Molcas Forum

andrewshyichuk

Member

Registered: 2020-02-13

Posts: 62

HDF5 output sensitive to thread use? [SOLVED]

Dear Users,

I have two versions of OpenMolcas compiled.
The two are exactly the same, except for one thing - the use OMP threading.
The issue is: HDF5 files are not saved by the non-threaded version.
HDF5 itself is threaded, but I do not see how is that relevant.

EDIT: found the solution.
After I manually set the HDF5 include dirs to /usr/local/easybuild/software/HDF5/1.10.7-gompi-2021a/include (the correct include dir in my case), the problem got resolved.
Apparently, in the threaded version, Molcas made an HDF5 call mediated by OMP and the call did happen due to HDF5 libs being included.
However, with the libs but without the HDF5 headers Molcas was unable do make a HDF5 call and the files were not saved.
 

The HDF5 part in the ccmake looks like so:

HDF5                             ON
 HDF5_CXX_COMPILER_EXECUTABLE     /usr/local/easybuild/software/HDF5/1.10.7-gompi-2021a/bin/h5c++
 HDF5_CXX_INCLUDE_DIR             HDF5_CXX_INCLUDE_DIR-NOTFOUND
 HDF5_CXX_LIBRARY_dl              /usr/lib64/libdl.so
 HDF5_CXX_LIBRARY_hdf5            /usr/local/easybuild/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.so
 HDF5_CXX_LIBRARY_hdf5_cpp        /usr/local/easybuild/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5_cpp.so
 HDF5_CXX_LIBRARY_m               /usr/lib64/libm.so
 HDF5_CXX_LIBRARY_pthread         /usr/lib64/libpthread.so
 HDF5_CXX_LIBRARY_sz              /usr/local/easybuild/software/Szip/2.1.1-GCCcore-10.3.0/lib/libsz.so  
 HDF5_CXX_LIBRARY_z               /usr/local/easybuild/software/zlib/1.2.11-GCCcore-10.3.0/lib/libz.so
 HDF5_C_COMPILER_EXECUTABLE       /usr/local/easybuild/software/HDF5/1.10.7-gompi-2021a/bin/h5pcc
 HDF5_C_INCLUDE_DIR               HDF5_C_INCLUDE_DIR-NOTFOUND
 HDF5_C_LIBRARY_dl                /usr/lib64/libdl.so
 HDF5_C_LIBRARY_hdf5              /usr/local/easybuild/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.so
 HDF5_C_LIBRARY_m                 /usr/lib64/libm.so
 HDF5_C_LIBRARY_pthread           /usr/lib64/libpthread.so
 HDF5_C_LIBRARY_sz                /usr/local/easybuild/software/Szip/2.1.1-GCCcore-10.3.0/lib/libsz.so
 HDF5_C_LIBRARY_z                 /usr/local/easybuild/software/zlib/1.2.11-GCCcore-10.3.0/lib/libz.so
 HDF5_DIFF_EXECUTABLE             /usr/local/easybuild/software/HDF5/1.10.7-gompi-2021a/bin/h5diff
 HDF5_DIR                         HDF5_DIR-NOTFOUND
 HDF5_IS_PARALLEL                 OFF
 HDF5_hdf5_LIBRARY_DEBUG          HDF5_hdf5_LIBRARY_DEBUG-NOTFOUND
 HDF5_hdf5_LIBRARY_RELEASE        HDF5_hdf5_LIBRARY_RELEASE-NOTFOUND
 HDF5_hdf5_cpp_LIBRARY_DEBUG      HDF5_hdf5_cpp_LIBRARY_DEBUG-NOTFOUND
 HDF5_hdf5_cpp_LIBRARY_RELEASE    HDF5_hdf5_cpp_LIBRARY_RELEASE-NOTFOUND

Note that HDF5 works (but only with OMP) despite the NOTFOUND elements above, it's libs are listed and, respectively, are found.

It is not much of an issue, but I ran into a suddent absence of the h5 files, at the rare instance I actually needed them.
Hence, I leave this information here for the Molcas users of the future.

Last edited by andrewshyichuk (2023-05-16 10:24:19)