank you for passing along your
> files. I
> > > > have
> > > > > a
> > > > > > > few
> > > > > > > > > > >> questions
> > > > > > > > > > >> > for you.
> > > > > > > > > > >> >
> > > > > > > > > > >> > 1) Are you installing the external libraries
> yourself
> > or
> > > > > were
> > > > > > > they
> > > > > > > > > > >> > previously installed?
> > > > > > > > > > >> > 2) Can you please verify that the external
libraries
> > and
> > > > MET
> > > > > > are
> > > > > > > > > being
> > > > > > > > > > >> > built with the same family of compilers (e.g.
all
> are
> > > > built
> > > > > > with
> > > > > > > > > GNU,
> > > > > > > > > > or
> > > > > > > > > > >> > all are build with Intel, etc.)? Which
compiler are
> > you
> > > > > > using?
> > > > > > > > > > >> > 3) Are you following the directions on this
page as
> > your
> > > > > > > > > instructions
> > > > > > > > > > >> for
> > > > > > > > > > >> > installation?
> > > > > > > > > > >> >
> > > > > > > > > > >> >
> > > > > > > > > > >>
> > > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > > > > > > > >> >
> > > > > > > > > > >> > Thank you!
> > > > > > > > > > >> >
> > > > > > > > > > >> > Julie
> > > > > > > > > > >> >
> > > > > > > > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor
Mandelbaum
> via
> > > RT <
> > > > > > > > > > >> > met_help at ucar.edu>
> > > > > > > > > > >> > wrote:
> > > > > > > > > > >> >
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > <URL:
> > > > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > >
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > Hey Julie,
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > I attached the config and make_install logs
here.
> We
> > > > could
> > > > > > do
> > > > > > > a
> > > > > > > > > > >> hangouts
> > > > > > > > > > >> > > session as well if you can't pinpoint the
issue;
> I'm
> > > > > > remoting
> > > > > > > in
> > > > > > > > > > from
> > > > > > > > > > >> my
> > > > > > > > > > >> > > home windows computer so it will be a bit
hacky.
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie
Prestopnik
> via
> > > RT
> > > > <
> > > > > > > > > > >> > met_help at ucar.edu
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > wrote:
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > > Hi Taylor. It is difficult to tell what
is
> going
> > > > > without
> > > > > > > more
> > > > > > > > > > >> context.
> > > > > > > > > > >> > > > Could you please send me your config.log
file
> and
> > > your
> > > > > > > > make.log
> > > > > > > > > > >> file?
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > We could also consider doing a hangouts
session
> > > where
> > > > > you
> > > > > > > can
> > > > > > > > > > share
> > > > > > > > > > >> > your
> > > > > > > > > > >> > > > screen, and I can directly help that way.
> Either
> > > way
> > > > > > > though,
> > > > > > > > if
> > > > > > > > > > you
> > > > > > > > > > >> > > could
> > > > > > > > > > >> > > > please send those files, I would
appreciate it.
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > Thanks,
> > > > > > > > > > >> > > > Julie
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > Thanks!
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > Julie
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor
> Mandelbaum
> > > via
> > > > > RT <
> > > > > > > > > > >> > > > met_help at ucar.edu>
> > > > > > > > > > >> > > > wrote:
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > Mon Jan 14 15:05:33 2019: Request 88502
was
> > acted
> > > > > upon.
> > > > > > > > > > >> > > > > Transaction: Ticket created by
> > > > > > > > > taylor.mandelbaum at stonybrook.edu
> > > > > > > > > > >> > > > > Queue: met_help
> > > > > > > > > > >> > > > > Subject: met install help
> > > > > > > > > > >> > > > > Owner: Nobody
> > > > > > > > > > >> > > > > Requestors:
> taylor.mandelbaum at stonybrook.edu
> > > > > > > > > > >> > > > > Status: new
> > > > > > > > > > >> > > > > Ticket <URL:
> > > > > > > > > > >> >
> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > Hey all,
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > I'm presently trying to compile MET 8.0
on our
> > > HPC;
> > > > > > when I
> > > > > > > > > > >> configure
> > > > > > > > > > >> > > it,
> > > > > > > > > > >> > > > > I'm getting a few warnings on .h files:
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > configure: WARNING: errno.h: present
but
> cannot
> > be
> > > > > > > compiled
> > > > > > > > > > >> > > > > configure: WARNING: errno.h: check
for
> > missing
> > > > > > > > > prerequisite
> > > > > > > > > > >> > > headers?
> > > > > > > > > > >> > > > > configure: WARNING: errno.h: see the
Autoconf
> > > > > > > documentation
> > > > > > > > > > >> > > > > configure: WARNING: errno.h:
section
> > "Present
> > > > But
> > > > > > > Cannot
> > > > > > > > > Be
> > > > > > > > > > >> > > Compiled"
> > > > > > > > > > >> > > > > configure: WARNING: errno.h: proceeding
with
> the
> > > > > > > compiler's
> > > > > > > > > > result
> > > > > > > > > > >> > > > > configure: WARNING: ##
> > > > > > > --------------------------------
> > > > > > > > ##
> > > > > > > > > > >> > > > > configure: WARNING: ## Report this
to
> > > > > > > met_help at ucar.edu
> > > > > > > > > ##
> > > > > > > > > > >> > > > > configure: WARNING: ##
> > > > > > > --------------------------------
> > > > > > > > ##
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > and the same for fcntl.h, limits.h,
stddef.h,
> > > file.h
> > > > > and
> > > > > > > > > > param.h.
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > When I try to make install, I get this
error
> on
> > > the
> > > > > tail
> > > > > > > of
> > > > > > > > > the
> > > > > > > > > > >> log:
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > > > > configalloc(yy_size_t)’:
> > > > > > > > > > >> > > > > config_scanner.cc:2179:31: error:
‘rpl_malloc’
> > was
> > > > not
> > > > > > > > > declared
> > > > > > > > > > in
> > > > > > > > > > >> > this
> > > > > > > > > > >> > > > > scope
> > > > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > > configrealloc(void*,
> > > > > > > > > > >> > yy_size_t)’:
> > > > > > > > > > >> > > > > config_scanner.cc:2191:46: error:
> ‘rpl_realloc’
> > > was
> > > > > not
> > > > > > > > > declared
> > > > > > > > > > >> in
> > > > > > > > > > >> > > this
> > > > > > > > > > >> > > > > scope
> > > > > > > > > > >> > > > > /* The cast to (char *) in the
following
> > > > > accommodates
> > > > > > > both
> > > > > > > > > > >> > > > >
> ^
> > > > > > > > > > >> > > > > make[3]: *** [libvx_config_a-
config_scanner.o]
> > > > Error 1
> > > > > > > > > > >> > > > > make[3]: Leaving directory
> > > > > > > > > > >> > > > >
> > > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > > > > > > > > >> > > > > make[2]: *** [install-recursive] Error
1
> > > > > > > > > > >> > > > > make[2]: Leaving directory
> > > > > > > > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > > > > > > > >> > > > > make[1]: *** [install-recursive] Error
1
> > > > > > > > > > >> > > > > make[1]: Leaving directory
> > > > > > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > > > > > > > >> > > > > make: *** [install-recursive] Error 1
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > Not sure how to address either of
these,
> > hopefully
> > > > you
> > > > > > > guys
> > > > > > > > > can
> > > > > > > > > > >> > provide
> > > > > > > > > > >> > > > > some insight.
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > > Thanks!
> > > > > > > > > > >> > > > > --
> > > > > > > > > > >> > > > > *Taylor Mandelbaum*
> > > > > > > > > > >> > > > > Research Technician
> > > > > > > > > > >> > > > > SoMAS | Stony Brook University
> > > > > > > > > > >> > > > > 678.468.5789
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > > >
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > > >
> > > > > > > > > > >> > >
> > > > > > > > > > >> > > --
> > > > > > > > > > >> > > *Taylor Mandelbaum*
> > > > > > > > > > >> > > Research Technician
> > > > > > > > > > >> > > SoMAS | Stony Brook University
> > > > > > > > > > >> > > 678.468.5789
> > > > > > > > > > >> > >
> > > > > > > > > > >> > >
> > > > > > > > > > >> >
> > > > > > > > > > >> >
> > > > > > > > > > >>
> > > > > > > > > > >> --
> > > > > > > > > > >> *Taylor Mandelbaum*
> > > > > > > > > > >> Research Technician
> > > > > > > > > > >> SoMAS | Stony Brook University
> > > > > > > > > > >> 678.468.5789
> > > > > > > > > > >>
> > > > > > > > > > >>
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > > --
> > > > > > > > > *Taylor Mandelbaum*
> > > > > > > > > Research Technician
> > > > > > > > > SoMAS | Stony Brook University
> > > > > > > > > 678.468.5789
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > *Taylor Mandelbaum*
> > > > > > > Research Technician
> > > > > > > SoMAS | Stony Brook University
> > > > > > > 678.468.5789
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > > --
> > > > > *Taylor Mandelbaum*
> > > > > Research Technician
> > > > > SoMAS | Stony Brook University
> > > > > 678.468.5789
> > > > >
> > > > >
> > > >
> > > >
> > >
> > > --
> > > *Taylor Mandelbaum*
> > > Research Technician
> > > SoMAS | Stony Brook University
> > > 678.468.5789
> > >
> > >
> >
> >
>
> --
> *Taylor Mandelbaum*
> Research Technician
> SoMAS | Stony Brook University
> 678.468.5789
>
>
------------------------------------------------
Subject: met install help
From: Taylor Mandelbaum
Time: Wed Feb 20 16:38:12 2019
I merged them, had an issue with grib2c which i re-made onto my local
directory... and I think I got MET compiled!
On Wed, Feb 20, 2019 at 4:59 PM Julie Prestopnik via RT
<met_help at ucar.edu>
wrote:
> Hi Taylor, for met-8.0 both the NetCDF-C package and the NetCDF-CXX
package
> are required. I see you said that you have installed version 4.6.2
for
> NetCDF-C and version 4.3.0 for NetCDF-CXX. I usually install
netcdf
> -c-4.4.1.1and netcdf-cxx4-4.3.0, but don't think that other versions
should
> be a problem.
>
> The error you received:
>
> nc_utils.h:22:18: error: netcdf: No such file or directory
> >
>
> indicates that MET is having a difficult time finding the file
"netcdf",
> which is included in the NetCDF-CXX installation.
>
> I see that you have MET_NETCDF set to /E1/taylorm/netcdf462. It is
> important to note that there is only one MET_NETCDF environment
variable,
> so both NetCDF packages are expected to be installed at the same
location.
> Is the file "netcdf" located at $MET_NETCDF/include/
> (/E1/taylorm/netcdf462/include)?
>
>
> Here is a quick reference checklist for NetCDF4 installation that
you can
> use to see if you have the necessary files:
>
> Files for NetCDF4 C:
>
> $MET_NETCDF/include/netcdf.h
> $MET_NETCDF/lib/libnetcdf.a
> $MET_NETCDF/lib/libnetcdf.so
>
> Files for NetCDF4 C++:
>
> $MET_NETCDF/include/netcdf
> $MET_NETCDF/lib/libnetcdf_c++4.a
> $MET_NETCDF/lib/libnetcdf_c++4.so
>
> I hope that helps. Please let me know if you have any questions.
>
> Thanks,
> Julie
>
> On Wed, Feb 20, 2019 at 12:37 PM Taylor Mandelbaum via RT <
> met_help at ucar.edu>
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> >
> > That solved that problem, onto the next one:
> >
> > nc_utils.h:22:18: fatal error: netcdf: No such file or directory
> >
> > I had installed netcdf 4.6.2 most recently and netcdfcxx 4.3.0, so
I'm
> not
> > sure what this is about.
> >
> >
> > On Wed, Feb 20, 2019 at 2:12 PM Julie Prestopnik via RT <
> met_help at ucar.edu
> > >
> > wrote:
> >
> > > Hi Taylor.
> > >
> > > I see the following in your config.log file:
> > >
> > > /usr/bin/ld: cannot find -lpython2.7-lpthread
> > >
> > > It looks like MET_PYTHON_LD was set in the following way:
> > >
> > > MET_PYTHON_LD='-L/cm/shared/apps/python/2.7.15/lib -lpython2.7-
lpthread
> > > > -ldl -lutil -lm -Xlinker -export-dynamic'
> > > >
> > >
> > > Note, the lack of space between "-lpython2.7" and "-lpthread"
in both
> > the
> > > error message and the setting of MET_PYTHON_LD.
> > >
> > > Please copy and paste the following:
> > >
> > > for csh:
> > > >
> > > > setenv MET_PYTHON_LD -L/cm/shared/apps/python/2.7.15/lib\
> -lpython2.7\
> > > > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> > > >
> > > > for bash:
> > > >
> > > > export MET_PYTHON_LD=-L/cm/shared/apps/python/2.7.15/lib\
> -lpython2.7\
> > > > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> > >
> > >
> > > Those lines should capture the proper spaces.
> > >
> > > Give that a try and reconfigure MET. Please let me know how it
goes.
> > > Thanks!
> > >
> > > Julie
> > >
> > > On Tue, Feb 19, 2019 at 6:11 PM Taylor Mandelbaum via RT <
> > > met_help at ucar.edu>
> > > wrote:
> > >
> > > >
> > > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
>
> > > >
> > > > Hey Julie,
> > > >
> > > > I set those up in my bashrc but am still having an issue with
the
> > config
> > > > not proceeding due to the c++ compiler:
> > > >
> > > > "checking whether the C++ compiler works... no
> > > > configure: error: in `/home/taylorm/MET8/met-8.0_bugfix':
> > > > configure: error: C++ compiler cannot create executables"
> > > >
> > > > attached the most recent config log.
> > > >
> > > > Thanks again!
> > > >
> > > > On Tue, Feb 19, 2019 at 12:47 PM Julie Prestopnik via RT <
> > > > met_help at ucar.edu>
> > > > wrote:
> > > >
> > > > > Hi Taylor,
> > > > >
> > > > > Great! Thanks for the update. Please try setting the
following:
> > > > >
> > > > > or csh:
> > > > >
> > > > > setenv MET_PYTHON_CC `python-config --cflags`
> > > > > setenv MET_PYTHON_LD -L/cm/shared/apps/python/2.7.15/lib\
> > -lpython2.7\
> > > > > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> > > > >
> > > > > for bash:
> > > > >
> > > > > export MET_PYTHON_CC=`python-config --cflags`
> > > > > export MET_PYTHON_LD=-L/cm/shared/apps/python/2.7.15/lib\
> > -lpython2.7\
> > > > > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> > > > >
> > > > > Please set up your other environment variables and then try
> > > reconfiguring
> > > > > and reinstalling MET. Please let me know how it goes.
> > > > >
> > > > > Thanks,
> > > > > Julie
> > > > >
> > > > > On Sat, Feb 16, 2019 at 2:36 PM Taylor Mandelbaum via RT <
> > > > > met_help at ucar.edu>
> > > > > wrote:
> > > > >
> > > > > >
> > > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > > >
> > > > > > Hey Julie,
> > > > > >
> > > > > > The libpython2.7.so file is in the first directory you
> > > > > > mentioned, /cm/shared/apps/python/2.7.15/lib.
> > > > > >
> > > > > > Sorry for the delay, busy week this week.
> > > > > >
> > > > > > On Mon, Feb 11, 2019 at 1:28 PM Julie Prestopnik via RT <
> > > > > met_help at ucar.edu
> > > > > > >
> > > > > > wrote:
> > > > > >
> > > > > > > Hi Taylor. Thanks for the update. I'm glad we are
making some
> > > > > progress.
> > > > > > >
> > > > > > > From your config.log file:
> > > > > > >
> > > > > > > > /usr/bin/ld: cannot find -lpython2.7
> > > > > > > > collect2: error: ld returned 1 exit status
> > > > > > > >
> > > > > > > and from the output you provided from running "python-
config
> > > > > --ldflags",
> > > > > > I
> > > > > > > can see what the problem is.
> > > > > > >
> > > > > > > It looks like the output "python-config --ldflags"
> unfortunately
> > > does
> > > > > not
> > > > > > > contain all of the information that the environment
variable
> > > > > > MET_PYTHON_LD
> > > > > > > needs to have.
> > > > > > >
> > > > > > > In order to proceed, we need to find the location of the
> > > libpython.a
> > > > > file
> > > > > > > or the libpython.so file. Based on the information from
the
> > output
> > > > > from
> > > > > > > running "python-config --cflags", I am going to guess
that the
> > > > > libpython
> > > > > > > file lives in /cm/shared/apps/python/2.7.15/lib or in
> > > > > > > /cm/shared/apps/python/2.7.15/lib/python2.7. Could you
please
> > > check
> > > > > > those
> > > > > > > directories and see if you can find a libpython.a file
or
> > > > libpython.so
> > > > > > > file? If so, please send me an email with the path to
the
> file.
> > > You
> > > > > > could
> > > > > > > just run "ls <path>" replacing <path> with the full path
and
> send
> > > me
> > > > > the
> > > > > > > output. Then, I will send you a command that you can
run to
> set
> > > the
> > > > > > value
> > > > > > > of the environment variable MET_PYTHON_LD.
> > > > > > >
> > > > > > > Thanks!
> > > > > > >
> > > > > > > Julie
> > > > > > >
> > > > > > > On Tue, Feb 5, 2019 at 7:16 PM Taylor Mandelbaum via RT
<
> > > > > > met_help at ucar.edu
> > > > > > > >
> > > > > > > wrote:
> > > > > > >
> > > > > > > >
> > > > > > > > <URL:
> https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > >
> > > > > > > >
> > > > > > > > Hey Julie,
> > > > > > > >
> > > > > > > > Sorry for the delayed response. We got python 2.7.15
set up
> as
> > a
> > > > > > module.
> > > > > > > I
> > > > > > > > ran python2.7-config --cflags and ..--ldflags:
> > > > > > > >
> > > > > > > > -I/cm/shared/apps/python/2.7.15/include/python2.7
> > > > > > > > -I/cm/shared/apps/python/2.7.15/include/python2.7
> > > > > -fno-strict-aliasing
> > > > > > -g
> > > > > > > > -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
> > > > > > > >
> > > > > > > > -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker
> -export-dynamic
> > > > > > > >
> > > > > > > > Those are the returned outputs. I updated my bashrc
with
> module
> > > > load
> > > > > > > > python/2.7; same issue is occurring with c++. Attached
the
> > config
> > > > > log.
> > > > > > > >
> > > > > > > > Thanks again for your help.
> > > > > > > >
> > > > > > > > On Mon, Jan 28, 2019 at 1:43 PM Julie Prestopnik via
RT <
> > > > > > > met_help at ucar.edu
> > > > > > > > >
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > > Hi Taylor.
> > > > > > > > >
> > > > > > > > > Thanks for getting HDF5 and NetCDF4 C and C++
installed.
> > > > > > > > >
> > > > > > > > > Thank you also for attaching your config.log file.
I see
> in
> > > your
> > > > > > > > > config.log file:
> > > > > > > > >
> > > > > > > > > > /cm/shared/apps/python/3.5.2/include/python3.5m:
file not
> > > > > > recognized:
> > > > > > > > Is
> > > > > > > > > a
> > > > > > > > > > directory
> > > > > > > > > >
> > > > > > > > > collect2: error: ld returned 1 exit status
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > > It looks like there is a problem with the linker in
that it
> > is
> > > > > > finding
> > > > > > > a
> > > > > > > > > directory instead of a file. However, before we
proceed, I
> > > > should
> > > > > > tell
> > > > > > > > you
> > > > > > > > > that the Python functionality with met-8.0 requires
Python
> > 2.7
> > > to
> > > > > be
> > > > > > > > used.
> > > > > > > > > Is Python 2.7 available on your system? If so,
please let
> me
> > > > know.
> > > > > > > > >
> > > > > > > > > I can help you set up the necessary environment
variables
> > that
> > > > are
> > > > > > > > required
> > > > > > > > > to use the python embedding functionality. You'll
need to
> > set
> > > > > > > > > MET_PYTHON_CC and MET_PYTHON_LD prior to configuring
MET.
> > > > Usually
> > > > > > the
> > > > > > > > > following is sufficient for csh:
> > > > > > > > >
> > > > > > > > > setenv MET_PYTHON_CC `python-config --cflags`
> > > > > > > > >
> > > > > > > > > setenv MET_PYTHON_LD `python-config --ldflags`
> > > > > > > > >
> > > > > > > > > for bash:
> > > > > > > > >
> > > > > > > > > export MET_PYTHON_CC=`python-config --cflags`
> > > > > > > > >
> > > > > > > > > export MET_PYTHON_LD=`python-config --ldflags`
> > > > > > > > >
> > > > > > > > > However, it may not be. Please run the following
commands
> > > (using
> > > > > > > Python
> > > > > > > > > 2.7) and send me the output:
> > > > > > > > >
> > > > > > > > > python-config --cflags
> > > > > > > > > python-config --ldflags
> > > > > > > > >
> > > > > > > > > Thanks!
> > > > > > > > >
> > > > > > > > > Julie
> > > > > > > > >
> > > > > > > > > On Sun, Jan 27, 2019 at 9:11 AM Taylor Mandelbaum
via RT <
> > > > > > > > > met_help at ucar.edu>
> > > > > > > > > wrote:
> > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > <URL:
> > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > >
> > > > > > > > > >
> > > > > > > > > > Hey all,
> > > > > > > > > >
> > > > > > > > > > I got netcdf4 c and c++ installed; I'm running
into an
> > issue
> > > > now
> > > > > on
> > > > > > > > > > configuring MET which says error: C++ compiler
cannot
> > create
> > > > > > > > executables.
> > > > > > > > > > It looks like in the config log that g++ is
getting
> > imported
> > > > but
> > > > > > > > erroring
> > > > > > > > > > out when trying to use -V as a command option.
Attached
> the
> > > > > newest
> > > > > > > > config
> > > > > > > > > > log here.
> > > > > > > > > >
> > > > > > > > > > When I configure it, this is the command I'm
using:
> > > > > > > > > >
> > > > > > > > > > ./configure --prefix=/E1/taylorm/MET8 --enable-
grib2
> > > > > > --enable-python
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > On Wed, Jan 16, 2019 at 12:23 PM Julie Prestopnik
via RT
> <
> > > > > > > > > > met_help at ucar.edu>
> > > > > > > > > > wrote:
> > > > > > > > > >
> > > > > > > > > > > Hi Taylor. In talking with more with John about
your
> > > > > config.log
> > > > > > > file
> > > > > > > > > we
> > > > > > > > > > > see that CC is set to use icc (intel), but CXX
and F77
> > are
> > > > set
> > > > > to
> > > > > > > use
> > > > > > > > > g++
> > > > > > > > > > > and gfortran (GNU).
> > > > > > > > > > >
> > > > > > > > > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > > > > > > > > >
> > > > > > > > >
> > > > > > >
> > > > >
> > >
>
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > > > > > > > > CXX='g++'
> > > > > > > > > > > F77='gfortran'
> > > > > > > > > > >
> > > > > > > > > > > Let's see if we can solve the immediate problem
before
> > > > worrying
> > > > > > > about
> > > > > > > > > any
> > > > > > > > > > > potential problems with the external libraries.
For
> now,
> > > > > please
> > > > > > > > choose
> > > > > > > > > > > either the GNU compilers or the Intel compilers
and set
> > the
> > > > > > > following
> > > > > > > > > > > variables accordingly. You can chose one and
then
> simply
> > > run
> > > > > the
> > > > > > > > > > commands
> > > > > > > > > > > below.
> > > > > > > > > > >
> > > > > > > > > > > *For GNU:*
> > > > > > > > > > > export CC=`which gcc`
> > > > > > > > > > > export CXX=`which g++`
> > > > > > > > > > > export F77=`which gfortran`
> > > > > > > > > > >
> > > > > > > > > > > *For Intel:*
> > > > > > > > > > >
> > > > > > > > > > > export CC=`which icc`
> > > > > > > > > > > export CXX=`which icc`
> > > > > > > > > > > export F77=`which ifort`
> > > > > > > > > > >
> > > > > > > > > > > Then run "make clean", rerun the configure
command, and
> > > then
> > > > > try
> > > > > > to
> > > > > > > > > make
> > > > > > > > > > > MET again.
> > > > > > > > > > >
> > > > > > > > > > > Let's go from there and see how it works out.
Please
> let
> > > me
> > > > > > know.
> > > > > > > > > > >
> > > > > > > > > > > Julie
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > On Wed, Jan 16, 2019 at 10:06 AM Julie
Prestopnik <
> > > > > > > jpresto at ucar.edu>
> > > > > > > > > > > wrote:
> > > > > > > > > > >
> > > > > > > > > > > > Hi Taylor. Thank you for all of this
information.
> > > > > > > > > > > >
> > > > > > > > > > > > Since the libraries were previously installed
and we
> > > cannot
> > > > > be
> > > > > > > > > certain
> > > > > > > > > > > > which compiler was used, are you able and
would you
> be
> > > > > > > comfortable
> > > > > > > > > > > > installing each of the dependent libraries and
not
> > using
> > > > the
> > > > > > > > > previously
> > > > > > > > > > > > installed versions? If so, we have an install
script
> > > that
> > > > I
> > > > > > can
> > > > > > > > > point
> > > > > > > > > > > you
> > > > > > > > > > > > to, which would install all of the packages
and MET
> as
> > > > > well. I
> > > > > > > can
> > > > > > > > > > walk
> > > > > > > > > > > > through this with you via google hangouts and
you can
> > > share
> > > > > > your
> > > > > > > > > screen
> > > > > > > > > > > so
> > > > > > > > > > > > we can make sure it is going smoothly. I
could do a
> > > > > hangouts
> > > > > > > > > session
> > > > > > > > > > > with
> > > > > > > > > > > > you tomorrow at 1:15pm (Mountain time) or on
Friday
> at
> > > > 9:00am
> > > > > > > > > (Mountain
> > > > > > > > > > > > time). If those times don't work. I can get
you
> > started
> > > > > with
> > > > > > > very
> > > > > > > > > > > > specific instructions via email and we can
continue
> to
> > > work
> > > > > > > through
> > > > > > > > > any
> > > > > > > > > > > > problems. We can also set up a different time
for
> next
> > > > week,
> > > > > > > > > however,
> > > > > > > > > > I
> > > > > > > > > > > > didn't want you to have to wait that long.
Please
> let
> > me
> > > > > know
> > > > > > > your
> > > > > > > > > > > > preference.
> > > > > > > > > > > >
> > > > > > > > > > > > If you think that icc may not be working
properly,
> then
> > > you
> > > > > > > should
> > > > > > > > > > > > probably use the GNU set of compilers, unless
there
> is
> > > some
> > > > > > > reason
> > > > > > > > > not
> > > > > > > > > > > to,
> > > > > > > > > > > > in which case you may need to get a system
> > administrator
> > > > > > correct
> > > > > > > > the
> > > > > > > > > > > > problems with the intel compiler.
> > > > > > > > > > > >
> > > > > > > > > > > > Running "which g++" and running "which
gfortran" can
> > tell
> > > > you
> > > > > > > what
> > > > > > > > > the
> > > > > > > > > > > CXX
> > > > > > > > > > > > and F77 paths should be set to. Please let me
know
> if
> > > you
> > > > > have
> > > > > > > any
> > > > > > > > > > > issues
> > > > > > > > > > > > with that.
> > > > > > > > > > > >
> > > > > > > > > > > > Julie
> > > > > > > > > > > >
> > > > > > > > > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor
Mandelbaum via
> > RT
> > > <
> > > > > > > > > > > > met_help at ucar.edu> wrote:
> > > > > > > > > > > >
> > > > > > > > > > > >>
> > > > > > > > > > > >> <URL:
> > > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > >
> > > > > > > > > > > >>
> > > > > > > > > > > >> Hey Julie,
> > > > > > > > > > > >>
> > > > > > > > > > > >> 1) They were previously installed, but I just
tried
> > > > running
> > > > > it
> > > > > > > > with
> > > > > > > > > > some
> > > > > > > > > > > >> of
> > > > > > > > > > > >> my own installed versions and they're not
working
> > > properly
> > > > > > (e.g.
> > > > > > > > the
> > > > > > > > > > > make
> > > > > > > > > > > >> install fails due to gsl/gsl_cdf.h missing...
> though I
> > > set
> > > > > > > MET_GSL
> > > > > > > > > to
> > > > > > > > > > my
> > > > > > > > > > > >> gsl-2.5 directory).
> > > > > > > > > > > >>
> > > > > > > > > > > >> 2) Not sure how I can verify that one, though
I
> think
> > > > > they're
> > > > > > > not
> > > > > > > > as
> > > > > > > > > > > I've
> > > > > > > > > > > >> seen GNU and Intel prompts in the config
output. My
> CC
> > > var
> > > > > in
> > > > > > my
> > > > > > > > > > bashrc
> > > > > > > > > > > >> links to an Intel compiler.
> > > > > > > > > > > >>
> > > > > > > > > > > >> 3) I followed those for the packages, though
for the
> > > > > compilers
> > > > > > > > > > section,
> > > > > > > > > > > I
> > > > > > > > > > > >> do not know my CXX or F77 paths on the hpc
that I'm
> > > > using. I
> > > > > > > also
> > > > > > > > > > think
> > > > > > > > > > > >> the
> > > > > > > > > > > >> icc is not working properly as I could not
run icc
> > > > without a
> > > > > > > > license
> > > > > > > > > > > >> prompt
> > > > > > > > > > > >> coming up.
> > > > > > > > > > > >>
> > > > > > > > > > > >> I'm not sure if any of that helps, but let me
know.
> > > Maybe
> > > > > some
> > > > > > > of
> > > > > > > > > > these
> > > > > > > > > > > >> issues are still on our end. The fact that
met needs
> > to
> > > > only
> > > > > > use
> > > > > > > > one
> > > > > > > > > > > >> compiler might be the issue...
> > > > > > > > > > > >>
> > > > > > > > > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie
Prestopnik
> via
> > > RT <
> > > > > > > > > > > >> met_help at ucar.edu>
> > > > > > > > > > > >> wrote:
> > > > > > > > > > > >>
> > > > > > > > > > > >> > Hi Taylor. Thank you for passing along
your
> > files. I
> > > > > have
> > > > > > a
> > > > > > > > few
> > > > > > > > > > > >> questions
> > > > > > > > > > > >> > for you.
> > > > > > > > > > > >> >
> > > > > > > > > > > >> > 1) Are you installing the external
libraries
> > yourself
> > > or
> > > > > > were
> > > > > > > > they
> > > > > > > > > > > >> > previously installed?
> > > > > > > > > > > >> > 2) Can you please verify that the external
> libraries
> > > and
> > > > > MET
> > > > > > > are
> > > > > > > > > > being
> > > > > > > > > > > >> > built with the same family of compilers
(e.g. all
> > are
> > > > > built
> > > > > > > with
> > > > > > > > > > GNU,
> > > > > > > > > > > or
> > > > > > > > > > > >> > all are build with Intel, etc.)? Which
compiler
> are
> > > you
> > > > > > > using?
> > > > > > > > > > > >> > 3) Are you following the directions on this
page
> as
> > > your
> > > > > > > > > > instructions
> > > > > > > > > > > >> for
> > > > > > > > > > > >> > installation?
> > > > > > > > > > > >> >
> > > > > > > > > > > >> >
> > > > > > > > > > > >>
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > > > > > > > > >> >
> > > > > > > > > > > >> > Thank you!
> > > > > > > > > > > >> >
> > > > > > > > > > > >> > Julie
> > > > > > > > > > > >> >
> > > > > > > > > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor
Mandelbaum
> > via
> > > > RT <
> > > > > > > > > > > >> > met_help at ucar.edu>
> > > > > > > > > > > >> > wrote:
> > > > > > > > > > > >> >
> > > > > > > > > > > >> > >
> > > > > > > > > > > >> > > <URL:
> > > > > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > > >
> > > > > > > > > > > >> > >
> > > > > > > > > > > >> > > Hey Julie,
> > > > > > > > > > > >> > >
> > > > > > > > > > > >> > > I attached the config and make_install
logs
> here.
> > We
> > > > > could
> > > > > > > do
> > > > > > > > a
> > > > > > > > > > > >> hangouts
> > > > > > > > > > > >> > > session as well if you can't pinpoint the
issue;
> > I'm
> > > > > > > remoting
> > > > > > > > in
> > > > > > > > > > > from
> > > > > > > > > > > >> my
> > > > > > > > > > > >> > > home windows computer so it will be a bit
hacky.
> > > > > > > > > > > >> > >
> > > > > > > > > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie
Prestopnik
> > via
> > > > RT
> > > > > <
> > > > > > > > > > > >> > met_help at ucar.edu
> > > > > > > > > > > >> > > >
> > > > > > > > > > > >> > > wrote:
> > > > > > > > > > > >> > >
> > > > > > > > > > > >> > > > Hi Taylor. It is difficult to tell
what is
> > going
> > > > > > without
> > > > > > > > more
> > > > > > > > > > > >> context.
> > > > > > > > > > > >> > > > Could you please send me your
config.log file
> > and
> > > > your
> > > > > > > > > make.log
> > > > > > > > > > > >> file?
> > > > > > > > > > > >> > > >
> > > > > > > > > > > >> > > > We could also consider doing a hangouts
> session
> > > > where
> > > > > > you
> > > > > > > > can
> > > > > > > > > > > share
> > > > > > > > > > > >> > your
> > > > > > > > > > > >> > > > screen, and I can directly help that
way.
> > Either
> > > > way
> > > > > > > > though,
> > > > > > > > > if
> > > > > > > > > > > you
> > > > > > > > > > > >> > > could
> > > > > > > > > > > >> > > > please send those files, I would
appreciate
> it.
> > > > > > > > > > > >> > > >
> > > > > > > > > > > >> > > > Thanks,
> > > > > > > > > > > >> > > > Julie
> > > > > > > > > > > >> > > >
> > > > > > > > > > > >> > > > Thanks!
> > > > > > > > > > > >> > > >
> > > > > > > > > > > >> > > > Julie
> > > > > > > > > > > >> > > >
> > > > > > > > > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM Taylor
> > Mandelbaum
> > > > via
> > > > > > RT <
> > > > > > > > > > > >> > > > met_help at ucar.edu>
> > > > > > > > > > > >> > > > wrote:
> > > > > > > > > > > >> > > >
> > > > > > > > > > > >> > > > >
> > > > > > > > > > > >> > > > > Mon Jan 14 15:05:33 2019: Request
88502 was
> > > acted
> > > > > > upon.
> > > > > > > > > > > >> > > > > Transaction: Ticket created by
> > > > > > > > > > taylor.mandelbaum at stonybrook.edu
> > > > > > > > > > > >> > > > > Queue: met_help
> > > > > > > > > > > >> > > > > Subject: met install help
> > > > > > > > > > > >> > > > > Owner: Nobody
> > > > > > > > > > > >> > > > > Requestors:
> > taylor.mandelbaum at stonybrook.edu
> > > > > > > > > > > >> > > > > Status: new
> > > > > > > > > > > >> > > > > Ticket <URL:
> > > > > > > > > > > >> >
> > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > > > > > >> > > >
> > > > > > > > > > > >> > > > >
> > > > > > > > > > > >> > > > >
> > > > > > > > > > > >> > > > > Hey all,
> > > > > > > > > > > >> > > > >
> > > > > > > > > > > >> > > > > I'm presently trying to compile MET
8.0 on
> our
> > > > HPC;
> > > > > > > when I
> > > > > > > > > > > >> configure
> > > > > > > > > > > >> > > it,
> > > > > > > > > > > >> > > > > I'm getting a few warnings on .h
files:
> > > > > > > > > > > >> > > > >
> > > > > > > > > > > >> > > > > configure: WARNING: errno.h: present
but
> > cannot
> > > be
> > > > > > > > compiled
> > > > > > > > > > > >> > > > > configure: WARNING: errno.h:
check for
> > > missing
> > > > > > > > > > prerequisite
> > > > > > > > > > > >> > > headers?
> > > > > > > > > > > >> > > > > configure: WARNING: errno.h: see the
> Autoconf
> > > > > > > > documentation
> > > > > > > > > > > >> > > > > configure: WARNING: errno.h:
section
> > > "Present
> > > > > But
> > > > > > > > Cannot
> > > > > > > > > > Be
> > > > > > > > > > > >> > > Compiled"
> > > > > > > > > > > >> > > > > configure: WARNING: errno.h:
proceeding with
> > the
> > > > > > > > compiler's
> > > > > > > > > > > result
> > > > > > > > > > > >> > > > > configure: WARNING: ##
> > > > > > > > --------------------------------
> > > > > > > > > ##
> > > > > > > > > > > >> > > > > configure: WARNING: ## Report
this to
> > > > > > > > met_help at ucar.edu
> > > > > > > > > > ##
> > > > > > > > > > > >> > > > > configure: WARNING: ##
> > > > > > > > --------------------------------
> > > > > > > > > ##
> > > > > > > > > > > >> > > > >
> > > > > > > > > > > >> > > > > and the same for fcntl.h, limits.h,
> stddef.h,
> > > > file.h
> > > > > > and
> > > > > > > > > > > param.h.
> > > > > > > > > > > >> > > > >
> > > > > > > > > > > >> > > > > When I try to make install, I get
this error
> > on
> > > > the
> > > > > > tail
> > > > > > > > of
> > > > > > > > > > the
> > > > > > > > > > > >> log:
> > > > > > > > > > > >> > > > >
> > > > > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > > > > > configalloc(yy_size_t)’:
> > > > > > > > > > > >> > > > > config_scanner.cc:2179:31: error:
> ‘rpl_malloc’
> > > was
> > > > > not
> > > > > > > > > > declared
> > > > > > > > > > > in
> > > > > > > > > > > >> > this
> > > > > > > > > > > >> > > > > scope
> > > > > > > > > > > >> > > > > config_scanner.cc: In function ‘void*
> > > > > > > configrealloc(void*,
> > > > > > > > > > > >> > yy_size_t)’:
> > > > > > > > > > > >> > > > > config_scanner.cc:2191:46: error:
> > ‘rpl_realloc’
> > > > was
> > > > > > not
> > > > > > > > > > declared
> > > > > > > > > > > >> in
> > > > > > > > > > > >> > > this
> > > > > > > > > > > >> > > > > scope
> > > > > > > > > > > >> > > > > /* The cast to (char *) in the
following
> > > > > > accommodates
> > > > > > > > both
> > > > > > > > > > > >> > > > >
> > ^
> > > > > > > > > > > >> > > > > make[3]: ***
> [libvx_config_a-config_scanner.o]
> > > > > Error 1
> > > > > > > > > > > >> > > > > make[3]: Leaving directory
> > > > > > > > > > > >> > > > >
> > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > > > > > > > > > >> > > > > make[2]: *** [install-recursive]
Error 1
> > > > > > > > > > > >> > > > > make[2]: Leaving directory
> > > > > > > > > > > >> > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic'
> > > > > > > > > > > >> > > > > make[1]: *** [install-recursive]
Error 1
> > > > > > > > > > > >> > > > > make[1]: Leaving directory
> > > > > > > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > > > > > > > > >> > > > > make: *** [install-recursive] Error 1
> > > > > > > > > > > >> > > > >
> > > > > > > > > > > >> > > > > Not sure how to address either of
these,
> > > hopefully
> > > > > you
> > > > > > > > guys
> > > > > > > > > > can
> > > > > > > > > > > >> > provide
> > > > > > > > > > > >> > > > > some insight.
> > > > > > > > > > > >> > > > >
> > > > > > > > > > > >> > > > > Thanks!
> > > > > > > > > > > >> > > > > --
> > > > > > > > > > > >> > > > > *Taylor Mandelbaum*
> > > > > > > > > > > >> > > > > Research Technician
> > > > > > > > > > > >> > > > > SoMAS | Stony Brook University
> > > > > > > > > > > >> > > > > 678.468.5789
> > > > > > > > > > > >> > > > >
> > > > > > > > > > > >> > > > >
> > > > > > > > > > > >> > > >
> > > > > > > > > > > >> > > >
> > > > > > > > > > > >> > >
> > > > > > > > > > > >> > > --
> > > > > > > > > > > >> > > *Taylor Mandelbaum*
> > > > > > > > > > > >> > > Research Technician
> > > > > > > > > > > >> > > SoMAS | Stony Brook University
> > > > > > > > > > > >> > > 678.468.5789
> > > > > > > > > > > >> > >
> > > > > > > > > > > >> > >
> > > > > > > > > > > >> >
> > > > > > > > > > > >> >
> > > > > > > > > > > >>
> > > > > > > > > > > >> --
> > > > > > > > > > > >> *Taylor Mandelbaum*
> > > > > > > > > > > >> Research Technician
> > > > > > > > > > > >> SoMAS | Stony Brook University
> > > > > > > > > > > >> 678.468.5789
> > > > > > > > > > > >>
> > > > > > > > > > > >>
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > --
> > > > > > > > > > *Taylor Mandelbaum*
> > > > > > > > > > Research Technician
> > > > > > > > > > SoMAS | Stony Brook University
> > > > > > > > > > 678.468.5789
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > > *Taylor Mandelbaum*
> > > > > > > > Research Technician
> > > > > > > > SoMAS | Stony Brook University
> > > > > > > > 678.468.5789
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > > > --
> > > > > > *Taylor Mandelbaum*
> > > > > > Research Technician
> > > > > > SoMAS | Stony Brook University
> > > > > > 678.468.5789
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > > > --
> > > > *Taylor Mandelbaum*
> > > > Research Technician
> > > > SoMAS | Stony Brook University
> > > > 678.468.5789
> > > >
> > > >
> > >
> > >
> >
> > --
> > *Taylor Mandelbaum*
> > Research Technician
> > SoMAS | Stony Brook University
> > 678.468.5789
> >
> >
>
>
--
*Taylor Mandelbaum*
Research Technician
SoMAS | Stony Brook University
678.468.5789
------------------------------------------------
Subject: met install help
From: Julie Prestopnik
Time: Thu Feb 21 08:47:37 2019
Taylor, that is great news! Thank you for letting us know. I'll go
ahead
and close this ticket. Please don't hesitate to write again to
met_help at ucar.edu with any questions or issues you encounter.
Thanks!
Julie
On Wed, Feb 20, 2019 at 4:38 PM Taylor Mandelbaum via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
>
> I merged them, had an issue with grib2c which i re-made onto my
local
> directory... and I think I got MET compiled!
>
> On Wed, Feb 20, 2019 at 4:59 PM Julie Prestopnik via RT
<met_help at ucar.edu
> >
> wrote:
>
> > Hi Taylor, for met-8.0 both the NetCDF-C package and the NetCDF-
CXX
> package
> > are required. I see you said that you have installed version
4.6.2 for
> > NetCDF-C and version 4.3.0 for NetCDF-CXX. I usually install
netcdf
> > -c-4.4.1.1and netcdf-cxx4-4.3.0, but don't think that other
versions
> should
> > be a problem.
> >
> > The error you received:
> >
> > nc_utils.h:22:18: error: netcdf: No such file or directory
> > >
> >
> > indicates that MET is having a difficult time finding the file
"netcdf",
> > which is included in the NetCDF-CXX installation.
> >
> > I see that you have MET_NETCDF set to /E1/taylorm/netcdf462. It
is
> > important to note that there is only one MET_NETCDF environment
variable,
> > so both NetCDF packages are expected to be installed at the same
> location.
> > Is the file "netcdf" located at $MET_NETCDF/include/
> > (/E1/taylorm/netcdf462/include)?
> >
> >
> > Here is a quick reference checklist for NetCDF4 installation that
you can
> > use to see if you have the necessary files:
> >
> > Files for NetCDF4 C:
> >
> > $MET_NETCDF/include/netcdf.h
> > $MET_NETCDF/lib/libnetcdf.a
> > $MET_NETCDF/lib/libnetcdf.so
> >
> > Files for NetCDF4 C++:
> >
> > $MET_NETCDF/include/netcdf
> > $MET_NETCDF/lib/libnetcdf_c++4.a
> > $MET_NETCDF/lib/libnetcdf_c++4.so
> >
> > I hope that helps. Please let me know if you have any questions.
> >
> > Thanks,
> > Julie
> >
> > On Wed, Feb 20, 2019 at 12:37 PM Taylor Mandelbaum via RT <
> > met_help at ucar.edu>
> > wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > >
> > > That solved that problem, onto the next one:
> > >
> > > nc_utils.h:22:18: fatal error: netcdf: No such file or directory
> > >
> > > I had installed netcdf 4.6.2 most recently and netcdfcxx 4.3.0,
so I'm
> > not
> > > sure what this is about.
> > >
> > >
> > > On Wed, Feb 20, 2019 at 2:12 PM Julie Prestopnik via RT <
> > met_help at ucar.edu
> > > >
> > > wrote:
> > >
> > > > Hi Taylor.
> > > >
> > > > I see the following in your config.log file:
> > > >
> > > > /usr/bin/ld: cannot find -lpython2.7-lpthread
> > > >
> > > > It looks like MET_PYTHON_LD was set in the following way:
> > > >
> > > > MET_PYTHON_LD='-L/cm/shared/apps/python/2.7.15/lib
> -lpython2.7-lpthread
> > > > > -ldl -lutil -lm -Xlinker -export-dynamic'
> > > > >
> > > >
> > > > Note, the lack of space between "-lpython2.7" and "-lpthread"
in
> both
> > > the
> > > > error message and the setting of MET_PYTHON_LD.
> > > >
> > > > Please copy and paste the following:
> > > >
> > > > for csh:
> > > > >
> > > > > setenv MET_PYTHON_LD -L/cm/shared/apps/python/2.7.15/lib\
> > -lpython2.7\
> > > > > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> > > > >
> > > > > for bash:
> > > > >
> > > > > export MET_PYTHON_LD=-L/cm/shared/apps/python/2.7.15/lib\
> > -lpython2.7\
> > > > > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> > > >
> > > >
> > > > Those lines should capture the proper spaces.
> > > >
> > > > Give that a try and reconfigure MET. Please let me know how it
goes.
> > > > Thanks!
> > > >
> > > > Julie
> > > >
> > > > On Tue, Feb 19, 2019 at 6:11 PM Taylor Mandelbaum via RT <
> > > > met_help at ucar.edu>
> > > > wrote:
> > > >
> > > > >
> > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502 >
> > > > >
> > > > > Hey Julie,
> > > > >
> > > > > I set those up in my bashrc but am still having an issue
with the
> > > config
> > > > > not proceeding due to the c++ compiler:
> > > > >
> > > > > "checking whether the C++ compiler works... no
> > > > > configure: error: in `/home/taylorm/MET8/met-8.0_bugfix':
> > > > > configure: error: C++ compiler cannot create executables"
> > > > >
> > > > > attached the most recent config log.
> > > > >
> > > > > Thanks again!
> > > > >
> > > > > On Tue, Feb 19, 2019 at 12:47 PM Julie Prestopnik via RT <
> > > > > met_help at ucar.edu>
> > > > > wrote:
> > > > >
> > > > > > Hi Taylor,
> > > > > >
> > > > > > Great! Thanks for the update. Please try setting the
following:
> > > > > >
> > > > > > or csh:
> > > > > >
> > > > > > setenv MET_PYTHON_CC `python-config --cflags`
> > > > > > setenv MET_PYTHON_LD -L/cm/shared/apps/python/2.7.15/lib\
> > > -lpython2.7\
> > > > > > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> > > > > >
> > > > > > for bash:
> > > > > >
> > > > > > export MET_PYTHON_CC=`python-config --cflags`
> > > > > > export MET_PYTHON_LD=-L/cm/shared/apps/python/2.7.15/lib\
> > > -lpython2.7\
> > > > > > -lpthread\ -ldl\ -lutil\ -lm\ -Xlinker\ -export-dynamic
> > > > > >
> > > > > > Please set up your other environment variables and then
try
> > > > reconfiguring
> > > > > > and reinstalling MET. Please let me know how it goes.
> > > > > >
> > > > > > Thanks,
> > > > > > Julie
> > > > > >
> > > > > > On Sat, Feb 16, 2019 at 2:36 PM Taylor Mandelbaum via RT <
> > > > > > met_help at ucar.edu>
> > > > > > wrote:
> > > > > >
> > > > > > >
> > > > > > > <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> >
> > > > > > >
> > > > > > > Hey Julie,
> > > > > > >
> > > > > > > The libpython2.7.so file is in the first directory you
> > > > > > > mentioned, /cm/shared/apps/python/2.7.15/lib.
> > > > > > >
> > > > > > > Sorry for the delay, busy week this week.
> > > > > > >
> > > > > > > On Mon, Feb 11, 2019 at 1:28 PM Julie Prestopnik via RT
<
> > > > > > met_help at ucar.edu
> > > > > > > >
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi Taylor. Thanks for the update. I'm glad we are
making
> some
> > > > > > progress.
> > > > > > > >
> > > > > > > > From your config.log file:
> > > > > > > >
> > > > > > > > > /usr/bin/ld: cannot find -lpython2.7
> > > > > > > > > collect2: error: ld returned 1 exit status
> > > > > > > > >
> > > > > > > > and from the output you provided from running "python-
config
> > > > > > --ldflags",
> > > > > > > I
> > > > > > > > can see what the problem is.
> > > > > > > >
> > > > > > > > It looks like the output "python-config --ldflags"
> > unfortunately
> > > > does
> > > > > > not
> > > > > > > > contain all of the information that the environment
variable
> > > > > > > MET_PYTHON_LD
> > > > > > > > needs to have.
> > > > > > > >
> > > > > > > > In order to proceed, we need to find the location of
the
> > > > libpython.a
> > > > > > file
> > > > > > > > or the libpython.so file. Based on the information
from the
> > > output
> > > > > > from
> > > > > > > > running "python-config --cflags", I am going to guess
that
> the
> > > > > > libpython
> > > > > > > > file lives in /cm/shared/apps/python/2.7.15/lib or in
> > > > > > > > /cm/shared/apps/python/2.7.15/lib/python2.7. Could
you
> please
> > > > check
> > > > > > > those
> > > > > > > > directories and see if you can find a libpython.a file
or
> > > > > libpython.so
> > > > > > > > file? If so, please send me an email with the path to
the
> > file.
> > > > You
> > > > > > > could
> > > > > > > > just run "ls <path>" replacing <path> with the full
path and
> > send
> > > > me
> > > > > > the
> > > > > > > > output. Then, I will send you a command that you can
run to
> > set
> > > > the
> > > > > > > value
> > > > > > > > of the environment variable MET_PYTHON_LD.
> > > > > > > >
> > > > > > > > Thanks!
> > > > > > > >
> > > > > > > > Julie
> > > > > > > >
> > > > > > > > On Tue, Feb 5, 2019 at 7:16 PM Taylor Mandelbaum via
RT <
> > > > > > > met_help at ucar.edu
> > > > > > > > >
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > >
> > > > > > > > > <URL:
> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > >
> > > > > > > > >
> > > > > > > > > Hey Julie,
> > > > > > > > >
> > > > > > > > > Sorry for the delayed response. We got python 2.7.15
set up
> > as
> > > a
> > > > > > > module.
> > > > > > > > I
> > > > > > > > > ran python2.7-config --cflags and ..--ldflags:
> > > > > > > > >
> > > > > > > > > -I/cm/shared/apps/python/2.7.15/include/python2.7
> > > > > > > > > -I/cm/shared/apps/python/2.7.15/include/python2.7
> > > > > > -fno-strict-aliasing
> > > > > > > -g
> > > > > > > > > -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-
prototypes
> > > > > > > > >
> > > > > > > > > -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker
> > -export-dynamic
> > > > > > > > >
> > > > > > > > > Those are the returned outputs. I updated my bashrc
with
> > module
> > > > > load
> > > > > > > > > python/2.7; same issue is occurring with c++.
Attached the
> > > config
> > > > > > log.
> > > > > > > > >
> > > > > > > > > Thanks again for your help.
> > > > > > > > >
> > > > > > > > > On Mon, Jan 28, 2019 at 1:43 PM Julie Prestopnik via
RT <
> > > > > > > > met_help at ucar.edu
> > > > > > > > > >
> > > > > > > > > wrote:
> > > > > > > > >
> > > > > > > > > > Hi Taylor.
> > > > > > > > > >
> > > > > > > > > > Thanks for getting HDF5 and NetCDF4 C and C++
installed.
> > > > > > > > > >
> > > > > > > > > > Thank you also for attaching your config.log file.
I see
> > in
> > > > your
> > > > > > > > > > config.log file:
> > > > > > > > > >
> > > > > > > > > > > /cm/shared/apps/python/3.5.2/include/python3.5m:
file
> not
> > > > > > > recognized:
> > > > > > > > > Is
> > > > > > > > > > a
> > > > > > > > > > > directory
> > > > > > > > > > >
> > > > > > > > > > collect2: error: ld returned 1 exit status
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > It looks like there is a problem with the linker
in that
> it
> > > is
> > > > > > > finding
> > > > > > > > a
> > > > > > > > > > directory instead of a file. However, before we
> proceed, I
> > > > > should
> > > > > > > tell
> > > > > > > > > you
> > > > > > > > > > that the Python functionality with met-8.0
requires
> Python
> > > 2.7
> > > > to
> > > > > > be
> > > > > > > > > used.
> > > > > > > > > > Is Python 2.7 available on your system? If so,
please
> let
> > me
> > > > > know.
> > > > > > > > > >
> > > > > > > > > > I can help you set up the necessary environment
variables
> > > that
> > > > > are
> > > > > > > > > required
> > > > > > > > > > to use the python embedding functionality. You'll
need
> to
> > > set
> > > > > > > > > > MET_PYTHON_CC and MET_PYTHON_LD prior to
configuring MET.
> > > > > Usually
> > > > > > > the
> > > > > > > > > > following is sufficient for csh:
> > > > > > > > > >
> > > > > > > > > > setenv MET_PYTHON_CC `python-config --cflags`
> > > > > > > > > >
> > > > > > > > > > setenv MET_PYTHON_LD `python-config --ldflags`
> > > > > > > > > >
> > > > > > > > > > for bash:
> > > > > > > > > >
> > > > > > > > > > export MET_PYTHON_CC=`python-config --cflags`
> > > > > > > > > >
> > > > > > > > > > export MET_PYTHON_LD=`python-config --ldflags`
> > > > > > > > > >
> > > > > > > > > > However, it may not be. Please run the following
> commands
> > > > (using
> > > > > > > > Python
> > > > > > > > > > 2.7) and send me the output:
> > > > > > > > > >
> > > > > > > > > > python-config --cflags
> > > > > > > > > > python-config --ldflags
> > > > > > > > > >
> > > > > > > > > > Thanks!
> > > > > > > > > >
> > > > > > > > > > Julie
> > > > > > > > > >
> > > > > > > > > > On Sun, Jan 27, 2019 at 9:11 AM Taylor Mandelbaum
via RT
> <
> > > > > > > > > > met_help at ucar.edu>
> > > > > > > > > > wrote:
> > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > <URL:
> > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > >
> > > > > > > > > > >
> > > > > > > > > > > Hey all,
> > > > > > > > > > >
> > > > > > > > > > > I got netcdf4 c and c++ installed; I'm running
into an
> > > issue
> > > > > now
> > > > > > on
> > > > > > > > > > > configuring MET which says error: C++ compiler
cannot
> > > create
> > > > > > > > > executables.
> > > > > > > > > > > It looks like in the config log that g++ is
getting
> > > imported
> > > > > but
> > > > > > > > > erroring
> > > > > > > > > > > out when trying to use -V as a command option.
Attached
> > the
> > > > > > newest
> > > > > > > > > config
> > > > > > > > > > > log here.
> > > > > > > > > > >
> > > > > > > > > > > When I configure it, this is the command I'm
using:
> > > > > > > > > > >
> > > > > > > > > > > ./configure --prefix=/E1/taylorm/MET8 --enable-
grib2
> > > > > > > --enable-python
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > On Wed, Jan 16, 2019 at 12:23 PM Julie
Prestopnik via
> RT
> > <
> > > > > > > > > > > met_help at ucar.edu>
> > > > > > > > > > > wrote:
> > > > > > > > > > >
> > > > > > > > > > > > Hi Taylor. In talking with more with John
about your
> > > > > > config.log
> > > > > > > > file
> > > > > > > > > > we
> > > > > > > > > > > > see that CC is set to use icc (intel), but CXX
and
> F77
> > > are
> > > > > set
> > > > > > to
> > > > > > > > use
> > > > > > > > > > g++
> > > > > > > > > > > > and gfortran (GNU).
> > > > > > > > > > > >
> > > > > > > > > > > > CC='/home/taylorm/MET8/met-8.0_bugfix/compile
> > > > > > > > > > > >
> > > > > > > > > >
> > > > > > > >
> > > > > >
> > > >
> >
/cm/shared/apps/intel/compilers_and_libraries/2016.4.258/bin/intel64/icc'
> > > > > > > > > > > > CXX='g++'
> > > > > > > > > > > > F77='gfortran'
> > > > > > > > > > > >
> > > > > > > > > > > > Let's see if we can solve the immediate
problem
> before
> > > > > worrying
> > > > > > > > about
> > > > > > > > > > any
> > > > > > > > > > > > potential problems with the external
libraries. For
> > now,
> > > > > > please
> > > > > > > > > choose
> > > > > > > > > > > > either the GNU compilers or the Intel
compilers and
> set
> > > the
> > > > > > > > following
> > > > > > > > > > > > variables accordingly. You can chose one and
then
> > simply
> > > > run
> > > > > > the
> > > > > > > > > > > commands
> > > > > > > > > > > > below.
> > > > > > > > > > > >
> > > > > > > > > > > > *For GNU:*
> > > > > > > > > > > > export CC=`which gcc`
> > > > > > > > > > > > export CXX=`which g++`
> > > > > > > > > > > > export F77=`which gfortran`
> > > > > > > > > > > >
> > > > > > > > > > > > *For Intel:*
> > > > > > > > > > > >
> > > > > > > > > > > > export CC=`which icc`
> > > > > > > > > > > > export CXX=`which icc`
> > > > > > > > > > > > export F77=`which ifort`
> > > > > > > > > > > >
> > > > > > > > > > > > Then run "make clean", rerun the configure
command,
> and
> > > > then
> > > > > > try
> > > > > > > to
> > > > > > > > > > make
> > > > > > > > > > > > MET again.
> > > > > > > > > > > >
> > > > > > > > > > > > Let's go from there and see how it works out.
Please
> > let
> > > > me
> > > > > > > know.
> > > > > > > > > > > >
> > > > > > > > > > > > Julie
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > > On Wed, Jan 16, 2019 at 10:06 AM Julie
Prestopnik <
> > > > > > > > jpresto at ucar.edu>
> > > > > > > > > > > > wrote:
> > > > > > > > > > > >
> > > > > > > > > > > > > Hi Taylor. Thank you for all of this
information.
> > > > > > > > > > > > >
> > > > > > > > > > > > > Since the libraries were previously
installed and
> we
> > > > cannot
> > > > > > be
> > > > > > > > > > certain
> > > > > > > > > > > > > which compiler was used, are you able and
would you
> > be
> > > > > > > > comfortable
> > > > > > > > > > > > > installing each of the dependent libraries
and not
> > > using
> > > > > the
> > > > > > > > > > previously
> > > > > > > > > > > > > installed versions? If so, we have an
install
> script
> > > > that
> > > > > I
> > > > > > > can
> > > > > > > > > > point
> > > > > > > > > > > > you
> > > > > > > > > > > > > to, which would install all of the packages
and MET
> > as
> > > > > > well. I
> > > > > > > > can
> > > > > > > > > > > walk
> > > > > > > > > > > > > through this with you via google hangouts
and you
> can
> > > > share
> > > > > > > your
> > > > > > > > > > screen
> > > > > > > > > > > > so
> > > > > > > > > > > > > we can make sure it is going smoothly. I
could
> do a
> > > > > > hangouts
> > > > > > > > > > session
> > > > > > > > > > > > with
> > > > > > > > > > > > > you tomorrow at 1:15pm (Mountain time) or on
Friday
> > at
> > > > > 9:00am
> > > > > > > > > > (Mountain
> > > > > > > > > > > > > time). If those times don't work. I can
get you
> > > started
> > > > > > with
> > > > > > > > very
> > > > > > > > > > > > > specific instructions via email and we can
continue
> > to
> > > > work
> > > > > > > > through
> > > > > > > > > > any
> > > > > > > > > > > > > problems. We can also set up a different
time for
> > next
> > > > > week,
> > > > > > > > > > however,
> > > > > > > > > > > I
> > > > > > > > > > > > > didn't want you to have to wait that long.
Please
> > let
> > > me
> > > > > > know
> > > > > > > > your
> > > > > > > > > > > > > preference.
> > > > > > > > > > > > >
> > > > > > > > > > > > > If you think that icc may not be working
properly,
> > then
> > > > you
> > > > > > > > should
> > > > > > > > > > > > > probably use the GNU set of compilers,
unless there
> > is
> > > > some
> > > > > > > > reason
> > > > > > > > > > not
> > > > > > > > > > > > to,
> > > > > > > > > > > > > in which case you may need to get a system
> > > administrator
> > > > > > > correct
> > > > > > > > > the
> > > > > > > > > > > > > problems with the intel compiler.
> > > > > > > > > > > > >
> > > > > > > > > > > > > Running "which g++" and running "which
gfortran"
> can
> > > tell
> > > > > you
> > > > > > > > what
> > > > > > > > > > the
> > > > > > > > > > > > CXX
> > > > > > > > > > > > > and F77 paths should be set to. Please let
me know
> > if
> > > > you
> > > > > > have
> > > > > > > > any
> > > > > > > > > > > > issues
> > > > > > > > > > > > > with that.
> > > > > > > > > > > > >
> > > > > > > > > > > > > Julie
> > > > > > > > > > > > >
> > > > > > > > > > > > > On Tue, Jan 15, 2019 at 5:53 PM Taylor
Mandelbaum
> via
> > > RT
> > > > <
> > > > > > > > > > > > > met_help at ucar.edu> wrote:
> > > > > > > > > > > > >
> > > > > > > > > > > > >>
> > > > > > > > > > > > >> <URL:
> > > > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > >
> > > > > > > > > > > > >>
> > > > > > > > > > > > >> Hey Julie,
> > > > > > > > > > > > >>
> > > > > > > > > > > > >> 1) They were previously installed, but I
just
> tried
> > > > > running
> > > > > > it
> > > > > > > > > with
> > > > > > > > > > > some
> > > > > > > > > > > > >> of
> > > > > > > > > > > > >> my own installed versions and they're not
working
> > > > properly
> > > > > > > (e.g.
> > > > > > > > > the
> > > > > > > > > > > > make
> > > > > > > > > > > > >> install fails due to gsl/gsl_cdf.h
missing...
> > though I
> > > > set
> > > > > > > > MET_GSL
> > > > > > > > > > to
> > > > > > > > > > > my
> > > > > > > > > > > > >> gsl-2.5 directory).
> > > > > > > > > > > > >>
> > > > > > > > > > > > >> 2) Not sure how I can verify that one,
though I
> > think
> > > > > > they're
> > > > > > > > not
> > > > > > > > > as
> > > > > > > > > > > > I've
> > > > > > > > > > > > >> seen GNU and Intel prompts in the config
output.
> My
> > CC
> > > > var
> > > > > > in
> > > > > > > my
> > > > > > > > > > > bashrc
> > > > > > > > > > > > >> links to an Intel compiler.
> > > > > > > > > > > > >>
> > > > > > > > > > > > >> 3) I followed those for the packages,
though for
> the
> > > > > > compilers
> > > > > > > > > > > section,
> > > > > > > > > > > > I
> > > > > > > > > > > > >> do not know my CXX or F77 paths on the hpc
that
> I'm
> > > > > using. I
> > > > > > > > also
> > > > > > > > > > > think
> > > > > > > > > > > > >> the
> > > > > > > > > > > > >> icc is not working properly as I could not
run icc
> > > > > without a
> > > > > > > > > license
> > > > > > > > > > > > >> prompt
> > > > > > > > > > > > >> coming up.
> > > > > > > > > > > > >>
> > > > > > > > > > > > >> I'm not sure if any of that helps, but let
me
> know.
> > > > Maybe
> > > > > > some
> > > > > > > > of
> > > > > > > > > > > these
> > > > > > > > > > > > >> issues are still on our end. The fact that
met
> needs
> > > to
> > > > > only
> > > > > > > use
> > > > > > > > > one
> > > > > > > > > > > > >> compiler might be the issue...
> > > > > > > > > > > > >>
> > > > > > > > > > > > >> On Tue, Jan 15, 2019 at 11:35 AM Julie
Prestopnik
> > via
> > > > RT <
> > > > > > > > > > > > >> met_help at ucar.edu>
> > > > > > > > > > > > >> wrote:
> > > > > > > > > > > > >>
> > > > > > > > > > > > >> > Hi Taylor. Thank you for passing along
your
> > > files. I
> > > > > > have
> > > > > > > a
> > > > > > > > > few
> > > > > > > > > > > > >> questions
> > > > > > > > > > > > >> > for you.
> > > > > > > > > > > > >> >
> > > > > > > > > > > > >> > 1) Are you installing the external
libraries
> > > yourself
> > > > or
> > > > > > > were
> > > > > > > > > they
> > > > > > > > > > > > >> > previously installed?
> > > > > > > > > > > > >> > 2) Can you please verify that the
external
> > libraries
> > > > and
> > > > > > MET
> > > > > > > > are
> > > > > > > > > > > being
> > > > > > > > > > > > >> > built with the same family of compilers
(e.g.
> all
> > > are
> > > > > > built
> > > > > > > > with
> > > > > > > > > > > GNU,
> > > > > > > > > > > > or
> > > > > > > > > > > > >> > all are build with Intel, etc.)? Which
compiler
> > are
> > > > you
> > > > > > > > using?
> > > > > > > > > > > > >> > 3) Are you following the directions on
this page
> > as
> > > > your
> > > > > > > > > > > instructions
> > > > > > > > > > > > >> for
> > > > > > > > > > > > >> > installation?
> > > > > > > > > > > > >> >
> > > > > > > > > > > > >> >
> > > > > > > > > > > > >>
> > > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv6.1/tutorial.php?name=compilation&category=req_libs
> > > > > > > > > > > > >> >
> > > > > > > > > > > > >> > Thank you!
> > > > > > > > > > > > >> >
> > > > > > > > > > > > >> > Julie
> > > > > > > > > > > > >> >
> > > > > > > > > > > > >> > On Mon, Jan 14, 2019 at 4:41 PM Taylor
> Mandelbaum
> > > via
> > > > > RT <
> > > > > > > > > > > > >> > met_help at ucar.edu>
> > > > > > > > > > > > >> > wrote:
> > > > > > > > > > > > >> >
> > > > > > > > > > > > >> > >
> > > > > > > > > > > > >> > > <URL:
> > > > > > > >
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > > > >
> > > > > > > > > > > > >> > >
> > > > > > > > > > > > >> > > Hey Julie,
> > > > > > > > > > > > >> > >
> > > > > > > > > > > > >> > > I attached the config and make_install
logs
> > here.
> > > We
> > > > > > could
> > > > > > > > do
> > > > > > > > > a
> > > > > > > > > > > > >> hangouts
> > > > > > > > > > > > >> > > session as well if you can't pinpoint
the
> issue;
> > > I'm
> > > > > > > > remoting
> > > > > > > > > in
> > > > > > > > > > > > from
> > > > > > > > > > > > >> my
> > > > > > > > > > > > >> > > home windows computer so it will be a
bit
> hacky.
> > > > > > > > > > > > >> > >
> > > > > > > > > > > > >> > > On Mon, Jan 14, 2019 at 5:13 PM Julie
> Prestopnik
> > > via
> > > > > RT
> > > > > > <
> > > > > > > > > > > > >> > met_help at ucar.edu
> > > > > > > > > > > > >> > > >
> > > > > > > > > > > > >> > > wrote:
> > > > > > > > > > > > >> > >
> > > > > > > > > > > > >> > > > Hi Taylor. It is difficult to tell
what is
> > > going
> > > > > > > without
> > > > > > > > > more
> > > > > > > > > > > > >> context.
> > > > > > > > > > > > >> > > > Could you please send me your
config.log
> file
> > > and
> > > > > your
> > > > > > > > > > make.log
> > > > > > > > > > > > >> file?
> > > > > > > > > > > > >> > > >
> > > > > > > > > > > > >> > > > We could also consider doing a
hangouts
> > session
> > > > > where
> > > > > > > you
> > > > > > > > > can
> > > > > > > > > > > > share
> > > > > > > > > > > > >> > your
> > > > > > > > > > > > >> > > > screen, and I can directly help that
way.
> > > Either
> > > > > way
> > > > > > > > > though,
> > > > > > > > > > if
> > > > > > > > > > > > you
> > > > > > > > > > > > >> > > could
> > > > > > > > > > > > >> > > > please send those files, I would
appreciate
> > it.
> > > > > > > > > > > > >> > > >
> > > > > > > > > > > > >> > > > Thanks,
> > > > > > > > > > > > >> > > > Julie
> > > > > > > > > > > > >> > > >
> > > > > > > > > > > > >> > > > Thanks!
> > > > > > > > > > > > >> > > >
> > > > > > > > > > > > >> > > > Julie
> > > > > > > > > > > > >> > > >
> > > > > > > > > > > > >> > > > On Mon, Jan 14, 2019 at 3:05 PM
Taylor
> > > Mandelbaum
> > > > > via
> > > > > > > RT <
> > > > > > > > > > > > >> > > > met_help at ucar.edu>
> > > > > > > > > > > > >> > > > wrote:
> > > > > > > > > > > > >> > > >
> > > > > > > > > > > > >> > > > >
> > > > > > > > > > > > >> > > > > Mon Jan 14 15:05:33 2019: Request
88502
> was
> > > > acted
> > > > > > > upon.
> > > > > > > > > > > > >> > > > > Transaction: Ticket created by
> > > > > > > > > > > taylor.mandelbaum at stonybrook.edu
> > > > > > > > > > > > >> > > > > Queue: met_help
> > > > > > > > > > > > >> > > > > Subject: met install help
> > > > > > > > > > > > >> > > > > Owner: Nobody
> > > > > > > > > > > > >> > > > > Requestors:
> > > taylor.mandelbaum at stonybrook.edu
> > > > > > > > > > > > >> > > > > Status: new
> > > > > > > > > > > > >> > > > > Ticket <URL:
> > > > > > > > > > > > >> >
> > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88502
> > > > > > > > > > > > >> > > >
> > > > > > > > > > > > >> > > > >
> > > > > > > > > > > > >> > > > >
> > > > > > > > > > > > >> > > > > Hey all,
> > > > > > > > > > > > >> > > > >
> > > > > > > > > > > > >> > > > > I'm presently trying to compile MET
8.0 on
> > our
> > > > > HPC;
> > > > > > > > when I
> > > > > > > > > > > > >> configure
> > > > > > > > > > > > >> > > it,
> > > > > > > > > > > > >> > > > > I'm getting a few warnings on .h
files:
> > > > > > > > > > > > >> > > > >
> > > > > > > > > > > > >> > > > > configure: WARNING: errno.h:
present but
> > > cannot
> > > > be
> > > > > > > > > compiled
> > > > > > > > > > > > >> > > > > configure: WARNING: errno.h:
check for
> > > > missing
> > > > > > > > > > > prerequisite
> > > > > > > > > > > > >> > > headers?
> > > > > > > > > > > > >> > > > > configure: WARNING: errno.h: see
the
> > Autoconf
> > > > > > > > > documentation
> > > > > > > > > > > > >> > > > > configure: WARNING: errno.h:
section
> > > > "Present
> > > > > > But
> > > > > > > > > Cannot
> > > > > > > > > > > Be
> > > > > > > > > > > > >> > > Compiled"
> > > > > > > > > > > > >> > > > > configure: WARNING: errno.h:
proceeding
> with
> > > the
> > > > > > > > > compiler's
> > > > > > > > > > > > result
> > > > > > > > > > > > >> > > > > configure: WARNING: ##
> > > > > > > > > --------------------------------
> > > > > > > > > > ##
> > > > > > > > > > > > >> > > > > configure: WARNING: ## Report
this to
> > > > > > > > > met_help at ucar.edu
> > > > > > > > > > > ##
> > > > > > > > > > > > >> > > > > configure: WARNING: ##
> > > > > > > > > --------------------------------
> > > > > > > > > > ##
> > > > > > > > > > > > >> > > > >
> > > > > > > > > > > > >> > > > > and the same for fcntl.h, limits.h,
> > stddef.h,
> > > > > file.h
> > > > > > > and
> > > > > > > > > > > > param.h.
> > > > > > > > > > > > >> > > > >
> > > > > > > > > > > > >> > > > > When I try to make install, I get
this
> error
> > > on
> > > > > the
> > > > > > > tail
> > > > > > > > > of
> > > > > > > > > > > the
> > > > > > > > > > > > >> log:
> > > > > > > > > > > > >> > > > >
> > > > > > > > > > > > >> > > > > config_scanner.cc: In function
‘void*
> > > > > > > > > > configalloc(yy_size_t)’:
> > > > > > > > > > > > >> > > > > config_scanner.cc:2179:31: error:
> > ‘rpl_malloc’
> > > > was
> > > > > > not
> > > > > > > > > > > declared
> > > > > > > > > > > > in
> > > > > > > > > > > > >> > this
> > > > > > > > > > > > >> > > > > scope
> > > > > > > > > > > > >> > > > > config_scanner.cc: In function
‘void*
> > > > > > > > configrealloc(void*,
> > > > > > > > > > > > >> > yy_size_t)’:
> > > > > > > > > > > > >> > > > > config_scanner.cc:2191:46: error:
> > > ‘rpl_realloc’
> > > > > was
> > > > > > > not
> > > > > > > > > > > declared
> > > > > > > > > > > > >> in
> > > > > > > > > > > > >> > > this
> > > > > > > > > > > > >> > > > > scope
> > > > > > > > > > > > >> > > > > /* The cast to (char *) in the
following
> > > > > > > accommodates
> > > > > > > > > both
> > > > > > > > > > > > >> > > > >
> > > ^
> > > > > > > > > > > > >> > > > > make[3]: ***
> > [libvx_config_a-config_scanner.o]
> > > > > > Error 1
> > > > > > > > > > > > >> > > > > make[3]: Leaving directory
> > > > > > > > > > > > >> > > > >
> > > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src/basic/vx_config'
> > > > > > > > > > > > >> > > > > make[2]: *** [install-recursive]
Error 1
> > > > > > > > > > > > >> > > > > make[2]: Leaving directory
> > > > > > > > > > > > >> > `/E1/taylorm/MET8/met-
8.0_bugfix/src/basic'
> > > > > > > > > > > > >> > > > > make[1]: *** [install-recursive]
Error 1
> > > > > > > > > > > > >> > > > > make[1]: Leaving directory
> > > > > > > > > > > `/E1/taylorm/MET8/met-8.0_bugfix/src'
> > > > > > > > > > > > >> > > > > make: *** [install-recursive] Error
1
> > > > > > > > > > > > >> > > > >
> > > > > > > > > > > > >> > > > > Not sure how to address either of
these,
> > > > hopefully
> > > > > > you
> > > > > > > > > guys
> > > > > > > > > > > can
> > > > > > > > > > > > >> > provide
> > > > > > > > > > > > >> > > > > some insight.
> > > > > > > > > > > > >> > > > >
> > > > > > > > > > > > >> > > > > Thanks!
> > > > > > > > > > > > >> > > > > --
> > > > > > > > > > > > >> > > > > *Taylor Mandelbaum*
> > > > > > > > > > > > >> > > > > Research Technician
> > > > > > > > > > > > >> > > > > SoMAS | Stony Brook University
> > > > > > > > > > > > >> > > > > 678.468.5789
> > > > > > > > > > > > >> > > > >
> > > > > > > > > > > > >> > > > >
> > > > > > > > > > > > >> > > >
> > > > > > > > > > > > >> > > >
> > > > > > > > > > > > >> > >
> > > > > > > > > > > > >> > > --
> > > > > > > > > > > > >> > > *Taylor Mandelbaum*
> > > > > > > > > > > > >> > > Research Technician
> > > > > > > > > > > > >> > > SoMAS | Stony Brook University
> > > > > > > > > > > > >> > > 678.468.5789
> > > > > > > > > > > > >> > >
> > > > > > > > > > > > >> > >
> > > > > > > > > > > > >> >
> > > > > > > > > > > > >> >
> > > > > > > > > > > > >>
> > > > > > > > > > > > >> --
> > > > > > > > > > > > >> *Taylor Mandelbaum*
> > > > > > > > > > > > >> Research Technician
> > > > > > > > > > > > >> SoMAS | Stony Brook University
> > > > > > > > > > > > >> 678.468.5789
> > > > > > > > > > > > >>
> > > > > > > > > > > > >>
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > --
> > > > > > > > > > > *Taylor Mandelbaum*
> > > > > > > > > > > Research Technician
> > > > > > > > > > > SoMAS | Stony Brook University
> > > > > > > > > > > 678.468.5789
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > > --
> > > > > > > > > *Taylor Mandelbaum*
> > > > > > > > > Research Technician
> > > > > > > > > SoMAS | Stony Brook University
> > > > > > > > > 678.468.5789
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > *Taylor Mandelbaum*
> > > > > > > Research Technician
> > > > > > > SoMAS | Stony Brook University
> > > > > > > 678.468.5789
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > > --
> > > > > *Taylor Mandelbaum*
> > > > > Research Technician
> > > > > SoMAS | Stony Brook University
> > > > > 678.468.5789
> > > > >
> > > > >
> > > >
> > > >
> > >
> > > --
> > > *Taylor Mandelbaum*
> > > Research Technician
> > > SoMAS | Stony Brook University
> > > 678.468.5789
> > >
> > >
> >
> >
>
> --
> *Taylor Mandelbaum*
> Research Technician
> SoMAS | Stony Brook University
> 678.468.5789
>
>
------------------------------------------------
More information about the Met_help
mailing list