[petsc-users] Update DMDA attached to DMSWARM

Matthew Knepley knepley at gmail.com
Fri Jan 17 10:18:42 CST 2025 

On Fri, Jan 17, 2025 at 10:49 AM MIGUEL MOLINOS PEREZ <mmolinos at us.es>
wrote:

> Now the error is in the call to DMSwarmMigrate
>

You have almost certainly overwritten memory somewhere. Can you use
vlagrind or Address Sanitizer?

   Thanks,

      Matt


> Miguel
>
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see https://urldefense.us/v3/__https://petsc.org/release/faq/*valgrind__;Iw!!G_uCfscf7eWS!ZR4qEUJFauPbLf2xjFCCNpzP81yruUvFjLgv04TV-z8lOzwKA--hL3qV6DsYz5Y5lMba6urrC0JQwfeJkbHf$  and
> https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!ZR4qEUJFauPbLf2xjFCCNpzP81yruUvFjLgv04TV-z8lOzwKA--hL3qV6DsYz5Y5lMba6urrC0JQwcFiO800$ 
> [0]PETSC ERROR: ---------------------  Stack Frames
> ------------------------------------
> [0]PETSC ERROR: The line numbers in the error traceback are not always
> exact.
> [0]PETSC ERROR: #1 DMSwarmDataBucketGetSizes() at
> /Users/migmolper/petsc/src/dm/impls/swarm/data_bucket.c:297
> [0]PETSC ERROR: #2 DMSwarmMigrate_CellDMScatter() at
> /Users/migmolper/petsc/src/dm/impls/swarm/swarm_migrate.c:201
> [0]PETSC ERROR: #3 DMSwarmMigrate() at
> /Users/migmolper/petsc/src/dm/impls/swarm/swarm.c:1349
> [0]PETSC ERROR: #4 main() at
> /Users/migmolper/DMD/driver-tasting-SOLERA.cpp:41
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
> On Jan 17, 2025, at 4:22 PM, Matthew Knepley <knepley at gmail.com> wrote:
>
> On Fri, Jan 17, 2025 at 10:08 AM MIGUEL MOLINOS PEREZ <mmolinos at us.es>
> wrote:
>
>> Thank you Matt, this the piece of code I use to change the coordinates of
>> the DM obtained using:
>>
>
> You do not need the call to DMSetCoordinates(). What happens when you
> remove it?
>
>   Thanks,
>
>     Matt
>
>
>>
>> DMSwarmGetCellDM(Simulation.atomistic_data, &bounding_cell);
>> DMGetApplicationContext(bounding_cell, &background_mesh);
>>
>> Thanks,
>> Miguel
>>
>> /************************************************************************/
>>
>> PetscErrorCode Volumetric_Expansion(DM dm, const Eigen::Matrix3d& F) {
>> PetscErrorCode ierr;
>> Vec coordinates;
>> PetscScalar* coordArray;
>> PetscInt xs, ys, zs, xm, ym, zm, i, j, k;
>> PetscInt dim, M, N, P;
>>
>> PetscFunctionBegin;
>> // Get DMDA information
>> ierr = DMDAGetInfo(dm, &dim, &M, &N, &P, NULL, NULL, NULL, NULL, NULL,
>> NULL,
>> NULL, NULL, NULL);
>> CHKERRQ(ierr);
>> ierr = DMDAGetCorners(dm, &xs, &ys, &zs, &xm, &ym, &zm);
>> CHKERRQ(ierr);
>>
>> // Get the coordinates vector
>> ierr = DMGetCoordinates(dm, &coordinates);
>> CHKERRQ(ierr);
>> ierr = VecGetArray(coordinates, &coordArray);
>> CHKERRQ(ierr);
>>
>> // Update the coordinates based on the desired transformation
>> for (k = zs; k < zs + zm; k++) {
>> for (j = ys; j < ys + ym; j++) {
>> for (i = xs; i < xs + xm; i++) {
>> PetscInt idx =
>> ((k * N + j) * M + i) * dim; // Index for the i, j, k point
>> coordArray[idx] = coordArray[idx] * F(0,0); // Update x-coordinate
>> coordArray[idx + 1] = coordArray[idx + 1] * F(1,1); // Update
>> y-coordinate
>> coordArray[idx + 2] = coordArray[idx + 2] * F(2,2); // Update
>> z-coordinate
>> }
>> }
>> }
>>
>> // Restore the coordinates vector
>> ierr = VecRestoreArray(coordinates, &coordArray);
>> CHKERRQ(ierr);
>>
>> // Set the updated coordinates back to the DMDA
>> ierr = DMSetCoordinates(dm, coordinates);
>> CHKERRQ(ierr);
>>
>> PetscFunctionReturn(0);
>> }
>>
>> /************************************************************************/
>>
>> On 17 Jan 2025, at 16:00, Matthew Knepley <knepley at gmail.com> wrote:
>>
>> On Fri, Jan 17, 2025 at 9:45 AM MIGUEL MOLINOS PEREZ <mmolinos at us.es>
>> wrote:
>>
>>> I tried what you suggested, but still I got this error message. Maybe I
>>> should use main release?
>>>
>>
>> No. I suspect something is wrong with the way you are setting
>> coordinates. Can you share the code?
>>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> Miguel
>>>
>>> [4]PETSC ERROR:
>>> ------------------------------------------------------------------------
>>> [4]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>>> probably memory access out of range
>>> [4]PETSC ERROR: Try option -start_in_debugger or
>>> -on_error_attach_debugger
>>> [4]PETSC ERROR: or see https://urldefense.us/v3/__https://petsc.org/release/faq/*valgrind__;Iw!!G_uCfscf7eWS!ZR4qEUJFauPbLf2xjFCCNpzP81yruUvFjLgv04TV-z8lOzwKA--hL3qV6DsYz5Y5lMba6urrC0JQwfeJkbHf$  and
>>> https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!ZR4qEUJFauPbLf2xjFCCNpzP81yruUvFjLgv04TV-z8lOzwKA--hL3qV6DsYz5Y5lMba6urrC0JQwcFiO800$ 
>>> [4]PETSC ERROR: ---------------------  Stack Frames
>>> ------------------------------------
>>> [4]PETSC ERROR: The line numbers in the error traceback are not always
>>> exact.
>>> [4]PETSC ERROR: #1 Pack_PetscReal_1_0() at
>>> /Users/migmolper/petsc/src/vec/is/sf/impls/basic/sfpack.c:373
>>> [4]PETSC ERROR: #2 PetscSFLinkPackRootData_Private() at
>>> /Users/migmolper/petsc/src/vec/is/sf/impls/basic/sfpack.c:932
>>> [4]PETSC ERROR: #3 PetscSFLinkPackRootData() at
>>> /Users/migmolper/petsc/src/vec/is/sf/impls/basic/sfpack.c:966
>>> [4]PETSC ERROR: #4 PetscSFBcastBegin_Basic() at
>>> /Users/migmolper/petsc/src/vec/is/sf/impls/basic/sfbasic.c:357
>>> [4]PETSC ERROR: #5 PetscSFBcastWithMemTypeBegin() at
>>> /Users/migmolper/petsc/src/vec/is/sf/interface/sf.c:1513
>>> [4]PETSC ERROR: #6 VecScatterBegin_Internal() at
>>> /Users/migmolper/petsc/src/vec/is/sf/interface/vscat.c:70
>>> [4]PETSC ERROR: #7 VecScatterBegin() at
>>> /Users/migmolper/petsc/src/vec/is/sf/interface/vscat.c:1316
>>> [4]PETSC ERROR: #8 DMGlobalToLocalBegin_DA() at
>>> /Users/migmolper/petsc/src/dm/impls/da/dagtol.c:15
>>> [4]PETSC ERROR: #9 DMGlobalToLocalBegin() at
>>> /Users/migmolper/petsc/src/dm/interface/dm.c:2844
>>> [4]PETSC ERROR: #10 DMGetCoordinatesLocalSetUp() at
>>> /Users/migmolper/petsc/src/dm/interface/dmcoordinates.c:565
>>> [4]PETSC ERROR: #11 DMGetCoordinatesLocal() at
>>> /Users/migmolper/petsc/src/dm/interface/dmcoordinates.c:599
>>> [4]PETSC ERROR: #12 _DMLocatePoints_DMDARegular_IS() at
>>> /Users/migmolper/DMD/SOLERA/Atoms/Atom.cpp:531
>>> [4]PETSC ERROR: #13 DMLocatePoints_DMDARegular() at
>>> /Users/migmolper/DMD/SOLERA/Atoms/Atom.cpp:586
>>> [4]PETSC ERROR: #14 DMLocatePoints() at
>>> /Users/migmolper/petsc/src/dm/interface/dmcoordinates.c:1194
>>> [4]PETSC ERROR: #15 DMSwarmMigrate_CellDMScatter() at
>>> /Users/migmolper/petsc/src/dm/impls/swarm/swarm_migrate.c:219
>>> [4]PETSC ERROR: #16 DMSwarmMigrate() at
>>> /Users/migmolper/petsc/src/dm/impls/swarm/swarm.c:1349
>>> [4]PETSC ERROR: #17 main() at
>>> /Users/migmolper/DMD/driver-tasting-SOLERA.cpp:41
>>>
>>>
>>>
>>> On Jan 15, 2025, at 4:56 PM, MIGUEL MOLINOS PEREZ <mmolinos at us.es>
>>> wrote:
>>>
>>> Thank you Matt for the useful info. I’ll try your idea.
>>>
>>> Miguel
>>>
>>> On 15 Jan 2025, at 16:48, Matthew Knepley <knepley at gmail.com> wrote:
>>>
>>> On Wed, Jan 15, 2025 at 10:41 AM MIGUEL MOLINOS PEREZ <mmolinos at us.es>
>>> wrote:
>>>
>>>> Thank you Matt.
>>>>
>>>> Yes, I am getting the "CellDM" from the DMSwarm.
>>>>
>>>> 1. I have recently overhauled this functionality because it was not
>>>> flexible enough for the plasma simulation we do. Thus main and release work
>>>> differently.
>>>>
>>>>
>>>> Nice to hear that. Should I move to main?
>>>>
>>>
>>> The changes allow you to have several cell DMs. I want to bin particles
>>> in space, but also in velocity, and then in the tensor product of space and
>>> velocity. Moreover, sometimes I want to use different Swarm fields as the
>>> DM field for the solver. You can do all that with main now. If you just
>>> need a single DM with the same DM fields, release is fine.
>>>
>>>
>>>> 2. I assume you are using release
>>>>
>>>>
>>>> You are correct.
>>>>
>>>> 3. In both main and release, if you change the coordinates of your
>>>> CellDM mesh, you need to rebin the particles. The easiest way to do this is
>>>> to call DMSwarmMigrate(sw, PETSC_FALSE).
>>>>
>>>>
>>>> What do you mean by rebin?
>>>>
>>>
>>> When you provide the cell DM, Swrm makes a "sort context" that bins the
>>> particles into DM cells. If you change the coordinates, this binning will
>>> change, so you need it to "rebin" or recreate the sort context.
>>>
>>>   Thanks,
>>>
>>>     Matt
>>>
>>>
>>>> Miguel
>>>>
>>>>
>>>>   Thanks,
>>>>
>>>>      Matt
>>>>
>>>>
>>>>> Best,
>>>>> Miguel
>>>>>
>>>> --
>>>> 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!ZR4qEUJFauPbLf2xjFCCNpzP81yruUvFjLgv04TV-z8lOzwKA--hL3qV6DsYz5Y5lMba6urrC0JQwZtiWUPK$ 
>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!ZR4qEUJFauPbLf2xjFCCNpzP81yruUvFjLgv04TV-z8lOzwKA--hL3qV6DsYz5Y5lMba6urrC0JQwRCb0BZR$ >
>>>>
>>>>
>>>>
>>>
>>> --
>>> 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!ZR4qEUJFauPbLf2xjFCCNpzP81yruUvFjLgv04TV-z8lOzwKA--hL3qV6DsYz5Y5lMba6urrC0JQwZtiWUPK$ 
>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!ZR4qEUJFauPbLf2xjFCCNpzP81yruUvFjLgv04TV-z8lOzwKA--hL3qV6DsYz5Y5lMba6urrC0JQwRCb0BZR$ >
>>>
>>>
>>>
>>>
>>
>> --
>> 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!ZR4qEUJFauPbLf2xjFCCNpzP81yruUvFjLgv04TV-z8lOzwKA--hL3qV6DsYz5Y5lMba6urrC0JQwZtiWUPK$ 
>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!ZR4qEUJFauPbLf2xjFCCNpzP81yruUvFjLgv04TV-z8lOzwKA--hL3qV6DsYz5Y5lMba6urrC0JQwRCb0BZR$ >
>>
>>
>>
>
> --
> 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!ZR4qEUJFauPbLf2xjFCCNpzP81yruUvFjLgv04TV-z8lOzwKA--hL3qV6DsYz5Y5lMba6urrC0JQwZtiWUPK$ 
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!ZR4qEUJFauPbLf2xjFCCNpzP81yruUvFjLgv04TV-z8lOzwKA--hL3qV6DsYz5Y5lMba6urrC0JQwRCb0BZR$ >
>
>
>

-- 
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!ZR4qEUJFauPbLf2xjFCCNpzP81yruUvFjLgv04TV-z8lOzwKA--hL3qV6DsYz5Y5lMba6urrC0JQwZtiWUPK$  <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!ZR4qEUJFauPbLf2xjFCCNpzP81yruUvFjLgv04TV-z8lOzwKA--hL3qV6DsYz5Y5lMba6urrC0JQwRCb0BZR$ >
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