[petsc-users] VecLoad from HDF5 file
Thibault Bridel-Bertomeu
thibault.bridelbertomeu at gmail.com
Thu Apr 8 08:00:29 CDT 2021
Hello everyone,
So i figured it out, and I got a work-around, but it's not pretty and I
think there might be a nicer solution that you guys will see.
Here is the stack of calls for the VecLoad of a vector generated via a
DMPlex :
CALLING PETSCVIEWERHDF5SETTIMESTEP FROM FORTRAN
TOTOTOTOTO :::>>> IN PETSCVIEWERHDF5SETTIMESTEP. <hdf5v.c>
TOTOTOTOTO :::>>> HDF5->TIMESTEP = 20. <hdf5v.c>
CALLING VECLOAD FROM FORTRAN
TOTOTOTOTO :::>>> INSIDE VECLOAD <vector.c>
TOTOTOTOTO :::>>> FORMAT = PETSC_VIEWER_RAW. <vector.c>
TOTOTOTOTO :::>>> IN VECLOAD_PLEX. <plex.c>
TOTOTOTOTO :::>>> IN VECLOAD_PLEX_HDF5_INTERNAL <plexhdf5.c>
TOTOTOTOTO :::>>> IN PETSCVIEWERHDF5SETTIMESTEP. <hdf5v.c>
TOTOTOTOTO :::>>> HDF5->TIMESTEP = 20. <hdf5v.c>
TOTOTOTOTO :::>>> IN VECLOAD_DEFAULT. <vecio.c>
TOTOTOTOTO :::>>> IN VECLOAD_HDF5 <vecio.c>.
TOTOTOTOTO :::>>> IN PETSCVIEWERHDF5LOAD. <hdf5io.c>
TOTOTOTOTO :::>>> IN PETSCVIEWERHDF5READINITIALIZE_PRIVATE. <hdf5io.c>
TOTOTOTOTO :::>>> TIMESTEP = 20. <hdf5io.c>
TOTOTOTOTO :::>>> LENIND = 1, TIMESTEP = 20. <hdf5io.c>
Not everything is there, I just stopped at line 78 of hdf5io.c as Matt
suggested.
The thing is, you can call
call PetscViewerHDF5SetTimestep(hdf5Viewer, restartiter, ierr);
CHKERRA(ierr)
all you want before calling
call VecLoad(sol, hdf5Viewer, ierr); CHKERRA(ierr)
it won't have any effect.
The timestep that is set by the ..SetTimestep routine is overriden inside
the
VecLoad_Plex_HDF5_Internal
routine because of these lines :
ierr = DMGetOutputSequenceNumber(dm, &seqnum, NULL);CHKERRQ(ierr);
ierr = PetscViewerHDF5SetTimestep(viewer, seqnum);CHKERRQ(ierr);
Since my point is to "restart" a computation from such a HDF5 file, when i
read the file the DMPlex is brand new and has no idea what happened during
another run of the program --> the "seqnum" is set to -1.
As a consequence, the viewer always sees its "timestep" variable as being
-1 even if you try forcing it with
call PetscViewerHDF5SetTimestep(hdf5Viewer, restartiter, ierr);
CHKERRA(ierr)
Anyways, one way to do it is then to add :
call DMSetOutputSequenceNumber(dm, restartiter, PETSC_NULL_REAL, ierr);
CHKERRA(ierr)
to the code, that thus becomes :
call DMSetOutputSequenceNumber(dm, restartiter, PETSC_NULL_REAL, ierr);
CHKERRA(ierr)
call PetscViewerHDF5Open(PETSC_COMM_WORLD, trim(restartname),
FILE_MODE_READ, hdf5Viewer, ierr); CHKERRA(ierr)
call PetscViewerHDF5PushGroup(hdf5Viewer, "/fields", ierr); CHKERRA(ierr)
call PetscViewerHDF5SetTimestep(hdf5Viewer, restartiter, ierr);
CHKERRA(ierr)
call VecLoad(sol, hdf5Viewer, ierr); CHKERRA(ierr)
call PetscViewerDestroy(hdf5Viewer, ierr); CHKERRA(ierr)
By the way, it even works if you remove the PushGroup(..., "/fields", ...)
because this is also forced in VecLoad_Plex_HDF5_Internal.
Might be a better idea would be to do a DMLoad, what do you think ?
Thanks !!
Thibault
Le jeu. 8 avr. 2021 à 13:35, Thibault Bridel-Bertomeu <
thibault.bridelbertomeu at gmail.com> a écrit :
> Argh no I don't, I implemented it straight in a larger CFD code because
> everything is already there for setting-up the DM, DS, PetscFV etc...
> Now that you guys gave me some more pointers I'll dig around with a
> debugger ..
>
> Thanks !
>
> Le jeu. 8 avr. 2021 à 13:25, Matthew Knepley <knepley at gmail.com> a écrit :
>
>> 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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