[petsc-users] VecLoad from HDF5 file
Matthew Knepley
knepley at gmail.com
Thu Apr 8 15:16:53 CDT 2021
On Thu, Apr 8, 2021 at 9:00 AM Thibault Bridel-Bertomeu <
thibault.bridelbertomeu at gmail.com> wrote:
> 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 ?
>
Okay, this is correct. I should have thought of this. If a Vec comes from a
DM, then the DM controls the I/O. We should be
more explicit about this in the documentation. From this decision flows the
decision to have the Solver (TS) communicate
with the DM instead of the Viewer.
Thus, if you want to load a certain output in the absence of a solver, you
too should communicate with it through the DM. I think
the problem here is lack of documentation rather than the choice. I will
think about where to document this. If you have a suggestion,
maybe where you looked first, it would be appreciated.
Thanks,
Matt
> 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/>
>>>
>>
--
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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