[petsc-users] VecLoad from HDF5 file
Matthew Knepley
knepley at gmail.com
Thu Apr 8 06:11:19 CDT 2021
On Thu, Apr 8, 2021 at 4:08 AM Thibault Bridel-Bertomeu <
thibault.bridelbertomeu at gmail.com> wrote:
> 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).
>
This is the one I do not believe. If the Viewer has a non-negative
timestep, it will increase the length index:
https://gitlab.com/petsc/petsc/-/blob/main/src/vec/is/utils/hdf5io.c#L78
and we can see all the sizes in your HDF5 file. Are you sure you are
running the one with the changed code?
Thanks,
Matt
>
> 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/>
>>
>>
>>
--
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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