How to use the hdf5 library

[lvkas521424]

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Hello, I’m facing the following problem: I want to embed an external Fortran programme into my current Moose application, and this Fortran programme uses the HDF5 library. I wish to use the external programme to link against the HDF5 link files located in the /moose/petsc/arc-moose/ directory, but I have discovered that, under Moose’s default offline compilation settings, the corresponding HDF5 link files for the Fortran option (h5fc) are not generated. I have checked the build script update_and_rebuild_petsc.sh, and it does not appear that this option is enabled anywhere. I would be grateful if you could assist me in resolving this issue. Thank you.

Note: I installed Moose on the supercomputing platform using the offline method. When I link my Fortran programme with the externally compiled HDF5 library, although the executable application compiles successfully, I am warned that there may be a library conflict. Furthermore, when I run the calculations, numerous exceptions occur when calling the HDF5 data-reading module in the external Fortran programme.
I want PETSC to generate libhdf5_fortran.so.200 at the same time as it generates the HDF5 file.
Below are the HDF5 libraries generated by PETSC and those I compiled myself.

[ssct0095t@login07 user]$ ls ../tools/hdf5-1.12.2/lib/
libhdf5.a           libhdf5_fortran.so.200      libhdf5hl_fortran.a    libhdf5hl_fortran.so.200      libhdf5_hl.so.200      libhdf5.so
libhdf5_fortran.a   libhdf5_fortran.so.200.1.1  libhdf5hl_fortran.la   libhdf5hl_fortran.so.200.0.2  libhdf5_hl.so.200.1.0  libhdf5.so.200
libhdf5_fortran.la  libhdf5_hl.a                libhdf5_hl_fortran.so  libhdf5_hl.la                 libhdf5.la             libhdf5.so.200.2.0
libhdf5_fortran.so  libhdf5_hl_fortran.a        libhdf5hl_fortran.so   libhdf5_hl.so                 libhdf5.settings
[ssct0095t@login07 user]$ ls ../tools/projects/moose/petsc/arch-moose/lib/
adm2dgr                libHYPRE.so                   libpetsc.so.3.24.2               libscalapack.so.2.2.2       libsmumps.a
cmake                  libkokkosalgorithms.so        libpord.a                        libscotcherrexit.so         libstrumpack.so
libceed.so             libkokkosalgorithms.so.4.7    libptesmumps.so                  libscotcherrexit.so.7.0     libstrumpack.so.8.0
libcmumps.a            libkokkosalgorithms.so.4.7.1  libptesmumps.so.7.0              libscotcherrexit.so.7.0.10  libstrumpack.so.8.0.0
libdmumps.a            libkokkoscontainers.so        libptesmumps.so.7.0.10           libscotcherr.so             libsuperlu_dist_python.so
libesmumps.so          libkokkoscontainers.so.4.7    libptscotcherrexit.so            libscotcherr.so.7.0         libsuperlu_dist_python.so.9
libesmumps.so.7.0      libkokkoscontainers.so.4.7.1  libptscotcherrexit.so.7.0        libscotcherr.so.7.0.10      libsuperlu_dist_python.so.9.2.0
libesmumps.so.7.0.10   libkokkoscore.so              libptscotcherrexit.so.7.0.10     libscotchmetisv3.so         libsuperlu_dist.so
libfblas.a             libkokkoscore.so.4.7          libptscotcherr.so                libscotchmetisv3.so.7.0     libsuperlu_dist.so.9
libflapack.a           libkokkoscore.so.4.7.1        libptscotcherr.so.7.0            libscotchmetisv3.so.7.0.10  libsuperlu_dist.so.9.2.0
libhdf5_hl.so          libkokkoskernels.so           libptscotcherr.so.7.0.10         libscotchmetisv5.so         libzmumps.a
libhdf5_hl.so.310      libkokkossimd.so              libptscotchparmetisv3.so         libscotchmetisv5.so.7.0     petsc
libhdf5_hl.so.310.0.6  libkokkossimd.so.4.7          libptscotchparmetisv3.so.7.0     libscotchmetisv5.so.7.0.10  pkgconfig
libhdf5.settings       libkokkossimd.so.4.7.1        libptscotchparmetisv3.so.7.0.10  libscotch.so                PYTHON
libhdf5.so             libmetis.so                   libptscotch.so                   libscotch.so.7.0            slepc
libhdf5.so.310         libmumps_common.a             libptscotch.so.7.0               libscotch.so.7.0.10
libhdf5.so.310.5.1     libparmetis.so                libptscotch.so.7.0.10            libslepc.so
libhpddm_petsc.so      libpetsc.so                   libscalapack.so                  libslepc.so.3.24
libHYPRE-3.0.0.so      libpetsc.so.3.24              libscalapack.so.2.2              libslepc.so.3.24.0
[ssct0095t@login07 user]$  

(Optional) code in question / simulation log / errors

No response

Encountering Errors? Please include diagnostic output

No response

[lindsayad]

Can your system administrators provide the HDF5 libraries you need? HDF5 is a pretty ubiquitous package. Then you wouldn't need PETSc to build HDF5 for you

[GiudGiud]

Did you export HDF5_DIR/_ROOT before recompiling petsc

[lvkas521424]

I’m afraid I didn’t do that; I simply added the HDF5 information to my environment（.bashrc）.

#hdf5-1.12.2
export PATH=/work/home/ssct0095t/tools/hdf5-1.12.2/bin:$PATH
export LD_LIBRARY_PATH=/work/home/ssct0095t/tools/hdf5-1.12.2/lib:$LD_LIBRARY_PATH

[GiudGiud]

It might have been enough.
I ll try dig out all the places where petsc looks for hdf5, it's in a thread somewhere

[loganharbour]

moose/scripts/configure_petsc.sh

Line 60 in 227076f

if [ -n "$HDF5_DIR" ]; then

Before calling update_and_rebuild_petsc.sh, call:

export HDF5_DIR=/work/home/ssct0095t/tools/hdf5-1.12.2

[lvkas521424]

Thank you very much, I understand now. I’m very grateful to all of you for your guidance. I think I’ve figured out why HDF5 wasn’t raising any errors on my small server: at the time, I had simply used HDF5_ROOT as the root directory for HDF5, and then added the path and ld_library_path on top of that.