[petsc-users] Update DMDA attached to DMSWARM

Fri Jan 17 09:49:56 CST 2025

Now the error is in the call to DMSwarmMigrate

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!ad4_CYmqVLwmuIANP7o2NXvoqCPGFSZpW_gVLp8pQweudrYWPdqW4De1CaYkE5a1sPrs7JUO_n5fznRPbEaqpg$  and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!ad4_CYmqVLwmuIANP7o2NXvoqCPGFSZpW_gVLp8pQweudrYWPdqW4De1CaYkE5a1sPrs7JUO_n5fznTEGnkpAg$ 
[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<mailto: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<mailto:knepley at gmail.com>> wrote:

On Fri, Jan 17, 2025 at 9:45 AM MIGUEL MOLINOS PEREZ <mmolinos at us.es<mailto: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!ad4_CYmqVLwmuIANP7o2NXvoqCPGFSZpW_gVLp8pQweudrYWPdqW4De1CaYkE5a1sPrs7JUO_n5fznRPbEaqpg$  and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!ad4_CYmqVLwmuIANP7o2NXvoqCPGFSZpW_gVLp8pQweudrYWPdqW4De1CaYkE5a1sPrs7JUO_n5fznTEGnkpAg$ 
[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<mailto: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<mailto:knepley at gmail.com>> wrote:

On Wed, Jan 15, 2025 at 10:41 AM MIGUEL MOLINOS PEREZ <mmolinos at us.es<mailto: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

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--
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!ad4_CYmqVLwmuIANP7o2NXvoqCPGFSZpW_gVLp8pQweudrYWPdqW4De1CaYkE5a1sPrs7JUO_n5fznQzmH4m9w$ <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!ad4_CYmqVLwmuIANP7o2NXvoqCPGFSZpW_gVLp8pQweudrYWPdqW4De1CaYkE5a1sPrs7JUO_n5fznSXl1mkRA$ >

--
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!ad4_CYmqVLwmuIANP7o2NXvoqCPGFSZpW_gVLp8pQweudrYWPdqW4De1CaYkE5a1sPrs7JUO_n5fznQzmH4m9w$ <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!ad4_CYmqVLwmuIANP7o2NXvoqCPGFSZpW_gVLp8pQweudrYWPdqW4De1CaYkE5a1sPrs7JUO_n5fznSXl1mkRA$ >

--
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!ad4_CYmqVLwmuIANP7o2NXvoqCPGFSZpW_gVLp8pQweudrYWPdqW4De1CaYkE5a1sPrs7JUO_n5fznQzmH4m9w$ <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!ad4_CYmqVLwmuIANP7o2NXvoqCPGFSZpW_gVLp8pQweudrYWPdqW4De1CaYkE5a1sPrs7JUO_n5fznSXl1mkRA$ >

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