[petsc-users] VecLoad from HDF5 file
Thibault Bridel-Bertomeu
thibault.bridelbertomeu at gmail.com
Wed Apr 7 15:09:47 CDT 2021
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 <vaclav.hapla at erdw.ethz.ch> a
écrit :
> Dear Thibault
>
> On 7 Apr 2021, at 08:18, Thibault Bridel-Bertomeu <
> thibault.bridelbertomeu at gmail.com> 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
>
>
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