[BUG] - PetscViewerHDF5GetGroup() requires HDF5

[guit-hub]

Describe the bug

• What is the bug? .After struggling with the installation of it for two weeks,I finally pip it on my Ubuntu virtual system successfully.However,when I run './test.sh' as the github page showed,I encountered a unexpected error which I failed to fix it with huge effort.By trying some other simple example,I found that the problem occurs when using "uw.meshing.UnstructuredSimplexBox(minCoords=(0.0, 0.0), maxCoords=(1.0, 1.0), cellSize=1.0 / 3.0, qdegree=2)".The following is the error report: [0]PETSC ERROR: No support for this operation for this object type [0]PETSC ERROR: PetscViewerHDF5GetGroup() requires HDF5 [0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program crashed before usage or a spelling mistake, etc! [0]PETSC ERROR: Option left: name:-dm_plex_hash_location (no value) source: code [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.21.4, unknown [0]PETSC ERROR: test_0004_pointwise_fns.py on a named DESKTOP-GNG87D4 by root Wed Aug 21 11:25:42 2024 [0]PETSC ERROR: Configure options --prefix=/usr/local/lib/python3.10/dist-packages/petsc PETSC_ARCH=arch-python --with-shared-libraries=1 --with-debugging=0 --with-c2html=0 --with-hdf5-dir=/usr/local/hdf5 --with-cc=/usr/local/bin/mpicc --with-cxx=/usr/local/bin/mpicxx --with-fc=0 --with-sowing=0 [0]PETSC ERROR: #1 PetscViewerHDF5GetGroup() at src/lib-petsc/compat/hdf5.h:14 [0]PETSC ERROR: #2 PetscViewerHDF5HasAttribute() at /opt/petsc/src/sys/classes/viewer/impls/hdf5/hdf5v.c:1527 [0]PETSC ERROR: #3 PetscViewerHDF5GetDMPlexStorageVersionWriting() at /opt/petsc/src/dm/impls/plex/plexhdf5.c:144 [0]PETSC ERROR: #4 DMPlexCoordinatesView_HDF5_Internal() at /opt/petsc/src/dm/impls/plex/plexhdf5.c:1042 [0]PETSC ERROR: #5 DMPlexView_HDF5_Internal() at /opt/petsc/src/dm/impls/plex/plexhdf5.c:1300 [0]PETSC ERROR: #6 DMView_Plex() at /opt/petsc/src/dm/impls/plex/plex.c:1941 [0]PETSC ERROR: #7 DMView() at /opt/petsc/src/dm/interface/dm.c:1001 [0]PETSC ERROR: #8 PetscObjectView() at /opt/petsc/src/sys/objects/destroy.c:76 Traceback (most recent call last): File "/opt/underworld/tests/test_0004_pointwise_fns.py", line 20, in mesh = uw.meshing.UnstructuredSimplexBox( File "/opt/underworld/src/underworld3/meshing.py", line 230, in UnstructuredSimplexBox new_mesh = Mesh( File "/opt/underworld/src/underworld3/discretisation.py", line 168, in init self.sf0, self.dm = _from_gmsh( File "/opt/underworld/src/underworld3/discretisation.py", line 75, in _from_gmsh viewer(plex_0) File "petsc4py/PETSc/Viewer.pyx", line 135, in petsc4py.PETSc.Viewer.call petsc4py.PETSc.Error: error code 56 WARNING! There are options you set that were not used! WARNING! could be spelling mistake, etc! There is one unused database option. It is: Option left: name:-dm_plex_hash_location (no value) source: code BTW,I'm sure I have installed HDF5 with the latest version correctly.
• What version code? underworld3 0.9b0
• What system are you running the code on? Ubuntu 22.04.4 LTS (GNU/Linux 5.15.133.1-microsoft-standard-WSL2 x86_64)
• Steps to reproduce? Here is my source code: mesh = uw.meshing.UnstructuredSimplexBox( minCoords=(0.0, 0.0), maxCoords=(1.0, 1.0), cellSize=1.0 / 3.0, qdegree=2 ) mesh.dm.view() Screenshots

[bknight1]

Looks like hdf5 isn't installed? You can try to pip install, but this will be the serial version.

[guit-hub]

Looks like hdf5 isn't installed? You can try to pip install, but this will be the serial version.

Sorry,when I type pip install hdf5,an error just occured: btw,I have installed h5py,but it doesn't work to fix the bug.

[bknight1]

Try:

pip install h5py

[julesghub]

@bknight1 is right, petsc wasn't compiled against your hdf5.

@guit-hub How are you installing petsc?

When configuring petsc, if you're compiling it, you need something like --with-hdf5-dir=/your/path/to/hdf5 to refer to a previously install hdf5 installation or --download-hdf5=1 to make petsc download and install a compatible hdf5 automatically.

[guit-hub]

@bknight1 is right, petsc wasn't compiled against your hdf5.

@guit-hub How are you installing petsc?

When configuring petsc, if you're compiling it, you need something like --with-hdf5-dir=/your/path/to/hdf5 to refer to a previously install hdf5 installation or --download-hdf5=1 to make petsc download and install a compatible hdf5 automatically.

Thanks for both of your answers,but I think I've compiled PETSc against hdf5-1.14.4.3,

maybe this version doesn't work or maybe I should run the installation again

[knepley]

Post your $PETSC_DIR/configure.log which will show exactly what was configured. You cannot get that error message if PETSc was successfully configured with HDF5.