[Met_help] [rt.rap.ucar.edu #80647] History for Error with Compiling MET-6.0
Howard Soh via RT
met_help at ucar.edu
Thu May 16 14:13:49 MDT 2019
----------------------------------------------------------------
Initial Request
----------------------------------------------------------------
Dear MET Help
Hi.
I am trying to compile MET-6.0 bugfixed version on a Linux cluster (Redhat)
at Purdue University.
I am using a few system-wide libraries (e.g., netcdf-3.6.3, hdf5) and I
installed most of the other library myself. Also I set up all the
environment variables required.
# MET
export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
export MET_GSL=/home/yoo108/build_MET/gsl-2.3
export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
export MET_UPP=/home/yoo108/UPPV3.1
export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
export MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
However, I got an error with the compilation of the MET-6.0 and it failed.
The error message reads as below:
MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
libvx_nc_util_a-nc_var_info.o -MD -MP -MF
.deps/libvx_nc_util_a-nc_var_info.Tpo -c -o libvx_nc_util_a-nc_var_info.o
`test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
In file included from nc_var_info.cc(24):
nc_utils.h(22): catastrophic error: cannot open source file "netcdf"
#include <netcdf>
^
compilation aborted for nc_var_info.cc (code 4)
make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
make[3]: Leaving directory
`/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/home/yoo108/build_MET/src/met-6.0/src/libcode'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/yoo108/build_MET/src/met-6.0/src'
make: *** [install-recursive] Error 1
^C[1]+ Exit 2 make install &>make_install.log
I wonder if this error is related with the 64 bit cluster while MET wants
32 bit software or else.
Your input will be highly appreciated.
Thank you.
Regards,
Jinwoong Yoo
Purdue Climate Change Research Center
----------------------------------------------------------------
Complete Ticket History
----------------------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Jinwoong Yoo
Time: Fri May 26 11:32:34 2017
Hi,
For a test, I compiled netcdf for MET.
And I set $LD_LIBRARY_PATH for netcdf and gsl.
However, I got the same compile error message as before.
BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
libvx_nc_util_a-nc_var_info.o -MD -MP -MF
.deps/libvx_nc_util_a-nc_var_info.Tpo -c -o libvx_nc_util_a-
nc_var_info.o
`test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
In file included from nc_var_info.cc(24):
nc_utils.h(22): catastrophic error: cannot open source file "netcdf"
#include <netcdf>
^
compilation aborted for nc_var_info.cc (code 4)
make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
make[3]: Leaving directory
`/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/home/yoo108/build_MET/src/met-
6.0/src/libcode'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/yoo108/build_MET/src/met-6.0/src'
make: *** [install-recursive] Error 1
Thank you.
Regards,
Jinwoong
On Fri, May 26, 2017 at 11:39 AM, met_help at ucar.edu via RT <
met_help at ucar.edu> wrote:
> NOTE: THE MET TEAM HAS LIMITED AVAILABILITY BETWEEN 5/23/17 AND
5/30/17.
> RESPONSES MAY BE DELAYED.
>
> Greetings,
>
> This message has been automatically generated in response to the
> creation of a trouble ticket regarding:
> "Error with Compiling MET-6.0",
> a summary of which appears below.
>
> There is no need to reply to this message right now. Your ticket
has been
> assigned an ID of [rt.rap.ucar.edu #80647].
>
> Please include the string:
>
> [rt.rap.ucar.edu #80647]
>
> in the subject line of all future correspondence about this issue.
To do
> so,
> you may reply to this message.
>
> Thank you,
> met_help at ucar.edu
>
>
-------------------------------------------------------------------------
> Dear MET Help
>
> Hi.
> I am trying to compile MET-6.0 bugfixed version on a Linux cluster
(Redhat)
> at Purdue University.
> I am using a few system-wide libraries (e.g., netcdf-3.6.3, hdf5)
and I
> installed most of the other library myself. Also I set up all the
> environment variables required.
>
> # MET
>
> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
>
> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
>
> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
>
> export MET_UPP=/home/yoo108/UPPV3.1
>
> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
>
> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
>
> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
>
> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
>
> export MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
>
> export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
>
> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
>
>
>
> However, I got an error with the compilation of the MET-6.0 and it
failed.
> The error message reads as below:
>
> MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o libvx_nc_util_a-
nc_var_info.o
> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
>
> In file included from nc_var_info.cc(24):
>
> nc_utils.h(22): catastrophic error: cannot open source file "netcdf"
>
> #include <netcdf>
>
> ^
>
>
> compilation aborted for nc_var_info.cc (code 4)
>
> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
>
> make[3]: Leaving directory
> `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
>
> make[2]: *** [install-recursive] Error 1
>
> make[2]: Leaving directory `/home/yoo108/build_MET/src/
> met-6.0/src/libcode'
>
> make[1]: *** [install-recursive] Error 1
>
> make[1]: Leaving directory `/home/yoo108/build_MET/src/met-6.0/src'
>
> make: *** [install-recursive] Error 1
>
> ^C[1]+ Exit 2 make install &>make_install.log
>
>
> I wonder if this error is related with the 64 bit cluster while MET
wants
> 32 bit software or else.
>
> Your input will be highly appreciated.
>
> Thank you.
>
> Regards,
>
>
> Jinwoong Yoo
>
> Purdue Climate Change Research Center
>
>
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Howard Soh
Time: Fri May 26 12:05:54 2017
Most engineers are out of office today.
I see that you are having problems compiling met-6.0 due to the error:
With version 6.0, MET includes support for NetCDF4. MET is looking for
the file "netcdf" that is included from the NetCDF4 C++ package.
Perhaps
that package is not installed on your system or at least not in the
location that MET_NETCDF is pointing to.
When installing these NetCDF packages, MET expects them to be
installed in
one location where all of the files are accessible, and that is what
you
would point MET_NETCDF to. Here is a list of files included in the
NetCDF4 C and C++ packages that MET will need, so you can check to see
if
they are installed in the MET_NETCDF location:
*Checklist to NetCDF4 C++ installation*
Files for NetCDF4 C:
- $MET_NETCDF/include/netcdf.h
- $MET_NETCDF/lib/libnetcdf.a
- $MET_NETCDF/lib/libnetcdf.so
Files for NetCDF4 C++:
- $MET_NETCDF/include/netcdf
- $MET_NETCDF/lib/libnetcdf_c++4.a
- $MET_NETCDF/lib/libnetcdf_c++4.so
If you find they are not installed and you need to install them, you
can
find instructions on ouronlinetutorialat this location:
http://www.dtcenter.org/met/users/support/online_tutorial/METv6.0/tutorial.php?name=compilation&category=req_libs
<http://www.dtcenter.org/met/users/support/online_tutorial/METv6.0/tutorial.php?name=compilation&category=req_libs>
You can continue on from that page for further instruction on setting
up
your environment and configuring MET.
Please check on those NetCDF files and let us know if you need any
further
assistance in getting met-6.0 installed.
I hope this helps!
Howard
On 5/26/2017 11:32 AM, Jinwoong Yoo via RT wrote:
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>
> Hi,
>
> For a test, I compiled netcdf for MET.
> And I set $LD_LIBRARY_PATH for netcdf and gsl.
> However, I got the same compile error message as before.
>
> BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o libvx_nc_util_a-
nc_var_info.o
> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
>
> In file included from nc_var_info.cc(24):
>
> nc_utils.h(22): catastrophic error: cannot open source file "netcdf"
>
> #include <netcdf>
>
> ^
>
>
> compilation aborted for nc_var_info.cc (code 4)
>
> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
>
> make[3]: Leaving directory
> `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
>
> make[2]: *** [install-recursive] Error 1
>
> make[2]: Leaving directory `/home/yoo108/build_MET/src/met-
6.0/src/libcode'
>
> make[1]: *** [install-recursive] Error 1
>
> make[1]: Leaving directory `/home/yoo108/build_MET/src/met-6.0/src'
>
> make: *** [install-recursive] Error 1
>
>
>
> Thank you.
>
> Regards,
>
>
> Jinwoong
>
> On Fri, May 26, 2017 at 11:39 AM, met_help at ucar.edu via RT <
> met_help at ucar.edu> wrote:
>
>> NOTE: THE MET TEAM HAS LIMITED AVAILABILITY BETWEEN 5/23/17 AND
5/30/17.
>> RESPONSES MAY BE DELAYED.
>>
>> Greetings,
>>
>> This message has been automatically generated in response to the
>> creation of a trouble ticket regarding:
>> "Error with Compiling MET-6.0",
>> a summary of which appears below.
>>
>> There is no need to reply to this message right now. Your ticket
has been
>> assigned an ID of [rt.rap.ucar.edu #80647].
>>
>> Please include the string:
>>
>> [rt.rap.ucar.edu #80647]
>>
>> in the subject line of all future correspondence about this issue.
To do
>> so,
>> you may reply to this message.
>>
>> Thank you,
>> met_help at ucar.edu
>>
>>
-------------------------------------------------------------------------
>> Dear MET Help
>>
>> Hi.
>> I am trying to compile MET-6.0 bugfixed version on a Linux cluster
(Redhat)
>> at Purdue University.
>> I am using a few system-wide libraries (e.g., netcdf-3.6.3, hdf5)
and I
>> installed most of the other library myself. Also I set up all the
>> environment variables required.
>>
>> # MET
>>
>> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
>>
>> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
>>
>> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
>>
>> export MET_UPP=/home/yoo108/UPPV3.1
>>
>> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
>>
>> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
>>
>> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
>>
>> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
>>
>> export MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
>>
>> export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
>>
>> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
>>
>>
>>
>> However, I got an error with the compilation of the MET-6.0 and it
failed.
>> The error message reads as below:
>>
>> MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
>> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
>> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o libvx_nc_util_a-
nc_var_info.o
>> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
>>
>> In file included from nc_var_info.cc(24):
>>
>> nc_utils.h(22): catastrophic error: cannot open source file
"netcdf"
>>
>> #include <netcdf>
>>
>> ^
>>
>>
>> compilation aborted for nc_var_info.cc (code 4)
>>
>> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
>>
>> make[3]: Leaving directory
>> `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
>>
>> make[2]: *** [install-recursive] Error 1
>>
>> make[2]: Leaving directory `/home/yoo108/build_MET/src/
>> met-6.0/src/libcode'
>>
>> make[1]: *** [install-recursive] Error 1
>>
>> make[1]: Leaving directory `/home/yoo108/build_MET/src/met-6.0/src'
>>
>> make: *** [install-recursive] Error 1
>>
>> ^C[1]+ Exit 2 make install &>make_install.log
>>
>>
>> I wonder if this error is related with the 64 bit cluster while MET
wants
>> 32 bit software or else.
>>
>> Your input will be highly appreciated.
>>
>> Thank you.
>>
>> Regards,
>>
>>
>> Jinwoong Yoo
>>
>> Purdue Climate Change Research Center
>>
>>
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Jinwoong Yoo
Time: Fri May 26 13:25:06 2017
Dear Howard,
Thank you very much for your reply.
Let me try with the netcdf4 C++.
Thank you.
Regards,
Jinwoong
On Fri, May 26, 2017 at 2:05 PM, Howard Soh via RT <met_help at ucar.edu>
wrote:
> Most engineers are out of office today.
>
> I see that you are having problems compiling met-6.0 due to the
error:
>
> With version 6.0, MET includes support for NetCDF4. MET is looking
for
> the file "netcdf" that is included from the NetCDF4 C++ package.
Perhaps
> that package is not installed on your system or at least not in the
> location that MET_NETCDF is pointing to.
>
> When installing these NetCDF packages, MET expects them to be
installed in
> one location where all of the files are accessible, and that is what
you
> would point MET_NETCDF to. Here is a list of files included in the
> NetCDF4 C and C++ packages that MET will need, so you can check to
see if
> they are installed in the MET_NETCDF location:
>
> *Checklist to NetCDF4 C++ installation*
>
> Files for NetCDF4 C:
>
> - $MET_NETCDF/include/netcdf.h
> - $MET_NETCDF/lib/libnetcdf.a
> - $MET_NETCDF/lib/libnetcdf.so
>
> Files for NetCDF4 C++:
>
> - $MET_NETCDF/include/netcdf
> - $MET_NETCDF/lib/libnetcdf_c++4.a
> - $MET_NETCDF/lib/libnetcdf_c++4.so
>
> If you find they are not installed and you need to install them, you
can
> find instructions on ouronlinetutorialat this location:
>
> http://www.dtcenter.org/met/users/support/online_tutorial/
> METv6.0/tutorial.php?name=compilation&category=req_libs
> <http://www.dtcenter.org/met/users/support/online_tutorial/
> METv6.0/tutorial.php?name=compilation&category=req_libs>
>
> You can continue on from that page for further instruction on
setting up
> your environment and configuring MET.
>
> Please check on those NetCDF files and let us know if you need any
further
> assistance in getting met-6.0 installed.
>
> I hope this helps!
>
>
> Howard
>
> On 5/26/2017 11:32 AM, Jinwoong Yoo via RT wrote:
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >
> > Hi,
> >
> > For a test, I compiled netcdf for MET.
> > And I set $LD_LIBRARY_PATH for netcdf and gsl.
> > However, I got the same compile error message as before.
> >
> > BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
> > libvx_nc_util_a-nc_var_info.o -MD -MP -MF
> > .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
> libvx_nc_util_a-nc_var_info.o
> > `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
> >
> > In file included from nc_var_info.cc(24):
> >
> > nc_utils.h(22): catastrophic error: cannot open source file
"netcdf"
> >
> > #include <netcdf>
> >
> > ^
> >
> >
> > compilation aborted for nc_var_info.cc (code 4)
> >
> > make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
> >
> > make[3]: Leaving directory
> > `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
> >
> > make[2]: *** [install-recursive] Error 1
> >
> > make[2]: Leaving directory `/home/yoo108/build_MET/src/
> met-6.0/src/libcode'
> >
> > make[1]: *** [install-recursive] Error 1
> >
> > make[1]: Leaving directory `/home/yoo108/build_MET/src/met-
6.0/src'
> >
> > make: *** [install-recursive] Error 1
> >
> >
> >
> > Thank you.
> >
> > Regards,
> >
> >
> > Jinwoong
> >
> > On Fri, May 26, 2017 at 11:39 AM, met_help at ucar.edu via RT <
> > met_help at ucar.edu> wrote:
> >
> >> NOTE: THE MET TEAM HAS LIMITED AVAILABILITY BETWEEN 5/23/17 AND
5/30/17.
> >> RESPONSES MAY BE DELAYED.
> >>
> >> Greetings,
> >>
> >> This message has been automatically generated in response to the
> >> creation of a trouble ticket regarding:
> >> "Error with Compiling MET-6.0",
> >> a summary of which appears below.
> >>
> >> There is no need to reply to this message right now. Your ticket
has
> been
> >> assigned an ID of [rt.rap.ucar.edu #80647].
> >>
> >> Please include the string:
> >>
> >> [rt.rap.ucar.edu #80647]
> >>
> >> in the subject line of all future correspondence about this
issue. To do
> >> so,
> >> you may reply to this message.
> >>
> >> Thank you,
> >> met_help at ucar.edu
> >>
> >> ------------------------------------------------------------
> -------------
> >> Dear MET Help
> >>
> >> Hi.
> >> I am trying to compile MET-6.0 bugfixed version on a Linux
cluster
> (Redhat)
> >> at Purdue University.
> >> I am using a few system-wide libraries (e.g., netcdf-3.6.3, hdf5)
and I
> >> installed most of the other library myself. Also I set up all the
> >> environment variables required.
> >>
> >> # MET
> >>
> >> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
> >>
> >> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
> >>
> >> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
> >>
> >> export MET_UPP=/home/yoo108/UPPV3.1
> >>
> >> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
> >>
> >> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
> >>
> >> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
> >>
> >> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
> >>
> >> export MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
> >>
> >> export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
> >>
> >> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
> >>
> >>
> >>
> >> However, I got an error with the compilation of the MET-6.0 and
it
> failed.
> >> The error message reads as below:
> >>
> >> MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
> >> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
> >> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
> libvx_nc_util_a-nc_var_info.o
> >> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
> >>
> >> In file included from nc_var_info.cc(24):
> >>
> >> nc_utils.h(22): catastrophic error: cannot open source file
"netcdf"
> >>
> >> #include <netcdf>
> >>
> >> ^
> >>
> >>
> >> compilation aborted for nc_var_info.cc (code 4)
> >>
> >> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
> >>
> >> make[3]: Leaving directory
> >> `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
> >>
> >> make[2]: *** [install-recursive] Error 1
> >>
> >> make[2]: Leaving directory `/home/yoo108/build_MET/src/
> >> met-6.0/src/libcode'
> >>
> >> make[1]: *** [install-recursive] Error 1
> >>
> >> make[1]: Leaving directory `/home/yoo108/build_MET/src/met-
6.0/src'
> >>
> >> make: *** [install-recursive] Error 1
> >>
> >> ^C[1]+ Exit 2 make install &>make_install.log
> >>
> >>
> >> I wonder if this error is related with the 64 bit cluster while
MET
> wants
> >> 32 bit software or else.
> >>
> >> Your input will be highly appreciated.
> >>
> >> Thank you.
> >>
> >> Regards,
> >>
> >>
> >> Jinwoong Yoo
> >>
> >> Purdue Climate Change Research Center
> >>
> >>
>
>
>
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Randy Bullock
Time: Tue May 30 11:04:48 2017
Hello -
Most of our team is out due to the Memorial Day holiday. We'll have a
look
at your issue when the team is back sometime later this week.
On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
<met_help at ucar.edu>
wrote:
>
> Fri May 26 09:39:58 2017: Request 80647 was acted upon.
> Transaction: Ticket created by jinwoong.yoo at gmail.com
> Queue: met_help
> Subject: Error with Compiling MET-6.0
> Owner: Nobody
> Requestors: jinwoong.yoo at gmail.com
> Status: new
> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>
>
> Dear MET Help
>
> Hi.
> I am trying to compile MET-6.0 bugfixed version on a Linux cluster
(Redhat)
> at Purdue University.
> I am using a few system-wide libraries (e.g., netcdf-3.6.3, hdf5)
and I
> installed most of the other library myself. Also I set up all the
> environment variables required.
>
> # MET
>
> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
>
> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
>
> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
>
> export MET_UPP=/home/yoo108/UPPV3.1
>
> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
>
> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
>
> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
>
> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
>
> export MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
>
> export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
>
> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
>
>
>
> However, I got an error with the compilation of the MET-6.0 and it
failed.
> The error message reads as below:
>
> MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o libvx_nc_util_a-
nc_var_info.o
> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
>
> In file included from nc_var_info.cc(24):
>
> nc_utils.h(22): catastrophic error: cannot open source file "netcdf"
>
> #include <netcdf>
>
> ^
>
>
> compilation aborted for nc_var_info.cc (code 4)
>
> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
>
> make[3]: Leaving directory
> `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
>
> make[2]: *** [install-recursive] Error 1
>
> make[2]: Leaving directory `/home/yoo108/build_MET/src/
> met-6.0/src/libcode'
>
> make[1]: *** [install-recursive] Error 1
>
> make[1]: Leaving directory `/home/yoo108/build_MET/src/met-6.0/src'
>
> make: *** [install-recursive] Error 1
>
> ^C[1]+ Exit 2 make install &>make_install.log
>
>
> I wonder if this error is related with the 64 bit cluster while MET
wants
> 32 bit software or else.
>
> Your input will be highly appreciated.
>
> Thank you.
>
> Regards,
>
>
> Jinwoong Yoo
>
> Purdue Climate Change Research Center
>
>
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Jinwoong Yoo
Time: Tue May 30 11:22:03 2017
Hi,
Thank you for your reply.
I realized that I have to have netcdf4-c and netcdf4-cxx to install
MET-6.0.
So far, I have compiled HDF5 following directions at
http://www.dtcenter.org/met/users/support/online_tutorial/METv6.0/tutorial.php?name=compilation&category=req_libs
.
I have built HDF5 successfully using the `--enable-hl` function and I
got
hdf5_h1.1 in my target directory. Previously I got error installing
netcdf4
with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared" message (as shown
in
https://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg13749.html
).
I am referring to unidata webpage for the compilation of netcdf4 at
http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html
.
But now I get an error with h5_test within the netcdf make check and
it
fails.
Attached please find configure and make log.
Do you have any know-how to overcome this issue?
Thank you very much in advance.
Regards,
Jinwoong Yoo
Purdue Climate Change Research Center
On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
<met_help at ucar.edu>
wrote:
> Hello -
>
> Most of our team is out due to the Memorial Day holiday. We'll have
a look
> at your issue when the team is back sometime later this week.
>
> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
<met_help at ucar.edu>
> wrote:
>
> >
> > Fri May 26 09:39:58 2017: Request 80647 was acted upon.
> > Transaction: Ticket created by jinwoong.yoo at gmail.com
> > Queue: met_help
> > Subject: Error with Compiling MET-6.0
> > Owner: Nobody
> > Requestors: jinwoong.yoo at gmail.com
> > Status: new
> > Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >
> >
> > Dear MET Help
> >
> > Hi.
> > I am trying to compile MET-6.0 bugfixed version on a Linux cluster
> (Redhat)
> > at Purdue University.
> > I am using a few system-wide libraries (e.g., netcdf-3.6.3, hdf5)
and I
> > installed most of the other library myself. Also I set up all the
> > environment variables required.
> >
> > # MET
> >
> > export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
> >
> > export MET_GSL=/home/yoo108/build_MET/gsl-2.3
> >
> > export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
> >
> > export MET_UPP=/home/yoo108/UPPV3.1
> >
> > export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
> >
> > export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
> >
> > export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
> >
> > export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
> >
> > export MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
> >
> > export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
> >
> > export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
> >
> >
> >
> > However, I got an error with the compilation of the MET-6.0 and it
> failed.
> > The error message reads as below:
> >
> > MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
> > libvx_nc_util_a-nc_var_info.o -MD -MP -MF
> > .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
> libvx_nc_util_a-nc_var_info.o
> > `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
> >
> > In file included from nc_var_info.cc(24):
> >
> > nc_utils.h(22): catastrophic error: cannot open source file
"netcdf"
> >
> > #include <netcdf>
> >
> > ^
> >
> >
> > compilation aborted for nc_var_info.cc (code 4)
> >
> > make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
> >
> > make[3]: Leaving directory
> > `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
> >
> > make[2]: *** [install-recursive] Error 1
> >
> > make[2]: Leaving directory `/home/yoo108/build_MET/src/
> > met-6.0/src/libcode'
> >
> > make[1]: *** [install-recursive] Error 1
> >
> > make[1]: Leaving directory `/home/yoo108/build_MET/src/met-
6.0/src'
> >
> > make: *** [install-recursive] Error 1
> >
> > ^C[1]+ Exit 2 make install &>make_install.log
> >
> >
> > I wonder if this error is related with the 64 bit cluster while
MET wants
> > 32 bit software or else.
> >
> > Your input will be highly appreciated.
> >
> > Thank you.
> >
> > Regards,
> >
> >
> > Jinwoong Yoo
> >
> > Purdue Climate Change Research Center
> >
> >
>
>
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Jinwoong Yoo
Time: Tue May 30 11:24:46 2017
I forgot to attach my log file.
Thanks!
On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo <jinwoong.yoo at gmail.com>
wrote:
> Hi,
> Thank you for your reply.
>
> I realized that I have to have netcdf4-c and netcdf4-cxx to install
> MET-6.0.
> So far, I have compiled HDF5 following directions at
> http://www.dtcenter.org/met/users/support/online_tutorial/
> METv6.0/tutorial.php?name=compilation&category=req_libs.
>
> I have built HDF5 successfully using the `--enable-hl` function and
I got
> hdf5_h1.1 in my target directory. Previously I got error installing
netcdf4
> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared" message (as
shown in
> https://www.unidata.ucar.edu/support/help/MailArchives/
> netcdf/msg13749.html).
>
> I am referring to unidata webpage for the compilation of netcdf4 at
> http://www.unidata.ucar.edu/software/netcdf/docs/getting_
> and_building_netcdf.html.
> But now I get an error with h5_test within the netcdf make check and
it
> fails.
> Attached please find configure and make log.
> Do you have any know-how to overcome this issue?
> Thank you very much in advance.
>
> Regards,
>
> Jinwoong Yoo
> Purdue Climate Change Research Center
>
> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
<met_help at ucar.edu>
> wrote:
>
>> Hello -
>>
>> Most of our team is out due to the Memorial Day holiday. We'll
have a
>> look
>> at your issue when the team is back sometime later this week.
>>
>> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
<met_help at ucar.edu>
>> wrote:
>>
>> >
>> > Fri May 26 09:39:58 2017: Request 80647 was acted upon.
>> > Transaction: Ticket created by jinwoong.yoo at gmail.com
>> > Queue: met_help
>> > Subject: Error with Compiling MET-6.0
>> > Owner: Nobody
>> > Requestors: jinwoong.yoo at gmail.com
>> > Status: new
>> > Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>> >
>> >
>> > Dear MET Help
>> >
>> > Hi.
>> > I am trying to compile MET-6.0 bugfixed version on a Linux
cluster
>> (Redhat)
>> > at Purdue University.
>> > I am using a few system-wide libraries (e.g., netcdf-3.6.3, hdf5)
and I
>> > installed most of the other library myself. Also I set up all the
>> > environment variables required.
>> >
>> > # MET
>> >
>> > export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
>> >
>> > export MET_GSL=/home/yoo108/build_MET/gsl-2.3
>> >
>> > export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
>> >
>> > export MET_UPP=/home/yoo108/UPPV3.1
>> >
>> > export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
>> >
>> > export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
>> >
>> > export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
>> >
>> > export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
>> >
>> > export MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
>> >
>> > export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
>> >
>> > export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
>> >
>> >
>> >
>> > However, I got an error with the compilation of the MET-6.0 and
it
>> failed.
>> > The error message reads as below:
>> >
>> > MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
>> > libvx_nc_util_a-nc_var_info.o -MD -MP -MF
>> > .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
>> libvx_nc_util_a-nc_var_info.o
>> > `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
>> >
>> > In file included from nc_var_info.cc(24):
>> >
>> > nc_utils.h(22): catastrophic error: cannot open source file
"netcdf"
>> >
>> > #include <netcdf>
>> >
>> > ^
>> >
>> >
>> > compilation aborted for nc_var_info.cc (code 4)
>> >
>> > make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
>> >
>> > make[3]: Leaving directory
>> > `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
>> >
>> > make[2]: *** [install-recursive] Error 1
>> >
>> > make[2]: Leaving directory `/home/yoo108/build_MET/src/
>> > met-6.0/src/libcode'
>> >
>> > make[1]: *** [install-recursive] Error 1
>> >
>> > make[1]: Leaving directory `/home/yoo108/build_MET/src/met-
6.0/src'
>> >
>> > make: *** [install-recursive] Error 1
>> >
>> > ^C[1]+ Exit 2 make install &>make_install.log
>> >
>> >
>> > I wonder if this error is related with the 64 bit cluster while
MET
>> wants
>> > 32 bit software or else.
>> >
>> > Your input will be highly appreciated.
>> >
>> > Thank you.
>> >
>> > Regards,
>> >
>> >
>> > Jinwoong Yoo
>> >
>> > Purdue Climate Change Research Center
>> >
>> >
>>
>>
>
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Howard Soh
Time: Tue May 30 12:22:10 2017
Hi Jinwoong.
I am sorry to hear that you are still having difficulty with the
netcdf library
files.
One unit test related with HDF5 was failed. Would you check
h5_test/test-suite.log
and contact Unidata?
The full path will be /home/yoo108/METwithGNU/src/netcdf-c-
4.4.1.1/h5_test
/test-suite.log.
It would help to understand your problem if you send us
h5_test/test-suite.log.
Cheers,
Howard
FYI:
FAIL: tst_h_vars
============================================================================
Testsuite summary for netCDF 4.4.1.1
============================================================================
# TOTAL: 26
# PASS: 25
# SKIP: 0
# XFAIL: 0
# FAIL: 1
# XPASS: 0
# ERROR: 0
============================================================================
See h5_test/test-suite.log
Please report to support-netcdf at unidata.ucar.edu
============================================================================
On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
<URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
I forgot to attach my log file.
Thanks!
On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo <jinwoong.yoo at gmail.com>
<jinwoong.yoo at gmail.com>
wrote:
Hi,
Thank you for your reply.
I realized that I have to have netcdf4-c and netcdf4-cxx to install
MET-6.0.
So far, I have compiled HDF5 following directions
athttp://www.dtcenter.org/met/users/support/online_tutorial/
METv6.0/tutorial.php?name=compilation&category=req_libs.
I have built HDF5 successfully using the `--enable-hl` function and I
got
hdf5_h1.1 in my target directory. Previously I got error installing
netcdf4
with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared" message (as shown
inhttps://www.unidata.ucar.edu/support/help/MailArchives/
netcdf/msg13749.html).
I am referring to unidata webpage for the compilation of netcdf4
athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
and_building_netcdf.html.
But now I get an error with h5_test within the netcdf make check and
it
fails.
Attached please find configure and make log.
Do you have any know-how to overcome this issue?
Thank you very much in advance.
Regards,
Jinwoong Yoo
Purdue Climate Change Research Center
On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
<met_help at ucar.edu> <met_help at ucar.edu>
wrote:
Hello -
Most of our team is out due to the Memorial Day holiday. We'll have a
look
at your issue when the team is back sometime later this week.
On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
<met_help at ucar.edu> <met_help at ucar.edu>
wrote:
Fri May 26 09:39:58 2017: Request 80647 was acted upon.
Transaction: Ticket created by jinwoong.yoo at gmail.com
Queue: met_help
Subject: Error with Compiling MET-6.0
Owner: Nobody
Requestors: jinwoong.yoo at gmail.com
Status: new
Ticket <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>
Dear MET Help
Hi.
I am trying to compile MET-6.0 bugfixed version on a Linux cluster
(Redhat)
at Purdue University.
I am using a few system-wide libraries (e.g., netcdf-3.6.3, hdf5) and
I
installed most of the other library myself. Also I set up all the
environment variables required.
# MET
export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
export MET_GSL=/home/yoo108/build_MET/gsl-2.3
export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
export MET_UPP=/home/yoo108/UPPV3.1
export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
export MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
However, I got an error with the compilation of the MET-6.0 and it
failed.
The error message reads as below:
MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
libvx_nc_util_a-nc_var_info.o -MD -MP -MF
.deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
libvx_nc_util_a-nc_var_info.o
`test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
In file included from nc_var_info.cc(24):
nc_utils.h(22): catastrophic error: cannot open source file "netcdf"
#include <netcdf>
^
compilation aborted for nc_var_info.cc (code 4)
make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
make[3]: Leaving directory
`/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/home/yoo108/build_MET/src/
met-6.0/src/libcode'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/yoo108/build_MET/src/met-6.0/src'
make: *** [install-recursive] Error 1
^C[1]+ Exit 2 make install &>make_install.log
I wonder if this error is related with the 64 bit cluster while MET
wants
32 bit software or else.
Your input will be highly appreciated.
Thank you.
Regards,
Jinwoong Yoo
Purdue Climate Change Research Center
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Jinwoong Yoo
Time: Tue May 30 12:33:49 2017
Hi Howard,
I contacted Unidata regarding the issue already.
Attached please find the file, and see its contents below.
============================================
netCDF 4.4.1.1: h5_test/test-suite.log
============================================
# TOTAL: 26
# PASS: 25
# SKIP: 0
# XFAIL: 0
# FAIL: 1
# XPASS: 0
# ERROR: 0
.. contents:: :depth: 2
FAIL: tst_h_vars
================
*** Checking HDF5 variable functions.
*** Checking HDF5 boolen variables...ok.
*** Checking HDF5 variable with unlimited dimension...ok.
*** Checking HDF5 deflate filter setting and getting...Sorry!
Unexpected
result, tst_h_vars.c, line: 230
FAIL tst_h_vars (exit status: 2)
Thank you.
Regards,
Jinwoong
On Tue, May 30, 2017 at 2:22 PM, Howard Soh via RT <met_help at ucar.edu>
wrote:
> Hi Jinwoong.
>
> I am sorry to hear that you are still having difficulty with the
netcdf
> library
> files.
> One unit test related with HDF5 was failed. Would you check
> h5_test/test-suite.log
> and contact Unidata?
> The full path will be /home/yoo108/METwithGNU/src/netcdf-c-
4.4.1.1/h5_test
> /test-suite.log.
>
> It would help to understand your problem if you send us
> h5_test/test-suite.log.
>
> Cheers,
> Howard
>
> FYI:
>
>
> FAIL: tst_h_vars
>
> ============================================================
> ================
> Testsuite summary for netCDF 4.4.1.1
> ============================================================
> ================
> # TOTAL: 26
> # PASS: 25
> # SKIP: 0
> # XFAIL: 0
> # FAIL: 1
> # XPASS: 0
> # ERROR: 0
> ============================================================
> ================
> See h5_test/test-suite.log
> Please report to support-netcdf at unidata.ucar.edu
> ============================================================
> ================
>
>
> On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>
> I forgot to attach my log file.
> Thanks!
>
>
> On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo
<jinwoong.yoo at gmail.com>
> <jinwoong.yoo at gmail.com>
> wrote:
>
>
> Hi,
> Thank you for your reply.
>
> I realized that I have to have netcdf4-c and netcdf4-cxx to install
> MET-6.0.
> So far, I have compiled HDF5 following directions
> athttp://www.dtcenter.org/met/users/support/online_tutorial/
> METv6.0/tutorial.php?name=compilation&category=req_libs.
>
> I have built HDF5 successfully using the `--enable-hl` function and
I got
> hdf5_h1.1 in my target directory. Previously I got error installing
netcdf4
> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared" message (as
shown
> inhttps://www.unidata.ucar.edu/support/help/MailArchives/
> netcdf/msg13749.html).
>
> I am referring to unidata webpage for the compilation of netcdf4
> athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
> and_building_netcdf.html.
> But now I get an error with h5_test within the netcdf make check and
it
> fails.
> Attached please find configure and make log.
> Do you have any know-how to overcome this issue?
> Thank you very much in advance.
>
> Regards,
>
> Jinwoong Yoo
> Purdue Climate Change Research Center
>
> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
> <met_help at ucar.edu> <met_help at ucar.edu>
> wrote:
>
>
> Hello -
>
> Most of our team is out due to the Memorial Day holiday. We'll have
a
> look
> at your issue when the team is back sometime later this week.
>
> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
> <met_help at ucar.edu> <met_help at ucar.edu>
> wrote:
>
>
> Fri May 26 09:39:58 2017: Request 80647 was acted upon.
> Transaction: Ticket created by jinwoong.yoo at gmail.com
> Queue: met_help
> Subject: Error with Compiling MET-6.0
> Owner: Nobody
> Requestors: jinwoong.yoo at gmail.com
> Status: new
> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>
>
> Dear MET Help
>
> Hi.
> I am trying to compile MET-6.0 bugfixed version on a Linux cluster
>
> (Redhat)
>
> at Purdue University.
> I am using a few system-wide libraries (e.g., netcdf-3.6.3, hdf5)
and I
> installed most of the other library myself. Also I set up all the
> environment variables required.
>
> # MET
>
> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
>
> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
>
> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
>
> export MET_UPP=/home/yoo108/UPPV3.1
>
> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
>
> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
>
> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
>
> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
>
> export MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
>
> export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
>
> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
>
>
>
> However, I got an error with the compilation of the MET-6.0 and it
>
> failed.
>
> The error message reads as below:
>
> MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
>
> libvx_nc_util_a-nc_var_info.o
>
> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
>
> In file included from nc_var_info.cc(24):
>
> nc_utils.h(22): catastrophic error: cannot open source file "netcdf"
>
> #include <netcdf>
>
> ^
>
>
> compilation aborted for nc_var_info.cc (code 4)
>
> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
>
> make[3]: Leaving directory
> `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
>
> make[2]: *** [install-recursive] Error 1
>
> make[2]: Leaving directory `/home/yoo108/build_MET/src/
> met-6.0/src/libcode'
>
> make[1]: *** [install-recursive] Error 1
>
> make[1]: Leaving directory `/home/yoo108/build_MET/src/met-6.0/src'
>
> make: *** [install-recursive] Error 1
>
> ^C[1]+ Exit 2 make install &>make_install.log
>
>
> I wonder if this error is related with the 64 bit cluster while MET
>
> wants
>
> 32 bit software or else.
>
> Your input will be highly appreciated.
>
> Thank you.
>
> Regards,
>
>
> Jinwoong Yoo
>
> Purdue Climate Change Research Center
>
>
------------------------------------------------
Subject: Re: [rt.rap.ucar.edu #80647] Error with Compiling MET-6.0
From: Howard Soh
Time: Tue May 30 13:18:27 2017
Thank you, Jinwoong.
Howard
On 5/30/2017 12:33 PM, Jinwoong Yoo via RT wrote:
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>
> Hi Howard,
>
> I contacted Unidata regarding the issue already.
> Attached please find the file, and see its contents below.
>
>
>
> ============================================
>
> netCDF 4.4.1.1: h5_test/test-suite.log
>
> ============================================
>
>
> # TOTAL: 26
>
> # PASS: 25
>
> # SKIP: 0
>
> # XFAIL: 0
>
> # FAIL: 1
>
> # XPASS: 0
>
> # ERROR: 0
>
>
> .. contents:: :depth: 2
>
>
> FAIL: tst_h_vars
>
> ================
>
>
>
> *** Checking HDF5 variable functions.
>
> *** Checking HDF5 boolen variables...ok.
>
> *** Checking HDF5 variable with unlimited dimension...ok.
>
> *** Checking HDF5 deflate filter setting and getting...Sorry!
Unexpected
> result, tst_h_vars.c, line: 230
>
> FAIL tst_h_vars (exit status: 2)
>
>
> Thank you.
>
> Regards,
>
>
> Jinwoong
>
>
>
>
>
>
>
> On Tue, May 30, 2017 at 2:22 PM, Howard Soh via RT
<met_help at ucar.edu>
> wrote:
>
>> Hi Jinwoong.
>>
>> I am sorry to hear that you are still having difficulty with the
netcdf
>> library
>> files.
>> One unit test related with HDF5 was failed. Would you check
>> h5_test/test-suite.log
>> and contact Unidata?
>> The full path will be /home/yoo108/METwithGNU/src/netcdf-c-
4.4.1.1/h5_test
>> /test-suite.log.
>>
>> It would help to understand your problem if you send us
>> h5_test/test-suite.log.
>>
>> Cheers,
>> Howard
>>
>> FYI:
>>
>>
>> FAIL: tst_h_vars
>>
>> ============================================================
>> ================
>> Testsuite summary for netCDF 4.4.1.1
>> ============================================================
>> ================
>> # TOTAL: 26
>> # PASS: 25
>> # SKIP: 0
>> # XFAIL: 0
>> # FAIL: 1
>> # XPASS: 0
>> # ERROR: 0
>> ============================================================
>> ================
>> See h5_test/test-suite.log
>> Please report to support-netcdf at unidata.ucar.edu
>> ============================================================
>> ================
>>
>>
>> On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
>>
>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>
>> I forgot to attach my log file.
>> Thanks!
>>
>>
>> On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo
<jinwoong.yoo at gmail.com>
>> <jinwoong.yoo at gmail.com>
>> wrote:
>>
>>
>> Hi,
>> Thank you for your reply.
>>
>> I realized that I have to have netcdf4-c and netcdf4-cxx to install
>> MET-6.0.
>> So far, I have compiled HDF5 following directions
>> athttp://www.dtcenter.org/met/users/support/online_tutorial/
>> METv6.0/tutorial.php?name=compilation&category=req_libs.
>>
>> I have built HDF5 successfully using the `--enable-hl` function and
I got
>> hdf5_h1.1 in my target directory. Previously I got error installing
netcdf4
>> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared" message (as
shown
>> inhttps://www.unidata.ucar.edu/support/help/MailArchives/
>> netcdf/msg13749.html).
>>
>> I am referring to unidata webpage for the compilation of netcdf4
>> athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
>> and_building_netcdf.html.
>> But now I get an error with h5_test within the netcdf make check
and it
>> fails.
>> Attached please find configure and make log.
>> Do you have any know-how to overcome this issue?
>> Thank you very much in advance.
>>
>> Regards,
>>
>> Jinwoong Yoo
>> Purdue Climate Change Research Center
>>
>> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
>> <met_help at ucar.edu> <met_help at ucar.edu>
>> wrote:
>>
>>
>> Hello -
>>
>> Most of our team is out due to the Memorial Day holiday. We'll
have a
>> look
>> at your issue when the team is back sometime later this week.
>>
>> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
>> <met_help at ucar.edu> <met_help at ucar.edu>
>> wrote:
>>
>>
>> Fri May 26 09:39:58 2017: Request 80647 was acted upon.
>> Transaction: Ticket created by jinwoong.yoo at gmail.com
>> Queue: met_help
>> Subject: Error with Compiling MET-6.0
>> Owner: Nobody
>> Requestors: jinwoong.yoo at gmail.com
>> Status: new
>> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>
>>
>> Dear MET Help
>>
>> Hi.
>> I am trying to compile MET-6.0 bugfixed version on a Linux cluster
>>
>> (Redhat)
>>
>> at Purdue University.
>> I am using a few system-wide libraries (e.g., netcdf-3.6.3, hdf5)
and I
>> installed most of the other library myself. Also I set up all the
>> environment variables required.
>>
>> # MET
>>
>> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
>>
>> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
>>
>> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
>>
>> export MET_UPP=/home/yoo108/UPPV3.1
>>
>> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
>>
>> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
>>
>> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
>>
>> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
>>
>> export MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
>>
>> export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
>>
>> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
>>
>>
>>
>> However, I got an error with the compilation of the MET-6.0 and it
>>
>> failed.
>>
>> The error message reads as below:
>>
>> MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
>> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
>> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
>>
>> libvx_nc_util_a-nc_var_info.o
>>
>> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
>>
>> In file included from nc_var_info.cc(24):
>>
>> nc_utils.h(22): catastrophic error: cannot open source file
"netcdf"
>>
>> #include <netcdf>
>>
>> ^
>>
>>
>> compilation aborted for nc_var_info.cc (code 4)
>>
>> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
>>
>> make[3]: Leaving directory
>> `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
>>
>> make[2]: *** [install-recursive] Error 1
>>
>> make[2]: Leaving directory `/home/yoo108/build_MET/src/
>> met-6.0/src/libcode'
>>
>> make[1]: *** [install-recursive] Error 1
>>
>> make[1]: Leaving directory `/home/yoo108/build_MET/src/met-6.0/src'
>>
>> make: *** [install-recursive] Error 1
>>
>> ^C[1]+ Exit 2 make install &>make_install.log
>>
>>
>> I wonder if this error is related with the 64 bit cluster while MET
>>
>> wants
>>
>> 32 bit software or else.
>>
>> Your input will be highly appreciated.
>>
>> Thank you.
>>
>> Regards,
>>
>>
>> Jinwoong Yoo
>>
>> Purdue Climate Change Research Center
>>
>>
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Jinwoong Yoo
Time: Tue May 30 14:12:23 2017
Hi Howard,
I was able to compile HDF5, Netcdf4-C, and NetCDF-CXX successfully
finally.
I happened to know that there were a few typos in the MET Online
Tutorial
For METv6.0, which led into various confusions.
In the "Compiling HDF5" section,
I had to configure hdf5 with the "--enable-hl" option along with "
*--with-zlib=${ZDIR}*".
In the "Compiling NetCDF" section,
both for NetCDF-C and NetCDF-CXX,
LDFLAGS and CPPFLAGS directories should be assigned to HDF5 directory,
not
the NetCDF4 installation directory in
"LDFLAGS=-L${MET_LIB_DIR}/lib CPPFLAGS=-I${MET_LIB_DIR}/include" while
the
target directory in "--prefix=${MET_LIB_DIR}" should be netcdf4
directory.
You might want to make changes for these error for other METv6.0 users
on
your webpage at "
http://www.dtcenter.org/met/users/support/online_tutorial/METv6.0/tutorial.php?name=compilation&category=req_libs
".
Thank you.
Regards,
Jinwoong
On Tue, May 30, 2017 at 3:18 PM, Howard Soh via RT <met_help at ucar.edu>
wrote:
> Thank you, Jinwoong.
>
> Howard
>
> On 5/30/2017 12:33 PM, Jinwoong Yoo via RT wrote:
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >
> > Hi Howard,
> >
> > I contacted Unidata regarding the issue already.
> > Attached please find the file, and see its contents below.
> >
> >
> >
> > ============================================
> >
> > netCDF 4.4.1.1: h5_test/test-suite.log
> >
> > ============================================
> >
> >
> > # TOTAL: 26
> >
> > # PASS: 25
> >
> > # SKIP: 0
> >
> > # XFAIL: 0
> >
> > # FAIL: 1
> >
> > # XPASS: 0
> >
> > # ERROR: 0
> >
> >
> > .. contents:: :depth: 2
> >
> >
> > FAIL: tst_h_vars
> >
> > ================
> >
> >
> >
> > *** Checking HDF5 variable functions.
> >
> > *** Checking HDF5 boolen variables...ok.
> >
> > *** Checking HDF5 variable with unlimited dimension...ok.
> >
> > *** Checking HDF5 deflate filter setting and getting...Sorry!
Unexpected
> > result, tst_h_vars.c, line: 230
> >
> > FAIL tst_h_vars (exit status: 2)
> >
> >
> > Thank you.
> >
> > Regards,
> >
> >
> > Jinwoong
> >
> >
> >
> >
> >
> >
> >
> > On Tue, May 30, 2017 at 2:22 PM, Howard Soh via RT
<met_help at ucar.edu>
> > wrote:
> >
> >> Hi Jinwoong.
> >>
> >> I am sorry to hear that you are still having difficulty with the
netcdf
> >> library
> >> files.
> >> One unit test related with HDF5 was failed. Would you check
> >> h5_test/test-suite.log
> >> and contact Unidata?
> >> The full path will be /home/yoo108/METwithGNU/src/
> netcdf-c-4.4.1.1/h5_test
> >> /test-suite.log.
> >>
> >> It would help to understand your problem if you send us
> >> h5_test/test-suite.log.
> >>
> >> Cheers,
> >> Howard
> >>
> >> FYI:
> >>
> >>
> >> FAIL: tst_h_vars
> >>
> >> ============================================================
> >> ================
> >> Testsuite summary for netCDF 4.4.1.1
> >> ============================================================
> >> ================
> >> # TOTAL: 26
> >> # PASS: 25
> >> # SKIP: 0
> >> # XFAIL: 0
> >> # FAIL: 1
> >> # XPASS: 0
> >> # ERROR: 0
> >> ============================================================
> >> ================
> >> See h5_test/test-suite.log
> >> Please report to support-netcdf at unidata.ucar.edu
> >> ============================================================
> >> ================
> >>
> >>
> >> On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
> >>
> >> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >>
> >> I forgot to attach my log file.
> >> Thanks!
> >>
> >>
> >> On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo
<jinwoong.yoo at gmail.com>
> >> <jinwoong.yoo at gmail.com>
> >> wrote:
> >>
> >>
> >> Hi,
> >> Thank you for your reply.
> >>
> >> I realized that I have to have netcdf4-c and netcdf4-cxx to
install
> >> MET-6.0.
> >> So far, I have compiled HDF5 following directions
> >> athttp://www.dtcenter.org/met/users/support/online_tutorial/
> >> METv6.0/tutorial.php?name=compilation&category=req_libs.
> >>
> >> I have built HDF5 successfully using the `--enable-hl` function
and I
> got
> >> hdf5_h1.1 in my target directory. Previously I got error
installing
> netcdf4
> >> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared" message (as
shown
> >> inhttps://www.unidata.ucar.edu/support/help/MailArchives/
> >> netcdf/msg13749.html).
> >>
> >> I am referring to unidata webpage for the compilation of netcdf4
> >> athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
> >> and_building_netcdf.html.
> >> But now I get an error with h5_test within the netcdf make check
and it
> >> fails.
> >> Attached please find configure and make log.
> >> Do you have any know-how to overcome this issue?
> >> Thank you very much in advance.
> >>
> >> Regards,
> >>
> >> Jinwoong Yoo
> >> Purdue Climate Change Research Center
> >>
> >> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
> >> <met_help at ucar.edu> <met_help at ucar.edu>
> >> wrote:
> >>
> >>
> >> Hello -
> >>
> >> Most of our team is out due to the Memorial Day holiday. We'll
have a
> >> look
> >> at your issue when the team is back sometime later this week.
> >>
> >> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
> >> <met_help at ucar.edu> <met_help at ucar.edu>
> >> wrote:
> >>
> >>
> >> Fri May 26 09:39:58 2017: Request 80647 was acted upon.
> >> Transaction: Ticket created by jinwoong.yoo at gmail.com
> >> Queue: met_help
> >> Subject: Error with Compiling MET-6.0
> >> Owner: Nobody
> >> Requestors: jinwoong.yoo at gmail.com
> >> Status: new
> >> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
> >
> >>
> >>
> >> Dear MET Help
> >>
> >> Hi.
> >> I am trying to compile MET-6.0 bugfixed version on a Linux
cluster
> >>
> >> (Redhat)
> >>
> >> at Purdue University.
> >> I am using a few system-wide libraries (e.g., netcdf-3.6.3, hdf5)
and I
> >> installed most of the other library myself. Also I set up all the
> >> environment variables required.
> >>
> >> # MET
> >>
> >> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
> >>
> >> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
> >>
> >> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
> >>
> >> export MET_UPP=/home/yoo108/UPPV3.1
> >>
> >> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
> >>
> >> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
> >>
> >> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
> >>
> >> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
> >>
> >> export MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
> >>
> >> export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
> >>
> >> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
> >>
> >>
> >>
> >> However, I got an error with the compilation of the MET-6.0 and
it
> >>
> >> failed.
> >>
> >> The error message reads as below:
> >>
> >> MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
> >> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
> >> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
> >>
> >> libvx_nc_util_a-nc_var_info.o
> >>
> >> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
> >>
> >> In file included from nc_var_info.cc(24):
> >>
> >> nc_utils.h(22): catastrophic error: cannot open source file
"netcdf"
> >>
> >> #include <netcdf>
> >>
> >> ^
> >>
> >>
> >> compilation aborted for nc_var_info.cc (code 4)
> >>
> >> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
> >>
> >> make[3]: Leaving directory
> >> `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
> >>
> >> make[2]: *** [install-recursive] Error 1
> >>
> >> make[2]: Leaving directory `/home/yoo108/build_MET/src/
> >> met-6.0/src/libcode'
> >>
> >> make[1]: *** [install-recursive] Error 1
> >>
> >> make[1]: Leaving directory `/home/yoo108/build_MET/src/met-
6.0/src'
> >>
> >> make: *** [install-recursive] Error 1
> >>
> >> ^C[1]+ Exit 2 make install &>make_install.log
> >>
> >>
> >> I wonder if this error is related with the 64 bit cluster while
MET
> >>
> >> wants
> >>
> >> 32 bit software or else.
> >>
> >> Your input will be highly appreciated.
> >>
> >> Thank you.
> >>
> >> Regards,
> >>
> >>
> >> Jinwoong Yoo
> >>
> >> Purdue Climate Change Research Center
> >>
> >>
>
>
>
------------------------------------------------
Subject: Re: [rt.rap.ucar.edu #80647] Error with Compiling MET-6.0
From: Howard Soh
Time: Tue May 30 16:21:19 2017
I'm glad to hear that you can build HDF5 and NetCDF4.
I appreciated your advice. We will review online tutorial and make it
clear.
Cheers,
Howard
FYI:
hdf5-1.8.17$ ./configure --help | grep enable-hl
--enable-hl Enable the high level library [default=yes]
hdf5-1.8.18$ ./configure --help | grep enable-hl
--enable-hl Enable the high level library [default=yes]
On 5/30/2017 2:12 PM, Jinwoong Yoo via RT wrote:
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>
> Hi Howard,
>
> I was able to compile HDF5, Netcdf4-C, and NetCDF-CXX successfully
finally.
> I happened to know that there were a few typos in the MET Online
Tutorial
> For METv6.0, which led into various confusions.
>
> In the "Compiling HDF5" section,
> I had to configure hdf5 with the "--enable-hl" option along with "
> *--with-zlib=${ZDIR}*".
>
>
> In the "Compiling NetCDF" section,
> both for NetCDF-C and NetCDF-CXX,
>
> LDFLAGS and CPPFLAGS directories should be assigned to HDF5
directory, not
> the NetCDF4 installation directory in
> "LDFLAGS=-L${MET_LIB_DIR}/lib CPPFLAGS=-I${MET_LIB_DIR}/include"
while the
> target directory in "--prefix=${MET_LIB_DIR}" should be netcdf4
directory.
>
> You might want to make changes for these error for other METv6.0
users on
> your webpage at "
>
http://www.dtcenter.org/met/users/support/online_tutorial/METv6.0/tutorial.php?name=compilation&category=req_libs
> ".
>
> Thank you.
> Regards,
>
> Jinwoong
>
>
>
>
>
>
>
>
>
> On Tue, May 30, 2017 at 3:18 PM, Howard Soh via RT
<met_help at ucar.edu>
> wrote:
>
>> Thank you, Jinwoong.
>>
>> Howard
>>
>> On 5/30/2017 12:33 PM, Jinwoong Yoo via RT wrote:
>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>
>>> Hi Howard,
>>>
>>> I contacted Unidata regarding the issue already.
>>> Attached please find the file, and see its contents below.
>>>
>>>
>>>
>>> ============================================
>>>
>>> netCDF 4.4.1.1: h5_test/test-suite.log
>>>
>>> ============================================
>>>
>>>
>>> # TOTAL: 26
>>>
>>> # PASS: 25
>>>
>>> # SKIP: 0
>>>
>>> # XFAIL: 0
>>>
>>> # FAIL: 1
>>>
>>> # XPASS: 0
>>>
>>> # ERROR: 0
>>>
>>>
>>> .. contents:: :depth: 2
>>>
>>>
>>> FAIL: tst_h_vars
>>>
>>> ================
>>>
>>>
>>>
>>> *** Checking HDF5 variable functions.
>>>
>>> *** Checking HDF5 boolen variables...ok.
>>>
>>> *** Checking HDF5 variable with unlimited dimension...ok.
>>>
>>> *** Checking HDF5 deflate filter setting and getting...Sorry!
Unexpected
>>> result, tst_h_vars.c, line: 230
>>>
>>> FAIL tst_h_vars (exit status: 2)
>>>
>>>
>>> Thank you.
>>>
>>> Regards,
>>>
>>>
>>> Jinwoong
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Tue, May 30, 2017 at 2:22 PM, Howard Soh via RT
<met_help at ucar.edu>
>>> wrote:
>>>
>>>> Hi Jinwoong.
>>>>
>>>> I am sorry to hear that you are still having difficulty with the
netcdf
>>>> library
>>>> files.
>>>> One unit test related with HDF5 was failed. Would you check
>>>> h5_test/test-suite.log
>>>> and contact Unidata?
>>>> The full path will be /home/yoo108/METwithGNU/src/
>> netcdf-c-4.4.1.1/h5_test
>>>> /test-suite.log.
>>>>
>>>> It would help to understand your problem if you send us
>>>> h5_test/test-suite.log.
>>>>
>>>> Cheers,
>>>> Howard
>>>>
>>>> FYI:
>>>>
>>>>
>>>> FAIL: tst_h_vars
>>>>
>>>> ============================================================
>>>> ================
>>>> Testsuite summary for netCDF 4.4.1.1
>>>> ============================================================
>>>> ================
>>>> # TOTAL: 26
>>>> # PASS: 25
>>>> # SKIP: 0
>>>> # XFAIL: 0
>>>> # FAIL: 1
>>>> # XPASS: 0
>>>> # ERROR: 0
>>>> ============================================================
>>>> ================
>>>> See h5_test/test-suite.log
>>>> Please report to support-netcdf at unidata.ucar.edu
>>>> ============================================================
>>>> ================
>>>>
>>>>
>>>> On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
>>>>
>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>>
>>>> I forgot to attach my log file.
>>>> Thanks!
>>>>
>>>>
>>>> On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo
<jinwoong.yoo at gmail.com>
>>>> <jinwoong.yoo at gmail.com>
>>>> wrote:
>>>>
>>>>
>>>> Hi,
>>>> Thank you for your reply.
>>>>
>>>> I realized that I have to have netcdf4-c and netcdf4-cxx to
install
>>>> MET-6.0.
>>>> So far, I have compiled HDF5 following directions
>>>> athttp://www.dtcenter.org/met/users/support/online_tutorial/
>>>> METv6.0/tutorial.php?name=compilation&category=req_libs.
>>>>
>>>> I have built HDF5 successfully using the `--enable-hl` function
and I
>> got
>>>> hdf5_h1.1 in my target directory. Previously I got error
installing
>> netcdf4
>>>> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared" message (as
shown
>>>> inhttps://www.unidata.ucar.edu/support/help/MailArchives/
>>>> netcdf/msg13749.html).
>>>>
>>>> I am referring to unidata webpage for the compilation of netcdf4
>>>> athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
>>>> and_building_netcdf.html.
>>>> But now I get an error with h5_test within the netcdf make check
and it
>>>> fails.
>>>> Attached please find configure and make log.
>>>> Do you have any know-how to overcome this issue?
>>>> Thank you very much in advance.
>>>>
>>>> Regards,
>>>>
>>>> Jinwoong Yoo
>>>> Purdue Climate Change Research Center
>>>>
>>>> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
>>>> <met_help at ucar.edu> <met_help at ucar.edu>
>>>> wrote:
>>>>
>>>>
>>>> Hello -
>>>>
>>>> Most of our team is out due to the Memorial Day holiday. We'll
have a
>>>> look
>>>> at your issue when the team is back sometime later this week.
>>>>
>>>> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
>>>> <met_help at ucar.edu> <met_help at ucar.edu>
>>>> wrote:
>>>>
>>>>
>>>> Fri May 26 09:39:58 2017: Request 80647 was acted upon.
>>>> Transaction: Ticket created by jinwoong.yoo at gmail.com
>>>> Queue: met_help
>>>> Subject: Error with Compiling MET-6.0
>>>> Owner: Nobody
>>>> Requestors: jinwoong.yoo at gmail.com
>>>> Status: new
>>>> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>>>>
>>>> Dear MET Help
>>>>
>>>> Hi.
>>>> I am trying to compile MET-6.0 bugfixed version on a Linux
cluster
>>>>
>>>> (Redhat)
>>>>
>>>> at Purdue University.
>>>> I am using a few system-wide libraries (e.g., netcdf-3.6.3, hdf5)
and I
>>>> installed most of the other library myself. Also I set up all the
>>>> environment variables required.
>>>>
>>>> # MET
>>>>
>>>> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
>>>>
>>>> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
>>>>
>>>> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
>>>>
>>>> export MET_UPP=/home/yoo108/UPPV3.1
>>>>
>>>> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
>>>>
>>>> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
>>>>
>>>> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
>>>>
>>>> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
>>>>
>>>> export MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
>>>>
>>>> export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
>>>>
>>>> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
>>>>
>>>>
>>>>
>>>> However, I got an error with the compilation of the MET-6.0 and
it
>>>>
>>>> failed.
>>>>
>>>> The error message reads as below:
>>>>
>>>> MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
>>>> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
>>>> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
>>>>
>>>> libvx_nc_util_a-nc_var_info.o
>>>>
>>>> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
>>>>
>>>> In file included from nc_var_info.cc(24):
>>>>
>>>> nc_utils.h(22): catastrophic error: cannot open source file
"netcdf"
>>>>
>>>> #include <netcdf>
>>>>
>>>> ^
>>>>
>>>>
>>>> compilation aborted for nc_var_info.cc (code 4)
>>>>
>>>> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
>>>>
>>>> make[3]: Leaving directory
>>>> `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
>>>>
>>>> make[2]: *** [install-recursive] Error 1
>>>>
>>>> make[2]: Leaving directory `/home/yoo108/build_MET/src/
>>>> met-6.0/src/libcode'
>>>>
>>>> make[1]: *** [install-recursive] Error 1
>>>>
>>>> make[1]: Leaving directory `/home/yoo108/build_MET/src/met-
6.0/src'
>>>>
>>>> make: *** [install-recursive] Error 1
>>>>
>>>> ^C[1]+ Exit 2 make install &>make_install.log
>>>>
>>>>
>>>> I wonder if this error is related with the 64 bit cluster while
MET
>>>>
>>>> wants
>>>>
>>>> 32 bit software or else.
>>>>
>>>> Your input will be highly appreciated.
>>>>
>>>> Thank you.
>>>>
>>>> Regards,
>>>>
>>>>
>>>> Jinwoong Yoo
>>>>
>>>> Purdue Climate Change Research Center
>>>>
>>>>
>>
>>
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Jinwoong Yoo
Time: Wed May 31 08:03:57 2017
Hi Howard,
Although, after compiling of all the dependency libraries,
I am getting error with installing the MET.
I set all the environment libraries as directed in the online
tutorial.
But it seems the installer cannot find hdf.h file.
Please see error message below:
*lidar2nc.cc:69:17:* *fatal error: *hdf.h: No such file or directory
compilation terminated.
make[5]: *** [lidar2nc-lidar2nc.o] Error 1
make[5]: Leaving directory
`/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools/other/lidar2nc'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory
`/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools/other'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/yoo108/METwithGNU/src/met-
6.0_bugfix/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/yoo108/METwithGNU/src/met-
6.0_bugfix'
make: *** [all] Error 2
Do you have any idea?
Thank you.
Regards,
Jinwoong
On Tue, May 30, 2017 at 6:21 PM, Howard Soh via RT <met_help at ucar.edu>
wrote:
> I'm glad to hear that you can build HDF5 and NetCDF4.
>
> I appreciated your advice. We will review online tutorial and make
it
> clear.
>
> Cheers,
> Howard
>
> FYI:
> hdf5-1.8.17$ ./configure --help | grep enable-hl
> --enable-hl Enable the high level library
[default=yes]
>
> hdf5-1.8.18$ ./configure --help | grep enable-hl
> --enable-hl Enable the high level library
[default=yes]
>
>
>
> On 5/30/2017 2:12 PM, Jinwoong Yoo via RT wrote:
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >
> > Hi Howard,
> >
> > I was able to compile HDF5, Netcdf4-C, and NetCDF-CXX successfully
> finally.
> > I happened to know that there were a few typos in the MET Online
Tutorial
> > For METv6.0, which led into various confusions.
> >
> > In the "Compiling HDF5" section,
> > I had to configure hdf5 with the "--enable-hl" option along with "
> > *--with-zlib=${ZDIR}*".
> >
> >
> > In the "Compiling NetCDF" section,
> > both for NetCDF-C and NetCDF-CXX,
> >
> > LDFLAGS and CPPFLAGS directories should be assigned to HDF5
directory,
> not
> > the NetCDF4 installation directory in
> > "LDFLAGS=-L${MET_LIB_DIR}/lib CPPFLAGS=-I${MET_LIB_DIR}/include"
while
> the
> > target directory in "--prefix=${MET_LIB_DIR}" should be netcdf4
> directory.
> >
> > You might want to make changes for these error for other METv6.0
users on
> > your webpage at "
> > http://www.dtcenter.org/met/users/support/online_tutorial/
> METv6.0/tutorial.php?name=compilation&category=req_libs
> > ".
> >
> > Thank you.
> > Regards,
> >
> > Jinwoong
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > On Tue, May 30, 2017 at 3:18 PM, Howard Soh via RT
<met_help at ucar.edu>
> > wrote:
> >
> >> Thank you, Jinwoong.
> >>
> >> Howard
> >>
> >> On 5/30/2017 12:33 PM, Jinwoong Yoo via RT wrote:
> >>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >>>
> >>> Hi Howard,
> >>>
> >>> I contacted Unidata regarding the issue already.
> >>> Attached please find the file, and see its contents below.
> >>>
> >>>
> >>>
> >>> ============================================
> >>>
> >>> netCDF 4.4.1.1: h5_test/test-suite.log
> >>>
> >>> ============================================
> >>>
> >>>
> >>> # TOTAL: 26
> >>>
> >>> # PASS: 25
> >>>
> >>> # SKIP: 0
> >>>
> >>> # XFAIL: 0
> >>>
> >>> # FAIL: 1
> >>>
> >>> # XPASS: 0
> >>>
> >>> # ERROR: 0
> >>>
> >>>
> >>> .. contents:: :depth: 2
> >>>
> >>>
> >>> FAIL: tst_h_vars
> >>>
> >>> ================
> >>>
> >>>
> >>>
> >>> *** Checking HDF5 variable functions.
> >>>
> >>> *** Checking HDF5 boolen variables...ok.
> >>>
> >>> *** Checking HDF5 variable with unlimited dimension...ok.
> >>>
> >>> *** Checking HDF5 deflate filter setting and getting...Sorry!
> Unexpected
> >>> result, tst_h_vars.c, line: 230
> >>>
> >>> FAIL tst_h_vars (exit status: 2)
> >>>
> >>>
> >>> Thank you.
> >>>
> >>> Regards,
> >>>
> >>>
> >>> Jinwoong
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Tue, May 30, 2017 at 2:22 PM, Howard Soh via RT
<met_help at ucar.edu>
> >>> wrote:
> >>>
> >>>> Hi Jinwoong.
> >>>>
> >>>> I am sorry to hear that you are still having difficulty with
the
> netcdf
> >>>> library
> >>>> files.
> >>>> One unit test related with HDF5 was failed. Would you check
> >>>> h5_test/test-suite.log
> >>>> and contact Unidata?
> >>>> The full path will be /home/yoo108/METwithGNU/src/
> >> netcdf-c-4.4.1.1/h5_test
> >>>> /test-suite.log.
> >>>>
> >>>> It would help to understand your problem if you send us
> >>>> h5_test/test-suite.log.
> >>>>
> >>>> Cheers,
> >>>> Howard
> >>>>
> >>>> FYI:
> >>>>
> >>>>
> >>>> FAIL: tst_h_vars
> >>>>
> >>>> ============================================================
> >>>> ================
> >>>> Testsuite summary for netCDF 4.4.1.1
> >>>> ============================================================
> >>>> ================
> >>>> # TOTAL: 26
> >>>> # PASS: 25
> >>>> # SKIP: 0
> >>>> # XFAIL: 0
> >>>> # FAIL: 1
> >>>> # XPASS: 0
> >>>> # ERROR: 0
> >>>> ============================================================
> >>>> ================
> >>>> See h5_test/test-suite.log
> >>>> Please report to support-netcdf at unidata.ucar.edu
> >>>> ============================================================
> >>>> ================
> >>>>
> >>>>
> >>>> On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
> >>>>
> >>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >>>>
> >>>> I forgot to attach my log file.
> >>>> Thanks!
> >>>>
> >>>>
> >>>> On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo
<jinwoong.yoo at gmail.com
> >
> >>>> <jinwoong.yoo at gmail.com>
> >>>> wrote:
> >>>>
> >>>>
> >>>> Hi,
> >>>> Thank you for your reply.
> >>>>
> >>>> I realized that I have to have netcdf4-c and netcdf4-cxx to
install
> >>>> MET-6.0.
> >>>> So far, I have compiled HDF5 following directions
> >>>> athttp://www.dtcenter.org/met/users/support/online_tutorial/
> >>>> METv6.0/tutorial.php?name=compilation&category=req_libs.
> >>>>
> >>>> I have built HDF5 successfully using the `--enable-hl` function
and I
> >> got
> >>>> hdf5_h1.1 in my target directory. Previously I got error
installing
> >> netcdf4
> >>>> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared" message
(as shown
> >>>> inhttps://www.unidata.ucar.edu/support/help/MailArchives/
> >>>> netcdf/msg13749.html).
> >>>>
> >>>> I am referring to unidata webpage for the compilation of
netcdf4
> >>>> athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
> >>>> and_building_netcdf.html.
> >>>> But now I get an error with h5_test within the netcdf make
check and
> it
> >>>> fails.
> >>>> Attached please find configure and make log.
> >>>> Do you have any know-how to overcome this issue?
> >>>> Thank you very much in advance.
> >>>>
> >>>> Regards,
> >>>>
> >>>> Jinwoong Yoo
> >>>> Purdue Climate Change Research Center
> >>>>
> >>>> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
> >>>> <met_help at ucar.edu> <met_help at ucar.edu>
> >>>> wrote:
> >>>>
> >>>>
> >>>> Hello -
> >>>>
> >>>> Most of our team is out due to the Memorial Day holiday. We'll
have a
> >>>> look
> >>>> at your issue when the team is back sometime later this week.
> >>>>
> >>>> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
> >>>> <met_help at ucar.edu> <met_help at ucar.edu>
> >>>> wrote:
> >>>>
> >>>>
> >>>> Fri May 26 09:39:58 2017: Request 80647 was acted upon.
> >>>> Transaction: Ticket created by jinwoong.yoo at gmail.com
> >>>> Queue: met_help
> >>>> Subject: Error with Compiling MET-6.0
> >>>> Owner: Nobody
> >>>> Requestors: jinwoong.yoo at gmail.com
> >>>> Status: new
> >>>> Ticket <URL: https://rt.rap.ucar.edu/rt/
> Ticket/Display.html?id=80647
> >>>>
> >>>> Dear MET Help
> >>>>
> >>>> Hi.
> >>>> I am trying to compile MET-6.0 bugfixed version on a Linux
cluster
> >>>>
> >>>> (Redhat)
> >>>>
> >>>> at Purdue University.
> >>>> I am using a few system-wide libraries (e.g., netcdf-3.6.3,
hdf5) and
> I
> >>>> installed most of the other library myself. Also I set up all
the
> >>>> environment variables required.
> >>>>
> >>>> # MET
> >>>>
> >>>> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
> >>>>
> >>>> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
> >>>>
> >>>> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
> >>>>
> >>>> export MET_UPP=/home/yoo108/UPPV3.1
> >>>>
> >>>> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
> >>>>
> >>>> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
> >>>>
> >>>> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
> >>>>
> >>>> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
> >>>>
> >>>> export MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
> >>>>
> >>>> export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
> >>>>
> >>>> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
> >>>>
> >>>>
> >>>>
> >>>> However, I got an error with the compilation of the MET-6.0 and
it
> >>>>
> >>>> failed.
> >>>>
> >>>> The error message reads as below:
> >>>>
> >>>> MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__ -MT
> >>>> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
> >>>> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
> >>>>
> >>>> libvx_nc_util_a-nc_var_info.o
> >>>>
> >>>> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
> >>>>
> >>>> In file included from nc_var_info.cc(24):
> >>>>
> >>>> nc_utils.h(22): catastrophic error: cannot open source file
"netcdf"
> >>>>
> >>>> #include <netcdf>
> >>>>
> >>>> ^
> >>>>
> >>>>
> >>>> compilation aborted for nc_var_info.cc (code 4)
> >>>>
> >>>> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
> >>>>
> >>>> make[3]: Leaving directory
> >>>> `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
> >>>>
> >>>> make[2]: *** [install-recursive] Error 1
> >>>>
> >>>> make[2]: Leaving directory `/home/yoo108/build_MET/src/
> >>>> met-6.0/src/libcode'
> >>>>
> >>>> make[1]: *** [install-recursive] Error 1
> >>>>
> >>>> make[1]: Leaving directory `/home/yoo108/build_MET/src/met-
6.0/src'
> >>>>
> >>>> make: *** [install-recursive] Error 1
> >>>>
> >>>> ^C[1]+ Exit 2 make install &>make_install.log
> >>>>
> >>>>
> >>>> I wonder if this error is related with the 64 bit cluster while
MET
> >>>>
> >>>> wants
> >>>>
> >>>> 32 bit software or else.
> >>>>
> >>>> Your input will be highly appreciated.
> >>>>
> >>>> Thank you.
> >>>>
> >>>> Regards,
> >>>>
> >>>>
> >>>> Jinwoong Yoo
> >>>>
> >>>> Purdue Climate Change Research Center
> >>>>
> >>>>
> >>
> >>
>
>
>
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Howard Soh
Time: Wed May 31 09:58:52 2017
MET still uses HDF4 library instead of HDF5 because of another
dependency,
HDF-EOS.
Note: hdf.h is for HDF4 and hdf5.h is for HDF5
NetCDF4 requires HDF5 on building and running. Once NetCDF library is
built, HDF5 is not required to build MET, but required to run MET.
Please set *$MET_HDF* to point to the HDF4 directory.
Cheers,
Howard
On Wed, May 31, 2017 at 8:03 AM, Jinwoong Yoo via RT
<met_help at ucar.edu>
wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>
> Hi Howard,
> Although, after compiling of all the dependency libraries,
> I am getting error with installing the MET.
>
> I set all the environment libraries as directed in the online
tutorial.
> But it seems the installer cannot find hdf.h file.
> Please see error message below:
>
> *lidar2nc.cc:69:17:* *fatal error: *hdf.h: No such file or directory
>
> compilation terminated.
>
> make[5]: *** [lidar2nc-lidar2nc.o] Error 1
>
> make[5]: Leaving directory
> `/home/yoo108/METwithGNU/src/met-
6.0_bugfix/src/tools/other/lidar2nc'
>
> make[4]: *** [all-recursive] Error 1
>
> make[4]: Leaving directory
> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools/other'
>
> make[3]: *** [all-recursive] Error 1
>
> make[3]: Leaving directory
> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools'
>
> make[2]: *** [all-recursive] Error 1
>
> make[2]: Leaving directory `/home/yoo108/METwithGNU/src/
> met-6.0_bugfix/src'
>
> make[1]: *** [all-recursive] Error 1
>
> make[1]: Leaving directory `/home/yoo108/METwithGNU/src/met-
6.0_bugfix'
>
> make: *** [all] Error 2
>
> Do you have any idea?
> Thank you.
>
> Regards,
>
> Jinwoong
>
> On Tue, May 30, 2017 at 6:21 PM, Howard Soh via RT
<met_help at ucar.edu>
> wrote:
>
> > I'm glad to hear that you can build HDF5 and NetCDF4.
> >
> > I appreciated your advice. We will review online tutorial and make
it
> > clear.
> >
> > Cheers,
> > Howard
> >
> > FYI:
> > hdf5-1.8.17$ ./configure --help | grep enable-hl
> > --enable-hl Enable the high level library
[default=yes]
> >
> > hdf5-1.8.18$ ./configure --help | grep enable-hl
> > --enable-hl Enable the high level library
[default=yes]
> >
> >
> >
> > On 5/30/2017 2:12 PM, Jinwoong Yoo via RT wrote:
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> > >
> > > Hi Howard,
> > >
> > > I was able to compile HDF5, Netcdf4-C, and NetCDF-CXX
successfully
> > finally.
> > > I happened to know that there were a few typos in the MET Online
> Tutorial
> > > For METv6.0, which led into various confusions.
> > >
> > > In the "Compiling HDF5" section,
> > > I had to configure hdf5 with the "--enable-hl" option along with
"
> > > *--with-zlib=${ZDIR}*".
> > >
> > >
> > > In the "Compiling NetCDF" section,
> > > both for NetCDF-C and NetCDF-CXX,
> > >
> > > LDFLAGS and CPPFLAGS directories should be assigned to HDF5
directory,
> > not
> > > the NetCDF4 installation directory in
> > > "LDFLAGS=-L${MET_LIB_DIR}/lib CPPFLAGS=-I${MET_LIB_DIR}/include"
while
> > the
> > > target directory in "--prefix=${MET_LIB_DIR}" should be netcdf4
> > directory.
> > >
> > > You might want to make changes for these error for other METv6.0
users
> on
> > > your webpage at "
> > > http://www.dtcenter.org/met/users/support/online_tutorial/
> > METv6.0/tutorial.php?name=compilation&category=req_libs
> > > ".
> > >
> > > Thank you.
> > > Regards,
> > >
> > > Jinwoong
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > On Tue, May 30, 2017 at 3:18 PM, Howard Soh via RT
<met_help at ucar.edu>
> > > wrote:
> > >
> > >> Thank you, Jinwoong.
> > >>
> > >> Howard
> > >>
> > >> On 5/30/2017 12:33 PM, Jinwoong Yoo via RT wrote:
> > >>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>
> > >>>
> > >>> Hi Howard,
> > >>>
> > >>> I contacted Unidata regarding the issue already.
> > >>> Attached please find the file, and see its contents below.
> > >>>
> > >>>
> > >>>
> > >>> ============================================
> > >>>
> > >>> netCDF 4.4.1.1: h5_test/test-suite.log
> > >>>
> > >>> ============================================
> > >>>
> > >>>
> > >>> # TOTAL: 26
> > >>>
> > >>> # PASS: 25
> > >>>
> > >>> # SKIP: 0
> > >>>
> > >>> # XFAIL: 0
> > >>>
> > >>> # FAIL: 1
> > >>>
> > >>> # XPASS: 0
> > >>>
> > >>> # ERROR: 0
> > >>>
> > >>>
> > >>> .. contents:: :depth: 2
> > >>>
> > >>>
> > >>> FAIL: tst_h_vars
> > >>>
> > >>> ================
> > >>>
> > >>>
> > >>>
> > >>> *** Checking HDF5 variable functions.
> > >>>
> > >>> *** Checking HDF5 boolen variables...ok.
> > >>>
> > >>> *** Checking HDF5 variable with unlimited dimension...ok.
> > >>>
> > >>> *** Checking HDF5 deflate filter setting and getting...Sorry!
> > Unexpected
> > >>> result, tst_h_vars.c, line: 230
> > >>>
> > >>> FAIL tst_h_vars (exit status: 2)
> > >>>
> > >>>
> > >>> Thank you.
> > >>>
> > >>> Regards,
> > >>>
> > >>>
> > >>> Jinwoong
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>> On Tue, May 30, 2017 at 2:22 PM, Howard Soh via RT <
> met_help at ucar.edu>
> > >>> wrote:
> > >>>
> > >>>> Hi Jinwoong.
> > >>>>
> > >>>> I am sorry to hear that you are still having difficulty with
the
> > netcdf
> > >>>> library
> > >>>> files.
> > >>>> One unit test related with HDF5 was failed. Would you check
> > >>>> h5_test/test-suite.log
> > >>>> and contact Unidata?
> > >>>> The full path will be /home/yoo108/METwithGNU/src/
> > >> netcdf-c-4.4.1.1/h5_test
> > >>>> /test-suite.log.
> > >>>>
> > >>>> It would help to understand your problem if you send us
> > >>>> h5_test/test-suite.log.
> > >>>>
> > >>>> Cheers,
> > >>>> Howard
> > >>>>
> > >>>> FYI:
> > >>>>
> > >>>>
> > >>>> FAIL: tst_h_vars
> > >>>>
> > >>>> ============================================================
> > >>>> ================
> > >>>> Testsuite summary for netCDF 4.4.1.1
> > >>>> ============================================================
> > >>>> ================
> > >>>> # TOTAL: 26
> > >>>> # PASS: 25
> > >>>> # SKIP: 0
> > >>>> # XFAIL: 0
> > >>>> # FAIL: 1
> > >>>> # XPASS: 0
> > >>>> # ERROR: 0
> > >>>> ============================================================
> > >>>> ================
> > >>>> See h5_test/test-suite.log
> > >>>> Please report to support-netcdf at unidata.ucar.edu
> > >>>> ============================================================
> > >>>> ================
> > >>>>
> > >>>>
> > >>>> On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
> > >>>>
> > >>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>
> > >>>>
> > >>>> I forgot to attach my log file.
> > >>>> Thanks!
> > >>>>
> > >>>>
> > >>>> On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo <
> jinwoong.yoo at gmail.com
> > >
> > >>>> <jinwoong.yoo at gmail.com>
> > >>>> wrote:
> > >>>>
> > >>>>
> > >>>> Hi,
> > >>>> Thank you for your reply.
> > >>>>
> > >>>> I realized that I have to have netcdf4-c and netcdf4-cxx to
install
> > >>>> MET-6.0.
> > >>>> So far, I have compiled HDF5 following directions
> > >>>> athttp://www.dtcenter.org/met/users/support/online_tutorial/
> > >>>> METv6.0/tutorial.php?name=compilation&category=req_libs.
> > >>>>
> > >>>> I have built HDF5 successfully using the `--enable-hl`
function and
> I
> > >> got
> > >>>> hdf5_h1.1 in my target directory. Previously I got error
installing
> > >> netcdf4
> > >>>> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared" message
(as
> shown
> > >>>> inhttps://www.unidata.ucar.edu/support/help/MailArchives/
> > >>>> netcdf/msg13749.html).
> > >>>>
> > >>>> I am referring to unidata webpage for the compilation of
netcdf4
> > >>>> athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
> > >>>> and_building_netcdf.html.
> > >>>> But now I get an error with h5_test within the netcdf make
check and
> > it
> > >>>> fails.
> > >>>> Attached please find configure and make log.
> > >>>> Do you have any know-how to overcome this issue?
> > >>>> Thank you very much in advance.
> > >>>>
> > >>>> Regards,
> > >>>>
> > >>>> Jinwoong Yoo
> > >>>> Purdue Climate Change Research Center
> > >>>>
> > >>>> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
> > >>>> <met_help at ucar.edu> <met_help at ucar.edu>
> > >>>> wrote:
> > >>>>
> > >>>>
> > >>>> Hello -
> > >>>>
> > >>>> Most of our team is out due to the Memorial Day holiday.
We'll
> have a
> > >>>> look
> > >>>> at your issue when the team is back sometime later this week.
> > >>>>
> > >>>> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
> > >>>> <met_help at ucar.edu> <met_help at ucar.edu>
> > >>>> wrote:
> > >>>>
> > >>>>
> > >>>> Fri May 26 09:39:58 2017: Request 80647 was acted upon.
> > >>>> Transaction: Ticket created by jinwoong.yoo at gmail.com
> > >>>> Queue: met_help
> > >>>> Subject: Error with Compiling MET-6.0
> > >>>> Owner: Nobody
> > >>>> Requestors: jinwoong.yoo at gmail.com
> > >>>> Status: new
> > >>>> Ticket <URL: https://rt.rap.ucar.edu/rt/
> > Ticket/Display.html?id=80647
> > >>>>
> > >>>> Dear MET Help
> > >>>>
> > >>>> Hi.
> > >>>> I am trying to compile MET-6.0 bugfixed version on a Linux
cluster
> > >>>>
> > >>>> (Redhat)
> > >>>>
> > >>>> at Purdue University.
> > >>>> I am using a few system-wide libraries (e.g., netcdf-3.6.3,
hdf5)
> and
> > I
> > >>>> installed most of the other library myself. Also I set up all
the
> > >>>> environment variables required.
> > >>>>
> > >>>> # MET
> > >>>>
> > >>>> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
> > >>>>
> > >>>> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
> > >>>>
> > >>>> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
> > >>>>
> > >>>> export MET_UPP=/home/yoo108/UPPV3.1
> > >>>>
> > >>>> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
> > >>>>
> > >>>> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
> > >>>>
> > >>>> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
> > >>>>
> > >>>> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
> > >>>>
> > >>>> export
MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
> > >>>>
> > >>>> export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
> > >>>>
> > >>>> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
> > >>>>
> > >>>>
> > >>>>
> > >>>> However, I got an error with the compilation of the MET-6.0
and it
> > >>>>
> > >>>> failed.
> > >>>>
> > >>>> The error message reads as below:
> > >>>>
> > >>>> MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__
-MT
> > >>>> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
> > >>>> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
> > >>>>
> > >>>> libvx_nc_util_a-nc_var_info.o
> > >>>>
> > >>>> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
> > >>>>
> > >>>> In file included from nc_var_info.cc(24):
> > >>>>
> > >>>> nc_utils.h(22): catastrophic error: cannot open source file
"netcdf"
> > >>>>
> > >>>> #include <netcdf>
> > >>>>
> > >>>> ^
> > >>>>
> > >>>>
> > >>>> compilation aborted for nc_var_info.cc (code 4)
> > >>>>
> > >>>> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
> > >>>>
> > >>>> make[3]: Leaving directory
> > >>>> `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
> > >>>>
> > >>>> make[2]: *** [install-recursive] Error 1
> > >>>>
> > >>>> make[2]: Leaving directory `/home/yoo108/build_MET/src/
> > >>>> met-6.0/src/libcode'
> > >>>>
> > >>>> make[1]: *** [install-recursive] Error 1
> > >>>>
> > >>>> make[1]: Leaving directory `/home/yoo108/build_MET/src/met-
6.0/src'
> > >>>>
> > >>>> make: *** [install-recursive] Error 1
> > >>>>
> > >>>> ^C[1]+ Exit 2 make install
&>make_install.log
> > >>>>
> > >>>>
> > >>>> I wonder if this error is related with the 64 bit cluster
while MET
> > >>>>
> > >>>> wants
> > >>>>
> > >>>> 32 bit software or else.
> > >>>>
> > >>>> Your input will be highly appreciated.
> > >>>>
> > >>>> Thank you.
> > >>>>
> > >>>> Regards,
> > >>>>
> > >>>>
> > >>>> Jinwoong Yoo
> > >>>>
> > >>>> Purdue Climate Change Research Center
> > >>>>
> > >>>>
> > >>
> > >>
> >
> >
> >
>
>
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Jinwoong Yoo
Time: Wed May 31 11:45:55 2017
Hi Howard,
Thank you much for your note.
Finally I was able to complete the installation of MET-6.0.
But I should let you know that I encountered several errors probably
due to
the outdated make file for the new include directory structures of
recent
versions of HDF-EOS2, Cairo, and Freetype.
Thank you.
Regards,
Jinwoong
On Wed, May 31, 2017 at 11:58 AM, Howard Soh via RT
<met_help at ucar.edu>
wrote:
> MET still uses HDF4 library instead of HDF5 because of another
dependency,
> HDF-EOS.
>
> Note: hdf.h is for HDF4 and hdf5.h is for HDF5
>
> NetCDF4 requires HDF5 on building and running. Once NetCDF library
is
> built, HDF5 is not required to build MET, but required to run MET.
>
> Please set *$MET_HDF* to point to the HDF4 directory.
>
> Cheers,
> Howard
>
>
> On Wed, May 31, 2017 at 8:03 AM, Jinwoong Yoo via RT
<met_help at ucar.edu>
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >
> > Hi Howard,
> > Although, after compiling of all the dependency libraries,
> > I am getting error with installing the MET.
> >
> > I set all the environment libraries as directed in the online
tutorial.
> > But it seems the installer cannot find hdf.h file.
> > Please see error message below:
> >
> > *lidar2nc.cc:69:17:* *fatal error: *hdf.h: No such file or
directory
> >
> > compilation terminated.
> >
> > make[5]: *** [lidar2nc-lidar2nc.o] Error 1
> >
> > make[5]: Leaving directory
> > `/home/yoo108/METwithGNU/src/met-
6.0_bugfix/src/tools/other/lidar2nc'
> >
> > make[4]: *** [all-recursive] Error 1
> >
> > make[4]: Leaving directory
> > `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools/other'
> >
> > make[3]: *** [all-recursive] Error 1
> >
> > make[3]: Leaving directory
> > `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools'
> >
> > make[2]: *** [all-recursive] Error 1
> >
> > make[2]: Leaving directory `/home/yoo108/METwithGNU/src/
> > met-6.0_bugfix/src'
> >
> > make[1]: *** [all-recursive] Error 1
> >
> > make[1]: Leaving directory `/home/yoo108/METwithGNU/src/met-
6.0_bugfix'
> >
> > make: *** [all] Error 2
> >
> > Do you have any idea?
> > Thank you.
> >
> > Regards,
> >
> > Jinwoong
> >
> > On Tue, May 30, 2017 at 6:21 PM, Howard Soh via RT
<met_help at ucar.edu>
> > wrote:
> >
> > > I'm glad to hear that you can build HDF5 and NetCDF4.
> > >
> > > I appreciated your advice. We will review online tutorial and
make it
> > > clear.
> > >
> > > Cheers,
> > > Howard
> > >
> > > FYI:
> > > hdf5-1.8.17$ ./configure --help | grep enable-hl
> > > --enable-hl Enable the high level library
[default=yes]
> > >
> > > hdf5-1.8.18$ ./configure --help | grep enable-hl
> > > --enable-hl Enable the high level library
[default=yes]
> > >
> > >
> > >
> > > On 5/30/2017 2:12 PM, Jinwoong Yoo via RT wrote:
> > > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>
> > > >
> > > > Hi Howard,
> > > >
> > > > I was able to compile HDF5, Netcdf4-C, and NetCDF-CXX
successfully
> > > finally.
> > > > I happened to know that there were a few typos in the MET
Online
> > Tutorial
> > > > For METv6.0, which led into various confusions.
> > > >
> > > > In the "Compiling HDF5" section,
> > > > I had to configure hdf5 with the "--enable-hl" option along
with "
> > > > *--with-zlib=${ZDIR}*".
> > > >
> > > >
> > > > In the "Compiling NetCDF" section,
> > > > both for NetCDF-C and NetCDF-CXX,
> > > >
> > > > LDFLAGS and CPPFLAGS directories should be assigned to HDF5
> directory,
> > > not
> > > > the NetCDF4 installation directory in
> > > > "LDFLAGS=-L${MET_LIB_DIR}/lib CPPFLAGS=-
I${MET_LIB_DIR}/include"
> while
> > > the
> > > > target directory in "--prefix=${MET_LIB_DIR}" should be
netcdf4
> > > directory.
> > > >
> > > > You might want to make changes for these error for other
METv6.0
> users
> > on
> > > > your webpage at "
> > > > http://www.dtcenter.org/met/users/support/online_tutorial/
> > > METv6.0/tutorial.php?name=compilation&category=req_libs
> > > > ".
> > > >
> > > > Thank you.
> > > > Regards,
> > > >
> > > > Jinwoong
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On Tue, May 30, 2017 at 3:18 PM, Howard Soh via RT <
> met_help at ucar.edu>
> > > > wrote:
> > > >
> > > >> Thank you, Jinwoong.
> > > >>
> > > >> Howard
> > > >>
> > > >> On 5/30/2017 12:33 PM, Jinwoong Yoo via RT wrote:
> > > >>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> > > >>>
> > > >>> Hi Howard,
> > > >>>
> > > >>> I contacted Unidata regarding the issue already.
> > > >>> Attached please find the file, and see its contents below.
> > > >>>
> > > >>>
> > > >>>
> > > >>> ============================================
> > > >>>
> > > >>> netCDF 4.4.1.1: h5_test/test-suite.log
> > > >>>
> > > >>> ============================================
> > > >>>
> > > >>>
> > > >>> # TOTAL: 26
> > > >>>
> > > >>> # PASS: 25
> > > >>>
> > > >>> # SKIP: 0
> > > >>>
> > > >>> # XFAIL: 0
> > > >>>
> > > >>> # FAIL: 1
> > > >>>
> > > >>> # XPASS: 0
> > > >>>
> > > >>> # ERROR: 0
> > > >>>
> > > >>>
> > > >>> .. contents:: :depth: 2
> > > >>>
> > > >>>
> > > >>> FAIL: tst_h_vars
> > > >>>
> > > >>> ================
> > > >>>
> > > >>>
> > > >>>
> > > >>> *** Checking HDF5 variable functions.
> > > >>>
> > > >>> *** Checking HDF5 boolen variables...ok.
> > > >>>
> > > >>> *** Checking HDF5 variable with unlimited dimension...ok.
> > > >>>
> > > >>> *** Checking HDF5 deflate filter setting and
getting...Sorry!
> > > Unexpected
> > > >>> result, tst_h_vars.c, line: 230
> > > >>>
> > > >>> FAIL tst_h_vars (exit status: 2)
> > > >>>
> > > >>>
> > > >>> Thank you.
> > > >>>
> > > >>> Regards,
> > > >>>
> > > >>>
> > > >>> Jinwoong
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>> On Tue, May 30, 2017 at 2:22 PM, Howard Soh via RT <
> > met_help at ucar.edu>
> > > >>> wrote:
> > > >>>
> > > >>>> Hi Jinwoong.
> > > >>>>
> > > >>>> I am sorry to hear that you are still having difficulty
with the
> > > netcdf
> > > >>>> library
> > > >>>> files.
> > > >>>> One unit test related with HDF5 was failed. Would you check
> > > >>>> h5_test/test-suite.log
> > > >>>> and contact Unidata?
> > > >>>> The full path will be /home/yoo108/METwithGNU/src/
> > > >> netcdf-c-4.4.1.1/h5_test
> > > >>>> /test-suite.log.
> > > >>>>
> > > >>>> It would help to understand your problem if you send us
> > > >>>> h5_test/test-suite.log.
> > > >>>>
> > > >>>> Cheers,
> > > >>>> Howard
> > > >>>>
> > > >>>> FYI:
> > > >>>>
> > > >>>>
> > > >>>> FAIL: tst_h_vars
> > > >>>>
> > > >>>>
============================================================
> > > >>>> ================
> > > >>>> Testsuite summary for netCDF 4.4.1.1
> > > >>>>
============================================================
> > > >>>> ================
> > > >>>> # TOTAL: 26
> > > >>>> # PASS: 25
> > > >>>> # SKIP: 0
> > > >>>> # XFAIL: 0
> > > >>>> # FAIL: 1
> > > >>>> # XPASS: 0
> > > >>>> # ERROR: 0
> > > >>>>
============================================================
> > > >>>> ================
> > > >>>> See h5_test/test-suite.log
> > > >>>> Please report to support-netcdf at unidata.ucar.edu
> > > >>>>
============================================================
> > > >>>> ================
> > > >>>>
> > > >>>>
> > > >>>> On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
> > > >>>>
> > > >>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> > > >>>>
> > > >>>> I forgot to attach my log file.
> > > >>>> Thanks!
> > > >>>>
> > > >>>>
> > > >>>> On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo <
> > jinwoong.yoo at gmail.com
> > > >
> > > >>>> <jinwoong.yoo at gmail.com>
> > > >>>> wrote:
> > > >>>>
> > > >>>>
> > > >>>> Hi,
> > > >>>> Thank you for your reply.
> > > >>>>
> > > >>>> I realized that I have to have netcdf4-c and netcdf4-cxx to
> install
> > > >>>> MET-6.0.
> > > >>>> So far, I have compiled HDF5 following directions
> > > >>>>
athttp://www.dtcenter.org/met/users/support/online_tutorial/
> > > >>>> METv6.0/tutorial.php?name=compilation&category=req_libs.
> > > >>>>
> > > >>>> I have built HDF5 successfully using the `--enable-hl`
function
> and
> > I
> > > >> got
> > > >>>> hdf5_h1.1 in my target directory. Previously I got error
> installing
> > > >> netcdf4
> > > >>>> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared"
message (as
> > shown
> > > >>>> inhttps://www.unidata.ucar.edu/support/help/MailArchives/
> > > >>>> netcdf/msg13749.html).
> > > >>>>
> > > >>>> I am referring to unidata webpage for the compilation of
netcdf4
> > > >>>> athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
> > > >>>> and_building_netcdf.html.
> > > >>>> But now I get an error with h5_test within the netcdf make
check
> and
> > > it
> > > >>>> fails.
> > > >>>> Attached please find configure and make log.
> > > >>>> Do you have any know-how to overcome this issue?
> > > >>>> Thank you very much in advance.
> > > >>>>
> > > >>>> Regards,
> > > >>>>
> > > >>>> Jinwoong Yoo
> > > >>>> Purdue Climate Change Research Center
> > > >>>>
> > > >>>> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
> > > >>>> <met_help at ucar.edu> <met_help at ucar.edu>
> > > >>>> wrote:
> > > >>>>
> > > >>>>
> > > >>>> Hello -
> > > >>>>
> > > >>>> Most of our team is out due to the Memorial Day holiday.
We'll
> > have a
> > > >>>> look
> > > >>>> at your issue when the team is back sometime later this
week.
> > > >>>>
> > > >>>> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
> > > >>>> <met_help at ucar.edu> <met_help at ucar.edu>
> > > >>>> wrote:
> > > >>>>
> > > >>>>
> > > >>>> Fri May 26 09:39:58 2017: Request 80647 was acted upon.
> > > >>>> Transaction: Ticket created by jinwoong.yoo at gmail.com
> > > >>>> Queue: met_help
> > > >>>> Subject: Error with Compiling MET-6.0
> > > >>>> Owner: Nobody
> > > >>>> Requestors: jinwoong.yoo at gmail.com
> > > >>>> Status: new
> > > >>>> Ticket <URL: https://rt.rap.ucar.edu/rt/
> > > Ticket/Display.html?id=80647
> > > >>>>
> > > >>>> Dear MET Help
> > > >>>>
> > > >>>> Hi.
> > > >>>> I am trying to compile MET-6.0 bugfixed version on a Linux
cluster
> > > >>>>
> > > >>>> (Redhat)
> > > >>>>
> > > >>>> at Purdue University.
> > > >>>> I am using a few system-wide libraries (e.g., netcdf-3.6.3,
hdf5)
> > and
> > > I
> > > >>>> installed most of the other library myself. Also I set up
all the
> > > >>>> environment variables required.
> > > >>>>
> > > >>>> # MET
> > > >>>>
> > > >>>> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
> > > >>>>
> > > >>>> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
> > > >>>>
> > > >>>> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
> > > >>>>
> > > >>>> export MET_UPP=/home/yoo108/UPPV3.1
> > > >>>>
> > > >>>> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
> > > >>>>
> > > >>>> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
> > > >>>>
> > > >>>> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
> > > >>>>
> > > >>>> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
> > > >>>>
> > > >>>> export
MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
> > > >>>>
> > > >>>> export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
> > > >>>>
> > > >>>> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
> > > >>>>
> > > >>>>
> > > >>>>
> > > >>>> However, I got an error with the compilation of the MET-6.0
and it
> > > >>>>
> > > >>>> failed.
> > > >>>>
> > > >>>> The error message reads as below:
> > > >>>>
> > > >>>> MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__
-MT
> > > >>>> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
> > > >>>> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
> > > >>>>
> > > >>>> libvx_nc_util_a-nc_var_info.o
> > > >>>>
> > > >>>> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
> > > >>>>
> > > >>>> In file included from nc_var_info.cc(24):
> > > >>>>
> > > >>>> nc_utils.h(22): catastrophic error: cannot open source file
> "netcdf"
> > > >>>>
> > > >>>> #include <netcdf>
> > > >>>>
> > > >>>> ^
> > > >>>>
> > > >>>>
> > > >>>> compilation aborted for nc_var_info.cc (code 4)
> > > >>>>
> > > >>>> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
> > > >>>>
> > > >>>> make[3]: Leaving directory
> > > >>>> `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
> > > >>>>
> > > >>>> make[2]: *** [install-recursive] Error 1
> > > >>>>
> > > >>>> make[2]: Leaving directory `/home/yoo108/build_MET/src/
> > > >>>> met-6.0/src/libcode'
> > > >>>>
> > > >>>> make[1]: *** [install-recursive] Error 1
> > > >>>>
> > > >>>> make[1]: Leaving directory `/home/yoo108/build_MET/src/
> met-6.0/src'
> > > >>>>
> > > >>>> make: *** [install-recursive] Error 1
> > > >>>>
> > > >>>> ^C[1]+ Exit 2 make install
&>make_install.log
> > > >>>>
> > > >>>>
> > > >>>> I wonder if this error is related with the 64 bit cluster
while
> MET
> > > >>>>
> > > >>>> wants
> > > >>>>
> > > >>>> 32 bit software or else.
> > > >>>>
> > > >>>> Your input will be highly appreciated.
> > > >>>>
> > > >>>> Thank you.
> > > >>>>
> > > >>>> Regards,
> > > >>>>
> > > >>>>
> > > >>>> Jinwoong Yoo
> > > >>>>
> > > >>>> Purdue Climate Change Research Center
> > > >>>>
> > > >>>>
> > > >>
> > > >>
> > >
> > >
> > >
> >
> >
>
>
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Howard Soh
Time: Wed May 31 12:03:41 2017
You're very welcome.
Please let us know if you encounter any other difficulties.**I'll go
ahead and close this ticket for now then. Please open a new ticket if
further questions or problems.
Thanks,
Howard
On 5/31/2017 11:45 AM, Jinwoong Yoo via RT wrote:
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>
> Hi Howard,
>
> Thank you much for your note.
> Finally I was able to complete the installation of MET-6.0.
> But I should let you know that I encountered several errors probably
due to
> the outdated make file for the new include directory structures of
recent
> versions of HDF-EOS2, Cairo, and Freetype.
>
> Thank you.
> Regards,
>
> Jinwoong
>
> On Wed, May 31, 2017 at 11:58 AM, Howard Soh via RT
<met_help at ucar.edu>
> wrote:
>
>> MET still uses HDF4 library instead of HDF5 because of another
dependency,
>> HDF-EOS.
>>
>> Note: hdf.h is for HDF4 and hdf5.h is for HDF5
>>
>> NetCDF4 requires HDF5 on building and running. Once NetCDF library
is
>> built, HDF5 is not required to build MET, but required to run MET.
>>
>> Please set *$MET_HDF* to point to the HDF4 directory.
>>
>> Cheers,
>> Howard
>>
>>
>> On Wed, May 31, 2017 at 8:03 AM, Jinwoong Yoo via RT
<met_help at ucar.edu>
>> wrote:
>>
>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>
>>> Hi Howard,
>>> Although, after compiling of all the dependency libraries,
>>> I am getting error with installing the MET.
>>>
>>> I set all the environment libraries as directed in the online
tutorial.
>>> But it seems the installer cannot find hdf.h file.
>>> Please see error message below:
>>>
>>> *lidar2nc.cc:69:17:* *fatal error: *hdf.h: No such file or
directory
>>>
>>> compilation terminated.
>>>
>>> make[5]: *** [lidar2nc-lidar2nc.o] Error 1
>>>
>>> make[5]: Leaving directory
>>> `/home/yoo108/METwithGNU/src/met-
6.0_bugfix/src/tools/other/lidar2nc'
>>>
>>> make[4]: *** [all-recursive] Error 1
>>>
>>> make[4]: Leaving directory
>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools/other'
>>>
>>> make[3]: *** [all-recursive] Error 1
>>>
>>> make[3]: Leaving directory
>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools'
>>>
>>> make[2]: *** [all-recursive] Error 1
>>>
>>> make[2]: Leaving directory `/home/yoo108/METwithGNU/src/
>>> met-6.0_bugfix/src'
>>>
>>> make[1]: *** [all-recursive] Error 1
>>>
>>> make[1]: Leaving directory `/home/yoo108/METwithGNU/src/met-
6.0_bugfix'
>>>
>>> make: *** [all] Error 2
>>>
>>> Do you have any idea?
>>> Thank you.
>>>
>>> Regards,
>>>
>>> Jinwoong
>>>
>>> On Tue, May 30, 2017 at 6:21 PM, Howard Soh via RT
<met_help at ucar.edu>
>>> wrote:
>>>
>>>> I'm glad to hear that you can build HDF5 and NetCDF4.
>>>>
>>>> I appreciated your advice. We will review online tutorial and
make it
>>>> clear.
>>>>
>>>> Cheers,
>>>> Howard
>>>>
>>>> FYI:
>>>> hdf5-1.8.17$ ./configure --help | grep enable-hl
>>>> --enable-hl Enable the high level library
[default=yes]
>>>>
>>>> hdf5-1.8.18$ ./configure --help | grep enable-hl
>>>> --enable-hl Enable the high level library
[default=yes]
>>>>
>>>>
>>>>
>>>> On 5/30/2017 2:12 PM, Jinwoong Yoo via RT wrote:
>>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>>>
>>>>> Hi Howard,
>>>>>
>>>>> I was able to compile HDF5, Netcdf4-C, and NetCDF-CXX
successfully
>>>> finally.
>>>>> I happened to know that there were a few typos in the MET Online
>>> Tutorial
>>>>> For METv6.0, which led into various confusions.
>>>>>
>>>>> In the "Compiling HDF5" section,
>>>>> I had to configure hdf5 with the "--enable-hl" option along with
"
>>>>> *--with-zlib=${ZDIR}*".
>>>>>
>>>>>
>>>>> In the "Compiling NetCDF" section,
>>>>> both for NetCDF-C and NetCDF-CXX,
>>>>>
>>>>> LDFLAGS and CPPFLAGS directories should be assigned to HDF5
>> directory,
>>>> not
>>>>> the NetCDF4 installation directory in
>>>>> "LDFLAGS=-L${MET_LIB_DIR}/lib CPPFLAGS=-I${MET_LIB_DIR}/include"
>> while
>>>> the
>>>>> target directory in "--prefix=${MET_LIB_DIR}" should be netcdf4
>>>> directory.
>>>>> You might want to make changes for these error for other METv6.0
>> users
>>> on
>>>>> your webpage at "
>>>>> http://www.dtcenter.org/met/users/support/online_tutorial/
>>>> METv6.0/tutorial.php?name=compilation&category=req_libs
>>>>> ".
>>>>>
>>>>> Thank you.
>>>>> Regards,
>>>>>
>>>>> Jinwoong
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Tue, May 30, 2017 at 3:18 PM, Howard Soh via RT <
>> met_help at ucar.edu>
>>>>> wrote:
>>>>>
>>>>>> Thank you, Jinwoong.
>>>>>>
>>>>>> Howard
>>>>>>
>>>>>> On 5/30/2017 12:33 PM, Jinwoong Yoo via RT wrote:
>>>>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>
>>>>>>>
>>>>>>> Hi Howard,
>>>>>>>
>>>>>>> I contacted Unidata regarding the issue already.
>>>>>>> Attached please find the file, and see its contents below.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ============================================
>>>>>>>
>>>>>>> netCDF 4.4.1.1: h5_test/test-suite.log
>>>>>>>
>>>>>>> ============================================
>>>>>>>
>>>>>>>
>>>>>>> # TOTAL: 26
>>>>>>>
>>>>>>> # PASS: 25
>>>>>>>
>>>>>>> # SKIP: 0
>>>>>>>
>>>>>>> # XFAIL: 0
>>>>>>>
>>>>>>> # FAIL: 1
>>>>>>>
>>>>>>> # XPASS: 0
>>>>>>>
>>>>>>> # ERROR: 0
>>>>>>>
>>>>>>>
>>>>>>> .. contents:: :depth: 2
>>>>>>>
>>>>>>>
>>>>>>> FAIL: tst_h_vars
>>>>>>>
>>>>>>> ================
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> *** Checking HDF5 variable functions.
>>>>>>>
>>>>>>> *** Checking HDF5 boolen variables...ok.
>>>>>>>
>>>>>>> *** Checking HDF5 variable with unlimited dimension...ok.
>>>>>>>
>>>>>>> *** Checking HDF5 deflate filter setting and getting...Sorry!
>>>> Unexpected
>>>>>>> result, tst_h_vars.c, line: 230
>>>>>>>
>>>>>>> FAIL tst_h_vars (exit status: 2)
>>>>>>>
>>>>>>>
>>>>>>> Thank you.
>>>>>>>
>>>>>>> Regards,
>>>>>>>
>>>>>>>
>>>>>>> Jinwoong
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Tue, May 30, 2017 at 2:22 PM, Howard Soh via RT <
>>> met_help at ucar.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi Jinwoong.
>>>>>>>>
>>>>>>>> I am sorry to hear that you are still having difficulty with
the
>>>> netcdf
>>>>>>>> library
>>>>>>>> files.
>>>>>>>> One unit test related with HDF5 was failed. Would you check
>>>>>>>> h5_test/test-suite.log
>>>>>>>> and contact Unidata?
>>>>>>>> The full path will be /home/yoo108/METwithGNU/src/
>>>>>> netcdf-c-4.4.1.1/h5_test
>>>>>>>> /test-suite.log.
>>>>>>>>
>>>>>>>> It would help to understand your problem if you send us
>>>>>>>> h5_test/test-suite.log.
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>> Howard
>>>>>>>>
>>>>>>>> FYI:
>>>>>>>>
>>>>>>>>
>>>>>>>> FAIL: tst_h_vars
>>>>>>>>
>>>>>>>> ============================================================
>>>>>>>> ================
>>>>>>>> Testsuite summary for netCDF 4.4.1.1
>>>>>>>> ============================================================
>>>>>>>> ================
>>>>>>>> # TOTAL: 26
>>>>>>>> # PASS: 25
>>>>>>>> # SKIP: 0
>>>>>>>> # XFAIL: 0
>>>>>>>> # FAIL: 1
>>>>>>>> # XPASS: 0
>>>>>>>> # ERROR: 0
>>>>>>>> ============================================================
>>>>>>>> ================
>>>>>>>> See h5_test/test-suite.log
>>>>>>>> Please report to support-netcdf at unidata.ucar.edu
>>>>>>>> ============================================================
>>>>>>>> ================
>>>>>>>>
>>>>>>>>
>>>>>>>> On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
>>>>>>>>
>>>>>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>
>>>>>>>>
>>>>>>>> I forgot to attach my log file.
>>>>>>>> Thanks!
>>>>>>>>
>>>>>>>>
>>>>>>>> On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo <
>>> jinwoong.yoo at gmail.com
>>>>>>>> <jinwoong.yoo at gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>> Hi,
>>>>>>>> Thank you for your reply.
>>>>>>>>
>>>>>>>> I realized that I have to have netcdf4-c and netcdf4-cxx to
>> install
>>>>>>>> MET-6.0.
>>>>>>>> So far, I have compiled HDF5 following directions
>>>>>>>> athttp://www.dtcenter.org/met/users/support/online_tutorial/
>>>>>>>> METv6.0/tutorial.php?name=compilation&category=req_libs.
>>>>>>>>
>>>>>>>> I have built HDF5 successfully using the `--enable-hl`
function
>> and
>>> I
>>>>>> got
>>>>>>>> hdf5_h1.1 in my target directory. Previously I got error
>> installing
>>>>>> netcdf4
>>>>>>>> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared" message
(as
>>> shown
>>>>>>>> inhttps://www.unidata.ucar.edu/support/help/MailArchives/
>>>>>>>> netcdf/msg13749.html).
>>>>>>>>
>>>>>>>> I am referring to unidata webpage for the compilation of
netcdf4
>>>>>>>> athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
>>>>>>>> and_building_netcdf.html.
>>>>>>>> But now I get an error with h5_test within the netcdf make
check
>> and
>>>> it
>>>>>>>> fails.
>>>>>>>> Attached please find configure and make log.
>>>>>>>> Do you have any know-how to overcome this issue?
>>>>>>>> Thank you very much in advance.
>>>>>>>>
>>>>>>>> Regards,
>>>>>>>>
>>>>>>>> Jinwoong Yoo
>>>>>>>> Purdue Climate Change Research Center
>>>>>>>>
>>>>>>>> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
>>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>> Hello -
>>>>>>>>
>>>>>>>> Most of our team is out due to the Memorial Day holiday.
We'll
>>> have a
>>>>>>>> look
>>>>>>>> at your issue when the team is back sometime later this week.
>>>>>>>>
>>>>>>>> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
>>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>> Fri May 26 09:39:58 2017: Request 80647 was acted upon.
>>>>>>>> Transaction: Ticket created by jinwoong.yoo at gmail.com
>>>>>>>> Queue: met_help
>>>>>>>> Subject: Error with Compiling MET-6.0
>>>>>>>> Owner: Nobody
>>>>>>>> Requestors: jinwoong.yoo at gmail.com
>>>>>>>> Status: new
>>>>>>>> Ticket <URL: https://rt.rap.ucar.edu/rt/
>>>> Ticket/Display.html?id=80647
>>>>>>>> Dear MET Help
>>>>>>>>
>>>>>>>> Hi.
>>>>>>>> I am trying to compile MET-6.0 bugfixed version on a Linux
cluster
>>>>>>>>
>>>>>>>> (Redhat)
>>>>>>>>
>>>>>>>> at Purdue University.
>>>>>>>> I am using a few system-wide libraries (e.g., netcdf-3.6.3,
hdf5)
>>> and
>>>> I
>>>>>>>> installed most of the other library myself. Also I set up all
the
>>>>>>>> environment variables required.
>>>>>>>>
>>>>>>>> # MET
>>>>>>>>
>>>>>>>> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
>>>>>>>>
>>>>>>>> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
>>>>>>>>
>>>>>>>> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
>>>>>>>>
>>>>>>>> export MET_UPP=/home/yoo108/UPPV3.1
>>>>>>>>
>>>>>>>> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
>>>>>>>>
>>>>>>>> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
>>>>>>>>
>>>>>>>> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
>>>>>>>>
>>>>>>>> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
>>>>>>>>
>>>>>>>> export
MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
>>>>>>>>
>>>>>>>> export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
>>>>>>>>
>>>>>>>> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> However, I got an error with the compilation of the MET-6.0
and it
>>>>>>>>
>>>>>>>> failed.
>>>>>>>>
>>>>>>>> The error message reads as below:
>>>>>>>>
>>>>>>>> MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__
-MT
>>>>>>>> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
>>>>>>>> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
>>>>>>>>
>>>>>>>> libvx_nc_util_a-nc_var_info.o
>>>>>>>>
>>>>>>>> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
>>>>>>>>
>>>>>>>> In file included from nc_var_info.cc(24):
>>>>>>>>
>>>>>>>> nc_utils.h(22): catastrophic error: cannot open source file
>> "netcdf"
>>>>>>>> #include <netcdf>
>>>>>>>>
>>>>>>>> ^
>>>>>>>>
>>>>>>>>
>>>>>>>> compilation aborted for nc_var_info.cc (code 4)
>>>>>>>>
>>>>>>>> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
>>>>>>>>
>>>>>>>> make[3]: Leaving directory
>>>>>>>> `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
>>>>>>>>
>>>>>>>> make[2]: *** [install-recursive] Error 1
>>>>>>>>
>>>>>>>> make[2]: Leaving directory `/home/yoo108/build_MET/src/
>>>>>>>> met-6.0/src/libcode'
>>>>>>>>
>>>>>>>> make[1]: *** [install-recursive] Error 1
>>>>>>>>
>>>>>>>> make[1]: Leaving directory `/home/yoo108/build_MET/src/
>> met-6.0/src'
>>>>>>>> make: *** [install-recursive] Error 1
>>>>>>>>
>>>>>>>> ^C[1]+ Exit 2 make install
&>make_install.log
>>>>>>>>
>>>>>>>>
>>>>>>>> I wonder if this error is related with the 64 bit cluster
while
>> MET
>>>>>>>> wants
>>>>>>>>
>>>>>>>> 32 bit software or else.
>>>>>>>>
>>>>>>>> Your input will be highly appreciated.
>>>>>>>>
>>>>>>>> Thank you.
>>>>>>>>
>>>>>>>> Regards,
>>>>>>>>
>>>>>>>>
>>>>>>>> Jinwoong Yoo
>>>>>>>>
>>>>>>>> Purdue Climate Change Research Center
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>
>>>>
>>>
>>
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Jinwoong Yoo
Time: Wed May 31 13:00:25 2017
Hi Howard,
I thought my MET compilation completed.
But it seems not.
When I typed in met commands in bin directory,
I got errors as below:
yoo108 at halstead-fe00:*~/MET-6.0* $ bin/pcp_combine
bin/pcp_combine: error while loading shared libraries: libimf.so:
cannot
open shared object file: No such file or directory
yoo108 at halstead-fe00:*~/MET-6.0* $ which ascii2nc
~/MET-6.0/bin/ascii2nc
yoo108 at halstead-fe00:*~/MET-6.0* $ ascii2nc
ascii2nc: error while loading shared libraries: libimf.so: cannot open
shared object file: No such file or directory
yoo108 at halstead-fe00:*~/MET-6.0* $ mode
mode: error while loading shared libraries: libimf.so: cannot open
shared
object file: No such file or directory
yoo108 at halstead-fe00:*~/MET-6.0* $ mtd
mtd: error while loading shared libraries: libimf.so: cannot open
shared
object file: No such file or directory
yoo108 at halstead-fe00:*~/MET-6.0* $ pb2nc
pb2nc: error while loading shared libraries: libimf.so: cannot open
shared
object file: No such file or directory
What I should do?
It seems there is no lib directory compiled with MET-6.0.
I am not sure which libimf.so file is needed.
Thank you.
Regards,
Jinwoong
On Wed, May 31, 2017 at 2:03 PM, Howard Soh via RT <met_help at ucar.edu>
wrote:
> You're very welcome.
>
> Please let us know if you encounter any other difficulties.**I'll go
> ahead and close this ticket for now then. Please open a new ticket
if
> further questions or problems.
>
> Thanks,
> Howard
>
>
> On 5/31/2017 11:45 AM, Jinwoong Yoo via RT wrote:
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >
> > Hi Howard,
> >
> > Thank you much for your note.
> > Finally I was able to complete the installation of MET-6.0.
> > But I should let you know that I encountered several errors
probably due
> to
> > the outdated make file for the new include directory structures of
recent
> > versions of HDF-EOS2, Cairo, and Freetype.
> >
> > Thank you.
> > Regards,
> >
> > Jinwoong
> >
> > On Wed, May 31, 2017 at 11:58 AM, Howard Soh via RT
<met_help at ucar.edu>
> > wrote:
> >
> >> MET still uses HDF4 library instead of HDF5 because of another
> dependency,
> >> HDF-EOS.
> >>
> >> Note: hdf.h is for HDF4 and hdf5.h is for HDF5
> >>
> >> NetCDF4 requires HDF5 on building and running. Once NetCDF
library is
> >> built, HDF5 is not required to build MET, but required to run
MET.
> >>
> >> Please set *$MET_HDF* to point to the HDF4 directory.
> >>
> >> Cheers,
> >> Howard
> >>
> >>
> >> On Wed, May 31, 2017 at 8:03 AM, Jinwoong Yoo via RT
<met_help at ucar.edu
> >
> >> wrote:
> >>
> >>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >>>
> >>> Hi Howard,
> >>> Although, after compiling of all the dependency libraries,
> >>> I am getting error with installing the MET.
> >>>
> >>> I set all the environment libraries as directed in the online
tutorial.
> >>> But it seems the installer cannot find hdf.h file.
> >>> Please see error message below:
> >>>
> >>> *lidar2nc.cc:69:17:* *fatal error: *hdf.h: No such file or
directory
> >>>
> >>> compilation terminated.
> >>>
> >>> make[5]: *** [lidar2nc-lidar2nc.o] Error 1
> >>>
> >>> make[5]: Leaving directory
> >>> `/home/yoo108/METwithGNU/src/met-
6.0_bugfix/src/tools/other/lidar2nc'
> >>>
> >>> make[4]: *** [all-recursive] Error 1
> >>>
> >>> make[4]: Leaving directory
> >>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools/other'
> >>>
> >>> make[3]: *** [all-recursive] Error 1
> >>>
> >>> make[3]: Leaving directory
> >>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools'
> >>>
> >>> make[2]: *** [all-recursive] Error 1
> >>>
> >>> make[2]: Leaving directory `/home/yoo108/METwithGNU/src/
> >>> met-6.0_bugfix/src'
> >>>
> >>> make[1]: *** [all-recursive] Error 1
> >>>
> >>> make[1]: Leaving directory `/home/yoo108/METwithGNU/src/
> met-6.0_bugfix'
> >>>
> >>> make: *** [all] Error 2
> >>>
> >>> Do you have any idea?
> >>> Thank you.
> >>>
> >>> Regards,
> >>>
> >>> Jinwoong
> >>>
> >>> On Tue, May 30, 2017 at 6:21 PM, Howard Soh via RT
<met_help at ucar.edu>
> >>> wrote:
> >>>
> >>>> I'm glad to hear that you can build HDF5 and NetCDF4.
> >>>>
> >>>> I appreciated your advice. We will review online tutorial and
make it
> >>>> clear.
> >>>>
> >>>> Cheers,
> >>>> Howard
> >>>>
> >>>> FYI:
> >>>> hdf5-1.8.17$ ./configure --help | grep enable-hl
> >>>> --enable-hl Enable the high level library
> [default=yes]
> >>>>
> >>>> hdf5-1.8.18$ ./configure --help | grep enable-hl
> >>>> --enable-hl Enable the high level library
> [default=yes]
> >>>>
> >>>>
> >>>>
> >>>> On 5/30/2017 2:12 PM, Jinwoong Yoo via RT wrote:
> >>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>
> >>>>>
> >>>>> Hi Howard,
> >>>>>
> >>>>> I was able to compile HDF5, Netcdf4-C, and NetCDF-CXX
successfully
> >>>> finally.
> >>>>> I happened to know that there were a few typos in the MET
Online
> >>> Tutorial
> >>>>> For METv6.0, which led into various confusions.
> >>>>>
> >>>>> In the "Compiling HDF5" section,
> >>>>> I had to configure hdf5 with the "--enable-hl" option along
with "
> >>>>> *--with-zlib=${ZDIR}*".
> >>>>>
> >>>>>
> >>>>> In the "Compiling NetCDF" section,
> >>>>> both for NetCDF-C and NetCDF-CXX,
> >>>>>
> >>>>> LDFLAGS and CPPFLAGS directories should be assigned to HDF5
> >> directory,
> >>>> not
> >>>>> the NetCDF4 installation directory in
> >>>>> "LDFLAGS=-L${MET_LIB_DIR}/lib CPPFLAGS=-
I${MET_LIB_DIR}/include"
> >> while
> >>>> the
> >>>>> target directory in "--prefix=${MET_LIB_DIR}" should be
netcdf4
> >>>> directory.
> >>>>> You might want to make changes for these error for other
METv6.0
> >> users
> >>> on
> >>>>> your webpage at "
> >>>>> http://www.dtcenter.org/met/users/support/online_tutorial/
> >>>> METv6.0/tutorial.php?name=compilation&category=req_libs
> >>>>> ".
> >>>>>
> >>>>> Thank you.
> >>>>> Regards,
> >>>>>
> >>>>> Jinwoong
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> On Tue, May 30, 2017 at 3:18 PM, Howard Soh via RT <
> >> met_help at ucar.edu>
> >>>>> wrote:
> >>>>>
> >>>>>> Thank you, Jinwoong.
> >>>>>>
> >>>>>> Howard
> >>>>>>
> >>>>>> On 5/30/2017 12:33 PM, Jinwoong Yoo via RT wrote:
> >>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >>>>>>>
> >>>>>>> Hi Howard,
> >>>>>>>
> >>>>>>> I contacted Unidata regarding the issue already.
> >>>>>>> Attached please find the file, and see its contents below.
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> ============================================
> >>>>>>>
> >>>>>>> netCDF 4.4.1.1: h5_test/test-suite.log
> >>>>>>>
> >>>>>>> ============================================
> >>>>>>>
> >>>>>>>
> >>>>>>> # TOTAL: 26
> >>>>>>>
> >>>>>>> # PASS: 25
> >>>>>>>
> >>>>>>> # SKIP: 0
> >>>>>>>
> >>>>>>> # XFAIL: 0
> >>>>>>>
> >>>>>>> # FAIL: 1
> >>>>>>>
> >>>>>>> # XPASS: 0
> >>>>>>>
> >>>>>>> # ERROR: 0
> >>>>>>>
> >>>>>>>
> >>>>>>> .. contents:: :depth: 2
> >>>>>>>
> >>>>>>>
> >>>>>>> FAIL: tst_h_vars
> >>>>>>>
> >>>>>>> ================
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> *** Checking HDF5 variable functions.
> >>>>>>>
> >>>>>>> *** Checking HDF5 boolen variables...ok.
> >>>>>>>
> >>>>>>> *** Checking HDF5 variable with unlimited dimension...ok.
> >>>>>>>
> >>>>>>> *** Checking HDF5 deflate filter setting and
getting...Sorry!
> >>>> Unexpected
> >>>>>>> result, tst_h_vars.c, line: 230
> >>>>>>>
> >>>>>>> FAIL tst_h_vars (exit status: 2)
> >>>>>>>
> >>>>>>>
> >>>>>>> Thank you.
> >>>>>>>
> >>>>>>> Regards,
> >>>>>>>
> >>>>>>>
> >>>>>>> Jinwoong
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> On Tue, May 30, 2017 at 2:22 PM, Howard Soh via RT <
> >>> met_help at ucar.edu>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>>> Hi Jinwoong.
> >>>>>>>>
> >>>>>>>> I am sorry to hear that you are still having difficulty
with the
> >>>> netcdf
> >>>>>>>> library
> >>>>>>>> files.
> >>>>>>>> One unit test related with HDF5 was failed. Would you check
> >>>>>>>> h5_test/test-suite.log
> >>>>>>>> and contact Unidata?
> >>>>>>>> The full path will be /home/yoo108/METwithGNU/src/
> >>>>>> netcdf-c-4.4.1.1/h5_test
> >>>>>>>> /test-suite.log.
> >>>>>>>>
> >>>>>>>> It would help to understand your problem if you send us
> >>>>>>>> h5_test/test-suite.log.
> >>>>>>>>
> >>>>>>>> Cheers,
> >>>>>>>> Howard
> >>>>>>>>
> >>>>>>>> FYI:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> FAIL: tst_h_vars
> >>>>>>>>
> >>>>>>>>
============================================================
> >>>>>>>> ================
> >>>>>>>> Testsuite summary for netCDF 4.4.1.1
> >>>>>>>>
============================================================
> >>>>>>>> ================
> >>>>>>>> # TOTAL: 26
> >>>>>>>> # PASS: 25
> >>>>>>>> # SKIP: 0
> >>>>>>>> # XFAIL: 0
> >>>>>>>> # FAIL: 1
> >>>>>>>> # XPASS: 0
> >>>>>>>> # ERROR: 0
> >>>>>>>>
============================================================
> >>>>>>>> ================
> >>>>>>>> See h5_test/test-suite.log
> >>>>>>>> Please report to support-netcdf at unidata.ucar.edu
> >>>>>>>>
============================================================
> >>>>>>>> ================
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
> >>>>>>>>
> >>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >>>>>>>>
> >>>>>>>> I forgot to attach my log file.
> >>>>>>>> Thanks!
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo <
> >>> jinwoong.yoo at gmail.com
> >>>>>>>> <jinwoong.yoo at gmail.com>
> >>>>>>>> wrote:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> Hi,
> >>>>>>>> Thank you for your reply.
> >>>>>>>>
> >>>>>>>> I realized that I have to have netcdf4-c and netcdf4-cxx to
> >> install
> >>>>>>>> MET-6.0.
> >>>>>>>> So far, I have compiled HDF5 following directions
> >>>>>>>>
athttp://www.dtcenter.org/met/users/support/online_tutorial/
> >>>>>>>> METv6.0/tutorial.php?name=compilation&category=req_libs.
> >>>>>>>>
> >>>>>>>> I have built HDF5 successfully using the `--enable-hl`
function
> >> and
> >>> I
> >>>>>> got
> >>>>>>>> hdf5_h1.1 in my target directory. Previously I got error
> >> installing
> >>>>>> netcdf4
> >>>>>>>> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared"
message (as
> >>> shown
> >>>>>>>> inhttps://www.unidata.ucar.edu/support/help/MailArchives/
> >>>>>>>> netcdf/msg13749.html).
> >>>>>>>>
> >>>>>>>> I am referring to unidata webpage for the compilation of
netcdf4
> >>>>>>>> athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
> >>>>>>>> and_building_netcdf.html.
> >>>>>>>> But now I get an error with h5_test within the netcdf make
check
> >> and
> >>>> it
> >>>>>>>> fails.
> >>>>>>>> Attached please find configure and make log.
> >>>>>>>> Do you have any know-how to overcome this issue?
> >>>>>>>> Thank you very much in advance.
> >>>>>>>>
> >>>>>>>> Regards,
> >>>>>>>>
> >>>>>>>> Jinwoong Yoo
> >>>>>>>> Purdue Climate Change Research Center
> >>>>>>>>
> >>>>>>>> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
> >>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
> >>>>>>>> wrote:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> Hello -
> >>>>>>>>
> >>>>>>>> Most of our team is out due to the Memorial Day holiday.
We'll
> >>> have a
> >>>>>>>> look
> >>>>>>>> at your issue when the team is back sometime later this
week.
> >>>>>>>>
> >>>>>>>> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
> >>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
> >>>>>>>> wrote:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> Fri May 26 09:39:58 2017: Request 80647 was acted upon.
> >>>>>>>> Transaction: Ticket created by jinwoong.yoo at gmail.com
> >>>>>>>> Queue: met_help
> >>>>>>>> Subject: Error with Compiling MET-6.0
> >>>>>>>> Owner: Nobody
> >>>>>>>> Requestors: jinwoong.yoo at gmail.com
> >>>>>>>> Status: new
> >>>>>>>> Ticket <URL: https://rt.rap.ucar.edu/rt/
> >>>> Ticket/Display.html?id=80647
> >>>>>>>> Dear MET Help
> >>>>>>>>
> >>>>>>>> Hi.
> >>>>>>>> I am trying to compile MET-6.0 bugfixed version on a Linux
cluster
> >>>>>>>>
> >>>>>>>> (Redhat)
> >>>>>>>>
> >>>>>>>> at Purdue University.
> >>>>>>>> I am using a few system-wide libraries (e.g., netcdf-3.6.3,
hdf5)
> >>> and
> >>>> I
> >>>>>>>> installed most of the other library myself. Also I set up
all the
> >>>>>>>> environment variables required.
> >>>>>>>>
> >>>>>>>> # MET
> >>>>>>>>
> >>>>>>>> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
> >>>>>>>>
> >>>>>>>> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
> >>>>>>>>
> >>>>>>>> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
> >>>>>>>>
> >>>>>>>> export MET_UPP=/home/yoo108/UPPV3.1
> >>>>>>>>
> >>>>>>>> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
> >>>>>>>>
> >>>>>>>> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
> >>>>>>>>
> >>>>>>>> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
> >>>>>>>>
> >>>>>>>> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
> >>>>>>>>
> >>>>>>>> export
MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
> >>>>>>>>
> >>>>>>>> export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
> >>>>>>>>
> >>>>>>>> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> However, I got an error with the compilation of the MET-6.0
and it
> >>>>>>>>
> >>>>>>>> failed.
> >>>>>>>>
> >>>>>>>> The error message reads as below:
> >>>>>>>>
> >>>>>>>> MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__
-MT
> >>>>>>>> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
> >>>>>>>> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
> >>>>>>>>
> >>>>>>>> libvx_nc_util_a-nc_var_info.o
> >>>>>>>>
> >>>>>>>> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
> >>>>>>>>
> >>>>>>>> In file included from nc_var_info.cc(24):
> >>>>>>>>
> >>>>>>>> nc_utils.h(22): catastrophic error: cannot open source file
> >> "netcdf"
> >>>>>>>> #include <netcdf>
> >>>>>>>>
> >>>>>>>> ^
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> compilation aborted for nc_var_info.cc (code 4)
> >>>>>>>>
> >>>>>>>> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
> >>>>>>>>
> >>>>>>>> make[3]: Leaving directory
> >>>>>>>> `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
> >>>>>>>>
> >>>>>>>> make[2]: *** [install-recursive] Error 1
> >>>>>>>>
> >>>>>>>> make[2]: Leaving directory `/home/yoo108/build_MET/src/
> >>>>>>>> met-6.0/src/libcode'
> >>>>>>>>
> >>>>>>>> make[1]: *** [install-recursive] Error 1
> >>>>>>>>
> >>>>>>>> make[1]: Leaving directory `/home/yoo108/build_MET/src/
> >> met-6.0/src'
> >>>>>>>> make: *** [install-recursive] Error 1
> >>>>>>>>
> >>>>>>>> ^C[1]+ Exit 2 make install
&>make_install.log
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> I wonder if this error is related with the 64 bit cluster
while
> >> MET
> >>>>>>>> wants
> >>>>>>>>
> >>>>>>>> 32 bit software or else.
> >>>>>>>>
> >>>>>>>> Your input will be highly appreciated.
> >>>>>>>>
> >>>>>>>> Thank you.
> >>>>>>>>
> >>>>>>>> Regards,
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> Jinwoong Yoo
> >>>>>>>>
> >>>>>>>> Purdue Climate Change Research Center
> >>>>>>>>
> >>>>>>>>
> >>>>>>
> >>>>
> >>>>
> >>>
> >>
>
>
>
------------------------------------------------
Subject: Re: [rt.rap.ucar.edu #80647] Error with Compiling MET-6.0
From: Howard Soh
Time: Wed May 31 14:02:13 2017
I am sorry to hear that you are still having difficulty with running
MET.
The error message implies that the MET was compiled with Intel but the
Intel libraries are not available at runtime.
It puzzles me why the build environment and the running environment
are different.
It's better to use one compiler for MET and dependent libraries. The
log file for HDF5 and NetCDF4 shows they were built with gcc 5.2.0.
Would you check which compilers were used to build MET and other
dependent libraries?
The first step will be finding which libraries not not available.
Would you execute ldd command and send me the output?
ldd bin/ascii2nc
Cheers,
Howard
FYI:
If there is "not found", the path for those libraries should be added
LD_LIBRARY_PATH.
For example,
libnetcdf_c++4.so.1 => not found
libnetcdf_c++.so.4 => not found
libnetcdf.so.7 => not found
libimf.so => not found
NetCDF library and Intel libraries are missing. In case of Intel
library, it's better to be resolved not by using LD_LIBRARY_PATH. If
"module" command is available, please use it "module load intel".
On 5/31/2017 1:00 PM, Jinwoong Yoo via RT wrote:
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>
> Hi Howard,
>
> I thought my MET compilation completed.
> But it seems not.
>
> When I typed in met commands in bin directory,
> I got errors as below:
>
> yoo108 at halstead-fe00:*~/MET-6.0* $ bin/pcp_combine
>
> bin/pcp_combine: error while loading shared libraries: libimf.so:
cannot
> open shared object file: No such file or directory
>
> yoo108 at halstead-fe00:*~/MET-6.0* $ which ascii2nc
>
> ~/MET-6.0/bin/ascii2nc
>
> yoo108 at halstead-fe00:*~/MET-6.0* $ ascii2nc
>
> ascii2nc: error while loading shared libraries: libimf.so: cannot
open
> shared object file: No such file or directory
>
> yoo108 at halstead-fe00:*~/MET-6.0* $ mode
>
> mode: error while loading shared libraries: libimf.so: cannot open
shared
> object file: No such file or directory
>
> yoo108 at halstead-fe00:*~/MET-6.0* $ mtd
>
> mtd: error while loading shared libraries: libimf.so: cannot open
shared
> object file: No such file or directory
>
> yoo108 at halstead-fe00:*~/MET-6.0* $ pb2nc
>
> pb2nc: error while loading shared libraries: libimf.so: cannot open
shared
> object file: No such file or directory
>
>
> What I should do?
>
> It seems there is no lib directory compiled with MET-6.0.
>
> I am not sure which libimf.so file is needed.
>
> Thank you.
>
>
> Regards,
>
>
> Jinwoong
>
>
>
>
> On Wed, May 31, 2017 at 2:03 PM, Howard Soh via RT
<met_help at ucar.edu>
> wrote:
>
>> You're very welcome.
>>
>> Please let us know if you encounter any other difficulties.**I'll
go
>> ahead and close this ticket for now then. Please open a new ticket
if
>> further questions or problems.
>>
>> Thanks,
>> Howard
>>
>>
>> On 5/31/2017 11:45 AM, Jinwoong Yoo via RT wrote:
>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>
>>> Hi Howard,
>>>
>>> Thank you much for your note.
>>> Finally I was able to complete the installation of MET-6.0.
>>> But I should let you know that I encountered several errors
probably due
>> to
>>> the outdated make file for the new include directory structures of
recent
>>> versions of HDF-EOS2, Cairo, and Freetype.
>>>
>>> Thank you.
>>> Regards,
>>>
>>> Jinwoong
>>>
>>> On Wed, May 31, 2017 at 11:58 AM, Howard Soh via RT
<met_help at ucar.edu>
>>> wrote:
>>>
>>>> MET still uses HDF4 library instead of HDF5 because of another
>> dependency,
>>>> HDF-EOS.
>>>>
>>>> Note: hdf.h is for HDF4 and hdf5.h is for HDF5
>>>>
>>>> NetCDF4 requires HDF5 on building and running. Once NetCDF
library is
>>>> built, HDF5 is not required to build MET, but required to run
MET.
>>>>
>>>> Please set *$MET_HDF* to point to the HDF4 directory.
>>>>
>>>> Cheers,
>>>> Howard
>>>>
>>>>
>>>> On Wed, May 31, 2017 at 8:03 AM, Jinwoong Yoo via RT
<met_help at ucar.edu
>>>> wrote:
>>>>
>>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>>>
>>>>> Hi Howard,
>>>>> Although, after compiling of all the dependency libraries,
>>>>> I am getting error with installing the MET.
>>>>>
>>>>> I set all the environment libraries as directed in the online
tutorial.
>>>>> But it seems the installer cannot find hdf.h file.
>>>>> Please see error message below:
>>>>>
>>>>> *lidar2nc.cc:69:17:* *fatal error: *hdf.h: No such file or
directory
>>>>>
>>>>> compilation terminated.
>>>>>
>>>>> make[5]: *** [lidar2nc-lidar2nc.o] Error 1
>>>>>
>>>>> make[5]: Leaving directory
>>>>> `/home/yoo108/METwithGNU/src/met-
6.0_bugfix/src/tools/other/lidar2nc'
>>>>>
>>>>> make[4]: *** [all-recursive] Error 1
>>>>>
>>>>> make[4]: Leaving directory
>>>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools/other'
>>>>>
>>>>> make[3]: *** [all-recursive] Error 1
>>>>>
>>>>> make[3]: Leaving directory
>>>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools'
>>>>>
>>>>> make[2]: *** [all-recursive] Error 1
>>>>>
>>>>> make[2]: Leaving directory `/home/yoo108/METwithGNU/src/
>>>>> met-6.0_bugfix/src'
>>>>>
>>>>> make[1]: *** [all-recursive] Error 1
>>>>>
>>>>> make[1]: Leaving directory `/home/yoo108/METwithGNU/src/
>> met-6.0_bugfix'
>>>>> make: *** [all] Error 2
>>>>>
>>>>> Do you have any idea?
>>>>> Thank you.
>>>>>
>>>>> Regards,
>>>>>
>>>>> Jinwoong
>>>>>
>>>>> On Tue, May 30, 2017 at 6:21 PM, Howard Soh via RT
<met_help at ucar.edu>
>>>>> wrote:
>>>>>
>>>>>> I'm glad to hear that you can build HDF5 and NetCDF4.
>>>>>>
>>>>>> I appreciated your advice. We will review online tutorial and
make it
>>>>>> clear.
>>>>>>
>>>>>> Cheers,
>>>>>> Howard
>>>>>>
>>>>>> FYI:
>>>>>> hdf5-1.8.17$ ./configure --help | grep enable-hl
>>>>>> --enable-hl Enable the high level library
>> [default=yes]
>>>>>> hdf5-1.8.18$ ./configure --help | grep enable-hl
>>>>>> --enable-hl Enable the high level library
>> [default=yes]
>>>>>>
>>>>>>
>>>>>> On 5/30/2017 2:12 PM, Jinwoong Yoo via RT wrote:
>>>>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>
>>>>>>>
>>>>>>> Hi Howard,
>>>>>>>
>>>>>>> I was able to compile HDF5, Netcdf4-C, and NetCDF-CXX
successfully
>>>>>> finally.
>>>>>>> I happened to know that there were a few typos in the MET
Online
>>>>> Tutorial
>>>>>>> For METv6.0, which led into various confusions.
>>>>>>>
>>>>>>> In the "Compiling HDF5" section,
>>>>>>> I had to configure hdf5 with the "--enable-hl" option along
with "
>>>>>>> *--with-zlib=${ZDIR}*".
>>>>>>>
>>>>>>>
>>>>>>> In the "Compiling NetCDF" section,
>>>>>>> both for NetCDF-C and NetCDF-CXX,
>>>>>>>
>>>>>>> LDFLAGS and CPPFLAGS directories should be assigned to HDF5
>>>> directory,
>>>>>> not
>>>>>>> the NetCDF4 installation directory in
>>>>>>> "LDFLAGS=-L${MET_LIB_DIR}/lib CPPFLAGS=-
I${MET_LIB_DIR}/include"
>>>> while
>>>>>> the
>>>>>>> target directory in "--prefix=${MET_LIB_DIR}" should be
netcdf4
>>>>>> directory.
>>>>>>> You might want to make changes for these error for other
METv6.0
>>>> users
>>>>> on
>>>>>>> your webpage at "
>>>>>>> http://www.dtcenter.org/met/users/support/online_tutorial/
>>>>>> METv6.0/tutorial.php?name=compilation&category=req_libs
>>>>>>> ".
>>>>>>>
>>>>>>> Thank you.
>>>>>>> Regards,
>>>>>>>
>>>>>>> Jinwoong
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Tue, May 30, 2017 at 3:18 PM, Howard Soh via RT <
>>>> met_help at ucar.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Thank you, Jinwoong.
>>>>>>>>
>>>>>>>> Howard
>>>>>>>>
>>>>>>>> On 5/30/2017 12:33 PM, Jinwoong Yoo via RT wrote:
>>>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>>>>>>>
>>>>>>>>> Hi Howard,
>>>>>>>>>
>>>>>>>>> I contacted Unidata regarding the issue already.
>>>>>>>>> Attached please find the file, and see its contents below.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ============================================
>>>>>>>>>
>>>>>>>>> netCDF 4.4.1.1: h5_test/test-suite.log
>>>>>>>>>
>>>>>>>>> ============================================
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> # TOTAL: 26
>>>>>>>>>
>>>>>>>>> # PASS: 25
>>>>>>>>>
>>>>>>>>> # SKIP: 0
>>>>>>>>>
>>>>>>>>> # XFAIL: 0
>>>>>>>>>
>>>>>>>>> # FAIL: 1
>>>>>>>>>
>>>>>>>>> # XPASS: 0
>>>>>>>>>
>>>>>>>>> # ERROR: 0
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> .. contents:: :depth: 2
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> FAIL: tst_h_vars
>>>>>>>>>
>>>>>>>>> ================
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> *** Checking HDF5 variable functions.
>>>>>>>>>
>>>>>>>>> *** Checking HDF5 boolen variables...ok.
>>>>>>>>>
>>>>>>>>> *** Checking HDF5 variable with unlimited dimension...ok.
>>>>>>>>>
>>>>>>>>> *** Checking HDF5 deflate filter setting and
getting...Sorry!
>>>>>> Unexpected
>>>>>>>>> result, tst_h_vars.c, line: 230
>>>>>>>>>
>>>>>>>>> FAIL tst_h_vars (exit status: 2)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thank you.
>>>>>>>>>
>>>>>>>>> Regards,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Jinwoong
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, May 30, 2017 at 2:22 PM, Howard Soh via RT <
>>>>> met_help at ucar.edu>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Jinwoong.
>>>>>>>>>>
>>>>>>>>>> I am sorry to hear that you are still having difficulty
with the
>>>>>> netcdf
>>>>>>>>>> library
>>>>>>>>>> files.
>>>>>>>>>> One unit test related with HDF5 was failed. Would you check
>>>>>>>>>> h5_test/test-suite.log
>>>>>>>>>> and contact Unidata?
>>>>>>>>>> The full path will be /home/yoo108/METwithGNU/src/
>>>>>>>> netcdf-c-4.4.1.1/h5_test
>>>>>>>>>> /test-suite.log.
>>>>>>>>>>
>>>>>>>>>> It would help to understand your problem if you send us
>>>>>>>>>> h5_test/test-suite.log.
>>>>>>>>>>
>>>>>>>>>> Cheers,
>>>>>>>>>> Howard
>>>>>>>>>>
>>>>>>>>>> FYI:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> FAIL: tst_h_vars
>>>>>>>>>>
>>>>>>>>>>
============================================================
>>>>>>>>>> ================
>>>>>>>>>> Testsuite summary for netCDF 4.4.1.1
>>>>>>>>>>
============================================================
>>>>>>>>>> ================
>>>>>>>>>> # TOTAL: 26
>>>>>>>>>> # PASS: 25
>>>>>>>>>> # SKIP: 0
>>>>>>>>>> # XFAIL: 0
>>>>>>>>>> # FAIL: 1
>>>>>>>>>> # XPASS: 0
>>>>>>>>>> # ERROR: 0
>>>>>>>>>>
============================================================
>>>>>>>>>> ================
>>>>>>>>>> See h5_test/test-suite.log
>>>>>>>>>> Please report to support-netcdf at unidata.ucar.edu
>>>>>>>>>>
============================================================
>>>>>>>>>> ================
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
>>>>>>>>>>
>>>>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>>>>>>>>
>>>>>>>>>> I forgot to attach my log file.
>>>>>>>>>> Thanks!
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo <
>>>>> jinwoong.yoo at gmail.com
>>>>>>>>>> <jinwoong.yoo at gmail.com>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>> Thank you for your reply.
>>>>>>>>>>
>>>>>>>>>> I realized that I have to have netcdf4-c and netcdf4-cxx to
>>>> install
>>>>>>>>>> MET-6.0.
>>>>>>>>>> So far, I have compiled HDF5 following directions
>>>>>>>>>>
athttp://www.dtcenter.org/met/users/support/online_tutorial/
>>>>>>>>>> METv6.0/tutorial.php?name=compilation&category=req_libs.
>>>>>>>>>>
>>>>>>>>>> I have built HDF5 successfully using the `--enable-hl`
function
>>>> and
>>>>> I
>>>>>>>> got
>>>>>>>>>> hdf5_h1.1 in my target directory. Previously I got error
>>>> installing
>>>>>>>> netcdf4
>>>>>>>>>> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared"
message (as
>>>>> shown
>>>>>>>>>> inhttps://www.unidata.ucar.edu/support/help/MailArchives/
>>>>>>>>>> netcdf/msg13749.html).
>>>>>>>>>>
>>>>>>>>>> I am referring to unidata webpage for the compilation of
netcdf4
>>>>>>>>>> athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
>>>>>>>>>> and_building_netcdf.html.
>>>>>>>>>> But now I get an error with h5_test within the netcdf make
check
>>>> and
>>>>>> it
>>>>>>>>>> fails.
>>>>>>>>>> Attached please find configure and make log.
>>>>>>>>>> Do you have any know-how to overcome this issue?
>>>>>>>>>> Thank you very much in advance.
>>>>>>>>>>
>>>>>>>>>> Regards,
>>>>>>>>>>
>>>>>>>>>> Jinwoong Yoo
>>>>>>>>>> Purdue Climate Change Research Center
>>>>>>>>>>
>>>>>>>>>> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
>>>>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Hello -
>>>>>>>>>>
>>>>>>>>>> Most of our team is out due to the Memorial Day holiday.
We'll
>>>>> have a
>>>>>>>>>> look
>>>>>>>>>> at your issue when the team is back sometime later this
week.
>>>>>>>>>>
>>>>>>>>>> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
>>>>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Fri May 26 09:39:58 2017: Request 80647 was acted upon.
>>>>>>>>>> Transaction: Ticket created by jinwoong.yoo at gmail.com
>>>>>>>>>> Queue: met_help
>>>>>>>>>> Subject: Error with Compiling MET-6.0
>>>>>>>>>> Owner: Nobody
>>>>>>>>>> Requestors: jinwoong.yoo at gmail.com
>>>>>>>>>> Status: new
>>>>>>>>>> Ticket <URL: https://rt.rap.ucar.edu/rt/
>>>>>> Ticket/Display.html?id=80647
>>>>>>>>>> Dear MET Help
>>>>>>>>>>
>>>>>>>>>> Hi.
>>>>>>>>>> I am trying to compile MET-6.0 bugfixed version on a Linux
cluster
>>>>>>>>>>
>>>>>>>>>> (Redhat)
>>>>>>>>>>
>>>>>>>>>> at Purdue University.
>>>>>>>>>> I am using a few system-wide libraries (e.g., netcdf-3.6.3,
hdf5)
>>>>> and
>>>>>> I
>>>>>>>>>> installed most of the other library myself. Also I set up
all the
>>>>>>>>>> environment variables required.
>>>>>>>>>>
>>>>>>>>>> # MET
>>>>>>>>>>
>>>>>>>>>> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-16.0.1.150
>>>>>>>>>>
>>>>>>>>>> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
>>>>>>>>>>
>>>>>>>>>> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-1.2.7
>>>>>>>>>>
>>>>>>>>>> export MET_UPP=/home/yoo108/UPPV3.1
>>>>>>>>>>
>>>>>>>>>> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
>>>>>>>>>>
>>>>>>>>>> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
>>>>>>>>>>
>>>>>>>>>> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
>>>>>>>>>>
>>>>>>>>>> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
>>>>>>>>>>
>>>>>>>>>> export
MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
>>>>>>>>>>
>>>>>>>>>> export MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
>>>>>>>>>>
>>>>>>>>>> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> However, I got an error with the compilation of the MET-6.0
and it
>>>>>>>>>>
>>>>>>>>>> failed.
>>>>>>>>>>
>>>>>>>>>> The error message reads as below:
>>>>>>>>>>
>>>>>>>>>> MET_BASE="\"/home/yoo108/MET-6.0/share/met\"" -D__64BIT__
-MT
>>>>>>>>>> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
>>>>>>>>>> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
>>>>>>>>>>
>>>>>>>>>> libvx_nc_util_a-nc_var_info.o
>>>>>>>>>>
>>>>>>>>>> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
>>>>>>>>>>
>>>>>>>>>> In file included from nc_var_info.cc(24):
>>>>>>>>>>
>>>>>>>>>> nc_utils.h(22): catastrophic error: cannot open source file
>>>> "netcdf"
>>>>>>>>>> #include <netcdf>
>>>>>>>>>>
>>>>>>>>>> ^
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> compilation aborted for nc_var_info.cc (code 4)
>>>>>>>>>>
>>>>>>>>>> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
>>>>>>>>>>
>>>>>>>>>> make[3]: Leaving directory
>>>>>>>>>> `/home/yoo108/build_MET/src/met-6.0/src/libcode/vx_nc_util'
>>>>>>>>>>
>>>>>>>>>> make[2]: *** [install-recursive] Error 1
>>>>>>>>>>
>>>>>>>>>> make[2]: Leaving directory `/home/yoo108/build_MET/src/
>>>>>>>>>> met-6.0/src/libcode'
>>>>>>>>>>
>>>>>>>>>> make[1]: *** [install-recursive] Error 1
>>>>>>>>>>
>>>>>>>>>> make[1]: Leaving directory `/home/yoo108/build_MET/src/
>>>> met-6.0/src'
>>>>>>>>>> make: *** [install-recursive] Error 1
>>>>>>>>>>
>>>>>>>>>> ^C[1]+ Exit 2 make install
&>make_install.log
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> I wonder if this error is related with the 64 bit cluster
while
>>>> MET
>>>>>>>>>> wants
>>>>>>>>>>
>>>>>>>>>> 32 bit software or else.
>>>>>>>>>>
>>>>>>>>>> Your input will be highly appreciated.
>>>>>>>>>>
>>>>>>>>>> Thank you.
>>>>>>>>>>
>>>>>>>>>> Regards,
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Jinwoong Yoo
>>>>>>>>>>
>>>>>>>>>> Purdue Climate Change Research Center
>>>>>>>>>>
>>>>>>>>>>
>>>>>>
>>
>>
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Jinwoong Yoo
Time: Wed May 31 14:08:35 2017
Hi Howard,
I used GNU gcc, g++, and gfortran to compile MET as well as other
libraries.
Below is output from "ldd bin/ascii2nc":
yoo108 at halstead-fe00:*~/MET-6.0* $ ldd bin/ascii2nc
linux-vdso.so.1 => (0x00007fff967cc000)
libjasper.so.1 => /home/yoo108/CDO/lib/libjasper.so.1
(0x00002b5ef0826000)
libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00000036f6000000)
libz.so.1 => /home/yoo108/METwithGNU/zlib-1.2.11/lib/libz.so.1
(0x00002b5ef0a94000)
libnetcdf_c++4.so.1 =>
/home/yoo108/METwithGNU/netcdf-4.4.1.1/lib/libnetcdf_c++4.so.1
(0x00002b5ef0cb0000)
libnetcdf.so.11 =>
/home/yoo108/METwithGNU/netcdf-4.4.1.1/lib/libnetcdf.so.11
(0x00002b5ef0efb000)
libgsl.so.19 => /home/yoo108/METwithGNU/gsl-2.3/lib/libgsl.so.19
(0x00002b5ef4291000)
libgslcblas.so.0 => /home/yoo108/METwithGNU/gsl-
2.3/lib/libgslcblas.so.0
(0x00002b5ef47b9000)
libstdc++.so.6 => /apps/rhel6/gcc/5.2.0/lib64/libstdc++.so.6
(0x00002b5ef4a11000)
libm.so.6 => /lib64/libm.so.6 (0x00000036f0000000)
libgcc_s.so.1 => /apps/rhel6/gcc/5.2.0/lib64/libgcc_s.so.1
(0x00002b5ef4dc2000)
libc.so.6 => /lib64/libc.so.6 (0x00000036efc00000)
libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x00000036f7000000)
libmpifort.so.12 => /apps/rhel6/intel/impi/
5.1.2.150/intel64/lib/libmpifort.so.12 (0x00002b5ef4fd9000)
libmpi.so.12 => /apps/rhel6/intel/impi/
5.1.2.150/intel64/lib/release_mt/libmpi.so.12 (0x00002b5ef536a000)
libdl.so.2 => /lib64/libdl.so.2 (0x00000036f0400000)
librt.so.1 => /lib64/librt.so.1 (0x00000036f0c00000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00000036f0800000)
libimf.so => not found
libsvml.so => not found
libirng.so => not found
libintlc.so.5 => not found
libnetcdf.so.6 => /usr/lib64/libnetcdf.so.6 (0x00000036fce00000)
libhdf5_hl.so.10 =>
/home/yoo108/METwithGNU/hdf5-1.8.18/lib/libhdf5_hl.so.10
(0x00002b5ef5b2f000)
libhdf5.so.10 => /home/yoo108/METwithGNU/hdf5-1.8.18/lib/libhdf5.so.10
(0x00002b5ef5d51000)
libcurl.so.4 => /usr/lib64/libcurl.so.4 (0x00000036fbc00000)
/lib64/ld-linux-x86-64.so.2 (0x00000036ef400000)
libhdf5_hl.so.6 => /usr/lib64/libhdf5_hl.so.6 (0x00000036fe600000)
libhdf5.so.6 => /usr/lib64/libhdf5.so.6 (0x00000036fc800000)
libidn.so.11 => /lib64/libidn.so.11 (0x00000036fb400000)
libldap-2.4.so.2 => /lib64/libldap-2.4.so.2 (0x00000036f9000000)
libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2 (0x00000036f3800000)
libkrb5.so.3 => /lib64/libkrb5.so.3 (0x00000036f3000000)
libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x00000036f5800000)
libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00000036f2400000)
libssl3.so => /usr/lib64/libssl3.so (0x00000036f7400000)
libsmime3.so => /usr/lib64/libsmime3.so (0x00000036f7c00000)
libnss3.so => /usr/lib64/libnss3.so (0x00000036f5000000)
libnssutil3.so => /usr/lib64/libnssutil3.so (0x00000036f2c00000)
libplds4.so => /lib64/libplds4.so (0x00000036f3c00000)
libplc4.so => /lib64/libplc4.so (0x00000036f4800000)
libnspr4.so => /lib64/libnspr4.so (0x00000036f3400000)
libssh2.so.1 => /usr/lib64/libssh2.so.1 (0x00000036fac00000)
liblber-2.4.so.2 => /lib64/liblber-2.4.so.2 (0x00000036f8400000)
libresolv.so.2 => /lib64/libresolv.so.2 (0x00000036f1c00000)
libsasl2.so.2 => /usr/lib64/libsasl2.so.2 (0x00000036f9800000)
libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x00000036f5400000)
libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00000036f4000000)
libssl.so.10 => /usr/lib64/libssl.so.10 (0x00000036f5c00000)
libcrypto.so.10 => /usr/lib64/libcrypto.so.10 (0x00000036f2000000)
libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00000036f4400000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x00000036f1400000)
libfreebl3.so => /usr/lib64/libfreebl3.so (0x00000036f2800000)
Thank you.
Regards,
Jinwoong
On Wed, May 31, 2017 at 4:02 PM, Howard Soh via RT <met_help at ucar.edu>
wrote:
> I am sorry to hear that you are still having difficulty with running
MET.
>
> The error message implies that the MET was compiled with Intel but
the
> Intel libraries are not available at runtime.
> It puzzles me why the build environment and the running environment
are
> different.
> It's better to use one compiler for MET and dependent libraries. The
log
> file for HDF5 and NetCDF4 shows they were built with gcc 5.2.0.
> Would you check which compilers were used to build MET and other
dependent
> libraries?
>
> The first step will be finding which libraries not not available.
> Would you execute ldd command and send me the output?
>
> ldd bin/ascii2nc
>
>
> Cheers,
> Howard
>
> FYI:
> If there is "not found", the path for those libraries should be
added
> LD_LIBRARY_PATH.
>
> For example,
> libnetcdf_c++4.so.1 => not found
> libnetcdf_c++.so.4 => not found
> libnetcdf.so.7 => not found
> libimf.so => not found
>
> NetCDF library and Intel libraries are missing. In case of Intel
library,
> it's better to be resolved not by using LD_LIBRARY_PATH. If "module"
> command is available, please use it "module load intel".
>
>
> On 5/31/2017 1:00 PM, Jinwoong Yoo via RT wrote:
>
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >
> > Hi Howard,
> >
> > I thought my MET compilation completed.
> > But it seems not.
> >
> > When I typed in met commands in bin directory,
> > I got errors as below:
> >
> > yoo108 at halstead-fe00:*~/MET-6.0* $ bin/pcp_combine
> >
> > bin/pcp_combine: error while loading shared libraries: libimf.so:
cannot
> > open shared object file: No such file or directory
> >
> > yoo108 at halstead-fe00:*~/MET-6.0* $ which ascii2nc
> >
> > ~/MET-6.0/bin/ascii2nc
> >
> > yoo108 at halstead-fe00:*~/MET-6.0* $ ascii2nc
> >
> > ascii2nc: error while loading shared libraries: libimf.so: cannot
open
> > shared object file: No such file or directory
> >
> > yoo108 at halstead-fe00:*~/MET-6.0* $ mode
> >
> > mode: error while loading shared libraries: libimf.so: cannot open
shared
> > object file: No such file or directory
> >
> > yoo108 at halstead-fe00:*~/MET-6.0* $ mtd
> >
> > mtd: error while loading shared libraries: libimf.so: cannot open
shared
> > object file: No such file or directory
> >
> > yoo108 at halstead-fe00:*~/MET-6.0* $ pb2nc
> >
> > pb2nc: error while loading shared libraries: libimf.so: cannot
open
> shared
> > object file: No such file or directory
> >
> >
> > What I should do?
> >
> > It seems there is no lib directory compiled with MET-6.0.
> >
> > I am not sure which libimf.so file is needed.
> >
> > Thank you.
> >
> >
> > Regards,
> >
> >
> > Jinwoong
> >
> >
> >
> >
> > On Wed, May 31, 2017 at 2:03 PM, Howard Soh via RT
<met_help at ucar.edu>
> > wrote:
> >
> >> You're very welcome.
> >>
> >> Please let us know if you encounter any other difficulties.**I'll
go
> >> ahead and close this ticket for now then. Please open a new
ticket if
> >> further questions or problems.
> >>
> >> Thanks,
> >> Howard
> >>
> >>
> >> On 5/31/2017 11:45 AM, Jinwoong Yoo via RT wrote:
> >>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >>>
> >>> Hi Howard,
> >>>
> >>> Thank you much for your note.
> >>> Finally I was able to complete the installation of MET-6.0.
> >>> But I should let you know that I encountered several errors
probably
> due
> >> to
> >>> the outdated make file for the new include directory structures
of
> recent
> >>> versions of HDF-EOS2, Cairo, and Freetype.
> >>>
> >>> Thank you.
> >>> Regards,
> >>>
> >>> Jinwoong
> >>>
> >>> On Wed, May 31, 2017 at 11:58 AM, Howard Soh via RT
<met_help at ucar.edu
> >
> >>> wrote:
> >>>
> >>>> MET still uses HDF4 library instead of HDF5 because of another
> >> dependency,
> >>>> HDF-EOS.
> >>>>
> >>>> Note: hdf.h is for HDF4 and hdf5.h is for HDF5
> >>>>
> >>>> NetCDF4 requires HDF5 on building and running. Once NetCDF
library is
> >>>> built, HDF5 is not required to build MET, but required to run
MET.
> >>>>
> >>>> Please set *$MET_HDF* to point to the HDF4 directory.
> >>>>
> >>>> Cheers,
> >>>> Howard
> >>>>
> >>>>
> >>>> On Wed, May 31, 2017 at 8:03 AM, Jinwoong Yoo via RT <
> met_help at ucar.edu
> >>>> wrote:
> >>>>
> >>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>
> >>>>>
> >>>>> Hi Howard,
> >>>>> Although, after compiling of all the dependency libraries,
> >>>>> I am getting error with installing the MET.
> >>>>>
> >>>>> I set all the environment libraries as directed in the online
> tutorial.
> >>>>> But it seems the installer cannot find hdf.h file.
> >>>>> Please see error message below:
> >>>>>
> >>>>> *lidar2nc.cc:69:17:* *fatal error: *hdf.h: No such file or
directory
> >>>>>
> >>>>> compilation terminated.
> >>>>>
> >>>>> make[5]: *** [lidar2nc-lidar2nc.o] Error 1
> >>>>>
> >>>>> make[5]: Leaving directory
> >>>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools/
> other/lidar2nc'
> >>>>>
> >>>>> make[4]: *** [all-recursive] Error 1
> >>>>>
> >>>>> make[4]: Leaving directory
> >>>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools/other'
> >>>>>
> >>>>> make[3]: *** [all-recursive] Error 1
> >>>>>
> >>>>> make[3]: Leaving directory
> >>>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools'
> >>>>>
> >>>>> make[2]: *** [all-recursive] Error 1
> >>>>>
> >>>>> make[2]: Leaving directory `/home/yoo108/METwithGNU/src/
> >>>>> met-6.0_bugfix/src'
> >>>>>
> >>>>> make[1]: *** [all-recursive] Error 1
> >>>>>
> >>>>> make[1]: Leaving directory `/home/yoo108/METwithGNU/src/
> >> met-6.0_bugfix'
> >>>>> make: *** [all] Error 2
> >>>>>
> >>>>> Do you have any idea?
> >>>>> Thank you.
> >>>>>
> >>>>> Regards,
> >>>>>
> >>>>> Jinwoong
> >>>>>
> >>>>> On Tue, May 30, 2017 at 6:21 PM, Howard Soh via RT <
> met_help at ucar.edu>
> >>>>> wrote:
> >>>>>
> >>>>>> I'm glad to hear that you can build HDF5 and NetCDF4.
> >>>>>>
> >>>>>> I appreciated your advice. We will review online tutorial and
make
> it
> >>>>>> clear.
> >>>>>>
> >>>>>> Cheers,
> >>>>>> Howard
> >>>>>>
> >>>>>> FYI:
> >>>>>> hdf5-1.8.17$ ./configure --help | grep enable-hl
> >>>>>> --enable-hl Enable the high level library
> >> [default=yes]
> >>>>>> hdf5-1.8.18$ ./configure --help | grep enable-hl
> >>>>>> --enable-hl Enable the high level library
> >> [default=yes]
> >>>>>>
> >>>>>>
> >>>>>> On 5/30/2017 2:12 PM, Jinwoong Yoo via RT wrote:
> >>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >>>>>>>
> >>>>>>> Hi Howard,
> >>>>>>>
> >>>>>>> I was able to compile HDF5, Netcdf4-C, and NetCDF-CXX
successfully
> >>>>>> finally.
> >>>>>>> I happened to know that there were a few typos in the MET
Online
> >>>>> Tutorial
> >>>>>>> For METv6.0, which led into various confusions.
> >>>>>>>
> >>>>>>> In the "Compiling HDF5" section,
> >>>>>>> I had to configure hdf5 with the "--enable-hl" option along
with "
> >>>>>>> *--with-zlib=${ZDIR}*".
> >>>>>>>
> >>>>>>>
> >>>>>>> In the "Compiling NetCDF" section,
> >>>>>>> both for NetCDF-C and NetCDF-CXX,
> >>>>>>>
> >>>>>>> LDFLAGS and CPPFLAGS directories should be assigned to HDF5
> >>>> directory,
> >>>>>> not
> >>>>>>> the NetCDF4 installation directory in
> >>>>>>> "LDFLAGS=-L${MET_LIB_DIR}/lib CPPFLAGS=-
I${MET_LIB_DIR}/include"
> >>>> while
> >>>>>> the
> >>>>>>> target directory in "--prefix=${MET_LIB_DIR}" should be
netcdf4
> >>>>>> directory.
> >>>>>>> You might want to make changes for these error for other
METv6.0
> >>>> users
> >>>>> on
> >>>>>>> your webpage at "
> >>>>>>> http://www.dtcenter.org/met/users/support/online_tutorial/
> >>>>>> METv6.0/tutorial.php?name=compilation&category=req_libs
> >>>>>>> ".
> >>>>>>>
> >>>>>>> Thank you.
> >>>>>>> Regards,
> >>>>>>>
> >>>>>>> Jinwoong
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> On Tue, May 30, 2017 at 3:18 PM, Howard Soh via RT <
> >>>> met_help at ucar.edu>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>>> Thank you, Jinwoong.
> >>>>>>>>
> >>>>>>>> Howard
> >>>>>>>>
> >>>>>>>> On 5/30/2017 12:33 PM, Jinwoong Yoo via RT wrote:
> >>>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >>>>>>>>>
> >>>>>>>>> Hi Howard,
> >>>>>>>>>
> >>>>>>>>> I contacted Unidata regarding the issue already.
> >>>>>>>>> Attached please find the file, and see its contents below.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> ============================================
> >>>>>>>>>
> >>>>>>>>> netCDF 4.4.1.1: h5_test/test-suite.log
> >>>>>>>>>
> >>>>>>>>> ============================================
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> # TOTAL: 26
> >>>>>>>>>
> >>>>>>>>> # PASS: 25
> >>>>>>>>>
> >>>>>>>>> # SKIP: 0
> >>>>>>>>>
> >>>>>>>>> # XFAIL: 0
> >>>>>>>>>
> >>>>>>>>> # FAIL: 1
> >>>>>>>>>
> >>>>>>>>> # XPASS: 0
> >>>>>>>>>
> >>>>>>>>> # ERROR: 0
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> .. contents:: :depth: 2
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> FAIL: tst_h_vars
> >>>>>>>>>
> >>>>>>>>> ================
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> *** Checking HDF5 variable functions.
> >>>>>>>>>
> >>>>>>>>> *** Checking HDF5 boolen variables...ok.
> >>>>>>>>>
> >>>>>>>>> *** Checking HDF5 variable with unlimited dimension...ok.
> >>>>>>>>>
> >>>>>>>>> *** Checking HDF5 deflate filter setting and
getting...Sorry!
> >>>>>> Unexpected
> >>>>>>>>> result, tst_h_vars.c, line: 230
> >>>>>>>>>
> >>>>>>>>> FAIL tst_h_vars (exit status: 2)
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Thank you.
> >>>>>>>>>
> >>>>>>>>> Regards,
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Jinwoong
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On Tue, May 30, 2017 at 2:22 PM, Howard Soh via RT <
> >>>>> met_help at ucar.edu>
> >>>>>>>>> wrote:
> >>>>>>>>>
> >>>>>>>>>> Hi Jinwoong.
> >>>>>>>>>>
> >>>>>>>>>> I am sorry to hear that you are still having difficulty
with the
> >>>>>> netcdf
> >>>>>>>>>> library
> >>>>>>>>>> files.
> >>>>>>>>>> One unit test related with HDF5 was failed. Would you
check
> >>>>>>>>>> h5_test/test-suite.log
> >>>>>>>>>> and contact Unidata?
> >>>>>>>>>> The full path will be /home/yoo108/METwithGNU/src/
> >>>>>>>> netcdf-c-4.4.1.1/h5_test
> >>>>>>>>>> /test-suite.log.
> >>>>>>>>>>
> >>>>>>>>>> It would help to understand your problem if you send us
> >>>>>>>>>> h5_test/test-suite.log.
> >>>>>>>>>>
> >>>>>>>>>> Cheers,
> >>>>>>>>>> Howard
> >>>>>>>>>>
> >>>>>>>>>> FYI:
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> FAIL: tst_h_vars
> >>>>>>>>>>
> >>>>>>>>>>
============================================================
> >>>>>>>>>> ================
> >>>>>>>>>> Testsuite summary for netCDF 4.4.1.1
> >>>>>>>>>>
============================================================
> >>>>>>>>>> ================
> >>>>>>>>>> # TOTAL: 26
> >>>>>>>>>> # PASS: 25
> >>>>>>>>>> # SKIP: 0
> >>>>>>>>>> # XFAIL: 0
> >>>>>>>>>> # FAIL: 1
> >>>>>>>>>> # XPASS: 0
> >>>>>>>>>> # ERROR: 0
> >>>>>>>>>>
============================================================
> >>>>>>>>>> ================
> >>>>>>>>>> See h5_test/test-suite.log
> >>>>>>>>>> Please report to support-netcdf at unidata.ucar.edu
> >>>>>>>>>>
============================================================
> >>>>>>>>>> ================
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
> >>>>>>>>>>
> >>>>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >>>>>>>>>>
> >>>>>>>>>> I forgot to attach my log file.
> >>>>>>>>>> Thanks!
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo <
> >>>>> jinwoong.yoo at gmail.com
> >>>>>>>>>> <jinwoong.yoo at gmail.com>
> >>>>>>>>>> wrote:
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> Hi,
> >>>>>>>>>> Thank you for your reply.
> >>>>>>>>>>
> >>>>>>>>>> I realized that I have to have netcdf4-c and netcdf4-cxx
to
> >>>> install
> >>>>>>>>>> MET-6.0.
> >>>>>>>>>> So far, I have compiled HDF5 following directions
> >>>>>>>>>>
athttp://www.dtcenter.org/met/users/support/online_tutorial/
> >>>>>>>>>> METv6.0/tutorial.php?name=compilation&category=req_libs.
> >>>>>>>>>>
> >>>>>>>>>> I have built HDF5 successfully using the `--enable-hl`
function
> >>>> and
> >>>>> I
> >>>>>>>> got
> >>>>>>>>>> hdf5_h1.1 in my target directory. Previously I got error
> >>>> installing
> >>>>>>>> netcdf4
> >>>>>>>>>> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared"
message (as
> >>>>> shown
> >>>>>>>>>> inhttps://www.unidata.ucar.edu/support/help/MailArchives/
> >>>>>>>>>> netcdf/msg13749.html).
> >>>>>>>>>>
> >>>>>>>>>> I am referring to unidata webpage for the compilation of
netcdf4
> >>>>>>>>>>
athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
> >>>>>>>>>> and_building_netcdf.html.
> >>>>>>>>>> But now I get an error with h5_test within the netcdf
make check
> >>>> and
> >>>>>> it
> >>>>>>>>>> fails.
> >>>>>>>>>> Attached please find configure and make log.
> >>>>>>>>>> Do you have any know-how to overcome this issue?
> >>>>>>>>>> Thank you very much in advance.
> >>>>>>>>>>
> >>>>>>>>>> Regards,
> >>>>>>>>>>
> >>>>>>>>>> Jinwoong Yoo
> >>>>>>>>>> Purdue Climate Change Research Center
> >>>>>>>>>>
> >>>>>>>>>> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
> >>>>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
> >>>>>>>>>> wrote:
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> Hello -
> >>>>>>>>>>
> >>>>>>>>>> Most of our team is out due to the Memorial Day holiday.
We'll
> >>>>> have a
> >>>>>>>>>> look
> >>>>>>>>>> at your issue when the team is back sometime later this
week.
> >>>>>>>>>>
> >>>>>>>>>> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
> >>>>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
> >>>>>>>>>> wrote:
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> Fri May 26 09:39:58 2017: Request 80647 was acted upon.
> >>>>>>>>>> Transaction: Ticket created by jinwoong.yoo at gmail.com
> >>>>>>>>>> Queue: met_help
> >>>>>>>>>> Subject: Error with Compiling MET-6.0
> >>>>>>>>>> Owner: Nobody
> >>>>>>>>>> Requestors: jinwoong.yoo at gmail.com
> >>>>>>>>>> Status: new
> >>>>>>>>>> Ticket <URL: https://rt.rap.ucar.edu/rt/
> >>>>>> Ticket/Display.html?id=80647
> >>>>>>>>>> Dear MET Help
> >>>>>>>>>>
> >>>>>>>>>> Hi.
> >>>>>>>>>> I am trying to compile MET-6.0 bugfixed version on a
Linux
> cluster
> >>>>>>>>>>
> >>>>>>>>>> (Redhat)
> >>>>>>>>>>
> >>>>>>>>>> at Purdue University.
> >>>>>>>>>> I am using a few system-wide libraries (e.g., netcdf-
3.6.3,
> hdf5)
> >>>>> and
> >>>>>> I
> >>>>>>>>>> installed most of the other library myself. Also I set up
all
> the
> >>>>>>>>>> environment variables required.
> >>>>>>>>>>
> >>>>>>>>>> # MET
> >>>>>>>>>>
> >>>>>>>>>> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-
16.0.1.150
> >>>>>>>>>>
> >>>>>>>>>> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
> >>>>>>>>>>
> >>>>>>>>>> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-
1.2.7
> >>>>>>>>>>
> >>>>>>>>>> export MET_UPP=/home/yoo108/UPPV3.1
> >>>>>>>>>>
> >>>>>>>>>> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
> >>>>>>>>>>
> >>>>>>>>>> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
> >>>>>>>>>>
> >>>>>>>>>> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
> >>>>>>>>>>
> >>>>>>>>>> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
> >>>>>>>>>>
> >>>>>>>>>> export
MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
> >>>>>>>>>>
> >>>>>>>>>> export
MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
> >>>>>>>>>>
> >>>>>>>>>> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> However, I got an error with the compilation of the MET-
6.0 and
> it
> >>>>>>>>>>
> >>>>>>>>>> failed.
> >>>>>>>>>>
> >>>>>>>>>> The error message reads as below:
> >>>>>>>>>>
> >>>>>>>>>> MET_BASE="\"/home/yoo108/MET-6.0/share/met\""
-D__64BIT__ -MT
> >>>>>>>>>> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
> >>>>>>>>>> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
> >>>>>>>>>>
> >>>>>>>>>> libvx_nc_util_a-nc_var_info.o
> >>>>>>>>>>
> >>>>>>>>>> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
> >>>>>>>>>>
> >>>>>>>>>> In file included from nc_var_info.cc(24):
> >>>>>>>>>>
> >>>>>>>>>> nc_utils.h(22): catastrophic error: cannot open source
file
> >>>> "netcdf"
> >>>>>>>>>> #include <netcdf>
> >>>>>>>>>>
> >>>>>>>>>> ^
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> compilation aborted for nc_var_info.cc (code 4)
> >>>>>>>>>>
> >>>>>>>>>> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
> >>>>>>>>>>
> >>>>>>>>>> make[3]: Leaving directory
> >>>>>>>>>> `/home/yoo108/build_MET/src/met-
6.0/src/libcode/vx_nc_util'
> >>>>>>>>>>
> >>>>>>>>>> make[2]: *** [install-recursive] Error 1
> >>>>>>>>>>
> >>>>>>>>>> make[2]: Leaving directory `/home/yoo108/build_MET/src/
> >>>>>>>>>> met-6.0/src/libcode'
> >>>>>>>>>>
> >>>>>>>>>> make[1]: *** [install-recursive] Error 1
> >>>>>>>>>>
> >>>>>>>>>> make[1]: Leaving directory `/home/yoo108/build_MET/src/
> >>>> met-6.0/src'
> >>>>>>>>>> make: *** [install-recursive] Error 1
> >>>>>>>>>>
> >>>>>>>>>> ^C[1]+ Exit 2 make install
&>make_install.log
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> I wonder if this error is related with the 64 bit cluster
while
> >>>> MET
> >>>>>>>>>> wants
> >>>>>>>>>>
> >>>>>>>>>> 32 bit software or else.
> >>>>>>>>>>
> >>>>>>>>>> Your input will be highly appreciated.
> >>>>>>>>>>
> >>>>>>>>>> Thank you.
> >>>>>>>>>>
> >>>>>>>>>> Regards,
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> Jinwoong Yoo
> >>>>>>>>>>
> >>>>>>>>>> Purdue Climate Change Research Center
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>
> >>
> >>
>
>
>
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Jinwoong Yoo
Time: Wed May 31 15:08:28 2017
Hi Howard,
It seems there were some interferences from my other libraries that
were
built using intel compilers.
When I removed them from my environment and re-compiled the MET-6.0,
it
works without any previous error message.
Thank you very much for your clue.
Regards,
Jinwoong
On Wed, May 31, 2017 at 4:08 PM, Jinwoong Yoo <jinwoong.yoo at gmail.com>
wrote:
> Hi Howard,
>
> I used GNU gcc, g++, and gfortran to compile MET as well as other
> libraries.
>
> Below is output from "ldd bin/ascii2nc":
>
> yoo108 at halstead-fe00:*~/MET-6.0* $ ldd bin/ascii2nc
>
> linux-vdso.so.1 => (0x00007fff967cc000)
>
> libjasper.so.1 => /home/yoo108/CDO/lib/libjasper.so.1
(0x00002b5ef0826000)
>
> libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00000036f6000000)
>
> libz.so.1 => /home/yoo108/METwithGNU/zlib-1.2.11/lib/libz.so.1
> (0x00002b5ef0a94000)
>
> libnetcdf_c++4.so.1 => /home/yoo108/METwithGNU/
> netcdf-4.4.1.1/lib/libnetcdf_c++4.so.1 (0x00002b5ef0cb0000)
>
> libnetcdf.so.11 => /home/yoo108/METwithGNU/netcdf-
4.4.1.1/lib/libnetcdf.so.11
> (0x00002b5ef0efb000)
>
> libgsl.so.19 => /home/yoo108/METwithGNU/gsl-2.3/lib/libgsl.so.19
> (0x00002b5ef4291000)
>
> libgslcblas.so.0 => /home/yoo108/METwithGNU/gsl-
2.3/lib/libgslcblas.so.0
> (0x00002b5ef47b9000)
>
> libstdc++.so.6 => /apps/rhel6/gcc/5.2.0/lib64/libstdc++.so.6
> (0x00002b5ef4a11000)
>
> libm.so.6 => /lib64/libm.so.6 (0x00000036f0000000)
>
> libgcc_s.so.1 => /apps/rhel6/gcc/5.2.0/lib64/libgcc_s.so.1
> (0x00002b5ef4dc2000)
>
> libc.so.6 => /lib64/libc.so.6 (0x00000036efc00000)
>
> libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x00000036f7000000)
>
> libmpifort.so.12 => /apps/rhel6/intel/impi/5.1.2.
> 150/intel64/lib/libmpifort.so.12 (0x00002b5ef4fd9000)
>
> libmpi.so.12 =>
/apps/rhel6/intel/impi/5.1.2.150/intel64/lib/release_mt/
> libmpi.so.12 (0x00002b5ef536a000)
>
> libdl.so.2 => /lib64/libdl.so.2 (0x00000036f0400000)
>
> librt.so.1 => /lib64/librt.so.1 (0x00000036f0c00000)
>
> libpthread.so.0 => /lib64/libpthread.so.0 (0x00000036f0800000)
>
> libimf.so => not found
>
> libsvml.so => not found
>
> libirng.so => not found
>
> libintlc.so.5 => not found
>
> libnetcdf.so.6 => /usr/lib64/libnetcdf.so.6 (0x00000036fce00000)
>
> libhdf5_hl.so.10 => /home/yoo108/METwithGNU/hdf5-
1.8.18/lib/libhdf5_hl.so.10
> (0x00002b5ef5b2f000)
>
> libhdf5.so.10 => /home/yoo108/METwithGNU/hdf5-
1.8.18/lib/libhdf5.so.10
> (0x00002b5ef5d51000)
>
> libcurl.so.4 => /usr/lib64/libcurl.so.4 (0x00000036fbc00000)
>
> /lib64/ld-linux-x86-64.so.2 (0x00000036ef400000)
>
> libhdf5_hl.so.6 => /usr/lib64/libhdf5_hl.so.6 (0x00000036fe600000)
>
> libhdf5.so.6 => /usr/lib64/libhdf5.so.6 (0x00000036fc800000)
>
> libidn.so.11 => /lib64/libidn.so.11 (0x00000036fb400000)
>
> libldap-2.4.so.2 => /lib64/libldap-2.4.so.2 (0x00000036f9000000)
>
> libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2
(0x00000036f3800000)
>
> libkrb5.so.3 => /lib64/libkrb5.so.3 (0x00000036f3000000)
>
> libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x00000036f5800000)
>
> libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00000036f2400000)
>
> libssl3.so => /usr/lib64/libssl3.so (0x00000036f7400000)
>
> libsmime3.so => /usr/lib64/libsmime3.so (0x00000036f7c00000)
>
> libnss3.so => /usr/lib64/libnss3.so (0x00000036f5000000)
>
> libnssutil3.so => /usr/lib64/libnssutil3.so (0x00000036f2c00000)
>
> libplds4.so => /lib64/libplds4.so (0x00000036f3c00000)
>
> libplc4.so => /lib64/libplc4.so (0x00000036f4800000)
>
> libnspr4.so => /lib64/libnspr4.so (0x00000036f3400000)
>
> libssh2.so.1 => /usr/lib64/libssh2.so.1 (0x00000036fac00000)
>
> liblber-2.4.so.2 => /lib64/liblber-2.4.so.2 (0x00000036f8400000)
>
> libresolv.so.2 => /lib64/libresolv.so.2 (0x00000036f1c00000)
>
> libsasl2.so.2 => /usr/lib64/libsasl2.so.2 (0x00000036f9800000)
>
> libkrb5support.so.0 => /lib64/libkrb5support.so.0
(0x00000036f5400000)
>
> libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00000036f4000000)
>
> libssl.so.10 => /usr/lib64/libssl.so.10 (0x00000036f5c00000)
>
> libcrypto.so.10 => /usr/lib64/libcrypto.so.10 (0x00000036f2000000)
>
> libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00000036f4400000)
>
> libselinux.so.1 => /lib64/libselinux.so.1 (0x00000036f1400000)
>
> libfreebl3.so => /usr/lib64/libfreebl3.so (0x00000036f2800000)
>
>
> Thank you.
>
> Regards,
>
>
> Jinwoong
>
>
> On Wed, May 31, 2017 at 4:02 PM, Howard Soh via RT
<met_help at ucar.edu>
> wrote:
>
>> I am sorry to hear that you are still having difficulty with
running MET.
>>
>> The error message implies that the MET was compiled with Intel but
the
>> Intel libraries are not available at runtime.
>> It puzzles me why the build environment and the running environment
are
>> different.
>> It's better to use one compiler for MET and dependent libraries.
The log
>> file for HDF5 and NetCDF4 shows they were built with gcc 5.2.0.
>> Would you check which compilers were used to build MET and other
>> dependent libraries?
>>
>> The first step will be finding which libraries not not available.
>> Would you execute ldd command and send me the output?
>>
>> ldd bin/ascii2nc
>>
>>
>> Cheers,
>> Howard
>>
>> FYI:
>> If there is "not found", the path for those libraries should be
added
>> LD_LIBRARY_PATH.
>>
>> For example,
>> libnetcdf_c++4.so.1 => not found
>> libnetcdf_c++.so.4 => not found
>> libnetcdf.so.7 => not found
>> libimf.so => not found
>>
>> NetCDF library and Intel libraries are missing. In case of Intel
library,
>> it's better to be resolved not by using LD_LIBRARY_PATH. If
"module"
>> command is available, please use it "module load intel".
>>
>>
>> On 5/31/2017 1:00 PM, Jinwoong Yoo via RT wrote:
>>
>> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>> >
>> > Hi Howard,
>> >
>> > I thought my MET compilation completed.
>> > But it seems not.
>> >
>> > When I typed in met commands in bin directory,
>> > I got errors as below:
>> >
>> > yoo108 at halstead-fe00:*~/MET-6.0* $ bin/pcp_combine
>> >
>> > bin/pcp_combine: error while loading shared libraries: libimf.so:
cannot
>> > open shared object file: No such file or directory
>> >
>> > yoo108 at halstead-fe00:*~/MET-6.0* $ which ascii2nc
>> >
>> > ~/MET-6.0/bin/ascii2nc
>> >
>> > yoo108 at halstead-fe00:*~/MET-6.0* $ ascii2nc
>> >
>> > ascii2nc: error while loading shared libraries: libimf.so: cannot
open
>> > shared object file: No such file or directory
>> >
>> > yoo108 at halstead-fe00:*~/MET-6.0* $ mode
>> >
>> > mode: error while loading shared libraries: libimf.so: cannot
open
>> shared
>> > object file: No such file or directory
>> >
>> > yoo108 at halstead-fe00:*~/MET-6.0* $ mtd
>> >
>> > mtd: error while loading shared libraries: libimf.so: cannot open
shared
>> > object file: No such file or directory
>> >
>> > yoo108 at halstead-fe00:*~/MET-6.0* $ pb2nc
>> >
>> > pb2nc: error while loading shared libraries: libimf.so: cannot
open
>> shared
>> > object file: No such file or directory
>> >
>> >
>> > What I should do?
>> >
>> > It seems there is no lib directory compiled with MET-6.0.
>> >
>> > I am not sure which libimf.so file is needed.
>> >
>> > Thank you.
>> >
>> >
>> > Regards,
>> >
>> >
>> > Jinwoong
>> >
>> >
>> >
>> >
>> > On Wed, May 31, 2017 at 2:03 PM, Howard Soh via RT
<met_help at ucar.edu>
>> > wrote:
>> >
>> >> You're very welcome.
>> >>
>> >> Please let us know if you encounter any other
difficulties.**I'll go
>> >> ahead and close this ticket for now then. Please open a new
ticket if
>> >> further questions or problems.
>> >>
>> >> Thanks,
>> >> Howard
>> >>
>> >>
>> >> On 5/31/2017 11:45 AM, Jinwoong Yoo via RT wrote:
>> >>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>> >>>
>> >>> Hi Howard,
>> >>>
>> >>> Thank you much for your note.
>> >>> Finally I was able to complete the installation of MET-6.0.
>> >>> But I should let you know that I encountered several errors
probably
>> due
>> >> to
>> >>> the outdated make file for the new include directory structures
of
>> recent
>> >>> versions of HDF-EOS2, Cairo, and Freetype.
>> >>>
>> >>> Thank you.
>> >>> Regards,
>> >>>
>> >>> Jinwoong
>> >>>
>> >>> On Wed, May 31, 2017 at 11:58 AM, Howard Soh via RT <
>> met_help at ucar.edu>
>> >>> wrote:
>> >>>
>> >>>> MET still uses HDF4 library instead of HDF5 because of another
>> >> dependency,
>> >>>> HDF-EOS.
>> >>>>
>> >>>> Note: hdf.h is for HDF4 and hdf5.h is for HDF5
>> >>>>
>> >>>> NetCDF4 requires HDF5 on building and running. Once NetCDF
library is
>> >>>> built, HDF5 is not required to build MET, but required to run
MET.
>> >>>>
>> >>>> Please set *$MET_HDF* to point to the HDF4 directory.
>> >>>>
>> >>>> Cheers,
>> >>>> Howard
>> >>>>
>> >>>>
>> >>>> On Wed, May 31, 2017 at 8:03 AM, Jinwoong Yoo via RT <
>> met_help at ucar.edu
>> >>>> wrote:
>> >>>>
>> >>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>
>> >>>>>
>> >>>>> Hi Howard,
>> >>>>> Although, after compiling of all the dependency libraries,
>> >>>>> I am getting error with installing the MET.
>> >>>>>
>> >>>>> I set all the environment libraries as directed in the online
>> tutorial.
>> >>>>> But it seems the installer cannot find hdf.h file.
>> >>>>> Please see error message below:
>> >>>>>
>> >>>>> *lidar2nc.cc:69:17:* *fatal error: *hdf.h: No such file or
directory
>> >>>>>
>> >>>>> compilation terminated.
>> >>>>>
>> >>>>> make[5]: *** [lidar2nc-lidar2nc.o] Error 1
>> >>>>>
>> >>>>> make[5]: Leaving directory
>> >>>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools/other/
>> lidar2nc'
>> >>>>>
>> >>>>> make[4]: *** [all-recursive] Error 1
>> >>>>>
>> >>>>> make[4]: Leaving directory
>> >>>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools/other'
>> >>>>>
>> >>>>> make[3]: *** [all-recursive] Error 1
>> >>>>>
>> >>>>> make[3]: Leaving directory
>> >>>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools'
>> >>>>>
>> >>>>> make[2]: *** [all-recursive] Error 1
>> >>>>>
>> >>>>> make[2]: Leaving directory `/home/yoo108/METwithGNU/src/
>> >>>>> met-6.0_bugfix/src'
>> >>>>>
>> >>>>> make[1]: *** [all-recursive] Error 1
>> >>>>>
>> >>>>> make[1]: Leaving directory `/home/yoo108/METwithGNU/src/
>> >> met-6.0_bugfix'
>> >>>>> make: *** [all] Error 2
>> >>>>>
>> >>>>> Do you have any idea?
>> >>>>> Thank you.
>> >>>>>
>> >>>>> Regards,
>> >>>>>
>> >>>>> Jinwoong
>> >>>>>
>> >>>>> On Tue, May 30, 2017 at 6:21 PM, Howard Soh via RT <
>> met_help at ucar.edu>
>> >>>>> wrote:
>> >>>>>
>> >>>>>> I'm glad to hear that you can build HDF5 and NetCDF4.
>> >>>>>>
>> >>>>>> I appreciated your advice. We will review online tutorial
and make
>> it
>> >>>>>> clear.
>> >>>>>>
>> >>>>>> Cheers,
>> >>>>>> Howard
>> >>>>>>
>> >>>>>> FYI:
>> >>>>>> hdf5-1.8.17$ ./configure --help | grep enable-hl
>> >>>>>> --enable-hl Enable the high level library
>> >> [default=yes]
>> >>>>>> hdf5-1.8.18$ ./configure --help | grep enable-hl
>> >>>>>> --enable-hl Enable the high level library
>> >> [default=yes]
>> >>>>>>
>> >>>>>>
>> >>>>>> On 5/30/2017 2:12 PM, Jinwoong Yoo via RT wrote:
>> >>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>> >>>>>>>
>> >>>>>>> Hi Howard,
>> >>>>>>>
>> >>>>>>> I was able to compile HDF5, Netcdf4-C, and NetCDF-CXX
successfully
>> >>>>>> finally.
>> >>>>>>> I happened to know that there were a few typos in the MET
Online
>> >>>>> Tutorial
>> >>>>>>> For METv6.0, which led into various confusions.
>> >>>>>>>
>> >>>>>>> In the "Compiling HDF5" section,
>> >>>>>>> I had to configure hdf5 with the "--enable-hl" option along
with "
>> >>>>>>> *--with-zlib=${ZDIR}*".
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> In the "Compiling NetCDF" section,
>> >>>>>>> both for NetCDF-C and NetCDF-CXX,
>> >>>>>>>
>> >>>>>>> LDFLAGS and CPPFLAGS directories should be assigned to HDF5
>> >>>> directory,
>> >>>>>> not
>> >>>>>>> the NetCDF4 installation directory in
>> >>>>>>> "LDFLAGS=-L${MET_LIB_DIR}/lib CPPFLAGS=-
I${MET_LIB_DIR}/include"
>> >>>> while
>> >>>>>> the
>> >>>>>>> target directory in "--prefix=${MET_LIB_DIR}" should be
netcdf4
>> >>>>>> directory.
>> >>>>>>> You might want to make changes for these error for other
METv6.0
>> >>>> users
>> >>>>> on
>> >>>>>>> your webpage at "
>> >>>>>>> http://www.dtcenter.org/met/users/support/online_tutorial/
>> >>>>>> METv6.0/tutorial.php?name=compilation&category=req_libs
>> >>>>>>> ".
>> >>>>>>>
>> >>>>>>> Thank you.
>> >>>>>>> Regards,
>> >>>>>>>
>> >>>>>>> Jinwoong
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> On Tue, May 30, 2017 at 3:18 PM, Howard Soh via RT <
>> >>>> met_help at ucar.edu>
>> >>>>>>> wrote:
>> >>>>>>>
>> >>>>>>>> Thank you, Jinwoong.
>> >>>>>>>>
>> >>>>>>>> Howard
>> >>>>>>>>
>> >>>>>>>> On 5/30/2017 12:33 PM, Jinwoong Yoo via RT wrote:
>> >>>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>> >>>>>>>>>
>> >>>>>>>>> Hi Howard,
>> >>>>>>>>>
>> >>>>>>>>> I contacted Unidata regarding the issue already.
>> >>>>>>>>> Attached please find the file, and see its contents
below.
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> ============================================
>> >>>>>>>>>
>> >>>>>>>>> netCDF 4.4.1.1: h5_test/test-suite.log
>> >>>>>>>>>
>> >>>>>>>>> ============================================
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> # TOTAL: 26
>> >>>>>>>>>
>> >>>>>>>>> # PASS: 25
>> >>>>>>>>>
>> >>>>>>>>> # SKIP: 0
>> >>>>>>>>>
>> >>>>>>>>> # XFAIL: 0
>> >>>>>>>>>
>> >>>>>>>>> # FAIL: 1
>> >>>>>>>>>
>> >>>>>>>>> # XPASS: 0
>> >>>>>>>>>
>> >>>>>>>>> # ERROR: 0
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> .. contents:: :depth: 2
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> FAIL: tst_h_vars
>> >>>>>>>>>
>> >>>>>>>>> ================
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> *** Checking HDF5 variable functions.
>> >>>>>>>>>
>> >>>>>>>>> *** Checking HDF5 boolen variables...ok.
>> >>>>>>>>>
>> >>>>>>>>> *** Checking HDF5 variable with unlimited dimension...ok.
>> >>>>>>>>>
>> >>>>>>>>> *** Checking HDF5 deflate filter setting and
getting...Sorry!
>> >>>>>> Unexpected
>> >>>>>>>>> result, tst_h_vars.c, line: 230
>> >>>>>>>>>
>> >>>>>>>>> FAIL tst_h_vars (exit status: 2)
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> Thank you.
>> >>>>>>>>>
>> >>>>>>>>> Regards,
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> Jinwoong
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> On Tue, May 30, 2017 at 2:22 PM, Howard Soh via RT <
>> >>>>> met_help at ucar.edu>
>> >>>>>>>>> wrote:
>> >>>>>>>>>
>> >>>>>>>>>> Hi Jinwoong.
>> >>>>>>>>>>
>> >>>>>>>>>> I am sorry to hear that you are still having difficulty
with
>> the
>> >>>>>> netcdf
>> >>>>>>>>>> library
>> >>>>>>>>>> files.
>> >>>>>>>>>> One unit test related with HDF5 was failed. Would you
check
>> >>>>>>>>>> h5_test/test-suite.log
>> >>>>>>>>>> and contact Unidata?
>> >>>>>>>>>> The full path will be /home/yoo108/METwithGNU/src/
>> >>>>>>>> netcdf-c-4.4.1.1/h5_test
>> >>>>>>>>>> /test-suite.log.
>> >>>>>>>>>>
>> >>>>>>>>>> It would help to understand your problem if you send us
>> >>>>>>>>>> h5_test/test-suite.log.
>> >>>>>>>>>>
>> >>>>>>>>>> Cheers,
>> >>>>>>>>>> Howard
>> >>>>>>>>>>
>> >>>>>>>>>> FYI:
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> FAIL: tst_h_vars
>> >>>>>>>>>>
>> >>>>>>>>>>
============================================================
>> >>>>>>>>>> ================
>> >>>>>>>>>> Testsuite summary for netCDF 4.4.1.1
>> >>>>>>>>>>
============================================================
>> >>>>>>>>>> ================
>> >>>>>>>>>> # TOTAL: 26
>> >>>>>>>>>> # PASS: 25
>> >>>>>>>>>> # SKIP: 0
>> >>>>>>>>>> # XFAIL: 0
>> >>>>>>>>>> # FAIL: 1
>> >>>>>>>>>> # XPASS: 0
>> >>>>>>>>>> # ERROR: 0
>> >>>>>>>>>>
============================================================
>> >>>>>>>>>> ================
>> >>>>>>>>>> See h5_test/test-suite.log
>> >>>>>>>>>> Please report to support-netcdf at unidata.ucar.edu
>> >>>>>>>>>>
============================================================
>> >>>>>>>>>> ================
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
>> >>>>>>>>>>
>> >>>>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>> >
>> >>>>>>>>>>
>> >>>>>>>>>> I forgot to attach my log file.
>> >>>>>>>>>> Thanks!
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo <
>> >>>>> jinwoong.yoo at gmail.com
>> >>>>>>>>>> <jinwoong.yoo at gmail.com>
>> >>>>>>>>>> wrote:
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> Hi,
>> >>>>>>>>>> Thank you for your reply.
>> >>>>>>>>>>
>> >>>>>>>>>> I realized that I have to have netcdf4-c and netcdf4-cxx
to
>> >>>> install
>> >>>>>>>>>> MET-6.0.
>> >>>>>>>>>> So far, I have compiled HDF5 following directions
>> >>>>>>>>>>
athttp://www.dtcenter.org/met/users/support/online_tutorial/
>> >>>>>>>>>> METv6.0/tutorial.php?name=compilation&category=req_libs.
>> >>>>>>>>>>
>> >>>>>>>>>> I have built HDF5 successfully using the `--enable-hl`
function
>> >>>> and
>> >>>>> I
>> >>>>>>>> got
>> >>>>>>>>>> hdf5_h1.1 in my target directory. Previously I got error
>> >>>> installing
>> >>>>>>>> netcdf4
>> >>>>>>>>>> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared"
message
>> (as
>> >>>>> shown
>> >>>>>>>>>>
inhttps://www.unidata.ucar.edu/support/help/MailArchives/
>> >>>>>>>>>> netcdf/msg13749.html).
>> >>>>>>>>>>
>> >>>>>>>>>> I am referring to unidata webpage for the compilation of
>> netcdf4
>> >>>>>>>>>>
athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
>> >>>>>>>>>> and_building_netcdf.html.
>> >>>>>>>>>> But now I get an error with h5_test within the netcdf
make
>> check
>> >>>> and
>> >>>>>> it
>> >>>>>>>>>> fails.
>> >>>>>>>>>> Attached please find configure and make log.
>> >>>>>>>>>> Do you have any know-how to overcome this issue?
>> >>>>>>>>>> Thank you very much in advance.
>> >>>>>>>>>>
>> >>>>>>>>>> Regards,
>> >>>>>>>>>>
>> >>>>>>>>>> Jinwoong Yoo
>> >>>>>>>>>> Purdue Climate Change Research Center
>> >>>>>>>>>>
>> >>>>>>>>>> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
>> >>>>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
>> >>>>>>>>>> wrote:
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> Hello -
>> >>>>>>>>>>
>> >>>>>>>>>> Most of our team is out due to the Memorial Day holiday.
We'll
>> >>>>> have a
>> >>>>>>>>>> look
>> >>>>>>>>>> at your issue when the team is back sometime later this
week.
>> >>>>>>>>>>
>> >>>>>>>>>> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
>> >>>>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
>> >>>>>>>>>> wrote:
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> Fri May 26 09:39:58 2017: Request 80647 was acted upon.
>> >>>>>>>>>> Transaction: Ticket created by jinwoong.yoo at gmail.com
>> >>>>>>>>>> Queue: met_help
>> >>>>>>>>>> Subject: Error with Compiling MET-6.0
>> >>>>>>>>>> Owner: Nobody
>> >>>>>>>>>> Requestors: jinwoong.yoo at gmail.com
>> >>>>>>>>>> Status: new
>> >>>>>>>>>> Ticket <URL: https://rt.rap.ucar.edu/rt/
>> >>>>>> Ticket/Display.html?id=80647
>> >>>>>>>>>> Dear MET Help
>> >>>>>>>>>>
>> >>>>>>>>>> Hi.
>> >>>>>>>>>> I am trying to compile MET-6.0 bugfixed version on a
Linux
>> cluster
>> >>>>>>>>>>
>> >>>>>>>>>> (Redhat)
>> >>>>>>>>>>
>> >>>>>>>>>> at Purdue University.
>> >>>>>>>>>> I am using a few system-wide libraries (e.g., netcdf-
3.6.3,
>> hdf5)
>> >>>>> and
>> >>>>>> I
>> >>>>>>>>>> installed most of the other library myself. Also I set
up all
>> the
>> >>>>>>>>>> environment variables required.
>> >>>>>>>>>>
>> >>>>>>>>>> # MET
>> >>>>>>>>>>
>> >>>>>>>>>> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-
16.0.1.150
>> >>>>>>>>>>
>> >>>>>>>>>> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
>> >>>>>>>>>>
>> >>>>>>>>>> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-
1.2.7
>> >>>>>>>>>>
>> >>>>>>>>>> export MET_UPP=/home/yoo108/UPPV3.1
>> >>>>>>>>>>
>> >>>>>>>>>> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
>> >>>>>>>>>>
>> >>>>>>>>>> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
>> >>>>>>>>>>
>> >>>>>>>>>> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
>> >>>>>>>>>>
>> >>>>>>>>>> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
>> >>>>>>>>>>
>> >>>>>>>>>> export MET_HDFEOS2INC=/home/yoo108/bu
>> ild_MET/src/hdfeos/include
>> >>>>>>>>>>
>> >>>>>>>>>> export
MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
>> >>>>>>>>>>
>> >>>>>>>>>> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> However, I got an error with the compilation of the MET-
6.0
>> and it
>> >>>>>>>>>>
>> >>>>>>>>>> failed.
>> >>>>>>>>>>
>> >>>>>>>>>> The error message reads as below:
>> >>>>>>>>>>
>> >>>>>>>>>> MET_BASE="\"/home/yoo108/MET-6.0/share/met\""
-D__64BIT__ -MT
>> >>>>>>>>>> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
>> >>>>>>>>>> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
>> >>>>>>>>>>
>> >>>>>>>>>> libvx_nc_util_a-nc_var_info.o
>> >>>>>>>>>>
>> >>>>>>>>>> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
>> >>>>>>>>>>
>> >>>>>>>>>> In file included from nc_var_info.cc(24):
>> >>>>>>>>>>
>> >>>>>>>>>> nc_utils.h(22): catastrophic error: cannot open source
file
>> >>>> "netcdf"
>> >>>>>>>>>> #include <netcdf>
>> >>>>>>>>>>
>> >>>>>>>>>> ^
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> compilation aborted for nc_var_info.cc (code 4)
>> >>>>>>>>>>
>> >>>>>>>>>> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
>> >>>>>>>>>>
>> >>>>>>>>>> make[3]: Leaving directory
>> >>>>>>>>>> `/home/yoo108/build_MET/src/met-
6.0/src/libcode/vx_nc_util'
>> >>>>>>>>>>
>> >>>>>>>>>> make[2]: *** [install-recursive] Error 1
>> >>>>>>>>>>
>> >>>>>>>>>> make[2]: Leaving directory `/home/yoo108/build_MET/src/
>> >>>>>>>>>> met-6.0/src/libcode'
>> >>>>>>>>>>
>> >>>>>>>>>> make[1]: *** [install-recursive] Error 1
>> >>>>>>>>>>
>> >>>>>>>>>> make[1]: Leaving directory `/home/yoo108/build_MET/src/
>> >>>> met-6.0/src'
>> >>>>>>>>>> make: *** [install-recursive] Error 1
>> >>>>>>>>>>
>> >>>>>>>>>> ^C[1]+ Exit 2 make install
&>make_install.log
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> I wonder if this error is related with the 64 bit
cluster while
>> >>>> MET
>> >>>>>>>>>> wants
>> >>>>>>>>>>
>> >>>>>>>>>> 32 bit software or else.
>> >>>>>>>>>>
>> >>>>>>>>>> Your input will be highly appreciated.
>> >>>>>>>>>>
>> >>>>>>>>>> Thank you.
>> >>>>>>>>>>
>> >>>>>>>>>> Regards,
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> Jinwoong Yoo
>> >>>>>>>>>>
>> >>>>>>>>>> Purdue Climate Change Research Center
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>
>> >>
>> >>
>>
>>
>>
>
------------------------------------------------
Subject: Re: [rt.rap.ucar.edu #80647] Error with Compiling MET-6.0
From: Howard Soh
Time: Wed May 31 15:33:17 2017
Hi Jinwoong.
acscii2nc does not need that many libraries. I built ascii2nc with gcc
4.9.2 and it uses 18 library files.
The MET was compiled with some libraries which were compiled with
Intel.
The following actions will help to find out Intel compiled libraries.
Action 1. Finding system libraries linked with MET but built with
Intel
compiler.
Would you run ldd for HDF5 library you built and other dependent
libraries which were not built by you for ascii2nc?
It will show which library was built with Intel compiler.
For example,
ldd /home/yoo108/METwithGNU/hdf5-1.8.18/lib/libhdf5_hl.so.10 | grep
intel
ldd /home/yoo108/METwithGNU/hdf5-1.8.18/lib/libhdf5_hl.so.10 | grep
libimf.so
HDF5 and NetCDF4 have the circular dependency. Above commands show if
the system NetCDF library was built with Intel or not.
Action 2. Finding extra libraries linked to ascii2nc
Would you send me the make log file for ascii2nc?
- Go to <MET_SOURCE_DIR>/src/tools/other/ascii2nc
- delete "ascii2nc"
- build again
cd <MET_SOURCE_DIR>/src/tools/other/ascii2nc
rm ./ascii2nc
make > ascii2nc.log
The last g++ command has the library paths and library list
to
be linked with.
Cheers,
Howard
Here is my library list for ascii2nc.
ldd bin/ascii2nc
linux-vdso.so.1 (0x00007fff2b9f3000)
libjasper.so.1 => /usr/lib/x86_64-linux-gnu/libjasper.so.1
(0x00007fd6817ff000)
libpng12.so.0 => /lib/x86_64-linux-gnu/libpng12.so.0
(0x00007fd6815d8000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1
(0x00007fd6813bc000)
libnetcdf_c++4.so.1 =>
/usr/local/netcdf/lib/libnetcdf_c++4.so.1 (0x00007fd68116c000)
libnetcdf.so.7 => /usr/local/netcdf/lib/libnetcdf.so.7
(0x00007fd680e5d000)
libgsl.so.0 => /usr/lib/libgsl.so.0 (0x00007fd680a2f000)
libgslcblas.so.0 => /usr/lib/libgslcblas.so.0
(0x00007fd6807f1000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
(0x00007fd6804e6000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6
(0x00007fd6801e4000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
(0x00007fd67ffce000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6
(0x00007fd67fc23000)
libjpeg.so.62 => /usr/lib/x86_64-linux-gnu/libjpeg.so.62
(0x00007fd67f9cb000)
libhdf5_hl.so.9 => /usr/local/hdf5-1.8.14/lib/libhdf5_hl.so.9
(0x00007fd67f7aa000)
libhdf5.so.9 => /usr/local/hdf5-1.8.14/lib/libhdf5.so.9
(0x00007fd67f2bf000)
libsz.so.2 => /usr/local/szip-2.1/lib/libsz.so.2
(0x00007fd67f0ac000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2
(0x00007fd67eea8000)
/lib64/ld-linux-x86-64.so.2 (0x0000564184cd8000)
On 5/31/2017 2:08 PM, Jinwoong Yoo via RT wrote:
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>
> Hi Howard,
>
> I used GNU gcc, g++, and gfortran to compile MET as well as other
libraries.
>
> Below is output from "ldd bin/ascii2nc":
>
> yoo108 at halstead-fe00:*~/MET-6.0* $ ldd bin/ascii2nc
>
> linux-vdso.so.1 => (0x00007fff967cc000)
>
> libjasper.so.1 => /home/yoo108/CDO/lib/libjasper.so.1
(0x00002b5ef0826000)
>
> libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00000036f6000000)
>
> libz.so.1 => /home/yoo108/METwithGNU/zlib-1.2.11/lib/libz.so.1
> (0x00002b5ef0a94000)
>
> libnetcdf_c++4.so.1 =>
> /home/yoo108/METwithGNU/netcdf-4.4.1.1/lib/libnetcdf_c++4.so.1
> (0x00002b5ef0cb0000)
>
> libnetcdf.so.11 =>
> /home/yoo108/METwithGNU/netcdf-4.4.1.1/lib/libnetcdf.so.11
> (0x00002b5ef0efb000)
>
> libgsl.so.19 => /home/yoo108/METwithGNU/gsl-2.3/lib/libgsl.so.19
> (0x00002b5ef4291000)
>
> libgslcblas.so.0 => /home/yoo108/METwithGNU/gsl-
2.3/lib/libgslcblas.so.0
> (0x00002b5ef47b9000)
>
> libstdc++.so.6 => /apps/rhel6/gcc/5.2.0/lib64/libstdc++.so.6
> (0x00002b5ef4a11000)
>
> libm.so.6 => /lib64/libm.so.6 (0x00000036f0000000)
>
> libgcc_s.so.1 => /apps/rhel6/gcc/5.2.0/lib64/libgcc_s.so.1
> (0x00002b5ef4dc2000)
>
> libc.so.6 => /lib64/libc.so.6 (0x00000036efc00000)
>
> libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x00000036f7000000)
>
> libmpifort.so.12 => /apps/rhel6/intel/impi/
> 5.1.2.150/intel64/lib/libmpifort.so.12 (0x00002b5ef4fd9000)
>
> libmpi.so.12 => /apps/rhel6/intel/impi/
> 5.1.2.150/intel64/lib/release_mt/libmpi.so.12 (0x00002b5ef536a000)
>
> libdl.so.2 => /lib64/libdl.so.2 (0x00000036f0400000)
>
> librt.so.1 => /lib64/librt.so.1 (0x00000036f0c00000)
>
> libpthread.so.0 => /lib64/libpthread.so.0 (0x00000036f0800000)
>
> libimf.so => not found
>
> libsvml.so => not found
>
> libirng.so => not found
>
> libintlc.so.5 => not found
>
> libnetcdf.so.6 => /usr/lib64/libnetcdf.so.6 (0x00000036fce00000)
>
> libhdf5_hl.so.10 =>
> /home/yoo108/METwithGNU/hdf5-1.8.18/lib/libhdf5_hl.so.10
> (0x00002b5ef5b2f000)
>
> libhdf5.so.10 => /home/yoo108/METwithGNU/hdf5-
1.8.18/lib/libhdf5.so.10
> (0x00002b5ef5d51000)
>
> libcurl.so.4 => /usr/lib64/libcurl.so.4 (0x00000036fbc00000)
>
> /lib64/ld-linux-x86-64.so.2 (0x00000036ef400000)
>
> libhdf5_hl.so.6 => /usr/lib64/libhdf5_hl.so.6 (0x00000036fe600000)
>
> libhdf5.so.6 => /usr/lib64/libhdf5.so.6 (0x00000036fc800000)
>
> libidn.so.11 => /lib64/libidn.so.11 (0x00000036fb400000)
>
> libldap-2.4.so.2 => /lib64/libldap-2.4.so.2 (0x00000036f9000000)
>
> libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2
(0x00000036f3800000)
>
> libkrb5.so.3 => /lib64/libkrb5.so.3 (0x00000036f3000000)
>
> libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x00000036f5800000)
>
> libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00000036f2400000)
>
> libssl3.so => /usr/lib64/libssl3.so (0x00000036f7400000)
>
> libsmime3.so => /usr/lib64/libsmime3.so (0x00000036f7c00000)
>
> libnss3.so => /usr/lib64/libnss3.so (0x00000036f5000000)
>
> libnssutil3.so => /usr/lib64/libnssutil3.so (0x00000036f2c00000)
>
> libplds4.so => /lib64/libplds4.so (0x00000036f3c00000)
>
> libplc4.so => /lib64/libplc4.so (0x00000036f4800000)
>
> libnspr4.so => /lib64/libnspr4.so (0x00000036f3400000)
>
> libssh2.so.1 => /usr/lib64/libssh2.so.1 (0x00000036fac00000)
>
> liblber-2.4.so.2 => /lib64/liblber-2.4.so.2 (0x00000036f8400000)
>
> libresolv.so.2 => /lib64/libresolv.so.2 (0x00000036f1c00000)
>
> libsasl2.so.2 => /usr/lib64/libsasl2.so.2 (0x00000036f9800000)
>
> libkrb5support.so.0 => /lib64/libkrb5support.so.0
(0x00000036f5400000)
>
> libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00000036f4000000)
>
> libssl.so.10 => /usr/lib64/libssl.so.10 (0x00000036f5c00000)
>
> libcrypto.so.10 => /usr/lib64/libcrypto.so.10 (0x00000036f2000000)
>
> libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00000036f4400000)
>
> libselinux.so.1 => /lib64/libselinux.so.1 (0x00000036f1400000)
>
> libfreebl3.so => /usr/lib64/libfreebl3.so (0x00000036f2800000)
>
>
> Thank you.
>
> Regards,
>
>
> Jinwoong
>
>
> On Wed, May 31, 2017 at 4:02 PM, Howard Soh via RT
<met_help at ucar.edu>
> wrote:
>
>> I am sorry to hear that you are still having difficulty with
running MET.
>>
>> The error message implies that the MET was compiled with Intel but
the
>> Intel libraries are not available at runtime.
>> It puzzles me why the build environment and the running environment
are
>> different.
>> It's better to use one compiler for MET and dependent libraries.
The log
>> file for HDF5 and NetCDF4 shows they were built with gcc 5.2.0.
>> Would you check which compilers were used to build MET and other
dependent
>> libraries?
>>
>> The first step will be finding which libraries not not available.
>> Would you execute ldd command and send me the output?
>>
>> ldd bin/ascii2nc
>>
>>
>> Cheers,
>> Howard
>>
>> FYI:
>> If there is "not found", the path for those libraries should be
added
>> LD_LIBRARY_PATH.
>>
>> For example,
>> libnetcdf_c++4.so.1 => not found
>> libnetcdf_c++.so.4 => not found
>> libnetcdf.so.7 => not found
>> libimf.so => not found
>>
>> NetCDF library and Intel libraries are missing. In case of Intel
library,
>> it's better to be resolved not by using LD_LIBRARY_PATH. If
"module"
>> command is available, please use it "module load intel".
>>
>>
>> On 5/31/2017 1:00 PM, Jinwoong Yoo via RT wrote:
>>
>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>
>>> Hi Howard,
>>>
>>> I thought my MET compilation completed.
>>> But it seems not.
>>>
>>> When I typed in met commands in bin directory,
>>> I got errors as below:
>>>
>>> yoo108 at halstead-fe00:*~/MET-6.0* $ bin/pcp_combine
>>>
>>> bin/pcp_combine: error while loading shared libraries: libimf.so:
cannot
>>> open shared object file: No such file or directory
>>>
>>> yoo108 at halstead-fe00:*~/MET-6.0* $ which ascii2nc
>>>
>>> ~/MET-6.0/bin/ascii2nc
>>>
>>> yoo108 at halstead-fe00:*~/MET-6.0* $ ascii2nc
>>>
>>> ascii2nc: error while loading shared libraries: libimf.so: cannot
open
>>> shared object file: No such file or directory
>>>
>>> yoo108 at halstead-fe00:*~/MET-6.0* $ mode
>>>
>>> mode: error while loading shared libraries: libimf.so: cannot open
shared
>>> object file: No such file or directory
>>>
>>> yoo108 at halstead-fe00:*~/MET-6.0* $ mtd
>>>
>>> mtd: error while loading shared libraries: libimf.so: cannot open
shared
>>> object file: No such file or directory
>>>
>>> yoo108 at halstead-fe00:*~/MET-6.0* $ pb2nc
>>>
>>> pb2nc: error while loading shared libraries: libimf.so: cannot
open
>> shared
>>> object file: No such file or directory
>>>
>>>
>>> What I should do?
>>>
>>> It seems there is no lib directory compiled with MET-6.0.
>>>
>>> I am not sure which libimf.so file is needed.
>>>
>>> Thank you.
>>>
>>>
>>> Regards,
>>>
>>>
>>> Jinwoong
>>>
>>>
>>>
>>>
>>> On Wed, May 31, 2017 at 2:03 PM, Howard Soh via RT
<met_help at ucar.edu>
>>> wrote:
>>>
>>>> You're very welcome.
>>>>
>>>> Please let us know if you encounter any other difficulties.**I'll
go
>>>> ahead and close this ticket for now then. Please open a new
ticket if
>>>> further questions or problems.
>>>>
>>>> Thanks,
>>>> Howard
>>>>
>>>>
>>>> On 5/31/2017 11:45 AM, Jinwoong Yoo via RT wrote:
>>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>>>
>>>>> Hi Howard,
>>>>>
>>>>> Thank you much for your note.
>>>>> Finally I was able to complete the installation of MET-6.0.
>>>>> But I should let you know that I encountered several errors
probably
>> due
>>>> to
>>>>> the outdated make file for the new include directory structures
of
>> recent
>>>>> versions of HDF-EOS2, Cairo, and Freetype.
>>>>>
>>>>> Thank you.
>>>>> Regards,
>>>>>
>>>>> Jinwoong
>>>>>
>>>>> On Wed, May 31, 2017 at 11:58 AM, Howard Soh via RT
<met_help at ucar.edu
>>>>> wrote:
>>>>>
>>>>>> MET still uses HDF4 library instead of HDF5 because of another
>>>> dependency,
>>>>>> HDF-EOS.
>>>>>>
>>>>>> Note: hdf.h is for HDF4 and hdf5.h is for HDF5
>>>>>>
>>>>>> NetCDF4 requires HDF5 on building and running. Once NetCDF
library is
>>>>>> built, HDF5 is not required to build MET, but required to run
MET.
>>>>>>
>>>>>> Please set *$MET_HDF* to point to the HDF4 directory.
>>>>>>
>>>>>> Cheers,
>>>>>> Howard
>>>>>>
>>>>>>
>>>>>> On Wed, May 31, 2017 at 8:03 AM, Jinwoong Yoo via RT <
>> met_help at ucar.edu
>>>>>> wrote:
>>>>>>
>>>>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>
>>>>>>>
>>>>>>> Hi Howard,
>>>>>>> Although, after compiling of all the dependency libraries,
>>>>>>> I am getting error with installing the MET.
>>>>>>>
>>>>>>> I set all the environment libraries as directed in the online
>> tutorial.
>>>>>>> But it seems the installer cannot find hdf.h file.
>>>>>>> Please see error message below:
>>>>>>>
>>>>>>> *lidar2nc.cc:69:17:* *fatal error: *hdf.h: No such file or
directory
>>>>>>>
>>>>>>> compilation terminated.
>>>>>>>
>>>>>>> make[5]: *** [lidar2nc-lidar2nc.o] Error 1
>>>>>>>
>>>>>>> make[5]: Leaving directory
>>>>>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools/
>> other/lidar2nc'
>>>>>>> make[4]: *** [all-recursive] Error 1
>>>>>>>
>>>>>>> make[4]: Leaving directory
>>>>>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools/other'
>>>>>>>
>>>>>>> make[3]: *** [all-recursive] Error 1
>>>>>>>
>>>>>>> make[3]: Leaving directory
>>>>>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools'
>>>>>>>
>>>>>>> make[2]: *** [all-recursive] Error 1
>>>>>>>
>>>>>>> make[2]: Leaving directory `/home/yoo108/METwithGNU/src/
>>>>>>> met-6.0_bugfix/src'
>>>>>>>
>>>>>>> make[1]: *** [all-recursive] Error 1
>>>>>>>
>>>>>>> make[1]: Leaving directory `/home/yoo108/METwithGNU/src/
>>>> met-6.0_bugfix'
>>>>>>> make: *** [all] Error 2
>>>>>>>
>>>>>>> Do you have any idea?
>>>>>>> Thank you.
>>>>>>>
>>>>>>> Regards,
>>>>>>>
>>>>>>> Jinwoong
>>>>>>>
>>>>>>> On Tue, May 30, 2017 at 6:21 PM, Howard Soh via RT <
>> met_help at ucar.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> I'm glad to hear that you can build HDF5 and NetCDF4.
>>>>>>>>
>>>>>>>> I appreciated your advice. We will review online tutorial and
make
>> it
>>>>>>>> clear.
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>> Howard
>>>>>>>>
>>>>>>>> FYI:
>>>>>>>> hdf5-1.8.17$ ./configure --help | grep enable-hl
>>>>>>>> --enable-hl Enable the high level library
>>>> [default=yes]
>>>>>>>> hdf5-1.8.18$ ./configure --help | grep enable-hl
>>>>>>>> --enable-hl Enable the high level library
>>>> [default=yes]
>>>>>>>>
>>>>>>>> On 5/30/2017 2:12 PM, Jinwoong Yoo via RT wrote:
>>>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>>>>>>>
>>>>>>>>> Hi Howard,
>>>>>>>>>
>>>>>>>>> I was able to compile HDF5, Netcdf4-C, and NetCDF-CXX
successfully
>>>>>>>> finally.
>>>>>>>>> I happened to know that there were a few typos in the MET
Online
>>>>>>> Tutorial
>>>>>>>>> For METv6.0, which led into various confusions.
>>>>>>>>>
>>>>>>>>> In the "Compiling HDF5" section,
>>>>>>>>> I had to configure hdf5 with the "--enable-hl" option along
with "
>>>>>>>>> *--with-zlib=${ZDIR}*".
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> In the "Compiling NetCDF" section,
>>>>>>>>> both for NetCDF-C and NetCDF-CXX,
>>>>>>>>>
>>>>>>>>> LDFLAGS and CPPFLAGS directories should be assigned to HDF5
>>>>>> directory,
>>>>>>>> not
>>>>>>>>> the NetCDF4 installation directory in
>>>>>>>>> "LDFLAGS=-L${MET_LIB_DIR}/lib CPPFLAGS=-
I${MET_LIB_DIR}/include"
>>>>>> while
>>>>>>>> the
>>>>>>>>> target directory in "--prefix=${MET_LIB_DIR}" should be
netcdf4
>>>>>>>> directory.
>>>>>>>>> You might want to make changes for these error for other
METv6.0
>>>>>> users
>>>>>>> on
>>>>>>>>> your webpage at "
>>>>>>>>> http://www.dtcenter.org/met/users/support/online_tutorial/
>>>>>>>> METv6.0/tutorial.php?name=compilation&category=req_libs
>>>>>>>>> ".
>>>>>>>>>
>>>>>>>>> Thank you.
>>>>>>>>> Regards,
>>>>>>>>>
>>>>>>>>> Jinwoong
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, May 30, 2017 at 3:18 PM, Howard Soh via RT <
>>>>>> met_help at ucar.edu>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> Thank you, Jinwoong.
>>>>>>>>>>
>>>>>>>>>> Howard
>>>>>>>>>>
>>>>>>>>>> On 5/30/2017 12:33 PM, Jinwoong Yoo via RT wrote:
>>>>>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>>>>>>>>>
>>>>>>>>>>> Hi Howard,
>>>>>>>>>>>
>>>>>>>>>>> I contacted Unidata regarding the issue already.
>>>>>>>>>>> Attached please find the file, and see its contents below.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ============================================
>>>>>>>>>>>
>>>>>>>>>>> netCDF 4.4.1.1: h5_test/test-suite.log
>>>>>>>>>>>
>>>>>>>>>>> ============================================
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> # TOTAL: 26
>>>>>>>>>>>
>>>>>>>>>>> # PASS: 25
>>>>>>>>>>>
>>>>>>>>>>> # SKIP: 0
>>>>>>>>>>>
>>>>>>>>>>> # XFAIL: 0
>>>>>>>>>>>
>>>>>>>>>>> # FAIL: 1
>>>>>>>>>>>
>>>>>>>>>>> # XPASS: 0
>>>>>>>>>>>
>>>>>>>>>>> # ERROR: 0
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> .. contents:: :depth: 2
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> FAIL: tst_h_vars
>>>>>>>>>>>
>>>>>>>>>>> ================
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> *** Checking HDF5 variable functions.
>>>>>>>>>>>
>>>>>>>>>>> *** Checking HDF5 boolen variables...ok.
>>>>>>>>>>>
>>>>>>>>>>> *** Checking HDF5 variable with unlimited dimension...ok.
>>>>>>>>>>>
>>>>>>>>>>> *** Checking HDF5 deflate filter setting and
getting...Sorry!
>>>>>>>> Unexpected
>>>>>>>>>>> result, tst_h_vars.c, line: 230
>>>>>>>>>>>
>>>>>>>>>>> FAIL tst_h_vars (exit status: 2)
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Thank you.
>>>>>>>>>>>
>>>>>>>>>>> Regards,
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Jinwoong
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Tue, May 30, 2017 at 2:22 PM, Howard Soh via RT <
>>>>>>> met_help at ucar.edu>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Jinwoong.
>>>>>>>>>>>>
>>>>>>>>>>>> I am sorry to hear that you are still having difficulty
with the
>>>>>>>> netcdf
>>>>>>>>>>>> library
>>>>>>>>>>>> files.
>>>>>>>>>>>> One unit test related with HDF5 was failed. Would you
check
>>>>>>>>>>>> h5_test/test-suite.log
>>>>>>>>>>>> and contact Unidata?
>>>>>>>>>>>> The full path will be /home/yoo108/METwithGNU/src/
>>>>>>>>>> netcdf-c-4.4.1.1/h5_test
>>>>>>>>>>>> /test-suite.log.
>>>>>>>>>>>>
>>>>>>>>>>>> It would help to understand your problem if you send us
>>>>>>>>>>>> h5_test/test-suite.log.
>>>>>>>>>>>>
>>>>>>>>>>>> Cheers,
>>>>>>>>>>>> Howard
>>>>>>>>>>>>
>>>>>>>>>>>> FYI:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> FAIL: tst_h_vars
>>>>>>>>>>>>
>>>>>>>>>>>>
============================================================
>>>>>>>>>>>> ================
>>>>>>>>>>>> Testsuite summary for netCDF 4.4.1.1
>>>>>>>>>>>>
============================================================
>>>>>>>>>>>> ================
>>>>>>>>>>>> # TOTAL: 26
>>>>>>>>>>>> # PASS: 25
>>>>>>>>>>>> # SKIP: 0
>>>>>>>>>>>> # XFAIL: 0
>>>>>>>>>>>> # FAIL: 1
>>>>>>>>>>>> # XPASS: 0
>>>>>>>>>>>> # ERROR: 0
>>>>>>>>>>>>
============================================================
>>>>>>>>>>>> ================
>>>>>>>>>>>> See h5_test/test-suite.log
>>>>>>>>>>>> Please report to support-netcdf at unidata.ucar.edu
>>>>>>>>>>>>
============================================================
>>>>>>>>>>>> ================
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>>>>>>>>>>
>>>>>>>>>>>> I forgot to attach my log file.
>>>>>>>>>>>> Thanks!
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo <
>>>>>>> jinwoong.yoo at gmail.com
>>>>>>>>>>>> <jinwoong.yoo at gmail.com>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Hi,
>>>>>>>>>>>> Thank you for your reply.
>>>>>>>>>>>>
>>>>>>>>>>>> I realized that I have to have netcdf4-c and netcdf4-cxx
to
>>>>>> install
>>>>>>>>>>>> MET-6.0.
>>>>>>>>>>>> So far, I have compiled HDF5 following directions
>>>>>>>>>>>>
athttp://www.dtcenter.org/met/users/support/online_tutorial/
>>>>>>>>>>>> METv6.0/tutorial.php?name=compilation&category=req_libs.
>>>>>>>>>>>>
>>>>>>>>>>>> I have built HDF5 successfully using the `--enable-hl`
function
>>>>>> and
>>>>>>> I
>>>>>>>>>> got
>>>>>>>>>>>> hdf5_h1.1 in my target directory. Previously I got error
>>>>>> installing
>>>>>>>>>> netcdf4
>>>>>>>>>>>> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared"
message (as
>>>>>>> shown
>>>>>>>>>>>> inhttps://www.unidata.ucar.edu/support/help/MailArchives/
>>>>>>>>>>>> netcdf/msg13749.html).
>>>>>>>>>>>>
>>>>>>>>>>>> I am referring to unidata webpage for the compilation of
netcdf4
>>>>>>>>>>>>
athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
>>>>>>>>>>>> and_building_netcdf.html.
>>>>>>>>>>>> But now I get an error with h5_test within the netcdf
make check
>>>>>> and
>>>>>>>> it
>>>>>>>>>>>> fails.
>>>>>>>>>>>> Attached please find configure and make log.
>>>>>>>>>>>> Do you have any know-how to overcome this issue?
>>>>>>>>>>>> Thank you very much in advance.
>>>>>>>>>>>>
>>>>>>>>>>>> Regards,
>>>>>>>>>>>>
>>>>>>>>>>>> Jinwoong Yoo
>>>>>>>>>>>> Purdue Climate Change Research Center
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
>>>>>>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Hello -
>>>>>>>>>>>>
>>>>>>>>>>>> Most of our team is out due to the Memorial Day holiday.
We'll
>>>>>>> have a
>>>>>>>>>>>> look
>>>>>>>>>>>> at your issue when the team is back sometime later this
week.
>>>>>>>>>>>>
>>>>>>>>>>>> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
>>>>>>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Fri May 26 09:39:58 2017: Request 80647 was acted upon.
>>>>>>>>>>>> Transaction: Ticket created by jinwoong.yoo at gmail.com
>>>>>>>>>>>> Queue: met_help
>>>>>>>>>>>> Subject: Error with Compiling MET-6.0
>>>>>>>>>>>> Owner: Nobody
>>>>>>>>>>>> Requestors: jinwoong.yoo at gmail.com
>>>>>>>>>>>> Status: new
>>>>>>>>>>>> Ticket <URL: https://rt.rap.ucar.edu/rt/
>>>>>>>> Ticket/Display.html?id=80647
>>>>>>>>>>>> Dear MET Help
>>>>>>>>>>>>
>>>>>>>>>>>> Hi.
>>>>>>>>>>>> I am trying to compile MET-6.0 bugfixed version on a
Linux
>> cluster
>>>>>>>>>>>> (Redhat)
>>>>>>>>>>>>
>>>>>>>>>>>> at Purdue University.
>>>>>>>>>>>> I am using a few system-wide libraries (e.g., netcdf-
3.6.3,
>> hdf5)
>>>>>>> and
>>>>>>>> I
>>>>>>>>>>>> installed most of the other library myself. Also I set up
all
>> the
>>>>>>>>>>>> environment variables required.
>>>>>>>>>>>>
>>>>>>>>>>>> # MET
>>>>>>>>>>>>
>>>>>>>>>>>> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-
16.0.1.150
>>>>>>>>>>>>
>>>>>>>>>>>> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
>>>>>>>>>>>>
>>>>>>>>>>>> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-
1.2.7
>>>>>>>>>>>>
>>>>>>>>>>>> export MET_UPP=/home/yoo108/UPPV3.1
>>>>>>>>>>>>
>>>>>>>>>>>> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
>>>>>>>>>>>>
>>>>>>>>>>>> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
>>>>>>>>>>>>
>>>>>>>>>>>> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
>>>>>>>>>>>>
>>>>>>>>>>>> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
>>>>>>>>>>>>
>>>>>>>>>>>> export
MET_HDFEOS2INC=/home/yoo108/build_MET/src/hdfeos/include
>>>>>>>>>>>>
>>>>>>>>>>>> export
MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
>>>>>>>>>>>>
>>>>>>>>>>>> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> However, I got an error with the compilation of the MET-
6.0 and
>> it
>>>>>>>>>>>> failed.
>>>>>>>>>>>>
>>>>>>>>>>>> The error message reads as below:
>>>>>>>>>>>>
>>>>>>>>>>>> MET_BASE="\"/home/yoo108/MET-6.0/share/met\""
-D__64BIT__ -MT
>>>>>>>>>>>> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
>>>>>>>>>>>> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
>>>>>>>>>>>>
>>>>>>>>>>>> libvx_nc_util_a-nc_var_info.o
>>>>>>>>>>>>
>>>>>>>>>>>> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
>>>>>>>>>>>>
>>>>>>>>>>>> In file included from nc_var_info.cc(24):
>>>>>>>>>>>>
>>>>>>>>>>>> nc_utils.h(22): catastrophic error: cannot open source
file
>>>>>> "netcdf"
>>>>>>>>>>>> #include <netcdf>
>>>>>>>>>>>>
>>>>>>>>>>>> ^
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> compilation aborted for nc_var_info.cc (code 4)
>>>>>>>>>>>>
>>>>>>>>>>>> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
>>>>>>>>>>>>
>>>>>>>>>>>> make[3]: Leaving directory
>>>>>>>>>>>> `/home/yoo108/build_MET/src/met-
6.0/src/libcode/vx_nc_util'
>>>>>>>>>>>>
>>>>>>>>>>>> make[2]: *** [install-recursive] Error 1
>>>>>>>>>>>>
>>>>>>>>>>>> make[2]: Leaving directory `/home/yoo108/build_MET/src/
>>>>>>>>>>>> met-6.0/src/libcode'
>>>>>>>>>>>>
>>>>>>>>>>>> make[1]: *** [install-recursive] Error 1
>>>>>>>>>>>>
>>>>>>>>>>>> make[1]: Leaving directory `/home/yoo108/build_MET/src/
>>>>>> met-6.0/src'
>>>>>>>>>>>> make: *** [install-recursive] Error 1
>>>>>>>>>>>>
>>>>>>>>>>>> ^C[1]+ Exit 2 make install
&>make_install.log
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> I wonder if this error is related with the 64 bit cluster
while
>>>>>> MET
>>>>>>>>>>>> wants
>>>>>>>>>>>>
>>>>>>>>>>>> 32 bit software or else.
>>>>>>>>>>>>
>>>>>>>>>>>> Your input will be highly appreciated.
>>>>>>>>>>>>
>>>>>>>>>>>> Thank you.
>>>>>>>>>>>>
>>>>>>>>>>>> Regards,
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Jinwoong Yoo
>>>>>>>>>>>>
>>>>>>>>>>>> Purdue Climate Change Research Center
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>
>>
>>
------------------------------------------------
Subject: Re: [rt.rap.ucar.edu #80647] Error with Compiling MET-6.0
From: Howard Soh
Time: Wed May 31 15:48:24 2017
Hi Jinwoong.
You solved it by yourself. Please ignore the previous mail.
I will close the ticket.
Cheers,
Howard
On 5/31/2017 3:08 PM, Jinwoong Yoo via RT wrote:
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>
> Hi Howard,
>
> It seems there were some interferences from my other libraries that
were
> built using intel compilers.
> When I removed them from my environment and re-compiled the MET-6.0,
it
> works without any previous error message.
> Thank you very much for your clue.
> Regards,
>
> Jinwoong
>
> On Wed, May 31, 2017 at 4:08 PM, Jinwoong Yoo
<jinwoong.yoo at gmail.com>
> wrote:
>
>> Hi Howard,
>>
>> I used GNU gcc, g++, and gfortran to compile MET as well as other
>> libraries.
>>
>> Below is output from "ldd bin/ascii2nc":
>>
>> yoo108 at halstead-fe00:*~/MET-6.0* $ ldd bin/ascii2nc
>>
>> linux-vdso.so.1 => (0x00007fff967cc000)
>>
>> libjasper.so.1 => /home/yoo108/CDO/lib/libjasper.so.1
(0x00002b5ef0826000)
>>
>> libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00000036f6000000)
>>
>> libz.so.1 => /home/yoo108/METwithGNU/zlib-1.2.11/lib/libz.so.1
>> (0x00002b5ef0a94000)
>>
>> libnetcdf_c++4.so.1 => /home/yoo108/METwithGNU/
>> netcdf-4.4.1.1/lib/libnetcdf_c++4.so.1 (0x00002b5ef0cb0000)
>>
>> libnetcdf.so.11 => /home/yoo108/METwithGNU/netcdf-
4.4.1.1/lib/libnetcdf.so.11
>> (0x00002b5ef0efb000)
>>
>> libgsl.so.19 => /home/yoo108/METwithGNU/gsl-2.3/lib/libgsl.so.19
>> (0x00002b5ef4291000)
>>
>> libgslcblas.so.0 => /home/yoo108/METwithGNU/gsl-
2.3/lib/libgslcblas.so.0
>> (0x00002b5ef47b9000)
>>
>> libstdc++.so.6 => /apps/rhel6/gcc/5.2.0/lib64/libstdc++.so.6
>> (0x00002b5ef4a11000)
>>
>> libm.so.6 => /lib64/libm.so.6 (0x00000036f0000000)
>>
>> libgcc_s.so.1 => /apps/rhel6/gcc/5.2.0/lib64/libgcc_s.so.1
>> (0x00002b5ef4dc2000)
>>
>> libc.so.6 => /lib64/libc.so.6 (0x00000036efc00000)
>>
>> libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x00000036f7000000)
>>
>> libmpifort.so.12 => /apps/rhel6/intel/impi/5.1.2.
>> 150/intel64/lib/libmpifort.so.12 (0x00002b5ef4fd9000)
>>
>> libmpi.so.12 =>
/apps/rhel6/intel/impi/5.1.2.150/intel64/lib/release_mt/
>> libmpi.so.12 (0x00002b5ef536a000)
>>
>> libdl.so.2 => /lib64/libdl.so.2 (0x00000036f0400000)
>>
>> librt.so.1 => /lib64/librt.so.1 (0x00000036f0c00000)
>>
>> libpthread.so.0 => /lib64/libpthread.so.0 (0x00000036f0800000)
>>
>> libimf.so => not found
>>
>> libsvml.so => not found
>>
>> libirng.so => not found
>>
>> libintlc.so.5 => not found
>>
>> libnetcdf.so.6 => /usr/lib64/libnetcdf.so.6 (0x00000036fce00000)
>>
>> libhdf5_hl.so.10 => /home/yoo108/METwithGNU/hdf5-
1.8.18/lib/libhdf5_hl.so.10
>> (0x00002b5ef5b2f000)
>>
>> libhdf5.so.10 => /home/yoo108/METwithGNU/hdf5-
1.8.18/lib/libhdf5.so.10
>> (0x00002b5ef5d51000)
>>
>> libcurl.so.4 => /usr/lib64/libcurl.so.4 (0x00000036fbc00000)
>>
>> /lib64/ld-linux-x86-64.so.2 (0x00000036ef400000)
>>
>> libhdf5_hl.so.6 => /usr/lib64/libhdf5_hl.so.6 (0x00000036fe600000)
>>
>> libhdf5.so.6 => /usr/lib64/libhdf5.so.6 (0x00000036fc800000)
>>
>> libidn.so.11 => /lib64/libidn.so.11 (0x00000036fb400000)
>>
>> libldap-2.4.so.2 => /lib64/libldap-2.4.so.2 (0x00000036f9000000)
>>
>> libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2
(0x00000036f3800000)
>>
>> libkrb5.so.3 => /lib64/libkrb5.so.3 (0x00000036f3000000)
>>
>> libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x00000036f5800000)
>>
>> libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00000036f2400000)
>>
>> libssl3.so => /usr/lib64/libssl3.so (0x00000036f7400000)
>>
>> libsmime3.so => /usr/lib64/libsmime3.so (0x00000036f7c00000)
>>
>> libnss3.so => /usr/lib64/libnss3.so (0x00000036f5000000)
>>
>> libnssutil3.so => /usr/lib64/libnssutil3.so (0x00000036f2c00000)
>>
>> libplds4.so => /lib64/libplds4.so (0x00000036f3c00000)
>>
>> libplc4.so => /lib64/libplc4.so (0x00000036f4800000)
>>
>> libnspr4.so => /lib64/libnspr4.so (0x00000036f3400000)
>>
>> libssh2.so.1 => /usr/lib64/libssh2.so.1 (0x00000036fac00000)
>>
>> liblber-2.4.so.2 => /lib64/liblber-2.4.so.2 (0x00000036f8400000)
>>
>> libresolv.so.2 => /lib64/libresolv.so.2 (0x00000036f1c00000)
>>
>> libsasl2.so.2 => /usr/lib64/libsasl2.so.2 (0x00000036f9800000)
>>
>> libkrb5support.so.0 => /lib64/libkrb5support.so.0
(0x00000036f5400000)
>>
>> libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00000036f4000000)
>>
>> libssl.so.10 => /usr/lib64/libssl.so.10 (0x00000036f5c00000)
>>
>> libcrypto.so.10 => /usr/lib64/libcrypto.so.10 (0x00000036f2000000)
>>
>> libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00000036f4400000)
>>
>> libselinux.so.1 => /lib64/libselinux.so.1 (0x00000036f1400000)
>>
>> libfreebl3.so => /usr/lib64/libfreebl3.so (0x00000036f2800000)
>>
>>
>> Thank you.
>>
>> Regards,
>>
>>
>> Jinwoong
>>
>>
>> On Wed, May 31, 2017 at 4:02 PM, Howard Soh via RT
<met_help at ucar.edu>
>> wrote:
>>
>>> I am sorry to hear that you are still having difficulty with
running MET.
>>>
>>> The error message implies that the MET was compiled with Intel but
the
>>> Intel libraries are not available at runtime.
>>> It puzzles me why the build environment and the running
environment are
>>> different.
>>> It's better to use one compiler for MET and dependent libraries.
The log
>>> file for HDF5 and NetCDF4 shows they were built with gcc 5.2.0.
>>> Would you check which compilers were used to build MET and other
>>> dependent libraries?
>>>
>>> The first step will be finding which libraries not not available.
>>> Would you execute ldd command and send me the output?
>>>
>>> ldd bin/ascii2nc
>>>
>>>
>>> Cheers,
>>> Howard
>>>
>>> FYI:
>>> If there is "not found", the path for those libraries should be
added
>>> LD_LIBRARY_PATH.
>>>
>>> For example,
>>> libnetcdf_c++4.so.1 => not found
>>> libnetcdf_c++.so.4 => not found
>>> libnetcdf.so.7 => not found
>>> libimf.so => not found
>>>
>>> NetCDF library and Intel libraries are missing. In case of Intel
library,
>>> it's better to be resolved not by using LD_LIBRARY_PATH. If
"module"
>>> command is available, please use it "module load intel".
>>>
>>>
>>> On 5/31/2017 1:00 PM, Jinwoong Yoo via RT wrote:
>>>
>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>>
>>>> Hi Howard,
>>>>
>>>> I thought my MET compilation completed.
>>>> But it seems not.
>>>>
>>>> When I typed in met commands in bin directory,
>>>> I got errors as below:
>>>>
>>>> yoo108 at halstead-fe00:*~/MET-6.0* $ bin/pcp_combine
>>>>
>>>> bin/pcp_combine: error while loading shared libraries: libimf.so:
cannot
>>>> open shared object file: No such file or directory
>>>>
>>>> yoo108 at halstead-fe00:*~/MET-6.0* $ which ascii2nc
>>>>
>>>> ~/MET-6.0/bin/ascii2nc
>>>>
>>>> yoo108 at halstead-fe00:*~/MET-6.0* $ ascii2nc
>>>>
>>>> ascii2nc: error while loading shared libraries: libimf.so: cannot
open
>>>> shared object file: No such file or directory
>>>>
>>>> yoo108 at halstead-fe00:*~/MET-6.0* $ mode
>>>>
>>>> mode: error while loading shared libraries: libimf.so: cannot
open
>>> shared
>>>> object file: No such file or directory
>>>>
>>>> yoo108 at halstead-fe00:*~/MET-6.0* $ mtd
>>>>
>>>> mtd: error while loading shared libraries: libimf.so: cannot open
shared
>>>> object file: No such file or directory
>>>>
>>>> yoo108 at halstead-fe00:*~/MET-6.0* $ pb2nc
>>>>
>>>> pb2nc: error while loading shared libraries: libimf.so: cannot
open
>>> shared
>>>> object file: No such file or directory
>>>>
>>>>
>>>> What I should do?
>>>>
>>>> It seems there is no lib directory compiled with MET-6.0.
>>>>
>>>> I am not sure which libimf.so file is needed.
>>>>
>>>> Thank you.
>>>>
>>>>
>>>> Regards,
>>>>
>>>>
>>>> Jinwoong
>>>>
>>>>
>>>>
>>>>
>>>> On Wed, May 31, 2017 at 2:03 PM, Howard Soh via RT
<met_help at ucar.edu>
>>>> wrote:
>>>>
>>>>> You're very welcome.
>>>>>
>>>>> Please let us know if you encounter any other
difficulties.**I'll go
>>>>> ahead and close this ticket for now then. Please open a new
ticket if
>>>>> further questions or problems.
>>>>>
>>>>> Thanks,
>>>>> Howard
>>>>>
>>>>>
>>>>> On 5/31/2017 11:45 AM, Jinwoong Yoo via RT wrote:
>>>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>>>>
>>>>>> Hi Howard,
>>>>>>
>>>>>> Thank you much for your note.
>>>>>> Finally I was able to complete the installation of MET-6.0.
>>>>>> But I should let you know that I encountered several errors
probably
>>> due
>>>>> to
>>>>>> the outdated make file for the new include directory structures
of
>>> recent
>>>>>> versions of HDF-EOS2, Cairo, and Freetype.
>>>>>>
>>>>>> Thank you.
>>>>>> Regards,
>>>>>>
>>>>>> Jinwoong
>>>>>>
>>>>>> On Wed, May 31, 2017 at 11:58 AM, Howard Soh via RT <
>>> met_help at ucar.edu>
>>>>>> wrote:
>>>>>>
>>>>>>> MET still uses HDF4 library instead of HDF5 because of another
>>>>> dependency,
>>>>>>> HDF-EOS.
>>>>>>>
>>>>>>> Note: hdf.h is for HDF4 and hdf5.h is for HDF5
>>>>>>>
>>>>>>> NetCDF4 requires HDF5 on building and running. Once NetCDF
library is
>>>>>>> built, HDF5 is not required to build MET, but required to run
MET.
>>>>>>>
>>>>>>> Please set *$MET_HDF* to point to the HDF4 directory.
>>>>>>>
>>>>>>> Cheers,
>>>>>>> Howard
>>>>>>>
>>>>>>>
>>>>>>> On Wed, May 31, 2017 at 8:03 AM, Jinwoong Yoo via RT <
>>> met_help at ucar.edu
>>>>>>> wrote:
>>>>>>>
>>>>>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>
>>>>>>>>
>>>>>>>> Hi Howard,
>>>>>>>> Although, after compiling of all the dependency libraries,
>>>>>>>> I am getting error with installing the MET.
>>>>>>>>
>>>>>>>> I set all the environment libraries as directed in the online
>>> tutorial.
>>>>>>>> But it seems the installer cannot find hdf.h file.
>>>>>>>> Please see error message below:
>>>>>>>>
>>>>>>>> *lidar2nc.cc:69:17:* *fatal error: *hdf.h: No such file or
directory
>>>>>>>>
>>>>>>>> compilation terminated.
>>>>>>>>
>>>>>>>> make[5]: *** [lidar2nc-lidar2nc.o] Error 1
>>>>>>>>
>>>>>>>> make[5]: Leaving directory
>>>>>>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools/other/
>>> lidar2nc'
>>>>>>>> make[4]: *** [all-recursive] Error 1
>>>>>>>>
>>>>>>>> make[4]: Leaving directory
>>>>>>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools/other'
>>>>>>>>
>>>>>>>> make[3]: *** [all-recursive] Error 1
>>>>>>>>
>>>>>>>> make[3]: Leaving directory
>>>>>>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools'
>>>>>>>>
>>>>>>>> make[2]: *** [all-recursive] Error 1
>>>>>>>>
>>>>>>>> make[2]: Leaving directory `/home/yoo108/METwithGNU/src/
>>>>>>>> met-6.0_bugfix/src'
>>>>>>>>
>>>>>>>> make[1]: *** [all-recursive] Error 1
>>>>>>>>
>>>>>>>> make[1]: Leaving directory `/home/yoo108/METwithGNU/src/
>>>>> met-6.0_bugfix'
>>>>>>>> make: *** [all] Error 2
>>>>>>>>
>>>>>>>> Do you have any idea?
>>>>>>>> Thank you.
>>>>>>>>
>>>>>>>> Regards,
>>>>>>>>
>>>>>>>> Jinwoong
>>>>>>>>
>>>>>>>> On Tue, May 30, 2017 at 6:21 PM, Howard Soh via RT <
>>> met_help at ucar.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> I'm glad to hear that you can build HDF5 and NetCDF4.
>>>>>>>>>
>>>>>>>>> I appreciated your advice. We will review online tutorial
and make
>>> it
>>>>>>>>> clear.
>>>>>>>>>
>>>>>>>>> Cheers,
>>>>>>>>> Howard
>>>>>>>>>
>>>>>>>>> FYI:
>>>>>>>>> hdf5-1.8.17$ ./configure --help | grep enable-hl
>>>>>>>>> --enable-hl Enable the high level library
>>>>> [default=yes]
>>>>>>>>> hdf5-1.8.18$ ./configure --help | grep enable-hl
>>>>>>>>> --enable-hl Enable the high level library
>>>>> [default=yes]
>>>>>>>>>
>>>>>>>>> On 5/30/2017 2:12 PM, Jinwoong Yoo via RT wrote:
>>>>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>>>>>>>>
>>>>>>>>>> Hi Howard,
>>>>>>>>>>
>>>>>>>>>> I was able to compile HDF5, Netcdf4-C, and NetCDF-CXX
successfully
>>>>>>>>> finally.
>>>>>>>>>> I happened to know that there were a few typos in the MET
Online
>>>>>>>> Tutorial
>>>>>>>>>> For METv6.0, which led into various confusions.
>>>>>>>>>>
>>>>>>>>>> In the "Compiling HDF5" section,
>>>>>>>>>> I had to configure hdf5 with the "--enable-hl" option along
with "
>>>>>>>>>> *--with-zlib=${ZDIR}*".
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> In the "Compiling NetCDF" section,
>>>>>>>>>> both for NetCDF-C and NetCDF-CXX,
>>>>>>>>>>
>>>>>>>>>> LDFLAGS and CPPFLAGS directories should be assigned to HDF5
>>>>>>> directory,
>>>>>>>>> not
>>>>>>>>>> the NetCDF4 installation directory in
>>>>>>>>>> "LDFLAGS=-L${MET_LIB_DIR}/lib CPPFLAGS=-
I${MET_LIB_DIR}/include"
>>>>>>> while
>>>>>>>>> the
>>>>>>>>>> target directory in "--prefix=${MET_LIB_DIR}" should be
netcdf4
>>>>>>>>> directory.
>>>>>>>>>> You might want to make changes for these error for other
METv6.0
>>>>>>> users
>>>>>>>> on
>>>>>>>>>> your webpage at "
>>>>>>>>>> http://www.dtcenter.org/met/users/support/online_tutorial/
>>>>>>>>> METv6.0/tutorial.php?name=compilation&category=req_libs
>>>>>>>>>> ".
>>>>>>>>>>
>>>>>>>>>> Thank you.
>>>>>>>>>> Regards,
>>>>>>>>>>
>>>>>>>>>> Jinwoong
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Tue, May 30, 2017 at 3:18 PM, Howard Soh via RT <
>>>>>>> met_help at ucar.edu>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> Thank you, Jinwoong.
>>>>>>>>>>>
>>>>>>>>>>> Howard
>>>>>>>>>>>
>>>>>>>>>>> On 5/30/2017 12:33 PM, Jinwoong Yoo via RT wrote:
>>>>>>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
>>>>>>>>>>>>
>>>>>>>>>>>> Hi Howard,
>>>>>>>>>>>>
>>>>>>>>>>>> I contacted Unidata regarding the issue already.
>>>>>>>>>>>> Attached please find the file, and see its contents
below.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ============================================
>>>>>>>>>>>>
>>>>>>>>>>>> netCDF 4.4.1.1: h5_test/test-suite.log
>>>>>>>>>>>>
>>>>>>>>>>>> ============================================
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> # TOTAL: 26
>>>>>>>>>>>>
>>>>>>>>>>>> # PASS: 25
>>>>>>>>>>>>
>>>>>>>>>>>> # SKIP: 0
>>>>>>>>>>>>
>>>>>>>>>>>> # XFAIL: 0
>>>>>>>>>>>>
>>>>>>>>>>>> # FAIL: 1
>>>>>>>>>>>>
>>>>>>>>>>>> # XPASS: 0
>>>>>>>>>>>>
>>>>>>>>>>>> # ERROR: 0
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> .. contents:: :depth: 2
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> FAIL: tst_h_vars
>>>>>>>>>>>>
>>>>>>>>>>>> ================
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> *** Checking HDF5 variable functions.
>>>>>>>>>>>>
>>>>>>>>>>>> *** Checking HDF5 boolen variables...ok.
>>>>>>>>>>>>
>>>>>>>>>>>> *** Checking HDF5 variable with unlimited dimension...ok.
>>>>>>>>>>>>
>>>>>>>>>>>> *** Checking HDF5 deflate filter setting and
getting...Sorry!
>>>>>>>>> Unexpected
>>>>>>>>>>>> result, tst_h_vars.c, line: 230
>>>>>>>>>>>>
>>>>>>>>>>>> FAIL tst_h_vars (exit status: 2)
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Thank you.
>>>>>>>>>>>>
>>>>>>>>>>>> Regards,
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Jinwoong
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, May 30, 2017 at 2:22 PM, Howard Soh via RT <
>>>>>>>> met_help at ucar.edu>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Jinwoong.
>>>>>>>>>>>>>
>>>>>>>>>>>>> I am sorry to hear that you are still having difficulty
with
>>> the
>>>>>>>>> netcdf
>>>>>>>>>>>>> library
>>>>>>>>>>>>> files.
>>>>>>>>>>>>> One unit test related with HDF5 was failed. Would you
check
>>>>>>>>>>>>> h5_test/test-suite.log
>>>>>>>>>>>>> and contact Unidata?
>>>>>>>>>>>>> The full path will be /home/yoo108/METwithGNU/src/
>>>>>>>>>>> netcdf-c-4.4.1.1/h5_test
>>>>>>>>>>>>> /test-suite.log.
>>>>>>>>>>>>>
>>>>>>>>>>>>> It would help to understand your problem if you send us
>>>>>>>>>>>>> h5_test/test-suite.log.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>> Howard
>>>>>>>>>>>>>
>>>>>>>>>>>>> FYI:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> FAIL: tst_h_vars
>>>>>>>>>>>>>
>>>>>>>>>>>>>
============================================================
>>>>>>>>>>>>> ================
>>>>>>>>>>>>> Testsuite summary for netCDF 4.4.1.1
>>>>>>>>>>>>>
============================================================
>>>>>>>>>>>>> ================
>>>>>>>>>>>>> # TOTAL: 26
>>>>>>>>>>>>> # PASS: 25
>>>>>>>>>>>>> # SKIP: 0
>>>>>>>>>>>>> # XFAIL: 0
>>>>>>>>>>>>> # FAIL: 1
>>>>>>>>>>>>> # XPASS: 0
>>>>>>>>>>>>> # ERROR: 0
>>>>>>>>>>>>>
============================================================
>>>>>>>>>>>>> ================
>>>>>>>>>>>>> See h5_test/test-suite.log
>>>>>>>>>>>>> Please report to support-netcdf at unidata.ucar.edu
>>>>>>>>>>>>>
============================================================
>>>>>>>>>>>>> ================
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>>>>>>>>>>>>> I forgot to attach my log file.
>>>>>>>>>>>>> Thanks!
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo <
>>>>>>>> jinwoong.yoo at gmail.com
>>>>>>>>>>>>> <jinwoong.yoo at gmail.com>
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>> Thank you for your reply.
>>>>>>>>>>>>>
>>>>>>>>>>>>> I realized that I have to have netcdf4-c and netcdf4-cxx
to
>>>>>>> install
>>>>>>>>>>>>> MET-6.0.
>>>>>>>>>>>>> So far, I have compiled HDF5 following directions
>>>>>>>>>>>>>
athttp://www.dtcenter.org/met/users/support/online_tutorial/
>>>>>>>>>>>>> METv6.0/tutorial.php?name=compilation&category=req_libs.
>>>>>>>>>>>>>
>>>>>>>>>>>>> I have built HDF5 successfully using the `--enable-hl`
function
>>>>>>> and
>>>>>>>> I
>>>>>>>>>>> got
>>>>>>>>>>>>> hdf5_h1.1 in my target directory. Previously I got error
>>>>>>> installing
>>>>>>>>>>> netcdf4
>>>>>>>>>>>>> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared"
message
>>> (as
>>>>>>>> shown
>>>>>>>>>>>>>
inhttps://www.unidata.ucar.edu/support/help/MailArchives/
>>>>>>>>>>>>> netcdf/msg13749.html).
>>>>>>>>>>>>>
>>>>>>>>>>>>> I am referring to unidata webpage for the compilation of
>>> netcdf4
>>>>>>>>>>>>>
athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
>>>>>>>>>>>>> and_building_netcdf.html.
>>>>>>>>>>>>> But now I get an error with h5_test within the netcdf
make
>>> check
>>>>>>> and
>>>>>>>>> it
>>>>>>>>>>>>> fails.
>>>>>>>>>>>>> Attached please find configure and make log.
>>>>>>>>>>>>> Do you have any know-how to overcome this issue?
>>>>>>>>>>>>> Thank you very much in advance.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Regards,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Jinwoong Yoo
>>>>>>>>>>>>> Purdue Climate Change Research Center
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
>>>>>>>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Hello -
>>>>>>>>>>>>>
>>>>>>>>>>>>> Most of our team is out due to the Memorial Day holiday.
We'll
>>>>>>>> have a
>>>>>>>>>>>>> look
>>>>>>>>>>>>> at your issue when the team is back sometime later this
week.
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
>>>>>>>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Fri May 26 09:39:58 2017: Request 80647 was acted upon.
>>>>>>>>>>>>> Transaction: Ticket created by jinwoong.yoo at gmail.com
>>>>>>>>>>>>> Queue: met_help
>>>>>>>>>>>>> Subject: Error with Compiling MET-6.0
>>>>>>>>>>>>> Owner: Nobody
>>>>>>>>>>>>> Requestors: jinwoong.yoo at gmail.com
>>>>>>>>>>>>> Status: new
>>>>>>>>>>>>> Ticket <URL: https://rt.rap.ucar.edu/rt/
>>>>>>>>> Ticket/Display.html?id=80647
>>>>>>>>>>>>> Dear MET Help
>>>>>>>>>>>>>
>>>>>>>>>>>>> Hi.
>>>>>>>>>>>>> I am trying to compile MET-6.0 bugfixed version on a
Linux
>>> cluster
>>>>>>>>>>>>> (Redhat)
>>>>>>>>>>>>>
>>>>>>>>>>>>> at Purdue University.
>>>>>>>>>>>>> I am using a few system-wide libraries (e.g., netcdf-
3.6.3,
>>> hdf5)
>>>>>>>> and
>>>>>>>>> I
>>>>>>>>>>>>> installed most of the other library myself. Also I set
up all
>>> the
>>>>>>>>>>>>> environment variables required.
>>>>>>>>>>>>>
>>>>>>>>>>>>> # MET
>>>>>>>>>>>>>
>>>>>>>>>>>>> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-
16.0.1.150
>>>>>>>>>>>>>
>>>>>>>>>>>>> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
>>>>>>>>>>>>>
>>>>>>>>>>>>> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-
1.2.7
>>>>>>>>>>>>>
>>>>>>>>>>>>> export MET_UPP=/home/yoo108/UPPV3.1
>>>>>>>>>>>>>
>>>>>>>>>>>>> export MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
>>>>>>>>>>>>>
>>>>>>>>>>>>> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
>>>>>>>>>>>>>
>>>>>>>>>>>>> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
>>>>>>>>>>>>>
>>>>>>>>>>>>> export MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
>>>>>>>>>>>>>
>>>>>>>>>>>>> export MET_HDFEOS2INC=/home/yoo108/bu
>>> ild_MET/src/hdfeos/include
>>>>>>>>>>>>> export
MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
>>>>>>>>>>>>>
>>>>>>>>>>>>> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-16.0.1.150
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> However, I got an error with the compilation of the MET-
6.0
>>> and it
>>>>>>>>>>>>> failed.
>>>>>>>>>>>>>
>>>>>>>>>>>>> The error message reads as below:
>>>>>>>>>>>>>
>>>>>>>>>>>>> MET_BASE="\"/home/yoo108/MET-6.0/share/met\""
-D__64BIT__ -MT
>>>>>>>>>>>>> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
>>>>>>>>>>>>> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
>>>>>>>>>>>>>
>>>>>>>>>>>>> libvx_nc_util_a-nc_var_info.o
>>>>>>>>>>>>>
>>>>>>>>>>>>> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
>>>>>>>>>>>>>
>>>>>>>>>>>>> In file included from nc_var_info.cc(24):
>>>>>>>>>>>>>
>>>>>>>>>>>>> nc_utils.h(22): catastrophic error: cannot open source
file
>>>>>>> "netcdf"
>>>>>>>>>>>>> #include <netcdf>
>>>>>>>>>>>>>
>>>>>>>>>>>>> ^
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> compilation aborted for nc_var_info.cc (code 4)
>>>>>>>>>>>>>
>>>>>>>>>>>>> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
>>>>>>>>>>>>>
>>>>>>>>>>>>> make[3]: Leaving directory
>>>>>>>>>>>>> `/home/yoo108/build_MET/src/met-
6.0/src/libcode/vx_nc_util'
>>>>>>>>>>>>>
>>>>>>>>>>>>> make[2]: *** [install-recursive] Error 1
>>>>>>>>>>>>>
>>>>>>>>>>>>> make[2]: Leaving directory `/home/yoo108/build_MET/src/
>>>>>>>>>>>>> met-6.0/src/libcode'
>>>>>>>>>>>>>
>>>>>>>>>>>>> make[1]: *** [install-recursive] Error 1
>>>>>>>>>>>>>
>>>>>>>>>>>>> make[1]: Leaving directory `/home/yoo108/build_MET/src/
>>>>>>> met-6.0/src'
>>>>>>>>>>>>> make: *** [install-recursive] Error 1
>>>>>>>>>>>>>
>>>>>>>>>>>>> ^C[1]+ Exit 2 make install
&>make_install.log
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> I wonder if this error is related with the 64 bit
cluster while
>>>>>>> MET
>>>>>>>>>>>>> wants
>>>>>>>>>>>>>
>>>>>>>>>>>>> 32 bit software or else.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Your input will be highly appreciated.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Regards,
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Jinwoong Yoo
>>>>>>>>>>>>>
>>>>>>>>>>>>> Purdue Climate Change Research Center
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>
>>>
>>>
------------------------------------------------
Subject: Error with Compiling MET-6.0
From: Jinwoong Yoo
Time: Wed May 31 16:27:44 2017
Thank you very much for your kind efforts to resolve this issue.
I appreciate it.
Regards,
Jinwoong
On Wed, May 31, 2017 at 5:48 PM, Howard Soh via RT <met_help at ucar.edu>
wrote:
> Hi Jinwoong.
>
> You solved it by yourself. Please ignore the previous mail.
> I will close the ticket.
>
> Cheers,
> Howard
>
> On 5/31/2017 3:08 PM, Jinwoong Yoo via RT wrote:
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >
> > Hi Howard,
> >
> > It seems there were some interferences from my other libraries
that were
> > built using intel compilers.
> > When I removed them from my environment and re-compiled the MET-
6.0, it
> > works without any previous error message.
> > Thank you very much for your clue.
> > Regards,
> >
> > Jinwoong
> >
> > On Wed, May 31, 2017 at 4:08 PM, Jinwoong Yoo
<jinwoong.yoo at gmail.com>
> > wrote:
> >
> >> Hi Howard,
> >>
> >> I used GNU gcc, g++, and gfortran to compile MET as well as other
> >> libraries.
> >>
> >> Below is output from "ldd bin/ascii2nc":
> >>
> >> yoo108 at halstead-fe00:*~/MET-6.0* $ ldd bin/ascii2nc
> >>
> >> linux-vdso.so.1 => (0x00007fff967cc000)
> >>
> >> libjasper.so.1 => /home/yoo108/CDO/lib/libjasper.so.1
> (0x00002b5ef0826000)
> >>
> >> libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00000036f6000000)
> >>
> >> libz.so.1 => /home/yoo108/METwithGNU/zlib-1.2.11/lib/libz.so.1
> >> (0x00002b5ef0a94000)
> >>
> >> libnetcdf_c++4.so.1 => /home/yoo108/METwithGNU/
> >> netcdf-4.4.1.1/lib/libnetcdf_c++4.so.1 (0x00002b5ef0cb0000)
> >>
> >> libnetcdf.so.11 => /home/yoo108/METwithGNU/
> netcdf-4.4.1.1/lib/libnetcdf.so.11
> >> (0x00002b5ef0efb000)
> >>
> >> libgsl.so.19 => /home/yoo108/METwithGNU/gsl-2.3/lib/libgsl.so.19
> >> (0x00002b5ef4291000)
> >>
> >> libgslcblas.so.0 => /home/yoo108/METwithGNU/gsl-2.
> 3/lib/libgslcblas.so.0
> >> (0x00002b5ef47b9000)
> >>
> >> libstdc++.so.6 => /apps/rhel6/gcc/5.2.0/lib64/libstdc++.so.6
> >> (0x00002b5ef4a11000)
> >>
> >> libm.so.6 => /lib64/libm.so.6 (0x00000036f0000000)
> >>
> >> libgcc_s.so.1 => /apps/rhel6/gcc/5.2.0/lib64/libgcc_s.so.1
> >> (0x00002b5ef4dc2000)
> >>
> >> libc.so.6 => /lib64/libc.so.6 (0x00000036efc00000)
> >>
> >> libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x00000036f7000000)
> >>
> >> libmpifort.so.12 => /apps/rhel6/intel/impi/5.1.2.
> >> 150/intel64/lib/libmpifort.so.12 (0x00002b5ef4fd9000)
> >>
> >> libmpi.so.12 => /apps/rhel6/intel/impi/5.1.2.
> 150/intel64/lib/release_mt/
> >> libmpi.so.12 (0x00002b5ef536a000)
> >>
> >> libdl.so.2 => /lib64/libdl.so.2 (0x00000036f0400000)
> >>
> >> librt.so.1 => /lib64/librt.so.1 (0x00000036f0c00000)
> >>
> >> libpthread.so.0 => /lib64/libpthread.so.0 (0x00000036f0800000)
> >>
> >> libimf.so => not found
> >>
> >> libsvml.so => not found
> >>
> >> libirng.so => not found
> >>
> >> libintlc.so.5 => not found
> >>
> >> libnetcdf.so.6 => /usr/lib64/libnetcdf.so.6 (0x00000036fce00000)
> >>
> >> libhdf5_hl.so.10 => /home/yoo108/METwithGNU/hdf5-
> 1.8.18/lib/libhdf5_hl.so.10
> >> (0x00002b5ef5b2f000)
> >>
> >> libhdf5.so.10 => /home/yoo108/METwithGNU/hdf5-
1.8.18/lib/libhdf5.so.10
> >> (0x00002b5ef5d51000)
> >>
> >> libcurl.so.4 => /usr/lib64/libcurl.so.4 (0x00000036fbc00000)
> >>
> >> /lib64/ld-linux-x86-64.so.2 (0x00000036ef400000)
> >>
> >> libhdf5_hl.so.6 => /usr/lib64/libhdf5_hl.so.6
(0x00000036fe600000)
> >>
> >> libhdf5.so.6 => /usr/lib64/libhdf5.so.6 (0x00000036fc800000)
> >>
> >> libidn.so.11 => /lib64/libidn.so.11 (0x00000036fb400000)
> >>
> >> libldap-2.4.so.2 => /lib64/libldap-2.4.so.2 (0x00000036f9000000)
> >>
> >> libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2
(0x00000036f3800000)
> >>
> >> libkrb5.so.3 => /lib64/libkrb5.so.3 (0x00000036f3000000)
> >>
> >> libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x00000036f5800000)
> >>
> >> libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00000036f2400000)
> >>
> >> libssl3.so => /usr/lib64/libssl3.so (0x00000036f7400000)
> >>
> >> libsmime3.so => /usr/lib64/libsmime3.so (0x00000036f7c00000)
> >>
> >> libnss3.so => /usr/lib64/libnss3.so (0x00000036f5000000)
> >>
> >> libnssutil3.so => /usr/lib64/libnssutil3.so (0x00000036f2c00000)
> >>
> >> libplds4.so => /lib64/libplds4.so (0x00000036f3c00000)
> >>
> >> libplc4.so => /lib64/libplc4.so (0x00000036f4800000)
> >>
> >> libnspr4.so => /lib64/libnspr4.so (0x00000036f3400000)
> >>
> >> libssh2.so.1 => /usr/lib64/libssh2.so.1 (0x00000036fac00000)
> >>
> >> liblber-2.4.so.2 => /lib64/liblber-2.4.so.2 (0x00000036f8400000)
> >>
> >> libresolv.so.2 => /lib64/libresolv.so.2 (0x00000036f1c00000)
> >>
> >> libsasl2.so.2 => /usr/lib64/libsasl2.so.2 (0x00000036f9800000)
> >>
> >> libkrb5support.so.0 => /lib64/libkrb5support.so.0
(0x00000036f5400000)
> >>
> >> libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00000036f4000000)
> >>
> >> libssl.so.10 => /usr/lib64/libssl.so.10 (0x00000036f5c00000)
> >>
> >> libcrypto.so.10 => /usr/lib64/libcrypto.so.10
(0x00000036f2000000)
> >>
> >> libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00000036f4400000)
> >>
> >> libselinux.so.1 => /lib64/libselinux.so.1 (0x00000036f1400000)
> >>
> >> libfreebl3.so => /usr/lib64/libfreebl3.so (0x00000036f2800000)
> >>
> >>
> >> Thank you.
> >>
> >> Regards,
> >>
> >>
> >> Jinwoong
> >>
> >>
> >> On Wed, May 31, 2017 at 4:02 PM, Howard Soh via RT
<met_help at ucar.edu>
> >> wrote:
> >>
> >>> I am sorry to hear that you are still having difficulty with
running
> MET.
> >>>
> >>> The error message implies that the MET was compiled with Intel
but the
> >>> Intel libraries are not available at runtime.
> >>> It puzzles me why the build environment and the running
environment are
> >>> different.
> >>> It's better to use one compiler for MET and dependent libraries.
The
> log
> >>> file for HDF5 and NetCDF4 shows they were built with gcc 5.2.0.
> >>> Would you check which compilers were used to build MET and other
> >>> dependent libraries?
> >>>
> >>> The first step will be finding which libraries not not
available.
> >>> Would you execute ldd command and send me the output?
> >>>
> >>> ldd bin/ascii2nc
> >>>
> >>>
> >>> Cheers,
> >>> Howard
> >>>
> >>> FYI:
> >>> If there is "not found", the path for those libraries should be
added
> >>> LD_LIBRARY_PATH.
> >>>
> >>> For example,
> >>> libnetcdf_c++4.so.1 => not found
> >>> libnetcdf_c++.so.4 => not found
> >>> libnetcdf.so.7 => not found
> >>> libimf.so => not found
> >>>
> >>> NetCDF library and Intel libraries are missing. In case of Intel
> library,
> >>> it's better to be resolved not by using LD_LIBRARY_PATH. If
"module"
> >>> command is available, please use it "module load intel".
> >>>
> >>>
> >>> On 5/31/2017 1:00 PM, Jinwoong Yoo via RT wrote:
> >>>
> >>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >>>>
> >>>> Hi Howard,
> >>>>
> >>>> I thought my MET compilation completed.
> >>>> But it seems not.
> >>>>
> >>>> When I typed in met commands in bin directory,
> >>>> I got errors as below:
> >>>>
> >>>> yoo108 at halstead-fe00:*~/MET-6.0* $ bin/pcp_combine
> >>>>
> >>>> bin/pcp_combine: error while loading shared libraries:
libimf.so:
> cannot
> >>>> open shared object file: No such file or directory
> >>>>
> >>>> yoo108 at halstead-fe00:*~/MET-6.0* $ which ascii2nc
> >>>>
> >>>> ~/MET-6.0/bin/ascii2nc
> >>>>
> >>>> yoo108 at halstead-fe00:*~/MET-6.0* $ ascii2nc
> >>>>
> >>>> ascii2nc: error while loading shared libraries: libimf.so:
cannot open
> >>>> shared object file: No such file or directory
> >>>>
> >>>> yoo108 at halstead-fe00:*~/MET-6.0* $ mode
> >>>>
> >>>> mode: error while loading shared libraries: libimf.so: cannot
open
> >>> shared
> >>>> object file: No such file or directory
> >>>>
> >>>> yoo108 at halstead-fe00:*~/MET-6.0* $ mtd
> >>>>
> >>>> mtd: error while loading shared libraries: libimf.so: cannot
open
> shared
> >>>> object file: No such file or directory
> >>>>
> >>>> yoo108 at halstead-fe00:*~/MET-6.0* $ pb2nc
> >>>>
> >>>> pb2nc: error while loading shared libraries: libimf.so: cannot
open
> >>> shared
> >>>> object file: No such file or directory
> >>>>
> >>>>
> >>>> What I should do?
> >>>>
> >>>> It seems there is no lib directory compiled with MET-6.0.
> >>>>
> >>>> I am not sure which libimf.so file is needed.
> >>>>
> >>>> Thank you.
> >>>>
> >>>>
> >>>> Regards,
> >>>>
> >>>>
> >>>> Jinwoong
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> On Wed, May 31, 2017 at 2:03 PM, Howard Soh via RT
<met_help at ucar.edu
> >
> >>>> wrote:
> >>>>
> >>>>> You're very welcome.
> >>>>>
> >>>>> Please let us know if you encounter any other
difficulties.**I'll go
> >>>>> ahead and close this ticket for now then. Please open a new
ticket if
> >>>>> further questions or problems.
> >>>>>
> >>>>> Thanks,
> >>>>> Howard
> >>>>>
> >>>>>
> >>>>> On 5/31/2017 11:45 AM, Jinwoong Yoo via RT wrote:
> >>>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
>
> >>>>>>
> >>>>>> Hi Howard,
> >>>>>>
> >>>>>> Thank you much for your note.
> >>>>>> Finally I was able to complete the installation of MET-6.0.
> >>>>>> But I should let you know that I encountered several errors
probably
> >>> due
> >>>>> to
> >>>>>> the outdated make file for the new include directory
structures of
> >>> recent
> >>>>>> versions of HDF-EOS2, Cairo, and Freetype.
> >>>>>>
> >>>>>> Thank you.
> >>>>>> Regards,
> >>>>>>
> >>>>>> Jinwoong
> >>>>>>
> >>>>>> On Wed, May 31, 2017 at 11:58 AM, Howard Soh via RT <
> >>> met_help at ucar.edu>
> >>>>>> wrote:
> >>>>>>
> >>>>>>> MET still uses HDF4 library instead of HDF5 because of
another
> >>>>> dependency,
> >>>>>>> HDF-EOS.
> >>>>>>>
> >>>>>>> Note: hdf.h is for HDF4 and hdf5.h is for HDF5
> >>>>>>>
> >>>>>>> NetCDF4 requires HDF5 on building and running. Once NetCDF
library
> is
> >>>>>>> built, HDF5 is not required to build MET, but required to
run MET.
> >>>>>>>
> >>>>>>> Please set *$MET_HDF* to point to the HDF4 directory.
> >>>>>>>
> >>>>>>> Cheers,
> >>>>>>> Howard
> >>>>>>>
> >>>>>>>
> >>>>>>> On Wed, May 31, 2017 at 8:03 AM, Jinwoong Yoo via RT <
> >>> met_help at ucar.edu
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >>>>>>>>
> >>>>>>>> Hi Howard,
> >>>>>>>> Although, after compiling of all the dependency libraries,
> >>>>>>>> I am getting error with installing the MET.
> >>>>>>>>
> >>>>>>>> I set all the environment libraries as directed in the
online
> >>> tutorial.
> >>>>>>>> But it seems the installer cannot find hdf.h file.
> >>>>>>>> Please see error message below:
> >>>>>>>>
> >>>>>>>> *lidar2nc.cc:69:17:* *fatal error: *hdf.h: No such file or
> directory
> >>>>>>>>
> >>>>>>>> compilation terminated.
> >>>>>>>>
> >>>>>>>> make[5]: *** [lidar2nc-lidar2nc.o] Error 1
> >>>>>>>>
> >>>>>>>> make[5]: Leaving directory
> >>>>>>>> `/home/yoo108/METwithGNU/src/met-
6.0_bugfix/src/tools/other/
> >>> lidar2nc'
> >>>>>>>> make[4]: *** [all-recursive] Error 1
> >>>>>>>>
> >>>>>>>> make[4]: Leaving directory
> >>>>>>>> `/home/yoo108/METwithGNU/src/met-
6.0_bugfix/src/tools/other'
> >>>>>>>>
> >>>>>>>> make[3]: *** [all-recursive] Error 1
> >>>>>>>>
> >>>>>>>> make[3]: Leaving directory
> >>>>>>>> `/home/yoo108/METwithGNU/src/met-6.0_bugfix/src/tools'
> >>>>>>>>
> >>>>>>>> make[2]: *** [all-recursive] Error 1
> >>>>>>>>
> >>>>>>>> make[2]: Leaving directory `/home/yoo108/METwithGNU/src/
> >>>>>>>> met-6.0_bugfix/src'
> >>>>>>>>
> >>>>>>>> make[1]: *** [all-recursive] Error 1
> >>>>>>>>
> >>>>>>>> make[1]: Leaving directory `/home/yoo108/METwithGNU/src/
> >>>>> met-6.0_bugfix'
> >>>>>>>> make: *** [all] Error 2
> >>>>>>>>
> >>>>>>>> Do you have any idea?
> >>>>>>>> Thank you.
> >>>>>>>>
> >>>>>>>> Regards,
> >>>>>>>>
> >>>>>>>> Jinwoong
> >>>>>>>>
> >>>>>>>> On Tue, May 30, 2017 at 6:21 PM, Howard Soh via RT <
> >>> met_help at ucar.edu>
> >>>>>>>> wrote:
> >>>>>>>>
> >>>>>>>>> I'm glad to hear that you can build HDF5 and NetCDF4.
> >>>>>>>>>
> >>>>>>>>> I appreciated your advice. We will review online tutorial
and
> make
> >>> it
> >>>>>>>>> clear.
> >>>>>>>>>
> >>>>>>>>> Cheers,
> >>>>>>>>> Howard
> >>>>>>>>>
> >>>>>>>>> FYI:
> >>>>>>>>> hdf5-1.8.17$ ./configure --help | grep enable-hl
> >>>>>>>>> --enable-hl Enable the high level
library
> >>>>> [default=yes]
> >>>>>>>>> hdf5-1.8.18$ ./configure --help | grep enable-hl
> >>>>>>>>> --enable-hl Enable the high level
library
> >>>>> [default=yes]
> >>>>>>>>>
> >>>>>>>>> On 5/30/2017 2:12 PM, Jinwoong Yoo via RT wrote:
> >>>>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647 >
> >>>>>>>>>>
> >>>>>>>>>> Hi Howard,
> >>>>>>>>>>
> >>>>>>>>>> I was able to compile HDF5, Netcdf4-C, and NetCDF-CXX
> successfully
> >>>>>>>>> finally.
> >>>>>>>>>> I happened to know that there were a few typos in the MET
Online
> >>>>>>>> Tutorial
> >>>>>>>>>> For METv6.0, which led into various confusions.
> >>>>>>>>>>
> >>>>>>>>>> In the "Compiling HDF5" section,
> >>>>>>>>>> I had to configure hdf5 with the "--enable-hl" option
along
> with "
> >>>>>>>>>> *--with-zlib=${ZDIR}*".
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> In the "Compiling NetCDF" section,
> >>>>>>>>>> both for NetCDF-C and NetCDF-CXX,
> >>>>>>>>>>
> >>>>>>>>>> LDFLAGS and CPPFLAGS directories should be assigned to
HDF5
> >>>>>>> directory,
> >>>>>>>>> not
> >>>>>>>>>> the NetCDF4 installation directory in
> >>>>>>>>>> "LDFLAGS=-L${MET_LIB_DIR}/lib CPPFLAGS=-I${MET_LIB_DIR}/
> include"
> >>>>>>> while
> >>>>>>>>> the
> >>>>>>>>>> target directory in "--prefix=${MET_LIB_DIR}" should be
netcdf4
> >>>>>>>>> directory.
> >>>>>>>>>> You might want to make changes for these error for other
METv6.0
> >>>>>>> users
> >>>>>>>> on
> >>>>>>>>>> your webpage at "
> >>>>>>>>>>
http://www.dtcenter.org/met/users/support/online_tutorial/
> >>>>>>>>> METv6.0/tutorial.php?name=compilation&category=req_libs
> >>>>>>>>>> ".
> >>>>>>>>>>
> >>>>>>>>>> Thank you.
> >>>>>>>>>> Regards,
> >>>>>>>>>>
> >>>>>>>>>> Jinwoong
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> On Tue, May 30, 2017 at 3:18 PM, Howard Soh via RT <
> >>>>>>> met_help at ucar.edu>
> >>>>>>>>>> wrote:
> >>>>>>>>>>
> >>>>>>>>>>> Thank you, Jinwoong.
> >>>>>>>>>>>
> >>>>>>>>>>> Howard
> >>>>>>>>>>>
> >>>>>>>>>>> On 5/30/2017 12:33 PM, Jinwoong Yoo via RT wrote:
> >>>>>>>>>>>> <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=80647
> >
> >>>>>>>>>>>>
> >>>>>>>>>>>> Hi Howard,
> >>>>>>>>>>>>
> >>>>>>>>>>>> I contacted Unidata regarding the issue already.
> >>>>>>>>>>>> Attached please find the file, and see its contents
below.
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> ============================================
> >>>>>>>>>>>>
> >>>>>>>>>>>> netCDF 4.4.1.1: h5_test/test-suite.log
> >>>>>>>>>>>>
> >>>>>>>>>>>> ============================================
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> # TOTAL: 26
> >>>>>>>>>>>>
> >>>>>>>>>>>> # PASS: 25
> >>>>>>>>>>>>
> >>>>>>>>>>>> # SKIP: 0
> >>>>>>>>>>>>
> >>>>>>>>>>>> # XFAIL: 0
> >>>>>>>>>>>>
> >>>>>>>>>>>> # FAIL: 1
> >>>>>>>>>>>>
> >>>>>>>>>>>> # XPASS: 0
> >>>>>>>>>>>>
> >>>>>>>>>>>> # ERROR: 0
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> .. contents:: :depth: 2
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> FAIL: tst_h_vars
> >>>>>>>>>>>>
> >>>>>>>>>>>> ================
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> *** Checking HDF5 variable functions.
> >>>>>>>>>>>>
> >>>>>>>>>>>> *** Checking HDF5 boolen variables...ok.
> >>>>>>>>>>>>
> >>>>>>>>>>>> *** Checking HDF5 variable with unlimited
dimension...ok.
> >>>>>>>>>>>>
> >>>>>>>>>>>> *** Checking HDF5 deflate filter setting and
getting...Sorry!
> >>>>>>>>> Unexpected
> >>>>>>>>>>>> result, tst_h_vars.c, line: 230
> >>>>>>>>>>>>
> >>>>>>>>>>>> FAIL tst_h_vars (exit status: 2)
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> Thank you.
> >>>>>>>>>>>>
> >>>>>>>>>>>> Regards,
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> Jinwoong
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> On Tue, May 30, 2017 at 2:22 PM, Howard Soh via RT <
> >>>>>>>> met_help at ucar.edu>
> >>>>>>>>>>>> wrote:
> >>>>>>>>>>>>
> >>>>>>>>>>>>> Hi Jinwoong.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> I am sorry to hear that you are still having
difficulty with
> >>> the
> >>>>>>>>> netcdf
> >>>>>>>>>>>>> library
> >>>>>>>>>>>>> files.
> >>>>>>>>>>>>> One unit test related with HDF5 was failed. Would you
check
> >>>>>>>>>>>>> h5_test/test-suite.log
> >>>>>>>>>>>>> and contact Unidata?
> >>>>>>>>>>>>> The full path will be /home/yoo108/METwithGNU/src/
> >>>>>>>>>>> netcdf-c-4.4.1.1/h5_test
> >>>>>>>>>>>>> /test-suite.log.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> It would help to understand your problem if you send
us
> >>>>>>>>>>>>> h5_test/test-suite.log.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Cheers,
> >>>>>>>>>>>>> Howard
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> FYI:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> FAIL: tst_h_vars
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
============================================================
> >>>>>>>>>>>>> ================
> >>>>>>>>>>>>> Testsuite summary for netCDF 4.4.1.1
> >>>>>>>>>>>>>
============================================================
> >>>>>>>>>>>>> ================
> >>>>>>>>>>>>> # TOTAL: 26
> >>>>>>>>>>>>> # PASS: 25
> >>>>>>>>>>>>> # SKIP: 0
> >>>>>>>>>>>>> # XFAIL: 0
> >>>>>>>>>>>>> # FAIL: 1
> >>>>>>>>>>>>> # XPASS: 0
> >>>>>>>>>>>>> # ERROR: 0
> >>>>>>>>>>>>>
============================================================
> >>>>>>>>>>>>> ================
> >>>>>>>>>>>>> See h5_test/test-suite.log
> >>>>>>>>>>>>> Please report to support-netcdf at unidata.ucar.edu
> >>>>>>>>>>>>>
============================================================
> >>>>>>>>>>>>> ================
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> On 5/30/2017 11:24 AM, Jinwoong Yoo via RT wrote:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> <URL: https://rt.rap.ucar.edu/rt/
> Ticket/Display.html?id=80647
> >>>>>>>>>>>>> I forgot to attach my log file.
> >>>>>>>>>>>>> Thanks!
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> On Tue, May 30, 2017 at 1:21 PM, Jinwoong Yoo <
> >>>>>>>> jinwoong.yoo at gmail.com
> >>>>>>>>>>>>> <jinwoong.yoo at gmail.com>
> >>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Hi,
> >>>>>>>>>>>>> Thank you for your reply.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> I realized that I have to have netcdf4-c and netcdf4-
cxx to
> >>>>>>> install
> >>>>>>>>>>>>> MET-6.0.
> >>>>>>>>>>>>> So far, I have compiled HDF5 following directions
> >>>>>>>>>>>>>
athttp://www.dtcenter.org/met/users/support/online_tutorial/
> >>>>>>>>>>>>>
METv6.0/tutorial.php?name=compilation&category=req_libs.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> I have built HDF5 successfully using the `--enable-hl`
> function
> >>>>>>> and
> >>>>>>>> I
> >>>>>>>>>>> got
> >>>>>>>>>>>>> hdf5_h1.1 in my target directory. Previously I got
error
> >>>>>>> installing
> >>>>>>>>>>> netcdf4
> >>>>>>>>>>>>> with "error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared"
message
> >>> (as
> >>>>>>>> shown
> >>>>>>>>>>>>>
inhttps://www.unidata.ucar.edu/support/help/MailArchives/
> >>>>>>>>>>>>> netcdf/msg13749.html).
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> I am referring to unidata webpage for the compilation
of
> >>> netcdf4
> >>>>>>>>>>>>>
athttp://www.unidata.ucar.edu/software/netcdf/docs/getting_
> >>>>>>>>>>>>> and_building_netcdf.html.
> >>>>>>>>>>>>> But now I get an error with h5_test within the netcdf
make
> >>> check
> >>>>>>> and
> >>>>>>>>> it
> >>>>>>>>>>>>> fails.
> >>>>>>>>>>>>> Attached please find configure and make log.
> >>>>>>>>>>>>> Do you have any know-how to overcome this issue?
> >>>>>>>>>>>>> Thank you very much in advance.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Regards,
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Jinwoong Yoo
> >>>>>>>>>>>>> Purdue Climate Change Research Center
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> On Tue, May 30, 2017 at 1:04 PM, Randy Bullock via RT
> >>>>>>>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
> >>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Hello -
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Most of our team is out due to the Memorial Day
holiday.
> We'll
> >>>>>>>> have a
> >>>>>>>>>>>>> look
> >>>>>>>>>>>>> at your issue when the team is back sometime later
this week.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> On Fri, May 26, 2017 at 9:39 AM, Jinwoong Yoo via RT
> >>>>>>>>>>>>> <met_help at ucar.edu> <met_help at ucar.edu>
> >>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Fri May 26 09:39:58 2017: Request 80647 was acted
upon.
> >>>>>>>>>>>>> Transaction: Ticket created by jinwoong.yoo at gmail.com
> >>>>>>>>>>>>> Queue: met_help
> >>>>>>>>>>>>> Subject: Error with Compiling MET-6.0
> >>>>>>>>>>>>> Owner: Nobody
> >>>>>>>>>>>>> Requestors: jinwoong.yoo at gmail.com
> >>>>>>>>>>>>> Status: new
> >>>>>>>>>>>>> Ticket <URL: https://rt.rap.ucar.edu/rt/
> >>>>>>>>> Ticket/Display.html?id=80647
> >>>>>>>>>>>>> Dear MET Help
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Hi.
> >>>>>>>>>>>>> I am trying to compile MET-6.0 bugfixed version on a
Linux
> >>> cluster
> >>>>>>>>>>>>> (Redhat)
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> at Purdue University.
> >>>>>>>>>>>>> I am using a few system-wide libraries (e.g., netcdf-
3.6.3,
> >>> hdf5)
> >>>>>>>> and
> >>>>>>>>> I
> >>>>>>>>>>>>> installed most of the other library myself. Also I set
up all
> >>> the
> >>>>>>>>>>>>> environment variables required.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> # MET
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> export MET_NETCDF=/apps/rhel6/netcdf/3.6.3_intel-
16.0.1.150
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> export MET_GSL=/home/yoo108/build_MET/gsl-2.3
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> export MET_ZLIB=/home/yoo108/Build_WRF/LIBRARIES/zlib-
1.2.7
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> export MET_UPP=/home/yoo108/UPPV3.1
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> export
MET_GRIB2=/home/yoo108/Build_WRF/LIBRARIES/grib2
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> export MET_HDF4=/home/yoo108/build_MET/hdf-4.2.12
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> export MET_HDFEOS2=/home/yoo108/build_MET/hdfeos
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> export
MET_HDFEOS2LIB=/home/yoo108/build_MET/hdfeos/lib
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> export MET_HDFEOS2INC=/home/yoo108/bu
> >>> ild_MET/src/hdfeos/include
> >>>>>>>>>>>>> export
MET_BUFRLIB=/home/yoo108/Build_WRF/LIBRARIES/BUFRLIB
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> export MET_HDF5=/apps/rhel6/hdf5/1.8.16_intel-
16.0.1.150
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> However, I got an error with the compilation of the
MET-6.0
> >>> and it
> >>>>>>>>>>>>> failed.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> The error message reads as below:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> MET_BASE="\"/home/yoo108/MET-6.0/share/met\""
-D__64BIT__
> -MT
> >>>>>>>>>>>>> libvx_nc_util_a-nc_var_info.o -MD -MP -MF
> >>>>>>>>>>>>> .deps/libvx_nc_util_a-nc_var_info.Tpo -c -o
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> libvx_nc_util_a-nc_var_info.o
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> `test -f 'nc_var_info.cc' || echo './'`nc_var_info.cc
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> In file included from nc_var_info.cc(24):
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> nc_utils.h(22): catastrophic error: cannot open source
file
> >>>>>>> "netcdf"
> >>>>>>>>>>>>> #include <netcdf>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> ^
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> compilation aborted for nc_var_info.cc (code 4)
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> make[3]: *** [libvx_nc_util_a-nc_var_info.o] Error 4
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> make[3]: Leaving directory
> >>>>>>>>>>>>> `/home/yoo108/build_MET/src/met-
6.0/src/libcode/vx_nc_util'
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> make[2]: *** [install-recursive] Error 1
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> make[2]: Leaving directory
`/home/yoo108/build_MET/src/
> >>>>>>>>>>>>> met-6.0/src/libcode'
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> make[1]: *** [install-recursive] Error 1
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> make[1]: Leaving directory
`/home/yoo108/build_MET/src/
> >>>>>>> met-6.0/src'
> >>>>>>>>>>>>> make: *** [install-recursive] Error 1
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> ^C[1]+ Exit 2 make install
> &>make_install.log
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> I wonder if this error is related with the 64 bit
cluster
> while
> >>>>>>> MET
> >>>>>>>>>>>>> wants
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> 32 bit software or else.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Your input will be highly appreciated.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Thank you.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Regards,
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Jinwoong Yoo
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Purdue Climate Change Research Center
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>
> >>>
> >>>
>
>
>
------------------------------------------------
More information about the Met_help
mailing list