[petsc-users] VecLoad from HDF5 file
Thibault Bridel-Bertomeu
thibault.bridelbertomeu at gmail.com
Thu Apr 8 06:20:20 CDT 2021
Well ... I cleaned everything and did a fresh compile just now with
"print*, "foo"" here and there and it does print foo on the terminal ...
So yes, I am running the changed code ! ;)
call DMCreateGlobalVector(dm, sol, ierr); CHKERRA(ierr)
call VecZeroEntries(sol, ierr); CHKERRA(ierr)
call PetscObjectSetName(sol, "Solution", ierr); CHKERRA(ierr)
print*, "foo"
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, restartiter, ierr);
CHKERRA(ierr)
call PetscViewerHDF5PushGroup(hdf5Viewer, "/fields", ierr); CHKERRA(ierr)
call VecLoad(sol, hdf5Viewer, ierr); CHKERRA(ierr)
call PetscViewerDestroy(hdf5Viewer, ierr); CHKERRA(ierr)
In the snippet, restartiter is an integer equal to 20.
I agree with you the line you just sent me should fix the issue. Maybe it's
a fortran stub problem, I'll double check the stubs.
Thanks !
Thibault
Le jeu. 8 avr. 2021 à 13:11, Matthew Knepley <knepley at gmail.com> a écrit :
> 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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