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

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

Robert Sawko
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): [hidden email]
Email (STFC): [hidden email]
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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Re: [Build] Unable to access module symbol file for module h5fortran_types

Scot Breitenfeld
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 <[hidden email]> 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): [hidden email]
> Email (STFC): [hidden email]
> 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
>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> [hidden email]
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5