You need to ./configure PETSc for HDF5 using > --with-fortran-bindings=0 --with-mpi-dir=/usr --download-hdf5
It may need additional options, if it does then rerun the ./configure with the additional options it lists. > On Mar 12, 2024, at 8:19 PM, adigitoleo (Leon) <[email protected]> wrote: > > This Message Is From an External Sender > This message came from outside your organization. > Hello, > > I'm new to the list and have a limited knowledge of PETSc so far, but > I'm trying to use a software (underworld3) that relies on petsc4py. > I have built PETSc with the following configure options: > > --with-fortran-bindings=0 --with-mpi-dir=/usr > > and `make test` gives me 160 failures which all seem to be timeouts or > arising from my having insufficient "slots" (cores?). I subsequently > built underworld3 with something like > > cd $PETSC_DIR > PETSC_DIR=... PETSC_ARCH=... NUMPY_INCLUDE=... pip install > src/binding/petsc4py > cd /path/to/underworld3/tree > pip install h5py > pip install mpi4py > PETSC_DIR=... PETSC_ARCH=... NUMPY_INCLUDE=... pip install -e . > > following their instructions. Building their python wheel/package was > successful, however when I run their tests (using pytest) I get errors > during test collection, which all come from petsc4py and have a stack > trace that ends in the snippet attached below. Am I going about this > wrong? How do I ensure that the HDF5 types are defined? > > src/underworld3/discretisation.py:86: in _from_gmsh > viewer = PETSc.ViewerHDF5().create(filename + ".h5", "w", > comm=PETSc.COMM_SELF) > petsc4py/PETSc/Viewer.pyx:916: in petsc4py.PETSc.ViewerHDF5.create > ??? > E petsc4py.PETSc.Error: error code 86 > ------------------------------- Captured stderr > -------------------------------- > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Unknown type. Check for miss-spelling or missing package: > https://urldefense.us/v3/__https://petsc.org/release/install/install/*external-packages__;Iw!!G_uCfscf7eWS!duVp7PZwdvHgymCgufX290k3tptJCHEo3vrV7dNt9zumYwqzDVsb1AG1HHargxq0LL-1JO6mjgiS7Vbykb1_siyXWw$ > [0]PETSC ERROR: Unknown PetscViewer type given: hdf5 > [0]PETSC ERROR: See > https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!duVp7PZwdvHgymCgufX290k3tptJCHEo3vrV7dNt9zumYwqzDVsb1AG1HHargxq0LL-1JO6mjgiS7Vbykb1LEFOicQ$ > for trouble shooting. > [0]PETSC ERROR: Petsc Release Version 3.20.4, unknown > [0]PETSC ERROR: /home/leon/vcs/underworld3/.venv-underworld3/bin/pytest > on a arch-linux-c-debug named roci by leon Wed Mar 13 00:01:33 2024 > [0]PETSC ERROR: Configure options --with-fortran-bindings=0 > --with-mpi-dir=/usr > [0]PETSC ERROR: #1 PetscViewerSetType() at > /home/leon/vcs/petsc/src/sys/classes/viewer/interface/viewreg.c:535 > > Cheers, > Leon
