[petsc-users] [EXTERNAL] Re: Is there anything like a "DMPlexSetCones()" ?

Matthew Knepley knepley at gmail.com
Wed May 1 19:52:32 CDT 2024 

On Wed, May 1, 2024 at 4:23 PM Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
wrote:

> Matt:
>
> My bad again, I need to clarify something that I just realized doesn't
> make sense.
> I said: "The nature of the I/O makes it so that I need to read the
> connectivity before I get a semblance of buffer sizes."
> Scratch that, obviously, if I can read the connectivity, I know the buffer
> sizes.
>
> What I should have said is that I cannot know the "chart" that one sets in
> DMPlexSetChart() a priori like in most cases.
> I need to determine the chart from the connectivity lists.
>

You know the number of cells if you can read connectivity. Do you mean that
the format does not tell you
the number of vertices?

  Thanks,

    Matt


> ------------------------------
> *From:* Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
> *Sent:* Wednesday, May 1, 2024 8:17 PM
> *To:* Matthew Knepley <knepley at gmail.com>
> *Cc:* petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
> *Subject:* Re: [EXTERNAL] Re: [petsc-users] Is there anything like a
> "DMPlexSetCones()" ?
>
> 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!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbEGErkJ-$ > DMSetUp <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DMSetUp/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbHlKVRsv$ >(DM <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DM/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbLTlKr33$ > dm)*
> 817: {
> 818:   PetscFunctionBegin <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionBegin/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbO3Lr_yl$ >;
> 820:   if (dm->setupcalled) PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbIQ_4i0Z$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbEGErkJ-$ >);
> 821:   PetscTryTypeMethod <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscTryTypeMethod/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbAvZ6cYM$ >(dm, setup);
> 822:   dm->setupcalled = PETSC_TRUE <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PETSC_TRUE/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbDXZdzLl$ >;
> 823:   PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbIQ_4i0Z$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbEGErkJ-$ >);
> 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>
> 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
>
>     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!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbI8UMqBN$ 
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbKClgWhj$ >
>
> ------------------------------
> *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>
> 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
>
>     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!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbI8UMqBN$ 
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbKClgWhj$ >
>


-- 
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!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbI8UMqBN$  <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbKClgWhj$ >
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