[petsc-users] VecLoad from HDF5 file
Matthew Knepley
knepley at gmail.com
Wed Apr 7 18:32:57 CDT 2021
On Wed, Apr 7, 2021 at 4:10 PM Thibault Bridel-Bertomeu <
thibault.bridelbertomeu at gmail.com> wrote:
> 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 ?
>
I think I understand this. PETSc tries to be clever to allow you to store
timesteps. It gives the HDF5 array an extra dimension. Somehow
the Viewer has to know this. The TS does this automatically, so you have an
array
GROUP "fields" {
DATASET "Solution" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 21, 5060, 5 ) / ( H5S_UNLIMITED, 5060, 5 ) }
}
}
which has 21 timesteps. However, when you create a brand new Viewer, it
does not know, and mistakenly thinks there is a single vector
of length 21 * 5 = 105. You can tell your reader which timestep you want to
extract using
https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Viewer/PetscViewerHDF5SetTimestep.html
Thanks,
Matt
> 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
>>
>>
--
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/>
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