[petsc-users] VecLoad from HDF5 file
Matthew Knepley
knepley at gmail.com
Thu Apr 8 06:25:21 CDT 2021
Do you have a self-contained thing I could run? This should be easy to
clear up in the debugger.
Thanks,
Matt
On Thu, Apr 8, 2021 at 7:22 AM Thibault Bridel-Bertomeu <
thibault.bridelbertomeu at gmail.com> wrote:
> 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/>
>>>
>>
--
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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