[petsc-users] VecLoad from HDF5 file
Thibault Bridel-Bertomeu
thibault.bridelbertomeu at gmail.com
Thu Apr 8 06:22:23 CDT 2021
Doesn't seem to be a Fortran stub problem, it's automatically generated and
looks good to me ...
Le jeu. 8 avr. 2021 à 13:20, Thibault Bridel-Bertomeu <
thibault.bridelbertomeu at gmail.com> a écrit :
> 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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