[Build] Unable to access module symbol file for module h5fortran_types

Robert_Sawko · December 9, 2017, 9:38am

Dear HDFers,

I am building a parallel version of HDF5 sub-version 1.10.1. I went with the
cmake path. The build is on a P8 machine with RHEL, Xl compilers and Spectrum
MPI. The cmake configure step goes fine, but my compilation crashes around 93%
with the following error:

/path/to/hdf/source/fortran/src/H5f90global.F90", line 43.7: 1514-219 (S) Unable to access module symbol file for module h5fortran_types. Check path and file permissions of file. Use association not done for this module.
1501-511 Compilation failed for file H5f90global.F90.
make[3]: *** [fortran/src/CMakeFiles/hdf5_fortran-static.dir/H5f90global.F90.o] Error 1
make[2]: *** [fortran/src/CMakeFiles/hdf5_fortran-static.dir/H5f90global.F90.o.provides] Error 2
make[1]: *** [fortran/src/CMakeFiles/hdf5_fortran-static.dir/all] Error 2"

After rerunning with VERBOSE=2, I nailed down the compilation issue to the line
below. Apologies for cluster specific paths, but I am afraid I will
accidentally remove important information so I am not editing anything:

/opt/ibm/xlf/15.1.5/bin/xlf90_r \
    -WF,-DNDEBUG -WF,-D_FILE_OFFSET_BITS=64 \
    -WF,-D_LARGEFILE64_SOURCE -WF,-D_LARGEFILE_SOURCE \
    -I/gpfs/cds/local/package_build/build/rrs59-build/build/hdf/build_1.10.1_xl \
    -I/gpfs/cds/local/package_build/build/rrs59-build/build/hdf/1.10.1/src \
    -I/gpfs/cds/local/package_build/build/rrs59-build/build/hdf/build_1.10.1_xl/bin \
    -I/gpfs/paragon/local/apps/ibm/spectrum_mpi/10.1.0/include \
    -I/gpfs/cds/local/package_build/build/rrs59-build/build/hdf/build_1.10.1_xl/fortran \
    -I/gpfs/cds/local/package_build/build/rrs59-build/build/hdf/build_1.10.1_xl/fortran/src \
    -I/gpfs/cds/local/package_build/build/rrs59-build/build/hdf/1.10.1/fortran/src \
    -I/gpfs/cds/local/package_build/build/rrs59-build/build/hdf/build_1.10.1_xl/src \
    -qfloat=nans:subnormals -qmaxmem=-1 -qnosave -qsclk=micro -qsmp=omp \
    -qarch=pwr8 -qtune=pwr8:smt8 -qthreaded -qhalt=e \
    -qmoddir=../../bin/static -qpic \
    -c /gpfs/cds/local/package_build/build/rrs59-build/build/hdf/1.10.1/fortran/src/H5f90global.F90 \
    -o CMakeFiles/hdf5_fortran-static.dir/H5f90global.F90.o

Please let me know if you have any advice. I also didn't manage to build it
with GCC although for completely different errors. I will need C and Fortran
interfaces, so my cmake build directory was configured with:

cmake \
    -DCMAKE_INSTALL_PREFIX:PATH=${PREFIX} \
    -DBUILD_SHARED_LIBS:BOOL=ON \
    -DHDF5_ENABLE_PARALLEL:BOOL=ON \
    -DHDF5_BUILD_FORTRAN:BOOL=ON \
    -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF \
    -DHDF5_BUILD_CPP_LIB:BOOL=OFF \
    ../${version}

Many thanks,
Robert

···

--
Dr Robert Sawko
Research Staff Member, IBM
Daresbury Laboratory
Keckwick Lane, Warrington
WA4 4AD
United Kingdom
--
Email (IBM): RSawko@uk.ibm.com
Email (STFC): robert.sawko@stfc.ac.uk
Phone (office): +44 (0) 1925 60 3967
Phone (mobile): +44 778 830 8522
Profile page:
http://researcher.watson.ibm.com/researcher/view.php?person=uk-RSawko
--Unless stated otherwise above:
IBM United Kingdom Limited - Registered in England and Wales with number 741598.
Registered office: PO Box 41, North Harbour, Portsmouth, Hampshire PO6 3AU

brtnfld · December 18, 2017, 8:56pm

Thanks for the report Robert,

We’ve reproduced the issue, and it's slated to be fixed in the next release of HDF5 1.10.

Scot

···

On Dec 9, 2017, at 3:38 AM, Robert Sawko <RSawko@uk.ibm.com> wrote:

Dear HDFers,

I am building a parallel version of HDF5 sub-version 1.10.1. I went with the
cmake path. The build is on a P8 machine with RHEL, Xl compilers and Spectrum
MPI. The cmake configure step goes fine, but my compilation crashes around 93%
with the following error:

/path/to/hdf/source/fortran/src/H5f90global.F90", line 43.7: 1514-219 (S) Unable to access module symbol file for module h5fortran_types. Check path and file permissions of file. Use association not done for this module.
1501-511 Compilation failed for file H5f90global.F90.
make[3]: *** [fortran/src/CMakeFiles/hdf5_fortran-static.dir/H5f90global.F90.o] Error 1
make[2]: *** [fortran/src/CMakeFiles/hdf5_fortran-static.dir/H5f90global.F90.o.provides] Error 2
make[1]: *** [fortran/src/CMakeFiles/hdf5_fortran-static.dir/all] Error 2"

After rerunning with VERBOSE=2, I nailed down the compilation issue to the line
below. Apologies for cluster specific paths, but I am afraid I will
accidentally remove important information so I am not editing anything:

/opt/ibm/xlf/15.1.5/bin/xlf90_r \
   -WF,-DNDEBUG -WF,-D_FILE_OFFSET_BITS=64 \
   -WF,-D_LARGEFILE64_SOURCE -WF,-D_LARGEFILE_SOURCE \
   -I/gpfs/cds/local/package_build/build/rrs59-build/build/hdf/build_1.10.1_xl \
   -I/gpfs/cds/local/package_build/build/rrs59-build/build/hdf/1.10.1/src \
   -I/gpfs/cds/local/package_build/build/rrs59-build/build/hdf/build_1.10.1_xl/bin \
   -I/gpfs/paragon/local/apps/ibm/spectrum_mpi/10.1.0/include \
   -I/gpfs/cds/local/package_build/build/rrs59-build/build/hdf/build_1.10.1_xl/fortran \
   -I/gpfs/cds/local/package_build/build/rrs59-build/build/hdf/build_1.10.1_xl/fortran/src \
   -I/gpfs/cds/local/package_build/build/rrs59-build/build/hdf/1.10.1/fortran/src \
   -I/gpfs/cds/local/package_build/build/rrs59-build/build/hdf/build_1.10.1_xl/src \
   -qfloat=nans:subnormals -qmaxmem=-1 -qnosave -qsclk=micro -qsmp=omp \
   -qarch=pwr8 -qtune=pwr8:smt8 -qthreaded -qhalt=e \
   -qmoddir=../../bin/static -qpic \
   -c /gpfs/cds/local/package_build/build/rrs59-build/build/hdf/1.10.1/fortran/src/H5f90global.F90 \
   -o CMakeFiles/hdf5_fortran-static.dir/H5f90global.F90.o

Please let me know if you have any advice. I also didn't manage to build it
with GCC although for completely different errors. I will need C and Fortran
interfaces, so my cmake build directory was configured with:

cmake \
   -DCMAKE_INSTALL_PREFIX:PATH=${PREFIX} \
   -DBUILD_SHARED_LIBS:BOOL=ON \
   -DHDF5_ENABLE_PARALLEL:BOOL=ON \
   -DHDF5_BUILD_FORTRAN:BOOL=ON \
   -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF \
   -DHDF5_BUILD_CPP_LIB:BOOL=OFF \
   ../${version}

Many thanks,
Robert
--
Dr Robert Sawko
Research Staff Member, IBM
Daresbury Laboratory
Keckwick Lane, Warrington
WA4 4AD
United Kingdom
--
Email (IBM): RSawko@uk.ibm.com
Email (STFC): robert.sawko@stfc.ac.uk
Phone (office): +44 (0) 1925 60 3967
Phone (mobile): +44 778 830 8522
Profile page:
http://researcher.watson.ibm.com/researcher/view.php?person=uk-RSawko
--Unless stated otherwise above:
IBM United Kingdom Limited - Registered in England and Wales with number 741598.
Registered office: PO Box 41, North Harbour, Portsmouth, Hampshire PO6 3AU

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