[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: GoddamitMfckr #1 PetscViewerHDF5GetGroup() at src/lib-petsc/compat/hdf5.h:14
  [0]PETSC ERROR: DMSwarm and the shadow space — is this implemented and is it what we need. #2 PetscViewerHDF5HasAttribute() at /opt/petsc/src/sys/classes/viewer/impls/hdf5/hdf5v.c:1527
  [0]PETSC ERROR: Get rotations happening for stokes dirichlet conditions #3 PetscViewerHDF5GetDMPlexStorageVersionWriting() at /opt/petsc/src/dm/impls/plex/plexhdf5.c:144
  [0]PETSC ERROR: Create & Populate a DMSwarm  #4 DMPlexCoordinatesView_HDF5_Internal() at /opt/petsc/src/dm/impls/plex/plexhdf5.c:1042
  [0]PETSC ERROR: Create dockerfile for development #5 DMPlexView_HDF5_Internal() at /opt/petsc/src/dm/impls/plex/plexhdf5.c:1300
  [0]PETSC ERROR: Upload JG DMSwarm advection snippet #6 DMView_Plex() at /opt/petsc/src/dm/impls/plex/plex.c:1941
  [0]PETSC ERROR: Mesh API object #7 DMView() at /opt/petsc/src/dm/interface/dm.c:1001
  [0]PETSC ERROR: Steady State Heat system object #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.