[Met_help] [rt.rap.ucar.edu #88918] History for MET Install NETCDF Issue
Julie Prestopnik via RT
met_help at ucar.edu
Thu Apr 11 11:43:18 MDT 2019
----------------------------------------------------------------
Initial Request
----------------------------------------------------------------
Julie, when compiling MET I get the error:
c_var_info.cc
169 In file included from nc_var_info.cc:24:
170 nc_utils.h:22:18: error: netcdf: No such file or directory
171 In file included from nc_var_info.cc:24:
To fix this, in a previous email you said to go to the MET help page and run through the NETCDF-C install procedures. I ran "./configure --prefix=${MET_LIB_DIR}/external_libs LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include" and then "make install" but get the following error:
Making install in include
make[1]: Entering directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
make[2]: Entering directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
make[2]: Nothing to be done for `install-exec-am'.
/bin/mkdir -p '/external_libs/include'
/bin/mkdir: cannot create directory `/external_libs': Permission denied
make[2]: *** [install-includeHEADERS] Error 1
make[2]: Leaving directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
make: *** [install-recursive] Error 1
The permissions in the netcdf-c-4.4.1.1 directory are 777.
What is the problem?
Thanks
Bob Craig
----------------------------------------------------------------
Complete Ticket History
----------------------------------------------------------------
Subject: MET Install NETCDF Issue
From: Julie Prestopnik
Time: Wed Feb 13 15:50:22 2019
Hi Bob. Based on the error message you included (thank you!):
/bin/mkdir -p '/external_libs/include'
/bin/mkdir: cannot create directory `/external_libs': Permission
denied
It appears that MET_LIB_DIR is not set, as "/" is the beginning
character.
Please be sure to set MET_LIB_DIR and try again.
Please let me know if you have any other questions or encounter any
other
problems.
Julie
On Wed, Feb 13, 2019, 3:45 PM robert.craig.2 at us.af.mil via RT <
met_help at ucar.edu> wrote:
>
> Wed Feb 13 15:44:51 2019: Request 88918 was acted upon.
> Transaction: Ticket created by robert.craig.2 at us.af.mil
> Queue: met_help
> Subject: MET Install NETCDF Issue
> Owner: Nobody
> Requestors: robert.craig.2 at us.af.mil
> Status: new
> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
>
>
> Julie, when compiling MET I get the error:
>
> c_var_info.cc
> 169 In file included from nc_var_info.cc:24:
> 170 nc_utils.h:22:18: error: netcdf: No such file or directory
> 171 In file included from nc_var_info.cc:24:
>
> To fix this, in a previous email you said to go to the MET help
page and
> run through the NETCDF-C install procedures. I ran "./configure
> --prefix=${MET_LIB_DIR}/external_libs
> LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include" and then "make
install"
> but get the following error:
>
> Making install in include
> make[1]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> make[2]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> make[2]: Nothing to be done for `install-exec-am'.
> /bin/mkdir -p '/external_libs/include'
> /bin/mkdir: cannot create directory `/external_libs': Permission
denied
> make[2]: *** [install-includeHEADERS] Error 1
> make[2]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> make[1]: *** [install-am] Error 2
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> make: *** [install-recursive] Error 1
>
> The permissions in the netcdf-c-4.4.1.1 directory are 777.
>
> What is the problem?
>
> Thanks
> Bob Craig
>
>
------------------------------------------------
Subject: RE: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET Install NETCDF Issue
From: robert.craig.2 at us.af.mil
Time: Thu Feb 14 07:35:37 2019
Julie, should MET_LIB_DIR point to met-8.1_beta1/lib? I tried this.
I got a good compile of NETCDF-CXX but I get an error compiling
NETCDF-C:
Making install in include
make[1]: Entering directory `/gpfs/dev/h/WXQC/met-
8.1_beta1/lib/netcdf-c-4.4.1.1/include'
make[2]: Entering directory `/gpfs/dev/h/WXQC/met-
8.1_beta1/lib/netcdf-c-4.4.1.1/include'
make[2]: Nothing to be done for `install-exec-am'.
/bin/mkdir -p '/h/WXQC/met-
8.1_beta1/external_libs/external_libs/include'
/usr/bin/install -c -m 644 netcdf.h netcdf_meta.h netcdf_mem.h
'/h/WXQC/met-8.1_beta1/external_libs/external_libs/include'
make[2]: Leaving directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-
c-4.4.1.1/include'
make[1]: Leaving directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-
c-4.4.1.1/include'
Making install in oc2
make[1]: Entering directory `/gpfs/dev/h/WXQC/met-
8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
make[2]: Entering directory `/gpfs/dev/h/WXQC/met-
8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-
c-4.4.1.1/oc2'
make[1]: Leaving directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-
c-4.4.1.1/oc2'
Making install in h5_test
make[1]: Entering directory `/gpfs/dev/h/WXQC/met-
8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
make[2]: Entering directory `/gpfs/dev/h/WXQC/met-
8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-
c-4.4.1.1/h5_test'
make[1]: Leaving directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-
c-4.4.1.1/h5_test'
Making install in libdispatch
make[1]: Entering directory `/gpfs/dev/h/WXQC/met-
8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
make[2]: Entering directory `/gpfs/dev/h/WXQC/met-
8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-
c-4.4.1.1/libdispatch'
make[1]: Leaving directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-
c-4.4.1.1/libdispatch'
Making install in libsrc
make[1]: Entering directory `/gpfs/dev/h/WXQC/met-
8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
make[2]: Entering directory `/gpfs/dev/h/WXQC/met-
8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
make[2]: Nothing to be done for `install-exec-am'.
/bin/mkdir -p '/h/WXQC/met-
8.1_beta1/external_libs/external_libs/share/man/man3'
/usr/bin/install -c -m 644 netcdf.3 '/h/WXQC/met-
8.1_beta1/external_libs/external_libs/share/man/man3'
make[2]: Leaving directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-
c-4.4.1.1/libsrc'
make[1]: Leaving directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-
c-4.4.1.1/libsrc'
Making install in libsrc4
make[1]: Entering directory `/gpfs/dev/h/WXQC/met-
8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I.. -I../include -I../oc2 -I/h/WXQC/met-
8.1_beta1/external_libs/external_libs/include -MT libnetcdf4_la-
nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-nc4file.Tpo -c -o
libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo './'`nc4file.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I../oc2
-I/h/WXQC/met-8.1_beta1/external_libs/external_libs/include -MT
libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-nc4file.Tpo
-c nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-nc4file.o
nc4file.c: In function ‘nc4_open_file’:
nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared (first
use in this function)
nc4file.c:2316: error: (Each undeclared identifier is reported only
once
nc4file.c:2316: error: for each function it appears in.)
nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
(first use in this function)
make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
make[1]: Leaving directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-
c-4.4.1.1/libsrc4'
make: *** [install-recursive] Error 1
What do you think I did wrong?
Thanks
Bob
-----Original Message-----
From: Julie Prestopnik via RT <met_help at ucar.edu>
Sent: Wednesday, February 13, 2019 4:50 PM
To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
<robert.craig.2 at us.af.mil>
Subject: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET Install
NETCDF Issue
Hi Bob. Based on the error message you included (thank you!):
/bin/mkdir -p '/external_libs/include'
/bin/mkdir: cannot create directory `/external_libs': Permission
denied
It appears that MET_LIB_DIR is not set, as "/" is the beginning
character.
Please be sure to set MET_LIB_DIR and try again.
Please let me know if you have any other questions or encounter any
other problems.
Julie
On Wed, Feb 13, 2019, 3:45 PM robert.craig.2 at us.af.mil via RT <
met_help at ucar.edu> wrote:
>
> Wed Feb 13 15:44:51 2019: Request 88918 was acted upon.
> Transaction: Ticket created by robert.craig.2 at us.af.mil
> Queue: met_help
> Subject: MET Install NETCDF Issue
> Owner: Nobody
> Requestors: robert.craig.2 at us.af.mil
> Status: new
> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918
> >
>
>
> Julie, when compiling MET I get the error:
>
> c_var_info.cc
> 169 In file included from nc_var_info.cc:24:
> 170 nc_utils.h:22:18: error: netcdf: No such file or directory
> 171 In file included from nc_var_info.cc:24:
>
> To fix this, in a previous email you said to go to the MET help
page
> and run through the NETCDF-C install procedures. I ran
"./configure
> --prefix=${MET_LIB_DIR}/external_libs
> LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include" and then "make
install"
> but get the following error:
>
> Making install in include
> make[1]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> make[2]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> make[2]: Nothing to be done for `install-exec-am'.
> /bin/mkdir -p '/external_libs/include'
> /bin/mkdir: cannot create directory `/external_libs': Permission
> denied
> make[2]: *** [install-includeHEADERS] Error 1
> make[2]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> make[1]: *** [install-am] Error 2
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> make: *** [install-recursive] Error 1
>
> The permissions in the netcdf-c-4.4.1.1 directory are 777.
>
> What is the problem?
>
> Thanks
> Bob Craig
>
>
------------------------------------------------
Subject: MET Install NETCDF Issue
From: Julie Prestopnik
Time: Thu Feb 14 08:47:30 2019
Hi Bob.
should MET_LIB_DIR point to met-8.1_beta1/lib?
>
I will answer that question, by breaking down the command that you
previously ran:
> ./configure --prefix=${MET_LIB_DIR}/external_libs
> LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include
In the example above "-prefix=" should be set to the location where
you
want the NetCDF files to be put. In the case above, the NetCDF
library
files would be put at "${MET_LIB_DIR}/external_libs/lib" and the
NetCDF
include files would be put at "${MET_LIB_DIR}/external_libs/include".
You
can set this to whatever you'd like, based on where you want to put
the
NetCDF library and include files (note that the NetCDF package knows
to put
the library files in a lib subdirectory and the include files in an
include
subdirectory, so for the "prefix" option, you simply set it to the
upper
level directory). NetCDF4 depends on HDF5, so HDF5 must be installed
first. In the above configure command the values of LDFLAGS and
CPPFLAGS
tell NetCDF where it can find the library files and header files,
respectively, that it needs. When I install MET, I install of the
external
libraries in a directory called <path to>/external_libs. All of the
external library files go in <path to>/external_libs/lib and all of
the
external library include files go in <path to>/external_libs/include.
So,
when I install NetCDF the HDF5 files have already been put in those
locations and by setting LDFLAGS and CPPFLAGS to the location in the
above
configure command, NetCDF knows where to find the files it needs.
>From the error you sent, it seems that NetCDF-C cannot find the HDF5
files
that it needs. Did you install HDF5 first? If not, please install
HDF5
first and they reconfigure and reinstall NetCDF-C pointing the
appropriate
locations as described above.
I hope that helps. Please let me know if you have any questions or if
you
encounter any other problems.
Thanks!
Julie
On Thu, Feb 14, 2019 at 7:35 AM robert.craig.2 at us.af.mil via RT <
met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
>
> Julie, should MET_LIB_DIR point to met-8.1_beta1/lib? I tried this.
I
> got a good compile of NETCDF-CXX but I get an error compiling
NETCDF-C:
>
> Making install in include
> make[1]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> make[2]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> make[2]: Nothing to be done for `install-exec-am'.
> /bin/mkdir -p '/h/WXQC/met-
8.1_beta1/external_libs/external_libs/include'
> /usr/bin/install -c -m 644 netcdf.h netcdf_meta.h netcdf_mem.h
> '/h/WXQC/met-8.1_beta1/external_libs/external_libs/include'
> make[2]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> Making install in oc2
> make[1]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> make[2]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> make[2]: Nothing to be done for `install-exec-am'.
> make[2]: Nothing to be done for `install-data-am'.
> make[2]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> Making install in h5_test
> make[1]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> make[2]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> make[2]: Nothing to be done for `install-exec-am'.
> make[2]: Nothing to be done for `install-data-am'.
> make[2]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> Making install in libdispatch
> make[1]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> make[2]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> make[2]: Nothing to be done for `install-exec-am'.
> make[2]: Nothing to be done for `install-data-am'.
> make[2]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> Making install in libsrc
> make[1]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> make[2]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> make[2]: Nothing to be done for `install-exec-am'.
> /bin/mkdir -p
> '/h/WXQC/met-8.1_beta1/external_libs/external_libs/share/man/man3'
> /usr/bin/install -c -m 644 netcdf.3
> '/h/WXQC/met-8.1_beta1/external_libs/external_libs/share/man/man3'
> make[2]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> Making install in libsrc4
> make[1]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I.
> -I.. -I../include -I../oc2
> -I/h/WXQC/met-8.1_beta1/external_libs/external_libs/include -MT
> libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-nc4file.Tpo
-c -o
> libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo './'`nc4file.c
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
-I../oc2
> -I/h/WXQC/met-8.1_beta1/external_libs/external_libs/include -MT
> libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-nc4file.Tpo
-c
> nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-nc4file.o
> nc4file.c: In function ‘nc4_open_file’:
> nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared (first
use
> in this function)
> nc4file.c:2316: error: (Each undeclared identifier is reported only
once
> nc4file.c:2316: error: for each function it appears in.)
> nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
(first
> use in this function)
> make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> make: *** [install-recursive] Error 1
>
> What do you think I did wrong?
>
> Thanks
> Bob
>
> -----Original Message-----
> From: Julie Prestopnik via RT <met_help at ucar.edu>
> Sent: Wednesday, February 13, 2019 4:50 PM
> To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
<robert.craig.2 at us.af.mil>
> Subject: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET Install
NETCDF
> Issue
>
> Hi Bob. Based on the error message you included (thank you!):
>
> /bin/mkdir -p '/external_libs/include'
> /bin/mkdir: cannot create directory `/external_libs': Permission
denied
>
> It appears that MET_LIB_DIR is not set, as "/" is the beginning
character.
> Please be sure to set MET_LIB_DIR and try again.
>
> Please let me know if you have any other questions or encounter any
other
> problems.
>
> Julie
>
>
> On Wed, Feb 13, 2019, 3:45 PM robert.craig.2 at us.af.mil via RT <
> met_help at ucar.edu> wrote:
>
> >
> > Wed Feb 13 15:44:51 2019: Request 88918 was acted upon.
> > Transaction: Ticket created by robert.craig.2 at us.af.mil
> > Queue: met_help
> > Subject: MET Install NETCDF Issue
> > Owner: Nobody
> > Requestors: robert.craig.2 at us.af.mil
> > Status: new
> > Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918
> > >
> >
> >
> > Julie, when compiling MET I get the error:
> >
> > c_var_info.cc
> > 169 In file included from nc_var_info.cc:24:
> > 170 nc_utils.h:22:18: error: netcdf: No such file or directory
> > 171 In file included from nc_var_info.cc:24:
> >
> > To fix this, in a previous email you said to go to the MET help
page
> > and run through the NETCDF-C install procedures. I ran
"./configure
> > --prefix=${MET_LIB_DIR}/external_libs
> > LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> > CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include" and then "make
install"
> > but get the following error:
> >
> > Making install in include
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make[2]: Nothing to be done for `install-exec-am'.
> > /bin/mkdir -p '/external_libs/include'
> > /bin/mkdir: cannot create directory `/external_libs': Permission
> > denied
> > make[2]: *** [install-includeHEADERS] Error 1
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make[1]: *** [install-am] Error 2
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make: *** [install-recursive] Error 1
> >
> > The permissions in the netcdf-c-4.4.1.1 directory are 777.
> >
> > What is the problem?
> >
> > Thanks
> > Bob Craig
> >
> >
>
>
>
>
------------------------------------------------
Subject: RE: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET Install NETCDF Issue
From: robert.craig.2 at us.af.mil
Time: Thu Feb 14 11:01:29 2019
Well, I am still having problems. First of all my env variables are
set this way:
MET_BUFR=/h/WXQC/met-8.1_beta1/lib/BUFRLIB_v10-0-1
MET_BUFRLIB=/h/WXQC/met-8.1_beta1/lib/BUFRLIB_v10-0-1
MET_GRIB2CINC=/h/WXQC/met-8.1_beta1/lib/g2clib-1.4.0
MET_GRIB2CLIB=/h/WXQC/met-8.1_beta1/lib/g2clib-1.4.0
MET_GRIB_TABLES=/h/data/global/WXQC/data/met/config/grib2
MET_GSL=/h/WXQC/met-8.1_beta1/lib/gsl-1.15
MET_HD5=/h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18
MET_LIB_DIR=/h/WXQC/met-8.1_beta1/lib
MET_NETCDF=/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1
ZDIR=/h/WXQC/met-8.1_beta1/lib/zlib-1.2.6/lib
H5DIR=/h/WXQC/met-8.1_beta1/lib/hd55-1.8.18
The /h/WXQC/met-8.1_beta1/lib directory has the following dirs.:
bin hd55-1.8.18 HDF-EOS2.19v1.00.tar
libhdf5_hl.la libhdf5.so.100 libnetcdf_c++4.so.1.0.3
netcdf-c-4.4.1.1
BUFRLIB_v10-0-1 hdf-4.2.12 include
libhdf5_hl.so libhdf5.so.100.0.1 libnetcdf.la
netcdf-cxx4-4.3.0
BUFRLIB_v10-2-3 hdf-4.2.12.tar jasper
libhdf5_hl.so.100 libnetcdf.a libnetcdf.settings
share
external_libs hdf5-1.10.0-patch1 lib
libhdf5_hl.so.100.0.0 libnetcdf_c++4.a libnetcdf.so
tar
g2clib-1.4.0 hdf5-1.8.18 libf2c libhdf5.la
libnetcdf_c++4.la libnetcdf.so.11 zlib-1.2.6
GRIBI_copygb.exe hdf5-1.8.18.tar libhdf5.a
libhdf5.settings libnetcdf_c++4.so libnetcdf.so.11.0.4
gsl-1.15 hdfeos libhdf5_hl.a libhdf5.so
libnetcdf_c++4.so.1 libpng-1.2.34
In the external_libs dir is:
bin include lib share
I download the HDFS library per instruction on MET web site and
installed. It looked like it compiled correctly. Then when trying
to compile netcdf-c-4.4.1.1 I get the same error messages I sent you
earlier:
T libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-nc4file.Tpo
-c -o libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo
'./'`nc4file.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I../oc2
-I/h/WXQC/met-8.1_beta1/lib/external_libs/include -MT libnetcdf4_la-
nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-nc4file.Tpo -c nc4file.c
-fPIC -DPIC -o .libs/libnetcdf4_la-nc4file.o
nc4file.c: In function ‘nc4_open_file’:
nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared (first
use in this function)
nc4file.c:2316: error: (Each undeclared identifier is reported only
once
nc4file.c:2316: error: for each function it appears in.)
nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
(first use in this function)
make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
make[1]: Leaving directory `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-
c-4.4.1.1/libsrc4'
make: *** [install-recursive] Error 1
So, not sure what to try at this point. Did I miss something that is
obvious?
Thanks
Bob
-----Original Message-----
From: Julie Prestopnik via RT <met_help at ucar.edu>
Sent: Thursday, February 14, 2019 9:48 AM
To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
<robert.craig.2 at us.af.mil>
Subject: Re: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET Install
NETCDF Issue
Hi Bob.
should MET_LIB_DIR point to met-8.1_beta1/lib?
>
I will answer that question, by breaking down the command that you
previously ran:
> ./configure --prefix=${MET_LIB_DIR}/external_libs
> LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include
In the example above "-prefix=" should be set to the location where
you want the NetCDF files to be put. In the case above, the NetCDF
library files would be put at "${MET_LIB_DIR}/external_libs/lib" and
the NetCDF include files would be put at
"${MET_LIB_DIR}/external_libs/include". You can set this to whatever
you'd like, based on where you want to put the NetCDF library and
include files (note that the NetCDF package knows to put the library
files in a lib subdirectory and the include files in an include
subdirectory, so for the "prefix" option, you simply set it to the
upper level directory). NetCDF4 depends on HDF5, so HDF5 must be
installed first. In the above configure command the values of LDFLAGS
and CPPFLAGS tell NetCDF where it can find the library files and
header files, respectively, that it needs. When I install MET, I
install of the external libraries in a directory called <path
to>/external_libs. All of the external library files go in <path
to>/external_libs/lib and all of the external library include files go
in <path to>/external_libs/include. So, when I install NetCDF the
HDF5 files have already been put in those locations and by setting
LDFLAGS and CPPFLAGS to the location in the above configure command,
NetCDF knows where to find the files it needs.
>From the error you sent, it seems that NetCDF-C cannot find the HDF5
files that it needs. Did you install HDF5 first? If not, please
install HDF5 first and they reconfigure and reinstall NetCDF-C
pointing the appropriate locations as described above.
I hope that helps. Please let me know if you have any questions or if
you encounter any other problems.
Thanks!
Julie
On Thu, Feb 14, 2019 at 7:35 AM robert.craig.2 at us.af.mil via RT <
met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
>
> Julie, should MET_LIB_DIR point to met-8.1_beta1/lib? I tried this.
> I got a good compile of NETCDF-CXX but I get an error compiling
NETCDF-C:
>
> Making install in include
> make[1]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> make[2]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> make[2]: Nothing to be done for `install-exec-am'.
> /bin/mkdir -p '/h/WXQC/met-
8.1_beta1/external_libs/external_libs/include'
> /usr/bin/install -c -m 644 netcdf.h netcdf_meta.h netcdf_mem.h
> '/h/WXQC/met-8.1_beta1/external_libs/external_libs/include'
> make[2]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> Making install in oc2
> make[1]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> make[2]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> make[2]: Nothing to be done for `install-exec-am'.
> make[2]: Nothing to be done for `install-data-am'.
> make[2]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> Making install in h5_test
> make[1]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> make[2]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> make[2]: Nothing to be done for `install-exec-am'.
> make[2]: Nothing to be done for `install-data-am'.
> make[2]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> Making install in libdispatch
> make[1]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> make[2]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> make[2]: Nothing to be done for `install-exec-am'.
> make[2]: Nothing to be done for `install-data-am'.
> make[2]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> Making install in libsrc
> make[1]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> make[2]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> make[2]: Nothing to be done for `install-exec-am'.
> /bin/mkdir -p
> '/h/WXQC/met-8.1_beta1/external_libs/external_libs/share/man/man3'
> /usr/bin/install -c -m 644 netcdf.3
> '/h/WXQC/met-8.1_beta1/external_libs/external_libs/share/man/man3'
> make[2]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> Making install in libsrc4
> make[1]: Entering directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I.
> -I.. -I../include -I../oc2
> -I/h/WXQC/met-8.1_beta1/external_libs/external_libs/include -MT
> libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-nc4file.Tpo
> -c -o libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo
> './'`nc4file.c
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
-I../oc2
> -I/h/WXQC/met-8.1_beta1/external_libs/external_libs/include -MT
> libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-nc4file.Tpo
> -c nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-nc4file.o
> nc4file.c: In function ‘nc4_open_file’:
> nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared (first
> use in this function)
> nc4file.c:2316: error: (Each undeclared identifier is reported only
> once
> nc4file.c:2316: error: for each function it appears in.)
> nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
> (first use in this function)
> make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> make: *** [install-recursive] Error 1
>
> What do you think I did wrong?
>
> Thanks
> Bob
>
> -----Original Message-----
> From: Julie Prestopnik via RT <met_help at ucar.edu>
> Sent: Wednesday, February 13, 2019 4:50 PM
> To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
> <robert.craig.2 at us.af.mil>
> Subject: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET Install
> NETCDF Issue
>
> Hi Bob. Based on the error message you included (thank you!):
>
> /bin/mkdir -p '/external_libs/include'
> /bin/mkdir: cannot create directory `/external_libs': Permission
> denied
>
> It appears that MET_LIB_DIR is not set, as "/" is the beginning
character.
> Please be sure to set MET_LIB_DIR and try again.
>
> Please let me know if you have any other questions or encounter any
> other problems.
>
> Julie
>
>
> On Wed, Feb 13, 2019, 3:45 PM robert.craig.2 at us.af.mil via RT <
> met_help at ucar.edu> wrote:
>
> >
> > Wed Feb 13 15:44:51 2019: Request 88918 was acted upon.
> > Transaction: Ticket created by robert.craig.2 at us.af.mil
> > Queue: met_help
> > Subject: MET Install NETCDF Issue
> > Owner: Nobody
> > Requestors: robert.craig.2 at us.af.mil
> > Status: new
> > Ticket <URL:
> > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918
> > >
> >
> >
> > Julie, when compiling MET I get the error:
> >
> > c_var_info.cc
> > 169 In file included from nc_var_info.cc:24:
> > 170 nc_utils.h:22:18: error: netcdf: No such file or directory
> > 171 In file included from nc_var_info.cc:24:
> >
> > To fix this, in a previous email you said to go to the MET help
> > page and run through the NETCDF-C install procedures. I ran
> > "./configure --prefix=${MET_LIB_DIR}/external_libs
> > LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> > CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include" and then "make
install"
> > but get the following error:
> >
> > Making install in include
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make[2]: Nothing to be done for `install-exec-am'.
> > /bin/mkdir -p '/external_libs/include'
> > /bin/mkdir: cannot create directory `/external_libs': Permission
> > denied
> > make[2]: *** [install-includeHEADERS] Error 1
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make[1]: *** [install-am] Error 2
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make: *** [install-recursive] Error 1
> >
> > The permissions in the netcdf-c-4.4.1.1 directory are 777.
> >
> > What is the problem?
> >
> > Thanks
> > Bob Craig
> >
> >
>
>
>
>
------------------------------------------------
Subject: MET Install NETCDF Issue
From: Julie Prestopnik
Time: Thu Feb 14 11:35:28 2019
Hi Bob.
When you compile NetCDF-C, you'll need to tell it where the library
files
are (for HDF5, possibly other files too, but let's start with that)
using
LDFLAGS and where the include files are (for HDF5, possibly other
files
too, but let's start with that) using CPPFLAGS.
I see that you set "MET_HD5=/h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18".
Is
there a "lib" subdirectory under /h/WXQC/met-8.1_beta1/lib/hdf5-
1.8.18? Is
there an include subdirectory under /h/WXQC/met-8.1_beta1/lib/hdf5-
1.8.18?
It looks like your HDF5 library files were put directly in
/h/WXQC/met-8.1_beta1/lib instead of at
/h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18/lib, but I don't see any header
files
in /h/WXQC/met-8.1_beta1/lib. Are the header/include files in
/h/WXQC/met-8.1_beta1/include?
On a separate note, I see that you set
"MET_NETCDF=/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1". You will
need to
have your NetCDF-C and NetCDF-CXX files installed in the same
location,
since MET has only only MET_NETCDF variable to reference. This is one
reason that I install every external library file at, for example,
/d1/jpresto/8.1_beta/external_libs (with library files in
/d1/jpresto/8.1_beta/external_libs/lib and include files in
/d1/jpresto/8.1_beta/external_libs/include).
You would want to set your configure command to the following for
NetCDF-C
(using bash syntax below), replacing the <> with the actual location.
export PREFIX=<set to the location you want to install the NetCDF lib
and
include files> (the library files will be put in a "lib" subdir and
the
include files will be put in an "include" subdir. This should be the
same
location for your NetCDF-CXX files)
export LDFLAGS=<set to the location where your HDF5 library files are>
export CPPFLAGS=<set to the location where your HDF5 header/include
files
are>
./configure --prefix=${PREFIX} LDFLAGS=-L${LDFLAGS} CPPFLAGS=-
I${CPPFLAGS}
I hope this helps. Please let me know if you have any questions. I
am out
for the rest of the day and most of tomorrow. Monday is a holiday.
I
will be back in the office on Tuesday. Please respond to this ticket
with
any other questions, and I will do my best to respond as soon as I
can.
Below I'll paste an example of how my installation is structured on
our
machine "cheyenne", so you have it as an example.
Thanks,
Julie
cheyenne3:jpresto> pwd
/glade/p/ral/jntp/MET/MET_releases/8.0
cheyenne3:jpresto> ls
bin external_libs met-8.0 share
cheyenne3:jpresto> cd
/glade/p/ral/jntp/MET/MET_releases/8.0/external_libs
/glade/p/ral/jntp/MET/MET_releases/8.0/external_libs
cheyenne3:jpresto> ls
bin bufrlib cairo freetype g2clib gsl hdf hdf5 hdfeos include
jasper lib libpng man netcdf share zlib
cheyenne3:jpresto> ls
/glade/p/ral/jntp/MET/MET_releases/8.0/external_libs/lib
libbufr.a libgrib2c.a libgsl.so.19 libhdf5.la
libmfhdf.a
libnetcdf.so libpng.la
libdf.a libgsl.a libgsl.so.19.0.0 libhdf5.settings
libnetcdf.a
libnetcdf.so.11 libpng.so
libfreetype.a libgslcblas.a libhdf4.settings libhdf5.so
libnetcdf_c++4.a libnetcdf.so.11.0.4 libz.a
libfreetype.la libgslcblas.la libhdf5.a libhdf5.so.10
libnetcdf_c++4.la libpng16.a libz.so
libfreetype.so libgslcblas.so libhdf5_hl.a
libhdf5.so.10.2.1
libnetcdf_c++4.so libpng16.la libz.so.1
libfreetype.so.6 libgslcblas.so.0 libhdf5_hl.la
libhdfeos.a
libnetcdf_c++4.so.1 libpng16.so libz.so.1.2.11
libfreetype.so.6.12.5 libgslcblas.so.0.0.0 libhdf5_hl.so
libhdfeos.la
libnetcdf_c++4.so.1.0.3 libpng16.so.16 pkgconfig
libGctp.a libgsl.la libhdf5_hl.so.10 libjasper.a
libnetcdf.la libpng16.so.16.34.0
libGctp.la libgsl.so libhdf5_hl.so.10.1.1 libjasper.la
libnetcdf.settings
libpng.a
cheyenne3:jpresto> ls
/glade/p/ral/jntp/MET/MET_releases/8.0/external_libs/include
atom.h dfsd.h H5Dpublic.h H5IMpublic.h H5Tpublic.h hdfi.h
mffunc.f90 ncFloat.h netcdf
bitvect.h dfstubs.h H5DSpublic.h H5Ipublic.h H5version.h
hdf.inc
mffunc.inc ncGroupAtt.h netcdf.h
cdeflate.h dfufp2i.h H5Epubgen.h H5Lpublic.h H5Zpublic.h
HE2_config.h mfgr.h ncGroup.h netcdf_mem.h
cfortHdf.h drstemplates.h H5Epublic.h H5LTpublic.h hbitio.h
herr.h
mfhdf.h ncInt64.h netcdf_meta.h
cnbit.h dynarray.h H5FDcore.h H5MMpublic.h hchunks.h
hfile.h
mfhdfi.h ncInt.h pdstemplates.h
cnone.h ease.h H5FDdirect.h H5Opublic.h hcomp.h hkit.h
mstdio.h ncOpaqueType.h pngconf.h
crle.h freetype2 H5FDfamily.h H5overflow.h hcompi.h
hlimits.h
ncAtt.h ncShort.h png.h
cskphuff.h grib2.h H5FDlog.h H5PLextern.h hconv.h hntdefs.h
ncByte.h ncString.h pnglibconf.h
cszip.h gridtemplates.h H5FDmpi.h H5PLpublic.h hdf2netcdf.h
hproto_fortran.h ncChar.h ncType.h tbbt.h
dfan.h gsl H5FDmpio.h H5Ppublic.h hdf4_netcdf.h hproto.h
ncCheck.h ncUbyte.h vattr.h
dffunc.f90 h4config.h H5FDmulti.h H5PTpublic.h hdf5.h
htags.h
ncCompoundType.h ncUint64.h vg.h
dffunc.inc H5ACpublic.h H5FDpublic.h H5pubconf.h hdf5_hl.h
jasper
ncDim.h ncUint.h zconf.h
dfgr.h H5api_adpt.h H5FDsec2.h H5public.h HdfEosDef.h
libpng16
ncDouble.h ncUshort.h zlib.h
df.h H5Apublic.h H5FDstdio.h H5Rpublic.h HDFEOSVersion.h
linklist.h ncEnumType.h ncVarAtt.h
dfi.h H5Cpublic.h H5Fpublic.h H5Spublic.h hdf.f90
local_nc.h
ncException.h ncVar.h
dfrig.h H5DOpublic.h H5Gpublic.h H5TBpublic.h hdf.h
mfan.h
ncFile.h ncVlenType.h
On Thu, Feb 14, 2019 at 11:01 AM robert.craig.2 at us.af.mil via RT <
met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
>
> Well, I am still having problems. First of all my env variables
are set
> this way:
>
> MET_BUFR=/h/WXQC/met-8.1_beta1/lib/BUFRLIB_v10-0-1
> MET_BUFRLIB=/h/WXQC/met-8.1_beta1/lib/BUFRLIB_v10-0-1
> MET_GRIB2CINC=/h/WXQC/met-8.1_beta1/lib/g2clib-1.4.0
> MET_GRIB2CLIB=/h/WXQC/met-8.1_beta1/lib/g2clib-1.4.0
> MET_GRIB_TABLES=/h/data/global/WXQC/data/met/config/grib2
> MET_GSL=/h/WXQC/met-8.1_beta1/lib/gsl-1.15
> MET_HD5=/h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18
> MET_LIB_DIR=/h/WXQC/met-8.1_beta1/lib
> MET_NETCDF=/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1
> ZDIR=/h/WXQC/met-8.1_beta1/lib/zlib-1.2.6/lib
> H5DIR=/h/WXQC/met-8.1_beta1/lib/hd55-1.8.18
>
> The /h/WXQC/met-8.1_beta1/lib directory has the following dirs.:
>
> bin hd55-1.8.18 HDF-EOS2.19v1.00.tar
libhdf5_hl.la
> libhdf5.so.100 libnetcdf_c++4.so.1.0.3 netcdf-c-
4.4.1.1
> BUFRLIB_v10-0-1 hdf-4.2.12 include
libhdf5_hl.so
> libhdf5.so.100.0.1 libnetcdf.la netcdf-cxx4-
4.3.0
> BUFRLIB_v10-2-3 hdf-4.2.12.tar jasper
> libhdf5_hl.so.100 libnetcdf.a libnetcdf.settings
share
> external_libs hdf5-1.10.0-patch1 lib
> libhdf5_hl.so.100.0.0 libnetcdf_c++4.a libnetcdf.so
tar
> g2clib-1.4.0 hdf5-1.8.18 libf2c
libhdf5.la
> libnetcdf_c++4.la libnetcdf.so.11 zlib-1.2.6
> GRIBI_copygb.exe hdf5-1.8.18.tar libhdf5.a
> libhdf5.settings libnetcdf_c++4.so libnetcdf.so.11.0.4
> gsl-1.15 hdfeos libhdf5_hl.a
libhdf5.so
> libnetcdf_c++4.so.1 libpng-1.2.34
>
> In the external_libs dir is:
>
> bin include lib share
>
> I download the HDFS library per instruction on MET web site and
> installed. It looked like it compiled correctly. Then when trying
to
> compile netcdf-c-4.4.1.1 I get the same error messages I sent you
earlier:
>
> T libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.Tpo -c
> -o libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo
'./'`nc4file.c
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
-I../oc2
> -I/h/WXQC/met-8.1_beta1/lib/external_libs/include -MT
> libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-nc4file.Tpo
-c
> nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-nc4file.o
> nc4file.c: In function ‘nc4_open_file’:
> nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared (first
use
> in this function)
> nc4file.c:2316: error: (Each undeclared identifier is reported only
once
> nc4file.c:2316: error: for each function it appears in.)
> nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
(first
> use in this function)
> make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> make: *** [install-recursive] Error 1
>
> So, not sure what to try at this point. Did I miss something that
is
> obvious?
>
> Thanks
> Bob
>
>
> -----Original Message-----
> From: Julie Prestopnik via RT <met_help at ucar.edu>
> Sent: Thursday, February 14, 2019 9:48 AM
> To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
<robert.craig.2 at us.af.mil>
> Subject: Re: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET
Install
> NETCDF Issue
>
> Hi Bob.
>
> should MET_LIB_DIR point to met-8.1_beta1/lib?
> >
>
> I will answer that question, by breaking down the command that you
> previously ran:
>
> > ./configure --prefix=${MET_LIB_DIR}/external_libs
> > LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> > CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include
>
>
> In the example above "-prefix=" should be set to the location where
you
> want the NetCDF files to be put. In the case above, the NetCDF
library
> files would be put at "${MET_LIB_DIR}/external_libs/lib" and the
NetCDF
> include files would be put at
"${MET_LIB_DIR}/external_libs/include". You
> can set this to whatever you'd like, based on where you want to put
the
> NetCDF library and include files (note that the NetCDF package knows
to put
> the library files in a lib subdirectory and the include files in an
include
> subdirectory, so for the "prefix" option, you simply set it to the
upper
> level directory). NetCDF4 depends on HDF5, so HDF5 must be
installed
> first. In the above configure command the values of LDFLAGS and
CPPFLAGS
> tell NetCDF where it can find the library files and header files,
> respectively, that it needs. When I install MET, I install of the
external
> libraries in a directory called <path to>/external_libs. All of the
> external library files go in <path to>/externa!
> l_libs/lib and all of the external library include files go in
<path
> to>/external_libs/include. So, when I install NetCDF the HDF5 files
have
> already been put in those locations and by setting LDFLAGS and
CPPFLAGS to
> the location in the above configure command, NetCDF knows where to
find the
> files it needs.
>
> From the error you sent, it seems that NetCDF-C cannot find the HDF5
files
> that it needs. Did you install HDF5 first? If not, please install
HDF5
> first and they reconfigure and reinstall NetCDF-C pointing the
appropriate
> locations as described above.
>
> I hope that helps. Please let me know if you have any questions or
if you
> encounter any other problems.
>
> Thanks!
>
> Julie
>
> On Thu, Feb 14, 2019 at 7:35 AM robert.craig.2 at us.af.mil via RT <
> met_help at ucar.edu> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
> >
> > Julie, should MET_LIB_DIR point to met-8.1_beta1/lib? I tried
this.
> > I got a good compile of NETCDF-CXX but I get an error compiling
NETCDF-C:
> >
> > Making install in include
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make[2]: Nothing to be done for `install-exec-am'.
> > /bin/mkdir -p
> '/h/WXQC/met-8.1_beta1/external_libs/external_libs/include'
> > /usr/bin/install -c -m 644 netcdf.h netcdf_meta.h netcdf_mem.h
> > '/h/WXQC/met-8.1_beta1/external_libs/external_libs/include'
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > Making install in oc2
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > make[2]: Nothing to be done for `install-exec-am'.
> > make[2]: Nothing to be done for `install-data-am'.
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > Making install in h5_test
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > make[2]: Nothing to be done for `install-exec-am'.
> > make[2]: Nothing to be done for `install-data-am'.
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > Making install in libdispatch
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> > make[2]: Nothing to be done for `install-exec-am'.
> > make[2]: Nothing to be done for `install-data-am'.
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> > Making install in libsrc
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > make[2]: Nothing to be done for `install-exec-am'.
> > /bin/mkdir -p
> > '/h/WXQC/met-8.1_beta1/external_libs/external_libs/share/man/man3'
> > /usr/bin/install -c -m 644 netcdf.3
> > '/h/WXQC/met-8.1_beta1/external_libs/external_libs/share/man/man3'
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > Making install in libsrc4
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> > /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I.
> > -I.. -I../include -I../oc2
> > -I/h/WXQC/met-8.1_beta1/external_libs/external_libs/include -MT
> > libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.Tpo
> > -c -o libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo
> > './'`nc4file.c
> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
-I../oc2
> > -I/h/WXQC/met-8.1_beta1/external_libs/external_libs/include -MT
> > libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.Tpo
> > -c nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-nc4file.o
> > nc4file.c: In function ‘nc4_open_file’:
> > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared
(first
> > use in this function)
> > nc4file.c:2316: error: (Each undeclared identifier is reported
only
> > once
> > nc4file.c:2316: error: for each function it appears in.)
> > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
> > (first use in this function)
> > make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> > make: *** [install-recursive] Error 1
> >
> > What do you think I did wrong?
> >
> > Thanks
> > Bob
> >
> > -----Original Message-----
> > From: Julie Prestopnik via RT <met_help at ucar.edu>
> > Sent: Wednesday, February 13, 2019 4:50 PM
> > To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
> > <robert.craig.2 at us.af.mil>
> > Subject: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET Install
> > NETCDF Issue
> >
> > Hi Bob. Based on the error message you included (thank you!):
> >
> > /bin/mkdir -p '/external_libs/include'
> > /bin/mkdir: cannot create directory `/external_libs': Permission
> > denied
> >
> > It appears that MET_LIB_DIR is not set, as "/" is the beginning
> character.
> > Please be sure to set MET_LIB_DIR and try again.
> >
> > Please let me know if you have any other questions or encounter
any
> > other problems.
> >
> > Julie
> >
> >
> > On Wed, Feb 13, 2019, 3:45 PM robert.craig.2 at us.af.mil via RT <
> > met_help at ucar.edu> wrote:
> >
> > >
> > > Wed Feb 13 15:44:51 2019: Request 88918 was acted upon.
> > > Transaction: Ticket created by robert.craig.2 at us.af.mil
> > > Queue: met_help
> > > Subject: MET Install NETCDF Issue
> > > Owner: Nobody
> > > Requestors: robert.craig.2 at us.af.mil
> > > Status: new
> > > Ticket <URL:
> > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918
> > > >
> > >
> > >
> > > Julie, when compiling MET I get the error:
> > >
> > > c_var_info.cc
> > > 169 In file included from nc_var_info.cc:24:
> > > 170 nc_utils.h:22:18: error: netcdf: No such file or directory
> > > 171 In file included from nc_var_info.cc:24:
> > >
> > > To fix this, in a previous email you said to go to the MET help
> > > page and run through the NETCDF-C install procedures. I ran
> > > "./configure --prefix=${MET_LIB_DIR}/external_libs
> > > LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> > > CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include" and then "make
> install"
> > > but get the following error:
> > >
> > > Making install in include
> > > make[1]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make[2]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make[2]: Nothing to be done for `install-exec-am'.
> > > /bin/mkdir -p '/external_libs/include'
> > > /bin/mkdir: cannot create directory `/external_libs': Permission
> > > denied
> > > make[2]: *** [install-includeHEADERS] Error 1
> > > make[2]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make[1]: *** [install-am] Error 2
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make: *** [install-recursive] Error 1
> > >
> > > The permissions in the netcdf-c-4.4.1.1 directory are 777.
> > >
> > > What is the problem?
> > >
> > > Thanks
> > > Bob Craig
> > >
> > >
> >
> >
> >
> >
>
>
>
>
------------------------------------------------
Subject: RE: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET Install NETCDF Issue
From: robert.craig.2 at us.af.mil
Time: Tue Feb 19 07:56:06 2019
Hi John and Julie, I am reorganizing our met-8.1 directories to be
more inline with what the manual recommends and then I will try again
to compile NETCDF without errors. One thing I do need help with is
getting the following libraries since we are blocked from getting to
their web sites: cairo, freetype. Could you place those on ARLSafe so
we can then download them. I will set up an ARLsafe code for you to
do this.
Thanks
Bob
-----Original Message-----
From: Julie Prestopnik via RT <met_help at ucar.edu>
Sent: Thursday, February 14, 2019 12:35 PM
To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
<robert.craig.2 at us.af.mil>
Subject: Re: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET Install
NETCDF Issue
Hi Bob.
When you compile NetCDF-C, you'll need to tell it where the library
files are (for HDF5, possibly other files too, but let's start with
that) using LDFLAGS and where the include files are (for HDF5,
possibly other files too, but let's start with that) using CPPFLAGS.
I see that you set "MET_HD5=/h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18".
Is there a "lib" subdirectory under /h/WXQC/met-8.1_beta1/lib/hdf5-
1.8.18? Is there an include subdirectory under /h/WXQC/met-
8.1_beta1/lib/hdf5-1.8.18?
It looks like your HDF5 library files were put directly in
/h/WXQC/met-8.1_beta1/lib instead of at /h/WXQC/met-
8.1_beta1/lib/hdf5-1.8.18/lib, but I don't see any header files in
/h/WXQC/met-8.1_beta1/lib. Are the header/include files in
/h/WXQC/met-8.1_beta1/include?
On a separate note, I see that you set
"MET_NETCDF=/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1". You will
need to have your NetCDF-C and NetCDF-CXX files installed in the same
location, since MET has only only MET_NETCDF variable to reference.
This is one reason that I install every external library file at, for
example, /d1/jpresto/8.1_beta/external_libs (with library files in
/d1/jpresto/8.1_beta/external_libs/lib and include files in
/d1/jpresto/8.1_beta/external_libs/include).
You would want to set your configure command to the following for
NetCDF-C (using bash syntax below), replacing the <> with the actual
location.
export PREFIX=<set to the location you want to install the NetCDF lib
and include files> (the library files will be put in a "lib" subdir
and the include files will be put in an "include" subdir. This should
be the same location for your NetCDF-CXX files) export LDFLAGS=<set to
the location where your HDF5 library files are> export CPPFLAGS=<set
to the location where your HDF5 header/include files
are>
./configure --prefix=${PREFIX} LDFLAGS=-L${LDFLAGS} CPPFLAGS=-
I${CPPFLAGS}
I hope this helps. Please let me know if you have any questions. I
am out
for the rest of the day and most of tomorrow. Monday is a holiday.
I
will be back in the office on Tuesday. Please respond to this ticket
with any other questions, and I will do my best to respond as soon as
I can.
Below I'll paste an example of how my installation is structured on
our machine "cheyenne", so you have it as an example.
Thanks,
Julie
cheyenne3:jpresto> pwd
/glade/p/ral/jntp/MET/MET_releases/8.0
cheyenne3:jpresto> ls
bin external_libs met-8.0 share
cheyenne3:jpresto> cd
/glade/p/ral/jntp/MET/MET_releases/8.0/external_libs
/glade/p/ral/jntp/MET/MET_releases/8.0/external_libs
cheyenne3:jpresto> ls
bin bufrlib cairo freetype g2clib gsl hdf hdf5 hdfeos include
jasper lib libpng man netcdf share zlib
cheyenne3:jpresto> ls
/glade/p/ral/jntp/MET/MET_releases/8.0/external_libs/lib
libbufr.a libgrib2c.a libgsl.so.19 libhdf5.la
libmfhdf.a
libnetcdf.so libpng.la
libdf.a libgsl.a libgsl.so.19.0.0 libhdf5.settings
libnetcdf.a
libnetcdf.so.11 libpng.so
libfreetype.a libgslcblas.a libhdf4.settings libhdf5.so
libnetcdf_c++4.a libnetcdf.so.11.0.4 libz.a
libfreetype.la libgslcblas.la libhdf5.a libhdf5.so.10
libnetcdf_c++4.la libpng16.a libz.so
libfreetype.so libgslcblas.so libhdf5_hl.a
libhdf5.so.10.2.1
libnetcdf_c++4.so libpng16.la libz.so.1
libfreetype.so.6 libgslcblas.so.0 libhdf5_hl.la
libhdfeos.a
libnetcdf_c++4.so.1 libpng16.so libz.so.1.2.11
libfreetype.so.6.12.5 libgslcblas.so.0.0.0 libhdf5_hl.so
libhdfeos.la
libnetcdf_c++4.so.1.0.3 libpng16.so.16 pkgconfig
libGctp.a libgsl.la libhdf5_hl.so.10 libjasper.a
libnetcdf.la libpng16.so.16.34.0
libGctp.la libgsl.so libhdf5_hl.so.10.1.1 libjasper.la
libnetcdf.settings
libpng.a
cheyenne3:jpresto> ls
/glade/p/ral/jntp/MET/MET_releases/8.0/external_libs/include
atom.h dfsd.h H5Dpublic.h H5IMpublic.h H5Tpublic.h hdfi.h
mffunc.f90 ncFloat.h netcdf
bitvect.h dfstubs.h H5DSpublic.h H5Ipublic.h H5version.h
hdf.inc
mffunc.inc ncGroupAtt.h netcdf.h
cdeflate.h dfufp2i.h H5Epubgen.h H5Lpublic.h H5Zpublic.h
HE2_config.h mfgr.h ncGroup.h netcdf_mem.h
cfortHdf.h drstemplates.h H5Epublic.h H5LTpublic.h hbitio.h
herr.h
mfhdf.h ncInt64.h netcdf_meta.h
cnbit.h dynarray.h H5FDcore.h H5MMpublic.h hchunks.h
hfile.h
mfhdfi.h ncInt.h pdstemplates.h
cnone.h ease.h H5FDdirect.h H5Opublic.h hcomp.h hkit.h
mstdio.h ncOpaqueType.h pngconf.h
crle.h freetype2 H5FDfamily.h H5overflow.h hcompi.h
hlimits.h
ncAtt.h ncShort.h png.h
cskphuff.h grib2.h H5FDlog.h H5PLextern.h hconv.h hntdefs.h
ncByte.h ncString.h pnglibconf.h
cszip.h gridtemplates.h H5FDmpi.h H5PLpublic.h hdf2netcdf.h
hproto_fortran.h ncChar.h ncType.h tbbt.h
dfan.h gsl H5FDmpio.h H5Ppublic.h hdf4_netcdf.h hproto.h
ncCheck.h ncUbyte.h vattr.h
dffunc.f90 h4config.h H5FDmulti.h H5PTpublic.h hdf5.h
htags.h
ncCompoundType.h ncUint64.h vg.h
dffunc.inc H5ACpublic.h H5FDpublic.h H5pubconf.h hdf5_hl.h
jasper
ncDim.h ncUint.h zconf.h
dfgr.h H5api_adpt.h H5FDsec2.h H5public.h HdfEosDef.h
libpng16
ncDouble.h ncUshort.h zlib.h
df.h H5Apublic.h H5FDstdio.h H5Rpublic.h HDFEOSVersion.h
linklist.h ncEnumType.h ncVarAtt.h
dfi.h H5Cpublic.h H5Fpublic.h H5Spublic.h hdf.f90
local_nc.h
ncException.h ncVar.h
dfrig.h H5DOpublic.h H5Gpublic.h H5TBpublic.h hdf.h
mfan.h
ncFile.h ncVlenType.h
On Thu, Feb 14, 2019 at 11:01 AM robert.craig.2 at us.af.mil via RT <
met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
>
> Well, I am still having problems. First of all my env variables
are set
> this way:
>
> MET_BUFR=/h/WXQC/met-8.1_beta1/lib/BUFRLIB_v10-0-1
> MET_BUFRLIB=/h/WXQC/met-8.1_beta1/lib/BUFRLIB_v10-0-1
> MET_GRIB2CINC=/h/WXQC/met-8.1_beta1/lib/g2clib-1.4.0
> MET_GRIB2CLIB=/h/WXQC/met-8.1_beta1/lib/g2clib-1.4.0
> MET_GRIB_TABLES=/h/data/global/WXQC/data/met/config/grib2
> MET_GSL=/h/WXQC/met-8.1_beta1/lib/gsl-1.15
> MET_HD5=/h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18
> MET_LIB_DIR=/h/WXQC/met-8.1_beta1/lib
> MET_NETCDF=/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1
> ZDIR=/h/WXQC/met-8.1_beta1/lib/zlib-1.2.6/lib
> H5DIR=/h/WXQC/met-8.1_beta1/lib/hd55-1.8.18
>
> The /h/WXQC/met-8.1_beta1/lib directory has the following dirs.:
>
> bin hd55-1.8.18 HDF-EOS2.19v1.00.tar
libhdf5_hl.la
> libhdf5.so.100 libnetcdf_c++4.so.1.0.3 netcdf-c-
4.4.1.1
> BUFRLIB_v10-0-1 hdf-4.2.12 include
libhdf5_hl.so
> libhdf5.so.100.0.1 libnetcdf.la netcdf-cxx4-
4.3.0
> BUFRLIB_v10-2-3 hdf-4.2.12.tar jasper
> libhdf5_hl.so.100 libnetcdf.a libnetcdf.settings
share
> external_libs hdf5-1.10.0-patch1 lib
> libhdf5_hl.so.100.0.0 libnetcdf_c++4.a libnetcdf.so
tar
> g2clib-1.4.0 hdf5-1.8.18 libf2c
libhdf5.la
> libnetcdf_c++4.la libnetcdf.so.11 zlib-1.2.6
> GRIBI_copygb.exe hdf5-1.8.18.tar libhdf5.a
> libhdf5.settings libnetcdf_c++4.so libnetcdf.so.11.0.4
> gsl-1.15 hdfeos libhdf5_hl.a
libhdf5.so
> libnetcdf_c++4.so.1 libpng-1.2.34
>
> In the external_libs dir is:
>
> bin include lib share
>
> I download the HDFS library per instruction on MET web site and
> installed. It looked like it compiled correctly. Then when trying
to
> compile netcdf-c-4.4.1.1 I get the same error messages I sent you
earlier:
>
> T libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.Tpo
> -c -o libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo
> './'`nc4file.c
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
-I../oc2
> -I/h/WXQC/met-8.1_beta1/lib/external_libs/include -MT
> libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-nc4file.Tpo
> -c nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-nc4file.o
> nc4file.c: In function ‘nc4_open_file’:
> nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared (first
> use in this function)
> nc4file.c:2316: error: (Each undeclared identifier is reported only
> once
> nc4file.c:2316: error: for each function it appears in.)
> nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
> (first use in this function)
> make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> make: *** [install-recursive] Error 1
>
> So, not sure what to try at this point. Did I miss something that
is
> obvious?
>
> Thanks
> Bob
>
>
> -----Original Message-----
> From: Julie Prestopnik via RT <met_help at ucar.edu>
> Sent: Thursday, February 14, 2019 9:48 AM
> To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
> <robert.craig.2 at us.af.mil>
> Subject: Re: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET
Install
> NETCDF Issue
>
> Hi Bob.
>
> should MET_LIB_DIR point to met-8.1_beta1/lib?
> >
>
> I will answer that question, by breaking down the command that you
> previously ran:
>
> > ./configure --prefix=${MET_LIB_DIR}/external_libs
> > LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> > CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include
>
>
> In the example above "-prefix=" should be set to the location where
> you want the NetCDF files to be put. In the case above, the NetCDF
> library files would be put at "${MET_LIB_DIR}/external_libs/lib" and
> the NetCDF include files would be put at
> "${MET_LIB_DIR}/external_libs/include". You can set this to
whatever
> you'd like, based on where you want to put the NetCDF library and
> include files (note that the NetCDF package knows to put the library
> files in a lib subdirectory and the include files in an include
> subdirectory, so for the "prefix" option, you simply set it to the
> upper level directory). NetCDF4 depends on HDF5, so HDF5 must be
> installed first. In the above configure command the values of
LDFLAGS
> and CPPFLAGS tell NetCDF where it can find the library files and
> header files, respectively, that it needs. When I install MET, I
> install of the external libraries in a directory called <path
to>/external_libs. All of the external library files go in <path
to>/externa!
> l_libs/lib and all of the external library include files go in
<path
> to>/external_libs/include. So, when I install NetCDF the HDF5 files
> to>have
> already been put in those locations and by setting LDFLAGS and
> CPPFLAGS to the location in the above configure command, NetCDF
knows
> where to find the files it needs.
>
> From the error you sent, it seems that NetCDF-C cannot find the HDF5
> files that it needs. Did you install HDF5 first? If not, please
> install HDF5 first and they reconfigure and reinstall NetCDF-C
> pointing the appropriate locations as described above.
>
> I hope that helps. Please let me know if you have any questions or
if
> you encounter any other problems.
>
> Thanks!
>
> Julie
>
> On Thu, Feb 14, 2019 at 7:35 AM robert.craig.2 at us.af.mil via RT <
> met_help at ucar.edu> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
> >
> > Julie, should MET_LIB_DIR point to met-8.1_beta1/lib? I tried
this.
> > I got a good compile of NETCDF-CXX but I get an error compiling
NETCDF-C:
> >
> > Making install in include
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make[2]: Nothing to be done for `install-exec-am'.
> > /bin/mkdir -p
> '/h/WXQC/met-8.1_beta1/external_libs/external_libs/include'
> > /usr/bin/install -c -m 644 netcdf.h netcdf_meta.h netcdf_mem.h
> > '/h/WXQC/met-8.1_beta1/external_libs/external_libs/include'
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > Making install in oc2
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > make[2]: Nothing to be done for `install-exec-am'.
> > make[2]: Nothing to be done for `install-data-am'.
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > Making install in h5_test
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > make[2]: Nothing to be done for `install-exec-am'.
> > make[2]: Nothing to be done for `install-data-am'.
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > Making install in libdispatch
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> > make[2]: Nothing to be done for `install-exec-am'.
> > make[2]: Nothing to be done for `install-data-am'.
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> > Making install in libsrc
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > make[2]: Nothing to be done for `install-exec-am'.
> > /bin/mkdir -p
> > '/h/WXQC/met-8.1_beta1/external_libs/external_libs/share/man/man3'
> > /usr/bin/install -c -m 644 netcdf.3
> > '/h/WXQC/met-8.1_beta1/external_libs/external_libs/share/man/man3'
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > Making install in libsrc4
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> > /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I.
> > -I.. -I../include -I../oc2
> > -I/h/WXQC/met-8.1_beta1/external_libs/external_libs/include -MT
> > libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.Tpo
> > -c -o libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo
> > './'`nc4file.c
> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
> > -I../oc2 -I/h/WXQC/met-
8.1_beta1/external_libs/external_libs/include
> > -MT libnetcdf4_la-nc4file.lo -MD -MP -MF
> > .deps/libnetcdf4_la-nc4file.Tpo -c nc4file.c -fPIC -DPIC -o
> > .libs/libnetcdf4_la-nc4file.o
> > nc4file.c: In function ‘nc4_open_file’:
> > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared
(first
> > use in this function)
> > nc4file.c:2316: error: (Each undeclared identifier is reported
only
> > once
> > nc4file.c:2316: error: for each function it appears in.)
> > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
> > (first use in this function)
> > make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> > make: *** [install-recursive] Error 1
> >
> > What do you think I did wrong?
> >
> > Thanks
> > Bob
> >
> > -----Original Message-----
> > From: Julie Prestopnik via RT <met_help at ucar.edu>
> > Sent: Wednesday, February 13, 2019 4:50 PM
> > To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
> > <robert.craig.2 at us.af.mil>
> > Subject: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET Install
> > NETCDF Issue
> >
> > Hi Bob. Based on the error message you included (thank you!):
> >
> > /bin/mkdir -p '/external_libs/include'
> > /bin/mkdir: cannot create directory `/external_libs': Permission
> > denied
> >
> > It appears that MET_LIB_DIR is not set, as "/" is the beginning
> character.
> > Please be sure to set MET_LIB_DIR and try again.
> >
> > Please let me know if you have any other questions or encounter
any
> > other problems.
> >
> > Julie
> >
> >
> > On Wed, Feb 13, 2019, 3:45 PM robert.craig.2 at us.af.mil via RT <
> > met_help at ucar.edu> wrote:
> >
> > >
> > > Wed Feb 13 15:44:51 2019: Request 88918 was acted upon.
> > > Transaction: Ticket created by robert.craig.2 at us.af.mil
> > > Queue: met_help
> > > Subject: MET Install NETCDF Issue
> > > Owner: Nobody
> > > Requestors: robert.craig.2 at us.af.mil
> > > Status: new
> > > Ticket <URL:
> > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918
> > > >
> > >
> > >
> > > Julie, when compiling MET I get the error:
> > >
> > > c_var_info.cc
> > > 169 In file included from nc_var_info.cc:24:
> > > 170 nc_utils.h:22:18: error: netcdf: No such file or directory
> > > 171 In file included from nc_var_info.cc:24:
> > >
> > > To fix this, in a previous email you said to go to the MET help
> > > page and run through the NETCDF-C install procedures. I ran
> > > "./configure --prefix=${MET_LIB_DIR}/external_libs
> > > LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> > > CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include" and then "make
> install"
> > > but get the following error:
> > >
> > > Making install in include
> > > make[1]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make[2]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make[2]: Nothing to be done for `install-exec-am'.
> > > /bin/mkdir -p '/external_libs/include'
> > > /bin/mkdir: cannot create directory `/external_libs': Permission
> > > denied
> > > make[2]: *** [install-includeHEADERS] Error 1
> > > make[2]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make[1]: *** [install-am] Error 2
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make: *** [install-recursive] Error 1
> > >
> > > The permissions in the netcdf-c-4.4.1.1 directory are 777.
> > >
> > > What is the problem?
> > >
> > > Thanks
> > > Bob Craig
> > >
> > >
> >
> >
> >
> >
>
>
>
>
------------------------------------------------
Subject: RE: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET Install NETCDF Issue
From: robert.craig.2 at us.af.mil
Time: Tue Feb 19 09:05:02 2019
Julie, I moved things around so that all the library programs are in a
directory /met-8.1_beta1/external_libs. The directory looks like
this:
BUFRLIB_v10-2-3 freetype g2clib-1.4.0 hdf-4.2.12 hdreos jasper
netcdf-c-4.4.1.1 share
cairo g2clib gsl-1.15 hdf5-1.8.18 include lib
netcdf-cxx4-4.3.0 zlib-1.2.6
Under netcdf-c-4.4.1.1 the directory looks like this:
acinclude.m4 comps.txt CONTRIBUTING.md
h5_test libnetcdf.settings.in Makefile.in nctest
README.md
aclocal.m4 config.guess COPYRIGHT
include libsrc mclean nc_test
RELEASE_NOTES.md
cf config.h CTestConfig.cmake.in
INSTALL.md libsrc4 missing
nc_test4 stamp-h1
cf.cmake config.h.cmake.in CTestCustom.cmake
install-sh libsrcp nc-config
netCDFConfig.cmake.in test-driver
cmake config.h.in depcomp lib
libtool nc-config.cmake.in netcdf.pc
test_prog.c
CMakeInstallation.cmake config.log docs
libdap2 ltmain.sh nc-config.in
netcdf.pc.in test_prog.F
CMakeLists.txt config.status dods.m4
libdispatch m4 ncdap_test oc2
test_prog.f90
cmake_uninstall.cmake.in config.sub examples
lib_flags.am Make0 ncdump
PostInstall.cmake VERSION
compile configure external_libs
liblib Makefile ncgen
postinstall.sh wjna
COMPILE.cmake.txt configure.ac FixBundle.cmake.in
libnetcdf.settings Makefile.am ncgen3
postinstall.sh.in
Under the netcdf lib directory are all the libnet* files. Under the
netcdf nclude directory are the *.h files.
Also, my env variables are:
export MET_NETCDF=/h/WXQC/met-8.1_beta1/external_libs/netcdf-c-4.4.1.1
export BUFR_BASE=/h/WXQC/met-8.1_beta1/external_libs/BUFRLIB_v10-2-3
export GSL_BASE=/h/WXQC/met-8.1_beta1/external_libs/gsl-1.15
export MET_BUFR=/h/WXQC/met-8.1_beta1/external_libs/BUFRLIB_v10-2-3
export MET_GSL=/h/WXQC/met-8.1_beta1/external_libs/gsl-1.15
export MET_GRIB2C=/h/WXQC/met-8.1_beta1/external_libs/g2clib-1.4.0
export MET_GRIB2CINC=/h/WXQC/met-8.1_beta1/external_libs/g2clib-1.4.0
export MET_GRIB2CLIB=/h/WXQC/met-8.1_beta1/external_libs/g2clib-1.4.0
export MET_BUFRLIB=/h/WXQC/met-8.1_beta1/external_libs/BUFRLIB_v10-2-3
export LDFLAGS='-L/h/WXQC/met-8.1_beta1/external_libs/jasper/lib
-L/h/WXQC/met-8.1_beta1/external_libs/zlib-1.2.6/lib -L/h/WXQC/met-
8.1_beta1/external_libs/libpng-1.2.34/li
b'
export LD_LIBRARY_PATH=/gpfs/lsf/9.1/linux2.6-glibc2.3-
x86_64/lib:/usr/mpi/gcc/openmpi-1.8.4/lib64:/h/WXQC/met-
8.1_beta1/external_libs/gsl-1.15/lib
export MET_HDFEOS=/h/WXQC/met-8.1_beta1/external_libs/hdfeos
export MET_HDF5=/h/WXQC/met-8.1_beta1/external_libs/hdf5-1.8.18
export MET_HDF=/h/WXQC/met-8.1_beta1/external_libs/HDF4.2.12
export FC=/usr/bin/gfortran
export F77=/usr/bin/gfortran
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export MET_LIB_DIR=${MET_NETCDF}
Based on this set up, in the MET8.0 tutorial it says to run the
following under the NETCDF-C instructions:
./configure --prefix=${MET_LIB_DIR}/external_libs LDFLAGS=-
L${MET_LIB_DIR}/external_libs/lib CPPFLAGS=-
I${MET_LIB_DIR}/external_libs/include
Currently my external_libs/lib and external_libs/include have the
same files as in the external_libs/netcdf-c-4.4.1.1/lib and include
directories. Is that correct?
When I run the make install after the configure line I get the
following error:
4_la-nc4file.Tpo -c nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-
nc4file.o
nc4file.c: In function ‘nc4_open_file’:
nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared (first
use in this function)
nc4file.c:2316: error: (Each undeclared identifier is reported only
once
nc4file.c:2316: error: for each function it appears in.)
nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
(first use in this function)
make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
make[1]: Leaving directory `/gpfs/dev/h/WXQC/met-
8.1_beta1/external_libs/netcdf-c-4.4.1.1/libsrc4'
make: *** [install-recursive] Error 1
My H5DIR is /h/WXQC/met-8.1_beta1/external_libs/hdf5-1.8.18 and my
ZDIR is /h/WXQC/met-8.1_beta1/external_libs/zlib-1.2.6/lib. My make
of the hdf5-1.8.18 library seems to work okay with out errors
following the instructions on the tutorial page for compiling
libraries.
So, what am I missing?
Thanks
Bob
-----Original Message-----
From: Julie Prestopnik via RT <met_help at ucar.edu>
Sent: Thursday, February 14, 2019 12:35 PM
To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
<robert.craig.2 at us.af.mil>
Subject: Re: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET Install
NETCDF Issue
Hi Bob.
When you compile NetCDF-C, you'll need to tell it where the library
files are (for HDF5, possibly other files too, but let's start with
that) using LDFLAGS and where the include files are (for HDF5,
possibly other files too, but let's start with that) using CPPFLAGS.
I see that you set "MET_HD5=/h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18".
Is there a "lib" subdirectory under /h/WXQC/met-8.1_beta1/lib/hdf5-
1.8.18? Is there an include subdirectory under /h/WXQC/met-
8.1_beta1/lib/hdf5-1.8.18?
It looks like your HDF5 library files were put directly in
/h/WXQC/met-8.1_beta1/lib instead of at /h/WXQC/met-
8.1_beta1/lib/hdf5-1.8.18/lib, but I don't see any header files in
/h/WXQC/met-8.1_beta1/lib. Are the header/include files in
/h/WXQC/met-8.1_beta1/include?
On a separate note, I see that you set
"MET_NETCDF=/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1". You will
need to have your NetCDF-C and NetCDF-CXX files installed in the same
location, since MET has only only MET_NETCDF variable to reference.
This is one reason that I install every external library file at, for
example, /d1/jpresto/8.1_beta/external_libs (with library files in
/d1/jpresto/8.1_beta/external_libs/lib and include files in
/d1/jpresto/8.1_beta/external_libs/include).
You would want to set your configure command to the following for
NetCDF-C (using bash syntax below), replacing the <> with the actual
location.
export PREFIX=<set to the location you want to install the NetCDF lib
and include files> (the library files will be put in a "lib" subdir
and the include files will be put in an "include" subdir. This should
be the same location for your NetCDF-CXX files) export LDFLAGS=<set to
the location where your HDF5 library files are> export CPPFLAGS=<set
to the location where your HDF5 header/include files
are>
./configure --prefix=${PREFIX} LDFLAGS=-L${LDFLAGS} CPPFLAGS=-
I${CPPFLAGS}
I hope this helps. Please let me know if you have any questions. I
am out
for the rest of the day and most of tomorrow. Monday is a holiday.
I
will be back in the office on Tuesday. Please respond to this ticket
with any other questions, and I will do my best to respond as soon as
I can.
Below I'll paste an example of how my installation is structured on
our machine "cheyenne", so you have it as an example.
Thanks,
Julie
cheyenne3:jpresto> pwd
/glade/p/ral/jntp/MET/MET_releases/8.0
cheyenne3:jpresto> ls
bin external_libs met-8.0 share
cheyenne3:jpresto> cd
/glade/p/ral/jntp/MET/MET_releases/8.0/external_libs
/glade/p/ral/jntp/MET/MET_releases/8.0/external_libs
cheyenne3:jpresto> ls
bin bufrlib cairo freetype g2clib gsl hdf hdf5 hdfeos include
jasper lib libpng man netcdf share zlib
cheyenne3:jpresto> ls
/glade/p/ral/jntp/MET/MET_releases/8.0/external_libs/lib
libbufr.a libgrib2c.a libgsl.so.19 libhdf5.la
libmfhdf.a
libnetcdf.so libpng.la
libdf.a libgsl.a libgsl.so.19.0.0 libhdf5.settings
libnetcdf.a
libnetcdf.so.11 libpng.so
libfreetype.a libgslcblas.a libhdf4.settings libhdf5.so
libnetcdf_c++4.a libnetcdf.so.11.0.4 libz.a
libfreetype.la libgslcblas.la libhdf5.a libhdf5.so.10
libnetcdf_c++4.la libpng16.a libz.so
libfreetype.so libgslcblas.so libhdf5_hl.a
libhdf5.so.10.2.1
libnetcdf_c++4.so libpng16.la libz.so.1
libfreetype.so.6 libgslcblas.so.0 libhdf5_hl.la
libhdfeos.a
libnetcdf_c++4.so.1 libpng16.so libz.so.1.2.11
libfreetype.so.6.12.5 libgslcblas.so.0.0.0 libhdf5_hl.so
libhdfeos.la
libnetcdf_c++4.so.1.0.3 libpng16.so.16 pkgconfig
libGctp.a libgsl.la libhdf5_hl.so.10 libjasper.a
libnetcdf.la libpng16.so.16.34.0
libGctp.la libgsl.so libhdf5_hl.so.10.1.1 libjasper.la
libnetcdf.settings
libpng.a
cheyenne3:jpresto> ls
/glade/p/ral/jntp/MET/MET_releases/8.0/external_libs/include
atom.h dfsd.h H5Dpublic.h H5IMpublic.h H5Tpublic.h hdfi.h
mffunc.f90 ncFloat.h netcdf
bitvect.h dfstubs.h H5DSpublic.h H5Ipublic.h H5version.h
hdf.inc
mffunc.inc ncGroupAtt.h netcdf.h
cdeflate.h dfufp2i.h H5Epubgen.h H5Lpublic.h H5Zpublic.h
HE2_config.h mfgr.h ncGroup.h netcdf_mem.h
cfortHdf.h drstemplates.h H5Epublic.h H5LTpublic.h hbitio.h
herr.h
mfhdf.h ncInt64.h netcdf_meta.h
cnbit.h dynarray.h H5FDcore.h H5MMpublic.h hchunks.h
hfile.h
mfhdfi.h ncInt.h pdstemplates.h
cnone.h ease.h H5FDdirect.h H5Opublic.h hcomp.h hkit.h
mstdio.h ncOpaqueType.h pngconf.h
crle.h freetype2 H5FDfamily.h H5overflow.h hcompi.h
hlimits.h
ncAtt.h ncShort.h png.h
cskphuff.h grib2.h H5FDlog.h H5PLextern.h hconv.h hntdefs.h
ncByte.h ncString.h pnglibconf.h
cszip.h gridtemplates.h H5FDmpi.h H5PLpublic.h hdf2netcdf.h
hproto_fortran.h ncChar.h ncType.h tbbt.h
dfan.h gsl H5FDmpio.h H5Ppublic.h hdf4_netcdf.h hproto.h
ncCheck.h ncUbyte.h vattr.h
dffunc.f90 h4config.h H5FDmulti.h H5PTpublic.h hdf5.h
htags.h
ncCompoundType.h ncUint64.h vg.h
dffunc.inc H5ACpublic.h H5FDpublic.h H5pubconf.h hdf5_hl.h
jasper
ncDim.h ncUint.h zconf.h
dfgr.h H5api_adpt.h H5FDsec2.h H5public.h HdfEosDef.h
libpng16
ncDouble.h ncUshort.h zlib.h
df.h H5Apublic.h H5FDstdio.h H5Rpublic.h HDFEOSVersion.h
linklist.h ncEnumType.h ncVarAtt.h
dfi.h H5Cpublic.h H5Fpublic.h H5Spublic.h hdf.f90
local_nc.h
ncException.h ncVar.h
dfrig.h H5DOpublic.h H5Gpublic.h H5TBpublic.h hdf.h
mfan.h
ncFile.h ncVlenType.h
On Thu, Feb 14, 2019 at 11:01 AM robert.craig.2 at us.af.mil via RT <
met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
>
> Well, I am still having problems. First of all my env variables
are set
> this way:
>
> MET_BUFR=/h/WXQC/met-8.1_beta1/lib/BUFRLIB_v10-0-1
> MET_BUFRLIB=/h/WXQC/met-8.1_beta1/lib/BUFRLIB_v10-0-1
> MET_GRIB2CINC=/h/WXQC/met-8.1_beta1/lib/g2clib-1.4.0
> MET_GRIB2CLIB=/h/WXQC/met-8.1_beta1/lib/g2clib-1.4.0
> MET_GRIB_TABLES=/h/data/global/WXQC/data/met/config/grib2
> MET_GSL=/h/WXQC/met-8.1_beta1/lib/gsl-1.15
> MET_HD5=/h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18
> MET_LIB_DIR=/h/WXQC/met-8.1_beta1/lib
> MET_NETCDF=/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1
> ZDIR=/h/WXQC/met-8.1_beta1/lib/zlib-1.2.6/lib
> H5DIR=/h/WXQC/met-8.1_beta1/lib/hd55-1.8.18
>
> The /h/WXQC/met-8.1_beta1/lib directory has the following dirs.:
>
> bin hd55-1.8.18 HDF-EOS2.19v1.00.tar
libhdf5_hl.la
> libhdf5.so.100 libnetcdf_c++4.so.1.0.3 netcdf-c-
4.4.1.1
> BUFRLIB_v10-0-1 hdf-4.2.12 include
libhdf5_hl.so
> libhdf5.so.100.0.1 libnetcdf.la netcdf-cxx4-
4.3.0
> BUFRLIB_v10-2-3 hdf-4.2.12.tar jasper
> libhdf5_hl.so.100 libnetcdf.a libnetcdf.settings
share
> external_libs hdf5-1.10.0-patch1 lib
> libhdf5_hl.so.100.0.0 libnetcdf_c++4.a libnetcdf.so
tar
> g2clib-1.4.0 hdf5-1.8.18 libf2c
libhdf5.la
> libnetcdf_c++4.la libnetcdf.so.11 zlib-1.2.6
> GRIBI_copygb.exe hdf5-1.8.18.tar libhdf5.a
> libhdf5.settings libnetcdf_c++4.so libnetcdf.so.11.0.4
> gsl-1.15 hdfeos libhdf5_hl.a
libhdf5.so
> libnetcdf_c++4.so.1 libpng-1.2.34
>
> In the external_libs dir is:
>
> bin include lib share
>
> I download the HDFS library per instruction on MET web site and
> installed. It looked like it compiled correctly. Then when trying
to
> compile netcdf-c-4.4.1.1 I get the same error messages I sent you
earlier:
>
> T libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.Tpo
> -c -o libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo
> './'`nc4file.c
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
-I../oc2
> -I/h/WXQC/met-8.1_beta1/lib/external_libs/include -MT
> libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-nc4file.Tpo
> -c nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-nc4file.o
> nc4file.c: In function ‘nc4_open_file’:
> nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared (first
> use in this function)
> nc4file.c:2316: error: (Each undeclared identifier is reported only
> once
> nc4file.c:2316: error: for each function it appears in.)
> nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
> (first use in this function)
> make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> make: *** [install-recursive] Error 1
>
> So, not sure what to try at this point. Did I miss something that
is
> obvious?
>
> Thanks
> Bob
>
>
> -----Original Message-----
> From: Julie Prestopnik via RT <met_help at ucar.edu>
> Sent: Thursday, February 14, 2019 9:48 AM
> To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
> <robert.craig.2 at us.af.mil>
> Subject: Re: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET
Install
> NETCDF Issue
>
> Hi Bob.
>
> should MET_LIB_DIR point to met-8.1_beta1/lib?
> >
>
> I will answer that question, by breaking down the command that you
> previously ran:
>
> > ./configure --prefix=${MET_LIB_DIR}/external_libs
> > LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> > CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include
>
>
> In the example above "-prefix=" should be set to the location where
> you want the NetCDF files to be put. In the case above, the NetCDF
> library files would be put at "${MET_LIB_DIR}/external_libs/lib" and
> the NetCDF include files would be put at
> "${MET_LIB_DIR}/external_libs/include". You can set this to
whatever
> you'd like, based on where you want to put the NetCDF library and
> include files (note that the NetCDF package knows to put the library
> files in a lib subdirectory and the include files in an include
> subdirectory, so for the "prefix" option, you simply set it to the
> upper level directory). NetCDF4 depends on HDF5, so HDF5 must be
> installed first. In the above configure command the values of
LDFLAGS
> and CPPFLAGS tell NetCDF where it can find the library files and
> header files, respectively, that it needs. When I install MET, I
> install of the external libraries in a directory called <path
to>/external_libs. All of the external library files go in <path
to>/externa!
> l_libs/lib and all of the external library include files go in
<path
> to>/external_libs/include. So, when I install NetCDF the HDF5 files
> to>have
> already been put in those locations and by setting LDFLAGS and
> CPPFLAGS to the location in the above configure command, NetCDF
knows
> where to find the files it needs.
>
> From the error you sent, it seems that NetCDF-C cannot find the HDF5
> files that it needs. Did you install HDF5 first? If not, please
> install HDF5 first and they reconfigure and reinstall NetCDF-C
> pointing the appropriate locations as described above.
>
> I hope that helps. Please let me know if you have any questions or
if
> you encounter any other problems.
>
> Thanks!
>
> Julie
>
> On Thu, Feb 14, 2019 at 7:35 AM robert.craig.2 at us.af.mil via RT <
> met_help at ucar.edu> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
> >
> > Julie, should MET_LIB_DIR point to met-8.1_beta1/lib? I tried
this.
> > I got a good compile of NETCDF-CXX but I get an error compiling
NETCDF-C:
> >
> > Making install in include
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make[2]: Nothing to be done for `install-exec-am'.
> > /bin/mkdir -p
> '/h/WXQC/met-8.1_beta1/external_libs/external_libs/include'
> > /usr/bin/install -c -m 644 netcdf.h netcdf_meta.h netcdf_mem.h
> > '/h/WXQC/met-8.1_beta1/external_libs/external_libs/include'
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > Making install in oc2
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > make[2]: Nothing to be done for `install-exec-am'.
> > make[2]: Nothing to be done for `install-data-am'.
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > Making install in h5_test
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > make[2]: Nothing to be done for `install-exec-am'.
> > make[2]: Nothing to be done for `install-data-am'.
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > Making install in libdispatch
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> > make[2]: Nothing to be done for `install-exec-am'.
> > make[2]: Nothing to be done for `install-data-am'.
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libdispatch'
> > Making install in libsrc
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > make[2]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > make[2]: Nothing to be done for `install-exec-am'.
> > /bin/mkdir -p
> > '/h/WXQC/met-8.1_beta1/external_libs/external_libs/share/man/man3'
> > /usr/bin/install -c -m 644 netcdf.3
> > '/h/WXQC/met-8.1_beta1/external_libs/external_libs/share/man/man3'
> > make[2]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > Making install in libsrc4
> > make[1]: Entering directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> > /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I.
> > -I.. -I../include -I../oc2
> > -I/h/WXQC/met-8.1_beta1/external_libs/external_libs/include -MT
> > libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.Tpo
> > -c -o libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo
> > './'`nc4file.c
> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
> > -I../oc2 -I/h/WXQC/met-
8.1_beta1/external_libs/external_libs/include
> > -MT libnetcdf4_la-nc4file.lo -MD -MP -MF
> > .deps/libnetcdf4_la-nc4file.Tpo -c nc4file.c -fPIC -DPIC -o
> > .libs/libnetcdf4_la-nc4file.o
> > nc4file.c: In function ‘nc4_open_file’:
> > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared
(first
> > use in this function)
> > nc4file.c:2316: error: (Each undeclared identifier is reported
only
> > once
> > nc4file.c:2316: error: for each function it appears in.)
> > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
> > (first use in this function)
> > make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> > make: *** [install-recursive] Error 1
> >
> > What do you think I did wrong?
> >
> > Thanks
> > Bob
> >
> > -----Original Message-----
> > From: Julie Prestopnik via RT <met_help at ucar.edu>
> > Sent: Wednesday, February 13, 2019 4:50 PM
> > To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
> > <robert.craig.2 at us.af.mil>
> > Subject: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET Install
> > NETCDF Issue
> >
> > Hi Bob. Based on the error message you included (thank you!):
> >
> > /bin/mkdir -p '/external_libs/include'
> > /bin/mkdir: cannot create directory `/external_libs': Permission
> > denied
> >
> > It appears that MET_LIB_DIR is not set, as "/" is the beginning
> character.
> > Please be sure to set MET_LIB_DIR and try again.
> >
> > Please let me know if you have any other questions or encounter
any
> > other problems.
> >
> > Julie
> >
> >
> > On Wed, Feb 13, 2019, 3:45 PM robert.craig.2 at us.af.mil via RT <
> > met_help at ucar.edu> wrote:
> >
> > >
> > > Wed Feb 13 15:44:51 2019: Request 88918 was acted upon.
> > > Transaction: Ticket created by robert.craig.2 at us.af.mil
> > > Queue: met_help
> > > Subject: MET Install NETCDF Issue
> > > Owner: Nobody
> > > Requestors: robert.craig.2 at us.af.mil
> > > Status: new
> > > Ticket <URL:
> > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918
> > > >
> > >
> > >
> > > Julie, when compiling MET I get the error:
> > >
> > > c_var_info.cc
> > > 169 In file included from nc_var_info.cc:24:
> > > 170 nc_utils.h:22:18: error: netcdf: No such file or directory
> > > 171 In file included from nc_var_info.cc:24:
> > >
> > > To fix this, in a previous email you said to go to the MET help
> > > page and run through the NETCDF-C install procedures. I ran
> > > "./configure --prefix=${MET_LIB_DIR}/external_libs
> > > LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> > > CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include" and then "make
> install"
> > > but get the following error:
> > >
> > > Making install in include
> > > make[1]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make[2]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make[2]: Nothing to be done for `install-exec-am'.
> > > /bin/mkdir -p '/external_libs/include'
> > > /bin/mkdir: cannot create directory `/external_libs': Permission
> > > denied
> > > make[2]: *** [install-includeHEADERS] Error 1
> > > make[2]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make[1]: *** [install-am] Error 2
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make: *** [install-recursive] Error 1
> > >
> > > The permissions in the netcdf-c-4.4.1.1 directory are 777.
> > >
> > > What is the problem?
> > >
> > > Thanks
> > > Bob Craig
> > >
> > >
> >
> >
> >
> >
>
>
>
>
------------------------------------------------
Subject: MET Install NETCDF Issue
From: Julie Prestopnik
Time: Tue Feb 19 10:29:43 2019
Hi Bob.
John will take care of providing you with Cairo and Freetype though
ARLSafe.
NetCDF-C still cannot find the HDF5 files that it needs. Are your
HDF5
header files located at
"/h/WXQC/met-8.1_beta1/external_libs/hdf5-1.8.18/include"?
If so, please try setting CFLAGS to that location:
export CFLAGS="-I/h/WXQC/met-8.1_beta1/external_libs/hdf5-
1.8.18/include"
and then, in the same shell/environment, reconfigure and reinstall
NetCDF-C
and then NetCDF-CXX in the manner that I described in my email from
Feb 14,
2019, 8:47 AM. Then run "make clean" for MET and then reconfigure and
reinstall MET as well.
Please let me know if you have any questions. I hope this helps.
Thanks!
Julie
On Tue, Feb 19, 2019 at 9:05 AM robert.craig.2 at us.af.mil via RT <
met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
>
> Julie, I moved things around so that all the library programs are in
a
> directory /met-8.1_beta1/external_libs. The directory looks like
this:
>
> BUFRLIB_v10-2-3 freetype g2clib-1.4.0 hdf-4.2.12 hdreos
jasper
> netcdf-c-4.4.1.1 share
> cairo g2clib gsl-1.15 hdf5-1.8.18 include lib
> netcdf-cxx4-4.3.0 zlib-1.2.6
>
> Under netcdf-c-4.4.1.1 the directory looks like this:
>
> acinclude.m4 comps.txt CONTRIBUTING.md
> h5_test libnetcdf.settings.in Makefile.in
nctest
> README.md
> aclocal.m4 config.guess COPYRIGHT
> include libsrc mclean
nc_test
> RELEASE_NOTES.md
> cf config.h CTestConfig.cmake.in
> INSTALL.md libsrc4 missing
nc_test4
> stamp-h1
> cf.cmake config.h.cmake.in CTestCustom.cmake
> install-sh libsrcp nc-config
> netCDFConfig.cmake.in test-driver
> cmake config.h.in depcomp
lib
> libtool nc-config.cmake.in netcdf.pc
> test_prog.c
> CMakeInstallation.cmake config.log docs
> libdap2 ltmain.sh nc-config.in
> netcdf.pc.in test_prog.F
> CMakeLists.txt config.status dods.m4
> libdispatch m4 ncdap_test oc2
> test_prog.f90
> cmake_uninstall.cmake.in config.sub examples
> lib_flags.am Make0 ncdump
> PostInstall.cmake VERSION
> compile configure external_libs
liblib
> Makefile ncgen
postinstall.sh
> wjna
> COMPILE.cmake.txt configure.ac FixBundle.cmake.in
> libnetcdf.settings Makefile.am ncgen3
> postinstall.sh.in
>
> Under the netcdf lib directory are all the libnet* files. Under
the
> netcdf nclude directory are the *.h files.
>
> Also, my env variables are:
>
> export MET_NETCDF=/h/WXQC/met-8.1_beta1/external_libs/netcdf-c-
4.4.1.1
> export BUFR_BASE=/h/WXQC/met-8.1_beta1/external_libs/BUFRLIB_v10-2-3
> export GSL_BASE=/h/WXQC/met-8.1_beta1/external_libs/gsl-1.15
> export MET_BUFR=/h/WXQC/met-8.1_beta1/external_libs/BUFRLIB_v10-2-3
> export MET_GSL=/h/WXQC/met-8.1_beta1/external_libs/gsl-1.15
> export MET_GRIB2C=/h/WXQC/met-8.1_beta1/external_libs/g2clib-1.4.0
> export MET_GRIB2CINC=/h/WXQC/met-8.1_beta1/external_libs/g2clib-
1.4.0
> export MET_GRIB2CLIB=/h/WXQC/met-8.1_beta1/external_libs/g2clib-
1.4.0
> export MET_BUFRLIB=/h/WXQC/met-8.1_beta1/external_libs/BUFRLIB_v10-
2-3
> export LDFLAGS='-L/h/WXQC/met-8.1_beta1/external_libs/jasper/lib
> -L/h/WXQC/met-8.1_beta1/external_libs/zlib-1.2.6/lib
> -L/h/WXQC/met-8.1_beta1/external_libs/libpng-1.2.34/li
> b'
> export
> LD_LIBRARY_PATH=/gpfs/lsf/9.1/linux2.6-glibc2.3-
x86_64/lib:/usr/mpi/gcc/openmpi-1.8.4/lib64:/h/WXQC/met-
8.1_beta1/external_libs/gsl-1.15/lib
> export MET_HDFEOS=/h/WXQC/met-8.1_beta1/external_libs/hdfeos
> export MET_HDF5=/h/WXQC/met-8.1_beta1/external_libs/hdf5-1.8.18
> export MET_HDF=/h/WXQC/met-8.1_beta1/external_libs/HDF4.2.12
> export FC=/usr/bin/gfortran
> export F77=/usr/bin/gfortran
> export CC=/usr/bin/gcc
> export CXX=/usr/bin/g++
> export MET_LIB_DIR=${MET_NETCDF}
>
> Based on this set up, in the MET8.0 tutorial it says to run the
following
> under the NETCDF-C instructions:
>
> ./configure --prefix=${MET_LIB_DIR}/external_libs
> LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include
> Currently my external_libs/lib and external_libs/include have the
same
> files as in the external_libs/netcdf-c-4.4.1.1/lib and include
> directories. Is that correct?
>
> When I run the make install after the configure line I get the
following
> error:
>
> 4_la-nc4file.Tpo -c nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-
nc4file.o
> nc4file.c: In function ‘nc4_open_file’:
> nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared (first
use
> in this function)
> nc4file.c:2316: error: (Each undeclared identifier is reported only
once
> nc4file.c:2316: error: for each function it appears in.)
> nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
(first
> use in this function)
> make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/external_libs/netcdf-c-
4.4.1.1/libsrc4'
> make: *** [install-recursive] Error 1
>
> My H5DIR is /h/WXQC/met-8.1_beta1/external_libs/hdf5-1.8.18 and my
ZDIR is
> /h/WXQC/met-8.1_beta1/external_libs/zlib-1.2.6/lib. My make of the
> hdf5-1.8.18 library seems to work okay with out errors following the
> instructions on the tutorial page for compiling libraries.
>
> So, what am I missing?
>
> Thanks
> Bob
>
>
>
> -----Original Message-----
> From: Julie Prestopnik via RT <met_help at ucar.edu>
> Sent: Thursday, February 14, 2019 12:35 PM
> To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
<robert.craig.2 at us.af.mil>
> Subject: Re: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET
Install
> NETCDF Issue
>
> Hi Bob.
>
> When you compile NetCDF-C, you'll need to tell it where the library
files
> are (for HDF5, possibly other files too, but let's start with that)
using
> LDFLAGS and where the include files are (for HDF5, possibly other
files
> too, but let's start with that) using CPPFLAGS.
>
> I see that you set "MET_HD5=/h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18".
Is
> there a "lib" subdirectory under /h/WXQC/met-8.1_beta1/lib/hdf5-
1.8.18? Is
> there an include subdirectory under /h/WXQC/met-8.1_beta1/lib/hdf5-
1.8.18?
> It looks like your HDF5 library files were put directly in
> /h/WXQC/met-8.1_beta1/lib instead of at
> /h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18/lib, but I don't see any
header files
> in /h/WXQC/met-8.1_beta1/lib. Are the header/include files in
> /h/WXQC/met-8.1_beta1/include?
>
> On a separate note, I see that you set
> "MET_NETCDF=/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1". You will
need to
> have your NetCDF-C and NetCDF-CXX files installed in the same
location,
> since MET has only only MET_NETCDF variable to reference. This is
one
> reason that I install every external library file at, for example,
> /d1/jpresto/8.1_beta/external_libs (with library files in
> /d1/jpresto/8.1_beta/external_libs/lib and include files in
> /d1/jpresto/8.1_beta/external_libs/include).
>
> You would want to set your configure command to the following for
NetCDF-C
> (using bash syntax below), replacing the <> with the actual
location.
>
> export PREFIX=<set to the location you want to install the NetCDF
lib and
> include files> (the library files will be put in a "lib" subdir and
the
> include files will be put in an "include" subdir. This should be
the same
> location for your NetCDF-CXX files) export LDFLAGS=<set to the
location
> where your HDF5 library files are> export CPPFLAGS=<set to the
location
> where your HDF5 header/include files
> are>
>
> ./configure --prefix=${PREFIX} LDFLAGS=-L${LDFLAGS} CPPFLAGS=-
I${CPPFLAGS}
>
> I hope this helps. Please let me know if you have any questions. I
am out
> for the rest of the day and most of tomorrow. Monday is a holiday.
I
> will be back in the office on Tuesday. Please respond to this
ticket with
> any other questions, and I will do my best to respond as soon as I
can.
>
> Below I'll paste an example of how my installation is structured on
our
> machine "cheyenne", so you have it as an example.
>
> Thanks,
> Julie
>
> cheyenne3:jpresto> pwd
>
> /glade/p/ral/jntp/MET/MET_releases/8.0
>
>
> cheyenne3:jpresto> ls
>
> bin external_libs met-8.0 share
>
>
> cheyenne3:jpresto> cd
/glade/p/ral/jntp/MET/MET_releases/8.0/external_libs
>
> /glade/p/ral/jntp/MET/MET_releases/8.0/external_libs
>
>
>
> cheyenne3:jpresto> ls
>
> bin bufrlib cairo freetype g2clib gsl hdf hdf5 hdfeos
include
> jasper lib libpng man netcdf share zlib
>
>
>
> cheyenne3:jpresto> ls
> /glade/p/ral/jntp/MET/MET_releases/8.0/external_libs/lib
>
> libbufr.a libgrib2c.a libgsl.so.19 libhdf5.la
libmfhdf.a
> libnetcdf.so libpng.la
>
> libdf.a libgsl.a libgsl.so.19.0.0 libhdf5.settings
> libnetcdf.a
> libnetcdf.so.11 libpng.so
>
> libfreetype.a libgslcblas.a libhdf4.settings libhdf5.so
> libnetcdf_c++4.a libnetcdf.so.11.0.4 libz.a
>
> libfreetype.la libgslcblas.la libhdf5.a libhdf5.so.10
> libnetcdf_c++4.la libpng16.a libz.so
>
> libfreetype.so libgslcblas.so libhdf5_hl.a
libhdf5.so.10.2.1
> libnetcdf_c++4.so libpng16.la libz.so.1
>
> libfreetype.so.6 libgslcblas.so.0 libhdf5_hl.la
libhdfeos.a
> libnetcdf_c++4.so.1 libpng16.so libz.so.1.2.11
>
> libfreetype.so.6.12.5 libgslcblas.so.0.0.0 libhdf5_hl.so
libhdfeos.la
> libnetcdf_c++4.so.1.0.3 libpng16.so.16 pkgconfig
>
> libGctp.a libgsl.la libhdf5_hl.so.10 libjasper.a
> libnetcdf.la libpng16.so.16.34.0
>
> libGctp.la libgsl.so libhdf5_hl.so.10.1.1 libjasper.la
> libnetcdf.settings
> libpng.a
>
>
>
> cheyenne3:jpresto> ls
> /glade/p/ral/jntp/MET/MET_releases/8.0/external_libs/include
>
> atom.h dfsd.h H5Dpublic.h H5IMpublic.h H5Tpublic.h
hdfi.h
> mffunc.f90 ncFloat.h netcdf
>
> bitvect.h dfstubs.h H5DSpublic.h H5Ipublic.h H5version.h
hdf.inc
> mffunc.inc ncGroupAtt.h netcdf.h
>
> cdeflate.h dfufp2i.h H5Epubgen.h H5Lpublic.h H5Zpublic.h
> HE2_config.h mfgr.h ncGroup.h netcdf_mem.h
>
> cfortHdf.h drstemplates.h H5Epublic.h H5LTpublic.h hbitio.h
herr.h
> mfhdf.h ncInt64.h netcdf_meta.h
>
> cnbit.h dynarray.h H5FDcore.h H5MMpublic.h hchunks.h
hfile.h
> mfhdfi.h ncInt.h pdstemplates.h
>
> cnone.h ease.h H5FDdirect.h H5Opublic.h hcomp.h hkit.h
> mstdio.h ncOpaqueType.h pngconf.h
>
> crle.h freetype2 H5FDfamily.h H5overflow.h hcompi.h
hlimits.h
> ncAtt.h ncShort.h png.h
>
> cskphuff.h grib2.h H5FDlog.h H5PLextern.h hconv.h
hntdefs.h
> ncByte.h ncString.h pnglibconf.h
>
> cszip.h gridtemplates.h H5FDmpi.h H5PLpublic.h hdf2netcdf.h
> hproto_fortran.h ncChar.h ncType.h tbbt.h
>
> dfan.h gsl H5FDmpio.h H5Ppublic.h hdf4_netcdf.h
hproto.h
> ncCheck.h ncUbyte.h vattr.h
>
> dffunc.f90 h4config.h H5FDmulti.h H5PTpublic.h hdf5.h
htags.h
> ncCompoundType.h ncUint64.h vg.h
>
> dffunc.inc H5ACpublic.h H5FDpublic.h H5pubconf.h hdf5_hl.h
jasper
> ncDim.h ncUint.h zconf.h
>
> dfgr.h H5api_adpt.h H5FDsec2.h H5public.h HdfEosDef.h
libpng16
> ncDouble.h ncUshort.h zlib.h
>
> df.h H5Apublic.h H5FDstdio.h H5Rpublic.h HDFEOSVersion.h
> linklist.h ncEnumType.h ncVarAtt.h
>
> dfi.h H5Cpublic.h H5Fpublic.h H5Spublic.h hdf.f90
local_nc.h
> ncException.h ncVar.h
>
> dfrig.h H5DOpublic.h H5Gpublic.h H5TBpublic.h hdf.h
mfan.h
> ncFile.h ncVlenType.h
>
>
>
>
> On Thu, Feb 14, 2019 at 11:01 AM robert.craig.2 at us.af.mil via RT <
> met_help at ucar.edu> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
> >
> > Well, I am still having problems. First of all my env variables
are set
> > this way:
> >
> > MET_BUFR=/h/WXQC/met-8.1_beta1/lib/BUFRLIB_v10-0-1
> > MET_BUFRLIB=/h/WXQC/met-8.1_beta1/lib/BUFRLIB_v10-0-1
> > MET_GRIB2CINC=/h/WXQC/met-8.1_beta1/lib/g2clib-1.4.0
> > MET_GRIB2CLIB=/h/WXQC/met-8.1_beta1/lib/g2clib-1.4.0
> > MET_GRIB_TABLES=/h/data/global/WXQC/data/met/config/grib2
> > MET_GSL=/h/WXQC/met-8.1_beta1/lib/gsl-1.15
> > MET_HD5=/h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18
> > MET_LIB_DIR=/h/WXQC/met-8.1_beta1/lib
> > MET_NETCDF=/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1
> > ZDIR=/h/WXQC/met-8.1_beta1/lib/zlib-1.2.6/lib
> > H5DIR=/h/WXQC/met-8.1_beta1/lib/hd55-1.8.18
> >
> > The /h/WXQC/met-8.1_beta1/lib directory has the following dirs.:
> >
> > bin hd55-1.8.18 HDF-EOS2.19v1.00.tar
> libhdf5_hl.la
> > libhdf5.so.100 libnetcdf_c++4.so.1.0.3 netcdf-c-
4.4.1.1
> > BUFRLIB_v10-0-1 hdf-4.2.12 include
libhdf5_hl.so
> > libhdf5.so.100.0.1 libnetcdf.la netcdf-cxx4-
4.3.0
> > BUFRLIB_v10-2-3 hdf-4.2.12.tar jasper
> > libhdf5_hl.so.100 libnetcdf.a libnetcdf.settings
> share
> > external_libs hdf5-1.10.0-patch1 lib
> > libhdf5_hl.so.100.0.0 libnetcdf_c++4.a libnetcdf.so
tar
> > g2clib-1.4.0 hdf5-1.8.18 libf2c
libhdf5.la
> > libnetcdf_c++4.la libnetcdf.so.11 zlib-1.2.6
> > GRIBI_copygb.exe hdf5-1.8.18.tar libhdf5.a
> > libhdf5.settings libnetcdf_c++4.so libnetcdf.so.11.0.4
> > gsl-1.15 hdfeos libhdf5_hl.a
libhdf5.so
> > libnetcdf_c++4.so.1 libpng-1.2.34
> >
> > In the external_libs dir is:
> >
> > bin include lib share
> >
> > I download the HDFS library per instruction on MET web site and
> > installed. It looked like it compiled correctly. Then when
trying to
> > compile netcdf-c-4.4.1.1 I get the same error messages I sent you
> earlier:
> >
> > T libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.Tpo
> > -c -o libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo
> > './'`nc4file.c
> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
-I../oc2
> > -I/h/WXQC/met-8.1_beta1/lib/external_libs/include -MT
> > libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.Tpo
> > -c nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-nc4file.o
> > nc4file.c: In function ‘nc4_open_file’:
> > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared
(first
> > use in this function)
> > nc4file.c:2316: error: (Each undeclared identifier is reported
only
> > once
> > nc4file.c:2316: error: for each function it appears in.)
> > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
> > (first use in this function)
> > make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> > make: *** [install-recursive] Error 1
> >
> > So, not sure what to try at this point. Did I miss something that
is
> > obvious?
> >
> > Thanks
> > Bob
> >
> >
> > -----Original Message-----
> > From: Julie Prestopnik via RT <met_help at ucar.edu>
> > Sent: Thursday, February 14, 2019 9:48 AM
> > To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
> > <robert.craig.2 at us.af.mil>
> > Subject: Re: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET
Install
> > NETCDF Issue
> >
> > Hi Bob.
> >
> > should MET_LIB_DIR point to met-8.1_beta1/lib?
> > >
> >
> > I will answer that question, by breaking down the command that you
> > previously ran:
> >
> > > ./configure --prefix=${MET_LIB_DIR}/external_libs
> > > LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> > > CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include
> >
> >
> > In the example above "-prefix=" should be set to the location
where
> > you want the NetCDF files to be put. In the case above, the
NetCDF
> > library files would be put at "${MET_LIB_DIR}/external_libs/lib"
and
> > the NetCDF include files would be put at
> > "${MET_LIB_DIR}/external_libs/include". You can set this to
whatever
> > you'd like, based on where you want to put the NetCDF library and
> > include files (note that the NetCDF package knows to put the
library
> > files in a lib subdirectory and the include files in an include
> > subdirectory, so for the "prefix" option, you simply set it to the
> > upper level directory). NetCDF4 depends on HDF5, so HDF5 must be
> > installed first. In the above configure command the values of
LDFLAGS
> > and CPPFLAGS tell NetCDF where it can find the library files and
> > header files, respectively, that it needs. When I install MET, I
> > install of the external libraries in a directory called <path
> to>/external_libs. All of the external library files go in <path
> to>/externa!
> > l_libs/lib and all of the external library include files go in
<path
> > to>/external_libs/include. So, when I install NetCDF the HDF5
files
> > to>have
> > already been put in those locations and by setting LDFLAGS and
> > CPPFLAGS to the location in the above configure command, NetCDF
knows
> > where to find the files it needs.
> >
> > From the error you sent, it seems that NetCDF-C cannot find the
HDF5
> > files that it needs. Did you install HDF5 first? If not, please
> > install HDF5 first and they reconfigure and reinstall NetCDF-C
> > pointing the appropriate locations as described above.
> >
> > I hope that helps. Please let me know if you have any questions
or if
> > you encounter any other problems.
> >
> > Thanks!
> >
> > Julie
> >
> > On Thu, Feb 14, 2019 at 7:35 AM robert.craig.2 at us.af.mil via RT <
> > met_help at ucar.edu> wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
> > >
> > > Julie, should MET_LIB_DIR point to met-8.1_beta1/lib? I tried
this.
> > > I got a good compile of NETCDF-CXX but I get an error compiling
> NETCDF-C:
> > >
> > > Making install in include
> > > make[1]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make[2]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make[2]: Nothing to be done for `install-exec-am'.
> > > /bin/mkdir -p
> > '/h/WXQC/met-8.1_beta1/external_libs/external_libs/include'
> > > /usr/bin/install -c -m 644 netcdf.h netcdf_meta.h netcdf_mem.h
> > > '/h/WXQC/met-8.1_beta1/external_libs/external_libs/include'
> > > make[2]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > Making install in oc2
> > > make[1]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > > make[2]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > > make[2]: Nothing to be done for `install-exec-am'.
> > > make[2]: Nothing to be done for `install-data-am'.
> > > make[2]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > > Making install in h5_test
> > > make[1]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > > make[2]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > > make[2]: Nothing to be done for `install-exec-am'.
> > > make[2]: Nothing to be done for `install-data-am'.
> > > make[2]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > > Making install in libdispatch
> > > make[1]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/libdispatch'
> > > make[2]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/libdispatch'
> > > make[2]: Nothing to be done for `install-exec-am'.
> > > make[2]: Nothing to be done for `install-data-am'.
> > > make[2]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/libdispatch'
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/libdispatch'
> > > Making install in libsrc
> > > make[1]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > > make[2]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > > make[2]: Nothing to be done for `install-exec-am'.
> > > /bin/mkdir -p
> > > '/h/WXQC/met-
8.1_beta1/external_libs/external_libs/share/man/man3'
> > > /usr/bin/install -c -m 644 netcdf.3
> > > '/h/WXQC/met-
8.1_beta1/external_libs/external_libs/share/man/man3'
> > > make[2]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > > Making install in libsrc4
> > > make[1]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> > > /bin/sh ../libtool --tag=CC --mode=compile gcc
-DHAVE_CONFIG_H -I.
> > > -I.. -I../include -I../oc2
> > > -I/h/WXQC/met-8.1_beta1/external_libs/external_libs/include
-MT
> > > libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.Tpo
> > > -c -o libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo
> > > './'`nc4file.c
> > > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
> > > -I../oc2 -I/h/WXQC/met-
8.1_beta1/external_libs/external_libs/include
> > > -MT libnetcdf4_la-nc4file.lo -MD -MP -MF
> > > .deps/libnetcdf4_la-nc4file.Tpo -c nc4file.c -fPIC -DPIC -o
> > > .libs/libnetcdf4_la-nc4file.o
> > > nc4file.c: In function ‘nc4_open_file’:
> > > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared
(first
> > > use in this function)
> > > nc4file.c:2316: error: (Each undeclared identifier is reported
only
> > > once
> > > nc4file.c:2316: error: for each function it appears in.)
> > > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
> > > (first use in this function)
> > > make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> > > make: *** [install-recursive] Error 1
> > >
> > > What do you think I did wrong?
> > >
> > > Thanks
> > > Bob
> > >
> > > -----Original Message-----
> > > From: Julie Prestopnik via RT <met_help at ucar.edu>
> > > Sent: Wednesday, February 13, 2019 4:50 PM
> > > To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
> > > <robert.craig.2 at us.af.mil>
> > > Subject: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET
Install
> > > NETCDF Issue
> > >
> > > Hi Bob. Based on the error message you included (thank you!):
> > >
> > > /bin/mkdir -p '/external_libs/include'
> > > /bin/mkdir: cannot create directory `/external_libs': Permission
> > > denied
> > >
> > > It appears that MET_LIB_DIR is not set, as "/" is the beginning
> > character.
> > > Please be sure to set MET_LIB_DIR and try again.
> > >
> > > Please let me know if you have any other questions or encounter
any
> > > other problems.
> > >
> > > Julie
> > >
> > >
> > > On Wed, Feb 13, 2019, 3:45 PM robert.craig.2 at us.af.mil via RT <
> > > met_help at ucar.edu> wrote:
> > >
> > > >
> > > > Wed Feb 13 15:44:51 2019: Request 88918 was acted upon.
> > > > Transaction: Ticket created by robert.craig.2 at us.af.mil
> > > > Queue: met_help
> > > > Subject: MET Install NETCDF Issue
> > > > Owner: Nobody
> > > > Requestors: robert.craig.2 at us.af.mil
> > > > Status: new
> > > > Ticket <URL:
> > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918
> > > > >
> > > >
> > > >
> > > > Julie, when compiling MET I get the error:
> > > >
> > > > c_var_info.cc
> > > > 169 In file included from nc_var_info.cc:24:
> > > > 170 nc_utils.h:22:18: error: netcdf: No such file or directory
> > > > 171 In file included from nc_var_info.cc:24:
> > > >
> > > > To fix this, in a previous email you said to go to the MET
help
> > > > page and run through the NETCDF-C install procedures. I ran
> > > > "./configure --prefix=${MET_LIB_DIR}/external_libs
> > > > LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> > > > CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include" and then
"make
> > install"
> > > > but get the following error:
> > > >
> > > > Making install in include
> > > > make[1]: Entering directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > > make[2]: Entering directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > > make[2]: Nothing to be done for `install-exec-am'.
> > > > /bin/mkdir -p '/external_libs/include'
> > > > /bin/mkdir: cannot create directory `/external_libs':
Permission
> > > > denied
> > > > make[2]: *** [install-includeHEADERS] Error 1
> > > > make[2]: Leaving directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > > make[1]: *** [install-am] Error 2
> > > > make[1]: Leaving directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > > make: *** [install-recursive] Error 1
> > > >
> > > > The permissions in the netcdf-c-4.4.1.1 directory are 777.
> > > >
> > > > What is the problem?
> > > >
> > > > Thanks
> > > > Bob Craig
> > > >
> > > >
> > >
> > >
> > >
> > >
> >
> >
> >
> >
>
>
>
>
------------------------------------------------
Subject: RE: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET Install NETCDF Issue
From: robert.craig.2 at us.af.mil
Time: Tue Feb 19 12:41:34 2019
Julie, your CFLAGS variable fixed the NETCDF compile problem and made
it all the way through the compile. One other thing I had to do to
get it to complile bufrlib correctly was to place the libbufr.a file
in the external_libs/lib directory. I had my env MET_BUFR and
MET_BUFRLIB pointing to external_libs/BUFRLIB_v10-2-3 but that was
not sufficient it seemed.
Thanks
Bob
-----Original Message-----
From: Julie Prestopnik via RT <met_help at ucar.edu>
Sent: Tuesday, February 19, 2019 11:30 AM
To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
<robert.craig.2 at us.af.mil>
Subject: Re: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET Install
NETCDF Issue
Hi Bob.
John will take care of providing you with Cairo and Freetype though
ARLSafe.
NetCDF-C still cannot find the HDF5 files that it needs. Are your
HDF5 header files located at "/h/WXQC/met-
8.1_beta1/external_libs/hdf5-1.8.18/include"?
If so, please try setting CFLAGS to that location:
export CFLAGS="-I/h/WXQC/met-8.1_beta1/external_libs/hdf5-
1.8.18/include"
and then, in the same shell/environment, reconfigure and reinstall
NetCDF-C and then NetCDF-CXX in the manner that I described in my
email from Feb 14, 2019, 8:47 AM. Then run "make clean" for MET and
then reconfigure and reinstall MET as well.
Please let me know if you have any questions. I hope this helps.
Thanks!
Julie
On Tue, Feb 19, 2019 at 9:05 AM robert.craig.2 at us.af.mil via RT <
met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
>
> Julie, I moved things around so that all the library programs are in
a
> directory /met-8.1_beta1/external_libs. The directory looks like
this:
>
> BUFRLIB_v10-2-3 freetype g2clib-1.4.0 hdf-4.2.12 hdreos
jasper
> netcdf-c-4.4.1.1 share
> cairo g2clib gsl-1.15 hdf5-1.8.18 include lib
> netcdf-cxx4-4.3.0 zlib-1.2.6
>
> Under netcdf-c-4.4.1.1 the directory looks like this:
>
> acinclude.m4 comps.txt CONTRIBUTING.md
> h5_test libnetcdf.settings.in Makefile.in
nctest
> README.md
> aclocal.m4 config.guess COPYRIGHT
> include libsrc mclean
nc_test
> RELEASE_NOTES.md
> cf config.h CTestConfig.cmake.in
> INSTALL.md libsrc4 missing
nc_test4
> stamp-h1
> cf.cmake config.h.cmake.in CTestCustom.cmake
> install-sh libsrcp nc-config
> netCDFConfig.cmake.in test-driver
> cmake config.h.in depcomp
lib
> libtool nc-config.cmake.in netcdf.pc
> test_prog.c
> CMakeInstallation.cmake config.log docs
> libdap2 ltmain.sh nc-config.in
> netcdf.pc.in test_prog.F
> CMakeLists.txt config.status dods.m4
> libdispatch m4 ncdap_test oc2
> test_prog.f90
> cmake_uninstall.cmake.in config.sub examples
> lib_flags.am Make0 ncdump
> PostInstall.cmake VERSION
> compile configure external_libs
liblib
> Makefile ncgen
postinstall.sh
> wjna
> COMPILE.cmake.txt configure.ac FixBundle.cmake.in
> libnetcdf.settings Makefile.am ncgen3
> postinstall.sh.in
>
> Under the netcdf lib directory are all the libnet* files. Under
the
> netcdf nclude directory are the *.h files.
>
> Also, my env variables are:
>
> export MET_NETCDF=/h/WXQC/met-8.1_beta1/external_libs/netcdf-c-
4.4.1.1
> export BUFR_BASE=/h/WXQC/met-8.1_beta1/external_libs/BUFRLIB_v10-2-3
> export GSL_BASE=/h/WXQC/met-8.1_beta1/external_libs/gsl-1.15
> export MET_BUFR=/h/WXQC/met-8.1_beta1/external_libs/BUFRLIB_v10-2-3
> export MET_GSL=/h/WXQC/met-8.1_beta1/external_libs/gsl-1.15
> export MET_GRIB2C=/h/WXQC/met-8.1_beta1/external_libs/g2clib-1.4.0
> export MET_GRIB2CINC=/h/WXQC/met-8.1_beta1/external_libs/g2clib-
1.4.0
> export MET_GRIB2CLIB=/h/WXQC/met-8.1_beta1/external_libs/g2clib-
1.4.0
> export MET_BUFRLIB=/h/WXQC/met-8.1_beta1/external_libs/BUFRLIB_v10-
2-3
> export LDFLAGS='-L/h/WXQC/met-8.1_beta1/external_libs/jasper/lib
> -L/h/WXQC/met-8.1_beta1/external_libs/zlib-1.2.6/lib
> -L/h/WXQC/met-8.1_beta1/external_libs/libpng-1.2.34/li
> b'
> export
> LD_LIBRARY_PATH=/gpfs/lsf/9.1/linux2.6-glibc2.3-
x86_64/lib:/usr/mpi/gc
> c/openmpi-1.8.4/lib64:/h/WXQC/met-8.1_beta1/external_libs/gsl-
1.15/lib
> export MET_HDFEOS=/h/WXQC/met-8.1_beta1/external_libs/hdfeos
> export MET_HDF5=/h/WXQC/met-8.1_beta1/external_libs/hdf5-1.8.18
> export MET_HDF=/h/WXQC/met-8.1_beta1/external_libs/HDF4.2.12
> export FC=/usr/bin/gfortran
> export F77=/usr/bin/gfortran
> export CC=/usr/bin/gcc
> export CXX=/usr/bin/g++
> export MET_LIB_DIR=${MET_NETCDF}
>
> Based on this set up, in the MET8.0 tutorial it says to run the
> following under the NETCDF-C instructions:
>
> ./configure --prefix=${MET_LIB_DIR}/external_libs
> LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include
> Currently my external_libs/lib and external_libs/include have the
> same files as in the external_libs/netcdf-c-4.4.1.1/lib and include
> directories. Is that correct?
>
> When I run the make install after the configure line I get the
> following
> error:
>
> 4_la-nc4file.Tpo -c nc4file.c -fPIC -DPIC -o
> .libs/libnetcdf4_la-nc4file.o
> nc4file.c: In function ‘nc4_open_file’:
> nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared (first
> use in this function)
> nc4file.c:2316: error: (Each undeclared identifier is reported only
> once
> nc4file.c:2316: error: for each function it appears in.)
> nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
> (first use in this function)
> make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> make[1]: Leaving directory
> `/gpfs/dev/h/WXQC/met-8.1_beta1/external_libs/netcdf-c-
4.4.1.1/libsrc4'
> make: *** [install-recursive] Error 1
>
> My H5DIR is /h/WXQC/met-8.1_beta1/external_libs/hdf5-1.8.18 and my
> ZDIR is /h/WXQC/met-8.1_beta1/external_libs/zlib-1.2.6/lib. My make
> of the
> hdf5-1.8.18 library seems to work okay with out errors following the
> instructions on the tutorial page for compiling libraries.
>
> So, what am I missing?
>
> Thanks
> Bob
>
>
>
> -----Original Message-----
> From: Julie Prestopnik via RT <met_help at ucar.edu>
> Sent: Thursday, February 14, 2019 12:35 PM
> To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
> <robert.craig.2 at us.af.mil>
> Subject: Re: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET
Install
> NETCDF Issue
>
> Hi Bob.
>
> When you compile NetCDF-C, you'll need to tell it where the library
> files are (for HDF5, possibly other files too, but let's start with
> that) using LDFLAGS and where the include files are (for HDF5,
> possibly other files too, but let's start with that) using CPPFLAGS.
>
> I see that you set "MET_HD5=/h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18".
> Is there a "lib" subdirectory under
> /h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18? Is there an include
subdirectory under /h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18?
> It looks like your HDF5 library files were put directly in
> /h/WXQC/met-8.1_beta1/lib instead of at
> /h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18/lib, but I don't see any
header
> files in /h/WXQC/met-8.1_beta1/lib. Are the header/include files in
> /h/WXQC/met-8.1_beta1/include?
>
> On a separate note, I see that you set
> "MET_NETCDF=/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1". You will
> need to have your NetCDF-C and NetCDF-CXX files installed in the
same
> location, since MET has only only MET_NETCDF variable to reference.
> This is one reason that I install every external library file at,
for
> example, /d1/jpresto/8.1_beta/external_libs (with library files in
> /d1/jpresto/8.1_beta/external_libs/lib and include files in
> /d1/jpresto/8.1_beta/external_libs/include).
>
> You would want to set your configure command to the following for
> NetCDF-C (using bash syntax below), replacing the <> with the actual
location.
>
> export PREFIX=<set to the location you want to install the NetCDF
lib
> and include files> (the library files will be put in a "lib" subdir
> and the include files will be put in an "include" subdir. This
should
> be the same location for your NetCDF-CXX files) export LDFLAGS=<set
to
> the location where your HDF5 library files are> export CPPFLAGS=<set
> to the location where your HDF5 header/include files
> are>
>
> ./configure --prefix=${PREFIX} LDFLAGS=-L${LDFLAGS}
> CPPFLAGS=-I${CPPFLAGS}
>
> I hope this helps. Please let me know if you have any questions. I
am out
> for the rest of the day and most of tomorrow. Monday is a holiday.
I
> will be back in the office on Tuesday. Please respond to this
ticket
> with any other questions, and I will do my best to respond as soon
as I can.
>
> Below I'll paste an example of how my installation is structured on
> our machine "cheyenne", so you have it as an example.
>
> Thanks,
> Julie
>
> cheyenne3:jpresto> pwd
>
> /glade/p/ral/jntp/MET/MET_releases/8.0
>
>
> cheyenne3:jpresto> ls
>
> bin external_libs met-8.0 share
>
>
> cheyenne3:jpresto> cd
> /glade/p/ral/jntp/MET/MET_releases/8.0/external_libs
>
> /glade/p/ral/jntp/MET/MET_releases/8.0/external_libs
>
>
>
> cheyenne3:jpresto> ls
>
> bin bufrlib cairo freetype g2clib gsl hdf hdf5 hdfeos
include
> jasper lib libpng man netcdf share zlib
>
>
>
> cheyenne3:jpresto> ls
> /glade/p/ral/jntp/MET/MET_releases/8.0/external_libs/lib
>
> libbufr.a libgrib2c.a libgsl.so.19 libhdf5.la
libmfhdf.a
> libnetcdf.so libpng.la
>
> libdf.a libgsl.a libgsl.so.19.0.0 libhdf5.settings
> libnetcdf.a
> libnetcdf.so.11 libpng.so
>
> libfreetype.a libgslcblas.a libhdf4.settings libhdf5.so
> libnetcdf_c++4.a libnetcdf.so.11.0.4 libz.a
>
> libfreetype.la libgslcblas.la libhdf5.a libhdf5.so.10
> libnetcdf_c++4.la libpng16.a libz.so
>
> libfreetype.so libgslcblas.so libhdf5_hl.a
libhdf5.so.10.2.1
> libnetcdf_c++4.so libpng16.la libz.so.1
>
> libfreetype.so.6 libgslcblas.so.0 libhdf5_hl.la
libhdfeos.a
> libnetcdf_c++4.so.1 libpng16.so libz.so.1.2.11
>
> libfreetype.so.6.12.5 libgslcblas.so.0.0.0 libhdf5_hl.so
libhdfeos.la
> libnetcdf_c++4.so.1.0.3 libpng16.so.16 pkgconfig
>
> libGctp.a libgsl.la libhdf5_hl.so.10 libjasper.a
> libnetcdf.la libpng16.so.16.34.0
>
> libGctp.la libgsl.so libhdf5_hl.so.10.1.1 libjasper.la
> libnetcdf.settings
> libpng.a
>
>
>
> cheyenne3:jpresto> ls
> /glade/p/ral/jntp/MET/MET_releases/8.0/external_libs/include
>
> atom.h dfsd.h H5Dpublic.h H5IMpublic.h H5Tpublic.h
hdfi.h
> mffunc.f90 ncFloat.h netcdf
>
> bitvect.h dfstubs.h H5DSpublic.h H5Ipublic.h H5version.h
hdf.inc
> mffunc.inc ncGroupAtt.h netcdf.h
>
> cdeflate.h dfufp2i.h H5Epubgen.h H5Lpublic.h H5Zpublic.h
> HE2_config.h mfgr.h ncGroup.h netcdf_mem.h
>
> cfortHdf.h drstemplates.h H5Epublic.h H5LTpublic.h hbitio.h
herr.h
> mfhdf.h ncInt64.h netcdf_meta.h
>
> cnbit.h dynarray.h H5FDcore.h H5MMpublic.h hchunks.h
hfile.h
> mfhdfi.h ncInt.h pdstemplates.h
>
> cnone.h ease.h H5FDdirect.h H5Opublic.h hcomp.h hkit.h
> mstdio.h ncOpaqueType.h pngconf.h
>
> crle.h freetype2 H5FDfamily.h H5overflow.h hcompi.h
hlimits.h
> ncAtt.h ncShort.h png.h
>
> cskphuff.h grib2.h H5FDlog.h H5PLextern.h hconv.h
hntdefs.h
> ncByte.h ncString.h pnglibconf.h
>
> cszip.h gridtemplates.h H5FDmpi.h H5PLpublic.h hdf2netcdf.h
> hproto_fortran.h ncChar.h ncType.h tbbt.h
>
> dfan.h gsl H5FDmpio.h H5Ppublic.h hdf4_netcdf.h
hproto.h
> ncCheck.h ncUbyte.h vattr.h
>
> dffunc.f90 h4config.h H5FDmulti.h H5PTpublic.h hdf5.h
htags.h
> ncCompoundType.h ncUint64.h vg.h
>
> dffunc.inc H5ACpublic.h H5FDpublic.h H5pubconf.h hdf5_hl.h
jasper
> ncDim.h ncUint.h zconf.h
>
> dfgr.h H5api_adpt.h H5FDsec2.h H5public.h HdfEosDef.h
libpng16
> ncDouble.h ncUshort.h zlib.h
>
> df.h H5Apublic.h H5FDstdio.h H5Rpublic.h HDFEOSVersion.h
> linklist.h ncEnumType.h ncVarAtt.h
>
> dfi.h H5Cpublic.h H5Fpublic.h H5Spublic.h hdf.f90
local_nc.h
> ncException.h ncVar.h
>
> dfrig.h H5DOpublic.h H5Gpublic.h H5TBpublic.h hdf.h
mfan.h
> ncFile.h ncVlenType.h
>
>
>
>
> On Thu, Feb 14, 2019 at 11:01 AM robert.craig.2 at us.af.mil via RT <
> met_help at ucar.edu> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
> >
> > Well, I am still having problems. First of all my env variables
are set
> > this way:
> >
> > MET_BUFR=/h/WXQC/met-8.1_beta1/lib/BUFRLIB_v10-0-1
> > MET_BUFRLIB=/h/WXQC/met-8.1_beta1/lib/BUFRLIB_v10-0-1
> > MET_GRIB2CINC=/h/WXQC/met-8.1_beta1/lib/g2clib-1.4.0
> > MET_GRIB2CLIB=/h/WXQC/met-8.1_beta1/lib/g2clib-1.4.0
> > MET_GRIB_TABLES=/h/data/global/WXQC/data/met/config/grib2
> > MET_GSL=/h/WXQC/met-8.1_beta1/lib/gsl-1.15
> > MET_HD5=/h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18
> > MET_LIB_DIR=/h/WXQC/met-8.1_beta1/lib
> > MET_NETCDF=/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1
> > ZDIR=/h/WXQC/met-8.1_beta1/lib/zlib-1.2.6/lib
> > H5DIR=/h/WXQC/met-8.1_beta1/lib/hd55-1.8.18
> >
> > The /h/WXQC/met-8.1_beta1/lib directory has the following dirs.:
> >
> > bin hd55-1.8.18 HDF-EOS2.19v1.00.tar
> libhdf5_hl.la
> > libhdf5.so.100 libnetcdf_c++4.so.1.0.3 netcdf-c-
4.4.1.1
> > BUFRLIB_v10-0-1 hdf-4.2.12 include
libhdf5_hl.so
> > libhdf5.so.100.0.1 libnetcdf.la netcdf-cxx4-
4.3.0
> > BUFRLIB_v10-2-3 hdf-4.2.12.tar jasper
> > libhdf5_hl.so.100 libnetcdf.a libnetcdf.settings
> share
> > external_libs hdf5-1.10.0-patch1 lib
> > libhdf5_hl.so.100.0.0 libnetcdf_c++4.a libnetcdf.so
tar
> > g2clib-1.4.0 hdf5-1.8.18 libf2c
libhdf5.la
> > libnetcdf_c++4.la libnetcdf.so.11 zlib-1.2.6
> > GRIBI_copygb.exe hdf5-1.8.18.tar libhdf5.a
> > libhdf5.settings libnetcdf_c++4.so libnetcdf.so.11.0.4
> > gsl-1.15 hdfeos libhdf5_hl.a
libhdf5.so
> > libnetcdf_c++4.so.1 libpng-1.2.34
> >
> > In the external_libs dir is:
> >
> > bin include lib share
> >
> > I download the HDFS library per instruction on MET web site and
> > installed. It looked like it compiled correctly. Then when
trying to
> > compile netcdf-c-4.4.1.1 I get the same error messages I sent you
> earlier:
> >
> > T libnetcdf4_la-nc4file.lo -MD -MP -MF
> > .deps/libnetcdf4_la-nc4file.Tpo -c -o libnetcdf4_la-nc4file.lo
`test
> > -f 'nc4file.c' || echo './'`nc4file.c
> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
> > -I../oc2 -I/h/WXQC/met-8.1_beta1/lib/external_libs/include -MT
> > libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.Tpo
> > -c nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-nc4file.o
> > nc4file.c: In function ‘nc4_open_file’:
> > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared
(first
> > use in this function)
> > nc4file.c:2316: error: (Each undeclared identifier is reported
only
> > once
> > nc4file.c:2316: error: for each function it appears in.)
> > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
> > (first use in this function)
> > make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> > make: *** [install-recursive] Error 1
> >
> > So, not sure what to try at this point. Did I miss something that
> > is obvious?
> >
> > Thanks
> > Bob
> >
> >
> > -----Original Message-----
> > From: Julie Prestopnik via RT <met_help at ucar.edu>
> > Sent: Thursday, February 14, 2019 9:48 AM
> > To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
> > <robert.craig.2 at us.af.mil>
> > Subject: Re: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET
> > Install NETCDF Issue
> >
> > Hi Bob.
> >
> > should MET_LIB_DIR point to met-8.1_beta1/lib?
> > >
> >
> > I will answer that question, by breaking down the command that you
> > previously ran:
> >
> > > ./configure --prefix=${MET_LIB_DIR}/external_libs
> > > LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> > > CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include
> >
> >
> > In the example above "-prefix=" should be set to the location
where
> > you want the NetCDF files to be put. In the case above, the
NetCDF
> > library files would be put at "${MET_LIB_DIR}/external_libs/lib"
and
> > the NetCDF include files would be put at
> > "${MET_LIB_DIR}/external_libs/include". You can set this to
> > whatever you'd like, based on where you want to put the NetCDF
> > library and include files (note that the NetCDF package knows to
put
> > the library files in a lib subdirectory and the include files in
an
> > include subdirectory, so for the "prefix" option, you simply set
it
> > to the upper level directory). NetCDF4 depends on HDF5, so HDF5
> > must be installed first. In the above configure command the
values
> > of LDFLAGS and CPPFLAGS tell NetCDF where it can find the library
> > files and header files, respectively, that it needs. When I
install
> > MET, I install of the external libraries in a directory called
<path
> to>/external_libs. All of the external library files go in <path
> to>/externa!
> > l_libs/lib and all of the external library include files go in
> > <path
> > to>/external_libs/include. So, when I install NetCDF the HDF5
files
> > to>have
> > already been put in those locations and by setting LDFLAGS and
> > CPPFLAGS to the location in the above configure command, NetCDF
> > knows where to find the files it needs.
> >
> > From the error you sent, it seems that NetCDF-C cannot find the
HDF5
> > files that it needs. Did you install HDF5 first? If not, please
> > install HDF5 first and they reconfigure and reinstall NetCDF-C
> > pointing the appropriate locations as described above.
> >
> > I hope that helps. Please let me know if you have any questions
or
> > if you encounter any other problems.
> >
> > Thanks!
> >
> > Julie
> >
> > On Thu, Feb 14, 2019 at 7:35 AM robert.craig.2 at us.af.mil via RT <
> > met_help at ucar.edu> wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
> > >
> > > Julie, should MET_LIB_DIR point to met-8.1_beta1/lib? I tried
this.
> > > I got a good compile of NETCDF-CXX but I get an error compiling
> NETCDF-C:
> > >
> > > Making install in include
> > > make[1]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make[2]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make[2]: Nothing to be done for `install-exec-am'.
> > > /bin/mkdir -p
> > '/h/WXQC/met-8.1_beta1/external_libs/external_libs/include'
> > > /usr/bin/install -c -m 644 netcdf.h netcdf_meta.h netcdf_mem.h
> > > '/h/WXQC/met-8.1_beta1/external_libs/external_libs/include'
> > > make[2]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > Making install in oc2
> > > make[1]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > > make[2]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > > make[2]: Nothing to be done for `install-exec-am'.
> > > make[2]: Nothing to be done for `install-data-am'.
> > > make[2]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > > Making install in h5_test
> > > make[1]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > > make[2]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > > make[2]: Nothing to be done for `install-exec-am'.
> > > make[2]: Nothing to be done for `install-data-am'.
> > > make[2]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > > Making install in libdispatch
> > > make[1]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/libdispatch'
> > > make[2]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/libdispatch'
> > > make[2]: Nothing to be done for `install-exec-am'.
> > > make[2]: Nothing to be done for `install-data-am'.
> > > make[2]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/libdispatch'
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/libdispatch'
> > > Making install in libsrc
> > > make[1]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > > make[2]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > > make[2]: Nothing to be done for `install-exec-am'.
> > > /bin/mkdir -p
> > > '/h/WXQC/met-
8.1_beta1/external_libs/external_libs/share/man/man3'
> > > /usr/bin/install -c -m 644 netcdf.3
> > > '/h/WXQC/met-
8.1_beta1/external_libs/external_libs/share/man/man3'
> > > make[2]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > > Making install in libsrc4
> > > make[1]: Entering directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> > > /bin/sh ../libtool --tag=CC --mode=compile gcc
-DHAVE_CONFIG_H -I.
> > > -I.. -I../include -I../oc2
> > > -I/h/WXQC/met-8.1_beta1/external_libs/external_libs/include
-MT
> > > libnetcdf4_la-nc4file.lo -MD -MP -MF
> > > .deps/libnetcdf4_la-nc4file.Tpo -c -o libnetcdf4_la-nc4file.lo
> > > `test -f 'nc4file.c' || echo './'`nc4file.c
> > > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
> > > -I../oc2
> > > -I/h/WXQC/met-8.1_beta1/external_libs/external_libs/include
> > > -MT libnetcdf4_la-nc4file.lo -MD -MP -MF
> > > .deps/libnetcdf4_la-nc4file.Tpo -c nc4file.c -fPIC -DPIC -o
> > > .libs/libnetcdf4_la-nc4file.o
> > > nc4file.c: In function ‘nc4_open_file’:
> > > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared
> > > (first use in this function)
> > > nc4file.c:2316: error: (Each undeclared identifier is reported
> > > only once
> > > nc4file.c:2316: error: for each function it appears in.)
> > > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
> > > (first use in this function)
> > > make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> > > make: *** [install-recursive] Error 1
> > >
> > > What do you think I did wrong?
> > >
> > > Thanks
> > > Bob
> > >
> > > -----Original Message-----
> > > From: Julie Prestopnik via RT <met_help at ucar.edu>
> > > Sent: Wednesday, February 13, 2019 4:50 PM
> > > To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
> > > <robert.craig.2 at us.af.mil>
> > > Subject: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET
Install
> > > NETCDF Issue
> > >
> > > Hi Bob. Based on the error message you included (thank you!):
> > >
> > > /bin/mkdir -p '/external_libs/include'
> > > /bin/mkdir: cannot create directory `/external_libs': Permission
> > > denied
> > >
> > > It appears that MET_LIB_DIR is not set, as "/" is the beginning
> > character.
> > > Please be sure to set MET_LIB_DIR and try again.
> > >
> > > Please let me know if you have any other questions or encounter
> > > any other problems.
> > >
> > > Julie
> > >
> > >
> > > On Wed, Feb 13, 2019, 3:45 PM robert.craig.2 at us.af.mil via RT <
> > > met_help at ucar.edu> wrote:
> > >
> > > >
> > > > Wed Feb 13 15:44:51 2019: Request 88918 was acted upon.
> > > > Transaction: Ticket created by robert.craig.2 at us.af.mil
> > > > Queue: met_help
> > > > Subject: MET Install NETCDF Issue
> > > > Owner: Nobody
> > > > Requestors: robert.craig.2 at us.af.mil
> > > > Status: new
> > > > Ticket <URL:
> > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918
> > > > >
> > > >
> > > >
> > > > Julie, when compiling MET I get the error:
> > > >
> > > > c_var_info.cc
> > > > 169 In file included from nc_var_info.cc:24:
> > > > 170 nc_utils.h:22:18: error: netcdf: No such file or directory
> > > > 171 In file included from nc_var_info.cc:24:
> > > >
> > > > To fix this, in a previous email you said to go to the MET
help
> > > > page and run through the NETCDF-C install procedures. I ran
> > > > "./configure --prefix=${MET_LIB_DIR}/external_libs
> > > > LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> > > > CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include" and then
"make
> > install"
> > > > but get the following error:
> > > >
> > > > Making install in include
> > > > make[1]: Entering directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > > make[2]: Entering directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > > make[2]: Nothing to be done for `install-exec-am'.
> > > > /bin/mkdir -p '/external_libs/include'
> > > > /bin/mkdir: cannot create directory `/external_libs':
Permission
> > > > denied
> > > > make[2]: *** [install-includeHEADERS] Error 1
> > > > make[2]: Leaving directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > > make[1]: *** [install-am] Error 2
> > > > make[1]: Leaving directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > > make: *** [install-recursive] Error 1
> > > >
> > > > The permissions in the netcdf-c-4.4.1.1 directory are 777.
> > > >
> > > > What is the problem?
> > > >
> > > > Thanks
> > > > Bob Craig
> > > >
> > > >
> > >
> > >
> > >
> > >
> >
> >
> >
> >
>
>
>
>
------------------------------------------------
Subject: MET Install NETCDF Issue
From: Julie Prestopnik
Time: Tue Feb 19 12:51:34 2019
Great, Bob! Thanks for letting us know. Please let us know if you
run
into any other issues.
Julie
On Tue, Feb 19, 2019 at 12:42 PM robert.craig.2 at us.af.mil via RT <
met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
>
> Julie, your CFLAGS variable fixed the NETCDF compile problem and
made it
> all the way through the compile. One other thing I had to do to get
it to
> complile bufrlib correctly was to place the libbufr.a file in the
> external_libs/lib directory. I had my env MET_BUFR and MET_BUFRLIB
> pointing to external_libs/BUFRLIB_v10-2-3 but that was not
sufficient it
> seemed.
>
>
> Thanks
> Bob
>
>
>
> -----Original Message-----
> From: Julie Prestopnik via RT <met_help at ucar.edu>
> Sent: Tuesday, February 19, 2019 11:30 AM
> To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
<robert.craig.2 at us.af.mil>
> Subject: Re: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET
Install
> NETCDF Issue
>
> Hi Bob.
>
> John will take care of providing you with Cairo and Freetype though
> ARLSafe.
>
> NetCDF-C still cannot find the HDF5 files that it needs. Are your
HDF5
> header files located at
> "/h/WXQC/met-8.1_beta1/external_libs/hdf5-1.8.18/include"?
>
> If so, please try setting CFLAGS to that location:
>
> export CFLAGS="-I/h/WXQC/met-8.1_beta1/external_libs/hdf5-
1.8.18/include"
>
> and then, in the same shell/environment, reconfigure and reinstall
> NetCDF-C and then NetCDF-CXX in the manner that I described in my
email
> from Feb 14, 2019, 8:47 AM. Then run "make clean" for MET and then
> reconfigure and reinstall MET as well.
>
> Please let me know if you have any questions. I hope this helps.
>
> Thanks!
>
> Julie
>
> On Tue, Feb 19, 2019 at 9:05 AM robert.craig.2 at us.af.mil via RT <
> met_help at ucar.edu> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
> >
> > Julie, I moved things around so that all the library programs are
in a
> > directory /met-8.1_beta1/external_libs. The directory looks like
this:
> >
> > BUFRLIB_v10-2-3 freetype g2clib-1.4.0 hdf-4.2.12 hdreos
jasper
> > netcdf-c-4.4.1.1 share
> > cairo g2clib gsl-1.15 hdf5-1.8.18 include lib
> > netcdf-cxx4-4.3.0 zlib-1.2.6
> >
> > Under netcdf-c-4.4.1.1 the directory looks like this:
> >
> > acinclude.m4 comps.txt CONTRIBUTING.md
> > h5_test libnetcdf.settings.in Makefile.in
nctest
> > README.md
> > aclocal.m4 config.guess COPYRIGHT
> > include libsrc mclean
nc_test
> > RELEASE_NOTES.md
> > cf config.h CTestConfig.cmake.in
> > INSTALL.md libsrc4 missing
nc_test4
> > stamp-h1
> > cf.cmake config.h.cmake.in CTestCustom.cmake
> > install-sh libsrcp nc-config
> > netCDFConfig.cmake.in test-driver
> > cmake config.h.in depcomp
lib
> > libtool nc-config.cmake.in netcdf.pc
> > test_prog.c
> > CMakeInstallation.cmake config.log docs
> > libdap2 ltmain.sh nc-config.in
> > netcdf.pc.in test_prog.F
> > CMakeLists.txt config.status dods.m4
> > libdispatch m4 ncdap_test
oc2
> > test_prog.f90
> > cmake_uninstall.cmake.in config.sub examples
> > lib_flags.am Make0 ncdump
> > PostInstall.cmake VERSION
> > compile configure external_libs
liblib
> > Makefile ncgen
postinstall.sh
> > wjna
> > COMPILE.cmake.txt configure.ac FixBundle.cmake.in
> > libnetcdf.settings Makefile.am ncgen3
> > postinstall.sh.in
> >
> > Under the netcdf lib directory are all the libnet* files. Under
the
> > netcdf nclude directory are the *.h files.
> >
> > Also, my env variables are:
> >
> > export MET_NETCDF=/h/WXQC/met-8.1_beta1/external_libs/netcdf-c-
4.4.1.1
> > export BUFR_BASE=/h/WXQC/met-8.1_beta1/external_libs/BUFRLIB_v10-
2-3
> > export GSL_BASE=/h/WXQC/met-8.1_beta1/external_libs/gsl-1.15
> > export MET_BUFR=/h/WXQC/met-8.1_beta1/external_libs/BUFRLIB_v10-2-
3
> > export MET_GSL=/h/WXQC/met-8.1_beta1/external_libs/gsl-1.15
> > export MET_GRIB2C=/h/WXQC/met-8.1_beta1/external_libs/g2clib-1.4.0
> > export MET_GRIB2CINC=/h/WXQC/met-8.1_beta1/external_libs/g2clib-
1.4.0
> > export MET_GRIB2CLIB=/h/WXQC/met-8.1_beta1/external_libs/g2clib-
1.4.0
> > export MET_BUFRLIB=/h/WXQC/met-
8.1_beta1/external_libs/BUFRLIB_v10-2-3
> > export LDFLAGS='-L/h/WXQC/met-8.1_beta1/external_libs/jasper/lib
> > -L/h/WXQC/met-8.1_beta1/external_libs/zlib-1.2.6/lib
> > -L/h/WXQC/met-8.1_beta1/external_libs/libpng-1.2.34/li
> > b'
> > export
> > LD_LIBRARY_PATH=/gpfs/lsf/9.1/linux2.6-glibc2.3-
x86_64/lib:/usr/mpi/gc
> > c/openmpi-1.8.4/lib64:/h/WXQC/met-8.1_beta1/external_libs/gsl-
1.15/lib
> > export MET_HDFEOS=/h/WXQC/met-8.1_beta1/external_libs/hdfeos
> > export MET_HDF5=/h/WXQC/met-8.1_beta1/external_libs/hdf5-1.8.18
> > export MET_HDF=/h/WXQC/met-8.1_beta1/external_libs/HDF4.2.12
> > export FC=/usr/bin/gfortran
> > export F77=/usr/bin/gfortran
> > export CC=/usr/bin/gcc
> > export CXX=/usr/bin/g++
> > export MET_LIB_DIR=${MET_NETCDF}
> >
> > Based on this set up, in the MET8.0 tutorial it says to run the
> > following under the NETCDF-C instructions:
> >
> > ./configure --prefix=${MET_LIB_DIR}/external_libs
> > LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> > CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include
> > Currently my external_libs/lib and external_libs/include have the
> > same files as in the external_libs/netcdf-c-4.4.1.1/lib and
include
> > directories. Is that correct?
> >
> > When I run the make install after the configure line I get the
> > following
> > error:
> >
> > 4_la-nc4file.Tpo -c nc4file.c -fPIC -DPIC -o
> > .libs/libnetcdf4_la-nc4file.o
> > nc4file.c: In function ‘nc4_open_file’:
> > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared
(first
> > use in this function)
> > nc4file.c:2316: error: (Each undeclared identifier is reported
only
> > once
> > nc4file.c:2316: error: for each function it appears in.)
> > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
> > (first use in this function)
> > make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> > make[1]: Leaving directory
> > `/gpfs/dev/h/WXQC/met-8.1_beta1/external_libs/netcdf-c-
4.4.1.1/libsrc4'
> > make: *** [install-recursive] Error 1
> >
> > My H5DIR is /h/WXQC/met-8.1_beta1/external_libs/hdf5-1.8.18 and my
> > ZDIR is /h/WXQC/met-8.1_beta1/external_libs/zlib-1.2.6/lib. My
make
> > of the
> > hdf5-1.8.18 library seems to work okay with out errors following
the
> > instructions on the tutorial page for compiling libraries.
> >
> > So, what am I missing?
> >
> > Thanks
> > Bob
> >
> >
> >
> > -----Original Message-----
> > From: Julie Prestopnik via RT <met_help at ucar.edu>
> > Sent: Thursday, February 14, 2019 12:35 PM
> > To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
> > <robert.craig.2 at us.af.mil>
> > Subject: Re: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET
Install
> > NETCDF Issue
> >
> > Hi Bob.
> >
> > When you compile NetCDF-C, you'll need to tell it where the
library
> > files are (for HDF5, possibly other files too, but let's start
with
> > that) using LDFLAGS and where the include files are (for HDF5,
> > possibly other files too, but let's start with that) using
CPPFLAGS.
> >
> > I see that you set "MET_HD5=/h/WXQC/met-8.1_beta1/lib/hdf5-
1.8.18".
> > Is there a "lib" subdirectory under
> > /h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18? Is there an include
subdirectory
> under /h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18?
> > It looks like your HDF5 library files were put directly in
> > /h/WXQC/met-8.1_beta1/lib instead of at
> > /h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18/lib, but I don't see any
header
> > files in /h/WXQC/met-8.1_beta1/lib. Are the header/include files
in
> > /h/WXQC/met-8.1_beta1/include?
> >
> > On a separate note, I see that you set
> > "MET_NETCDF=/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1". You will
> > need to have your NetCDF-C and NetCDF-CXX files installed in the
same
> > location, since MET has only only MET_NETCDF variable to
reference.
> > This is one reason that I install every external library file at,
for
> > example, /d1/jpresto/8.1_beta/external_libs (with library files in
> > /d1/jpresto/8.1_beta/external_libs/lib and include files in
> > /d1/jpresto/8.1_beta/external_libs/include).
> >
> > You would want to set your configure command to the following for
> > NetCDF-C (using bash syntax below), replacing the <> with the
actual
> location.
> >
> > export PREFIX=<set to the location you want to install the NetCDF
lib
> > and include files> (the library files will be put in a "lib"
subdir
> > and the include files will be put in an "include" subdir. This
should
> > be the same location for your NetCDF-CXX files) export
LDFLAGS=<set to
> > the location where your HDF5 library files are> export
CPPFLAGS=<set
> > to the location where your HDF5 header/include files
> > are>
> >
> > ./configure --prefix=${PREFIX} LDFLAGS=-L${LDFLAGS}
> > CPPFLAGS=-I${CPPFLAGS}
> >
> > I hope this helps. Please let me know if you have any questions.
I am
> out
> > for the rest of the day and most of tomorrow. Monday is a
holiday. I
> > will be back in the office on Tuesday. Please respond to this
ticket
> > with any other questions, and I will do my best to respond as soon
as I
> can.
> >
> > Below I'll paste an example of how my installation is structured
on
> > our machine "cheyenne", so you have it as an example.
> >
> > Thanks,
> > Julie
> >
> > cheyenne3:jpresto> pwd
> >
> > /glade/p/ral/jntp/MET/MET_releases/8.0
> >
> >
> > cheyenne3:jpresto> ls
> >
> > bin external_libs met-8.0 share
> >
> >
> > cheyenne3:jpresto> cd
> > /glade/p/ral/jntp/MET/MET_releases/8.0/external_libs
> >
> > /glade/p/ral/jntp/MET/MET_releases/8.0/external_libs
> >
> >
> >
> > cheyenne3:jpresto> ls
> >
> > bin bufrlib cairo freetype g2clib gsl hdf hdf5 hdfeos
include
> > jasper lib libpng man netcdf share zlib
> >
> >
> >
> > cheyenne3:jpresto> ls
> > /glade/p/ral/jntp/MET/MET_releases/8.0/external_libs/lib
> >
> > libbufr.a libgrib2c.a libgsl.so.19 libhdf5.la
> libmfhdf.a
> > libnetcdf.so libpng.la
> >
> > libdf.a libgsl.a libgsl.so.19.0.0 libhdf5.settings
> > libnetcdf.a
> > libnetcdf.so.11 libpng.so
> >
> > libfreetype.a libgslcblas.a libhdf4.settings
libhdf5.so
> > libnetcdf_c++4.a libnetcdf.so.11.0.4 libz.a
> >
> > libfreetype.la libgslcblas.la libhdf5.a libhdf5.so.10
> > libnetcdf_c++4.la libpng16.a libz.so
> >
> > libfreetype.so libgslcblas.so libhdf5_hl.a
libhdf5.so.10.2.1
> > libnetcdf_c++4.so libpng16.la libz.so.1
> >
> > libfreetype.so.6 libgslcblas.so.0 libhdf5_hl.la
libhdfeos.a
> > libnetcdf_c++4.so.1 libpng16.so libz.so.1.2.11
> >
> > libfreetype.so.6.12.5 libgslcblas.so.0.0.0 libhdf5_hl.so
> libhdfeos.la
> > libnetcdf_c++4.so.1.0.3 libpng16.so.16 pkgconfig
> >
> > libGctp.a libgsl.la libhdf5_hl.so.10 libjasper.a
> > libnetcdf.la libpng16.so.16.34.0
> >
> > libGctp.la libgsl.so libhdf5_hl.so.10.1.1 libjasper.la
> > libnetcdf.settings
> > libpng.a
> >
> >
> >
> > cheyenne3:jpresto> ls
> > /glade/p/ral/jntp/MET/MET_releases/8.0/external_libs/include
> >
> > atom.h dfsd.h H5Dpublic.h H5IMpublic.h H5Tpublic.h
hdfi.h
> > mffunc.f90 ncFloat.h netcdf
> >
> > bitvect.h dfstubs.h H5DSpublic.h H5Ipublic.h H5version.h
hdf.inc
> > mffunc.inc ncGroupAtt.h netcdf.h
> >
> > cdeflate.h dfufp2i.h H5Epubgen.h H5Lpublic.h H5Zpublic.h
> > HE2_config.h mfgr.h ncGroup.h netcdf_mem.h
> >
> > cfortHdf.h drstemplates.h H5Epublic.h H5LTpublic.h hbitio.h
> herr.h
> > mfhdf.h ncInt64.h netcdf_meta.h
> >
> > cnbit.h dynarray.h H5FDcore.h H5MMpublic.h hchunks.h
> hfile.h
> > mfhdfi.h ncInt.h pdstemplates.h
> >
> > cnone.h ease.h H5FDdirect.h H5Opublic.h hcomp.h hkit.h
> > mstdio.h ncOpaqueType.h pngconf.h
> >
> > crle.h freetype2 H5FDfamily.h H5overflow.h hcompi.h
hlimits.h
> > ncAtt.h ncShort.h png.h
> >
> > cskphuff.h grib2.h H5FDlog.h H5PLextern.h hconv.h
hntdefs.h
> > ncByte.h ncString.h pnglibconf.h
> >
> > cszip.h gridtemplates.h H5FDmpi.h H5PLpublic.h
hdf2netcdf.h
> > hproto_fortran.h ncChar.h ncType.h tbbt.h
> >
> > dfan.h gsl H5FDmpio.h H5Ppublic.h hdf4_netcdf.h
hproto.h
> > ncCheck.h ncUbyte.h vattr.h
> >
> > dffunc.f90 h4config.h H5FDmulti.h H5PTpublic.h hdf5.h
htags.h
> > ncCompoundType.h ncUint64.h vg.h
> >
> > dffunc.inc H5ACpublic.h H5FDpublic.h H5pubconf.h hdf5_hl.h
jasper
> > ncDim.h ncUint.h zconf.h
> >
> > dfgr.h H5api_adpt.h H5FDsec2.h H5public.h HdfEosDef.h
> libpng16
> > ncDouble.h ncUshort.h zlib.h
> >
> > df.h H5Apublic.h H5FDstdio.h H5Rpublic.h
HDFEOSVersion.h
> > linklist.h ncEnumType.h ncVarAtt.h
> >
> > dfi.h H5Cpublic.h H5Fpublic.h H5Spublic.h hdf.f90
local_nc.h
> > ncException.h ncVar.h
> >
> > dfrig.h H5DOpublic.h H5Gpublic.h H5TBpublic.h hdf.h
mfan.h
> > ncFile.h ncVlenType.h
> >
> >
> >
> >
> > On Thu, Feb 14, 2019 at 11:01 AM robert.craig.2 at us.af.mil via RT <
> > met_help at ucar.edu> wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918 >
> > >
> > > Well, I am still having problems. First of all my env
variables are
> set
> > > this way:
> > >
> > > MET_BUFR=/h/WXQC/met-8.1_beta1/lib/BUFRLIB_v10-0-1
> > > MET_BUFRLIB=/h/WXQC/met-8.1_beta1/lib/BUFRLIB_v10-0-1
> > > MET_GRIB2CINC=/h/WXQC/met-8.1_beta1/lib/g2clib-1.4.0
> > > MET_GRIB2CLIB=/h/WXQC/met-8.1_beta1/lib/g2clib-1.4.0
> > > MET_GRIB_TABLES=/h/data/global/WXQC/data/met/config/grib2
> > > MET_GSL=/h/WXQC/met-8.1_beta1/lib/gsl-1.15
> > > MET_HD5=/h/WXQC/met-8.1_beta1/lib/hdf5-1.8.18
> > > MET_LIB_DIR=/h/WXQC/met-8.1_beta1/lib
> > > MET_NETCDF=/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1
> > > ZDIR=/h/WXQC/met-8.1_beta1/lib/zlib-1.2.6/lib
> > > H5DIR=/h/WXQC/met-8.1_beta1/lib/hd55-1.8.18
> > >
> > > The /h/WXQC/met-8.1_beta1/lib directory has the following dirs.:
> > >
> > > bin hd55-1.8.18 HDF-EOS2.19v1.00.tar
> > libhdf5_hl.la
> > > libhdf5.so.100 libnetcdf_c++4.so.1.0.3 netcdf-c-
4.4.1.1
> > > BUFRLIB_v10-0-1 hdf-4.2.12 include
> libhdf5_hl.so
> > > libhdf5.so.100.0.1 libnetcdf.la
> netcdf-cxx4-4.3.0
> > > BUFRLIB_v10-2-3 hdf-4.2.12.tar jasper
> > > libhdf5_hl.so.100 libnetcdf.a libnetcdf.settings
> > share
> > > external_libs hdf5-1.10.0-patch1 lib
> > > libhdf5_hl.so.100.0.0 libnetcdf_c++4.a libnetcdf.so
> tar
> > > g2clib-1.4.0 hdf5-1.8.18 libf2c
libhdf5.la
> > > libnetcdf_c++4.la libnetcdf.so.11 zlib-
1.2.6
> > > GRIBI_copygb.exe hdf5-1.8.18.tar libhdf5.a
> > > libhdf5.settings libnetcdf_c++4.so libnetcdf.so.11.0.4
> > > gsl-1.15 hdfeos libhdf5_hl.a
libhdf5.so
> > > libnetcdf_c++4.so.1 libpng-1.2.34
> > >
> > > In the external_libs dir is:
> > >
> > > bin include lib share
> > >
> > > I download the HDFS library per instruction on MET web site and
> > > installed. It looked like it compiled correctly. Then when
trying to
> > > compile netcdf-c-4.4.1.1 I get the same error messages I sent
you
> > earlier:
> > >
> > > T libnetcdf4_la-nc4file.lo -MD -MP -MF
> > > .deps/libnetcdf4_la-nc4file.Tpo -c -o libnetcdf4_la-nc4file.lo
`test
> > > -f 'nc4file.c' || echo './'`nc4file.c
> > > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
> > > -I../oc2 -I/h/WXQC/met-8.1_beta1/lib/external_libs/include -MT
> > > libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.Tpo
> > > -c nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-nc4file.o
> > > nc4file.c: In function ‘nc4_open_file’:
> > > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared
(first
> > > use in this function)
> > > nc4file.c:2316: error: (Each undeclared identifier is reported
only
> > > once
> > > nc4file.c:2316: error: for each function it appears in.)
> > > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’ undeclared
> > > (first use in this function)
> > > make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> > > make[1]: Leaving directory
> > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> > > make: *** [install-recursive] Error 1
> > >
> > > So, not sure what to try at this point. Did I miss something
that
> > > is obvious?
> > >
> > > Thanks
> > > Bob
> > >
> > >
> > > -----Original Message-----
> > > From: Julie Prestopnik via RT <met_help at ucar.edu>
> > > Sent: Thursday, February 14, 2019 9:48 AM
> > > To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
> > > <robert.craig.2 at us.af.mil>
> > > Subject: Re: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET
> > > Install NETCDF Issue
> > >
> > > Hi Bob.
> > >
> > > should MET_LIB_DIR point to met-8.1_beta1/lib?
> > > >
> > >
> > > I will answer that question, by breaking down the command that
you
> > > previously ran:
> > >
> > > > ./configure --prefix=${MET_LIB_DIR}/external_libs
> > > > LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> > > > CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include
> > >
> > >
> > > In the example above "-prefix=" should be set to the location
where
> > > you want the NetCDF files to be put. In the case above, the
NetCDF
> > > library files would be put at "${MET_LIB_DIR}/external_libs/lib"
and
> > > the NetCDF include files would be put at
> > > "${MET_LIB_DIR}/external_libs/include". You can set this to
> > > whatever you'd like, based on where you want to put the NetCDF
> > > library and include files (note that the NetCDF package knows to
put
> > > the library files in a lib subdirectory and the include files in
an
> > > include subdirectory, so for the "prefix" option, you simply set
it
> > > to the upper level directory). NetCDF4 depends on HDF5, so HDF5
> > > must be installed first. In the above configure command the
values
> > > of LDFLAGS and CPPFLAGS tell NetCDF where it can find the
library
> > > files and header files, respectively, that it needs. When I
install
> > > MET, I install of the external libraries in a directory called
<path
> > to>/external_libs. All of the external library files go in <path
> > to>/externa!
> > > l_libs/lib and all of the external library include files go in
> > > <path
> > > to>/external_libs/include. So, when I install NetCDF the HDF5
files
> > > to>have
> > > already been put in those locations and by setting LDFLAGS and
> > > CPPFLAGS to the location in the above configure command, NetCDF
> > > knows where to find the files it needs.
> > >
> > > From the error you sent, it seems that NetCDF-C cannot find the
HDF5
> > > files that it needs. Did you install HDF5 first? If not,
please
> > > install HDF5 first and they reconfigure and reinstall NetCDF-C
> > > pointing the appropriate locations as described above.
> > >
> > > I hope that helps. Please let me know if you have any questions
or
> > > if you encounter any other problems.
> > >
> > > Thanks!
> > >
> > > Julie
> > >
> > > On Thu, Feb 14, 2019 at 7:35 AM robert.craig.2 at us.af.mil via RT
<
> > > met_help at ucar.edu> wrote:
> > >
> > > >
> > > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918
>
> > > >
> > > > Julie, should MET_LIB_DIR point to met-8.1_beta1/lib? I tried
this.
> > > > I got a good compile of NETCDF-CXX but I get an error
compiling
> > NETCDF-C:
> > > >
> > > > Making install in include
> > > > make[1]: Entering directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > > make[2]: Entering directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > > make[2]: Nothing to be done for `install-exec-am'.
> > > > /bin/mkdir -p
> > > '/h/WXQC/met-8.1_beta1/external_libs/external_libs/include'
> > > > /usr/bin/install -c -m 644 netcdf.h netcdf_meta.h
netcdf_mem.h
> > > > '/h/WXQC/met-8.1_beta1/external_libs/external_libs/include'
> > > > make[2]: Leaving directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > > make[1]: Leaving directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/include'
> > > > Making install in oc2
> > > > make[1]: Entering directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > > > make[2]: Entering directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > > > make[2]: Nothing to be done for `install-exec-am'.
> > > > make[2]: Nothing to be done for `install-data-am'.
> > > > make[2]: Leaving directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > > > make[1]: Leaving directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/oc2'
> > > > Making install in h5_test
> > > > make[1]: Entering directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > > > make[2]: Entering directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > > > make[2]: Nothing to be done for `install-exec-am'.
> > > > make[2]: Nothing to be done for `install-data-am'.
> > > > make[2]: Leaving directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > > > make[1]: Leaving directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/h5_test'
> > > > Making install in libdispatch
> > > > make[1]: Entering directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/libdispatch'
> > > > make[2]: Entering directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/libdispatch'
> > > > make[2]: Nothing to be done for `install-exec-am'.
> > > > make[2]: Nothing to be done for `install-data-am'.
> > > > make[2]: Leaving directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/libdispatch'
> > > > make[1]: Leaving directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/libdispatch'
> > > > Making install in libsrc
> > > > make[1]: Entering directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > > > make[2]: Entering directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > > > make[2]: Nothing to be done for `install-exec-am'.
> > > > /bin/mkdir -p
> > > > '/h/WXQC/met-
8.1_beta1/external_libs/external_libs/share/man/man3'
> > > > /usr/bin/install -c -m 644 netcdf.3
> > > > '/h/WXQC/met-
8.1_beta1/external_libs/external_libs/share/man/man3'
> > > > make[2]: Leaving directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > > > make[1]: Leaving directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc'
> > > > Making install in libsrc4
> > > > make[1]: Entering directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> > > > /bin/sh ../libtool --tag=CC --mode=compile gcc
-DHAVE_CONFIG_H -I.
> > > > -I.. -I../include -I../oc2
> > > > -I/h/WXQC/met-8.1_beta1/external_libs/external_libs/include
-MT
> > > > libnetcdf4_la-nc4file.lo -MD -MP -MF
> > > > .deps/libnetcdf4_la-nc4file.Tpo -c -o libnetcdf4_la-nc4file.lo
> > > > `test -f 'nc4file.c' || echo './'`nc4file.c
> > > > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
> > > > -I../oc2
> > > > -I/h/WXQC/met-8.1_beta1/external_libs/external_libs/include
> > > > -MT libnetcdf4_la-nc4file.lo -MD -MP -MF
> > > > .deps/libnetcdf4_la-nc4file.Tpo -c nc4file.c -fPIC -DPIC -o
> > > > .libs/libnetcdf4_la-nc4file.o
> > > > nc4file.c: In function ‘nc4_open_file’:
> > > > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_COPY’ undeclared
> > > > (first use in this function)
> > > > nc4file.c:2316: error: (Each undeclared identifier is reported
> > > > only once
> > > > nc4file.c:2316: error: for each function it appears in.)
> > > > nc4file.c:2316: error: ‘H5LT_FILE_IMAGE_DONT_RELEASE’
undeclared
> > > > (first use in this function)
> > > > make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> > > > make[1]: Leaving directory
> > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-4.4.1.1/libsrc4'
> > > > make: *** [install-recursive] Error 1
> > > >
> > > > What do you think I did wrong?
> > > >
> > > > Thanks
> > > > Bob
> > > >
> > > > -----Original Message-----
> > > > From: Julie Prestopnik via RT <met_help at ucar.edu>
> > > > Sent: Wednesday, February 13, 2019 4:50 PM
> > > > To: CRAIG, ROBERT J GS-12 USAF ACC 16 WS/WXN
> > > > <robert.craig.2 at us.af.mil>
> > > > Subject: [Non-DoD Source] Re: [rt.rap.ucar.edu #88918] MET
Install
> > > > NETCDF Issue
> > > >
> > > > Hi Bob. Based on the error message you included (thank you!):
> > > >
> > > > /bin/mkdir -p '/external_libs/include'
> > > > /bin/mkdir: cannot create directory `/external_libs':
Permission
> > > > denied
> > > >
> > > > It appears that MET_LIB_DIR is not set, as "/" is the
beginning
> > > character.
> > > > Please be sure to set MET_LIB_DIR and try again.
> > > >
> > > > Please let me know if you have any other questions or
encounter
> > > > any other problems.
> > > >
> > > > Julie
> > > >
> > > >
> > > > On Wed, Feb 13, 2019, 3:45 PM robert.craig.2 at us.af.mil via RT
<
> > > > met_help at ucar.edu> wrote:
> > > >
> > > > >
> > > > > Wed Feb 13 15:44:51 2019: Request 88918 was acted upon.
> > > > > Transaction: Ticket created by robert.craig.2 at us.af.mil
> > > > > Queue: met_help
> > > > > Subject: MET Install NETCDF Issue
> > > > > Owner: Nobody
> > > > > Requestors: robert.craig.2 at us.af.mil
> > > > > Status: new
> > > > > Ticket <URL:
> > > > > https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88918
> > > > > >
> > > > >
> > > > >
> > > > > Julie, when compiling MET I get the error:
> > > > >
> > > > > c_var_info.cc
> > > > > 169 In file included from nc_var_info.cc:24:
> > > > > 170 nc_utils.h:22:18: error: netcdf: No such file or
directory
> > > > > 171 In file included from nc_var_info.cc:24:
> > > > >
> > > > > To fix this, in a previous email you said to go to the MET
help
> > > > > page and run through the NETCDF-C install procedures. I
ran
> > > > > "./configure --prefix=${MET_LIB_DIR}/external_libs
> > > > > LDFLAGS=-L${MET_LIB_DIR}/external_libs/lib
> > > > > CPPFLAGS=-I${MET_LIB_DIR}/external_libs/include" and then
"make
> > > install"
> > > > > but get the following error:
> > > > >
> > > > > Making install in include
> > > > > make[1]: Entering directory
> > > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/include'
> > > > > make[2]: Entering directory
> > > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/include'
> > > > > make[2]: Nothing to be done for `install-exec-am'.
> > > > > /bin/mkdir -p '/external_libs/include'
> > > > > /bin/mkdir: cannot create directory `/external_libs':
Permission
> > > > > denied
> > > > > make[2]: *** [install-includeHEADERS] Error 1
> > > > > make[2]: Leaving directory
> > > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/include'
> > > > > make[1]: *** [install-am] Error 2
> > > > > make[1]: Leaving directory
> > > > > `/gpfs/dev/h/WXQC/met-8.1_beta1/lib/netcdf-c-
4.4.1.1/include'
> > > > > make: *** [install-recursive] Error 1
> > > > >
> > > > > The permissions in the netcdf-c-4.4.1.1 directory are 777.
> > > > >
> > > > > What is the problem?
> > > > >
> > > > > Thanks
> > > > > Bob Craig
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> > >
> > >
> >
> >
> >
> >
>
>
>
>
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