Re: [petsc-users] Swarm view HDF5

2024-02-21 Thread Mark Adams 
On Thu, Jan 18, 2024 at 3:08 PM Matthew Knepley  wrote:

> On Thu, Jan 18, 2024 at 1:20 PM Mark Adams  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 
>> wrote:
>>
>>> On Thu, Jan 18, 2024 at 10:08 AM Mark Adams  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", ));
   PetscCall(PetscObjectSetName((PetscObject)f, "particle weights"));
   PetscCall(VecViewFromOptions(f, NULL, "-weights_view"));
   PetscCall(DMSwarmDestroyGlobalVectorFromField(sw, "w_q", ));

 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 +
 [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$
>>>  
>>> >>  >
>>>
>>
>
> --
> 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$
>  
>   >
>

Re: [petsc-users] Swarm view HDF5

2024-01-18 Thread Matthew Knepley 
On Thu, Jan 18, 2024 at 1:20 PM Mark Adams  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.

  Thanks,

Matt


> Thanks,
> Mark
>
>
> On Thu, Jan 18, 2024 at 11:26 AM Matthew Knepley 
> wrote:
>
>> On Thu, Jan 18, 2024 at 10:08 AM Mark Adams  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", ));
>>>   PetscCall(PetscObjectSetName((PetscObject)f, "particle weights"));
>>>   PetscCall(VecViewFromOptions(f, NULL, "-weights_view"));
>>>   PetscCall(DMSwarmDestroyGlobalVectorFromField(sw, "w_q", ));
>>>
>>> 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://petsc.org/release/faq/ for trouble shooting.
>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.20.3-461-g585a01bd688
>>>  GIT Date: 2024-01-16 23:32:45 +
>>> [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://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/

Re: [petsc-users] Swarm view HDF5

2024-01-18 Thread Mark Adams 
I had this working at one point.

Should I add PetscViewerHDF5PushTimestepping?
I don't create a viewer now, but I could make one.

Thanks,
Mark


On Thu, Jan 18, 2024 at 11:26 AM Matthew Knepley  wrote:

> On Thu, Jan 18, 2024 at 10:08 AM Mark Adams  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", ));
>>   PetscCall(PetscObjectSetName((PetscObject)f, "particle weights"));
>>   PetscCall(VecViewFromOptions(f, NULL, "-weights_view"));
>>   PetscCall(DMSwarmDestroyGlobalVectorFromField(sw, "w_q", ));
>>
>> 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://petsc.org/release/faq/ for trouble shooting.
>> [0]PETSC ERROR: Petsc Development GIT revision: v3.20.3-461-g585a01bd688
>>  GIT Date: 2024-01-16 23:32:45 +
>> [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://www.cse.buffalo.edu/~knepley/
> 
>

Re: [petsc-users] Swarm view HDF5

2024-01-18 Thread Matthew Knepley 
On Thu, Jan 18, 2024 at 10:08 AM Mark Adams  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", ));
>   PetscCall(PetscObjectSetName((PetscObject)f, "particle weights"));
>   PetscCall(VecViewFromOptions(f, NULL, "-weights_view"));
>   PetscCall(DMSwarmDestroyGlobalVectorFromField(sw, "w_q", ));
>
> 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://petsc.org/release/faq/ for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.20.3-461-g585a01bd688
>  GIT Date: 2024-01-16 23:32:45 +
> [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://www.cse.buffalo.edu/~knepley/