[petsc-users] VecLoad from HDF5 file
Thibault Bridel-Bertomeu
thibault.bridelbertomeu at gmail.com
Thu Apr 8 03:07:59 CDT 2021
Hi everyone,
Thank you for your answers.
Unfortunately, it does not work yet.
1/ I first tried just adding
call PetscViewerHDF5SetTimestep(hdf5Viewer, 20, ierr); CHKERRA(ierr)
(the latest iteration in the *.hdf5 is iter 20) before the VecLoad, i.e.:
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 PetscViewerHDF5SetTimestep(hdf5Viewer, 20, ierr); CHKERRA(ierr)
call PetscViewerHDF5PushGroup(hdf5Viewer, "/fields", ierr); CHKERRA(ierr)
call VecLoad(sol, hdf5Viewer, ierr); CHKERRA(ierr)
call PetscViewerDestroy(hdf5Viewer, ierr); CHKERRA(ierr)
but it does not change anything, the error is exactly the same as before
(with or without the PushGroup by the way).
2/ I then tried adding
call PetscViewerHDF5SetTimestep(hdf5Viewer, -1, ierr); CHKERRA(ierr)
before the VecView to "prevent blocking with timesteps" as the doc says (
https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Viewer/PetscViewerHDF5SetTimestep.html#PetscViewerHDF5SetTimestep),
i.e. :
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 PetscViewerHDF5SetTimestep(hdf5Viewer, -1, ierr); CHKERRA(ierr)
call VecView(X, hdf5Viewer, ierr); CHKERRA(ierr)
call PetscViewerDestroy(hdf5Viewer, ierr); CHKERRA(ierr)
but the hdf5 files keep increasing in size and each one stores more data
than the previous one ... can I not disable that "stacking" effect and just
keep the iteration I want ?
3/ I tried adding
call PetscViewerHDF5SetTimestep(hdf5Viewer, stepnum, ierr); CHKERRA(ierr)
before the VecView to try and just keep one iteration in the file, i.e. :
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 PetscViewerHDF5SetTimestep(hdf5Viewer, stepnum, ierr); CHKERRA(ierr)
call VecView(X, hdf5Viewer, ierr); CHKERRA(ierr)
call PetscViewerDestroy(hdf5Viewer, ierr); CHKERRA(ierr)
but it has no effect whatsoever on the hdf5 files that are written ... they
still store several timesteps, and then I cannot VecLoad what I want, i
still get the same error.
Any more idea ? I keep reading the doc on the HDF5 viewer and thinking that
this or that function could solve the issue but either it has zero effect
or does not solve the issue ...
Thanks !!!
Thibault
Le jeu. 8 avr. 2021 à 02:42, Barry Smith <bsmith at petsc.dev> a écrit :
>
> Matt,
>
> Is there anyway to provide this "extra meta-data" inside the generated
> HDF file? Then when a fresh viewer opens the file it uses this meta-data to
> know that the file contains "time-steps" and allows processing of them? The
> simplest thing would be to have the viewer generate an error if the file
> has time-steps but the user does not "request a (or more) time-steps"
> instead of getting confused about the vector sizes.
>
> Barry
>
>
>
> On Apr 7, 2021, at 6:32 PM, Matthew Knepley <knepley at gmail.com> wrote:
>
> 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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