problem compiling with hdf5

User Support
1

Hello everyone

i tried compiling openmc with hdf5 support. i downloaded HDF5 1.8.14. installed it with instruction given in section 2.2.1 of installation. used the command to

export FC=h5pfc

then this error happened.

[ 46%] Building Fortran object CMakeFiles/openmc.dir/hdf5_interface.F90.o
/home/khurrum/Work/openmc/src/hdf5_interface.F90:1791.47:

mem_space_id=dspace, xfer_prp = plist)
1
Error: There is no specific subroutine for the generic ‘h5dread_vl_f’ at (1)
/home/khurrum/Work/openmc/src/hdf5_interface.F90:1737.45:

mem_space_id=dspace, xfer_prp=plist)
1
Error: There is no specific subroutine for the generic ‘h5dwrite_vl_f’ at (1)
/home/khurrum/Work/openmc/src/hdf5_interface.F90:779.47:

mem_space_id=dspace, xfer_prp = plist)
1
Error: There is no specific subroutine for the generic ‘h5dread_vl_f’ at (1)
/home/khurrum/Work/openmc/src/hdf5_interface.F90:737.29:

mem_space_id=dspace)
1
Error: There is no specific subroutine for the generic ‘h5dwrite_vl_f’ at (1)
make[3]: *** [CMakeFiles/openmc.dir/hdf5_interface.F90.o] Error 1
make[2]: *** [CMakeFiles/openmc.dir/hdf5_interface.F90.o.provides] Error 2
make[1]: *** [CMakeFiles/openmc.dir/all] Error 2
make: *** [all] Error 2

i am working at ubuntu 12.04 LTS. your help in this regard will be highly appreciated.

2

These are my commands to build mpich and parallel hdf5:

Build MPICH

wget http://www.mpich.org/static/downloads/3.1.3/mpich-3.1.3.tar.gz
tar -xzvf mpich-3.1.3.tar.gz
cd mpich-3.1.3
./configure --prefix=/opt/mpich/3.1.3-gnu
make -j
make install
cd …

Build PHDF5

wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.14.tar.gz
tar -xzvf hdf5-1.8.14.tar.gz
cd hdf5-1.8.14
CC=/opt/mpich/3.1.3-gnu/bin/mpicc FC=/opt/mpich/3.1.3-gnu/bin/mpif90
./configure
–prefix=/opt/phdf5/1.8.14-gnu --enable-fortran
–enable-fortran2003 --enable-parallel
make -j
make install
cd …

Let me know if this gives you problems.

3

I have successfully installed mpich and hdf5 with parallel option enabled. The error I posted is during installation of openmc with parallel enabled Fortran wrapper of hdf5

4

this is the output of cmake showing that it detects the h5pfc fortran wrapper but don’t know what is the problem with the compilation

– The Fortran compiler identification is GNU
– Check for working Fortran compiler: /home/khurrum/Downloads/hdf5-1.8.14/build/bin/h5pfc
– Check for working Fortran compiler: /home/khurrum/Downloads/hdf5-1.8.14/build/bin/h5pfc – works
– Detecting Fortran compiler ABI info
– Detecting Fortran compiler ABI info - done
– Checking whether /home/khurrum/Downloads/hdf5-1.8.14/build/bin/h5pfc supports Fortran 90
– Checking whether /home/khurrum/Downloads/hdf5-1.8.14/build/bin/h5pfc supports Fortran 90 – yes
– Detected parallel HDF5 wrapper: /home/khurrum/Downloads/hdf5-1.8.14/build/bin/h5pfc
– Found PythonInterp: /usr/bin/python (found version “2.7.3”)
– Configuring done
– Generating done
– Build files have been written to: /home/khurrum/Work/openmc/src

5

When you built HDF5, did you use the --enable-fortran and --enable-fortran2003 options?

Paul

6

Yes I did. As in my last post I have shown output of cmake which detected f5pfs so this means Fortran was enabled. I have run some examples of hdf5 to check its installation and they are working fine