[Met_help] [rt.rap.ucar.edu #88728] History for Help compiling met with "undefined reference" errors
Julie Prestopnik via RT
met_help at ucar.edu
Thu Apr 11 11:44:21 MDT 2019
----------------------------------------------------------------
Initial Request
----------------------------------------------------------------
Hi MET support,
I have been struggling to compile MET 7 (or 8) using Intel compilers. The basic problem is undefined references to required libraries (netcdf, hdf, etc). Interestingly, they always seem to occur in the src/libcode/vx_* files. I have attached my latest compile log for the met-7.0_bugfix.20180924.tar.gz build. I have followed all the directions in the MET Users Guide but it dows not seem to make any difference. For this latest try, I setup the environment as follows:
------------------------------------------------------------------------------------------
module load other/comp/gcc-6.3
module load comp/intel-18.0.2.199
module load mpi/impi-18.0.2.199
module load lib/mkl-18.0.2.199
module load wrf-deps/intel-18.0.2.199
module load wgrib2/2.0.7_intel-18.0.2.199
setenv COMPVERS intel-18.0.2.199
setenv APPDIR ${NOBACKUP}/apps/sp3
setenv MET_NETCDF ${APPDIR}/netcdf/4.6.1_hdf4/${COMPVERS}
setenv MET_HDF5 ${APPDIR}/hdf5/1.10.2/${COMPVERS}
setenv MET_HDF ${APPDIR}/hdf/4.2.13_no-fortran/${COMPVERS}
setenv MET_HDFEOS ${APPDIR}/hdfeos/2.20v1.00/${COMPVERS}
setenv MET_GRIB2C ${APPDIR}/g2clib/1.6.0/${COMPVERS}
setenv MET_GSL ${APPDIR}/gsl/2.5/${COMPVERS}
setenv MET_BUFR ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}
setenv MET_BUFRLIB ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}/lib
setenv MET_CAIROINC /usr/include/cairo
setenv MET_CAIROLIB /usr/lib64
setenv MET_FREETYPEINC /usr/include/freetype2
setenv MET_FREETYPELIB /usr/lib64
setenv YACC ${APPDIR}/byacc/github/${COMPVERS}
setenv LDFLAGS -L${APPDIR}/wrf-deps/${COMPVERS}/lib
setenv CPPFLAGS -I${APPDIR}/wrf-deps/${COMPVERS}/include
setenv CFLAGS "-D__64BIT__"
./configure --prefix=${APPDIR}/MET/7.0/${COMPVERS} --enable-lidar2nc --enable-grib2 --enable-modis --enable-mode_graphics |& tee myConfigure.log
------------------------------------------------------------------------------------------
Then I ran "make install |& tee myMake.log" and got the resulting error logs (attached). Everything seems correct. I have not been able to successfully build MET 8 either because of similar errors. Please let me know any ideas on how to get this to compile correctly. I am out of ideas and have spent a while recompiling supporting libraries using different options. By the way, are there specific configure options necessary when building the netcdf and hdf libraries or does it not matter? I look forward to hearing from you soon.
Thanks,
Scott
----------------------------------------------------------------
Complete Ticket History
----------------------------------------------------------------
Subject: Help compiling met with "undefined reference" errors
From: Julie Prestopnik
Time: Thu Jan 31 15:51:22 2019
Hi Scott.
I see that you have been struggling to compile met-7.0 and/or met-8.0.
I'm
sorry to hear that. Thank you for taking the time to email met_help.
Based on the undefined references errors, there does seem to be a
problem
with the libraries as you indicated. We'd love to have you using the
latest version of MET and its patches (as of 20190130) which you can
get by
running:
wget
https://dtcenter.org/met/users/downloads/MET_releases/met-
8.0_bugfix/met-8.0_bugfix.20190130.tar.gz
I will say that I am unsure if we, the developers, have installed MET
using
that high of a version of the Intel compiler. I don't believe I have.
That may or may not be part of the problem. Do you have an earlier
version
(16.x.x.xxx?) of the Intel compiler that you could use. Thank you for
attaching your myConfigure.log file and your myMakeInstall.log file.
In
the future, it would be good to take a look at your config.log file,
which
has usually has additional information over configure.log.
I see that you have set the "-D__64BIT__" flag. As of recently there
were
problems with the compilation using that flag, so we ask that the you
remove the "-D__64BIT__" from the value of CFLAGS for the compilation
of
the libraries and for MET. This is noted under the "Compiling GRIB2
C-Library" section of the "Compilation" page of our newly posted met-
8.0
online tutorial. Please recompile the GRIB2 C-Library and MET without
that
flag set.
However, the undefined reference to error seems to be occurring with
NetCDF. I'm a little perplexed by the "undefined reference to
`_ZNK6netCDF5NcVar7getNameB5cxx11Ev'" error. I have not seen that
sort of
error, with the additional characters, previously. MET requires the C
and C++
interface to NetCDF. Here is a checklist of files that are necessary:
Files for NetCDF4 C:
- $MET_NETCDF/include/netcdf.h
- $MET_NETCDF/lib/libnetcdf.a
- $MET_NETCDF/lib/libnetcdf.so
Files for NetCDF4 C++:
- $MET_NETCDF/include/netcdf
- $MET_NETCDF/lib/libnetcdf_c++4.a
- $MET_NETCDF/lib/libnetcdf_c++4.so
You could take a look and see if you have all of those files.
By the way, are there specific configure options necessary when
building
> the netcdf and hdf libraries or does it not matter?
>
We have detailed installation instructions for each of the required
libraries posted in our online tutorial on the following page:
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
I hope this information is helpful. Please take a look and let us
know if
you have any questions. Please don't hesitate to follow up with any
additional questions.
Thanks,
Julie
On Thu, Jan 31, 2019 at 1:31 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>
> Thu Jan 31 13:31:33 2019: Request 88728 was acted upon.
> Transaction: Ticket created by scott.d.rabenhorst at nasa.gov
> Queue: met_help
> Subject: Help compiling met with "undefined reference" errors
> Owner: Nobody
> Requestors: scott.d.rabenhorst at nasa.gov
> Status: new
> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
>
>
> Hi MET support,
>
> I have been struggling to compile MET 7 (or 8) using Intel
compilers. The
> basic problem is undefined references to required libraries (netcdf,
hdf,
> etc). Interestingly, they always seem to occur in the
src/libcode/vx_*
> files. I have attached my latest compile log for the
> met-7.0_bugfix.20180924.tar.gz build. I have followed all the
directions in
> the MET Users Guide but it dows not seem to make any difference. For
this
> latest try, I setup the environment as follows:
>
>
>
------------------------------------------------------------------------------------------
> module load other/comp/gcc-6.3
> module load comp/intel-18.0.2.199
> module load mpi/impi-18.0.2.199
> module load lib/mkl-18.0.2.199
> module load wrf-deps/intel-18.0.2.199
> module load wgrib2/2.0.7_intel-18.0.2.199
>
> setenv COMPVERS intel-18.0.2.199
> setenv APPDIR ${NOBACKUP}/apps/sp3
>
> setenv MET_NETCDF ${APPDIR}/netcdf/4.6.1_hdf4/${COMPVERS}
> setenv MET_HDF5 ${APPDIR}/hdf5/1.10.2/${COMPVERS}
> setenv MET_HDF ${APPDIR}/hdf/4.2.13_no-fortran/${COMPVERS}
> setenv MET_HDFEOS ${APPDIR}/hdfeos/2.20v1.00/${COMPVERS}
> setenv MET_GRIB2C ${APPDIR}/g2clib/1.6.0/${COMPVERS}
> setenv MET_GSL ${APPDIR}/gsl/2.5/${COMPVERS}
> setenv MET_BUFR ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}
> setenv MET_BUFRLIB ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}/lib
> setenv MET_CAIROINC /usr/include/cairo
> setenv MET_CAIROLIB /usr/lib64
> setenv MET_FREETYPEINC /usr/include/freetype2
> setenv MET_FREETYPELIB /usr/lib64
> setenv YACC ${APPDIR}/byacc/github/${COMPVERS}
> setenv LDFLAGS -L${APPDIR}/wrf-deps/${COMPVERS}/lib
> setenv CPPFLAGS -I${APPDIR}/wrf-deps/${COMPVERS}/include
>
> setenv CFLAGS "-D__64BIT__"
>
> ./configure --prefix=${APPDIR}/MET/7.0/${COMPVERS} --enable-lidar2nc
> --enable-grib2 --enable-modis --enable-mode_graphics |& tee
myConfigure.log
>
>
>
------------------------------------------------------------------------------------------
>
> Then I ran "make install |& tee myMake.log" and got the resulting
error
> logs (attached). Everything seems correct. I have not been able to
> successfully build MET 8 either because of similar errors. Please
let me
> know any ideas on how to get this to compile correctly. I am out of
ideas
> and have spent a while recompiling supporting libraries using
different
> options. By the way, are there specific configure options necessary
when
> building the netcdf and hdf libraries or does it not matter? I look
forward
> to hearing from you soon.
>
>
> Thanks,
> Scott
>
>
------------------------------------------------
Subject: RE: [rt.rap.ucar.edu #88728] Help compiling met with "undefined reference" errors
From: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]
Time: Fri Feb 01 12:42:38 2019
Hi Julie,
Thanks so much for your prompt response. I will try compiling the
latest version of MET this afternoon with your suggestions (removing
the "-D__64BIT__" flag and compiler version). However, I can verify
that all the required netcdf files are present and passed self-
testing:
-rwxr-xr-x 1 sdrabenh g0620 1891 Jan 24 11:20 libbzip2.la
-rwxr-xr-x 1 sdrabenh g0620 113492 Jan 24 11:20 libbzip2.so
-rwxr-xr-x 1 sdrabenh g0620 1883 Jan 24 11:20 libmisc.la
-rwxr-xr-x 1 sdrabenh g0620 12777 Jan 24 11:20 libmisc.so
-rw-r--r-- 1 sdrabenh g0620 2629834 Jan 24 11:20 libnetcdf.a
-rw-r--r-- 1 sdrabenh g0620 1469428 Jan 24 11:33 libnetcdf_c++4.a
-rwxr-xr-x 1 sdrabenh g0620 2314 Jan 24 11:33 libnetcdf_c++4.la
lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33 libnetcdf_c++4.so ->
libnetcdf_c++4.so.1.0.3
lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33 libnetcdf_c++4.so.1
-> libnetcdf_c++4.so.1.0.3
-rwxr-xr-x 1 sdrabenh g0620 460080 Jan 24 11:33
libnetcdf_c++4.so.1.0.3
-rw-r--r-- 1 sdrabenh g0620 1053986 Jan 24 11:31 libnetcdff.a
-rwxr-xr-x 1 sdrabenh g0620 2295 Jan 24 11:31 libnetcdff.la
lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so ->
libnetcdff.so.6.1.1
lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so.6 ->
libnetcdff.so.6.1.1
-rwxr-xr-x 1 sdrabenh g0620 807278 Jan 24 11:31 libnetcdff.so.6.1.1
-rwxr-xr-x 1 sdrabenh g0620 2100 Jan 24 11:20 libnetcdf.la
-rw-r--r-- 1 sdrabenh g0620 1321 Jan 24 11:20 libnetcdf.settings
lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so ->
libnetcdf.so.13.1.1
lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so.13 ->
libnetcdf.so.13.1.1
-rwxr-xr-x 1 sdrabenh g0620 1908852 Jan 24 11:20 libnetcdf.so.13.1.1
drwxr-xr-x 2 sdrabenh g0620 512 Jan 24 11:33 pkgconfig
...and include files:
-rw-r--r-- 1 sdrabenh g0620 2965 Jan 24 11:33 ncAtt.h
-rw-r--r-- 1 sdrabenh g0620 480 Jan 24 11:33 ncByte.h
-rw-r--r-- 1 sdrabenh g0620 440 Jan 24 11:33 ncChar.h
-rw-r--r-- 1 sdrabenh g0620 1048 Jan 24 11:33 ncCheck.h
-rw-r--r-- 1 sdrabenh g0620 3684 Jan 24 11:33 ncCompoundType.h
-rw-r--r-- 1 sdrabenh g0620 1940 Jan 24 11:33 ncDim.h
-rw-r--r-- 1 sdrabenh g0620 483 Jan 24 11:33 ncDouble.h
-rw-r--r-- 1 sdrabenh g0620 3327 Jan 24 11:33 ncEnumType.h
-rw-r--r-- 1 sdrabenh g0620 12051 Jan 24 11:33 ncException.h
-rw-r--r-- 1 sdrabenh g0620 3469 Jan 24 11:33 ncFile.h
-rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncFloat.h
-rw-r--r-- 1 sdrabenh g0620 1055 Jan 24 11:33 ncGroupAtt.h
-rw-r--r-- 1 sdrabenh g0620 23965 Jan 24 11:33 ncGroup.h
-rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncInt64.h
-rw-r--r-- 1 sdrabenh g0620 453 Jan 24 11:33 ncInt.h
-rw-r--r-- 1 sdrabenh g0620 1501 Jan 24 11:33 ncOpaqueType.h
-rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncShort.h
-rw-r--r-- 1 sdrabenh g0620 482 Jan 24 11:33 ncString.h
-rw-r--r-- 1 sdrabenh g0620 5409 Jan 24 11:33 ncType.h
-rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncUbyte.h
-rw-r--r-- 1 sdrabenh g0620 481 Jan 24 11:33 ncUint64.h
-rw-r--r-- 1 sdrabenh g0620 462 Jan 24 11:33 ncUint.h
-rw-r--r-- 1 sdrabenh g0620 469 Jan 24 11:33 ncUshort.h
-rw-r--r-- 1 sdrabenh g0620 1151 Jan 24 11:33 ncVarAtt.h
-rw-r--r-- 1 sdrabenh g0620 54638 Jan 24 11:33 ncVar.h
-rw-r--r-- 1 sdrabenh g0620 1430 Jan 24 11:33 ncVlenType.h
-rw-r--r-- 1 sdrabenh g0620 651 Jan 24 11:33 netcdf
-rw-r--r-- 1 sdrabenh g0620 642 Jan 24 11:31 netcdf4_f03.mod
-rw-r--r-- 1 sdrabenh g0620 232820 Jan 24 11:31
netcdf4_nc_interfaces.mod
-rw-r--r-- 1 sdrabenh g0620 41808 Jan 24 11:31
netcdf4_nf_interfaces.mod
-rw-r--r-- 1 sdrabenh g0620 538 Jan 24 11:31 netcdf_f03.mod
-rw-r--r-- 1 sdrabenh g0620 200505 Jan 24 11:31
netcdf_fortv2_c_interfaces.mod
-rw-r--r-- 1 sdrabenh g0620 66697 Jan 24 11:20 netcdf.h
-rw-r--r-- 1 sdrabenh g0620 59877 Jan 24 11:31 netcdf.inc
-rw-r--r-- 1 sdrabenh g0620 520 Jan 24 11:20 netcdf_mem.h
-rw-r--r-- 1 sdrabenh g0620 2223 Jan 24 11:20 netcdf_meta.h
-rw-r--r-- 1 sdrabenh g0620 265880 Jan 24 11:31 netcdf.mod
-rw-r--r-- 1 sdrabenh g0620 26434 Jan 24 11:31 netcdf_nc_data.mod
-rw-r--r-- 1 sdrabenh g0620 155675 Jan 24 11:31
netcdf_nc_interfaces.mod
-rw-r--r-- 1 sdrabenh g0620 57449 Jan 24 11:31 netcdf_nf_data.mod
-rw-r--r-- 1 sdrabenh g0620 99023 Jan 24 11:31
netcdf_nf_interfaces.mod
-rw-r--r-- 1 sdrabenh g0620 1382 Jan 24 11:31 typesizes.mod
As you can see, all the c, c++, fortran files exist and I double
checked the MET_* environment variables all point correctly. It is
very strange that I keep encountering problems in the vx lib code. I
realize that the
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
provides some documentation on the required libs, but certainly not
all details. For instance, I know there have been many changes to the
recent versions of netcdf and hdf. Could you tell me if you have
successfully built MET8 (with Intel compilers), and if so, what
versions of netcdf-c, netcdf-cxx4, netcdf-fortran, hdf5, etc that you
used to make it work? That would be a very helpful starting point. I
have a feeling something I did may not be configured correctly, or I
may be using a library version that is either too old or new.
Currently, my libs have been built as follows:
1) szip/2.1.1
2) zlib/1.2.11
3) libpng/1.6.34 (--enable-shared --enable-static)
4) jpeg/9b (--enable-shared --enable-static)
5) jasper/1.900.1 (--enable-shared --enable-static --disable-opengl
--enable-libjpeg --with-PACKAGE=$JPEG --disable-asan --disable-leak)
6) hdf/4.2.13 (--with-zlib=$ZLIB --with-jpeg=$JPEG --with-szlib=$SZIP
--disable-fortran --enable-shared --enable-static --disable-netcdf)
7) hdfeos/2.20v1.00 (FC=$HDF/bin/h4fc
CXX=/usr/local/intel/2018/compilers_and_libraries_2018.2.199/linux/bin/intel64/icpc
F77=$HDF/bin/h4fc CC=$HDF/bin/h4cc --with-hdf4=$HDF --with-zlib=$ZLIB
--with-jpeg=$JPEG --with-szlib=$SZIP --disable-shared --enable-static)
8) hdf5/1.10.2 (--with-zlib=$ZLIB/include,$ZLIB/lib --with-szlib=$SZIP
--enable-cxx --enable-fortran --enable-fortran2003 --enable-hl
--enable-shared --enable-static --enable-codestack --enable-using-
memchecker --enable-filters=shuffle,fletcher32,nbit,scaleoffset)
9) netcdf-c/4.6.1 (--enable-hdf4 --enable-hdf4-file-tests --enable-
netcdf4 --enable-netcdf-4 --enable-dynamic-loading --enable-shared
--enable-static --enable-mmap --enable-fsync --enable-jna)
10) netcdf-fortran/4.4.4 (--enable-f03-compiler-check --enable-
fortran-type-check --enable-f03 --enable-largefile)
11) netcdf-cxx4/4.3.0 (--enable-shared --enable-static --enable-
largefile)
12) BUFRLIB/10.2.3 (FCFLAGS = CFLAGS = -DUNDERSCORE)
13) w3lib/2.0.6 (FFLAGS = CFLAGS = -O3 -g -m64 -DLINUX -D__64BIT__)
14) g2lib/3.1.0 (FFLAGS = -O3 -g -I $(MODDIR) -DLINUX -m64
-D__64BIT__; CFLAGS = -O3 -g -DLINUX $(INCDIR) -m64 -D__64BIT__)
15) g2clib/1.6.0 (INC = -I${JASPERINC} -I${SZIP}/include
-I${ZLIB}/include -I${PNG}/include -I${W3LIB}/include)
16) gsl/2.5 (--enable-shared --enable-static )
Please let me know if you have any further insight regarding what
versions and configuration of the required software will work with
intel compilers.
Thanks,
Scott
________________________________________
From: Julie Prestopnik via RT [met_help at ucar.edu]
Sent: Thursday, January 31, 2019 5:51 PM
To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS
INC]
Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
"undefined reference" errors
Hi Scott.
I see that you have been struggling to compile met-7.0 and/or met-8.0.
I'm
sorry to hear that. Thank you for taking the time to email met_help.
Based on the undefined references errors, there does seem to be a
problem
with the libraries as you indicated. We'd love to have you using the
latest version of MET and its patches (as of 20190130) which you can
get by
running:
wget
https://dtcenter.org/met/users/downloads/MET_releases/met-
8.0_bugfix/met-8.0_bugfix.20190130.tar.gz
I will say that I am unsure if we, the developers, have installed MET
using
that high of a version of the Intel compiler. I don't believe I have.
That may or may not be part of the problem. Do you have an earlier
version
(16.x.x.xxx?) of the Intel compiler that you could use. Thank you for
attaching your myConfigure.log file and your myMakeInstall.log file.
In
the future, it would be good to take a look at your config.log file,
which
has usually has additional information over configure.log.
I see that you have set the "-D__64BIT__" flag. As of recently there
were
problems with the compilation using that flag, so we ask that the you
remove the "-D__64BIT__" from the value of CFLAGS for the compilation
of
the libraries and for MET. This is noted under the "Compiling GRIB2
C-Library" section of the "Compilation" page of our newly posted met-
8.0
online tutorial. Please recompile the GRIB2 C-Library and MET without
that
flag set.
However, the undefined reference to error seems to be occurring with
NetCDF. I'm a little perplexed by the "undefined reference to
`_ZNK6netCDF5NcVar7getNameB5cxx11Ev'" error. I have not seen that
sort of
error, with the additional characters, previously. MET requires the C
and C++
interface to NetCDF. Here is a checklist of files that are necessary:
Files for NetCDF4 C:
- $MET_NETCDF/include/netcdf.h
- $MET_NETCDF/lib/libnetcdf.a
- $MET_NETCDF/lib/libnetcdf.so
Files for NetCDF4 C++:
- $MET_NETCDF/include/netcdf
- $MET_NETCDF/lib/libnetcdf_c++4.a
- $MET_NETCDF/lib/libnetcdf_c++4.so
You could take a look and see if you have all of those files.
By the way, are there specific configure options necessary when
building
> the netcdf and hdf libraries or does it not matter?
>
We have detailed installation instructions for each of the required
libraries posted in our online tutorial on the following page:
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
I hope this information is helpful. Please take a look and let us
know if
you have any questions. Please don't hesitate to follow up with any
additional questions.
Thanks,
Julie
On Thu, Jan 31, 2019 at 1:31 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>
> Thu Jan 31 13:31:33 2019: Request 88728 was acted upon.
> Transaction: Ticket created by scott.d.rabenhorst at nasa.gov
> Queue: met_help
> Subject: Help compiling met with "undefined reference" errors
> Owner: Nobody
> Requestors: scott.d.rabenhorst at nasa.gov
> Status: new
> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
>
>
> Hi MET support,
>
> I have been struggling to compile MET 7 (or 8) using Intel
compilers. The
> basic problem is undefined references to required libraries (netcdf,
hdf,
> etc). Interestingly, they always seem to occur in the
src/libcode/vx_*
> files. I have attached my latest compile log for the
> met-7.0_bugfix.20180924.tar.gz build. I have followed all the
directions in
> the MET Users Guide but it dows not seem to make any difference. For
this
> latest try, I setup the environment as follows:
>
>
>
------------------------------------------------------------------------------------------
> module load other/comp/gcc-6.3
> module load comp/intel-18.0.2.199
> module load mpi/impi-18.0.2.199
> module load lib/mkl-18.0.2.199
> module load wrf-deps/intel-18.0.2.199
> module load wgrib2/2.0.7_intel-18.0.2.199
>
> setenv COMPVERS intel-18.0.2.199
> setenv APPDIR ${NOBACKUP}/apps/sp3
>
> setenv MET_NETCDF ${APPDIR}/netcdf/4.6.1_hdf4/${COMPVERS}
> setenv MET_HDF5 ${APPDIR}/hdf5/1.10.2/${COMPVERS}
> setenv MET_HDF ${APPDIR}/hdf/4.2.13_no-fortran/${COMPVERS}
> setenv MET_HDFEOS ${APPDIR}/hdfeos/2.20v1.00/${COMPVERS}
> setenv MET_GRIB2C ${APPDIR}/g2clib/1.6.0/${COMPVERS}
> setenv MET_GSL ${APPDIR}/gsl/2.5/${COMPVERS}
> setenv MET_BUFR ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}
> setenv MET_BUFRLIB ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}/lib
> setenv MET_CAIROINC /usr/include/cairo
> setenv MET_CAIROLIB /usr/lib64
> setenv MET_FREETYPEINC /usr/include/freetype2
> setenv MET_FREETYPELIB /usr/lib64
> setenv YACC ${APPDIR}/byacc/github/${COMPVERS}
> setenv LDFLAGS -L${APPDIR}/wrf-deps/${COMPVERS}/lib
> setenv CPPFLAGS -I${APPDIR}/wrf-deps/${COMPVERS}/include
>
> setenv CFLAGS "-D__64BIT__"
>
> ./configure --prefix=${APPDIR}/MET/7.0/${COMPVERS} --enable-lidar2nc
> --enable-grib2 --enable-modis --enable-mode_graphics |& tee
myConfigure.log
>
>
>
------------------------------------------------------------------------------------------
>
> Then I ran "make install |& tee myMake.log" and got the resulting
error
> logs (attached). Everything seems correct. I have not been able to
> successfully build MET 8 either because of similar errors. Please
let me
> know any ideas on how to get this to compile correctly. I am out of
ideas
> and have spent a while recompiling supporting libraries using
different
> options. By the way, are there specific configure options necessary
when
> building the netcdf and hdf libraries or does it not matter? I look
forward
> to hearing from you soon.
>
>
> Thanks,
> Scott
>
>
------------------------------------------------
Subject: Help compiling met with "undefined reference" errors
From: Julie Prestopnik
Time: Fri Feb 01 12:54:13 2019
Hi Scott.
Sounds good! Thanks for recompiling later this afternoon. Thank you
also
for verifying that all of the required netcdf files are present (and
passed
self-testing!).
Could you tell me if you have successfully built MET8 (with Intel
> compilers), and if so, what versions of netcdf-c, netcdf-cxx4,
> netcdf-fortran, hdf5, etc that you used to make it work?
>
Yes. I mostly use the Intel compilers, but not with version 18.
Usually,
it's a lower version. Regarding the versions of the libraries, at the
bottom of the Downloads page on our website:
https://dtcenter.org/met/users/downloads/index.php
You can find a tarfile (
https://dtcenter.org/met/users/compile_scripts/tar_files.tar) that
contains
the versions of the libraries that we've been using along with a
script (
https://dtcenter.org/met/users/compile_scripts/compile_MET_all.sh)
that I
frequently use to compile MET and its dependent libraries on various
machines. There are some necessary environment variables that need to
be
set before running the script and those are described on the bottom of
the
Downloads page.
Please let me know if you have any other questions or problems. I'm
leaving now and won't be back until Monday. We have an three day MET
Tutorial this coming Monday - Wednesday at NCAR, so I may be a little
slower to respond, but I will get back to you as soon as I can.
I hope your next attempt will be successful! If not, let us know how
we can
help.
Thanks,
Julie
On Fri, Feb 1, 2019 at 12:42 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
>
> Hi Julie,
>
> Thanks so much for your prompt response. I will try compiling the
latest
> version of MET this afternoon with your suggestions (removing the
> "-D__64BIT__" flag and compiler version). However, I can verify that
all
> the required netcdf files are present and passed self-testing:
>
> -rwxr-xr-x 1 sdrabenh g0620 1891 Jan 24 11:20 libbzip2.la
> -rwxr-xr-x 1 sdrabenh g0620 113492 Jan 24 11:20 libbzip2.so
> -rwxr-xr-x 1 sdrabenh g0620 1883 Jan 24 11:20 libmisc.la
> -rwxr-xr-x 1 sdrabenh g0620 12777 Jan 24 11:20 libmisc.so
> -rw-r--r-- 1 sdrabenh g0620 2629834 Jan 24 11:20 libnetcdf.a
> -rw-r--r-- 1 sdrabenh g0620 1469428 Jan 24 11:33 libnetcdf_c++4.a
> -rwxr-xr-x 1 sdrabenh g0620 2314 Jan 24 11:33 libnetcdf_c++4.la
> lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33 libnetcdf_c++4.so
->
> libnetcdf_c++4.so.1.0.3
> lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33 libnetcdf_c++4.so.1
->
> libnetcdf_c++4.so.1.0.3
> -rwxr-xr-x 1 sdrabenh g0620 460080 Jan 24 11:33
libnetcdf_c++4.so.1.0.3
> -rw-r--r-- 1 sdrabenh g0620 1053986 Jan 24 11:31 libnetcdff.a
> -rwxr-xr-x 1 sdrabenh g0620 2295 Jan 24 11:31 libnetcdff.la
> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so ->
> libnetcdff.so.6.1.1
> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so.6 ->
> libnetcdff.so.6.1.1
> -rwxr-xr-x 1 sdrabenh g0620 807278 Jan 24 11:31 libnetcdff.so.6.1.1
> -rwxr-xr-x 1 sdrabenh g0620 2100 Jan 24 11:20 libnetcdf.la
> -rw-r--r-- 1 sdrabenh g0620 1321 Jan 24 11:20 libnetcdf.settings
> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so ->
> libnetcdf.so.13.1.1
> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so.13 ->
> libnetcdf.so.13.1.1
> -rwxr-xr-x 1 sdrabenh g0620 1908852 Jan 24 11:20 libnetcdf.so.13.1.1
> drwxr-xr-x 2 sdrabenh g0620 512 Jan 24 11:33 pkgconfig
>
> ...and include files:
>
> -rw-r--r-- 1 sdrabenh g0620 2965 Jan 24 11:33 ncAtt.h
> -rw-r--r-- 1 sdrabenh g0620 480 Jan 24 11:33 ncByte.h
> -rw-r--r-- 1 sdrabenh g0620 440 Jan 24 11:33 ncChar.h
> -rw-r--r-- 1 sdrabenh g0620 1048 Jan 24 11:33 ncCheck.h
> -rw-r--r-- 1 sdrabenh g0620 3684 Jan 24 11:33 ncCompoundType.h
> -rw-r--r-- 1 sdrabenh g0620 1940 Jan 24 11:33 ncDim.h
> -rw-r--r-- 1 sdrabenh g0620 483 Jan 24 11:33 ncDouble.h
> -rw-r--r-- 1 sdrabenh g0620 3327 Jan 24 11:33 ncEnumType.h
> -rw-r--r-- 1 sdrabenh g0620 12051 Jan 24 11:33 ncException.h
> -rw-r--r-- 1 sdrabenh g0620 3469 Jan 24 11:33 ncFile.h
> -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncFloat.h
> -rw-r--r-- 1 sdrabenh g0620 1055 Jan 24 11:33 ncGroupAtt.h
> -rw-r--r-- 1 sdrabenh g0620 23965 Jan 24 11:33 ncGroup.h
> -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncInt64.h
> -rw-r--r-- 1 sdrabenh g0620 453 Jan 24 11:33 ncInt.h
> -rw-r--r-- 1 sdrabenh g0620 1501 Jan 24 11:33 ncOpaqueType.h
> -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncShort.h
> -rw-r--r-- 1 sdrabenh g0620 482 Jan 24 11:33 ncString.h
> -rw-r--r-- 1 sdrabenh g0620 5409 Jan 24 11:33 ncType.h
> -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncUbyte.h
> -rw-r--r-- 1 sdrabenh g0620 481 Jan 24 11:33 ncUint64.h
> -rw-r--r-- 1 sdrabenh g0620 462 Jan 24 11:33 ncUint.h
> -rw-r--r-- 1 sdrabenh g0620 469 Jan 24 11:33 ncUshort.h
> -rw-r--r-- 1 sdrabenh g0620 1151 Jan 24 11:33 ncVarAtt.h
> -rw-r--r-- 1 sdrabenh g0620 54638 Jan 24 11:33 ncVar.h
> -rw-r--r-- 1 sdrabenh g0620 1430 Jan 24 11:33 ncVlenType.h
> -rw-r--r-- 1 sdrabenh g0620 651 Jan 24 11:33 netcdf
> -rw-r--r-- 1 sdrabenh g0620 642 Jan 24 11:31 netcdf4_f03.mod
> -rw-r--r-- 1 sdrabenh g0620 232820 Jan 24 11:31
netcdf4_nc_interfaces.mod
> -rw-r--r-- 1 sdrabenh g0620 41808 Jan 24 11:31
netcdf4_nf_interfaces.mod
> -rw-r--r-- 1 sdrabenh g0620 538 Jan 24 11:31 netcdf_f03.mod
> -rw-r--r-- 1 sdrabenh g0620 200505 Jan 24 11:31
> netcdf_fortv2_c_interfaces.mod
> -rw-r--r-- 1 sdrabenh g0620 66697 Jan 24 11:20 netcdf.h
> -rw-r--r-- 1 sdrabenh g0620 59877 Jan 24 11:31 netcdf.inc
> -rw-r--r-- 1 sdrabenh g0620 520 Jan 24 11:20 netcdf_mem.h
> -rw-r--r-- 1 sdrabenh g0620 2223 Jan 24 11:20 netcdf_meta.h
> -rw-r--r-- 1 sdrabenh g0620 265880 Jan 24 11:31 netcdf.mod
> -rw-r--r-- 1 sdrabenh g0620 26434 Jan 24 11:31 netcdf_nc_data.mod
> -rw-r--r-- 1 sdrabenh g0620 155675 Jan 24 11:31
netcdf_nc_interfaces.mod
> -rw-r--r-- 1 sdrabenh g0620 57449 Jan 24 11:31 netcdf_nf_data.mod
> -rw-r--r-- 1 sdrabenh g0620 99023 Jan 24 11:31
netcdf_nf_interfaces.mod
> -rw-r--r-- 1 sdrabenh g0620 1382 Jan 24 11:31 typesizes.mod
>
> As you can see, all the c, c++, fortran files exist and I double
checked
> the MET_* environment variables all point correctly. It is very
strange
> that I keep encountering problems in the vx lib code. I realize that
the
>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
> provides some documentation on the required libs, but certainly not
all
> details. For instance, I know there have been many changes to the
recent
> versions of netcdf and hdf. Could you tell me if you have
successfully
> built MET8 (with Intel compilers), and if so, what versions of
netcdf-c,
> netcdf-cxx4, netcdf-fortran, hdf5, etc that you used to make it
work? That
> would be a very helpful starting point. I have a feeling something I
did
> may not be configured correctly, or I may be using a library version
that
> is either too old or new. Currently, my libs have been built as
follows:
>
> 1) szip/2.1.1
>
> 2) zlib/1.2.11
>
> 3) libpng/1.6.34 (--enable-shared --enable-static)
>
> 4) jpeg/9b (--enable-shared --enable-static)
>
> 5) jasper/1.900.1 (--enable-shared --enable-static --disable-opengl
> --enable-libjpeg --with-PACKAGE=$JPEG --disable-asan --disable-leak)
>
> 6) hdf/4.2.13 (--with-zlib=$ZLIB --with-jpeg=$JPEG --with-
szlib=$SZIP
> --disable-fortran --enable-shared --enable-static --disable-netcdf)
>
> 7) hdfeos/2.20v1.00 (FC=$HDF/bin/h4fc
>
CXX=/usr/local/intel/2018/compilers_and_libraries_2018.2.199/linux/bin/intel64/icpc
> F77=$HDF/bin/h4fc CC=$HDF/bin/h4cc --with-hdf4=$HDF --with-
zlib=$ZLIB
> --with-jpeg=$JPEG --with-szlib=$SZIP --disable-shared --enable-
static)
>
> 8) hdf5/1.10.2 (--with-zlib=$ZLIB/include,$ZLIB/lib --with-
szlib=$SZIP
> --enable-cxx --enable-fortran --enable-fortran2003 --enable-hl
> --enable-shared --enable-static --enable-codestack
> --enable-using-memchecker
> --enable-filters=shuffle,fletcher32,nbit,scaleoffset)
>
> 9) netcdf-c/4.6.1 (--enable-hdf4 --enable-hdf4-file-tests --enable-
netcdf4
> --enable-netcdf-4 --enable-dynamic-loading --enable-shared --enable-
static
> --enable-mmap --enable-fsync --enable-jna)
>
> 10) netcdf-fortran/4.4.4 (--enable-f03-compiler-check
> --enable-fortran-type-check --enable-f03 --enable-largefile)
>
> 11) netcdf-cxx4/4.3.0 (--enable-shared --enable-static --enable-
largefile)
>
> 12) BUFRLIB/10.2.3 (FCFLAGS = CFLAGS = -DUNDERSCORE)
>
> 13) w3lib/2.0.6 (FFLAGS = CFLAGS = -O3 -g -m64 -DLINUX -D__64BIT__)
>
> 14) g2lib/3.1.0 (FFLAGS = -O3 -g -I $(MODDIR) -DLINUX -m64
-D__64BIT__;
> CFLAGS = -O3 -g -DLINUX $(INCDIR) -m64 -D__64BIT__)
>
> 15) g2clib/1.6.0 (INC = -I${JASPERINC} -I${SZIP}/include
-I${ZLIB}/include
> -I${PNG}/include -I${W3LIB}/include)
>
> 16) gsl/2.5 (--enable-shared --enable-static )
>
> Please let me know if you have any further insight regarding what
versions
> and configuration of the required software will work with intel
compilers.
>
> Thanks,
> Scott
>
>
> ________________________________________
> From: Julie Prestopnik via RT [met_help at ucar.edu]
> Sent: Thursday, January 31, 2019 5:51 PM
> To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
APPLICATIONS INC]
> Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
"undefined
> reference" errors
>
> Hi Scott.
>
> I see that you have been struggling to compile met-7.0 and/or met-
8.0. I'm
> sorry to hear that. Thank you for taking the time to email
met_help.
> Based on the undefined references errors, there does seem to be a
problem
> with the libraries as you indicated. We'd love to have you using
the
> latest version of MET and its patches (as of 20190130) which you can
get by
> running:
> wget
>
> https://dtcenter.org/met/users/downloads/MET_releases/met-
8.0_bugfix/met-8.0_bugfix.20190130.tar.gz
>
> I will say that I am unsure if we, the developers, have installed
MET using
> that high of a version of the Intel compiler. I don't believe I
have.
> That may or may not be part of the problem. Do you have an earlier
version
> (16.x.x.xxx?) of the Intel compiler that you could use. Thank you
for
> attaching your myConfigure.log file and your myMakeInstall.log file.
In
> the future, it would be good to take a look at your config.log file,
which
> has usually has additional information over configure.log.
>
> I see that you have set the "-D__64BIT__" flag. As of recently
there were
> problems with the compilation using that flag, so we ask that the
you
> remove the "-D__64BIT__" from the value of CFLAGS for the
compilation of
> the libraries and for MET. This is noted under the "Compiling GRIB2
> C-Library" section of the "Compilation" page of our newly posted
met-8.0
> online tutorial. Please recompile the GRIB2 C-Library and MET
without that
> flag set.
>
> However, the undefined reference to error seems to be occurring with
> NetCDF. I'm a little perplexed by the "undefined reference to
> `_ZNK6netCDF5NcVar7getNameB5cxx11Ev'" error. I have not seen that
sort of
> error, with the additional characters, previously. MET requires the
C and
> C++
> interface to NetCDF. Here is a checklist of files that are
necessary:
>
> Files for NetCDF4 C:
>
> - $MET_NETCDF/include/netcdf.h
> - $MET_NETCDF/lib/libnetcdf.a
> - $MET_NETCDF/lib/libnetcdf.so
>
> Files for NetCDF4 C++:
>
> - $MET_NETCDF/include/netcdf
> - $MET_NETCDF/lib/libnetcdf_c++4.a
> - $MET_NETCDF/lib/libnetcdf_c++4.so
>
> You could take a look and see if you have all of those files.
>
> By the way, are there specific configure options necessary when
building
> > the netcdf and hdf libraries or does it not matter?
> >
>
> We have detailed installation instructions for each of the required
> libraries posted in our online tutorial on the following page:
>
>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
>
> I hope this information is helpful. Please take a look and let us
know if
> you have any questions. Please don't hesitate to follow up with any
> additional questions.
>
> Thanks,
> Julie
>
> On Thu, Jan 31, 2019 at 1:31 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>
> >
> > Thu Jan 31 13:31:33 2019: Request 88728 was acted upon.
> > Transaction: Ticket created by scott.d.rabenhorst at nasa.gov
> > Queue: met_help
> > Subject: Help compiling met with "undefined reference" errors
> > Owner: Nobody
> > Requestors: scott.d.rabenhorst at nasa.gov
> > Status: new
> > Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
> >
> >
> > Hi MET support,
> >
> > I have been struggling to compile MET 7 (or 8) using Intel
compilers. The
> > basic problem is undefined references to required libraries
(netcdf, hdf,
> > etc). Interestingly, they always seem to occur in the
src/libcode/vx_*
> > files. I have attached my latest compile log for the
> > met-7.0_bugfix.20180924.tar.gz build. I have followed all the
directions
> in
> > the MET Users Guide but it dows not seem to make any difference.
For this
> > latest try, I setup the environment as follows:
> >
> >
> >
>
------------------------------------------------------------------------------------------
> > module load other/comp/gcc-6.3
> > module load comp/intel-18.0.2.199
> > module load mpi/impi-18.0.2.199
> > module load lib/mkl-18.0.2.199
> > module load wrf-deps/intel-18.0.2.199
> > module load wgrib2/2.0.7_intel-18.0.2.199
> >
> > setenv COMPVERS intel-18.0.2.199
> > setenv APPDIR ${NOBACKUP}/apps/sp3
> >
> > setenv MET_NETCDF ${APPDIR}/netcdf/4.6.1_hdf4/${COMPVERS}
> > setenv MET_HDF5 ${APPDIR}/hdf5/1.10.2/${COMPVERS}
> > setenv MET_HDF ${APPDIR}/hdf/4.2.13_no-
fortran/${COMPVERS}
> > setenv MET_HDFEOS ${APPDIR}/hdfeos/2.20v1.00/${COMPVERS}
> > setenv MET_GRIB2C ${APPDIR}/g2clib/1.6.0/${COMPVERS}
> > setenv MET_GSL ${APPDIR}/gsl/2.5/${COMPVERS}
> > setenv MET_BUFR ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}
> > setenv MET_BUFRLIB ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}/lib
> > setenv MET_CAIROINC /usr/include/cairo
> > setenv MET_CAIROLIB /usr/lib64
> > setenv MET_FREETYPEINC /usr/include/freetype2
> > setenv MET_FREETYPELIB /usr/lib64
> > setenv YACC ${APPDIR}/byacc/github/${COMPVERS}
> > setenv LDFLAGS -L${APPDIR}/wrf-deps/${COMPVERS}/lib
> > setenv CPPFLAGS -I${APPDIR}/wrf-deps/${COMPVERS}/include
> >
> > setenv CFLAGS "-D__64BIT__"
> >
> > ./configure --prefix=${APPDIR}/MET/7.0/${COMPVERS} --enable-
lidar2nc
> > --enable-grib2 --enable-modis --enable-mode_graphics |& tee
> myConfigure.log
> >
> >
> >
>
------------------------------------------------------------------------------------------
> >
> > Then I ran "make install |& tee myMake.log" and got the resulting
error
> > logs (attached). Everything seems correct. I have not been able to
> > successfully build MET 8 either because of similar errors. Please
let me
> > know any ideas on how to get this to compile correctly. I am out
of ideas
> > and have spent a while recompiling supporting libraries using
different
> > options. By the way, are there specific configure options
necessary when
> > building the netcdf and hdf libraries or does it not matter? I
look
> forward
> > to hearing from you soon.
> >
> >
> > Thanks,
> > Scott
> >
> >
>
>
>
>
------------------------------------------------
Subject: Help compiling met with "undefined reference" errors
From: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]
Time: Fri Feb 01 13:32:50 2019
Hi Julie,
No luck compiling MET8 using my existing libraries (as detailed in my
previous email). I attached my output logs for configure and make. It
is the same problem exists as before in the same src/libcode/vx_*
dirs. I can try using a intel-16.0.X.XXX compiler, but I'm skeptical
that is the source of the problem. First, I would have to rebuild all
the support libraries. Again, my suspicion is either some of the
required library versions are too new/old (incompatible versions) or I
might need to include some additional directives when building MET
(e.g. additional FLAGS or includes). If you have any versions that
successfully compiled with Intel, that might be the best starting
point. I can try to replicate that.
Thanks,
Scott
________________________________________
From: Julie Prestopnik via RT [met_help at ucar.edu]
Sent: Friday, February 01, 2019 2:54 PM
To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS
INC]
Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
"undefined reference" errors
Hi Scott.
Sounds good! Thanks for recompiling later this afternoon. Thank you
also
for verifying that all of the required netcdf files are present (and
passed
self-testing!).
Could you tell me if you have successfully built MET8 (with Intel
> compilers), and if so, what versions of netcdf-c, netcdf-cxx4,
> netcdf-fortran, hdf5, etc that you used to make it work?
>
Yes. I mostly use the Intel compilers, but not with version 18.
Usually,
it's a lower version. Regarding the versions of the libraries, at the
bottom of the Downloads page on our website:
https://dtcenter.org/met/users/downloads/index.php
You can find a tarfile (
https://dtcenter.org/met/users/compile_scripts/tar_files.tar) that
contains
the versions of the libraries that we've been using along with a
script (
https://dtcenter.org/met/users/compile_scripts/compile_MET_all.sh)
that I
frequently use to compile MET and its dependent libraries on various
machines. There are some necessary environment variables that need to
be
set before running the script and those are described on the bottom of
the
Downloads page.
Please let me know if you have any other questions or problems. I'm
leaving now and won't be back until Monday. We have an three day MET
Tutorial this coming Monday - Wednesday at NCAR, so I may be a little
slower to respond, but I will get back to you as soon as I can.
I hope your next attempt will be successful! If not, let us know how
we can
help.
Thanks,
Julie
On Fri, Feb 1, 2019 at 12:42 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
>
> Hi Julie,
>
> Thanks so much for your prompt response. I will try compiling the
latest
> version of MET this afternoon with your suggestions (removing the
> "-D__64BIT__" flag and compiler version). However, I can verify that
all
> the required netcdf files are present and passed self-testing:
>
> -rwxr-xr-x 1 sdrabenh g0620 1891 Jan 24 11:20 libbzip2.la
> -rwxr-xr-x 1 sdrabenh g0620 113492 Jan 24 11:20 libbzip2.so
> -rwxr-xr-x 1 sdrabenh g0620 1883 Jan 24 11:20 libmisc.la
> -rwxr-xr-x 1 sdrabenh g0620 12777 Jan 24 11:20 libmisc.so
> -rw-r--r-- 1 sdrabenh g0620 2629834 Jan 24 11:20 libnetcdf.a
> -rw-r--r-- 1 sdrabenh g0620 1469428 Jan 24 11:33 libnetcdf_c++4.a
> -rwxr-xr-x 1 sdrabenh g0620 2314 Jan 24 11:33 libnetcdf_c++4.la
> lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33 libnetcdf_c++4.so
->
> libnetcdf_c++4.so.1.0.3
> lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33 libnetcdf_c++4.so.1
->
> libnetcdf_c++4.so.1.0.3
> -rwxr-xr-x 1 sdrabenh g0620 460080 Jan 24 11:33
libnetcdf_c++4.so.1.0.3
> -rw-r--r-- 1 sdrabenh g0620 1053986 Jan 24 11:31 libnetcdff.a
> -rwxr-xr-x 1 sdrabenh g0620 2295 Jan 24 11:31 libnetcdff.la
> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so ->
> libnetcdff.so.6.1.1
> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so.6 ->
> libnetcdff.so.6.1.1
> -rwxr-xr-x 1 sdrabenh g0620 807278 Jan 24 11:31 libnetcdff.so.6.1.1
> -rwxr-xr-x 1 sdrabenh g0620 2100 Jan 24 11:20 libnetcdf.la
> -rw-r--r-- 1 sdrabenh g0620 1321 Jan 24 11:20 libnetcdf.settings
> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so ->
> libnetcdf.so.13.1.1
> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so.13 ->
> libnetcdf.so.13.1.1
> -rwxr-xr-x 1 sdrabenh g0620 1908852 Jan 24 11:20 libnetcdf.so.13.1.1
> drwxr-xr-x 2 sdrabenh g0620 512 Jan 24 11:33 pkgconfig
>
> ...and include files:
>
> -rw-r--r-- 1 sdrabenh g0620 2965 Jan 24 11:33 ncAtt.h
> -rw-r--r-- 1 sdrabenh g0620 480 Jan 24 11:33 ncByte.h
> -rw-r--r-- 1 sdrabenh g0620 440 Jan 24 11:33 ncChar.h
> -rw-r--r-- 1 sdrabenh g0620 1048 Jan 24 11:33 ncCheck.h
> -rw-r--r-- 1 sdrabenh g0620 3684 Jan 24 11:33 ncCompoundType.h
> -rw-r--r-- 1 sdrabenh g0620 1940 Jan 24 11:33 ncDim.h
> -rw-r--r-- 1 sdrabenh g0620 483 Jan 24 11:33 ncDouble.h
> -rw-r--r-- 1 sdrabenh g0620 3327 Jan 24 11:33 ncEnumType.h
> -rw-r--r-- 1 sdrabenh g0620 12051 Jan 24 11:33 ncException.h
> -rw-r--r-- 1 sdrabenh g0620 3469 Jan 24 11:33 ncFile.h
> -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncFloat.h
> -rw-r--r-- 1 sdrabenh g0620 1055 Jan 24 11:33 ncGroupAtt.h
> -rw-r--r-- 1 sdrabenh g0620 23965 Jan 24 11:33 ncGroup.h
> -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncInt64.h
> -rw-r--r-- 1 sdrabenh g0620 453 Jan 24 11:33 ncInt.h
> -rw-r--r-- 1 sdrabenh g0620 1501 Jan 24 11:33 ncOpaqueType.h
> -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncShort.h
> -rw-r--r-- 1 sdrabenh g0620 482 Jan 24 11:33 ncString.h
> -rw-r--r-- 1 sdrabenh g0620 5409 Jan 24 11:33 ncType.h
> -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncUbyte.h
> -rw-r--r-- 1 sdrabenh g0620 481 Jan 24 11:33 ncUint64.h
> -rw-r--r-- 1 sdrabenh g0620 462 Jan 24 11:33 ncUint.h
> -rw-r--r-- 1 sdrabenh g0620 469 Jan 24 11:33 ncUshort.h
> -rw-r--r-- 1 sdrabenh g0620 1151 Jan 24 11:33 ncVarAtt.h
> -rw-r--r-- 1 sdrabenh g0620 54638 Jan 24 11:33 ncVar.h
> -rw-r--r-- 1 sdrabenh g0620 1430 Jan 24 11:33 ncVlenType.h
> -rw-r--r-- 1 sdrabenh g0620 651 Jan 24 11:33 netcdf
> -rw-r--r-- 1 sdrabenh g0620 642 Jan 24 11:31 netcdf4_f03.mod
> -rw-r--r-- 1 sdrabenh g0620 232820 Jan 24 11:31
netcdf4_nc_interfaces.mod
> -rw-r--r-- 1 sdrabenh g0620 41808 Jan 24 11:31
netcdf4_nf_interfaces.mod
> -rw-r--r-- 1 sdrabenh g0620 538 Jan 24 11:31 netcdf_f03.mod
> -rw-r--r-- 1 sdrabenh g0620 200505 Jan 24 11:31
> netcdf_fortv2_c_interfaces.mod
> -rw-r--r-- 1 sdrabenh g0620 66697 Jan 24 11:20 netcdf.h
> -rw-r--r-- 1 sdrabenh g0620 59877 Jan 24 11:31 netcdf.inc
> -rw-r--r-- 1 sdrabenh g0620 520 Jan 24 11:20 netcdf_mem.h
> -rw-r--r-- 1 sdrabenh g0620 2223 Jan 24 11:20 netcdf_meta.h
> -rw-r--r-- 1 sdrabenh g0620 265880 Jan 24 11:31 netcdf.mod
> -rw-r--r-- 1 sdrabenh g0620 26434 Jan 24 11:31 netcdf_nc_data.mod
> -rw-r--r-- 1 sdrabenh g0620 155675 Jan 24 11:31
netcdf_nc_interfaces.mod
> -rw-r--r-- 1 sdrabenh g0620 57449 Jan 24 11:31 netcdf_nf_data.mod
> -rw-r--r-- 1 sdrabenh g0620 99023 Jan 24 11:31
netcdf_nf_interfaces.mod
> -rw-r--r-- 1 sdrabenh g0620 1382 Jan 24 11:31 typesizes.mod
>
> As you can see, all the c, c++, fortran files exist and I double
checked
> the MET_* environment variables all point correctly. It is very
strange
> that I keep encountering problems in the vx lib code. I realize that
the
>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
> provides some documentation on the required libs, but certainly not
all
> details. For instance, I know there have been many changes to the
recent
> versions of netcdf and hdf. Could you tell me if you have
successfully
> built MET8 (with Intel compilers), and if so, what versions of
netcdf-c,
> netcdf-cxx4, netcdf-fortran, hdf5, etc that you used to make it
work? That
> would be a very helpful starting point. I have a feeling something I
did
> may not be configured correctly, or I may be using a library version
that
> is either too old or new. Currently, my libs have been built as
follows:
>
> 1) szip/2.1.1
>
> 2) zlib/1.2.11
>
> 3) libpng/1.6.34 (--enable-shared --enable-static)
>
> 4) jpeg/9b (--enable-shared --enable-static)
>
> 5) jasper/1.900.1 (--enable-shared --enable-static --disable-opengl
> --enable-libjpeg --with-PACKAGE=$JPEG --disable-asan --disable-leak)
>
> 6) hdf/4.2.13 (--with-zlib=$ZLIB --with-jpeg=$JPEG --with-
szlib=$SZIP
> --disable-fortran --enable-shared --enable-static --disable-netcdf)
>
> 7) hdfeos/2.20v1.00 (FC=$HDF/bin/h4fc
>
CXX=/usr/local/intel/2018/compilers_and_libraries_2018.2.199/linux/bin/intel64/icpc
> F77=$HDF/bin/h4fc CC=$HDF/bin/h4cc --with-hdf4=$HDF --with-
zlib=$ZLIB
> --with-jpeg=$JPEG --with-szlib=$SZIP --disable-shared --enable-
static)
>
> 8) hdf5/1.10.2 (--with-zlib=$ZLIB/include,$ZLIB/lib --with-
szlib=$SZIP
> --enable-cxx --enable-fortran --enable-fortran2003 --enable-hl
> --enable-shared --enable-static --enable-codestack
> --enable-using-memchecker
> --enable-filters=shuffle,fletcher32,nbit,scaleoffset)
>
> 9) netcdf-c/4.6.1 (--enable-hdf4 --enable-hdf4-file-tests --enable-
netcdf4
> --enable-netcdf-4 --enable-dynamic-loading --enable-shared --enable-
static
> --enable-mmap --enable-fsync --enable-jna)
>
> 10) netcdf-fortran/4.4.4 (--enable-f03-compiler-check
> --enable-fortran-type-check --enable-f03 --enable-largefile)
>
> 11) netcdf-cxx4/4.3.0 (--enable-shared --enable-static --enable-
largefile)
>
> 12) BUFRLIB/10.2.3 (FCFLAGS = CFLAGS = -DUNDERSCORE)
>
> 13) w3lib/2.0.6 (FFLAGS = CFLAGS = -O3 -g -m64 -DLINUX -D__64BIT__)
>
> 14) g2lib/3.1.0 (FFLAGS = -O3 -g -I $(MODDIR) -DLINUX -m64
-D__64BIT__;
> CFLAGS = -O3 -g -DLINUX $(INCDIR) -m64 -D__64BIT__)
>
> 15) g2clib/1.6.0 (INC = -I${JASPERINC} -I${SZIP}/include
-I${ZLIB}/include
> -I${PNG}/include -I${W3LIB}/include)
>
> 16) gsl/2.5 (--enable-shared --enable-static )
>
> Please let me know if you have any further insight regarding what
versions
> and configuration of the required software will work with intel
compilers.
>
> Thanks,
> Scott
>
>
> ________________________________________
> From: Julie Prestopnik via RT [met_help at ucar.edu]
> Sent: Thursday, January 31, 2019 5:51 PM
> To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
APPLICATIONS INC]
> Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
"undefined
> reference" errors
>
> Hi Scott.
>
> I see that you have been struggling to compile met-7.0 and/or met-
8.0. I'm
> sorry to hear that. Thank you for taking the time to email
met_help.
> Based on the undefined references errors, there does seem to be a
problem
> with the libraries as you indicated. We'd love to have you using
the
> latest version of MET and its patches (as of 20190130) which you can
get by
> running:
> wget
>
> https://dtcenter.org/met/users/downloads/MET_releases/met-
8.0_bugfix/met-8.0_bugfix.20190130.tar.gz
>
> I will say that I am unsure if we, the developers, have installed
MET using
> that high of a version of the Intel compiler. I don't believe I
have.
> That may or may not be part of the problem. Do you have an earlier
version
> (16.x.x.xxx?) of the Intel compiler that you could use. Thank you
for
> attaching your myConfigure.log file and your myMakeInstall.log file.
In
> the future, it would be good to take a look at your config.log file,
which
> has usually has additional information over configure.log.
>
> I see that you have set the "-D__64BIT__" flag. As of recently
there were
> problems with the compilation using that flag, so we ask that the
you
> remove the "-D__64BIT__" from the value of CFLAGS for the
compilation of
> the libraries and for MET. This is noted under the "Compiling GRIB2
> C-Library" section of the "Compilation" page of our newly posted
met-8.0
> online tutorial. Please recompile the GRIB2 C-Library and MET
without that
> flag set.
>
> However, the undefined reference to error seems to be occurring with
> NetCDF. I'm a little perplexed by the "undefined reference to
> `_ZNK6netCDF5NcVar7getNameB5cxx11Ev'" error. I have not seen that
sort of
> error, with the additional characters, previously. MET requires the
C and
> C++
> interface to NetCDF. Here is a checklist of files that are
necessary:
>
> Files for NetCDF4 C:
>
> - $MET_NETCDF/include/netcdf.h
> - $MET_NETCDF/lib/libnetcdf.a
> - $MET_NETCDF/lib/libnetcdf.so
>
> Files for NetCDF4 C++:
>
> - $MET_NETCDF/include/netcdf
> - $MET_NETCDF/lib/libnetcdf_c++4.a
> - $MET_NETCDF/lib/libnetcdf_c++4.so
>
> You could take a look and see if you have all of those files.
>
> By the way, are there specific configure options necessary when
building
> > the netcdf and hdf libraries or does it not matter?
> >
>
> We have detailed installation instructions for each of the required
> libraries posted in our online tutorial on the following page:
>
>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
>
> I hope this information is helpful. Please take a look and let us
know if
> you have any questions. Please don't hesitate to follow up with any
> additional questions.
>
> Thanks,
> Julie
>
> On Thu, Jan 31, 2019 at 1:31 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>
> >
> > Thu Jan 31 13:31:33 2019: Request 88728 was acted upon.
> > Transaction: Ticket created by scott.d.rabenhorst at nasa.gov
> > Queue: met_help
> > Subject: Help compiling met with "undefined reference" errors
> > Owner: Nobody
> > Requestors: scott.d.rabenhorst at nasa.gov
> > Status: new
> > Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
> >
> >
> > Hi MET support,
> >
> > I have been struggling to compile MET 7 (or 8) using Intel
compilers. The
> > basic problem is undefined references to required libraries
(netcdf, hdf,
> > etc). Interestingly, they always seem to occur in the
src/libcode/vx_*
> > files. I have attached my latest compile log for the
> > met-7.0_bugfix.20180924.tar.gz build. I have followed all the
directions
> in
> > the MET Users Guide but it dows not seem to make any difference.
For this
> > latest try, I setup the environment as follows:
> >
> >
> >
>
------------------------------------------------------------------------------------------
> > module load other/comp/gcc-6.3
> > module load comp/intel-18.0.2.199
> > module load mpi/impi-18.0.2.199
> > module load lib/mkl-18.0.2.199
> > module load wrf-deps/intel-18.0.2.199
> > module load wgrib2/2.0.7_intel-18.0.2.199
> >
> > setenv COMPVERS intel-18.0.2.199
> > setenv APPDIR ${NOBACKUP}/apps/sp3
> >
> > setenv MET_NETCDF ${APPDIR}/netcdf/4.6.1_hdf4/${COMPVERS}
> > setenv MET_HDF5 ${APPDIR}/hdf5/1.10.2/${COMPVERS}
> > setenv MET_HDF ${APPDIR}/hdf/4.2.13_no-
fortran/${COMPVERS}
> > setenv MET_HDFEOS ${APPDIR}/hdfeos/2.20v1.00/${COMPVERS}
> > setenv MET_GRIB2C ${APPDIR}/g2clib/1.6.0/${COMPVERS}
> > setenv MET_GSL ${APPDIR}/gsl/2.5/${COMPVERS}
> > setenv MET_BUFR ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}
> > setenv MET_BUFRLIB ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}/lib
> > setenv MET_CAIROINC /usr/include/cairo
> > setenv MET_CAIROLIB /usr/lib64
> > setenv MET_FREETYPEINC /usr/include/freetype2
> > setenv MET_FREETYPELIB /usr/lib64
> > setenv YACC ${APPDIR}/byacc/github/${COMPVERS}
> > setenv LDFLAGS -L${APPDIR}/wrf-deps/${COMPVERS}/lib
> > setenv CPPFLAGS -I${APPDIR}/wrf-deps/${COMPVERS}/include
> >
> > setenv CFLAGS "-D__64BIT__"
> >
> > ./configure --prefix=${APPDIR}/MET/7.0/${COMPVERS} --enable-
lidar2nc
> > --enable-grib2 --enable-modis --enable-mode_graphics |& tee
> myConfigure.log
> >
> >
> >
>
------------------------------------------------------------------------------------------
> >
> > Then I ran "make install |& tee myMake.log" and got the resulting
error
> > logs (attached). Everything seems correct. I have not been able to
> > successfully build MET 8 either because of similar errors. Please
let me
> > know any ideas on how to get this to compile correctly. I am out
of ideas
> > and have spent a while recompiling supporting libraries using
different
> > options. By the way, are there specific configure options
necessary when
> > building the netcdf and hdf libraries or does it not matter? I
look
> forward
> > to hearing from you soon.
> >
> >
> > Thanks,
> > Scott
> >
> >
>
>
>
>
------------------------------------------------
Subject: Help compiling met with "undefined reference" errors
From: Julie Prestopnik
Time: Fri Feb 01 13:46:30 2019
Hi Scott. I'm replying from my phone, so this will be brief. I just
wanted
to make sure that it was clear that the tar file package I pointed you
to
in my last email contains the versions of all libraries that have
successfully compiled with Intel (and gnu and pgi).
Regarding flags, this would be indicated in the page in our online
tutorial
that I pointed you to in my first email.
Please take a look at the versions in the tarfile and follow up with
any
questions. You could also use the script I pointed to you to compile
only
MET or some or all of the supporting libraries.
Thanks, Julie
On Fri, Feb 1, 2019, 1:33 PM Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE
SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
>
> Hi Julie,
>
> No luck compiling MET8 using my existing libraries (as detailed in
my
> previous email). I attached my output logs for configure and make.
It is
> the same problem exists as before in the same src/libcode/vx_* dirs.
I can
> try using a intel-16.0.X.XXX compiler, but I'm skeptical that is the
source
> of the problem. First, I would have to rebuild all the support
libraries.
> Again, my suspicion is either some of the required library versions
are too
> new/old (incompatible versions) or I might need to include some
additional
> directives when building MET (e.g. additional FLAGS or includes). If
you
> have any versions that successfully compiled with Intel, that might
be the
> best starting point. I can try to replicate that.
>
> Thanks,
> Scott
>
> ________________________________________
> From: Julie Prestopnik via RT [met_help at ucar.edu]
> Sent: Friday, February 01, 2019 2:54 PM
> To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
APPLICATIONS INC]
> Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
"undefined
> reference" errors
>
> Hi Scott.
>
> Sounds good! Thanks for recompiling later this afternoon. Thank you
also
> for verifying that all of the required netcdf files are present (and
passed
> self-testing!).
>
> Could you tell me if you have successfully built MET8 (with Intel
> > compilers), and if so, what versions of netcdf-c, netcdf-cxx4,
> > netcdf-fortran, hdf5, etc that you used to make it work?
> >
>
> Yes. I mostly use the Intel compilers, but not with version 18.
Usually,
> it's a lower version. Regarding the versions of the libraries, at
the
> bottom of the Downloads page on our website:
> https://dtcenter.org/met/users/downloads/index.php
>
> You can find a tarfile (
> https://dtcenter.org/met/users/compile_scripts/tar_files.tar) that
> contains
> the versions of the libraries that we've been using along with a
script (
> https://dtcenter.org/met/users/compile_scripts/compile_MET_all.sh)
that I
> frequently use to compile MET and its dependent libraries on various
> machines. There are some necessary environment variables that need
to be
> set before running the script and those are described on the bottom
of the
> Downloads page.
>
> Please let me know if you have any other questions or problems. I'm
> leaving now and won't be back until Monday. We have an three day
MET
> Tutorial this coming Monday - Wednesday at NCAR, so I may be a
little
> slower to respond, but I will get back to you as soon as I can.
>
> I hope your next attempt will be successful! If not, let us know how
we can
> help.
>
> Thanks,
> Julie
>
> On Fri, Feb 1, 2019 at 12:42 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
> >
> > Hi Julie,
> >
> > Thanks so much for your prompt response. I will try compiling the
latest
> > version of MET this afternoon with your suggestions (removing the
> > "-D__64BIT__" flag and compiler version). However, I can verify
that all
> > the required netcdf files are present and passed self-testing:
> >
> > -rwxr-xr-x 1 sdrabenh g0620 1891 Jan 24 11:20 libbzip2.la
> > -rwxr-xr-x 1 sdrabenh g0620 113492 Jan 24 11:20 libbzip2.so
> > -rwxr-xr-x 1 sdrabenh g0620 1883 Jan 24 11:20 libmisc.la
> > -rwxr-xr-x 1 sdrabenh g0620 12777 Jan 24 11:20 libmisc.so
> > -rw-r--r-- 1 sdrabenh g0620 2629834 Jan 24 11:20 libnetcdf.a
> > -rw-r--r-- 1 sdrabenh g0620 1469428 Jan 24 11:33 libnetcdf_c++4.a
> > -rwxr-xr-x 1 sdrabenh g0620 2314 Jan 24 11:33 libnetcdf_c++4.la
> > lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33 libnetcdf_c++4.so
->
> > libnetcdf_c++4.so.1.0.3
> > lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33
libnetcdf_c++4.so.1 ->
> > libnetcdf_c++4.so.1.0.3
> > -rwxr-xr-x 1 sdrabenh g0620 460080 Jan 24 11:33
libnetcdf_c++4.so.1.0.3
> > -rw-r--r-- 1 sdrabenh g0620 1053986 Jan 24 11:31 libnetcdff.a
> > -rwxr-xr-x 1 sdrabenh g0620 2295 Jan 24 11:31 libnetcdff.la
> > lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so ->
> > libnetcdff.so.6.1.1
> > lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so.6
->
> > libnetcdff.so.6.1.1
> > -rwxr-xr-x 1 sdrabenh g0620 807278 Jan 24 11:31
libnetcdff.so.6.1.1
> > -rwxr-xr-x 1 sdrabenh g0620 2100 Jan 24 11:20 libnetcdf.la
> > -rw-r--r-- 1 sdrabenh g0620 1321 Jan 24 11:20
libnetcdf.settings
> > lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so ->
> > libnetcdf.so.13.1.1
> > lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so.13
->
> > libnetcdf.so.13.1.1
> > -rwxr-xr-x 1 sdrabenh g0620 1908852 Jan 24 11:20
libnetcdf.so.13.1.1
> > drwxr-xr-x 2 sdrabenh g0620 512 Jan 24 11:33 pkgconfig
> >
> > ...and include files:
> >
> > -rw-r--r-- 1 sdrabenh g0620 2965 Jan 24 11:33 ncAtt.h
> > -rw-r--r-- 1 sdrabenh g0620 480 Jan 24 11:33 ncByte.h
> > -rw-r--r-- 1 sdrabenh g0620 440 Jan 24 11:33 ncChar.h
> > -rw-r--r-- 1 sdrabenh g0620 1048 Jan 24 11:33 ncCheck.h
> > -rw-r--r-- 1 sdrabenh g0620 3684 Jan 24 11:33 ncCompoundType.h
> > -rw-r--r-- 1 sdrabenh g0620 1940 Jan 24 11:33 ncDim.h
> > -rw-r--r-- 1 sdrabenh g0620 483 Jan 24 11:33 ncDouble.h
> > -rw-r--r-- 1 sdrabenh g0620 3327 Jan 24 11:33 ncEnumType.h
> > -rw-r--r-- 1 sdrabenh g0620 12051 Jan 24 11:33 ncException.h
> > -rw-r--r-- 1 sdrabenh g0620 3469 Jan 24 11:33 ncFile.h
> > -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncFloat.h
> > -rw-r--r-- 1 sdrabenh g0620 1055 Jan 24 11:33 ncGroupAtt.h
> > -rw-r--r-- 1 sdrabenh g0620 23965 Jan 24 11:33 ncGroup.h
> > -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncInt64.h
> > -rw-r--r-- 1 sdrabenh g0620 453 Jan 24 11:33 ncInt.h
> > -rw-r--r-- 1 sdrabenh g0620 1501 Jan 24 11:33 ncOpaqueType.h
> > -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncShort.h
> > -rw-r--r-- 1 sdrabenh g0620 482 Jan 24 11:33 ncString.h
> > -rw-r--r-- 1 sdrabenh g0620 5409 Jan 24 11:33 ncType.h
> > -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncUbyte.h
> > -rw-r--r-- 1 sdrabenh g0620 481 Jan 24 11:33 ncUint64.h
> > -rw-r--r-- 1 sdrabenh g0620 462 Jan 24 11:33 ncUint.h
> > -rw-r--r-- 1 sdrabenh g0620 469 Jan 24 11:33 ncUshort.h
> > -rw-r--r-- 1 sdrabenh g0620 1151 Jan 24 11:33 ncVarAtt.h
> > -rw-r--r-- 1 sdrabenh g0620 54638 Jan 24 11:33 ncVar.h
> > -rw-r--r-- 1 sdrabenh g0620 1430 Jan 24 11:33 ncVlenType.h
> > -rw-r--r-- 1 sdrabenh g0620 651 Jan 24 11:33 netcdf
> > -rw-r--r-- 1 sdrabenh g0620 642 Jan 24 11:31 netcdf4_f03.mod
> > -rw-r--r-- 1 sdrabenh g0620 232820 Jan 24 11:31
netcdf4_nc_interfaces.mod
> > -rw-r--r-- 1 sdrabenh g0620 41808 Jan 24 11:31
netcdf4_nf_interfaces.mod
> > -rw-r--r-- 1 sdrabenh g0620 538 Jan 24 11:31 netcdf_f03.mod
> > -rw-r--r-- 1 sdrabenh g0620 200505 Jan 24 11:31
> > netcdf_fortv2_c_interfaces.mod
> > -rw-r--r-- 1 sdrabenh g0620 66697 Jan 24 11:20 netcdf.h
> > -rw-r--r-- 1 sdrabenh g0620 59877 Jan 24 11:31 netcdf.inc
> > -rw-r--r-- 1 sdrabenh g0620 520 Jan 24 11:20 netcdf_mem.h
> > -rw-r--r-- 1 sdrabenh g0620 2223 Jan 24 11:20 netcdf_meta.h
> > -rw-r--r-- 1 sdrabenh g0620 265880 Jan 24 11:31 netcdf.mod
> > -rw-r--r-- 1 sdrabenh g0620 26434 Jan 24 11:31 netcdf_nc_data.mod
> > -rw-r--r-- 1 sdrabenh g0620 155675 Jan 24 11:31
netcdf_nc_interfaces.mod
> > -rw-r--r-- 1 sdrabenh g0620 57449 Jan 24 11:31 netcdf_nf_data.mod
> > -rw-r--r-- 1 sdrabenh g0620 99023 Jan 24 11:31
netcdf_nf_interfaces.mod
> > -rw-r--r-- 1 sdrabenh g0620 1382 Jan 24 11:31 typesizes.mod
> >
> > As you can see, all the c, c++, fortran files exist and I double
checked
> > the MET_* environment variables all point correctly. It is very
strange
> > that I keep encountering problems in the vx lib code. I realize
that the
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
> > provides some documentation on the required libs, but certainly
not all
> > details. For instance, I know there have been many changes to the
recent
> > versions of netcdf and hdf. Could you tell me if you have
successfully
> > built MET8 (with Intel compilers), and if so, what versions of
netcdf-c,
> > netcdf-cxx4, netcdf-fortran, hdf5, etc that you used to make it
work?
> That
> > would be a very helpful starting point. I have a feeling something
I did
> > may not be configured correctly, or I may be using a library
version that
> > is either too old or new. Currently, my libs have been built as
follows:
> >
> > 1) szip/2.1.1
> >
> > 2) zlib/1.2.11
> >
> > 3) libpng/1.6.34 (--enable-shared --enable-static)
> >
> > 4) jpeg/9b (--enable-shared --enable-static)
> >
> > 5) jasper/1.900.1 (--enable-shared --enable-static --disable-
opengl
> > --enable-libjpeg --with-PACKAGE=$JPEG --disable-asan --disable-
leak)
> >
> > 6) hdf/4.2.13 (--with-zlib=$ZLIB --with-jpeg=$JPEG --with-
szlib=$SZIP
> > --disable-fortran --enable-shared --enable-static --disable-
netcdf)
> >
> > 7) hdfeos/2.20v1.00 (FC=$HDF/bin/h4fc
> >
>
CXX=/usr/local/intel/2018/compilers_and_libraries_2018.2.199/linux/bin/intel64/icpc
> > F77=$HDF/bin/h4fc CC=$HDF/bin/h4cc --with-hdf4=$HDF --with-
zlib=$ZLIB
> > --with-jpeg=$JPEG --with-szlib=$SZIP --disable-shared --enable-
static)
> >
> > 8) hdf5/1.10.2 (--with-zlib=$ZLIB/include,$ZLIB/lib --with-
szlib=$SZIP
> > --enable-cxx --enable-fortran --enable-fortran2003 --enable-hl
> > --enable-shared --enable-static --enable-codestack
> > --enable-using-memchecker
> > --enable-filters=shuffle,fletcher32,nbit,scaleoffset)
> >
> > 9) netcdf-c/4.6.1 (--enable-hdf4 --enable-hdf4-file-tests
> --enable-netcdf4
> > --enable-netcdf-4 --enable-dynamic-loading --enable-shared
> --enable-static
> > --enable-mmap --enable-fsync --enable-jna)
> >
> > 10) netcdf-fortran/4.4.4 (--enable-f03-compiler-check
> > --enable-fortran-type-check --enable-f03 --enable-largefile)
> >
> > 11) netcdf-cxx4/4.3.0 (--enable-shared --enable-static
> --enable-largefile)
> >
> > 12) BUFRLIB/10.2.3 (FCFLAGS = CFLAGS = -DUNDERSCORE)
> >
> > 13) w3lib/2.0.6 (FFLAGS = CFLAGS = -O3 -g -m64 -DLINUX
-D__64BIT__)
> >
> > 14) g2lib/3.1.0 (FFLAGS = -O3 -g -I $(MODDIR) -DLINUX -m64
-D__64BIT__;
> > CFLAGS = -O3 -g -DLINUX $(INCDIR) -m64 -D__64BIT__)
> >
> > 15) g2clib/1.6.0 (INC = -I${JASPERINC} -I${SZIP}/include
> -I${ZLIB}/include
> > -I${PNG}/include -I${W3LIB}/include)
> >
> > 16) gsl/2.5 (--enable-shared --enable-static )
> >
> > Please let me know if you have any further insight regarding what
> versions
> > and configuration of the required software will work with intel
> compilers.
> >
> > Thanks,
> > Scott
> >
> >
> > ________________________________________
> > From: Julie Prestopnik via RT [met_help at ucar.edu]
> > Sent: Thursday, January 31, 2019 5:51 PM
> > To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
APPLICATIONS
> INC]
> > Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
"undefined
> > reference" errors
> >
> > Hi Scott.
> >
> > I see that you have been struggling to compile met-7.0 and/or met-
8.0.
> I'm
> > sorry to hear that. Thank you for taking the time to email
met_help.
> > Based on the undefined references errors, there does seem to be a
problem
> > with the libraries as you indicated. We'd love to have you using
the
> > latest version of MET and its patches (as of 20190130) which you
can get
> by
> > running:
> > wget
> >
> >
> https://dtcenter.org/met/users/downloads/MET_releases/met-
8.0_bugfix/met-8.0_bugfix.20190130.tar.gz
> >
> > I will say that I am unsure if we, the developers, have installed
MET
> using
> > that high of a version of the Intel compiler. I don't believe I
have.
> > That may or may not be part of the problem. Do you have an
earlier
> version
> > (16.x.x.xxx?) of the Intel compiler that you could use. Thank you
for
> > attaching your myConfigure.log file and your myMakeInstall.log
file. In
> > the future, it would be good to take a look at your config.log
file,
> which
> > has usually has additional information over configure.log.
> >
> > I see that you have set the "-D__64BIT__" flag. As of recently
there
> were
> > problems with the compilation using that flag, so we ask that the
you
> > remove the "-D__64BIT__" from the value of CFLAGS for the
compilation of
> > the libraries and for MET. This is noted under the "Compiling
GRIB2
> > C-Library" section of the "Compilation" page of our newly posted
met-8.0
> > online tutorial. Please recompile the GRIB2 C-Library and MET
without
> that
> > flag set.
> >
> > However, the undefined reference to error seems to be occurring
with
> > NetCDF. I'm a little perplexed by the "undefined reference to
> > `_ZNK6netCDF5NcVar7getNameB5cxx11Ev'" error. I have not seen that
sort
> of
> > error, with the additional characters, previously. MET requires
the C
> and
> > C++
> > interface to NetCDF. Here is a checklist of files that are
necessary:
> >
> > Files for NetCDF4 C:
> >
> > - $MET_NETCDF/include/netcdf.h
> > - $MET_NETCDF/lib/libnetcdf.a
> > - $MET_NETCDF/lib/libnetcdf.so
> >
> > Files for NetCDF4 C++:
> >
> > - $MET_NETCDF/include/netcdf
> > - $MET_NETCDF/lib/libnetcdf_c++4.a
> > - $MET_NETCDF/lib/libnetcdf_c++4.so
> >
> > You could take a look and see if you have all of those files.
> >
> > By the way, are there specific configure options necessary when
building
> > > the netcdf and hdf libraries or does it not matter?
> > >
> >
> > We have detailed installation instructions for each of the
required
> > libraries posted in our online tutorial on the following page:
> >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
> >
> > I hope this information is helpful. Please take a look and let us
know
> if
> > you have any questions. Please don't hesitate to follow up with
any
> > additional questions.
> >
> > Thanks,
> > Julie
> >
> > On Thu, Jan 31, 2019 at 1:31 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
> > SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
> >
> > >
> > > Thu Jan 31 13:31:33 2019: Request 88728 was acted upon.
> > > Transaction: Ticket created by scott.d.rabenhorst at nasa.gov
> > > Queue: met_help
> > > Subject: Help compiling met with "undefined reference"
errors
> > > Owner: Nobody
> > > Requestors: scott.d.rabenhorst at nasa.gov
> > > Status: new
> > > Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728
> >
> > >
> > >
> > > Hi MET support,
> > >
> > > I have been struggling to compile MET 7 (or 8) using Intel
compilers.
> The
> > > basic problem is undefined references to required libraries
(netcdf,
> hdf,
> > > etc). Interestingly, they always seem to occur in the
src/libcode/vx_*
> > > files. I have attached my latest compile log for the
> > > met-7.0_bugfix.20180924.tar.gz build. I have followed all the
> directions
> > in
> > > the MET Users Guide but it dows not seem to make any difference.
For
> this
> > > latest try, I setup the environment as follows:
> > >
> > >
> > >
> >
>
------------------------------------------------------------------------------------------
> > > module load other/comp/gcc-6.3
> > > module load comp/intel-18.0.2.199
> > > module load mpi/impi-18.0.2.199
> > > module load lib/mkl-18.0.2.199
> > > module load wrf-deps/intel-18.0.2.199
> > > module load wgrib2/2.0.7_intel-18.0.2.199
> > >
> > > setenv COMPVERS intel-18.0.2.199
> > > setenv APPDIR ${NOBACKUP}/apps/sp3
> > >
> > > setenv MET_NETCDF ${APPDIR}/netcdf/4.6.1_hdf4/${COMPVERS}
> > > setenv MET_HDF5 ${APPDIR}/hdf5/1.10.2/${COMPVERS}
> > > setenv MET_HDF ${APPDIR}/hdf/4.2.13_no-
fortran/${COMPVERS}
> > > setenv MET_HDFEOS ${APPDIR}/hdfeos/2.20v1.00/${COMPVERS}
> > > setenv MET_GRIB2C ${APPDIR}/g2clib/1.6.0/${COMPVERS}
> > > setenv MET_GSL ${APPDIR}/gsl/2.5/${COMPVERS}
> > > setenv MET_BUFR ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}
> > > setenv MET_BUFRLIB ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}/lib
> > > setenv MET_CAIROINC /usr/include/cairo
> > > setenv MET_CAIROLIB /usr/lib64
> > > setenv MET_FREETYPEINC /usr/include/freetype2
> > > setenv MET_FREETYPELIB /usr/lib64
> > > setenv YACC ${APPDIR}/byacc/github/${COMPVERS}
> > > setenv LDFLAGS -L${APPDIR}/wrf-deps/${COMPVERS}/lib
> > > setenv CPPFLAGS -I${APPDIR}/wrf-deps/${COMPVERS}/include
> > >
> > > setenv CFLAGS "-D__64BIT__"
> > >
> > > ./configure --prefix=${APPDIR}/MET/7.0/${COMPVERS} --enable-
lidar2nc
> > > --enable-grib2 --enable-modis --enable-mode_graphics |& tee
> > myConfigure.log
> > >
> > >
> > >
> >
>
------------------------------------------------------------------------------------------
> > >
> > > Then I ran "make install |& tee myMake.log" and got the
resulting error
> > > logs (attached). Everything seems correct. I have not been able
to
> > > successfully build MET 8 either because of similar errors.
Please let
> me
> > > know any ideas on how to get this to compile correctly. I am out
of
> ideas
> > > and have spent a while recompiling supporting libraries using
different
> > > options. By the way, are there specific configure options
necessary
> when
> > > building the netcdf and hdf libraries or does it not matter? I
look
> > forward
> > > to hearing from you soon.
> > >
> > >
> > > Thanks,
> > > Scott
> > >
> > >
> >
> >
> >
> >
>
>
>
------------------------------------------------
Subject: RE: [rt.rap.ucar.edu #88728] Help compiling met with "undefined reference" errors
From: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]
Time: Fri Feb 01 14:04:53 2019
Hi Julie,
I am so sorry! I did not see your inline response with the tar file
and config script. That will be super helpful. I will give that a try
on my HPC system - I'm optimistic I can replicate things with that
level of detail.
Again, thanks so much for your prompt response to my emails. You have
been a terrific correspondent! I will let you know how things go.
Thanks,
Scott
________________________________________
From: Julie Prestopnik via RT [met_help at ucar.edu]
Sent: Friday, February 01, 2019 3:46 PM
To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS
INC]
Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
"undefined reference" errors
Hi Scott. I'm replying from my phone, so this will be brief. I just
wanted
to make sure that it was clear that the tar file package I pointed you
to
in my last email contains the versions of all libraries that have
successfully compiled with Intel (and gnu and pgi).
Regarding flags, this would be indicated in the page in our online
tutorial
that I pointed you to in my first email.
Please take a look at the versions in the tarfile and follow up with
any
questions. You could also use the script I pointed to you to compile
only
MET or some or all of the supporting libraries.
Thanks, Julie
On Fri, Feb 1, 2019, 1:33 PM Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE
SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
>
> Hi Julie,
>
> No luck compiling MET8 using my existing libraries (as detailed in
my
> previous email). I attached my output logs for configure and make.
It is
> the same problem exists as before in the same src/libcode/vx_* dirs.
I can
> try using a intel-16.0.X.XXX compiler, but I'm skeptical that is the
source
> of the problem. First, I would have to rebuild all the support
libraries.
> Again, my suspicion is either some of the required library versions
are too
> new/old (incompatible versions) or I might need to include some
additional
> directives when building MET (e.g. additional FLAGS or includes). If
you
> have any versions that successfully compiled with Intel, that might
be the
> best starting point. I can try to replicate that.
>
> Thanks,
> Scott
>
> ________________________________________
> From: Julie Prestopnik via RT [met_help at ucar.edu]
> Sent: Friday, February 01, 2019 2:54 PM
> To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
APPLICATIONS INC]
> Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
"undefined
> reference" errors
>
> Hi Scott.
>
> Sounds good! Thanks for recompiling later this afternoon. Thank you
also
> for verifying that all of the required netcdf files are present (and
passed
> self-testing!).
>
> Could you tell me if you have successfully built MET8 (with Intel
> > compilers), and if so, what versions of netcdf-c, netcdf-cxx4,
> > netcdf-fortran, hdf5, etc that you used to make it work?
> >
>
> Yes. I mostly use the Intel compilers, but not with version 18.
Usually,
> it's a lower version. Regarding the versions of the libraries, at
the
> bottom of the Downloads page on our website:
> https://dtcenter.org/met/users/downloads/index.php
>
> You can find a tarfile (
> https://dtcenter.org/met/users/compile_scripts/tar_files.tar) that
> contains
> the versions of the libraries that we've been using along with a
script (
> https://dtcenter.org/met/users/compile_scripts/compile_MET_all.sh)
that I
> frequently use to compile MET and its dependent libraries on various
> machines. There are some necessary environment variables that need
to be
> set before running the script and those are described on the bottom
of the
> Downloads page.
>
> Please let me know if you have any other questions or problems. I'm
> leaving now and won't be back until Monday. We have an three day
MET
> Tutorial this coming Monday - Wednesday at NCAR, so I may be a
little
> slower to respond, but I will get back to you as soon as I can.
>
> I hope your next attempt will be successful! If not, let us know how
we can
> help.
>
> Thanks,
> Julie
>
> On Fri, Feb 1, 2019 at 12:42 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
> >
> > Hi Julie,
> >
> > Thanks so much for your prompt response. I will try compiling the
latest
> > version of MET this afternoon with your suggestions (removing the
> > "-D__64BIT__" flag and compiler version). However, I can verify
that all
> > the required netcdf files are present and passed self-testing:
> >
> > -rwxr-xr-x 1 sdrabenh g0620 1891 Jan 24 11:20 libbzip2.la
> > -rwxr-xr-x 1 sdrabenh g0620 113492 Jan 24 11:20 libbzip2.so
> > -rwxr-xr-x 1 sdrabenh g0620 1883 Jan 24 11:20 libmisc.la
> > -rwxr-xr-x 1 sdrabenh g0620 12777 Jan 24 11:20 libmisc.so
> > -rw-r--r-- 1 sdrabenh g0620 2629834 Jan 24 11:20 libnetcdf.a
> > -rw-r--r-- 1 sdrabenh g0620 1469428 Jan 24 11:33 libnetcdf_c++4.a
> > -rwxr-xr-x 1 sdrabenh g0620 2314 Jan 24 11:33 libnetcdf_c++4.la
> > lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33 libnetcdf_c++4.so
->
> > libnetcdf_c++4.so.1.0.3
> > lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33
libnetcdf_c++4.so.1 ->
> > libnetcdf_c++4.so.1.0.3
> > -rwxr-xr-x 1 sdrabenh g0620 460080 Jan 24 11:33
libnetcdf_c++4.so.1.0.3
> > -rw-r--r-- 1 sdrabenh g0620 1053986 Jan 24 11:31 libnetcdff.a
> > -rwxr-xr-x 1 sdrabenh g0620 2295 Jan 24 11:31 libnetcdff.la
> > lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so ->
> > libnetcdff.so.6.1.1
> > lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so.6
->
> > libnetcdff.so.6.1.1
> > -rwxr-xr-x 1 sdrabenh g0620 807278 Jan 24 11:31
libnetcdff.so.6.1.1
> > -rwxr-xr-x 1 sdrabenh g0620 2100 Jan 24 11:20 libnetcdf.la
> > -rw-r--r-- 1 sdrabenh g0620 1321 Jan 24 11:20
libnetcdf.settings
> > lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so ->
> > libnetcdf.so.13.1.1
> > lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so.13
->
> > libnetcdf.so.13.1.1
> > -rwxr-xr-x 1 sdrabenh g0620 1908852 Jan 24 11:20
libnetcdf.so.13.1.1
> > drwxr-xr-x 2 sdrabenh g0620 512 Jan 24 11:33 pkgconfig
> >
> > ...and include files:
> >
> > -rw-r--r-- 1 sdrabenh g0620 2965 Jan 24 11:33 ncAtt.h
> > -rw-r--r-- 1 sdrabenh g0620 480 Jan 24 11:33 ncByte.h
> > -rw-r--r-- 1 sdrabenh g0620 440 Jan 24 11:33 ncChar.h
> > -rw-r--r-- 1 sdrabenh g0620 1048 Jan 24 11:33 ncCheck.h
> > -rw-r--r-- 1 sdrabenh g0620 3684 Jan 24 11:33 ncCompoundType.h
> > -rw-r--r-- 1 sdrabenh g0620 1940 Jan 24 11:33 ncDim.h
> > -rw-r--r-- 1 sdrabenh g0620 483 Jan 24 11:33 ncDouble.h
> > -rw-r--r-- 1 sdrabenh g0620 3327 Jan 24 11:33 ncEnumType.h
> > -rw-r--r-- 1 sdrabenh g0620 12051 Jan 24 11:33 ncException.h
> > -rw-r--r-- 1 sdrabenh g0620 3469 Jan 24 11:33 ncFile.h
> > -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncFloat.h
> > -rw-r--r-- 1 sdrabenh g0620 1055 Jan 24 11:33 ncGroupAtt.h
> > -rw-r--r-- 1 sdrabenh g0620 23965 Jan 24 11:33 ncGroup.h
> > -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncInt64.h
> > -rw-r--r-- 1 sdrabenh g0620 453 Jan 24 11:33 ncInt.h
> > -rw-r--r-- 1 sdrabenh g0620 1501 Jan 24 11:33 ncOpaqueType.h
> > -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncShort.h
> > -rw-r--r-- 1 sdrabenh g0620 482 Jan 24 11:33 ncString.h
> > -rw-r--r-- 1 sdrabenh g0620 5409 Jan 24 11:33 ncType.h
> > -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncUbyte.h
> > -rw-r--r-- 1 sdrabenh g0620 481 Jan 24 11:33 ncUint64.h
> > -rw-r--r-- 1 sdrabenh g0620 462 Jan 24 11:33 ncUint.h
> > -rw-r--r-- 1 sdrabenh g0620 469 Jan 24 11:33 ncUshort.h
> > -rw-r--r-- 1 sdrabenh g0620 1151 Jan 24 11:33 ncVarAtt.h
> > -rw-r--r-- 1 sdrabenh g0620 54638 Jan 24 11:33 ncVar.h
> > -rw-r--r-- 1 sdrabenh g0620 1430 Jan 24 11:33 ncVlenType.h
> > -rw-r--r-- 1 sdrabenh g0620 651 Jan 24 11:33 netcdf
> > -rw-r--r-- 1 sdrabenh g0620 642 Jan 24 11:31 netcdf4_f03.mod
> > -rw-r--r-- 1 sdrabenh g0620 232820 Jan 24 11:31
netcdf4_nc_interfaces.mod
> > -rw-r--r-- 1 sdrabenh g0620 41808 Jan 24 11:31
netcdf4_nf_interfaces.mod
> > -rw-r--r-- 1 sdrabenh g0620 538 Jan 24 11:31 netcdf_f03.mod
> > -rw-r--r-- 1 sdrabenh g0620 200505 Jan 24 11:31
> > netcdf_fortv2_c_interfaces.mod
> > -rw-r--r-- 1 sdrabenh g0620 66697 Jan 24 11:20 netcdf.h
> > -rw-r--r-- 1 sdrabenh g0620 59877 Jan 24 11:31 netcdf.inc
> > -rw-r--r-- 1 sdrabenh g0620 520 Jan 24 11:20 netcdf_mem.h
> > -rw-r--r-- 1 sdrabenh g0620 2223 Jan 24 11:20 netcdf_meta.h
> > -rw-r--r-- 1 sdrabenh g0620 265880 Jan 24 11:31 netcdf.mod
> > -rw-r--r-- 1 sdrabenh g0620 26434 Jan 24 11:31 netcdf_nc_data.mod
> > -rw-r--r-- 1 sdrabenh g0620 155675 Jan 24 11:31
netcdf_nc_interfaces.mod
> > -rw-r--r-- 1 sdrabenh g0620 57449 Jan 24 11:31 netcdf_nf_data.mod
> > -rw-r--r-- 1 sdrabenh g0620 99023 Jan 24 11:31
netcdf_nf_interfaces.mod
> > -rw-r--r-- 1 sdrabenh g0620 1382 Jan 24 11:31 typesizes.mod
> >
> > As you can see, all the c, c++, fortran files exist and I double
checked
> > the MET_* environment variables all point correctly. It is very
strange
> > that I keep encountering problems in the vx lib code. I realize
that the
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
> > provides some documentation on the required libs, but certainly
not all
> > details. For instance, I know there have been many changes to the
recent
> > versions of netcdf and hdf. Could you tell me if you have
successfully
> > built MET8 (with Intel compilers), and if so, what versions of
netcdf-c,
> > netcdf-cxx4, netcdf-fortran, hdf5, etc that you used to make it
work?
> That
> > would be a very helpful starting point. I have a feeling something
I did
> > may not be configured correctly, or I may be using a library
version that
> > is either too old or new. Currently, my libs have been built as
follows:
> >
> > 1) szip/2.1.1
> >
> > 2) zlib/1.2.11
> >
> > 3) libpng/1.6.34 (--enable-shared --enable-static)
> >
> > 4) jpeg/9b (--enable-shared --enable-static)
> >
> > 5) jasper/1.900.1 (--enable-shared --enable-static --disable-
opengl
> > --enable-libjpeg --with-PACKAGE=$JPEG --disable-asan --disable-
leak)
> >
> > 6) hdf/4.2.13 (--with-zlib=$ZLIB --with-jpeg=$JPEG --with-
szlib=$SZIP
> > --disable-fortran --enable-shared --enable-static --disable-
netcdf)
> >
> > 7) hdfeos/2.20v1.00 (FC=$HDF/bin/h4fc
> >
>
CXX=/usr/local/intel/2018/compilers_and_libraries_2018.2.199/linux/bin/intel64/icpc
> > F77=$HDF/bin/h4fc CC=$HDF/bin/h4cc --with-hdf4=$HDF --with-
zlib=$ZLIB
> > --with-jpeg=$JPEG --with-szlib=$SZIP --disable-shared --enable-
static)
> >
> > 8) hdf5/1.10.2 (--with-zlib=$ZLIB/include,$ZLIB/lib --with-
szlib=$SZIP
> > --enable-cxx --enable-fortran --enable-fortran2003 --enable-hl
> > --enable-shared --enable-static --enable-codestack
> > --enable-using-memchecker
> > --enable-filters=shuffle,fletcher32,nbit,scaleoffset)
> >
> > 9) netcdf-c/4.6.1 (--enable-hdf4 --enable-hdf4-file-tests
> --enable-netcdf4
> > --enable-netcdf-4 --enable-dynamic-loading --enable-shared
> --enable-static
> > --enable-mmap --enable-fsync --enable-jna)
> >
> > 10) netcdf-fortran/4.4.4 (--enable-f03-compiler-check
> > --enable-fortran-type-check --enable-f03 --enable-largefile)
> >
> > 11) netcdf-cxx4/4.3.0 (--enable-shared --enable-static
> --enable-largefile)
> >
> > 12) BUFRLIB/10.2.3 (FCFLAGS = CFLAGS = -DUNDERSCORE)
> >
> > 13) w3lib/2.0.6 (FFLAGS = CFLAGS = -O3 -g -m64 -DLINUX
-D__64BIT__)
> >
> > 14) g2lib/3.1.0 (FFLAGS = -O3 -g -I $(MODDIR) -DLINUX -m64
-D__64BIT__;
> > CFLAGS = -O3 -g -DLINUX $(INCDIR) -m64 -D__64BIT__)
> >
> > 15) g2clib/1.6.0 (INC = -I${JASPERINC} -I${SZIP}/include
> -I${ZLIB}/include
> > -I${PNG}/include -I${W3LIB}/include)
> >
> > 16) gsl/2.5 (--enable-shared --enable-static )
> >
> > Please let me know if you have any further insight regarding what
> versions
> > and configuration of the required software will work with intel
> compilers.
> >
> > Thanks,
> > Scott
> >
> >
> > ________________________________________
> > From: Julie Prestopnik via RT [met_help at ucar.edu]
> > Sent: Thursday, January 31, 2019 5:51 PM
> > To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
APPLICATIONS
> INC]
> > Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
"undefined
> > reference" errors
> >
> > Hi Scott.
> >
> > I see that you have been struggling to compile met-7.0 and/or met-
8.0.
> I'm
> > sorry to hear that. Thank you for taking the time to email
met_help.
> > Based on the undefined references errors, there does seem to be a
problem
> > with the libraries as you indicated. We'd love to have you using
the
> > latest version of MET and its patches (as of 20190130) which you
can get
> by
> > running:
> > wget
> >
> >
> https://dtcenter.org/met/users/downloads/MET_releases/met-
8.0_bugfix/met-8.0_bugfix.20190130.tar.gz
> >
> > I will say that I am unsure if we, the developers, have installed
MET
> using
> > that high of a version of the Intel compiler. I don't believe I
have.
> > That may or may not be part of the problem. Do you have an
earlier
> version
> > (16.x.x.xxx?) of the Intel compiler that you could use. Thank you
for
> > attaching your myConfigure.log file and your myMakeInstall.log
file. In
> > the future, it would be good to take a look at your config.log
file,
> which
> > has usually has additional information over configure.log.
> >
> > I see that you have set the "-D__64BIT__" flag. As of recently
there
> were
> > problems with the compilation using that flag, so we ask that the
you
> > remove the "-D__64BIT__" from the value of CFLAGS for the
compilation of
> > the libraries and for MET. This is noted under the "Compiling
GRIB2
> > C-Library" section of the "Compilation" page of our newly posted
met-8.0
> > online tutorial. Please recompile the GRIB2 C-Library and MET
without
> that
> > flag set.
> >
> > However, the undefined reference to error seems to be occurring
with
> > NetCDF. I'm a little perplexed by the "undefined reference to
> > `_ZNK6netCDF5NcVar7getNameB5cxx11Ev'" error. I have not seen that
sort
> of
> > error, with the additional characters, previously. MET requires
the C
> and
> > C++
> > interface to NetCDF. Here is a checklist of files that are
necessary:
> >
> > Files for NetCDF4 C:
> >
> > - $MET_NETCDF/include/netcdf.h
> > - $MET_NETCDF/lib/libnetcdf.a
> > - $MET_NETCDF/lib/libnetcdf.so
> >
> > Files for NetCDF4 C++:
> >
> > - $MET_NETCDF/include/netcdf
> > - $MET_NETCDF/lib/libnetcdf_c++4.a
> > - $MET_NETCDF/lib/libnetcdf_c++4.so
> >
> > You could take a look and see if you have all of those files.
> >
> > By the way, are there specific configure options necessary when
building
> > > the netcdf and hdf libraries or does it not matter?
> > >
> >
> > We have detailed installation instructions for each of the
required
> > libraries posted in our online tutorial on the following page:
> >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
> >
> > I hope this information is helpful. Please take a look and let us
know
> if
> > you have any questions. Please don't hesitate to follow up with
any
> > additional questions.
> >
> > Thanks,
> > Julie
> >
> > On Thu, Jan 31, 2019 at 1:31 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
> > SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
> >
> > >
> > > Thu Jan 31 13:31:33 2019: Request 88728 was acted upon.
> > > Transaction: Ticket created by scott.d.rabenhorst at nasa.gov
> > > Queue: met_help
> > > Subject: Help compiling met with "undefined reference"
errors
> > > Owner: Nobody
> > > Requestors: scott.d.rabenhorst at nasa.gov
> > > Status: new
> > > Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728
> >
> > >
> > >
> > > Hi MET support,
> > >
> > > I have been struggling to compile MET 7 (or 8) using Intel
compilers.
> The
> > > basic problem is undefined references to required libraries
(netcdf,
> hdf,
> > > etc). Interestingly, they always seem to occur in the
src/libcode/vx_*
> > > files. I have attached my latest compile log for the
> > > met-7.0_bugfix.20180924.tar.gz build. I have followed all the
> directions
> > in
> > > the MET Users Guide but it dows not seem to make any difference.
For
> this
> > > latest try, I setup the environment as follows:
> > >
> > >
> > >
> >
>
------------------------------------------------------------------------------------------
> > > module load other/comp/gcc-6.3
> > > module load comp/intel-18.0.2.199
> > > module load mpi/impi-18.0.2.199
> > > module load lib/mkl-18.0.2.199
> > > module load wrf-deps/intel-18.0.2.199
> > > module load wgrib2/2.0.7_intel-18.0.2.199
> > >
> > > setenv COMPVERS intel-18.0.2.199
> > > setenv APPDIR ${NOBACKUP}/apps/sp3
> > >
> > > setenv MET_NETCDF ${APPDIR}/netcdf/4.6.1_hdf4/${COMPVERS}
> > > setenv MET_HDF5 ${APPDIR}/hdf5/1.10.2/${COMPVERS}
> > > setenv MET_HDF ${APPDIR}/hdf/4.2.13_no-
fortran/${COMPVERS}
> > > setenv MET_HDFEOS ${APPDIR}/hdfeos/2.20v1.00/${COMPVERS}
> > > setenv MET_GRIB2C ${APPDIR}/g2clib/1.6.0/${COMPVERS}
> > > setenv MET_GSL ${APPDIR}/gsl/2.5/${COMPVERS}
> > > setenv MET_BUFR ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}
> > > setenv MET_BUFRLIB ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}/lib
> > > setenv MET_CAIROINC /usr/include/cairo
> > > setenv MET_CAIROLIB /usr/lib64
> > > setenv MET_FREETYPEINC /usr/include/freetype2
> > > setenv MET_FREETYPELIB /usr/lib64
> > > setenv YACC ${APPDIR}/byacc/github/${COMPVERS}
> > > setenv LDFLAGS -L${APPDIR}/wrf-deps/${COMPVERS}/lib
> > > setenv CPPFLAGS -I${APPDIR}/wrf-deps/${COMPVERS}/include
> > >
> > > setenv CFLAGS "-D__64BIT__"
> > >
> > > ./configure --prefix=${APPDIR}/MET/7.0/${COMPVERS} --enable-
lidar2nc
> > > --enable-grib2 --enable-modis --enable-mode_graphics |& tee
> > myConfigure.log
> > >
> > >
> > >
> >
>
------------------------------------------------------------------------------------------
> > >
> > > Then I ran "make install |& tee myMake.log" and got the
resulting error
> > > logs (attached). Everything seems correct. I have not been able
to
> > > successfully build MET 8 either because of similar errors.
Please let
> me
> > > know any ideas on how to get this to compile correctly. I am out
of
> ideas
> > > and have spent a while recompiling supporting libraries using
different
> > > options. By the way, are there specific configure options
necessary
> when
> > > building the netcdf and hdf libraries or does it not matter? I
look
> > forward
> > > to hearing from you soon.
> > >
> > >
> > > Thanks,
> > > Scott
> > >
> > >
> >
> >
> >
> >
>
>
>
------------------------------------------------
Subject: Help compiling met with "undefined reference" errors
From: Julie Prestopnik
Time: Tue Feb 05 09:47:02 2019
It's no problem! I hope the installation is going well. Please let
us
know how things go.
Thanks!
Julie
On Fri, Feb 1, 2019 at 2:04 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
>
> Hi Julie,
>
> I am so sorry! I did not see your inline response with the tar file
and
> config script. That will be super helpful. I will give that a try on
my HPC
> system - I'm optimistic I can replicate things with that level of
detail.
>
> Again, thanks so much for your prompt response to my emails. You
have been
> a terrific correspondent! I will let you know how things go.
>
> Thanks,
> Scott
>
> ________________________________________
> From: Julie Prestopnik via RT [met_help at ucar.edu]
> Sent: Friday, February 01, 2019 3:46 PM
> To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
APPLICATIONS INC]
> Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
"undefined
> reference" errors
>
> Hi Scott. I'm replying from my phone, so this will be brief. I just
wanted
> to make sure that it was clear that the tar file package I pointed
you to
> in my last email contains the versions of all libraries that have
> successfully compiled with Intel (and gnu and pgi).
>
> Regarding flags, this would be indicated in the page in our online
tutorial
> that I pointed you to in my first email.
>
> Please take a look at the versions in the tarfile and follow up with
any
> questions. You could also use the script I pointed to you to compile
only
> MET or some or all of the supporting libraries.
>
> Thanks, Julie
>
> On Fri, Feb 1, 2019, 1:33 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
> >
> > Hi Julie,
> >
> > No luck compiling MET8 using my existing libraries (as detailed in
my
> > previous email). I attached my output logs for configure and make.
It is
> > the same problem exists as before in the same src/libcode/vx_*
dirs. I
> can
> > try using a intel-16.0.X.XXX compiler, but I'm skeptical that is
the
> source
> > of the problem. First, I would have to rebuild all the support
libraries.
> > Again, my suspicion is either some of the required library
versions are
> too
> > new/old (incompatible versions) or I might need to include some
> additional
> > directives when building MET (e.g. additional FLAGS or includes).
If you
> > have any versions that successfully compiled with Intel, that
might be
> the
> > best starting point. I can try to replicate that.
> >
> > Thanks,
> > Scott
> >
> > ________________________________________
> > From: Julie Prestopnik via RT [met_help at ucar.edu]
> > Sent: Friday, February 01, 2019 2:54 PM
> > To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
APPLICATIONS
> INC]
> > Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
"undefined
> > reference" errors
> >
> > Hi Scott.
> >
> > Sounds good! Thanks for recompiling later this afternoon. Thank
you also
> > for verifying that all of the required netcdf files are present
(and
> passed
> > self-testing!).
> >
> > Could you tell me if you have successfully built MET8 (with Intel
> > > compilers), and if so, what versions of netcdf-c, netcdf-cxx4,
> > > netcdf-fortran, hdf5, etc that you used to make it work?
> > >
> >
> > Yes. I mostly use the Intel compilers, but not with version 18.
> Usually,
> > it's a lower version. Regarding the versions of the libraries, at
the
> > bottom of the Downloads page on our website:
> > https://dtcenter.org/met/users/downloads/index.php
> >
> > You can find a tarfile (
> > https://dtcenter.org/met/users/compile_scripts/tar_files.tar) that
> > contains
> > the versions of the libraries that we've been using along with a
script (
> > https://dtcenter.org/met/users/compile_scripts/compile_MET_all.sh)
that
> I
> > frequently use to compile MET and its dependent libraries on
various
> > machines. There are some necessary environment variables that
need to be
> > set before running the script and those are described on the
bottom of
> the
> > Downloads page.
> >
> > Please let me know if you have any other questions or problems.
I'm
> > leaving now and won't be back until Monday. We have an three day
MET
> > Tutorial this coming Monday - Wednesday at NCAR, so I may be a
little
> > slower to respond, but I will get back to you as soon as I can.
> >
> > I hope your next attempt will be successful! If not, let us know
how we
> can
> > help.
> >
> > Thanks,
> > Julie
> >
> > On Fri, Feb 1, 2019 at 12:42 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
> > SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
> > >
> > > Hi Julie,
> > >
> > > Thanks so much for your prompt response. I will try compiling
the
> latest
> > > version of MET this afternoon with your suggestions (removing
the
> > > "-D__64BIT__" flag and compiler version). However, I can verify
that
> all
> > > the required netcdf files are present and passed self-testing:
> > >
> > > -rwxr-xr-x 1 sdrabenh g0620 1891 Jan 24 11:20 libbzip2.la
> > > -rwxr-xr-x 1 sdrabenh g0620 113492 Jan 24 11:20 libbzip2.so
> > > -rwxr-xr-x 1 sdrabenh g0620 1883 Jan 24 11:20 libmisc.la
> > > -rwxr-xr-x 1 sdrabenh g0620 12777 Jan 24 11:20 libmisc.so
> > > -rw-r--r-- 1 sdrabenh g0620 2629834 Jan 24 11:20 libnetcdf.a
> > > -rw-r--r-- 1 sdrabenh g0620 1469428 Jan 24 11:33
libnetcdf_c++4.a
> > > -rwxr-xr-x 1 sdrabenh g0620 2314 Jan 24 11:33
libnetcdf_c++4.la
> > > lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33
libnetcdf_c++4.so ->
> > > libnetcdf_c++4.so.1.0.3
> > > lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33
libnetcdf_c++4.so.1 ->
> > > libnetcdf_c++4.so.1.0.3
> > > -rwxr-xr-x 1 sdrabenh g0620 460080 Jan 24 11:33
> libnetcdf_c++4.so.1.0.3
> > > -rw-r--r-- 1 sdrabenh g0620 1053986 Jan 24 11:31 libnetcdff.a
> > > -rwxr-xr-x 1 sdrabenh g0620 2295 Jan 24 11:31 libnetcdff.la
> > > lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so
->
> > > libnetcdff.so.6.1.1
> > > lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so.6
->
> > > libnetcdff.so.6.1.1
> > > -rwxr-xr-x 1 sdrabenh g0620 807278 Jan 24 11:31
libnetcdff.so.6.1.1
> > > -rwxr-xr-x 1 sdrabenh g0620 2100 Jan 24 11:20 libnetcdf.la
> > > -rw-r--r-- 1 sdrabenh g0620 1321 Jan 24 11:20
libnetcdf.settings
> > > lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so ->
> > > libnetcdf.so.13.1.1
> > > lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so.13
->
> > > libnetcdf.so.13.1.1
> > > -rwxr-xr-x 1 sdrabenh g0620 1908852 Jan 24 11:20
libnetcdf.so.13.1.1
> > > drwxr-xr-x 2 sdrabenh g0620 512 Jan 24 11:33 pkgconfig
> > >
> > > ...and include files:
> > >
> > > -rw-r--r-- 1 sdrabenh g0620 2965 Jan 24 11:33 ncAtt.h
> > > -rw-r--r-- 1 sdrabenh g0620 480 Jan 24 11:33 ncByte.h
> > > -rw-r--r-- 1 sdrabenh g0620 440 Jan 24 11:33 ncChar.h
> > > -rw-r--r-- 1 sdrabenh g0620 1048 Jan 24 11:33 ncCheck.h
> > > -rw-r--r-- 1 sdrabenh g0620 3684 Jan 24 11:33 ncCompoundType.h
> > > -rw-r--r-- 1 sdrabenh g0620 1940 Jan 24 11:33 ncDim.h
> > > -rw-r--r-- 1 sdrabenh g0620 483 Jan 24 11:33 ncDouble.h
> > > -rw-r--r-- 1 sdrabenh g0620 3327 Jan 24 11:33 ncEnumType.h
> > > -rw-r--r-- 1 sdrabenh g0620 12051 Jan 24 11:33 ncException.h
> > > -rw-r--r-- 1 sdrabenh g0620 3469 Jan 24 11:33 ncFile.h
> > > -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncFloat.h
> > > -rw-r--r-- 1 sdrabenh g0620 1055 Jan 24 11:33 ncGroupAtt.h
> > > -rw-r--r-- 1 sdrabenh g0620 23965 Jan 24 11:33 ncGroup.h
> > > -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncInt64.h
> > > -rw-r--r-- 1 sdrabenh g0620 453 Jan 24 11:33 ncInt.h
> > > -rw-r--r-- 1 sdrabenh g0620 1501 Jan 24 11:33 ncOpaqueType.h
> > > -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncShort.h
> > > -rw-r--r-- 1 sdrabenh g0620 482 Jan 24 11:33 ncString.h
> > > -rw-r--r-- 1 sdrabenh g0620 5409 Jan 24 11:33 ncType.h
> > > -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncUbyte.h
> > > -rw-r--r-- 1 sdrabenh g0620 481 Jan 24 11:33 ncUint64.h
> > > -rw-r--r-- 1 sdrabenh g0620 462 Jan 24 11:33 ncUint.h
> > > -rw-r--r-- 1 sdrabenh g0620 469 Jan 24 11:33 ncUshort.h
> > > -rw-r--r-- 1 sdrabenh g0620 1151 Jan 24 11:33 ncVarAtt.h
> > > -rw-r--r-- 1 sdrabenh g0620 54638 Jan 24 11:33 ncVar.h
> > > -rw-r--r-- 1 sdrabenh g0620 1430 Jan 24 11:33 ncVlenType.h
> > > -rw-r--r-- 1 sdrabenh g0620 651 Jan 24 11:33 netcdf
> > > -rw-r--r-- 1 sdrabenh g0620 642 Jan 24 11:31 netcdf4_f03.mod
> > > -rw-r--r-- 1 sdrabenh g0620 232820 Jan 24 11:31
> netcdf4_nc_interfaces.mod
> > > -rw-r--r-- 1 sdrabenh g0620 41808 Jan 24 11:31
> netcdf4_nf_interfaces.mod
> > > -rw-r--r-- 1 sdrabenh g0620 538 Jan 24 11:31 netcdf_f03.mod
> > > -rw-r--r-- 1 sdrabenh g0620 200505 Jan 24 11:31
> > > netcdf_fortv2_c_interfaces.mod
> > > -rw-r--r-- 1 sdrabenh g0620 66697 Jan 24 11:20 netcdf.h
> > > -rw-r--r-- 1 sdrabenh g0620 59877 Jan 24 11:31 netcdf.inc
> > > -rw-r--r-- 1 sdrabenh g0620 520 Jan 24 11:20 netcdf_mem.h
> > > -rw-r--r-- 1 sdrabenh g0620 2223 Jan 24 11:20 netcdf_meta.h
> > > -rw-r--r-- 1 sdrabenh g0620 265880 Jan 24 11:31 netcdf.mod
> > > -rw-r--r-- 1 sdrabenh g0620 26434 Jan 24 11:31
netcdf_nc_data.mod
> > > -rw-r--r-- 1 sdrabenh g0620 155675 Jan 24 11:31
> netcdf_nc_interfaces.mod
> > > -rw-r--r-- 1 sdrabenh g0620 57449 Jan 24 11:31
netcdf_nf_data.mod
> > > -rw-r--r-- 1 sdrabenh g0620 99023 Jan 24 11:31
> netcdf_nf_interfaces.mod
> > > -rw-r--r-- 1 sdrabenh g0620 1382 Jan 24 11:31 typesizes.mod
> > >
> > > As you can see, all the c, c++, fortran files exist and I double
> checked
> > > the MET_* environment variables all point correctly. It is very
strange
> > > that I keep encountering problems in the vx lib code. I realize
that
> the
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
> > > provides some documentation on the required libs, but certainly
not all
> > > details. For instance, I know there have been many changes to
the
> recent
> > > versions of netcdf and hdf. Could you tell me if you have
successfully
> > > built MET8 (with Intel compilers), and if so, what versions of
> netcdf-c,
> > > netcdf-cxx4, netcdf-fortran, hdf5, etc that you used to make it
work?
> > That
> > > would be a very helpful starting point. I have a feeling
something I
> did
> > > may not be configured correctly, or I may be using a library
version
> that
> > > is either too old or new. Currently, my libs have been built as
> follows:
> > >
> > > 1) szip/2.1.1
> > >
> > > 2) zlib/1.2.11
> > >
> > > 3) libpng/1.6.34 (--enable-shared --enable-static)
> > >
> > > 4) jpeg/9b (--enable-shared --enable-static)
> > >
> > > 5) jasper/1.900.1 (--enable-shared --enable-static --disable-
opengl
> > > --enable-libjpeg --with-PACKAGE=$JPEG --disable-asan --disable-
leak)
> > >
> > > 6) hdf/4.2.13 (--with-zlib=$ZLIB --with-jpeg=$JPEG --with-
szlib=$SZIP
> > > --disable-fortran --enable-shared --enable-static --disable-
netcdf)
> > >
> > > 7) hdfeos/2.20v1.00 (FC=$HDF/bin/h4fc
> > >
> >
>
CXX=/usr/local/intel/2018/compilers_and_libraries_2018.2.199/linux/bin/intel64/icpc
> > > F77=$HDF/bin/h4fc CC=$HDF/bin/h4cc --with-hdf4=$HDF --with-
zlib=$ZLIB
> > > --with-jpeg=$JPEG --with-szlib=$SZIP --disable-shared --enable-
static)
> > >
> > > 8) hdf5/1.10.2 (--with-zlib=$ZLIB/include,$ZLIB/lib --with-
szlib=$SZIP
> > > --enable-cxx --enable-fortran --enable-fortran2003 --enable-hl
> > > --enable-shared --enable-static --enable-codestack
> > > --enable-using-memchecker
> > > --enable-filters=shuffle,fletcher32,nbit,scaleoffset)
> > >
> > > 9) netcdf-c/4.6.1 (--enable-hdf4 --enable-hdf4-file-tests
> > --enable-netcdf4
> > > --enable-netcdf-4 --enable-dynamic-loading --enable-shared
> > --enable-static
> > > --enable-mmap --enable-fsync --enable-jna)
> > >
> > > 10) netcdf-fortran/4.4.4 (--enable-f03-compiler-check
> > > --enable-fortran-type-check --enable-f03 --enable-largefile)
> > >
> > > 11) netcdf-cxx4/4.3.0 (--enable-shared --enable-static
> > --enable-largefile)
> > >
> > > 12) BUFRLIB/10.2.3 (FCFLAGS = CFLAGS = -DUNDERSCORE)
> > >
> > > 13) w3lib/2.0.6 (FFLAGS = CFLAGS = -O3 -g -m64 -DLINUX
-D__64BIT__)
> > >
> > > 14) g2lib/3.1.0 (FFLAGS = -O3 -g -I $(MODDIR) -DLINUX -m64
> -D__64BIT__;
> > > CFLAGS = -O3 -g -DLINUX $(INCDIR) -m64 -D__64BIT__)
> > >
> > > 15) g2clib/1.6.0 (INC = -I${JASPERINC} -I${SZIP}/include
> > -I${ZLIB}/include
> > > -I${PNG}/include -I${W3LIB}/include)
> > >
> > > 16) gsl/2.5 (--enable-shared --enable-static )
> > >
> > > Please let me know if you have any further insight regarding
what
> > versions
> > > and configuration of the required software will work with intel
> > compilers.
> > >
> > > Thanks,
> > > Scott
> > >
> > >
> > > ________________________________________
> > > From: Julie Prestopnik via RT [met_help at ucar.edu]
> > > Sent: Thursday, January 31, 2019 5:51 PM
> > > To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
APPLICATIONS
> > INC]
> > > Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
> "undefined
> > > reference" errors
> > >
> > > Hi Scott.
> > >
> > > I see that you have been struggling to compile met-7.0 and/or
met-8.0.
> > I'm
> > > sorry to hear that. Thank you for taking the time to email
met_help.
> > > Based on the undefined references errors, there does seem to be
a
> problem
> > > with the libraries as you indicated. We'd love to have you
using the
> > > latest version of MET and its patches (as of 20190130) which you
can
> get
> > by
> > > running:
> > > wget
> > >
> > >
> >
> https://dtcenter.org/met/users/downloads/MET_releases/met-
8.0_bugfix/met-8.0_bugfix.20190130.tar.gz
> > >
> > > I will say that I am unsure if we, the developers, have
installed MET
> > using
> > > that high of a version of the Intel compiler. I don't believe I
have.
> > > That may or may not be part of the problem. Do you have an
earlier
> > version
> > > (16.x.x.xxx?) of the Intel compiler that you could use. Thank
you for
> > > attaching your myConfigure.log file and your myMakeInstall.log
file.
> In
> > > the future, it would be good to take a look at your config.log
file,
> > which
> > > has usually has additional information over configure.log.
> > >
> > > I see that you have set the "-D__64BIT__" flag. As of recently
there
> > were
> > > problems with the compilation using that flag, so we ask that
the you
> > > remove the "-D__64BIT__" from the value of CFLAGS for the
compilation
> of
> > > the libraries and for MET. This is noted under the "Compiling
GRIB2
> > > C-Library" section of the "Compilation" page of our newly posted
> met-8.0
> > > online tutorial. Please recompile the GRIB2 C-Library and MET
without
> > that
> > > flag set.
> > >
> > > However, the undefined reference to error seems to be occurring
with
> > > NetCDF. I'm a little perplexed by the "undefined reference to
> > > `_ZNK6netCDF5NcVar7getNameB5cxx11Ev'" error. I have not seen
that sort
> > of
> > > error, with the additional characters, previously. MET requires
the C
> > and
> > > C++
> > > interface to NetCDF. Here is a checklist of files that are
necessary:
> > >
> > > Files for NetCDF4 C:
> > >
> > > - $MET_NETCDF/include/netcdf.h
> > > - $MET_NETCDF/lib/libnetcdf.a
> > > - $MET_NETCDF/lib/libnetcdf.so
> > >
> > > Files for NetCDF4 C++:
> > >
> > > - $MET_NETCDF/include/netcdf
> > > - $MET_NETCDF/lib/libnetcdf_c++4.a
> > > - $MET_NETCDF/lib/libnetcdf_c++4.so
> > >
> > > You could take a look and see if you have all of those files.
> > >
> > > By the way, are there specific configure options necessary when
> building
> > > > the netcdf and hdf libraries or does it not matter?
> > > >
> > >
> > > We have detailed installation instructions for each of the
required
> > > libraries posted in our online tutorial on the following page:
> > >
> > >
> >
>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
> > >
> > > I hope this information is helpful. Please take a look and let
us know
> > if
> > > you have any questions. Please don't hesitate to follow up with
any
> > > additional questions.
> > >
> > > Thanks,
> > > Julie
> > >
> > > On Thu, Jan 31, 2019 at 1:31 PM Rabenhorst, Scott D.
> (GSFC-610.1)[SCIENCE
> > > SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
> > >
> > > >
> > > > Thu Jan 31 13:31:33 2019: Request 88728 was acted upon.
> > > > Transaction: Ticket created by scott.d.rabenhorst at nasa.gov
> > > > Queue: met_help
> > > > Subject: Help compiling met with "undefined reference"
errors
> > > > Owner: Nobody
> > > > Requestors: scott.d.rabenhorst at nasa.gov
> > > > Status: new
> > > > Ticket <URL:
> https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728
> > >
> > > >
> > > >
> > > > Hi MET support,
> > > >
> > > > I have been struggling to compile MET 7 (or 8) using Intel
compilers.
> > The
> > > > basic problem is undefined references to required libraries
(netcdf,
> > hdf,
> > > > etc). Interestingly, they always seem to occur in the
> src/libcode/vx_*
> > > > files. I have attached my latest compile log for the
> > > > met-7.0_bugfix.20180924.tar.gz build. I have followed all the
> > directions
> > > in
> > > > the MET Users Guide but it dows not seem to make any
difference. For
> > this
> > > > latest try, I setup the environment as follows:
> > > >
> > > >
> > > >
> > >
> >
>
------------------------------------------------------------------------------------------
> > > > module load other/comp/gcc-6.3
> > > > module load comp/intel-18.0.2.199
> > > > module load mpi/impi-18.0.2.199
> > > > module load lib/mkl-18.0.2.199
> > > > module load wrf-deps/intel-18.0.2.199
> > > > module load wgrib2/2.0.7_intel-18.0.2.199
> > > >
> > > > setenv COMPVERS intel-18.0.2.199
> > > > setenv APPDIR ${NOBACKUP}/apps/sp3
> > > >
> > > > setenv MET_NETCDF
${APPDIR}/netcdf/4.6.1_hdf4/${COMPVERS}
> > > > setenv MET_HDF5 ${APPDIR}/hdf5/1.10.2/${COMPVERS}
> > > > setenv MET_HDF ${APPDIR}/hdf/4.2.13_no-
fortran/${COMPVERS}
> > > > setenv MET_HDFEOS ${APPDIR}/hdfeos/2.20v1.00/${COMPVERS}
> > > > setenv MET_GRIB2C ${APPDIR}/g2clib/1.6.0/${COMPVERS}
> > > > setenv MET_GSL ${APPDIR}/gsl/2.5/${COMPVERS}
> > > > setenv MET_BUFR ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}
> > > > setenv MET_BUFRLIB
${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}/lib
> > > > setenv MET_CAIROINC /usr/include/cairo
> > > > setenv MET_CAIROLIB /usr/lib64
> > > > setenv MET_FREETYPEINC /usr/include/freetype2
> > > > setenv MET_FREETYPELIB /usr/lib64
> > > > setenv YACC ${APPDIR}/byacc/github/${COMPVERS}
> > > > setenv LDFLAGS -L${APPDIR}/wrf-deps/${COMPVERS}/lib
> > > > setenv CPPFLAGS -I${APPDIR}/wrf-
deps/${COMPVERS}/include
> > > >
> > > > setenv CFLAGS "-D__64BIT__"
> > > >
> > > > ./configure --prefix=${APPDIR}/MET/7.0/${COMPVERS} --enable-
lidar2nc
> > > > --enable-grib2 --enable-modis --enable-mode_graphics |& tee
> > > myConfigure.log
> > > >
> > > >
> > > >
> > >
> >
>
------------------------------------------------------------------------------------------
> > > >
> > > > Then I ran "make install |& tee myMake.log" and got the
resulting
> error
> > > > logs (attached). Everything seems correct. I have not been
able to
> > > > successfully build MET 8 either because of similar errors.
Please let
> > me
> > > > know any ideas on how to get this to compile correctly. I am
out of
> > ideas
> > > > and have spent a while recompiling supporting libraries using
> different
> > > > options. By the way, are there specific configure options
necessary
> > when
> > > > building the netcdf and hdf libraries or does it not matter? I
look
> > > forward
> > > > to hearing from you soon.
> > > >
> > > >
> > > > Thanks,
> > > > Scott
> > > >
> > > >
> > >
> > >
> > >
> > >
> >
> >
> >
>
>
>
>
------------------------------------------------
Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with "undefined reference" errors
From: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]
Time: Fri Feb 15 09:51:44 2019
Hi Julie,
Sorry for my delayed response. I had to take care of more pressing
projects this week and have just now returning to getting MET up and
running.
I am trying to replicate your compile script. However, I ran into a
problem. I am having trouble building hd4 (your version of HDF4.2r3
from
2008) using my version of jpeg (9c). The make check fails with jpeg
related issues. In the files you posted for me the other week, I could
not find a jpeg source tar file. Neither could I figure out what
version
you are using based on the compile script. However, the jpeg library
is
required. Would you mind letting me know what version your are using?
I
hope that may solve some issues here.
Thanks,
Scott
On 2/5/19 11:47 AM, Julie Prestopnik via RT wrote:
> It's no problem! I hope the installation is going well. Please let
us
> know how things go.
>
> Thanks!
>
> Julie
>
> On Fri, Feb 1, 2019 at 2:04 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>
>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
>>
>> Hi Julie,
>>
>> I am so sorry! I did not see your inline response with the tar file
and
>> config script. That will be super helpful. I will give that a try
on my HPC
>> system - I'm optimistic I can replicate things with that level of
detail.
>>
>> Again, thanks so much for your prompt response to my emails. You
have been
>> a terrific correspondent! I will let you know how things go.
>>
>> Thanks,
>> Scott
>>
>> ________________________________________
>> From: Julie Prestopnik via RT [met_help at ucar.edu]
>> Sent: Friday, February 01, 2019 3:46 PM
>> To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
APPLICATIONS INC]
>> Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
"undefined
>> reference" errors
>>
>> Hi Scott. I'm replying from my phone, so this will be brief. I just
wanted
>> to make sure that it was clear that the tar file package I pointed
you to
>> in my last email contains the versions of all libraries that have
>> successfully compiled with Intel (and gnu and pgi).
>>
>> Regarding flags, this would be indicated in the page in our online
tutorial
>> that I pointed you to in my first email.
>>
>> Please take a look at the versions in the tarfile and follow up
with any
>> questions. You could also use the script I pointed to you to
compile only
>> MET or some or all of the supporting libraries.
>>
>> Thanks, Julie
>>
>> On Fri, Feb 1, 2019, 1:33 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
>> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>>
>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
>>>
>>> Hi Julie,
>>>
>>> No luck compiling MET8 using my existing libraries (as detailed in
my
>>> previous email). I attached my output logs for configure and make.
It is
>>> the same problem exists as before in the same src/libcode/vx_*
dirs. I
>> can
>>> try using a intel-16.0.X.XXX compiler, but I'm skeptical that is
the
>> source
>>> of the problem. First, I would have to rebuild all the support
libraries.
>>> Again, my suspicion is either some of the required library
versions are
>> too
>>> new/old (incompatible versions) or I might need to include some
>> additional
>>> directives when building MET (e.g. additional FLAGS or includes).
If you
>>> have any versions that successfully compiled with Intel, that
might be
>> the
>>> best starting point. I can try to replicate that.
>>>
>>> Thanks,
>>> Scott
>>>
>>> ________________________________________
>>> From: Julie Prestopnik via RT [met_help at ucar.edu]
>>> Sent: Friday, February 01, 2019 2:54 PM
>>> To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
APPLICATIONS
>> INC]
>>> Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
"undefined
>>> reference" errors
>>>
>>> Hi Scott.
>>>
>>> Sounds good! Thanks for recompiling later this afternoon. Thank
you also
>>> for verifying that all of the required netcdf files are present
(and
>> passed
>>> self-testing!).
>>>
>>> Could you tell me if you have successfully built MET8 (with Intel
>>>> compilers), and if so, what versions of netcdf-c, netcdf-cxx4,
>>>> netcdf-fortran, hdf5, etc that you used to make it work?
>>>>
>>> Yes. I mostly use the Intel compilers, but not with version 18.
>> Usually,
>>> it's a lower version. Regarding the versions of the libraries, at
the
>>> bottom of the Downloads page on our website:
>>> https://dtcenter.org/met/users/downloads/index.php
>>>
>>> You can find a tarfile (
>>> https://dtcenter.org/met/users/compile_scripts/tar_files.tar) that
>>> contains
>>> the versions of the libraries that we've been using along with a
script (
>>> https://dtcenter.org/met/users/compile_scripts/compile_MET_all.sh)
that
>> I
>>> frequently use to compile MET and its dependent libraries on
various
>>> machines. There are some necessary environment variables that
need to be
>>> set before running the script and those are described on the
bottom of
>> the
>>> Downloads page.
>>>
>>> Please let me know if you have any other questions or problems.
I'm
>>> leaving now and won't be back until Monday. We have an three day
MET
>>> Tutorial this coming Monday - Wednesday at NCAR, so I may be a
little
>>> slower to respond, but I will get back to you as soon as I can.
>>>
>>> I hope your next attempt will be successful! If not, let us know
how we
>> can
>>> help.
>>>
>>> Thanks,
>>> Julie
>>>
>>> On Fri, Feb 1, 2019 at 12:42 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
>>> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>>>
>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
>>>>
>>>> Hi Julie,
>>>>
>>>> Thanks so much for your prompt response. I will try compiling the
>> latest
>>>> version of MET this afternoon with your suggestions (removing the
>>>> "-D__64BIT__" flag and compiler version). However, I can verify
that
>> all
>>>> the required netcdf files are present and passed self-testing:
>>>>
>>>> -rwxr-xr-x 1 sdrabenh g0620 1891 Jan 24 11:20 libbzip2.la
>>>> -rwxr-xr-x 1 sdrabenh g0620 113492 Jan 24 11:20 libbzip2.so
>>>> -rwxr-xr-x 1 sdrabenh g0620 1883 Jan 24 11:20 libmisc.la
>>>> -rwxr-xr-x 1 sdrabenh g0620 12777 Jan 24 11:20 libmisc.so
>>>> -rw-r--r-- 1 sdrabenh g0620 2629834 Jan 24 11:20 libnetcdf.a
>>>> -rw-r--r-- 1 sdrabenh g0620 1469428 Jan 24 11:33 libnetcdf_c++4.a
>>>> -rwxr-xr-x 1 sdrabenh g0620 2314 Jan 24 11:33
libnetcdf_c++4.la
>>>> lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33
libnetcdf_c++4.so ->
>>>> libnetcdf_c++4.so.1.0.3
>>>> lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33
libnetcdf_c++4.so.1 ->
>>>> libnetcdf_c++4.so.1.0.3
>>>> -rwxr-xr-x 1 sdrabenh g0620 460080 Jan 24 11:33
>> libnetcdf_c++4.so.1.0.3
>>>> -rw-r--r-- 1 sdrabenh g0620 1053986 Jan 24 11:31 libnetcdff.a
>>>> -rwxr-xr-x 1 sdrabenh g0620 2295 Jan 24 11:31 libnetcdff.la
>>>> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so ->
>>>> libnetcdff.so.6.1.1
>>>> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so.6
->
>>>> libnetcdff.so.6.1.1
>>>> -rwxr-xr-x 1 sdrabenh g0620 807278 Jan 24 11:31
libnetcdff.so.6.1.1
>>>> -rwxr-xr-x 1 sdrabenh g0620 2100 Jan 24 11:20 libnetcdf.la
>>>> -rw-r--r-- 1 sdrabenh g0620 1321 Jan 24 11:20
libnetcdf.settings
>>>> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so ->
>>>> libnetcdf.so.13.1.1
>>>> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so.13
->
>>>> libnetcdf.so.13.1.1
>>>> -rwxr-xr-x 1 sdrabenh g0620 1908852 Jan 24 11:20
libnetcdf.so.13.1.1
>>>> drwxr-xr-x 2 sdrabenh g0620 512 Jan 24 11:33 pkgconfig
>>>>
>>>> ...and include files:
>>>>
>>>> -rw-r--r-- 1 sdrabenh g0620 2965 Jan 24 11:33 ncAtt.h
>>>> -rw-r--r-- 1 sdrabenh g0620 480 Jan 24 11:33 ncByte.h
>>>> -rw-r--r-- 1 sdrabenh g0620 440 Jan 24 11:33 ncChar.h
>>>> -rw-r--r-- 1 sdrabenh g0620 1048 Jan 24 11:33 ncCheck.h
>>>> -rw-r--r-- 1 sdrabenh g0620 3684 Jan 24 11:33 ncCompoundType.h
>>>> -rw-r--r-- 1 sdrabenh g0620 1940 Jan 24 11:33 ncDim.h
>>>> -rw-r--r-- 1 sdrabenh g0620 483 Jan 24 11:33 ncDouble.h
>>>> -rw-r--r-- 1 sdrabenh g0620 3327 Jan 24 11:33 ncEnumType.h
>>>> -rw-r--r-- 1 sdrabenh g0620 12051 Jan 24 11:33 ncException.h
>>>> -rw-r--r-- 1 sdrabenh g0620 3469 Jan 24 11:33 ncFile.h
>>>> -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncFloat.h
>>>> -rw-r--r-- 1 sdrabenh g0620 1055 Jan 24 11:33 ncGroupAtt.h
>>>> -rw-r--r-- 1 sdrabenh g0620 23965 Jan 24 11:33 ncGroup.h
>>>> -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncInt64.h
>>>> -rw-r--r-- 1 sdrabenh g0620 453 Jan 24 11:33 ncInt.h
>>>> -rw-r--r-- 1 sdrabenh g0620 1501 Jan 24 11:33 ncOpaqueType.h
>>>> -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncShort.h
>>>> -rw-r--r-- 1 sdrabenh g0620 482 Jan 24 11:33 ncString.h
>>>> -rw-r--r-- 1 sdrabenh g0620 5409 Jan 24 11:33 ncType.h
>>>> -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncUbyte.h
>>>> -rw-r--r-- 1 sdrabenh g0620 481 Jan 24 11:33 ncUint64.h
>>>> -rw-r--r-- 1 sdrabenh g0620 462 Jan 24 11:33 ncUint.h
>>>> -rw-r--r-- 1 sdrabenh g0620 469 Jan 24 11:33 ncUshort.h
>>>> -rw-r--r-- 1 sdrabenh g0620 1151 Jan 24 11:33 ncVarAtt.h
>>>> -rw-r--r-- 1 sdrabenh g0620 54638 Jan 24 11:33 ncVar.h
>>>> -rw-r--r-- 1 sdrabenh g0620 1430 Jan 24 11:33 ncVlenType.h
>>>> -rw-r--r-- 1 sdrabenh g0620 651 Jan 24 11:33 netcdf
>>>> -rw-r--r-- 1 sdrabenh g0620 642 Jan 24 11:31 netcdf4_f03.mod
>>>> -rw-r--r-- 1 sdrabenh g0620 232820 Jan 24 11:31
>> netcdf4_nc_interfaces.mod
>>>> -rw-r--r-- 1 sdrabenh g0620 41808 Jan 24 11:31
>> netcdf4_nf_interfaces.mod
>>>> -rw-r--r-- 1 sdrabenh g0620 538 Jan 24 11:31 netcdf_f03.mod
>>>> -rw-r--r-- 1 sdrabenh g0620 200505 Jan 24 11:31
>>>> netcdf_fortv2_c_interfaces.mod
>>>> -rw-r--r-- 1 sdrabenh g0620 66697 Jan 24 11:20 netcdf.h
>>>> -rw-r--r-- 1 sdrabenh g0620 59877 Jan 24 11:31 netcdf.inc
>>>> -rw-r--r-- 1 sdrabenh g0620 520 Jan 24 11:20 netcdf_mem.h
>>>> -rw-r--r-- 1 sdrabenh g0620 2223 Jan 24 11:20 netcdf_meta.h
>>>> -rw-r--r-- 1 sdrabenh g0620 265880 Jan 24 11:31 netcdf.mod
>>>> -rw-r--r-- 1 sdrabenh g0620 26434 Jan 24 11:31
netcdf_nc_data.mod
>>>> -rw-r--r-- 1 sdrabenh g0620 155675 Jan 24 11:31
>> netcdf_nc_interfaces.mod
>>>> -rw-r--r-- 1 sdrabenh g0620 57449 Jan 24 11:31
netcdf_nf_data.mod
>>>> -rw-r--r-- 1 sdrabenh g0620 99023 Jan 24 11:31
>> netcdf_nf_interfaces.mod
>>>> -rw-r--r-- 1 sdrabenh g0620 1382 Jan 24 11:31 typesizes.mod
>>>>
>>>> As you can see, all the c, c++, fortran files exist and I double
>> checked
>>>> the MET_* environment variables all point correctly. It is very
strange
>>>> that I keep encountering problems in the vx lib code. I realize
that
>> the
>>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
>>>> provides some documentation on the required libs, but certainly
not all
>>>> details. For instance, I know there have been many changes to the
>> recent
>>>> versions of netcdf and hdf. Could you tell me if you have
successfully
>>>> built MET8 (with Intel compilers), and if so, what versions of
>> netcdf-c,
>>>> netcdf-cxx4, netcdf-fortran, hdf5, etc that you used to make it
work?
>>> That
>>>> would be a very helpful starting point. I have a feeling
something I
>> did
>>>> may not be configured correctly, or I may be using a library
version
>> that
>>>> is either too old or new. Currently, my libs have been built as
>> follows:
>>>> 1) szip/2.1.1
>>>>
>>>> 2) zlib/1.2.11
>>>>
>>>> 3) libpng/1.6.34 (--enable-shared --enable-static)
>>>>
>>>> 4) jpeg/9b (--enable-shared --enable-static)
>>>>
>>>> 5) jasper/1.900.1 (--enable-shared --enable-static --disable-
opengl
>>>> --enable-libjpeg --with-PACKAGE=$JPEG --disable-asan --disable-
leak)
>>>>
>>>> 6) hdf/4.2.13 (--with-zlib=$ZLIB --with-jpeg=$JPEG --with-
szlib=$SZIP
>>>> --disable-fortran --enable-shared --enable-static --disable-
netcdf)
>>>>
>>>> 7) hdfeos/2.20v1.00 (FC=$HDF/bin/h4fc
>>>>
>>
CXX=/usr/local/intel/2018/compilers_and_libraries_2018.2.199/linux/bin/intel64/icpc
>>>> F77=$HDF/bin/h4fc CC=$HDF/bin/h4cc --with-hdf4=$HDF --with-
zlib=$ZLIB
>>>> --with-jpeg=$JPEG --with-szlib=$SZIP --disable-shared --enable-
static)
>>>>
>>>> 8) hdf5/1.10.2 (--with-zlib=$ZLIB/include,$ZLIB/lib --with-
szlib=$SZIP
>>>> --enable-cxx --enable-fortran --enable-fortran2003 --enable-hl
>>>> --enable-shared --enable-static --enable-codestack
>>>> --enable-using-memchecker
>>>> --enable-filters=shuffle,fletcher32,nbit,scaleoffset)
>>>>
>>>> 9) netcdf-c/4.6.1 (--enable-hdf4 --enable-hdf4-file-tests
>>> --enable-netcdf4
>>>> --enable-netcdf-4 --enable-dynamic-loading --enable-shared
>>> --enable-static
>>>> --enable-mmap --enable-fsync --enable-jna)
>>>>
>>>> 10) netcdf-fortran/4.4.4 (--enable-f03-compiler-check
>>>> --enable-fortran-type-check --enable-f03 --enable-largefile)
>>>>
>>>> 11) netcdf-cxx4/4.3.0 (--enable-shared --enable-static
>>> --enable-largefile)
>>>> 12) BUFRLIB/10.2.3 (FCFLAGS = CFLAGS = -DUNDERSCORE)
>>>>
>>>> 13) w3lib/2.0.6 (FFLAGS = CFLAGS = -O3 -g -m64 -DLINUX
-D__64BIT__)
>>>>
>>>> 14) g2lib/3.1.0 (FFLAGS = -O3 -g -I $(MODDIR) -DLINUX -m64
>> -D__64BIT__;
>>>> CFLAGS = -O3 -g -DLINUX $(INCDIR) -m64 -D__64BIT__)
>>>>
>>>> 15) g2clib/1.6.0 (INC = -I${JASPERINC} -I${SZIP}/include
>>> -I${ZLIB}/include
>>>> -I${PNG}/include -I${W3LIB}/include)
>>>>
>>>> 16) gsl/2.5 (--enable-shared --enable-static )
>>>>
>>>> Please let me know if you have any further insight regarding what
>>> versions
>>>> and configuration of the required software will work with intel
>>> compilers.
>>>> Thanks,
>>>> Scott
>>>>
>>>>
>>>> ________________________________________
>>>> From: Julie Prestopnik via RT [met_help at ucar.edu]
>>>> Sent: Thursday, January 31, 2019 5:51 PM
>>>> To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
APPLICATIONS
>>> INC]
>>>> Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
>> "undefined
>>>> reference" errors
>>>>
>>>> Hi Scott.
>>>>
>>>> I see that you have been struggling to compile met-7.0 and/or
met-8.0.
>>> I'm
>>>> sorry to hear that. Thank you for taking the time to email
met_help.
>>>> Based on the undefined references errors, there does seem to be a
>> problem
>>>> with the libraries as you indicated. We'd love to have you using
the
>>>> latest version of MET and its patches (as of 20190130) which you
can
>> get
>>> by
>>>> running:
>>>> wget
>>>>
>>>>
>> https://dtcenter.org/met/users/downloads/MET_releases/met-
8.0_bugfix/met-8.0_bugfix.20190130.tar.gz
>>>> I will say that I am unsure if we, the developers, have installed
MET
>>> using
>>>> that high of a version of the Intel compiler. I don't believe I
have.
>>>> That may or may not be part of the problem. Do you have an
earlier
>>> version
>>>> (16.x.x.xxx?) of the Intel compiler that you could use. Thank you
for
>>>> attaching your myConfigure.log file and your myMakeInstall.log
file.
>> In
>>>> the future, it would be good to take a look at your config.log
file,
>>> which
>>>> has usually has additional information over configure.log.
>>>>
>>>> I see that you have set the "-D__64BIT__" flag. As of recently
there
>>> were
>>>> problems with the compilation using that flag, so we ask that the
you
>>>> remove the "-D__64BIT__" from the value of CFLAGS for the
compilation
>> of
>>>> the libraries and for MET. This is noted under the "Compiling
GRIB2
>>>> C-Library" section of the "Compilation" page of our newly posted
>> met-8.0
>>>> online tutorial. Please recompile the GRIB2 C-Library and MET
without
>>> that
>>>> flag set.
>>>>
>>>> However, the undefined reference to error seems to be occurring
with
>>>> NetCDF. I'm a little perplexed by the "undefined reference to
>>>> `_ZNK6netCDF5NcVar7getNameB5cxx11Ev'" error. I have not seen
that sort
>>> of
>>>> error, with the additional characters, previously. MET requires
the C
>>> and
>>>> C++
>>>> interface to NetCDF. Here is a checklist of files that are
necessary:
>>>>
>>>> Files for NetCDF4 C:
>>>>
>>>> - $MET_NETCDF/include/netcdf.h
>>>> - $MET_NETCDF/lib/libnetcdf.a
>>>> - $MET_NETCDF/lib/libnetcdf.so
>>>>
>>>> Files for NetCDF4 C++:
>>>>
>>>> - $MET_NETCDF/include/netcdf
>>>> - $MET_NETCDF/lib/libnetcdf_c++4.a
>>>> - $MET_NETCDF/lib/libnetcdf_c++4.so
>>>>
>>>> You could take a look and see if you have all of those files.
>>>>
>>>> By the way, are there specific configure options necessary when
>> building
>>>>> the netcdf and hdf libraries or does it not matter?
>>>>>
>>>> We have detailed installation instructions for each of the
required
>>>> libraries posted in our online tutorial on the following page:
>>>>
>>>>
>>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
>>>> I hope this information is helpful. Please take a look and let
us know
>>> if
>>>> you have any questions. Please don't hesitate to follow up with
any
>>>> additional questions.
>>>>
>>>> Thanks,
>>>> Julie
>>>>
>>>> On Thu, Jan 31, 2019 at 1:31 PM Rabenhorst, Scott D.
>> (GSFC-610.1)[SCIENCE
>>>> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>>>>
>>>>> Thu Jan 31 13:31:33 2019: Request 88728 was acted upon.
>>>>> Transaction: Ticket created by scott.d.rabenhorst at nasa.gov
>>>>> Queue: met_help
>>>>> Subject: Help compiling met with "undefined reference"
errors
>>>>> Owner: Nobody
>>>>> Requestors: scott.d.rabenhorst at nasa.gov
>>>>> Status: new
>>>>> Ticket <URL:
>> https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728
>>>>>
>>>>> Hi MET support,
>>>>>
>>>>> I have been struggling to compile MET 7 (or 8) using Intel
compilers.
>>> The
>>>>> basic problem is undefined references to required libraries
(netcdf,
>>> hdf,
>>>>> etc). Interestingly, they always seem to occur in the
>> src/libcode/vx_*
>>>>> files. I have attached my latest compile log for the
>>>>> met-7.0_bugfix.20180924.tar.gz build. I have followed all the
>>> directions
>>>> in
>>>>> the MET Users Guide but it dows not seem to make any difference.
For
>>> this
>>>>> latest try, I setup the environment as follows:
>>>>>
>>>>>
>>>>>
>>
------------------------------------------------------------------------------------------
>>>>> module load other/comp/gcc-6.3
>>>>> module load comp/intel-18.0.2.199
>>>>> module load mpi/impi-18.0.2.199
>>>>> module load lib/mkl-18.0.2.199
>>>>> module load wrf-deps/intel-18.0.2.199
>>>>> module load wgrib2/2.0.7_intel-18.0.2.199
>>>>>
>>>>> setenv COMPVERS intel-18.0.2.199
>>>>> setenv APPDIR ${NOBACKUP}/apps/sp3
>>>>>
>>>>> setenv MET_NETCDF ${APPDIR}/netcdf/4.6.1_hdf4/${COMPVERS}
>>>>> setenv MET_HDF5 ${APPDIR}/hdf5/1.10.2/${COMPVERS}
>>>>> setenv MET_HDF ${APPDIR}/hdf/4.2.13_no-
fortran/${COMPVERS}
>>>>> setenv MET_HDFEOS ${APPDIR}/hdfeos/2.20v1.00/${COMPVERS}
>>>>> setenv MET_GRIB2C ${APPDIR}/g2clib/1.6.0/${COMPVERS}
>>>>> setenv MET_GSL ${APPDIR}/gsl/2.5/${COMPVERS}
>>>>> setenv MET_BUFR ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}
>>>>> setenv MET_BUFRLIB ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}/lib
>>>>> setenv MET_CAIROINC /usr/include/cairo
>>>>> setenv MET_CAIROLIB /usr/lib64
>>>>> setenv MET_FREETYPEINC /usr/include/freetype2
>>>>> setenv MET_FREETYPELIB /usr/lib64
>>>>> setenv YACC ${APPDIR}/byacc/github/${COMPVERS}
>>>>> setenv LDFLAGS -L${APPDIR}/wrf-deps/${COMPVERS}/lib
>>>>> setenv CPPFLAGS -I${APPDIR}/wrf-deps/${COMPVERS}/include
>>>>>
>>>>> setenv CFLAGS "-D__64BIT__"
>>>>>
>>>>> ./configure --prefix=${APPDIR}/MET/7.0/${COMPVERS} --enable-
lidar2nc
>>>>> --enable-grib2 --enable-modis --enable-mode_graphics |& tee
>>>> myConfigure.log
>>>>>
>>>>>
>>
------------------------------------------------------------------------------------------
>>>>> Then I ran "make install |& tee myMake.log" and got the
resulting
>> error
>>>>> logs (attached). Everything seems correct. I have not been able
to
>>>>> successfully build MET 8 either because of similar errors.
Please let
>>> me
>>>>> know any ideas on how to get this to compile correctly. I am out
of
>>> ideas
>>>>> and have spent a while recompiling supporting libraries using
>> different
>>>>> options. By the way, are there specific configure options
necessary
>>> when
>>>>> building the netcdf and hdf libraries or does it not matter? I
look
>>>> forward
>>>>> to hearing from you soon.
>>>>>
>>>>>
>>>>> Thanks,
>>>>> Scott
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
------------------------------------------------
Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with "undefined reference" errors
From: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]
Time: Fri Feb 15 13:19:08 2019
Hi Julie,
After reading additional documentation I saw the required version is
jpegsrc.v6b.tar.gz. I was able to get the latest version of MET
compiled
sucessfully. Thanks you so much for your help and scripts. Apparently,
all the supporting library versions have to be just right for a
successful build. FYI, I used intel-18.0.3.222 compilers.
On an unrelated question, can the input grid for gen_vx_mask be a
netcdf
file? If so, do you have any examples on what the contents (i.e.
ncdump)
would look like?
Thanks,
Scott
On 2/15/19 11:51 AM, Scott Daniel Rabenhorst wrote:
> Hi Julie,
>
> Sorry for my delayed response. I had to take care of more pressing
> projects this week and have just now returning to getting MET up and
> running.
>
> I am trying to replicate your compile script. However, I ran into a
> problem. I am having trouble building hd4 (your version of HDF4.2r3
> from 2008) using my version of jpeg (9c). The make check fails with
> jpeg related issues. In the files you posted for me the other week,
I
> could not find a jpeg source tar file. Neither could I figure out
what
> version you are using based on the compile script. However, the jpeg
> library is required. Would you mind letting me know what version
your
> are using? I hope that may solve some issues here.
>
> Thanks,
> Scott
>
>
> On 2/5/19 11:47 AM, Julie Prestopnik via RT wrote:
>> It's no problem! I hope the installation is going well. Please
let us
>> know how things go.
>>
>> Thanks!
>>
>> Julie
>>
>> On Fri, Feb 1, 2019 at 2:04 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
>> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>>
>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
>>>
>>> Hi Julie,
>>>
>>> I am so sorry! I did not see your inline response with the tar
file and
>>> config script. That will be super helpful. I will give that a try
on
>>> my HPC
>>> system - I'm optimistic I can replicate things with that level of
>>> detail.
>>>
>>> Again, thanks so much for your prompt response to my emails. You
>>> have been
>>> a terrific correspondent! I will let you know how things go.
>>>
>>> Thanks,
>>> Scott
>>>
>>> ________________________________________
>>> From: Julie Prestopnik via RT [met_help at ucar.edu]
>>> Sent: Friday, February 01, 2019 3:46 PM
>>> To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
>>> APPLICATIONS INC]
>>> Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
>>> "undefined
>>> reference" errors
>>>
>>> Hi Scott. I'm replying from my phone, so this will be brief. I
just
>>> wanted
>>> to make sure that it was clear that the tar file package I pointed
>>> you to
>>> in my last email contains the versions of all libraries that have
>>> successfully compiled with Intel (and gnu and pgi).
>>>
>>> Regarding flags, this would be indicated in the page in our online
>>> tutorial
>>> that I pointed you to in my first email.
>>>
>>> Please take a look at the versions in the tarfile and follow up
with
>>> any
>>> questions. You could also use the script I pointed to you to
compile
>>> only
>>> MET or some or all of the supporting libraries.
>>>
>>> Thanks, Julie
>>>
>>> On Fri, Feb 1, 2019, 1:33 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
>>> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>>>
>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
>>>>
>>>> Hi Julie,
>>>>
>>>> No luck compiling MET8 using my existing libraries (as detailed
in my
>>>> previous email). I attached my output logs for configure and
make.
>>>> It is
>>>> the same problem exists as before in the same src/libcode/vx_*
dirs. I
>>> can
>>>> try using a intel-16.0.X.XXX compiler, but I'm skeptical that is
the
>>> source
>>>> of the problem. First, I would have to rebuild all the support
>>>> libraries.
>>>> Again, my suspicion is either some of the required library
versions
>>>> are
>>> too
>>>> new/old (incompatible versions) or I might need to include some
>>> additional
>>>> directives when building MET (e.g. additional FLAGS or includes).
>>>> If you
>>>> have any versions that successfully compiled with Intel, that
might be
>>> the
>>>> best starting point. I can try to replicate that.
>>>>
>>>> Thanks,
>>>> Scott
>>>>
>>>> ________________________________________
>>>> From: Julie Prestopnik via RT [met_help at ucar.edu]
>>>> Sent: Friday, February 01, 2019 2:54 PM
>>>> To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
APPLICATIONS
>>> INC]
>>>> Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
>>>> "undefined
>>>> reference" errors
>>>>
>>>> Hi Scott.
>>>>
>>>> Sounds good! Thanks for recompiling later this afternoon. Thank
>>>> you also
>>>> for verifying that all of the required netcdf files are present
(and
>>> passed
>>>> self-testing!).
>>>>
>>>> Could you tell me if you have successfully built MET8 (with Intel
>>>>> compilers), and if so, what versions of netcdf-c, netcdf-cxx4,
>>>>> netcdf-fortran, hdf5, etc that you used to make it work?
>>>>>
>>>> Yes. I mostly use the Intel compilers, but not with version 18.
>>> Usually,
>>>> it's a lower version. Regarding the versions of the libraries, at
the
>>>> bottom of the Downloads page on our website:
>>>> https://dtcenter.org/met/users/downloads/index.php
>>>>
>>>> You can find a tarfile (
>>>> https://dtcenter.org/met/users/compile_scripts/tar_files.tar)
that
>>>> contains
>>>> the versions of the libraries that we've been using along with a
>>>> script (
>>>>
https://dtcenter.org/met/users/compile_scripts/compile_MET_all.sh)
>>>> that
>>> I
>>>> frequently use to compile MET and its dependent libraries on
various
>>>> machines. There are some necessary environment variables that
need
>>>> to be
>>>> set before running the script and those are described on the
bottom of
>>> the
>>>> Downloads page.
>>>>
>>>> Please let me know if you have any other questions or problems.
I'm
>>>> leaving now and won't be back until Monday. We have an three day
MET
>>>> Tutorial this coming Monday - Wednesday at NCAR, so I may be a
little
>>>> slower to respond, but I will get back to you as soon as I can.
>>>>
>>>> I hope your next attempt will be successful! If not, let us know
>>>> how we
>>> can
>>>> help.
>>>>
>>>> Thanks,
>>>> Julie
>>>>
>>>> On Fri, Feb 1, 2019 at 12:42 PM Rabenhorst, Scott D.
>>>> (GSFC-610.1)[SCIENCE
>>>> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>>>>
>>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
>>>>>
>>>>> Hi Julie,
>>>>>
>>>>> Thanks so much for your prompt response. I will try compiling
the
>>> latest
>>>>> version of MET this afternoon with your suggestions (removing
the
>>>>> "-D__64BIT__" flag and compiler version). However, I can verify
that
>>> all
>>>>> the required netcdf files are present and passed self-testing:
>>>>>
>>>>> -rwxr-xr-x 1 sdrabenh g0620 1891 Jan 24 11:20 libbzip2.la
>>>>> -rwxr-xr-x 1 sdrabenh g0620 113492 Jan 24 11:20 libbzip2.so
>>>>> -rwxr-xr-x 1 sdrabenh g0620 1883 Jan 24 11:20 libmisc.la
>>>>> -rwxr-xr-x 1 sdrabenh g0620 12777 Jan 24 11:20 libmisc.so
>>>>> -rw-r--r-- 1 sdrabenh g0620 2629834 Jan 24 11:20 libnetcdf.a
>>>>> -rw-r--r-- 1 sdrabenh g0620 1469428 Jan 24 11:33
libnetcdf_c++4.a
>>>>> -rwxr-xr-x 1 sdrabenh g0620 2314 Jan 24 11:33
libnetcdf_c++4.la
>>>>> lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33
libnetcdf_c++4.so ->
>>>>> libnetcdf_c++4.so.1.0.3
>>>>> lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33
>>>>> libnetcdf_c++4.so.1 ->
>>>>> libnetcdf_c++4.so.1.0.3
>>>>> -rwxr-xr-x 1 sdrabenh g0620 460080 Jan 24 11:33
>>> libnetcdf_c++4.so.1.0.3
>>>>> -rw-r--r-- 1 sdrabenh g0620 1053986 Jan 24 11:31 libnetcdff.a
>>>>> -rwxr-xr-x 1 sdrabenh g0620 2295 Jan 24 11:31 libnetcdff.la
>>>>> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so
->
>>>>> libnetcdff.so.6.1.1
>>>>> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so.6
->
>>>>> libnetcdff.so.6.1.1
>>>>> -rwxr-xr-x 1 sdrabenh g0620 807278 Jan 24 11:31
libnetcdff.so.6.1.1
>>>>> -rwxr-xr-x 1 sdrabenh g0620 2100 Jan 24 11:20 libnetcdf.la
>>>>> -rw-r--r-- 1 sdrabenh g0620 1321 Jan 24 11:20
libnetcdf.settings
>>>>> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so ->
>>>>> libnetcdf.so.13.1.1
>>>>> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so.13
->
>>>>> libnetcdf.so.13.1.1
>>>>> -rwxr-xr-x 1 sdrabenh g0620 1908852 Jan 24 11:20
libnetcdf.so.13.1.1
>>>>> drwxr-xr-x 2 sdrabenh g0620 512 Jan 24 11:33 pkgconfig
>>>>>
>>>>> ...and include files:
>>>>>
>>>>> -rw-r--r-- 1 sdrabenh g0620 2965 Jan 24 11:33 ncAtt.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 480 Jan 24 11:33 ncByte.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 440 Jan 24 11:33 ncChar.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 1048 Jan 24 11:33 ncCheck.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 3684 Jan 24 11:33 ncCompoundType.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 1940 Jan 24 11:33 ncDim.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 483 Jan 24 11:33 ncDouble.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 3327 Jan 24 11:33 ncEnumType.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 12051 Jan 24 11:33 ncException.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 3469 Jan 24 11:33 ncFile.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncFloat.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 1055 Jan 24 11:33 ncGroupAtt.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 23965 Jan 24 11:33 ncGroup.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncInt64.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 453 Jan 24 11:33 ncInt.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 1501 Jan 24 11:33 ncOpaqueType.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncShort.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 482 Jan 24 11:33 ncString.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 5409 Jan 24 11:33 ncType.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncUbyte.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 481 Jan 24 11:33 ncUint64.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 462 Jan 24 11:33 ncUint.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 469 Jan 24 11:33 ncUshort.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 1151 Jan 24 11:33 ncVarAtt.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 54638 Jan 24 11:33 ncVar.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 1430 Jan 24 11:33 ncVlenType.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 651 Jan 24 11:33 netcdf
>>>>> -rw-r--r-- 1 sdrabenh g0620 642 Jan 24 11:31 netcdf4_f03.mod
>>>>> -rw-r--r-- 1 sdrabenh g0620 232820 Jan 24 11:31
>>> netcdf4_nc_interfaces.mod
>>>>> -rw-r--r-- 1 sdrabenh g0620 41808 Jan 24 11:31
>>> netcdf4_nf_interfaces.mod
>>>>> -rw-r--r-- 1 sdrabenh g0620 538 Jan 24 11:31 netcdf_f03.mod
>>>>> -rw-r--r-- 1 sdrabenh g0620 200505 Jan 24 11:31
>>>>> netcdf_fortv2_c_interfaces.mod
>>>>> -rw-r--r-- 1 sdrabenh g0620 66697 Jan 24 11:20 netcdf.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 59877 Jan 24 11:31 netcdf.inc
>>>>> -rw-r--r-- 1 sdrabenh g0620 520 Jan 24 11:20 netcdf_mem.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 2223 Jan 24 11:20 netcdf_meta.h
>>>>> -rw-r--r-- 1 sdrabenh g0620 265880 Jan 24 11:31 netcdf.mod
>>>>> -rw-r--r-- 1 sdrabenh g0620 26434 Jan 24 11:31
netcdf_nc_data.mod
>>>>> -rw-r--r-- 1 sdrabenh g0620 155675 Jan 24 11:31
>>> netcdf_nc_interfaces.mod
>>>>> -rw-r--r-- 1 sdrabenh g0620 57449 Jan 24 11:31
netcdf_nf_data.mod
>>>>> -rw-r--r-- 1 sdrabenh g0620 99023 Jan 24 11:31
>>> netcdf_nf_interfaces.mod
>>>>> -rw-r--r-- 1 sdrabenh g0620 1382 Jan 24 11:31 typesizes.mod
>>>>>
>>>>> As you can see, all the c, c++, fortran files exist and I double
>>> checked
>>>>> the MET_* environment variables all point correctly. It is very
>>>>> strange
>>>>> that I keep encountering problems in the vx lib code. I realize
that
>>> the
>>>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
>>>
>>>>> provides some documentation on the required libs, but certainly
>>>>> not all
>>>>> details. For instance, I know there have been many changes to
the
>>> recent
>>>>> versions of netcdf and hdf. Could you tell me if you have
>>>>> successfully
>>>>> built MET8 (with Intel compilers), and if so, what versions of
>>> netcdf-c,
>>>>> netcdf-cxx4, netcdf-fortran, hdf5, etc that you used to make it
work?
>>>> That
>>>>> would be a very helpful starting point. I have a feeling
something I
>>> did
>>>>> may not be configured correctly, or I may be using a library
version
>>> that
>>>>> is either too old or new. Currently, my libs have been built as
>>> follows:
>>>>> 1) szip/2.1.1
>>>>>
>>>>> 2) zlib/1.2.11
>>>>>
>>>>> 3) libpng/1.6.34 (--enable-shared --enable-static)
>>>>>
>>>>> 4) jpeg/9b (--enable-shared --enable-static)
>>>>>
>>>>> 5) jasper/1.900.1 (--enable-shared --enable-static --disable-
opengl
>>>>> --enable-libjpeg --with-PACKAGE=$JPEG --disable-asan --disable-
leak)
>>>>>
>>>>> 6) hdf/4.2.13 (--with-zlib=$ZLIB --with-jpeg=$JPEG --with-
szlib=$SZIP
>>>>> --disable-fortran --enable-shared --enable-static --disable-
netcdf)
>>>>>
>>>>> 7) hdfeos/2.20v1.00 (FC=$HDF/bin/h4fc
>>>>>
>>>
CXX=/usr/local/intel/2018/compilers_and_libraries_2018.2.199/linux/bin/intel64/icpc
>>>
>>>>> F77=$HDF/bin/h4fc CC=$HDF/bin/h4cc --with-hdf4=$HDF --with-
zlib=$ZLIB
>>>>> --with-jpeg=$JPEG --with-szlib=$SZIP --disable-shared
>>>>> --enable-static)
>>>>>
>>>>> 8) hdf5/1.10.2 (--with-zlib=$ZLIB/include,$ZLIB/lib
>>>>> --with-szlib=$SZIP
>>>>> --enable-cxx --enable-fortran --enable-fortran2003 --enable-hl
>>>>> --enable-shared --enable-static --enable-codestack
>>>>> --enable-using-memchecker
>>>>> --enable-filters=shuffle,fletcher32,nbit,scaleoffset)
>>>>>
>>>>> 9) netcdf-c/4.6.1 (--enable-hdf4 --enable-hdf4-file-tests
>>>> --enable-netcdf4
>>>>> --enable-netcdf-4 --enable-dynamic-loading --enable-shared
>>>> --enable-static
>>>>> --enable-mmap --enable-fsync --enable-jna)
>>>>>
>>>>> 10) netcdf-fortran/4.4.4 (--enable-f03-compiler-check
>>>>> --enable-fortran-type-check --enable-f03 --enable-largefile)
>>>>>
>>>>> 11) netcdf-cxx4/4.3.0 (--enable-shared --enable-static
>>>> --enable-largefile)
>>>>> 12) BUFRLIB/10.2.3 (FCFLAGS = CFLAGS = -DUNDERSCORE)
>>>>>
>>>>> 13) w3lib/2.0.6 (FFLAGS = CFLAGS = -O3 -g -m64 -DLINUX
-D__64BIT__)
>>>>>
>>>>> 14) g2lib/3.1.0 (FFLAGS = -O3 -g -I $(MODDIR) -DLINUX -m64
>>> -D__64BIT__;
>>>>> CFLAGS = -O3 -g -DLINUX $(INCDIR) -m64 -D__64BIT__)
>>>>>
>>>>> 15) g2clib/1.6.0 (INC = -I${JASPERINC} -I${SZIP}/include
>>>> -I${ZLIB}/include
>>>>> -I${PNG}/include -I${W3LIB}/include)
>>>>>
>>>>> 16) gsl/2.5 (--enable-shared --enable-static )
>>>>>
>>>>> Please let me know if you have any further insight regarding
what
>>>> versions
>>>>> and configuration of the required software will work with intel
>>>> compilers.
>>>>> Thanks,
>>>>> Scott
>>>>>
>>>>>
>>>>> ________________________________________
>>>>> From: Julie Prestopnik via RT [met_help at ucar.edu]
>>>>> Sent: Thursday, January 31, 2019 5:51 PM
>>>>> To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
>>>>> APPLICATIONS
>>>> INC]
>>>>> Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
>>> "undefined
>>>>> reference" errors
>>>>>
>>>>> Hi Scott.
>>>>>
>>>>> I see that you have been struggling to compile met-7.0 and/or
>>>>> met-8.0.
>>>> I'm
>>>>> sorry to hear that. Thank you for taking the time to email
met_help.
>>>>> Based on the undefined references errors, there does seem to be
a
>>> problem
>>>>> with the libraries as you indicated. We'd love to have you
using the
>>>>> latest version of MET and its patches (as of 20190130) which you
can
>>> get
>>>> by
>>>>> running:
>>>>> wget
>>>>>
>>>>>
>>> https://dtcenter.org/met/users/downloads/MET_releases/met-
8.0_bugfix/met-8.0_bugfix.20190130.tar.gz
>>>
>>>>> I will say that I am unsure if we, the developers, have
installed MET
>>>> using
>>>>> that high of a version of the Intel compiler. I don't believe I
>>>>> have.
>>>>> That may or may not be part of the problem. Do you have an
earlier
>>>> version
>>>>> (16.x.x.xxx?) of the Intel compiler that you could use. Thank
you for
>>>>> attaching your myConfigure.log file and your myMakeInstall.log
file.
>>> In
>>>>> the future, it would be good to take a look at your config.log
file,
>>>> which
>>>>> has usually has additional information over configure.log.
>>>>>
>>>>> I see that you have set the "-D__64BIT__" flag. As of recently
there
>>>> were
>>>>> problems with the compilation using that flag, so we ask that
the you
>>>>> remove the "-D__64BIT__" from the value of CFLAGS for the
compilation
>>> of
>>>>> the libraries and for MET. This is noted under the "Compiling
GRIB2
>>>>> C-Library" section of the "Compilation" page of our newly posted
>>> met-8.0
>>>>> online tutorial. Please recompile the GRIB2 C-Library and MET
>>>>> without
>>>> that
>>>>> flag set.
>>>>>
>>>>> However, the undefined reference to error seems to be occurring
with
>>>>> NetCDF. I'm a little perplexed by the "undefined reference to
>>>>> `_ZNK6netCDF5NcVar7getNameB5cxx11Ev'" error. I have not seen
that
>>>>> sort
>>>> of
>>>>> error, with the additional characters, previously. MET requires
>>>>> the C
>>>> and
>>>>> C++
>>>>> interface to NetCDF. Here is a checklist of files that are
necessary:
>>>>>
>>>>> Files for NetCDF4 C:
>>>>>
>>>>> - $MET_NETCDF/include/netcdf.h
>>>>> - $MET_NETCDF/lib/libnetcdf.a
>>>>> - $MET_NETCDF/lib/libnetcdf.so
>>>>>
>>>>> Files for NetCDF4 C++:
>>>>>
>>>>> - $MET_NETCDF/include/netcdf
>>>>> - $MET_NETCDF/lib/libnetcdf_c++4.a
>>>>> - $MET_NETCDF/lib/libnetcdf_c++4.so
>>>>>
>>>>> You could take a look and see if you have all of those files.
>>>>>
>>>>> By the way, are there specific configure options necessary when
>>> building
>>>>>> the netcdf and hdf libraries or does it not matter?
>>>>>>
>>>>> We have detailed installation instructions for each of the
required
>>>>> libraries posted in our online tutorial on the following page:
>>>>>
>>>>>
>>>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
>>>
>>>>> I hope this information is helpful. Please take a look and let
us
>>>>> know
>>>> if
>>>>> you have any questions. Please don't hesitate to follow up with
any
>>>>> additional questions.
>>>>>
>>>>> Thanks,
>>>>> Julie
>>>>>
>>>>> On Thu, Jan 31, 2019 at 1:31 PM Rabenhorst, Scott D.
>>> (GSFC-610.1)[SCIENCE
>>>>> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>>>>>
>>>>>> Thu Jan 31 13:31:33 2019: Request 88728 was acted upon.
>>>>>> Transaction: Ticket created by scott.d.rabenhorst at nasa.gov
>>>>>> Queue: met_help
>>>>>> Subject: Help compiling met with "undefined reference"
errors
>>>>>> Owner: Nobody
>>>>>> Requestors: scott.d.rabenhorst at nasa.gov
>>>>>> Status: new
>>>>>> Ticket <URL:
>>> https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728
>>>>>>
>>>>>> Hi MET support,
>>>>>>
>>>>>> I have been struggling to compile MET 7 (or 8) using Intel
>>>>>> compilers.
>>>> The
>>>>>> basic problem is undefined references to required libraries
(netcdf,
>>>> hdf,
>>>>>> etc). Interestingly, they always seem to occur in the
>>> src/libcode/vx_*
>>>>>> files. I have attached my latest compile log for the
>>>>>> met-7.0_bugfix.20180924.tar.gz build. I have followed all the
>>>> directions
>>>>> in
>>>>>> the MET Users Guide but it dows not seem to make any
difference. For
>>>> this
>>>>>> latest try, I setup the environment as follows:
>>>>>>
>>>>>>
>>>>>>
>>>
------------------------------------------------------------------------------------------
>>>
>>>>>> module load other/comp/gcc-6.3
>>>>>> module load comp/intel-18.0.2.199
>>>>>> module load mpi/impi-18.0.2.199
>>>>>> module load lib/mkl-18.0.2.199
>>>>>> module load wrf-deps/intel-18.0.2.199
>>>>>> module load wgrib2/2.0.7_intel-18.0.2.199
>>>>>>
>>>>>> setenv COMPVERS intel-18.0.2.199
>>>>>> setenv APPDIR ${NOBACKUP}/apps/sp3
>>>>>>
>>>>>> setenv MET_NETCDF ${APPDIR}/netcdf/4.6.1_hdf4/${COMPVERS}
>>>>>> setenv MET_HDF5 ${APPDIR}/hdf5/1.10.2/${COMPVERS}
>>>>>> setenv MET_HDF ${APPDIR}/hdf/4.2.13_no-fortran/${COMPVERS}
>>>>>> setenv MET_HDFEOS ${APPDIR}/hdfeos/2.20v1.00/${COMPVERS}
>>>>>> setenv MET_GRIB2C ${APPDIR}/g2clib/1.6.0/${COMPVERS}
>>>>>> setenv MET_GSL ${APPDIR}/gsl/2.5/${COMPVERS}
>>>>>> setenv MET_BUFR ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}
>>>>>> setenv MET_BUFRLIB ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}/lib
>>>>>> setenv MET_CAIROINC /usr/include/cairo
>>>>>> setenv MET_CAIROLIB /usr/lib64
>>>>>> setenv MET_FREETYPEINC /usr/include/freetype2
>>>>>> setenv MET_FREETYPELIB /usr/lib64
>>>>>> setenv YACC ${APPDIR}/byacc/github/${COMPVERS}
>>>>>> setenv LDFLAGS -L${APPDIR}/wrf-deps/${COMPVERS}/lib
>>>>>> setenv CPPFLAGS -I${APPDIR}/wrf-deps/${COMPVERS}/include
>>>>>>
>>>>>> setenv CFLAGS "-D__64BIT__"
>>>>>>
>>>>>> ./configure --prefix=${APPDIR}/MET/7.0/${COMPVERS} --enable-
lidar2nc
>>>>>> --enable-grib2 --enable-modis --enable-mode_graphics |& tee
>>>>> myConfigure.log
>>>>>>
>>>>>>
>>>
------------------------------------------------------------------------------------------
>>>
>>>>>> Then I ran "make install |& tee myMake.log" and got the
resulting
>>> error
>>>>>> logs (attached). Everything seems correct. I have not been able
to
>>>>>> successfully build MET 8 either because of similar errors.
Please
>>>>>> let
>>>> me
>>>>>> know any ideas on how to get this to compile correctly. I am
out of
>>>> ideas
>>>>>> and have spent a while recompiling supporting libraries using
>>> different
>>>>>> options. By the way, are there specific configure options
necessary
>>>> when
>>>>>> building the netcdf and hdf libraries or does it not matter? I
look
>>>>> forward
>>>>>> to hearing from you soon.
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>>
------------------------------------------------
Subject: Help compiling met with "undefined reference" errors
From: John Halley Gotway
Time: Fri Feb 15 15:41:12 2019
Hi Scott,
This is John Halley Gotway. I work with Julie on support of MET.
Glad you
were able to get a successful build. I see you have a question about
inputs for the gen_vx_mask tool in MET. All of the tools in MET call
common library code for reading gridded data files. Therefore
anywhere the
MET tools read a gridded data file, they can read the full set of file
formats.
That includes GRIB1, GRIB2, CF-compliant NetCDF files, the NetCDF
output of
the wrf-interp or p-interp utility (for WRF-ARW output), or the NetCDF
files created by other MET tools (like pcp_combine for example). The
met-8.0 release includes one additional option and that's writing a
Python
script to load some data into a NumPy array, define the metadata, and
hand
it in memory to the MET tools. Examples of these sort of Python
scripts
can be found on the MET website:
https://dtcenter.org/met/users/downloads/analysis_scripts.php
It sounds like you have some data in NetCDF and are wondering if/how
MET
can read it. If it's already CF-compliant (i.e. global attribute with
"Conventions = "CF-1.?", then you're all set. If not, you could
either
make it CF-compliant, reformat it to look like the output of
pcp_combine,
or write a Python script to read it.
Hope that helps.
Thanks,
John
On Fri, Feb 15, 2019 at 1:19 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
>
> Hi Julie,
>
> After reading additional documentation I saw the required version is
> jpegsrc.v6b.tar.gz. I was able to get the latest version of MET
compiled
> sucessfully. Thanks you so much for your help and scripts.
Apparently,
> all the supporting library versions have to be just right for a
> successful build. FYI, I used intel-18.0.3.222 compilers.
>
> On an unrelated question, can the input grid for gen_vx_mask be a
netcdf
> file? If so, do you have any examples on what the contents (i.e.
ncdump)
> would look like?
>
> Thanks,
> Scott
>
>
> On 2/15/19 11:51 AM, Scott Daniel Rabenhorst wrote:
> > Hi Julie,
> >
> > Sorry for my delayed response. I had to take care of more pressing
> > projects this week and have just now returning to getting MET up
and
> > running.
> >
> > I am trying to replicate your compile script. However, I ran into
a
> > problem. I am having trouble building hd4 (your version of
HDF4.2r3
> > from 2008) using my version of jpeg (9c). The make check fails
with
> > jpeg related issues. In the files you posted for me the other
week, I
> > could not find a jpeg source tar file. Neither could I figure out
what
> > version you are using based on the compile script. However, the
jpeg
> > library is required. Would you mind letting me know what version
your
> > are using? I hope that may solve some issues here.
> >
> > Thanks,
> > Scott
> >
> >
> > On 2/5/19 11:47 AM, Julie Prestopnik via RT wrote:
> >> It's no problem! I hope the installation is going well. Please
let us
> >> know how things go.
> >>
> >> Thanks!
> >>
> >> Julie
> >>
> >> On Fri, Feb 1, 2019 at 2:04 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
> >> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
> >>
> >>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
> >>>
> >>> Hi Julie,
> >>>
> >>> I am so sorry! I did not see your inline response with the tar
file and
> >>> config script. That will be super helpful. I will give that a
try on
> >>> my HPC
> >>> system - I'm optimistic I can replicate things with that level
of
> >>> detail.
> >>>
> >>> Again, thanks so much for your prompt response to my emails. You
> >>> have been
> >>> a terrific correspondent! I will let you know how things go.
> >>>
> >>> Thanks,
> >>> Scott
> >>>
> >>> ________________________________________
> >>> From: Julie Prestopnik via RT [met_help at ucar.edu]
> >>> Sent: Friday, February 01, 2019 3:46 PM
> >>> To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
> >>> APPLICATIONS INC]
> >>> Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
> >>> "undefined
> >>> reference" errors
> >>>
> >>> Hi Scott. I'm replying from my phone, so this will be brief. I
just
> >>> wanted
> >>> to make sure that it was clear that the tar file package I
pointed
> >>> you to
> >>> in my last email contains the versions of all libraries that
have
> >>> successfully compiled with Intel (and gnu and pgi).
> >>>
> >>> Regarding flags, this would be indicated in the page in our
online
> >>> tutorial
> >>> that I pointed you to in my first email.
> >>>
> >>> Please take a look at the versions in the tarfile and follow up
with
> >>> any
> >>> questions. You could also use the script I pointed to you to
compile
> >>> only
> >>> MET or some or all of the supporting libraries.
> >>>
> >>> Thanks, Julie
> >>>
> >>> On Fri, Feb 1, 2019, 1:33 PM Rabenhorst, Scott D. (GSFC-
610.1)[SCIENCE
> >>> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
> >>>
> >>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728 >
> >>>>
> >>>> Hi Julie,
> >>>>
> >>>> No luck compiling MET8 using my existing libraries (as detailed
in my
> >>>> previous email). I attached my output logs for configure and
make.
> >>>> It is
> >>>> the same problem exists as before in the same src/libcode/vx_*
dirs. I
> >>> can
> >>>> try using a intel-16.0.X.XXX compiler, but I'm skeptical that
is the
> >>> source
> >>>> of the problem. First, I would have to rebuild all the support
> >>>> libraries.
> >>>> Again, my suspicion is either some of the required library
versions
> >>>> are
> >>> too
> >>>> new/old (incompatible versions) or I might need to include some
> >>> additional
> >>>> directives when building MET (e.g. additional FLAGS or
includes).
> >>>> If you
> >>>> have any versions that successfully compiled with Intel, that
might be
> >>> the
> >>>> best starting point. I can try to replicate that.
> >>>>
> >>>> Thanks,
> >>>> Scott
> >>>>
> >>>> ________________________________________
> >>>> From: Julie Prestopnik via RT [met_help at ucar.edu]
> >>>> Sent: Friday, February 01, 2019 2:54 PM
> >>>> To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
APPLICATIONS
> >>> INC]
> >>>> Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
> >>>> "undefined
> >>>> reference" errors
> >>>>
> >>>> Hi Scott.
> >>>>
> >>>> Sounds good! Thanks for recompiling later this afternoon.
Thank
> >>>> you also
> >>>> for verifying that all of the required netcdf files are present
(and
> >>> passed
> >>>> self-testing!).
> >>>>
> >>>> Could you tell me if you have successfully built MET8 (with
Intel
> >>>>> compilers), and if so, what versions of netcdf-c, netcdf-cxx4,
> >>>>> netcdf-fortran, hdf5, etc that you used to make it work?
> >>>>>
> >>>> Yes. I mostly use the Intel compilers, but not with version
18.
> >>> Usually,
> >>>> it's a lower version. Regarding the versions of the libraries,
at the
> >>>> bottom of the Downloads page on our website:
> >>>> https://dtcenter.org/met/users/downloads/index.php
> >>>>
> >>>> You can find a tarfile (
> >>>> https://dtcenter.org/met/users/compile_scripts/tar_files.tar)
that
> >>>> contains
> >>>> the versions of the libraries that we've been using along with
a
> >>>> script (
> >>>>
https://dtcenter.org/met/users/compile_scripts/compile_MET_all.sh)
> >>>> that
> >>> I
> >>>> frequently use to compile MET and its dependent libraries on
various
> >>>> machines. There are some necessary environment variables that
need
> >>>> to be
> >>>> set before running the script and those are described on the
bottom of
> >>> the
> >>>> Downloads page.
> >>>>
> >>>> Please let me know if you have any other questions or problems.
I'm
> >>>> leaving now and won't be back until Monday. We have an three
day MET
> >>>> Tutorial this coming Monday - Wednesday at NCAR, so I may be a
little
> >>>> slower to respond, but I will get back to you as soon as I can.
> >>>>
> >>>> I hope your next attempt will be successful! If not, let us
know
> >>>> how we
> >>> can
> >>>> help.
> >>>>
> >>>> Thanks,
> >>>> Julie
> >>>>
> >>>> On Fri, Feb 1, 2019 at 12:42 PM Rabenhorst, Scott D.
> >>>> (GSFC-610.1)[SCIENCE
> >>>> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu> wrote:
> >>>>
> >>>>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728
>
> >>>>>
> >>>>> Hi Julie,
> >>>>>
> >>>>> Thanks so much for your prompt response. I will try compiling
the
> >>> latest
> >>>>> version of MET this afternoon with your suggestions (removing
the
> >>>>> "-D__64BIT__" flag and compiler version). However, I can
verify that
> >>> all
> >>>>> the required netcdf files are present and passed self-testing:
> >>>>>
> >>>>> -rwxr-xr-x 1 sdrabenh g0620 1891 Jan 24 11:20 libbzip2.la
> >>>>> -rwxr-xr-x 1 sdrabenh g0620 113492 Jan 24 11:20 libbzip2.so
> >>>>> -rwxr-xr-x 1 sdrabenh g0620 1883 Jan 24 11:20 libmisc.la
> >>>>> -rwxr-xr-x 1 sdrabenh g0620 12777 Jan 24 11:20 libmisc.so
> >>>>> -rw-r--r-- 1 sdrabenh g0620 2629834 Jan 24 11:20 libnetcdf.a
> >>>>> -rw-r--r-- 1 sdrabenh g0620 1469428 Jan 24 11:33
libnetcdf_c++4.a
> >>>>> -rwxr-xr-x 1 sdrabenh g0620 2314 Jan 24 11:33
libnetcdf_c++4.la
> >>>>> lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33
libnetcdf_c++4.so ->
> >>>>> libnetcdf_c++4.so.1.0.3
> >>>>> lrwxrwxrwx 1 sdrabenh g0620 23 Jan 24 11:33
> >>>>> libnetcdf_c++4.so.1 ->
> >>>>> libnetcdf_c++4.so.1.0.3
> >>>>> -rwxr-xr-x 1 sdrabenh g0620 460080 Jan 24 11:33
> >>> libnetcdf_c++4.so.1.0.3
> >>>>> -rw-r--r-- 1 sdrabenh g0620 1053986 Jan 24 11:31 libnetcdff.a
> >>>>> -rwxr-xr-x 1 sdrabenh g0620 2295 Jan 24 11:31 libnetcdff.la
> >>>>> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31 libnetcdff.so
->
> >>>>> libnetcdff.so.6.1.1
> >>>>> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:31
libnetcdff.so.6 ->
> >>>>> libnetcdff.so.6.1.1
> >>>>> -rwxr-xr-x 1 sdrabenh g0620 807278 Jan 24 11:31
libnetcdff.so.6.1.1
> >>>>> -rwxr-xr-x 1 sdrabenh g0620 2100 Jan 24 11:20 libnetcdf.la
> >>>>> -rw-r--r-- 1 sdrabenh g0620 1321 Jan 24 11:20
libnetcdf.settings
> >>>>> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20 libnetcdf.so
->
> >>>>> libnetcdf.so.13.1.1
> >>>>> lrwxrwxrwx 1 sdrabenh g0620 19 Jan 24 11:20
libnetcdf.so.13 ->
> >>>>> libnetcdf.so.13.1.1
> >>>>> -rwxr-xr-x 1 sdrabenh g0620 1908852 Jan 24 11:20
libnetcdf.so.13.1.1
> >>>>> drwxr-xr-x 2 sdrabenh g0620 512 Jan 24 11:33 pkgconfig
> >>>>>
> >>>>> ...and include files:
> >>>>>
> >>>>> -rw-r--r-- 1 sdrabenh g0620 2965 Jan 24 11:33 ncAtt.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 480 Jan 24 11:33 ncByte.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 440 Jan 24 11:33 ncChar.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 1048 Jan 24 11:33 ncCheck.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 3684 Jan 24 11:33
ncCompoundType.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 1940 Jan 24 11:33 ncDim.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 483 Jan 24 11:33 ncDouble.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 3327 Jan 24 11:33 ncEnumType.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 12051 Jan 24 11:33 ncException.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 3469 Jan 24 11:33 ncFile.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncFloat.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 1055 Jan 24 11:33 ncGroupAtt.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 23965 Jan 24 11:33 ncGroup.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 473 Jan 24 11:33 ncInt64.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 453 Jan 24 11:33 ncInt.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 1501 Jan 24 11:33 ncOpaqueType.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncShort.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 482 Jan 24 11:33 ncString.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 5409 Jan 24 11:33 ncType.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 472 Jan 24 11:33 ncUbyte.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 481 Jan 24 11:33 ncUint64.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 462 Jan 24 11:33 ncUint.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 469 Jan 24 11:33 ncUshort.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 1151 Jan 24 11:33 ncVarAtt.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 54638 Jan 24 11:33 ncVar.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 1430 Jan 24 11:33 ncVlenType.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 651 Jan 24 11:33 netcdf
> >>>>> -rw-r--r-- 1 sdrabenh g0620 642 Jan 24 11:31
netcdf4_f03.mod
> >>>>> -rw-r--r-- 1 sdrabenh g0620 232820 Jan 24 11:31
> >>> netcdf4_nc_interfaces.mod
> >>>>> -rw-r--r-- 1 sdrabenh g0620 41808 Jan 24 11:31
> >>> netcdf4_nf_interfaces.mod
> >>>>> -rw-r--r-- 1 sdrabenh g0620 538 Jan 24 11:31 netcdf_f03.mod
> >>>>> -rw-r--r-- 1 sdrabenh g0620 200505 Jan 24 11:31
> >>>>> netcdf_fortv2_c_interfaces.mod
> >>>>> -rw-r--r-- 1 sdrabenh g0620 66697 Jan 24 11:20 netcdf.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 59877 Jan 24 11:31 netcdf.inc
> >>>>> -rw-r--r-- 1 sdrabenh g0620 520 Jan 24 11:20 netcdf_mem.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 2223 Jan 24 11:20 netcdf_meta.h
> >>>>> -rw-r--r-- 1 sdrabenh g0620 265880 Jan 24 11:31 netcdf.mod
> >>>>> -rw-r--r-- 1 sdrabenh g0620 26434 Jan 24 11:31
netcdf_nc_data.mod
> >>>>> -rw-r--r-- 1 sdrabenh g0620 155675 Jan 24 11:31
> >>> netcdf_nc_interfaces.mod
> >>>>> -rw-r--r-- 1 sdrabenh g0620 57449 Jan 24 11:31
netcdf_nf_data.mod
> >>>>> -rw-r--r-- 1 sdrabenh g0620 99023 Jan 24 11:31
> >>> netcdf_nf_interfaces.mod
> >>>>> -rw-r--r-- 1 sdrabenh g0620 1382 Jan 24 11:31 typesizes.mod
> >>>>>
> >>>>> As you can see, all the c, c++, fortran files exist and I
double
> >>> checked
> >>>>> the MET_* environment variables all point correctly. It is
very
> >>>>> strange
> >>>>> that I keep encountering problems in the vx lib code. I
realize that
> >>> the
> >>>
>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
> >>>
> >>>>> provides some documentation on the required libs, but
certainly
> >>>>> not all
> >>>>> details. For instance, I know there have been many changes to
the
> >>> recent
> >>>>> versions of netcdf and hdf. Could you tell me if you have
> >>>>> successfully
> >>>>> built MET8 (with Intel compilers), and if so, what versions of
> >>> netcdf-c,
> >>>>> netcdf-cxx4, netcdf-fortran, hdf5, etc that you used to make
it work?
> >>>> That
> >>>>> would be a very helpful starting point. I have a feeling
something I
> >>> did
> >>>>> may not be configured correctly, or I may be using a library
version
> >>> that
> >>>>> is either too old or new. Currently, my libs have been built
as
> >>> follows:
> >>>>> 1) szip/2.1.1
> >>>>>
> >>>>> 2) zlib/1.2.11
> >>>>>
> >>>>> 3) libpng/1.6.34 (--enable-shared --enable-static)
> >>>>>
> >>>>> 4) jpeg/9b (--enable-shared --enable-static)
> >>>>>
> >>>>> 5) jasper/1.900.1 (--enable-shared --enable-static --disable-
opengl
> >>>>> --enable-libjpeg --with-PACKAGE=$JPEG --disable-asan
--disable-leak)
> >>>>>
> >>>>> 6) hdf/4.2.13 (--with-zlib=$ZLIB --with-jpeg=$JPEG --with-
szlib=$SZIP
> >>>>> --disable-fortran --enable-shared --enable-static --disable-
netcdf)
> >>>>>
> >>>>> 7) hdfeos/2.20v1.00 (FC=$HDF/bin/h4fc
> >>>>>
> >>>
>
CXX=/usr/local/intel/2018/compilers_and_libraries_2018.2.199/linux/bin/intel64/icpc
>
> >>>
> >>>>> F77=$HDF/bin/h4fc CC=$HDF/bin/h4cc --with-hdf4=$HDF --with-
zlib=$ZLIB
> >>>>> --with-jpeg=$JPEG --with-szlib=$SZIP --disable-shared
> >>>>> --enable-static)
> >>>>>
> >>>>> 8) hdf5/1.10.2 (--with-zlib=$ZLIB/include,$ZLIB/lib
> >>>>> --with-szlib=$SZIP
> >>>>> --enable-cxx --enable-fortran --enable-fortran2003 --enable-hl
> >>>>> --enable-shared --enable-static --enable-codestack
> >>>>> --enable-using-memchecker
> >>>>> --enable-filters=shuffle,fletcher32,nbit,scaleoffset)
> >>>>>
> >>>>> 9) netcdf-c/4.6.1 (--enable-hdf4 --enable-hdf4-file-tests
> >>>> --enable-netcdf4
> >>>>> --enable-netcdf-4 --enable-dynamic-loading --enable-shared
> >>>> --enable-static
> >>>>> --enable-mmap --enable-fsync --enable-jna)
> >>>>>
> >>>>> 10) netcdf-fortran/4.4.4 (--enable-f03-compiler-check
> >>>>> --enable-fortran-type-check --enable-f03 --enable-largefile)
> >>>>>
> >>>>> 11) netcdf-cxx4/4.3.0 (--enable-shared --enable-static
> >>>> --enable-largefile)
> >>>>> 12) BUFRLIB/10.2.3 (FCFLAGS = CFLAGS = -DUNDERSCORE)
> >>>>>
> >>>>> 13) w3lib/2.0.6 (FFLAGS = CFLAGS = -O3 -g -m64 -DLINUX
-D__64BIT__)
> >>>>>
> >>>>> 14) g2lib/3.1.0 (FFLAGS = -O3 -g -I $(MODDIR) -DLINUX -m64
> >>> -D__64BIT__;
> >>>>> CFLAGS = -O3 -g -DLINUX $(INCDIR) -m64 -D__64BIT__)
> >>>>>
> >>>>> 15) g2clib/1.6.0 (INC = -I${JASPERINC} -I${SZIP}/include
> >>>> -I${ZLIB}/include
> >>>>> -I${PNG}/include -I${W3LIB}/include)
> >>>>>
> >>>>> 16) gsl/2.5 (--enable-shared --enable-static )
> >>>>>
> >>>>> Please let me know if you have any further insight regarding
what
> >>>> versions
> >>>>> and configuration of the required software will work with
intel
> >>>> compilers.
> >>>>> Thanks,
> >>>>> Scott
> >>>>>
> >>>>>
> >>>>> ________________________________________
> >>>>> From: Julie Prestopnik via RT [met_help at ucar.edu]
> >>>>> Sent: Thursday, January 31, 2019 5:51 PM
> >>>>> To: Rabenhorst, Scott D. (GSFC-610.1)[SCIENCE SYSTEMS AND
> >>>>> APPLICATIONS
> >>>> INC]
> >>>>> Subject: Re: [rt.rap.ucar.edu #88728] Help compiling met with
> >>> "undefined
> >>>>> reference" errors
> >>>>>
> >>>>> Hi Scott.
> >>>>>
> >>>>> I see that you have been struggling to compile met-7.0 and/or
> >>>>> met-8.0.
> >>>> I'm
> >>>>> sorry to hear that. Thank you for taking the time to email
met_help.
> >>>>> Based on the undefined references errors, there does seem to
be a
> >>> problem
> >>>>> with the libraries as you indicated. We'd love to have you
using the
> >>>>> latest version of MET and its patches (as of 20190130) which
you can
> >>> get
> >>>> by
> >>>>> running:
> >>>>> wget
> >>>>>
> >>>>>
> >>>
> https://dtcenter.org/met/users/downloads/MET_releases/met-
8.0_bugfix/met-8.0_bugfix.20190130.tar.gz
> >>>
> >>>>> I will say that I am unsure if we, the developers, have
installed MET
> >>>> using
> >>>>> that high of a version of the Intel compiler. I don't believe
I
> >>>>> have.
> >>>>> That may or may not be part of the problem. Do you have an
earlier
> >>>> version
> >>>>> (16.x.x.xxx?) of the Intel compiler that you could use. Thank
you for
> >>>>> attaching your myConfigure.log file and your myMakeInstall.log
file.
> >>> In
> >>>>> the future, it would be good to take a look at your config.log
file,
> >>>> which
> >>>>> has usually has additional information over configure.log.
> >>>>>
> >>>>> I see that you have set the "-D__64BIT__" flag. As of
recently there
> >>>> were
> >>>>> problems with the compilation using that flag, so we ask that
the you
> >>>>> remove the "-D__64BIT__" from the value of CFLAGS for the
compilation
> >>> of
> >>>>> the libraries and for MET. This is noted under the "Compiling
GRIB2
> >>>>> C-Library" section of the "Compilation" page of our newly
posted
> >>> met-8.0
> >>>>> online tutorial. Please recompile the GRIB2 C-Library and MET
> >>>>> without
> >>>> that
> >>>>> flag set.
> >>>>>
> >>>>> However, the undefined reference to error seems to be
occurring with
> >>>>> NetCDF. I'm a little perplexed by the "undefined reference
to
> >>>>> `_ZNK6netCDF5NcVar7getNameB5cxx11Ev'" error. I have not seen
that
> >>>>> sort
> >>>> of
> >>>>> error, with the additional characters, previously. MET
requires
> >>>>> the C
> >>>> and
> >>>>> C++
> >>>>> interface to NetCDF. Here is a checklist of files that are
necessary:
> >>>>>
> >>>>> Files for NetCDF4 C:
> >>>>>
> >>>>> - $MET_NETCDF/include/netcdf.h
> >>>>> - $MET_NETCDF/lib/libnetcdf.a
> >>>>> - $MET_NETCDF/lib/libnetcdf.so
> >>>>>
> >>>>> Files for NetCDF4 C++:
> >>>>>
> >>>>> - $MET_NETCDF/include/netcdf
> >>>>> - $MET_NETCDF/lib/libnetcdf_c++4.a
> >>>>> - $MET_NETCDF/lib/libnetcdf_c++4.so
> >>>>>
> >>>>> You could take a look and see if you have all of those files.
> >>>>>
> >>>>> By the way, are there specific configure options necessary
when
> >>> building
> >>>>>> the netcdf and hdf libraries or does it not matter?
> >>>>>>
> >>>>> We have detailed installation instructions for each of the
required
> >>>>> libraries posted in our online tutorial on the following page:
> >>>>>
> >>>>>
> >>>
>
https://dtcenter.org/met/users/support/online_tutorial/METv8.0/tutorial.php?name=compilation&category=req_libs
> >>>
> >>>>> I hope this information is helpful. Please take a look and let
us
> >>>>> know
> >>>> if
> >>>>> you have any questions. Please don't hesitate to follow up
with any
> >>>>> additional questions.
> >>>>>
> >>>>> Thanks,
> >>>>> Julie
> >>>>>
> >>>>> On Thu, Jan 31, 2019 at 1:31 PM Rabenhorst, Scott D.
> >>> (GSFC-610.1)[SCIENCE
> >>>>> SYSTEMS AND APPLICATIONS INC] via RT <met_help at ucar.edu>
wrote:
> >>>>>
> >>>>>> Thu Jan 31 13:31:33 2019: Request 88728 was acted upon.
> >>>>>> Transaction: Ticket created by scott.d.rabenhorst at nasa.gov
> >>>>>> Queue: met_help
> >>>>>> Subject: Help compiling met with "undefined reference"
errors
> >>>>>> Owner: Nobody
> >>>>>> Requestors: scott.d.rabenhorst at nasa.gov
> >>>>>> Status: new
> >>>>>> Ticket <URL:
> >>> https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=88728
> >>>>>>
> >>>>>> Hi MET support,
> >>>>>>
> >>>>>> I have been struggling to compile MET 7 (or 8) using Intel
> >>>>>> compilers.
> >>>> The
> >>>>>> basic problem is undefined references to required libraries
(netcdf,
> >>>> hdf,
> >>>>>> etc). Interestingly, they always seem to occur in the
> >>> src/libcode/vx_*
> >>>>>> files. I have attached my latest compile log for the
> >>>>>> met-7.0_bugfix.20180924.tar.gz build. I have followed all the
> >>>> directions
> >>>>> in
> >>>>>> the MET Users Guide but it dows not seem to make any
difference. For
> >>>> this
> >>>>>> latest try, I setup the environment as follows:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>
>
------------------------------------------------------------------------------------------
>
> >>>
> >>>>>> module load other/comp/gcc-6.3
> >>>>>> module load comp/intel-18.0.2.199
> >>>>>> module load mpi/impi-18.0.2.199
> >>>>>> module load lib/mkl-18.0.2.199
> >>>>>> module load wrf-deps/intel-18.0.2.199
> >>>>>> module load wgrib2/2.0.7_intel-18.0.2.199
> >>>>>>
> >>>>>> setenv COMPVERS intel-18.0.2.199
> >>>>>> setenv APPDIR ${NOBACKUP}/apps/sp3
> >>>>>>
> >>>>>> setenv MET_NETCDF ${APPDIR}/netcdf/4.6.1_hdf4/${COMPVERS}
> >>>>>> setenv MET_HDF5 ${APPDIR}/hdf5/1.10.2/${COMPVERS}
> >>>>>> setenv MET_HDF ${APPDIR}/hdf/4.2.13_no-fortran/${COMPVERS}
> >>>>>> setenv MET_HDFEOS ${APPDIR}/hdfeos/2.20v1.00/${COMPVERS}
> >>>>>> setenv MET_GRIB2C ${APPDIR}/g2clib/1.6.0/${COMPVERS}
> >>>>>> setenv MET_GSL ${APPDIR}/gsl/2.5/${COMPVERS}
> >>>>>> setenv MET_BUFR ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}
> >>>>>> setenv MET_BUFRLIB ${APPDIR}/BUFRLIB/10.2.3/${COMPVERS}/lib
> >>>>>> setenv MET_CAIROINC /usr/include/cairo
> >>>>>> setenv MET_CAIROLIB /usr/lib64
> >>>>>> setenv MET_FREETYPEINC /usr/include/freetype2
> >>>>>> setenv MET_FREETYPELIB /usr/lib64
> >>>>>> setenv YACC ${APPDIR}/byacc/github/${COMPVERS}
> >>>>>> setenv LDFLAGS -L${APPDIR}/wrf-deps/${COMPVERS}/lib
> >>>>>> setenv CPPFLAGS -I${APPDIR}/wrf-deps/${COMPVERS}/include
> >>>>>>
> >>>>>> setenv CFLAGS "-D__64BIT__"
> >>>>>>
> >>>>>> ./configure --prefix=${APPDIR}/MET/7.0/${COMPVERS} --enable-
lidar2nc
> >>>>>> --enable-grib2 --enable-modis --enable-mode_graphics |& tee
> >>>>> myConfigure.log
> >>>>>>
> >>>>>>
> >>>
>
------------------------------------------------------------------------------------------
>
> >>>
> >>>>>> Then I ran "make install |& tee myMake.log" and got the
resulting
> >>> error
> >>>>>> logs (attached). Everything seems correct. I have not been
able to
> >>>>>> successfully build MET 8 either because of similar errors.
Please
> >>>>>> let
> >>>> me
> >>>>>> know any ideas on how to get this to compile correctly. I am
out of
> >>>> ideas
> >>>>>> and have spent a while recompiling supporting libraries using
> >>> different
> >>>>>> options. By the way, are there specific configure options
necessary
> >>>> when
> >>>>>> building the netcdf and hdf libraries or does it not matter?
I look
> >>>>> forward
> >>>>>> to hearing from you soon.
> >>>>>>
> >>>>>>
> >>>>>> Thanks,
> >>>>>> Scott
> >>>>>>
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>
> >>>
> >>>
>
>
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