[petsc-users] Swarm view HDF5

[Mark Adams]

On Thu, Jan 18, 2024 at 3:08 PM Matthew Knepley <knepley at gmail.com> wrote:

> On Thu, Jan 18, 2024 at 1:20 PM Mark Adams <mfadams at lbl.gov> wrote:
>
>> I had this working at one point.
>>
>> Should I add PetscViewerHDF5PushTimestepping?
>> I don't create a viewer now, but I could make one.
>>
>
> That will make it work. The real fix would be to check at swarm.c:45 to
> see whether timestepping is set.
>

Did you fix this? I do see PetscCall(PetscViewerHDF5SetTimestep(viewer,
seqnum)); at swarm.c:45

But, I still need to comment out the check to get this to work.

Thanks,
Mark


>   Thanks,
>
>     Matt
>
>
>> Thanks,
>> Mark
>>
>>
>> On Thu, Jan 18, 2024 at 11:26 AM Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> On Thu, Jan 18, 2024 at 10:08 AM Mark Adams <mfadams at lbl.gov> wrote:
>>>
>>>> I am trying to view a DMSwarm with: -weights_view hdf5:part.h5
>>>>
>>>>      Vec f;
>>>>       PetscCall(DMSetOutputSequenceNumber(sw, 0, 0.0));
>>>>       PetscCall(DMSwarmCreateGlobalVectorFromField(sw, "w_q", &f));
>>>>       PetscCall(PetscObjectSetName((PetscObject)f, "particle weights"));
>>>>       PetscCall(VecViewFromOptions(f, NULL, "-weights_view"));
>>>>       PetscCall(DMSwarmDestroyGlobalVectorFromField(sw, "w_q", &f));
>>>>
>>>> And I get this error. I had this working once and did not set
>>>> PetscViewerHDF5PushTimestepping, so I wanted to check.
>>>>
>>>
>>> We probably were not checking then. We might have to check there when we
>>> set the timestep.
>>>
>>>   Thanks,
>>>
>>>     Matt
>>>
>>>
>>>> Thanks,
>>>> Mark
>>>>
>>>>
>>>> [0]PETSC ERROR: Object is in wrong state
>>>> [0]PETSC ERROR: Timestepping has not been pushed yet. Call
>>>> PetscViewerHDF5PushTimestepping() first
>>>> [0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the
>>>> program crashed before usage or a spelling mistake, etc!
>>>> [0]PETSC ERROR:   Option left: name:-options_left (no value) source:
>>>> command line
>>>> [0]PETSC ERROR: See https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!cD7sluQj9NiJty0xU3K76VpLTY-Rrg5Yt76rcjqqqRBJrORnOfs8HUpFGI3GWx5NmacCoQMG4Rzh9rws_R_xRvs$  for trouble
>>>> shooting.
>>>> [0]PETSC ERROR: Petsc Development GIT revision:
>>>> v3.20.3-461-g585a01bd688  GIT Date: 2024-01-16 23:32:45 +0000
>>>> [0]PETSC ERROR: ./ex30k on a arch-macosx-gnu-O named MarksMac-302.local
>>>> by markadams Thu Jan 18 10:05:53 2024
>>>> [0]PETSC ERROR: Configure options CFLAGS="-g
>>>> -Wno-deprecated-declarations " CXXFLAGS="-g -Wno-deprecated-declarations "
>>>> COPTFLAGS=-O CXXOPTFLAGS=-O --with-cc=/usr/local/opt/llvm/bin/clang
>>>> --with-cxx=/usr/local/opt/llvm/bin/clang++ --download-mpich
>>>> --with-strict-petscerrorcode --download-triangle=1 --with-debugging=0
>>>> --download-hdf5=1 PETSC_ARCH=arch-macosx-gnu-O
>>>> [0]PETSC ERROR: #1 PetscViewerHDF5SetTimestep() at
>>>> /Users/markadams/Codes/petsc/src/sys/classes/viewer/impls/hdf5/hdf5v.c:990
>>>> [0]PETSC ERROR: #2 VecView_Swarm_HDF5_Internal() at
>>>> /Users/markadams/Codes/petsc/src/dm/impls/swarm/swarm.c:45
>>>> [0]PETSC ERROR: #3 VecView_Swarm() at
>>>> /Users/markadams/Codes/petsc/src/dm/impls/swarm/swarm.c:86
>>>> [0]PETSC ERROR: #4 VecView() at
>>>> /Users/markadams/Codes/petsc/src/vec/vec/interface/vector.c:806
>>>> [0]PETSC ERROR: #5 PetscObjectView() at
>>>> /Users/markadams/Codes/petsc/src/sys/objects/destroy.c:76
>>>> [0]PETSC ERROR: #6 PetscObjectViewFromOptions() at
>>>> /Users/markadams/Codes/petsc/src/sys/objects/destroy.c:128
>>>> [0]PETSC ERROR: #7 VecViewFromOptions() at
>>>> /Users/markadams/Codes/petsc/src/vec/vec/interface/vector.c:691
>>>>
>>>
>>>
>>> --
>>> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cD7sluQj9NiJty0xU3K76VpLTY-Rrg5Yt76rcjqqqRBJrORnOfs8HUpFGI3GWx5NmacCoQMG4Rzh9rwsjjsXQw0$ 
>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cD7sluQj9NiJty0xU3K76VpLTY-Rrg5Yt76rcjqqqRBJrORnOfs8HUpFGI3GWx5NmacCoQMG4Rzh9rws_GyIuzA$ >
>>>
>>
>
> --
> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cD7sluQj9NiJty0xU3K76VpLTY-Rrg5Yt76rcjqqqRBJrORnOfs8HUpFGI3GWx5NmacCoQMG4Rzh9rwsjjsXQw0$ 
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cD7sluQj9NiJty0xU3K76VpLTY-Rrg5Yt76rcjqqqRBJrORnOfs8HUpFGI3GWx5NmacCoQMG4Rzh9rws_GyIuzA$ >
>
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