[petsc-users] [EXTERNAL] Re: Is there anything like a "DMPlexSetCones()" ?
Ferrand, Jesus A.
FERRANJ2 at my.erau.edu
Wed May 1 19:17:15 CDT 2024
Matt:
"I do not understand the "flag check". What is that?"
My bad, I should have referred to the "dm->setupcalled".
I believe this PetscBool is checked by the other DM (not just DMPlex) APIs.
The subsequent checks for dm->setupcalled == PETSC_TRUE is what I meant to say.
Here's a copy of DMSetUp().
PetscErrorCode<https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!YFXAyokfQwnPYORwZQ6qcxVJHF6uyeDin1NgKfpvqUZafCX_TGDCu_5NYVR63aFhpdQwl9zaJ_woQpUfaXoUtLMeB-Q$ > DMSetUp<https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DMSetUp/__;!!G_uCfscf7eWS!YFXAyokfQwnPYORwZQ6qcxVJHF6uyeDin1NgKfpvqUZafCX_TGDCu_5NYVR63aFhpdQwl9zaJ_woQpUfaXoUPgF7MMU$ >(DM<https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DM/__;!!G_uCfscf7eWS!YFXAyokfQwnPYORwZQ6qcxVJHF6uyeDin1NgKfpvqUZafCX_TGDCu_5NYVR63aFhpdQwl9zaJ_woQpUfaXoUht3yJz4$ > dm)
817: {
818: PetscFunctionBegin<https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionBegin/__;!!G_uCfscf7eWS!YFXAyokfQwnPYORwZQ6qcxVJHF6uyeDin1NgKfpvqUZafCX_TGDCu_5NYVR63aFhpdQwl9zaJ_woQpUfaXoUFggIo3o$ >;
820: if (dm->setupcalled) PetscFunctionReturn<https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!YFXAyokfQwnPYORwZQ6qcxVJHF6uyeDin1NgKfpvqUZafCX_TGDCu_5NYVR63aFhpdQwl9zaJ_woQpUfaXoU7-1kX1w$ >(PETSC_SUCCESS<https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!YFXAyokfQwnPYORwZQ6qcxVJHF6uyeDin1NgKfpvqUZafCX_TGDCu_5NYVR63aFhpdQwl9zaJ_woQpUfaXoUtLMeB-Q$ >);
821: PetscTryTypeMethod<https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscTryTypeMethod/__;!!G_uCfscf7eWS!YFXAyokfQwnPYORwZQ6qcxVJHF6uyeDin1NgKfpvqUZafCX_TGDCu_5NYVR63aFhpdQwl9zaJ_woQpUfaXoUmqkFeuk$ >(dm, setup);
822: dm->setupcalled = PETSC_TRUE<https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PETSC_TRUE/__;!!G_uCfscf7eWS!YFXAyokfQwnPYORwZQ6qcxVJHF6uyeDin1NgKfpvqUZafCX_TGDCu_5NYVR63aFhpdQwl9zaJ_woQpUfaXoUVfOOOpc$ >;
823: PetscFunctionReturn<https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!YFXAyokfQwnPYORwZQ6qcxVJHF6uyeDin1NgKfpvqUZafCX_TGDCu_5NYVR63aFhpdQwl9zaJ_woQpUfaXoU7-1kX1w$ >(PETSC_SUCCESS<https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!YFXAyokfQwnPYORwZQ6qcxVJHF6uyeDin1NgKfpvqUZafCX_TGDCu_5NYVR63aFhpdQwl9zaJ_woQpUfaXoUtLMeB-Q$ >);
824: }
"We could make a DMPlexSetCones(), but as you point out, the workflow for DMSetUp() would have to change. Where does the memory come from for your connectivity?"
It's a memory that I myself allocate based on a file's contents.
The nature of the I/O makes it so that I need to read the connectivity before I get a semblance of buffer sizes.
Otherwise, I would stick to the tried and tested way.
Also, when replying to the PETSc developers, users must reply to petsc-users at mcs.anl.gov and not just to the individual email accounts of the developers, right?
________________________________
From: Matthew Knepley <knepley at gmail.com>
Sent: Wednesday, May 1, 2024 8:07 PM
To: Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
Cc: petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
Subject: [EXTERNAL] Re: [petsc-users] Is there anything like a "DMPlexSetCones()" ?
CAUTION: This email originated outside of Embry-Riddle Aeronautical University. Do not click links or open attachments unless you recognize the sender and know the content is safe.
On Wed, May 1, 2024 at 3:34 PM Ferrand, Jesus A. <FERRANJ2 at my.erau.edu<mailto:FERRANJ2 at my.erau.edu>> wrote:
This Message Is From an External Sender
This message came from outside your organization.
Dear PETSc team:
For a project that I'm working on, I need to manually build a DMPlex.
>From studying the source code of the various APIs in which the plex is built from some supported file format, I get that the workflow is this:
1.
DMPlexSetChart() <-- Input nCells + nVerts
2.
DMPlexSetConeSize() <-- Input ConeSize for each point in [0,nCells)
3.
DMSetUp() – Allocates memory internally.
4.
DMPlexGetCones() --> Gives you the memory onto which to write the cell connectivity.
5.
*Write connectivity*
6.
DMPlexReorderCell() <-- For each point in [0,nCells)
I'm in a situation where the memory given by step (4) is available a-priori.
I was hoping to skip steps 2, 3 , and 4 with something like a "DMPlexSetCones()", but such an API does not exist.
My current workaround is to implement steps 2 through 4 as always and have double the memory allocated in the interim (my instance + DM's internal instance).
I was thinking of looking for the name of the struct member and = it to my memory, but I can't overcome the flag check in DMSetUp() during later calls to DMPlexGetCones() or DMPlexGetTransitiveClosure().
I do not understand the "flag check". What is that?
We could make a DMPlexSetCones(), but as you point out, the workflow for DMSetUp() would have to change. Where does the memory come from for your connectivity?
Thanks,
Matt
Sincerely:
J.A. Ferrand
Embry-Riddle Aeronautical University - Daytona Beach - FL
Ph.D. Candidate, Aerospace Engineering
M.Sc. Aerospace Engineering
B.Sc. Aerospace Engineering
B.Sc. Computational Mathematics
Phone: (386)-843-1829
Email(s): ferranj2 at my.erau.edu<mailto:ferranj2 at my.erau.edu>
jesus.ferrand at gmail.com<mailto:jesus.ferrand at gmail.com>
--
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!YFXAyokfQwnPYORwZQ6qcxVJHF6uyeDin1NgKfpvqUZafCX_TGDCu_5NYVR63aFhpdQwl9zaJ_woQpUfaXoUdNOo-OU$ <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!YFXAyokfQwnPYORwZQ6qcxVJHF6uyeDin1NgKfpvqUZafCX_TGDCu_5NYVR63aFhpdQwl9zaJ_woQpUfaXoU4UlOUm0$ >
________________________________
From: Matthew Knepley <knepley at gmail.com>
Sent: Wednesday, May 1, 2024 8:07 PM
To: Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
Cc: petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
Subject: [EXTERNAL] Re: [petsc-users] Is there anything like a "DMPlexSetCones()" ?
CAUTION: This email originated outside of Embry-Riddle Aeronautical University. Do not click links or open attachments unless you recognize the sender and know the content is safe.
On Wed, May 1, 2024 at 3:34 PM Ferrand, Jesus A. <FERRANJ2 at my.erau.edu<mailto:FERRANJ2 at my.erau.edu>> wrote:
This Message Is From an External Sender
This message came from outside your organization.
Dear PETSc team:
For a project that I'm working on, I need to manually build a DMPlex.
>From studying the source code of the various APIs in which the plex is built from some supported file format, I get that the workflow is this:
1.
DMPlexSetChart() <-- Input nCells + nVerts
2.
DMPlexSetConeSize() <-- Input ConeSize for each point in [0,nCells)
3.
DMSetUp() – Allocates memory internally.
4.
DMPlexGetCones() --> Gives you the memory onto which to write the cell connectivity.
5.
*Write connectivity*
6.
DMPlexReorderCell() <-- For each point in [0,nCells)
I'm in a situation where the memory given by step (4) is available a-priori.
I was hoping to skip steps 2, 3 , and 4 with something like a "DMPlexSetCones()", but such an API does not exist.
My current workaround is to implement steps 2 through 4 as always and have double the memory allocated in the interim (my instance + DM's internal instance).
I was thinking of looking for the name of the struct member and = it to my memory, but I can't overcome the flag check in DMSetUp() during later calls to DMPlexGetCones() or DMPlexGetTransitiveClosure().
I do not understand the "flag check". What is that?
We could make a DMPlexSetCones(), but as you point out, the workflow for DMSetUp() would have to change. Where does the memory come from for your connectivity?
Thanks,
Matt
Sincerely:
J.A. Ferrand
Embry-Riddle Aeronautical University - Daytona Beach - FL
Ph.D. Candidate, Aerospace Engineering
M.Sc. Aerospace Engineering
B.Sc. Aerospace Engineering
B.Sc. Computational Mathematics
Phone: (386)-843-1829
Email(s): ferranj2 at my.erau.edu<mailto:ferranj2 at my.erau.edu>
jesus.ferrand at gmail.com<mailto:jesus.ferrand at gmail.com>
--
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!YFXAyokfQwnPYORwZQ6qcxVJHF6uyeDin1NgKfpvqUZafCX_TGDCu_5NYVR63aFhpdQwl9zaJ_woQpUfaXoUdNOo-OU$ <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!YFXAyokfQwnPYORwZQ6qcxVJHF6uyeDin1NgKfpvqUZafCX_TGDCu_5NYVR63aFhpdQwl9zaJ_woQpUfaXoU4UlOUm0$ >
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