Hello Vaclav, Thank you for your quick answer !! OK so, if I need to push the group, I added :
call PetscViewerHDF5PushGroup(hdf5Viewer, "/fields", ierr); CHKERRA(ierr) right after the call to PetscViewerFileSetName. The result is the same, it produces the following error : *[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------* [0]PETSC ERROR: Unexpected data in file [0]PETSC ERROR: Global size of array in file is 105, not 25300 as expected [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Development GIT revision: v3.14.4-671-g707297fd510 GIT Date: 2021-02-24 22:50:05 +0000 [0]PETSC ERROR: ../../../bin/eulerian3D on a named macbook-pro-de-thibault.home by tbridel Wed Apr 7 22:05:14 2021 [0]PETSC ERROR: Configure options --with-clean=1 --prefix=/Users/tbridel/Documents/1-CODES/04-PETSC/build_uns3D --with-make-np=2 --with-windows-graphics=0 --with-debugging=0 --download-fblaslapack --download-mpich-shared=0 --with-x=0 --with-pthread=0 --with-valgrind=0 --PETSC_ARCH=macosx_uns3D --with-fc=/usr/local/bin/mpifort --with-cc=/usr/local/bin/mpicc --with-cxx=/usr/local/bin/mpic++ --with-openmp=0 --download-hypre=yes --download-sowing=yes --download-metis=yes --download-parmetis=yes --download-triangle=yes --download-tetgen=yes --download-ctetgen=yes --download-p4est=yes --download-zlib=yes --download-c2html=yes --download-eigen=yes --download-pragmatic=yes --with-hdf5-dir=/usr/local/opt/hdf5-mpi --with-cmake-dir=/usr/local/opt/cmake --with-libtoolize=/usr/local/bin/glibtoolize --with-autoreconf=/usr/local/bin/autoreconf [0]PETSC ERROR: #1 PetscViewerHDF5ReadSizes_Private() line 114 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/vec/is/utils/hdf5io.c [0]PETSC ERROR: #2 PetscViewerHDF5Load() line 208 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/vec/is/utils/hdf5io.c [0]PETSC ERROR: #3 VecLoad_HDF5() line 132 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/vec/vec/utils/vecio.c [0]PETSC ERROR: #4 VecLoad_Default() line 257 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/vec/vec/utils/vecio.c [0]PETSC ERROR: #5 VecLoad_Plex_Local() line 474 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/dm/impls/plex/plex.c [0]PETSC ERROR: #6 VecLoad_Plex_HDF5_Internal() line 295 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/dm/impls/plex/plexhdf5.c [0]PETSC ERROR: #7 VecLoad_Plex() line 496 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/dm/impls/plex/plex.c [0]PETSC ERROR: #8 VecLoad() line 953 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/vec/vec/interface/vector.c [0]PETSC ERROR: #9 User provided function() line 0 in User file Do you know where it could come from ? As for what I am doing exactly : i am using the DMPlex with a PetscFV to solve the fluid mechanics Euler equations in 3D. The PetscFV linked to the DS of the DMPlex might be why there is a /fields before the /Solution maybe .. ? Cheers and thank you again for your help !! Thibault Le mer. 7 avr. 2021 à 10:07, Hapla Vaclav <[email protected]> a écrit : > Dear Thibault > > On 7 Apr 2021, at 08:18, Thibault Bridel-Bertomeu < > [email protected]> wrote: > > Dear all, > > I have been facing a problem with VecLoad recently, even though it seems > to me I did exactly like in the examples/tutorials. > > Basically, a program writes a vector with the HDF5 writer like this : > > call DMCreateGlobalVector(dm, sol, ierr); > CHKERRA(ierr) call VecZeroEntries(X, ierr); > CHKERRA(ierr) call PetscObjectSetName(X, "Solution", ierr); > CHKERRA(ierr) > > < do something with X to fill it up with relevant data > > > call PetscViewerCreate(PETSC_COMM_WORLD, hdf5Viewer, ierr); > CHKERRA(ierr) call PetscViewerSetType(hdf5Viewer, > PETSCVIEWERHDF5, ierr); CHKERRA(ierr) call > PetscViewerFileSetMode(hdf5Viewer, FILE_MODE_WRITE, ierr); CHKERRA(ierr); > write(filename,'(A,I5.5,A)') "restart_", stepnum, ".h5" > call PetscViewerFileSetName(hdf5Viewer, trim(filename), ierr); > CHKERRA(ierr) call VecView(X, hdf5Viewer, ierr); CHKERRA(ierr) > call PetscViewerDestroy(hdf5Viewer, ierr); CHKERRA(ierr) > > and the same program (but with different start-up options, say) re-reads > such a file like this : > > call DMCreateGlobalVector(dm, sol, ierr); > CHKERRA(ierr) call VecZeroEntries(sol, ierr); > CHKERRA(ierr) call PetscObjectSetName(sol, "Solution", > ierr); CHKERRA(ierr) > call PetscViewerCreate(PETSC_COMM_WORLD, hdf5Viewer, ierr); > CHKERRA(ierr) call PetscViewerSetType(hdf5Viewer, > PETSCVIEWERHDF5, ierr); CHKERRA(ierr) call > PetscViewerFileSetMode(hdf5Viewer, FILE_MODE_READ, ierr); CHKERRA(ierr) > call PetscViewerFileSetName(hdf5Viewer, trim(restartname), ierr); > CHKERRA(ierr) call VecLoad(sol, hdf5Viewer, ierr); > CHKERRA(ierr) call PetscViewerDestroy(hdf5Viewer, ierr); > CHKERRA(ierr) > > > Such a dataset can be found under this link : > https://drive.google.com/file/d/1owLAx5vknNhj61_5ieAwnWOR9cmkTseL/view?usp=sharing > > > I'm just looking at the HDF5 file. The structure is like this > > > $PETSC_DIR/$PETSC_ARCH/bin/h5dump -H restart_00020.h5 > > HDF5 "restart_00020.h5" { > GROUP "/" { > GROUP "cell_fields" { > DATASET "Solution_FV solver" { > DATATYPE H5T_IEEE_F64LE > DATASPACE SIMPLE { ( 21, 3884, 5 ) / ( H5S_UNLIMITED, 3884, 5 ) } > ATTRIBUTE "vector_field_type" { > DATATYPE H5T_STRING { > STRSIZE 7; > STRPAD H5T_STR_NULLTERM; > CSET H5T_CSET_ASCII; > CTYPE H5T_C_S1; > } > DATASPACE SCALAR > } > } > } > GROUP "fields" { > DATASET "Solution" { > DATATYPE H5T_IEEE_F64LE > DATASPACE SIMPLE { ( 21, 5060, 5 ) / ( H5S_UNLIMITED, 5060, 5 ) } > } > } > DATASET "time" { > DATATYPE H5T_IEEE_F64LE > DATASPACE SIMPLE { ( 21, 1 ) / ( H5S_UNLIMITED, 1 ) } > } > } > } > > > I would like the reader to read the /fields/Solution group basically, but > I am not even sure it tries to do that. > Anyhow, I got an error, saying that the size found in the file (105) does > not match the expected size (25300). If I look at the shape of > /fields/Solution it is given as (21, 5030, 5). First, it is weird, cause > the 21 seems to be 1 + current iteration number ... but anyways we find the > 5 variables and the 5030 cells. Only the reader seems to do 21 * 5 when it > should be doing 5030 * 5 ... > I tried adding 'PetscViewerHDF5PushGroup(hdf5Viewer, "/fields/Solution", > ierr)' to force it to read that group, but it does not change anything. > > > You definitely need to push the group, unless it's the root group "/". > There is no way the reader would guess the correct group if it's not the > root one [and I don't think it would be a good idea to implement such > searching]. > > If you tried adding > PetscViewerHDF5PushGroup(hdf5Viewer, "/fields/Solution", ierr) > you likely pushed a wrong group. If the Vec name was set to "Solution" > like in your snippet [using PetscObjectSetName()], the absolute dataset > name to look up would be "/fields/Solution/Solution". > > But in your file, there's just a dataset "/fields/Solution", so its parent > group is just "/fields". So please try pushing this. > > I would gladly try to reproduce your case - perhaps the error handling > should be improved so that it would guide you into the right direction. But > it would be helpful to know exactly what you're doing - the snippet with > VecView() above should produce "/Solution" dataset but in the file you're > sending, there's "/fields/Solution". > > Note also you don't need to do VecZeroEntries() before loading because > VecLoad() fully rewrites the Vec data in memory anyway. > > > I would appreciate it if anyone could give me pointers on this issue ... > > Thank you very much in advance !! > > Thibault > > > Thanks, > Vaclav > >
