Created
June 17, 2026 09:52
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(partial) EasyBuild log for failed build of /dev/shm/eb-2sqdx5fd/files_pr25224/g/G-ADOPT/G-ADOPT-4.1.0-foss-2025b.eb (PR(s) #25224)
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| [0]PETSC ERROR: /apps/Test/software/Python-bundle-PyPI/2025.07-GCCcore-14.3.0/bin/pytest with 1 MPI process(es) and PETSC_ARCH on vera-r08-07 by c3-builder Wed Jun 17 11:49:06 2026 | |
| [0]PETSC ERROR: Configure options: --prefix=/apps/Test/software/PETSc/3.24.0-foss-2025b --LIBS="-lm -lpthread -lrt" --with-mpi4py=0 --with-cc=mpicc --with-cxx=mpicxx --with-c++-support --with-fc=mpifort --COPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --CXXOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC -DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX" --FOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --with-mpi=1 --with-build-step-np=8 --with-shared-libraries=1 --with-debugging=0 --with-pic=1 --with-x=0 --with-windows-graphics=0 --with-numpy=1 --with-fftw=1 --with-fftw-lib="[/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/lib/libfftw3_mpi.a,libfftw3.a]" --with-fftw-include=/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/include --with-scalapack=1 --with-scalapack-lib="[/apps/Test/software/ScaLAPACK/2.2.2-gompi-2025b-fb/lib/libscalapack.a,libflexiblas.a,libgfortran.a]" --with-blaslapack-lib="[/apps/Test/software/FlexiBLAS/3.4.5-GCC-14.3.0/lib/libflexiblas.a,libgfortran.a]" --with-boost=1 --with-boost-dir=/apps/Test/software/Boost/1.88.0-GCC-14.3.0 --with-mumps=1 --with-mumps-dir=/apps/Test/software/MUMPS/5.8.1-foss-2025b-metis --with-python=1 --with-python-dir=/apps/Test/software/Python/3.13.5-GCCcore-14.3.0 --with-zlib=1 --with-zlib-dir=/apps/Test/software/zlib/1.3.1-GCCcore-14.3.0 --with-metis=1 --with-metis-dir=/apps/Test/software/METIS/5.1.0-GCCcore-14.3.0 --with-superlu_dist=1 --with-superlu_dist-dir=/apps/Test/software/SuperLU_DIST/9.1.0-foss-2025b --with-parmetis=1 --with-parmetis-dir=/apps/Test/software/ParMETIS/4.0.3-gompi-2025b --with-pnetcdf=1 --with-pnetcdf-dir=/apps/Test/software/PnetCDF/1.14.1-gompi-2025b --with-hypre=1 --with-hypre-dir=/apps/Test/software/Hypre/2.33.0-foss-2025b --with-hdf5=1 --with-hdf5-dir=/apps/Test/software/HDF5/1.14.6-gompi-2025b --with-hwloc=1 --with-hwloc-dir=/apps/Test/software/hwloc/2.12.1-GCCcore-14.3.0 --with-netcdf=1 --with-netcdf-dir=/apps/Test/software/netCDF/4.9.3-gompi-2025b --with-ptscotch=1 --with-ptscotch-include="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/include]" --with-ptscotch-lib="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotchparmetisv3.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotcherr.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotcherr.a]" --with-suitesparse=1 --with-suitesparse-include="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/include]" --with-suitesparse-lib="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libumfpack.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libklu.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspqr.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcholmod.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libbtf.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libccolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcxsparse.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libldl.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/librbio.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspex.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libamd.so]" | |
| [0]PETSC ERROR: #1 PetscViewerHDF5GetGroup() at src/lib-petsc/compat/hdf5.h:14 | |
| [0]PETSC ERROR: #2 PetscViewerHDF5HasAttribute() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/sys/classes/viewer/impls/hdf5/hdf5v.c:1599 | |
| [0]PETSC ERROR: #3 PetscViewerHDF5GetDMPlexStorageVersionWriting() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:242 | |
| [0]PETSC ERROR: #4 DMPlexTopologyView_HDF5_Internal() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:1046 | |
| [0]PETSC ERROR: #5 DMPlexTopologyView() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/plex.c:2162 | |
| _____________________________________________________________________________ test_recover_from_checkpoint[SquareMesh-2-args3] _____________________________________________________________________________ | |
| mesh_name = 'SquareMesh', ndim = 2, args = (20, 20, 10) | |
| @pytest.mark.parametrize("mesh_name,ndim,args", fd_supported_meshes) | |
| def test_recover_from_checkpoint(mesh_name, ndim, args): | |
| mesh_creator = getattr(fd, mesh_name) | |
| mesh_w = mesh_creator(*args) | |
| with tempfile.NamedTemporaryFile() as fp: | |
| cf = fd.CheckpointFile(fp.name, "w") | |
| > cf.save_mesh(mesh_w) | |
| test_boundary_detection.py:62: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:629: in save_mesh | |
| self._save_mesh_topology(tmesh) | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:747: in _save_mesh_topology | |
| topology_dm.topologyView(viewer=self.viewer) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| > ??? | |
| E petsc4py.PETSc.Error: error code 56 | |
| petsc4py/PETSc/DMPlex.pyx:3213: Error | |
| ------------------------------------------------------------------------------------------- Captured stderr call ------------------------------------------------------------------------------------------- | |
| [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- | |
| [0]PETSC ERROR: It appears a new error in the code was triggered after a previous error, possibly because: | |
| [0]PETSC ERROR: - The first error was not properly handled via (for example) the use of | |
| [0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or | |
| [0]PETSC ERROR: - The second error was triggered while handling the first error. | |
| [0]PETSC ERROR: Above is the traceback for the previous unhandled error, below the traceback for the next error | |
| [0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add the appropriate error checking to the code | |
| [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_view_hdf5_storage_version value: 3.0.0 source: code | |
| [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. | |
| [0]PETSC ERROR: PETSc Release Version 3.24.0, Sep 29, 2025 | |
| [0]PETSC ERROR: /apps/Test/software/Python-bundle-PyPI/2025.07-GCCcore-14.3.0/bin/pytest with 1 MPI process(es) and PETSC_ARCH on vera-r08-07 by c3-builder Wed Jun 17 11:49:06 2026 | |
| [0]PETSC ERROR: Configure options: --prefix=/apps/Test/software/PETSc/3.24.0-foss-2025b --LIBS="-lm -lpthread -lrt" --with-mpi4py=0 --with-cc=mpicc --with-cxx=mpicxx --with-c++-support --with-fc=mpifort --COPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --CXXOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC -DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX" --FOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --with-mpi=1 --with-build-step-np=8 --with-shared-libraries=1 --with-debugging=0 --with-pic=1 --with-x=0 --with-windows-graphics=0 --with-numpy=1 --with-fftw=1 --with-fftw-lib="[/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/lib/libfftw3_mpi.a,libfftw3.a]" --with-fftw-include=/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/include --with-scalapack=1 --with-scalapack-lib="[/apps/Test/software/ScaLAPACK/2.2.2-gompi-2025b-fb/lib/libscalapack.a,libflexiblas.a,libgfortran.a]" --with-blaslapack-lib="[/apps/Test/software/FlexiBLAS/3.4.5-GCC-14.3.0/lib/libflexiblas.a,libgfortran.a]" --with-boost=1 --with-boost-dir=/apps/Test/software/Boost/1.88.0-GCC-14.3.0 --with-mumps=1 --with-mumps-dir=/apps/Test/software/MUMPS/5.8.1-foss-2025b-metis --with-python=1 --with-python-dir=/apps/Test/software/Python/3.13.5-GCCcore-14.3.0 --with-zlib=1 --with-zlib-dir=/apps/Test/software/zlib/1.3.1-GCCcore-14.3.0 --with-metis=1 --with-metis-dir=/apps/Test/software/METIS/5.1.0-GCCcore-14.3.0 --with-superlu_dist=1 --with-superlu_dist-dir=/apps/Test/software/SuperLU_DIST/9.1.0-foss-2025b --with-parmetis=1 --with-parmetis-dir=/apps/Test/software/ParMETIS/4.0.3-gompi-2025b --with-pnetcdf=1 --with-pnetcdf-dir=/apps/Test/software/PnetCDF/1.14.1-gompi-2025b --with-hypre=1 --with-hypre-dir=/apps/Test/software/Hypre/2.33.0-foss-2025b --with-hdf5=1 --with-hdf5-dir=/apps/Test/software/HDF5/1.14.6-gompi-2025b --with-hwloc=1 --with-hwloc-dir=/apps/Test/software/hwloc/2.12.1-GCCcore-14.3.0 --with-netcdf=1 --with-netcdf-dir=/apps/Test/software/netCDF/4.9.3-gompi-2025b --with-ptscotch=1 --with-ptscotch-include="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/include]" --with-ptscotch-lib="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotchparmetisv3.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotcherr.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotcherr.a]" --with-suitesparse=1 --with-suitesparse-include="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/include]" --with-suitesparse-lib="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libumfpack.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libklu.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspqr.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcholmod.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libbtf.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libccolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcxsparse.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libldl.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/librbio.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspex.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libamd.so]" | |
| [0]PETSC ERROR: #1 PetscViewerHDF5GetGroup() at src/lib-petsc/compat/hdf5.h:14 | |
| [0]PETSC ERROR: #2 PetscViewerHDF5HasAttribute() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/sys/classes/viewer/impls/hdf5/hdf5v.c:1599 | |
| [0]PETSC ERROR: #3 PetscViewerHDF5GetDMPlexStorageVersionWriting() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:242 | |
| [0]PETSC ERROR: #4 DMPlexTopologyView_HDF5_Internal() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:1046 | |
| [0]PETSC ERROR: #5 DMPlexTopologyView() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/plex.c:2162 | |
| ___________________________________________________________________________ test_recover_from_checkpoint[UnitSquareMesh-2-args4] ___________________________________________________________________________ | |
| mesh_name = 'UnitSquareMesh', ndim = 2, args = (20, 20) | |
| @pytest.mark.parametrize("mesh_name,ndim,args", fd_supported_meshes) | |
| def test_recover_from_checkpoint(mesh_name, ndim, args): | |
| mesh_creator = getattr(fd, mesh_name) | |
| mesh_w = mesh_creator(*args) | |
| with tempfile.NamedTemporaryFile() as fp: | |
| cf = fd.CheckpointFile(fp.name, "w") | |
| > cf.save_mesh(mesh_w) | |
| test_boundary_detection.py:62: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:629: in save_mesh | |
| self._save_mesh_topology(tmesh) | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:747: in _save_mesh_topology | |
| topology_dm.topologyView(viewer=self.viewer) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| > ??? | |
| E petsc4py.PETSc.Error: error code 56 | |
| petsc4py/PETSc/DMPlex.pyx:3213: Error | |
| ------------------------------------------------------------------------------------------- Captured stderr call ------------------------------------------------------------------------------------------- | |
| [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- | |
| [0]PETSC ERROR: It appears a new error in the code was triggered after a previous error, possibly because: | |
| [0]PETSC ERROR: - The first error was not properly handled via (for example) the use of | |
| [0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or | |
| [0]PETSC ERROR: - The second error was triggered while handling the first error. | |
| [0]PETSC ERROR: Above is the traceback for the previous unhandled error, below the traceback for the next error | |
| [0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add the appropriate error checking to the code | |
| [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_view_hdf5_storage_version value: 3.0.0 source: code | |
| [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. | |
| [0]PETSC ERROR: PETSc Release Version 3.24.0, Sep 29, 2025 | |
| [0]PETSC ERROR: /apps/Test/software/Python-bundle-PyPI/2025.07-GCCcore-14.3.0/bin/pytest with 1 MPI process(es) and PETSC_ARCH on vera-r08-07 by c3-builder Wed Jun 17 11:49:06 2026 | |
| [0]PETSC ERROR: Configure options: --prefix=/apps/Test/software/PETSc/3.24.0-foss-2025b --LIBS="-lm -lpthread -lrt" --with-mpi4py=0 --with-cc=mpicc --with-cxx=mpicxx --with-c++-support --with-fc=mpifort --COPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --CXXOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC -DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX" --FOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --with-mpi=1 --with-build-step-np=8 --with-shared-libraries=1 --with-debugging=0 --with-pic=1 --with-x=0 --with-windows-graphics=0 --with-numpy=1 --with-fftw=1 --with-fftw-lib="[/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/lib/libfftw3_mpi.a,libfftw3.a]" --with-fftw-include=/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/include --with-scalapack=1 --with-scalapack-lib="[/apps/Test/software/ScaLAPACK/2.2.2-gompi-2025b-fb/lib/libscalapack.a,libflexiblas.a,libgfortran.a]" --with-blaslapack-lib="[/apps/Test/software/FlexiBLAS/3.4.5-GCC-14.3.0/lib/libflexiblas.a,libgfortran.a]" --with-boost=1 --with-boost-dir=/apps/Test/software/Boost/1.88.0-GCC-14.3.0 --with-mumps=1 --with-mumps-dir=/apps/Test/software/MUMPS/5.8.1-foss-2025b-metis --with-python=1 --with-python-dir=/apps/Test/software/Python/3.13.5-GCCcore-14.3.0 --with-zlib=1 --with-zlib-dir=/apps/Test/software/zlib/1.3.1-GCCcore-14.3.0 --with-metis=1 --with-metis-dir=/apps/Test/software/METIS/5.1.0-GCCcore-14.3.0 --with-superlu_dist=1 --with-superlu_dist-dir=/apps/Test/software/SuperLU_DIST/9.1.0-foss-2025b --with-parmetis=1 --with-parmetis-dir=/apps/Test/software/ParMETIS/4.0.3-gompi-2025b --with-pnetcdf=1 --with-pnetcdf-dir=/apps/Test/software/PnetCDF/1.14.1-gompi-2025b --with-hypre=1 --with-hypre-dir=/apps/Test/software/Hypre/2.33.0-foss-2025b --with-hdf5=1 --with-hdf5-dir=/apps/Test/software/HDF5/1.14.6-gompi-2025b --with-hwloc=1 --with-hwloc-dir=/apps/Test/software/hwloc/2.12.1-GCCcore-14.3.0 --with-netcdf=1 --with-netcdf-dir=/apps/Test/software/netCDF/4.9.3-gompi-2025b --with-ptscotch=1 --with-ptscotch-include="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/include]" --with-ptscotch-lib="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotchparmetisv3.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotcherr.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotcherr.a]" --with-suitesparse=1 --with-suitesparse-include="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/include]" --with-suitesparse-lib="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libumfpack.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libklu.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspqr.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcholmod.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libbtf.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libccolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcxsparse.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libldl.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/librbio.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspex.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libamd.so]" | |
| [0]PETSC ERROR: #1 PetscViewerHDF5GetGroup() at src/lib-petsc/compat/hdf5.h:14 | |
| [0]PETSC ERROR: #2 PetscViewerHDF5HasAttribute() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/sys/classes/viewer/impls/hdf5/hdf5v.c:1599 | |
| [0]PETSC ERROR: #3 PetscViewerHDF5GetDMPlexStorageVersionWriting() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:242 | |
| [0]PETSC ERROR: #4 DMPlexTopologyView_HDF5_Internal() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:1046 | |
| [0]PETSC ERROR: #5 DMPlexTopologyView() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/plex.c:2162 | |
| ______________________________________________________________________________ test_recover_from_checkpoint[BoxMesh-3-args5] _______________________________________________________________________________ | |
| mesh_name = 'BoxMesh', ndim = 3, args = (5, 10, 15, 5, 10, 15) | |
| @pytest.mark.parametrize("mesh_name,ndim,args", fd_supported_meshes) | |
| def test_recover_from_checkpoint(mesh_name, ndim, args): | |
| mesh_creator = getattr(fd, mesh_name) | |
| mesh_w = mesh_creator(*args) | |
| with tempfile.NamedTemporaryFile() as fp: | |
| cf = fd.CheckpointFile(fp.name, "w") | |
| > cf.save_mesh(mesh_w) | |
| test_boundary_detection.py:62: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:629: in save_mesh | |
| self._save_mesh_topology(tmesh) | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:747: in _save_mesh_topology | |
| topology_dm.topologyView(viewer=self.viewer) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| > ??? | |
| E petsc4py.PETSc.Error: error code 56 | |
| petsc4py/PETSc/DMPlex.pyx:3213: Error | |
| ------------------------------------------------------------------------------------------- Captured stderr call ------------------------------------------------------------------------------------------- | |
| [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- | |
| [0]PETSC ERROR: It appears a new error in the code was triggered after a previous error, possibly because: | |
| [0]PETSC ERROR: - The first error was not properly handled via (for example) the use of | |
| [0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or | |
| [0]PETSC ERROR: - The second error was triggered while handling the first error. | |
| [0]PETSC ERROR: Above is the traceback for the previous unhandled error, below the traceback for the next error | |
| [0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add the appropriate error checking to the code | |
| [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_view_hdf5_storage_version value: 3.0.0 source: code | |
| [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. | |
| [0]PETSC ERROR: PETSc Release Version 3.24.0, Sep 29, 2025 | |
| [0]PETSC ERROR: /apps/Test/software/Python-bundle-PyPI/2025.07-GCCcore-14.3.0/bin/pytest with 1 MPI process(es) and PETSC_ARCH on vera-r08-07 by c3-builder Wed Jun 17 11:49:06 2026 | |
| [0]PETSC ERROR: Configure options: --prefix=/apps/Test/software/PETSc/3.24.0-foss-2025b --LIBS="-lm -lpthread -lrt" --with-mpi4py=0 --with-cc=mpicc --with-cxx=mpicxx --with-c++-support --with-fc=mpifort --COPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --CXXOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC -DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX" --FOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --with-mpi=1 --with-build-step-np=8 --with-shared-libraries=1 --with-debugging=0 --with-pic=1 --with-x=0 --with-windows-graphics=0 --with-numpy=1 --with-fftw=1 --with-fftw-lib="[/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/lib/libfftw3_mpi.a,libfftw3.a]" --with-fftw-include=/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/include --with-scalapack=1 --with-scalapack-lib="[/apps/Test/software/ScaLAPACK/2.2.2-gompi-2025b-fb/lib/libscalapack.a,libflexiblas.a,libgfortran.a]" --with-blaslapack-lib="[/apps/Test/software/FlexiBLAS/3.4.5-GCC-14.3.0/lib/libflexiblas.a,libgfortran.a]" --with-boost=1 --with-boost-dir=/apps/Test/software/Boost/1.88.0-GCC-14.3.0 --with-mumps=1 --with-mumps-dir=/apps/Test/software/MUMPS/5.8.1-foss-2025b-metis --with-python=1 --with-python-dir=/apps/Test/software/Python/3.13.5-GCCcore-14.3.0 --with-zlib=1 --with-zlib-dir=/apps/Test/software/zlib/1.3.1-GCCcore-14.3.0 --with-metis=1 --with-metis-dir=/apps/Test/software/METIS/5.1.0-GCCcore-14.3.0 --with-superlu_dist=1 --with-superlu_dist-dir=/apps/Test/software/SuperLU_DIST/9.1.0-foss-2025b --with-parmetis=1 --with-parmetis-dir=/apps/Test/software/ParMETIS/4.0.3-gompi-2025b --with-pnetcdf=1 --with-pnetcdf-dir=/apps/Test/software/PnetCDF/1.14.1-gompi-2025b --with-hypre=1 --with-hypre-dir=/apps/Test/software/Hypre/2.33.0-foss-2025b --with-hdf5=1 --with-hdf5-dir=/apps/Test/software/HDF5/1.14.6-gompi-2025b --with-hwloc=1 --with-hwloc-dir=/apps/Test/software/hwloc/2.12.1-GCCcore-14.3.0 --with-netcdf=1 --with-netcdf-dir=/apps/Test/software/netCDF/4.9.3-gompi-2025b --with-ptscotch=1 --with-ptscotch-include="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/include]" --with-ptscotch-lib="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotchparmetisv3.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotcherr.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotcherr.a]" --with-suitesparse=1 --with-suitesparse-include="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/include]" --with-suitesparse-lib="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libumfpack.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libklu.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspqr.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcholmod.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libbtf.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libccolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcxsparse.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libldl.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/librbio.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspex.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libamd.so]" | |
| [0]PETSC ERROR: #1 PetscViewerHDF5GetGroup() at src/lib-petsc/compat/hdf5.h:14 | |
| [0]PETSC ERROR: #2 PetscViewerHDF5HasAttribute() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/sys/classes/viewer/impls/hdf5/hdf5v.c:1599 | |
| [0]PETSC ERROR: #3 PetscViewerHDF5GetDMPlexStorageVersionWriting() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:242 | |
| [0]PETSC ERROR: #4 DMPlexTopologyView_HDF5_Internal() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:1046 | |
| [0]PETSC ERROR: #5 DMPlexTopologyView() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/plex.c:2162 | |
| ______________________________________________________________________________ test_recover_from_checkpoint[CubeMesh-3-args6] ______________________________________________________________________________ | |
| mesh_name = 'CubeMesh', ndim = 3, args = (10, 10, 10, 10) | |
| @pytest.mark.parametrize("mesh_name,ndim,args", fd_supported_meshes) | |
| def test_recover_from_checkpoint(mesh_name, ndim, args): | |
| mesh_creator = getattr(fd, mesh_name) | |
| mesh_w = mesh_creator(*args) | |
| with tempfile.NamedTemporaryFile() as fp: | |
| cf = fd.CheckpointFile(fp.name, "w") | |
| > cf.save_mesh(mesh_w) | |
| test_boundary_detection.py:62: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:629: in save_mesh | |
| self._save_mesh_topology(tmesh) | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:747: in _save_mesh_topology | |
| topology_dm.topologyView(viewer=self.viewer) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| > ??? | |
| E petsc4py.PETSc.Error: error code 56 | |
| petsc4py/PETSc/DMPlex.pyx:3213: Error | |
| ------------------------------------------------------------------------------------------- Captured stderr call ------------------------------------------------------------------------------------------- | |
| [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- | |
| [0]PETSC ERROR: It appears a new error in the code was triggered after a previous error, possibly because: | |
| [0]PETSC ERROR: - The first error was not properly handled via (for example) the use of | |
| [0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or | |
| [0]PETSC ERROR: - The second error was triggered while handling the first error. | |
| [0]PETSC ERROR: Above is the traceback for the previous unhandled error, below the traceback for the next error | |
| [0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add the appropriate error checking to the code | |
| [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_view_hdf5_storage_version value: 3.0.0 source: code | |
| [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. | |
| [0]PETSC ERROR: PETSc Release Version 3.24.0, Sep 29, 2025 | |
| [0]PETSC ERROR: /apps/Test/software/Python-bundle-PyPI/2025.07-GCCcore-14.3.0/bin/pytest with 1 MPI process(es) and PETSC_ARCH on vera-r08-07 by c3-builder Wed Jun 17 11:49:06 2026 | |
| [0]PETSC ERROR: Configure options: --prefix=/apps/Test/software/PETSc/3.24.0-foss-2025b --LIBS="-lm -lpthread -lrt" --with-mpi4py=0 --with-cc=mpicc --with-cxx=mpicxx --with-c++-support --with-fc=mpifort --COPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --CXXOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC -DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX" --FOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --with-mpi=1 --with-build-step-np=8 --with-shared-libraries=1 --with-debugging=0 --with-pic=1 --with-x=0 --with-windows-graphics=0 --with-numpy=1 --with-fftw=1 --with-fftw-lib="[/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/lib/libfftw3_mpi.a,libfftw3.a]" --with-fftw-include=/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/include --with-scalapack=1 --with-scalapack-lib="[/apps/Test/software/ScaLAPACK/2.2.2-gompi-2025b-fb/lib/libscalapack.a,libflexiblas.a,libgfortran.a]" --with-blaslapack-lib="[/apps/Test/software/FlexiBLAS/3.4.5-GCC-14.3.0/lib/libflexiblas.a,libgfortran.a]" --with-boost=1 --with-boost-dir=/apps/Test/software/Boost/1.88.0-GCC-14.3.0 --with-mumps=1 --with-mumps-dir=/apps/Test/software/MUMPS/5.8.1-foss-2025b-metis --with-python=1 --with-python-dir=/apps/Test/software/Python/3.13.5-GCCcore-14.3.0 --with-zlib=1 --with-zlib-dir=/apps/Test/software/zlib/1.3.1-GCCcore-14.3.0 --with-metis=1 --with-metis-dir=/apps/Test/software/METIS/5.1.0-GCCcore-14.3.0 --with-superlu_dist=1 --with-superlu_dist-dir=/apps/Test/software/SuperLU_DIST/9.1.0-foss-2025b --with-parmetis=1 --with-parmetis-dir=/apps/Test/software/ParMETIS/4.0.3-gompi-2025b --with-pnetcdf=1 --with-pnetcdf-dir=/apps/Test/software/PnetCDF/1.14.1-gompi-2025b --with-hypre=1 --with-hypre-dir=/apps/Test/software/Hypre/2.33.0-foss-2025b --with-hdf5=1 --with-hdf5-dir=/apps/Test/software/HDF5/1.14.6-gompi-2025b --with-hwloc=1 --with-hwloc-dir=/apps/Test/software/hwloc/2.12.1-GCCcore-14.3.0 --with-netcdf=1 --with-netcdf-dir=/apps/Test/software/netCDF/4.9.3-gompi-2025b --with-ptscotch=1 --with-ptscotch-include="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/include]" --with-ptscotch-lib="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotchparmetisv3.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotcherr.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotcherr.a]" --with-suitesparse=1 --with-suitesparse-include="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/include]" --with-suitesparse-lib="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libumfpack.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libklu.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspqr.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcholmod.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libbtf.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libccolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcxsparse.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libldl.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/librbio.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspex.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libamd.so]" | |
| [0]PETSC ERROR: #1 PetscViewerHDF5GetGroup() at src/lib-petsc/compat/hdf5.h:14 | |
| [0]PETSC ERROR: #2 PetscViewerHDF5HasAttribute() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/sys/classes/viewer/impls/hdf5/hdf5v.c:1599 | |
| [0]PETSC ERROR: #3 PetscViewerHDF5GetDMPlexStorageVersionWriting() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:242 | |
| [0]PETSC ERROR: #4 DMPlexTopologyView_HDF5_Internal() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:1046 | |
| [0]PETSC ERROR: #5 DMPlexTopologyView() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/plex.c:2162 | |
| ____________________________________________________________________________ test_recover_from_checkpoint[UnitCubeMesh-3-args7] ____________________________________________________________________________ | |
| mesh_name = 'UnitCubeMesh', ndim = 3, args = (10, 10, 10) | |
| @pytest.mark.parametrize("mesh_name,ndim,args", fd_supported_meshes) | |
| def test_recover_from_checkpoint(mesh_name, ndim, args): | |
| mesh_creator = getattr(fd, mesh_name) | |
| mesh_w = mesh_creator(*args) | |
| with tempfile.NamedTemporaryFile() as fp: | |
| cf = fd.CheckpointFile(fp.name, "w") | |
| > cf.save_mesh(mesh_w) | |
| test_boundary_detection.py:62: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:629: in save_mesh | |
| self._save_mesh_topology(tmesh) | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:747: in _save_mesh_topology | |
| topology_dm.topologyView(viewer=self.viewer) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| > ??? | |
| E petsc4py.PETSc.Error: error code 56 | |
| petsc4py/PETSc/DMPlex.pyx:3213: Error | |
| ------------------------------------------------------------------------------------------- Captured stderr call ------------------------------------------------------------------------------------------- | |
| [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- | |
| [0]PETSC ERROR: It appears a new error in the code was triggered after a previous error, possibly because: | |
| [0]PETSC ERROR: - The first error was not properly handled via (for example) the use of | |
| [0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or | |
| [0]PETSC ERROR: - The second error was triggered while handling the first error. | |
| [0]PETSC ERROR: Above is the traceback for the previous unhandled error, below the traceback for the next error | |
| [0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add the appropriate error checking to the code | |
| [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_view_hdf5_storage_version value: 3.0.0 source: code | |
| [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. | |
| [0]PETSC ERROR: PETSc Release Version 3.24.0, Sep 29, 2025 | |
| [0]PETSC ERROR: /apps/Test/software/Python-bundle-PyPI/2025.07-GCCcore-14.3.0/bin/pytest with 1 MPI process(es) and PETSC_ARCH on vera-r08-07 by c3-builder Wed Jun 17 11:49:06 2026 | |
| [0]PETSC ERROR: Configure options: --prefix=/apps/Test/software/PETSc/3.24.0-foss-2025b --LIBS="-lm -lpthread -lrt" --with-mpi4py=0 --with-cc=mpicc --with-cxx=mpicxx --with-c++-support --with-fc=mpifort --COPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --CXXOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC -DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX" --FOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --with-mpi=1 --with-build-step-np=8 --with-shared-libraries=1 --with-debugging=0 --with-pic=1 --with-x=0 --with-windows-graphics=0 --with-numpy=1 --with-fftw=1 --with-fftw-lib="[/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/lib/libfftw3_mpi.a,libfftw3.a]" --with-fftw-include=/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/include --with-scalapack=1 --with-scalapack-lib="[/apps/Test/software/ScaLAPACK/2.2.2-gompi-2025b-fb/lib/libscalapack.a,libflexiblas.a,libgfortran.a]" --with-blaslapack-lib="[/apps/Test/software/FlexiBLAS/3.4.5-GCC-14.3.0/lib/libflexiblas.a,libgfortran.a]" --with-boost=1 --with-boost-dir=/apps/Test/software/Boost/1.88.0-GCC-14.3.0 --with-mumps=1 --with-mumps-dir=/apps/Test/software/MUMPS/5.8.1-foss-2025b-metis --with-python=1 --with-python-dir=/apps/Test/software/Python/3.13.5-GCCcore-14.3.0 --with-zlib=1 --with-zlib-dir=/apps/Test/software/zlib/1.3.1-GCCcore-14.3.0 --with-metis=1 --with-metis-dir=/apps/Test/software/METIS/5.1.0-GCCcore-14.3.0 --with-superlu_dist=1 --with-superlu_dist-dir=/apps/Test/software/SuperLU_DIST/9.1.0-foss-2025b --with-parmetis=1 --with-parmetis-dir=/apps/Test/software/ParMETIS/4.0.3-gompi-2025b --with-pnetcdf=1 --with-pnetcdf-dir=/apps/Test/software/PnetCDF/1.14.1-gompi-2025b --with-hypre=1 --with-hypre-dir=/apps/Test/software/Hypre/2.33.0-foss-2025b --with-hdf5=1 --with-hdf5-dir=/apps/Test/software/HDF5/1.14.6-gompi-2025b --with-hwloc=1 --with-hwloc-dir=/apps/Test/software/hwloc/2.12.1-GCCcore-14.3.0 --with-netcdf=1 --with-netcdf-dir=/apps/Test/software/netCDF/4.9.3-gompi-2025b --with-ptscotch=1 --with-ptscotch-include="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/include]" --with-ptscotch-lib="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotchparmetisv3.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotcherr.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotcherr.a]" --with-suitesparse=1 --with-suitesparse-include="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/include]" --with-suitesparse-lib="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libumfpack.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libklu.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspqr.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcholmod.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libbtf.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libccolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcxsparse.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libldl.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/librbio.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspex.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libamd.so]" | |
| [0]PETSC ERROR: #1 PetscViewerHDF5GetGroup() at src/lib-petsc/compat/hdf5.h:14 | |
| [0]PETSC ERROR: #2 PetscViewerHDF5HasAttribute() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/sys/classes/viewer/impls/hdf5/hdf5v.c:1599 | |
| [0]PETSC ERROR: #3 PetscViewerHDF5GetDMPlexStorageVersionWriting() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:242 | |
| [0]PETSC ERROR: #4 DMPlexTopologyView_HDF5_Internal() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:1046 | |
| [0]PETSC ERROR: #5 DMPlexTopologyView() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/plex.c:2162 | |
| _________________________________________________________________________ test_recover_from_checkpoint[CircleManifoldMesh-0-args8] _________________________________________________________________________ | |
| mesh_name = 'CircleManifoldMesh', ndim = 0, args = (50,) | |
| @pytest.mark.parametrize("mesh_name,ndim,args", fd_supported_meshes) | |
| def test_recover_from_checkpoint(mesh_name, ndim, args): | |
| mesh_creator = getattr(fd, mesh_name) | |
| mesh_w = mesh_creator(*args) | |
| with tempfile.NamedTemporaryFile() as fp: | |
| cf = fd.CheckpointFile(fp.name, "w") | |
| > cf.save_mesh(mesh_w) | |
| test_boundary_detection.py:62: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:629: in save_mesh | |
| self._save_mesh_topology(tmesh) | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:747: in _save_mesh_topology | |
| topology_dm.topologyView(viewer=self.viewer) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| > ??? | |
| E petsc4py.PETSc.Error: error code 56 | |
| petsc4py/PETSc/DMPlex.pyx:3213: Error | |
| ------------------------------------------------------------------------------------------- Captured stderr call ------------------------------------------------------------------------------------------- | |
| [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- | |
| [0]PETSC ERROR: It appears a new error in the code was triggered after a previous error, possibly because: | |
| [0]PETSC ERROR: - The first error was not properly handled via (for example) the use of | |
| [0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or | |
| [0]PETSC ERROR: - The second error was triggered while handling the first error. | |
| [0]PETSC ERROR: Above is the traceback for the previous unhandled error, below the traceback for the next error | |
| [0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add the appropriate error checking to the code | |
| [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_view_hdf5_storage_version value: 3.0.0 source: code | |
| [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. | |
| [0]PETSC ERROR: PETSc Release Version 3.24.0, Sep 29, 2025 | |
| [0]PETSC ERROR: /apps/Test/software/Python-bundle-PyPI/2025.07-GCCcore-14.3.0/bin/pytest with 1 MPI process(es) and PETSC_ARCH on vera-r08-07 by c3-builder Wed Jun 17 11:49:06 2026 | |
| [0]PETSC ERROR: Configure options: --prefix=/apps/Test/software/PETSc/3.24.0-foss-2025b --LIBS="-lm -lpthread -lrt" --with-mpi4py=0 --with-cc=mpicc --with-cxx=mpicxx --with-c++-support --with-fc=mpifort --COPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --CXXOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC -DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX" --FOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --with-mpi=1 --with-build-step-np=8 --with-shared-libraries=1 --with-debugging=0 --with-pic=1 --with-x=0 --with-windows-graphics=0 --with-numpy=1 --with-fftw=1 --with-fftw-lib="[/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/lib/libfftw3_mpi.a,libfftw3.a]" --with-fftw-include=/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/include --with-scalapack=1 --with-scalapack-lib="[/apps/Test/software/ScaLAPACK/2.2.2-gompi-2025b-fb/lib/libscalapack.a,libflexiblas.a,libgfortran.a]" --with-blaslapack-lib="[/apps/Test/software/FlexiBLAS/3.4.5-GCC-14.3.0/lib/libflexiblas.a,libgfortran.a]" --with-boost=1 --with-boost-dir=/apps/Test/software/Boost/1.88.0-GCC-14.3.0 --with-mumps=1 --with-mumps-dir=/apps/Test/software/MUMPS/5.8.1-foss-2025b-metis --with-python=1 --with-python-dir=/apps/Test/software/Python/3.13.5-GCCcore-14.3.0 --with-zlib=1 --with-zlib-dir=/apps/Test/software/zlib/1.3.1-GCCcore-14.3.0 --with-metis=1 --with-metis-dir=/apps/Test/software/METIS/5.1.0-GCCcore-14.3.0 --with-superlu_dist=1 --with-superlu_dist-dir=/apps/Test/software/SuperLU_DIST/9.1.0-foss-2025b --with-parmetis=1 --with-parmetis-dir=/apps/Test/software/ParMETIS/4.0.3-gompi-2025b --with-pnetcdf=1 --with-pnetcdf-dir=/apps/Test/software/PnetCDF/1.14.1-gompi-2025b --with-hypre=1 --with-hypre-dir=/apps/Test/software/Hypre/2.33.0-foss-2025b --with-hdf5=1 --with-hdf5-dir=/apps/Test/software/HDF5/1.14.6-gompi-2025b --with-hwloc=1 --with-hwloc-dir=/apps/Test/software/hwloc/2.12.1-GCCcore-14.3.0 --with-netcdf=1 --with-netcdf-dir=/apps/Test/software/netCDF/4.9.3-gompi-2025b --with-ptscotch=1 --with-ptscotch-include="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/include]" --with-ptscotch-lib="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotchparmetisv3.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotcherr.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotcherr.a]" --with-suitesparse=1 --with-suitesparse-include="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/include]" --with-suitesparse-lib="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libumfpack.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libklu.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspqr.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcholmod.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libbtf.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libccolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcxsparse.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libldl.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/librbio.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspex.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libamd.so]" | |
| [0]PETSC ERROR: #1 PetscViewerHDF5GetGroup() at src/lib-petsc/compat/hdf5.h:14 | |
| [0]PETSC ERROR: #2 PetscViewerHDF5HasAttribute() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/sys/classes/viewer/impls/hdf5/hdf5v.c:1599 | |
| [0]PETSC ERROR: #3 PetscViewerHDF5GetDMPlexStorageVersionWriting() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:242 | |
| [0]PETSC ERROR: #4 DMPlexTopologyView_HDF5_Internal() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:1046 | |
| [0]PETSC ERROR: #5 DMPlexTopologyView() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/plex.c:2162 | |
| __________________________________________________________________________ test_recover_from_checkpoint[CubedSphereMesh-0-args9] ___________________________________________________________________________ | |
| mesh_name = 'CubedSphereMesh', ndim = 0, args = (20, 2, 2) | |
| @pytest.mark.parametrize("mesh_name,ndim,args", fd_supported_meshes) | |
| def test_recover_from_checkpoint(mesh_name, ndim, args): | |
| mesh_creator = getattr(fd, mesh_name) | |
| mesh_w = mesh_creator(*args) | |
| with tempfile.NamedTemporaryFile() as fp: | |
| cf = fd.CheckpointFile(fp.name, "w") | |
| > cf.save_mesh(mesh_w) | |
| test_boundary_detection.py:62: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:629: in save_mesh | |
| self._save_mesh_topology(tmesh) | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:747: in _save_mesh_topology | |
| topology_dm.topologyView(viewer=self.viewer) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| > ??? | |
| E petsc4py.PETSc.Error: error code 56 | |
| petsc4py/PETSc/DMPlex.pyx:3213: Error | |
| ------------------------------------------------------------------------------------------- Captured stderr call ------------------------------------------------------------------------------------------- | |
| [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- | |
| [0]PETSC ERROR: It appears a new error in the code was triggered after a previous error, possibly because: | |
| [0]PETSC ERROR: - The first error was not properly handled via (for example) the use of | |
| [0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or | |
| [0]PETSC ERROR: - The second error was triggered while handling the first error. | |
| [0]PETSC ERROR: Above is the traceback for the previous unhandled error, below the traceback for the next error | |
| [0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add the appropriate error checking to the code | |
| [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_view_hdf5_storage_version value: 3.0.0 source: code | |
| [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. | |
| [0]PETSC ERROR: PETSc Release Version 3.24.0, Sep 29, 2025 | |
| [0]PETSC ERROR: /apps/Test/software/Python-bundle-PyPI/2025.07-GCCcore-14.3.0/bin/pytest with 1 MPI process(es) and PETSC_ARCH on vera-r08-07 by c3-builder Wed Jun 17 11:49:06 2026 | |
| [0]PETSC ERROR: Configure options: --prefix=/apps/Test/software/PETSc/3.24.0-foss-2025b --LIBS="-lm -lpthread -lrt" --with-mpi4py=0 --with-cc=mpicc --with-cxx=mpicxx --with-c++-support --with-fc=mpifort --COPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --CXXOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC -DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX" --FOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --with-mpi=1 --with-build-step-np=8 --with-shared-libraries=1 --with-debugging=0 --with-pic=1 --with-x=0 --with-windows-graphics=0 --with-numpy=1 --with-fftw=1 --with-fftw-lib="[/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/lib/libfftw3_mpi.a,libfftw3.a]" --with-fftw-include=/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/include --with-scalapack=1 --with-scalapack-lib="[/apps/Test/software/ScaLAPACK/2.2.2-gompi-2025b-fb/lib/libscalapack.a,libflexiblas.a,libgfortran.a]" --with-blaslapack-lib="[/apps/Test/software/FlexiBLAS/3.4.5-GCC-14.3.0/lib/libflexiblas.a,libgfortran.a]" --with-boost=1 --with-boost-dir=/apps/Test/software/Boost/1.88.0-GCC-14.3.0 --with-mumps=1 --with-mumps-dir=/apps/Test/software/MUMPS/5.8.1-foss-2025b-metis --with-python=1 --with-python-dir=/apps/Test/software/Python/3.13.5-GCCcore-14.3.0 --with-zlib=1 --with-zlib-dir=/apps/Test/software/zlib/1.3.1-GCCcore-14.3.0 --with-metis=1 --with-metis-dir=/apps/Test/software/METIS/5.1.0-GCCcore-14.3.0 --with-superlu_dist=1 --with-superlu_dist-dir=/apps/Test/software/SuperLU_DIST/9.1.0-foss-2025b --with-parmetis=1 --with-parmetis-dir=/apps/Test/software/ParMETIS/4.0.3-gompi-2025b --with-pnetcdf=1 --with-pnetcdf-dir=/apps/Test/software/PnetCDF/1.14.1-gompi-2025b --with-hypre=1 --with-hypre-dir=/apps/Test/software/Hypre/2.33.0-foss-2025b --with-hdf5=1 --with-hdf5-dir=/apps/Test/software/HDF5/1.14.6-gompi-2025b --with-hwloc=1 --with-hwloc-dir=/apps/Test/software/hwloc/2.12.1-GCCcore-14.3.0 --with-netcdf=1 --with-netcdf-dir=/apps/Test/software/netCDF/4.9.3-gompi-2025b --with-ptscotch=1 --with-ptscotch-include="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/include]" --with-ptscotch-lib="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotchparmetisv3.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotcherr.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotcherr.a]" --with-suitesparse=1 --with-suitesparse-include="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/include]" --with-suitesparse-lib="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libumfpack.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libklu.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspqr.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcholmod.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libbtf.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libccolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcxsparse.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libldl.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/librbio.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspex.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libamd.so]" | |
| [0]PETSC ERROR: #1 PetscViewerHDF5GetGroup() at src/lib-petsc/compat/hdf5.h:14 | |
| [0]PETSC ERROR: #2 PetscViewerHDF5HasAttribute() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/sys/classes/viewer/impls/hdf5/hdf5v.c:1599 | |
| [0]PETSC ERROR: #3 PetscViewerHDF5GetDMPlexStorageVersionWriting() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:242 | |
| [0]PETSC ERROR: #4 DMPlexTopologyView_HDF5_Internal() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:1046 | |
| [0]PETSC ERROR: #5 DMPlexTopologyView() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/plex.c:2162 | |
| ________________________________________________________________________ test_recover_from_checkpoint[UnitCubedSphereMesh-0-args10] ________________________________________________________________________ | |
| mesh_name = 'UnitCubedSphereMesh', ndim = 0, args = (2, 2) | |
| @pytest.mark.parametrize("mesh_name,ndim,args", fd_supported_meshes) | |
| def test_recover_from_checkpoint(mesh_name, ndim, args): | |
| mesh_creator = getattr(fd, mesh_name) | |
| mesh_w = mesh_creator(*args) | |
| with tempfile.NamedTemporaryFile() as fp: | |
| cf = fd.CheckpointFile(fp.name, "w") | |
| > cf.save_mesh(mesh_w) | |
| test_boundary_detection.py:62: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:629: in save_mesh | |
| self._save_mesh_topology(tmesh) | |
| petsc4py/PETSc/Log.pyx:250: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| petsc4py/PETSc/Log.pyx:251: in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func | |
| ??? | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/firedrake/checkpointing.py:747: in _save_mesh_topology | |
| topology_dm.topologyView(viewer=self.viewer) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| > ??? | |
| E petsc4py.PETSc.Error: error code 56 | |
| petsc4py/PETSc/DMPlex.pyx:3213: Error | |
| ------------------------------------------------------------------------------------------- Captured stderr call ------------------------------------------------------------------------------------------- | |
| [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- | |
| [0]PETSC ERROR: It appears a new error in the code was triggered after a previous error, possibly because: | |
| [0]PETSC ERROR: - The first error was not properly handled via (for example) the use of | |
| [0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or | |
| [0]PETSC ERROR: - The second error was triggered while handling the first error. | |
| [0]PETSC ERROR: Above is the traceback for the previous unhandled error, below the traceback for the next error | |
| [0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add the appropriate error checking to the code | |
| [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_view_hdf5_storage_version value: 3.0.0 source: code | |
| [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. | |
| [0]PETSC ERROR: PETSc Release Version 3.24.0, Sep 29, 2025 | |
| [0]PETSC ERROR: /apps/Test/software/Python-bundle-PyPI/2025.07-GCCcore-14.3.0/bin/pytest with 1 MPI process(es) and PETSC_ARCH on vera-r08-07 by c3-builder Wed Jun 17 11:49:06 2026 | |
| [0]PETSC ERROR: Configure options: --prefix=/apps/Test/software/PETSc/3.24.0-foss-2025b --LIBS="-lm -lpthread -lrt" --with-mpi4py=0 --with-cc=mpicc --with-cxx=mpicxx --with-c++-support --with-fc=mpifort --COPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --CXXOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC -DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX" --FOPTFLAGS="-O2 -ftree-vectorize -fopenmp -march=native -fno-math-errno -fPIC" --with-mpi=1 --with-build-step-np=8 --with-shared-libraries=1 --with-debugging=0 --with-pic=1 --with-x=0 --with-windows-graphics=0 --with-numpy=1 --with-fftw=1 --with-fftw-lib="[/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/lib/libfftw3_mpi.a,libfftw3.a]" --with-fftw-include=/apps/Test/software/FFTW.MPI/3.3.10-gompi-2025b/include --with-scalapack=1 --with-scalapack-lib="[/apps/Test/software/ScaLAPACK/2.2.2-gompi-2025b-fb/lib/libscalapack.a,libflexiblas.a,libgfortran.a]" --with-blaslapack-lib="[/apps/Test/software/FlexiBLAS/3.4.5-GCC-14.3.0/lib/libflexiblas.a,libgfortran.a]" --with-boost=1 --with-boost-dir=/apps/Test/software/Boost/1.88.0-GCC-14.3.0 --with-mumps=1 --with-mumps-dir=/apps/Test/software/MUMPS/5.8.1-foss-2025b-metis --with-python=1 --with-python-dir=/apps/Test/software/Python/3.13.5-GCCcore-14.3.0 --with-zlib=1 --with-zlib-dir=/apps/Test/software/zlib/1.3.1-GCCcore-14.3.0 --with-metis=1 --with-metis-dir=/apps/Test/software/METIS/5.1.0-GCCcore-14.3.0 --with-superlu_dist=1 --with-superlu_dist-dir=/apps/Test/software/SuperLU_DIST/9.1.0-foss-2025b --with-parmetis=1 --with-parmetis-dir=/apps/Test/software/ParMETIS/4.0.3-gompi-2025b --with-pnetcdf=1 --with-pnetcdf-dir=/apps/Test/software/PnetCDF/1.14.1-gompi-2025b --with-hypre=1 --with-hypre-dir=/apps/Test/software/Hypre/2.33.0-foss-2025b --with-hdf5=1 --with-hdf5-dir=/apps/Test/software/HDF5/1.14.6-gompi-2025b --with-hwloc=1 --with-hwloc-dir=/apps/Test/software/hwloc/2.12.1-GCCcore-14.3.0 --with-netcdf=1 --with-netcdf-dir=/apps/Test/software/netCDF/4.9.3-gompi-2025b --with-ptscotch=1 --with-ptscotch-include="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/include]" --with-ptscotch-lib="[/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotchparmetisv3.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libptscotcherr.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libesmumps.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotch.a,/apps/Test/software/SCOTCH/7.0.10-gompi-2025b/lib/libscotcherr.a]" --with-suitesparse=1 --with-suitesparse-include="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/include]" --with-suitesparse-lib="[/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libumfpack.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libklu.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspqr.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcholmod.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libbtf.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libccolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcolamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcxsparse.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libldl.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/librbio.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libspex.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libcamd.so,/apps/Test/software/SuiteSparse/7.11.0-gfbf-2025b/lib/libamd.so]" | |
| [0]PETSC ERROR: #1 PetscViewerHDF5GetGroup() at src/lib-petsc/compat/hdf5.h:14 | |
| [0]PETSC ERROR: #2 PetscViewerHDF5HasAttribute() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/sys/classes/viewer/impls/hdf5/hdf5v.c:1599 | |
| [0]PETSC ERROR: #3 PetscViewerHDF5GetDMPlexStorageVersionWriting() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:242 | |
| [0]PETSC ERROR: #4 DMPlexTopologyView_HDF5_Internal() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/hdf5/plexhdf5.c:1046 | |
| [0]PETSC ERROR: #5 DMPlexTopologyView() at /dev/shm/PETSc/3.24.0/foss-2025b/petsc-3.24.0/src/dm/impls/plex/plex.c:2162 | |
| ============================================================================================= warnings summary ============================================================================================= | |
| tests/unit/test_continuity.py::test_continuity | |
| tests/unit/test_continuity.py::test_continuity | |
| tests/unit/test_limiters.py::test_slope_limiters | |
| tests/unit/test_limiters.py::test_slope_limiters | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/finat/ufl/elementlist.py:427: UserWarning: Discontinuous Lagrange element requested on quadrilateral, creating DQ element. | |
| warnings.warn("Discontinuous Lagrange element requested on %s, creating DQ element." % cell.cellname()) | |
| tests/unit/test_continuity.py::test_continuity | |
| tests/unit/test_continuity.py::test_continuity | |
| tests/unit/test_limiters.py::test_slope_limiters | |
| tests/unit/test_limiters.py::test_slope_limiters | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/finat/ufl/elementlist.py:427: UserWarning: Discontinuous Lagrange element requested on interval * interval, creating DQ element. | |
| warnings.warn("Discontinuous Lagrange element requested on %s, creating DQ element." % cell.cellname()) | |
| tests/unit/test_gplates.py::test_gplates | |
| /dev/shm/eb-2sqdx5fd/tmpujfbz_3l/lib/python3.13/site-packages/gadopt/gplates/gplates.py:411: RuntimeWarning: pygplates couldn't assign plate IDs to some seeds due to irregularities in the reconstruction model. G-ADOPT will interpolate the nearest values. | |
| warnings.warn("pygplates couldn't assign plate IDs to some seeds due to irregularities in the reconstruction model. G-ADOPT will interpolate the nearest values.", category=RuntimeWarning) | |
| tests/unit/test_limiters.py: 16 warnings | |
| /apps/Test/software/Firedrake/2025.10.2-foss-2025b/lib/python3.13/site-packages/pyop2/types/glob.py:283: UserWarning: PyOP2.Global has no comm, this is likely to break in parallel! | |
| warnings.warn("PyOP2.Global has no comm, this is likely to break in parallel!") | |
| -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html | |
| ========================================================================================= short test summary info ========================================================================================== | |
| FAILED test_boundary_detection.py::test_recover_from_checkpoint[IntervalMesh-1-args0] - petsc4py.PETSc.Error: error code 56 | |
| FAILED test_boundary_detection.py::test_recover_from_checkpoint[UnitIntervalMesh-1-args1] - petsc4py.PETSc.Error: error code 56 | |
| FAILED test_boundary_detection.py::test_recover_from_checkpoint[RectangleMesh-2-args2] - petsc4py.PETSc.Error: error code 56 | |
| FAILED test_boundary_detection.py::test_recover_from_checkpoint[SquareMesh-2-args3] - petsc4py.PETSc.Error: error code 56 | |
| FAILED test_boundary_detection.py::test_recover_from_checkpoint[UnitSquareMesh-2-args4] - petsc4py.PETSc.Error: error code 56 | |
| FAILED test_boundary_detection.py::test_recover_from_checkpoint[BoxMesh-3-args5] - petsc4py.PETSc.Error: error code 56 | |
| FAILED test_boundary_detection.py::test_recover_from_checkpoint[CubeMesh-3-args6] - petsc4py.PETSc.Error: error code 56 | |
| FAILED test_boundary_detection.py::test_recover_from_checkpoint[UnitCubeMesh-3-args7] - petsc4py.PETSc.Error: error code 56 | |
| FAILED test_boundary_detection.py::test_recover_from_checkpoint[CircleManifoldMesh-0-args8] - petsc4py.PETSc.Error: error code 56 | |
| FAILED test_boundary_detection.py::test_recover_from_checkpoint[CubedSphereMesh-0-args9] - petsc4py.PETSc.Error: error code 56 | |
| FAILED test_boundary_detection.py::test_recover_from_checkpoint[UnitCubedSphereMesh-0-args10] - petsc4py.PETSc.Error: error code 56 | |
| ========================================================================== 11 failed, 27 passed, 25 warnings in 197.21s (0:03:17) ========================================================================== | |
| == 2026-06-17 11:52:24,100 easyblock.py:3127 WARNING shell command 'export PYTHONPATH=/dev/shm/eb-2sqdx5fd/tmpujfbz_3l/lib/python3.13/site-packages:$PYTHONPATH && export PATH=/dev/shm/eb-2sqdx5fd/tmpujfbz_3l/bin:$PATH && export EBPYTHONPREFIXES=/dev/shm/eb-2sqdx5fd/tmpujfbz_3l:$EBPYTHONPREFIXES && export OMP_NUM_THREADS=1 && cd /dev/shm/GADOPT/4.1.0/foss-2025b/gadopt/gadopt-4.1.0/demos/mantle_convection/gplates_global && wget https://data.gadopt.org/github-actions/Muller_etal_2022_SE_1Ga_Opt_PlateMotionModel_v1.2.zip && unzip Muller_etal_2022_SE_1Ga_Opt_PlateMotionModel_v1.2.zip && cd /dev/shm/GADOPT/4.1.0/foss-2025b/gadopt/gadopt-4.1.0/tests/unit && pytest && cd - && make -C /dev/shm/GADOPT/4.1.0/foss-2025b/gadopt/gadopt-4.1.0/demos/mantle_convection/base_case check' failed in test step for G-ADOPT-4.1.0-foss-2025b.eb | |
| == 2026-06-17 11:52:24,104 build_log.py:233 ERROR EasyBuild encountered an error: shell command 'export ...' failed in test step for G-ADOPT-4.1.0-foss-2025b.eb (at easybuild/framework/easyblock.py:2624 in report_test_failure) | |
| Callstack: | |
| easybuild/framework/easyblock.py:2624 in report_test_failure | |
| easybuild/framework/easyblock.py:3128 in _test_step | |
| easybuild/easyblocks/generic/pythonpackage.py:1176 in install_extension | |
| easybuild/framework/extension.py:311 in install_extension_substep | |
| easybuild/framework/easyblock.py:2205 in install_extensions_sequential | |
| easybuild/framework/easyblock.py:2156 in install_all_extensions | |
| easybuild/framework/easyblock.py:3276 in extensions_step | |
| easybuild/easyblocks/generic/pythonbundle.py:116 in extensions_step | |
| easybuild/framework/easyblock.py:4830 in run_step | |
| easybuild/framework/easyblock.py:4989 in run_all_steps | |
| easybuild/framework/easyblock.py:5177 in build_and_install_one | |
| easybuild/main.py:184 in build_and_install_software | |
| easybuild/main.py:630 in process_eb_args | |
| easybuild/main.py:814 in main | |
| easybuild/main.py:872 in main_with_hooks | |
| easybuild/main.py:891 in <module> | |
| == 2026-06-17 11:52:24,105 build_log.py:330 INFO ... (took 3 mins 49 secs) | |
| == 2026-06-17 11:52:24,109 run.py:526 INFO Running '/usr/share/lmod/lmod/libexec/lmod ...' command in /dev/shm/GADOPT/4.1.0/foss-2025b/gadopt/gadopt-4.1.0: | |
| /usr/share/lmod/lmod/libexec/lmod python unload G-ADOPT/4.1.0-foss-2025b | |
| == 2026-06-17 11:52:26,035 run.py:642 INFO '/usr/share/lmod/lmod/libexec/lmod ...' command completed successfully | |
| == 2026-06-17 11:52:26,051 filetools.py:421 INFO Path /dev/shm/eb-2sqdx5fd/tmpphcn9r6l successfully removed. | |
| == 2026-06-17 11:52:26,051 easyblock.py:1971 INFO Restoring environment after unloading fake module | |
| == 2026-06-17 11:52:26,062 build_log.py:330 INFO ... (took 13 mins 19 secs) | |
| == 2026-06-17 11:52:26,065 filetools.py:2150 INFO Removing lock /apps/Test/software/.locks/_apps_Test_software_G-ADOPT_4.1.0-foss-2025b.lock... | |
| == 2026-06-17 11:52:26,070 filetools.py:421 INFO Path /apps/Test/software/.locks/_apps_Test_software_G-ADOPT_4.1.0-foss-2025b.lock successfully removed. | |
| == 2026-06-17 11:52:26,070 filetools.py:2154 INFO Lock removed: /apps/Test/software/.locks/_apps_Test_software_G-ADOPT_4.1.0-foss-2025b.lock | |
| == 2026-06-17 11:52:26,070 easyblock.py:400 INFO Closing log for application name G-ADOPT version 4.1.0 |
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