PUMGen compilation and hdf5 on Shaheen about pumgen

[Thomas-Ulrich]

Hi, I can have a look if you share /home/vyasjc/meshing-soft-pumi-pumgen on shaheen.

[Thomas-Ulrich]

Hi, so the problem is the output of h5pcc -show -shlib on shaheen:

Shaheen

x_ulricht@cdl2:/project/k1488/meshing-soft-pumi-pumgen-TU/PUMGen> /opt/cray/pe/hdf5-parallel/1.10.5.2/bin/h5pcc -show  -shlib
cc -DpgiFortran -dynamic -Wl,-rpath -Wl,/opt/cray/pe/hdf5-parallel/1.10.5.2/CRAY/9.0/lib

SupermucNG:

di73yeq4@login03:~> h5pcc -show -shlib
/dss/dsshome1/lrz/sys/spack/release/19.2/opt/x86_avx512/intel-mpi/2019.6.154-intel-lmhtdss/bin/mpicc -I/dss/dsshome1/lrz/sys/spack/release/19.2/opt/x86_avx512/zlib/1.2.11-gcc-ajxhsmr/include -I/dss/dsshome1/lrz/sys/spack/release/19.2/opt/x86_avx512/libszip/2.1.1-gcc-v3th2mi/include -fPIC -L/dss/dsshome1/lrz/sys/spack/release/19.2/opt/x86_avx512/hdf5/1.8.20-intel-mhsivcc/lib -lhdf5_hl -lhdf5 -L/dss/dsshome1/lrz/sys/spack/release/19.2/opt/x86_avx512/zlib/1.2.11-gcc-ajxhsmr/lib -L/dss/dsshome1/lrz/sys/spack/release/19.2/opt/x86_avx512/libszip/2.1.1-gcc-v3th2mi/lib -lpthread -lsz -lz -ldl -lm -Wl,-rpath -Wl,/dss/dsshome1/lrz/sys/spack/release/19.2/opt/x86_avx512/hdf5/1.8.20-intel-mhsivcc/lib

@tum: any idea how to fix that?

Thomas.

[Thomas-Ulrich]

So the problem what that hdf5.py was looking for the -L option which is not there

1. A suggested workaround is to unload the hdf5 module and manually set the PKG_CONFIG_PATH. On shaheen this is done with:

export PKG_CONFIG_PATH=$PE_INTEL_FIXED_PKGCONFIG_PATH:$PKG_CONFIG_PATH

(but then another other problem arises at linking: build/src/pumgen.o:pumgen.cpp:function main: error: undefined reference to 'H5open').

2. it turned out that the problem had been fixed before but not properly documented, 2 lines need to be added to hdf5.py:

        utils.pkgconfig.appendPathes(env, flags)
        flags['LIBS'].append('hdf5_hl')
        flags['LIBS'].append('hdf5_hl_parallel')
        if not conf.CheckLibWithHeader(flags['LIBS'][0], 'hdf5.h', 'c', extra_libs=flags['LIBS'][1:]):

3. actually there is an (undocumented yet) cmake builder, so fixing the hdf5.py is not a priority...