Yes, I am getting the "CellDM" from the DMSwarm. Miguel On 15 Jan 2025, at 16:08, Mark Adams <[email protected]> wrote: Are you getting the "CellDM" from the DMSwarm? Mark On Wed, Jan 15, 2025 at 7:09 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> wrote: Dear all, It seems that we can not modify the coordinates of the background mesh attached to a DMSwarm simulation. This is a feature? Best, Miguel

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? 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? 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

Thank you Matt for the useful info. I’ll try your idea. Miguel On 15 Jan 2025, at 16:48, Matthew Knepley <[email protected]> wrote: On Wed, Jan 15, 2025 at 10:41 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

On Fri, Jan 17, 2025 at 9:45 AM MIGUEL MOLINOS PEREZ <[email protected]> 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_u... and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!f... [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 <[email protected]> wrote:

Thank you Matt for the useful info. I’ll try your idea.

Miguel

On 15 Jan 2025, at 16:48, Matthew Knepley <[email protected]> wrote:

On Wed, Jan 15, 2025 at 10:41 AM MIGUEL MOLINOS PEREZ <[email protected]> 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

-- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

-- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

On Fri, Jan 17, 2025 at 10:08 AM MIGUEL MOLINOS PEREZ <[email protected]> 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 <[email protected]> wrote:

On Fri, Jan 17, 2025 at 9:45 AM MIGUEL MOLINOS PEREZ <[email protected]> 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_u... and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!d... [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 <[email protected]> wrote:

Thank you Matt for the useful info. I’ll try your idea.

Miguel

On 15 Jan 2025, at 16:48, Matthew Knepley <[email protected]> wrote:

On Wed, Jan 15, 2025 at 10:41 AM MIGUEL MOLINOS PEREZ <[email protected]> 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

-- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

-- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

-- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

On Fri, Jan 17, 2025 at 10:49 AM MIGUEL MOLINOS PEREZ <[email protected]> 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_u... and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!Z... [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 <[email protected]> wrote:

On Fri, Jan 17, 2025 at 10:08 AM MIGUEL MOLINOS PEREZ <[email protected]> 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 <[email protected]> wrote:

On Fri, Jan 17, 2025 at 9:45 AM MIGUEL MOLINOS PEREZ <[email protected]> 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_u... and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!Z... [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 <[email protected]> wrote:

Thank you Matt for the useful info. I’ll try your idea.

Miguel

On 15 Jan 2025, at 16:48, Matthew Knepley <[email protected]> wrote:

On Wed, Jan 15, 2025 at 10:41 AM MIGUEL MOLINOS PEREZ <[email protected]> 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

-- 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

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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

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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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

Dear Matt, the error was in the implementation of the volume expansion function. I updated it, and it works finte under finite domains. However, if I include periodic boundary conditions the volume of the cell does not accommodate the volume expansion of the particles. The deformation gradient is not the identity… I guess I am missing the fine detail on how periodic bcc are implemented in DMDA mesh, I’m right? Thanks, Miguel static PetscErrorCode Volumetric_Expansion_DMDA(DM * da, const Eigen::Matrix3d& F) { PetscInt i, j, mstart, m, nstart, n, pstart, p, k; Vec local, global; DMDACoor3d ***coors, ***coorslocal; DM cda; PetscFunctionBeginUser; PetscCall(DMGetCoordinateDM(*da, &cda)); PetscCall(DMGetCoordinates(*da, &global)); PetscCall(DMGetCoordinatesLocal(*da, &local)); PetscCall(DMDAVecGetArray(cda, global, &coors)); PetscCall(DMDAVecGetArrayRead(cda, local, &coorslocal)); PetscCall(DMDAGetCorners(cda, &mstart, &nstart, &pstart, &m, &n, &p)); for (i = mstart; i < mstart + m; i++) { for (j = nstart; j < nstart + n; j++) { for (k = pstart; k < pstart + p; k++) { coors[k][j][i].x = coorslocal[k][j][i].x * F(0, 0); coors[k][j][i].y = coorslocal[k][j][i].y * F(1, 1); coors[k][j][i].z = coorslocal[k][j][i].z * F(2, 2); } } } PetscCall(DMDAVecRestoreArray(cda, global, &coors)); PetscCall(DMDAVecRestoreArrayRead(cda, local, &coorslocal)); PetscCall(DMGlobalToLocalBegin(cda, global, INSERT_VALUES, local)); PetscCall(DMGlobalToLocalEnd(cda, global, INSERT_VALUES, local)); PetscFunctionReturn(PETSC_SUCCESS); } On 17 Jan 2025, at 18:01, MIGUEL MOLINOS PEREZ <[email protected]> wrote: You are right!! Thank you again! Miguel On Jan 17, 2025, at 5:18 PM, Matthew Knepley <[email protected]> wrote: On Fri, Jan 17, 2025 at 10:49 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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_u... and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!f... [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 <[email protected]<mailto:[email protected]>> wrote: On Fri, Jan 17, 2025 at 10:08 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> wrote: On Fri, Jan 17, 2025 at 9:45 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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_u... and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!f... [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 <[email protected]<mailto:[email protected]>> wrote: Thank you Matt for the useful info. I’ll try your idea. Miguel On 15 Jan 2025, at 16:48, Matthew Knepley <[email protected]<mailto:[email protected]>> wrote: On Wed, Jan 15, 2025 at 10:41 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

Thanks Matt, I tried that too, and the problem remains. The box is updated only if I set no periodic bcc. Miguel On 24 Jan 2025, at 14:20, Matthew Knepley <[email protected]> wrote: On Fri, Jan 24, 2025 at 4:41 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> wrote: Dear Matt, the error was in the implementation of the volume expansion function. I updated it, and it works finte under finite domains. However, if I include periodic boundary conditions the volume of the cell does not accommodate the volume expansion of the particles. The deformation gradient is not the identity… I guess I am missing the fine detail on how periodic bcc are implemented in DMDA mesh, I’m right? DMDA identifies vertices using a VecScatter to implement periodic BC. This should be insensitive to coordinates. However, I don't think the algorithm below is correct for local coordinates. You use GlobalToLocal(), which means that some global coordinate "wins" for each local cell, so cells on the periodic boundary can be wrong. I would set the local coordinates by hand as well. Thanks, Matt Thanks, Miguel static PetscErrorCode Volumetric_Expansion_DMDA(DM * da, const Eigen::Matrix3d& F) { PetscInt i, j, mstart, m, nstart, n, pstart, p, k; Vec local, global; DMDACoor3d ***coors, ***coorslocal; DM cda; PetscFunctionBeginUser; PetscCall(DMGetCoordinateDM(*da, &cda)); PetscCall(DMGetCoordinates(*da, &global)); PetscCall(DMGetCoordinatesLocal(*da, &local)); PetscCall(DMDAVecGetArray(cda, global, &coors)); PetscCall(DMDAVecGetArrayRead(cda, local, &coorslocal)); PetscCall(DMDAGetCorners(cda, &mstart, &nstart, &pstart, &m, &n, &p)); for (i = mstart; i < mstart + m; i++) { for (j = nstart; j < nstart + n; j++) { for (k = pstart; k < pstart + p; k++) { coors[k][j][i].x = coorslocal[k][j][i].x * F(0, 0); coors[k][j][i].y = coorslocal[k][j][i].y * F(1, 1); coors[k][j][i].z = coorslocal[k][j][i].z * F(2, 2); } } } PetscCall(DMDAVecRestoreArray(cda, global, &coors)); PetscCall(DMDAVecRestoreArrayRead(cda, local, &coorslocal)); PetscCall(DMGlobalToLocalBegin(cda, global, INSERT_VALUES, local)); PetscCall(DMGlobalToLocalEnd(cda, global, INSERT_VALUES, local)); PetscFunctionReturn(PETSC_SUCCESS); } On 17 Jan 2025, at 18:01, MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> wrote: You are right!! Thank you again! Miguel On Jan 17, 2025, at 5:18 PM, Matthew Knepley <[email protected]<mailto:[email protected]>> wrote: On Fri, Jan 17, 2025 at 10:49 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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_u... and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!Y... [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 <[email protected]<mailto:[email protected]>> wrote: On Fri, Jan 17, 2025 at 10:08 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> wrote: On Fri, Jan 17, 2025 at 9:45 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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_u... and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!Y... [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 <[email protected]<mailto:[email protected]>> wrote: Thank you Matt for the useful info. I’ll try your idea. Miguel On 15 Jan 2025, at 16:48, Matthew Knepley <[email protected]<mailto:[email protected]>> wrote: On Wed, Jan 15, 2025 at 10:41 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

Sorry I wasn’t clear enough. By “the box is updated” I mean: I run DMGetBoundingBox and the resulting coordinates are updated according to the deformation gradient “F". Thanks, Miguel On 24 Jan 2025, at 16:50, Matthew Knepley <[email protected]> wrote: On Fri, Jan 24, 2025 at 10:36 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> wrote: Thanks Matt, I tried that too, and the problem remains. The box is updated only if I set no periodic bcc. What do you mean by "The box is updated"? I am trying to understand how you test things. Clearly the coordinates are updated, even in the periodic case. Thus, I need to understand the test. Once we do that, we can work backwards to the first broken thing. Thanks, Matt Miguel On 24 Jan 2025, at 14:20, Matthew Knepley <[email protected]<mailto:[email protected]>> wrote: On Fri, Jan 24, 2025 at 4:41 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> wrote: Dear Matt, the error was in the implementation of the volume expansion function. I updated it, and it works finte under finite domains. However, if I include periodic boundary conditions the volume of the cell does not accommodate the volume expansion of the particles. The deformation gradient is not the identity… I guess I am missing the fine detail on how periodic bcc are implemented in DMDA mesh, I’m right? DMDA identifies vertices using a VecScatter to implement periodic BC. This should be insensitive to coordinates. However, I don't think the algorithm below is correct for local coordinates. You use GlobalToLocal(), which means that some global coordinate "wins" for each local cell, so cells on the periodic boundary can be wrong. I would set the local coordinates by hand as well. Thanks, Matt Thanks, Miguel static PetscErrorCode Volumetric_Expansion_DMDA(DM * da, const Eigen::Matrix3d& F) { PetscInt i, j, mstart, m, nstart, n, pstart, p, k; Vec local, global; DMDACoor3d ***coors, ***coorslocal; DM cda; PetscFunctionBeginUser; PetscCall(DMGetCoordinateDM(*da, &cda)); PetscCall(DMGetCoordinates(*da, &global)); PetscCall(DMGetCoordinatesLocal(*da, &local)); PetscCall(DMDAVecGetArray(cda, global, &coors)); PetscCall(DMDAVecGetArrayRead(cda, local, &coorslocal)); PetscCall(DMDAGetCorners(cda, &mstart, &nstart, &pstart, &m, &n, &p)); for (i = mstart; i < mstart + m; i++) { for (j = nstart; j < nstart + n; j++) { for (k = pstart; k < pstart + p; k++) { coors[k][j][i].x = coorslocal[k][j][i].x * F(0, 0); coors[k][j][i].y = coorslocal[k][j][i].y * F(1, 1); coors[k][j][i].z = coorslocal[k][j][i].z * F(2, 2); } } } PetscCall(DMDAVecRestoreArray(cda, global, &coors)); PetscCall(DMDAVecRestoreArrayRead(cda, local, &coorslocal)); PetscCall(DMGlobalToLocalBegin(cda, global, INSERT_VALUES, local)); PetscCall(DMGlobalToLocalEnd(cda, global, INSERT_VALUES, local)); PetscFunctionReturn(PETSC_SUCCESS); } On 17 Jan 2025, at 18:01, MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> wrote: You are right!! Thank you again! Miguel On Jan 17, 2025, at 5:18 PM, Matthew Knepley <[email protected]<mailto:[email protected]>> wrote: On Fri, Jan 17, 2025 at 10:49 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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_u... and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!Y... [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 <[email protected]<mailto:[email protected]>> wrote: On Fri, Jan 17, 2025 at 10:08 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> wrote: On Fri, Jan 17, 2025 at 9:45 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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_u... and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!Y... [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 <[email protected]<mailto:[email protected]>> wrote: Thank you Matt for the useful info. I’ll try your idea. Miguel On 15 Jan 2025, at 16:48, Matthew Knepley <[email protected]<mailto:[email protected]>> wrote: On Wed, Jan 15, 2025 at 10:41 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

Ohh, I wasn't aware of this function. Thank you Matt, I’ll see if that solves the problem. Miguel On 24 Jan 2025, at 17:00, Matthew Knepley <[email protected]> wrote: On Fri, Jan 24, 2025 at 10:56 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> wrote: Sorry I wasn’t clear enough. By “the box is updated” I mean: I run DMGetBoundingBox and the resulting coordinates are updated according to the deformation gradient “F". Oh, if you change the periodic extent, which you are, you have to recall DMSetPeriodicity(), which is what DMGetBoundaingBox() consults for the periodic extent (because the coordinates cannot be trusted). Thanks, Matt Thanks, Miguel On 24 Jan 2025, at 16:50, Matthew Knepley <[email protected]<mailto:[email protected]>> wrote: On Fri, Jan 24, 2025 at 10:36 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> wrote: Thanks Matt, I tried that too, and the problem remains. The box is updated only if I set no periodic bcc. What do you mean by "The box is updated"? I am trying to understand how you test things. Clearly the coordinates are updated, even in the periodic case. Thus, I need to understand the test. Once we do that, we can work backwards to the first broken thing. Thanks, Matt Miguel On 24 Jan 2025, at 14:20, Matthew Knepley <[email protected]<mailto:[email protected]>> wrote: On Fri, Jan 24, 2025 at 4:41 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> wrote: Dear Matt, the error was in the implementation of the volume expansion function. I updated it, and it works finte under finite domains. However, if I include periodic boundary conditions the volume of the cell does not accommodate the volume expansion of the particles. The deformation gradient is not the identity… I guess I am missing the fine detail on how periodic bcc are implemented in DMDA mesh, I’m right? DMDA identifies vertices using a VecScatter to implement periodic BC. This should be insensitive to coordinates. However, I don't think the algorithm below is correct for local coordinates. You use GlobalToLocal(), which means that some global coordinate "wins" for each local cell, so cells on the periodic boundary can be wrong. I would set the local coordinates by hand as well. Thanks, Matt Thanks, Miguel static PetscErrorCode Volumetric_Expansion_DMDA(DM * da, const Eigen::Matrix3d& F) { PetscInt i, j, mstart, m, nstart, n, pstart, p, k; Vec local, global; DMDACoor3d ***coors, ***coorslocal; DM cda; PetscFunctionBeginUser; PetscCall(DMGetCoordinateDM(*da, &cda)); PetscCall(DMGetCoordinates(*da, &global)); PetscCall(DMGetCoordinatesLocal(*da, &local)); PetscCall(DMDAVecGetArray(cda, global, &coors)); PetscCall(DMDAVecGetArrayRead(cda, local, &coorslocal)); PetscCall(DMDAGetCorners(cda, &mstart, &nstart, &pstart, &m, &n, &p)); for (i = mstart; i < mstart + m; i++) { for (j = nstart; j < nstart + n; j++) { for (k = pstart; k < pstart + p; k++) { coors[k][j][i].x = coorslocal[k][j][i].x * F(0, 0); coors[k][j][i].y = coorslocal[k][j][i].y * F(1, 1); coors[k][j][i].z = coorslocal[k][j][i].z * F(2, 2); } } } PetscCall(DMDAVecRestoreArray(cda, global, &coors)); PetscCall(DMDAVecRestoreArrayRead(cda, local, &coorslocal)); PetscCall(DMGlobalToLocalBegin(cda, global, INSERT_VALUES, local)); PetscCall(DMGlobalToLocalEnd(cda, global, INSERT_VALUES, local)); PetscFunctionReturn(PETSC_SUCCESS); } On 17 Jan 2025, at 18:01, MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> wrote: You are right!! Thank you again! Miguel On Jan 17, 2025, at 5:18 PM, Matthew Knepley <[email protected]<mailto:[email protected]>> wrote: On Fri, Jan 17, 2025 at 10:49 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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_u... and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!c... [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 <[email protected]<mailto:[email protected]>> wrote: On Fri, Jan 17, 2025 at 10:08 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> wrote: On Fri, Jan 17, 2025 at 9:45 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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_u... and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!c... [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 <[email protected]<mailto:[email protected]>> wrote: Thank you Matt for the useful info. I’ll try your idea. Miguel On 15 Jan 2025, at 16:48, Matthew Knepley <[email protected]<mailto:[email protected]>> wrote: On Wed, Jan 15, 2025 at 10:41 AM MIGUEL MOLINOS PEREZ <[email protected]<mailto:[email protected]>> 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... > -- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

No problem. Sorry I did not think of it sooner. Matt On Tue, Jan 28, 2025 at 10:45 AM MIGUEL MOLINOS PEREZ <[email protected]> wrote:

It works! Thank you again Matt.

Miguel

On 24 Jan 2025, at 17:07, MIGUEL MOLINOS PEREZ <[email protected]> wrote:

Ohh, I wasn't aware of this function. Thank you Matt, I’ll see if that solves the problem.

Miguel

On 24 Jan 2025, at 17:00, Matthew Knepley <[email protected]> wrote:

On Fri, Jan 24, 2025 at 10:56 AM MIGUEL MOLINOS PEREZ <[email protected]> wrote:

...

Sorry I wasn’t clear enough. By “the box is updated” I mean: I run DMGetBoundingBox and the resulting coordinates are updated according to the deformation gradient “F".

Oh, if you change the periodic extent, which you are, you have to recall DMSetPeriodicity(), which is what DMGetBoundaingBox() consults for the periodic extent (because the coordinates cannot be trusted).

Thanks,

Matt

...

Thanks, Miguel

On 24 Jan 2025, at 16:50, Matthew Knepley <[email protected]> wrote:

On Fri, Jan 24, 2025 at 10:36 AM MIGUEL MOLINOS PEREZ <[email protected]> wrote:

...

Thanks Matt, I tried that too, and the problem remains. The box is updated only if I set no periodic bcc.

What do you mean by "The box is updated"? I am trying to understand how you test things. Clearly the coordinates are updated, even in the periodic case. Thus, I need to understand the test. Once we do that, we can work backwards to the first broken thing.

Thanks,

Matt

...

Miguel

On 24 Jan 2025, at 14:20, Matthew Knepley <[email protected]> wrote:

On Fri, Jan 24, 2025 at 4:41 AM MIGUEL MOLINOS PEREZ <[email protected]> wrote:

...

Dear Matt, the error was in the implementation of the volume expansion function. I updated it, and it works finte under finite domains. However, if I include periodic boundary conditions the volume of the cell does not accommodate the volume expansion of the particles. The deformation gradient is not the identity… I guess I am missing the fine detail on how periodic bcc are implemented in DMDA mesh, I’m right?

DMDA identifies vertices using a VecScatter to implement periodic BC. This should be insensitive to coordinates. However, I don't think the algorithm below is correct for local coordinates. You use GlobalToLocal(), which means that some global coordinate "wins" for each local cell, so cells on the periodic boundary can be wrong. I would set the local coordinates by hand as well.

Thanks,

Matt

...

Thanks, Miguel

static PetscErrorCode Volumetric_Expansion_DMDA(DM * da, const Eigen::Matrix3d& F) {

PetscInt i, j, mstart, m, nstart, n, pstart, p, k; Vec local, global; DMDACoor3d ***coors, ***coorslocal; DM cda;

PetscFunctionBeginUser; PetscCall(DMGetCoordinateDM(*da, &cda)); PetscCall(DMGetCoordinates(*da, &global)); PetscCall(DMGetCoordinatesLocal(*da, &local)); PetscCall(DMDAVecGetArray(cda, global, &coors)); PetscCall(DMDAVecGetArrayRead(cda, local, &coorslocal)); PetscCall(DMDAGetCorners(cda, &mstart, &nstart, &pstart, &m, &n, &p)); for (i = mstart; i < mstart + m; i++) { for (j = nstart; j < nstart + n; j++) { for (k = pstart; k < pstart + p; k++) { coors[k][j][i].x = coorslocal[k][j][i].x * F(0, 0); coors[k][j][i].y = coorslocal[k][j][i].y * F(1, 1); coors[k][j][i].z = coorslocal[k][j][i].z * F(2, 2); } } } PetscCall(DMDAVecRestoreArray(cda, global, &coors)); PetscCall(DMDAVecRestoreArrayRead(cda, local, &coorslocal));

PetscCall(DMGlobalToLocalBegin(cda, global, INSERT_VALUES, local)); PetscCall(DMGlobalToLocalEnd(cda, global, INSERT_VALUES, local));

PetscFunctionReturn(PETSC_SUCCESS); }

On 17 Jan 2025, at 18:01, MIGUEL MOLINOS PEREZ <[email protected]> wrote:

You are right!! Thank you again!

Miguel

On Jan 17, 2025, at 5:18 PM, Matthew Knepley <[email protected]> wrote:

On Fri, Jan 17, 2025 at 10:49 AM MIGUEL MOLINOS PEREZ <[email protected]> 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_u... and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!e... [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 <[email protected]> wrote:

On Fri, Jan 17, 2025 at 10:08 AM MIGUEL MOLINOS PEREZ <[email protected]> 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 <[email protected]> wrote:

On Fri, Jan 17, 2025 at 9:45 AM MIGUEL MOLINOS PEREZ <[email protected]> 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_u... and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!e... [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 <[email protected]> wrote:

Thank you Matt for the useful info. I’ll try your idea.

Miguel

On 15 Jan 2025, at 16:48, Matthew Knepley <[email protected]> wrote:

On Wed, Jan 15, 2025 at 10:41 AM MIGUEL MOLINOS PEREZ < [email protected]> 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

-- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

-- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

-- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

-- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

-- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

-- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

-- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >

-- 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_uCf... <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfs... >