On Mon, Dec 6, 2021 at 11:28 AM Quentin Chevalier < quentin.cheval...@polytechnique.edu> wrote:
> Hello PETSc users, > > This email is a duplicata of this gitlab issue > <https://gitlab.com/petsc/petsc/-/issues/1070>, sorry for any > inconvenience caused. > > I want to compute a PETSc vector in real mode, than perform calculations > with it in complex mode. I want as much of this process to be parallel as > possible. Right now, I compile PETSc in real mode, compute my vector and > save it to a file, then switch to complex mode, read it, and move on. > > This creates unexpected behaviour using MPIIO, so on Lisandro Dalcinl's > advice I'm moving to HDF5 format. My code is as follows (taking inspiration > from petsc4py doc > <https://www.mcs.anl.gov/petsc/petsc4py-current/docs/apiref/petsc4py.PETSc.Viewer-class.html#section-NestedClasses>, > a bitbucket example > <https://bitbucket.org/petsc/petsc4py/issues/70/difficulties-in-reading-from-hdf5-file> > and another one > <https://bitbucket.org/petsc/petsc4py/pull-requests/51/add-save-in-hdf5-format-demo>, > all top Google results for 'petsc hdf5') : > >> viewer = PETSc.Viewer().createHDF5(file_name, 'r', >> COMM_WORLD)q.load(viewer)q.ghostUpdate(addv=PETSc.InsertMode.INSERT, >> mode=PETSc.ScatterMode.FORWARD) >> >> > This crashes my code. I obtain traceback : > >> File "/home/shared/code.py", line 121, in Load viewer = >> PETSc.Viewer().createHDF5(file_name, 'r', COMM_WORLD) File >> "PETSc/Viewer.pyx", line 182, in >> petsc4py.PETSc.Viewer.createHDF5petsc4py.PETSc.Error: error code 86[0] >> PetscViewerSetType() at >> /usr/local/petsc/src/sys/classes/viewer/interface/viewreg.c:442[0] Unknown >> type. Check for miss-spelling or missing package: >> https://petsc.org/release/install/install/#external-packages[0] Unknown >> PetscViewer type given: hdf5 >> >> This means that PETSc has not been configured with HDF5 (--with-hdf5 or --download-hdf5), so the container should be updated. THanks, Matt > I have petsc4py 3.16 from this docker container > <https://hub.docker.com/r/dolfinx/dolfinx> (list of dependencies > <https://docs.fenicsproject.org/dolfinx/main/python/installation.html#dependencies> > include PETSc and petsc4py). > > I'm pretty sure this is not intended behaviour. Any insight as to how to > fix this issue (I tried running ./configure --with-hdf5 to no avail) or > more generally to perform this jiggling between real and complex would be > much appreciated, > > Kind regards. > > Quentin > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>