[petsc-users] [EXTERNAL] Re: Is there anything like a "DMPlexSetCones()" ?
Matthew Knepley
knepley at gmail.com
Mon May 6 16:14:35 CDT 2024
On Mon, May 6, 2024 at 4:33 PM Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
wrote:
> "What is the argument for this optimization?"
>
> Ah!
> That's all I had really.
> That you would skip this one malloc step but without regard to the grander
> picture.
> I had a gut feeling that it is a sizeable double malloc because it is the
> cell connectivity.
> However, once you bring into perspective all the other stuff
> (CellOrientation, Vecs, etc.) it does seem like a micro-optimization.
> If in your estimation this isn't worth the development, then I'll continue
> to follow the guidance from the PETSc source code.
>
Once everything is coded, we can put in monitoring, and see if it would
make a difference.
Thanks,
Matt
> ------------------------------
> *From:* Matthew Knepley <knepley at gmail.com>
> *Sent:* Monday, May 6, 2024 10:55 AM
> *To:* Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
> *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()" ?
>
> On Mon, May 6, 2024 at 10:17 AM Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
> wrote:
>
> "The cone sizes are used to allocate the array to hold the cones. How
> would you have an array holding the cone information without knowing the
> sizes?"
>
> You're right, I must first know the sizes (which I determine from the
> file).
> It lists the number of cells and their types by sequential chunks.
>
> The issue I am trying to describe, is that because I cannot know the
> number of local vertices a priori, the pipeline
> DMSetChart()->DMPlexSetConeSize()->DMSetUp() essentially produces a
> redundant array (because I already have the connectivity that I read from
> the file).
> As far as I can tell, in my case, the end result of calling these APIs is
> already available, hence my wish for a "DMPlexSetCones()".
> If such an API existed, I would then attempt to retroactively set the
> Chart and the ConeSizes.
>
> Like you hinted in a reply, for this extra array to be worthwhile, I would
> have to keep it as a global numbering list (which I want to by the way).
> I was hoping to at least keep them in the DM's global PetscSection as
> offsets.
> Unfortunately, PetscSection has a similar workflow to DM:
> PetscSectionSetChart(), PetscSectionAddDof(), PetscSectionSetUp(),
> PetscSectionSetOffset().
>
>
> I looked at the other parallel code. It does maintain two arrays, so that
> you can compute this stuff.
>
> I am reluctant to add this interface, since I think the optimization is
> very small and it is not a good pattern.
> You will save allocating the cell connectivity. However, if you
> interpolate the mesh, this is small. This is the
> same size as the cell orientations, which we will also have to allocate.
> We are likely to allocate vectors over the mesh. It does not seem likely
> that this allocation will increase the peak allocation, and it will be
> freed after creation, so total size will not be affected. What is the
> argument for this optimization?
>
> Thanks,
>
> Matt
>
>
> ------------------------------
> *From:* Matthew Knepley <knepley at gmail.com>
> *Sent:* Monday, May 6, 2024 7:52 AM
> *To:* Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
> *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()" ?
>
> On Fri, May 3, 2024 at 7:32 PM Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
> wrote:
>
> "Right, but that means that the connectivity you read in is not in local
> numbering. You will have to renumber it, so making a copy is probably
> necessary anyway. This is the same sort of processing I do for the parallel
> read."
>
> True, the connectivity is read in global numbering.
> Renumbering is facilitated by the table from PetscHashSetI.
> The connectivity list I am able to renumber in place though, I don't see
> the need to have another interim copy of the numbers.
> My concern is that I have two memory chunks that both contain the same
> information.
> The only reason It has to be this way is because I can't manually set the
> Cones first and the Chart/ConeSizes second.
>
>
> The cone sizes are used to allocate the array to hold the cones. How would
> you have an array holding the cone information without knowing the sizes?
>
> Thanks,
>
> Matt
>
>
> ------------------------------
> *From:* Matthew Knepley <knepley at gmail.com>
> *Sent:* Friday, May 3, 2024 6:45 PM
> *To:* Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
> *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()" ?
>
> On Wed, May 1, 2024 at 6:30 PM Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
> wrote:
>
> "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?"
>
> Sort of...
> So, the format does provide the number of vertices, however, due to the
> way I read the data in parallel I don't know immediately how many local
> vertices there will be.
> Which prevents me from knowing the chart a priori.
> I figured out the number of vertices using PetscHashSetI to determine the
> number of unique entries in the connectivity list.
>
>
> Right, but that means that the connectivity you read in is not in local
> numbering. You will have to renumber it, so making a copy is probably
> necessary anyway. This is the same sort of processing I do for the parallel
> read.
>
> Thanks,
>
> Matt
>
>
> ------------------------------
> *From:* Matthew Knepley <knepley at gmail.com>
> *Sent:* Wednesday, May 1, 2024 8:52 PM
> *To:* Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
> *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()" ?
>
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEKC-qu2V$ > DMSetUp <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DMSetUp/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEFRaFnFP$ >(DM <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DM/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOsMzn8I$ > dm)*
> 817: {
> 818: PetscFunctionBegin <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionBegin/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYECLIvlTF$ >;
> 820: if (dm->setupcalled) PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEPMSYHRs$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEKC-qu2V$ >);
> 821: PetscTryTypeMethod <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscTryTypeMethod/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEMNOEPZO$ >(dm, setup);
> 822: dm->setupcalled = PETSC_TRUE <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PETSC_TRUE/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEEwtC_Xx$ >;
> 823: PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEPMSYHRs$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEKC-qu2V$ >);
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
> ------------------------------
> *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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
>
>
> --
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
> ------------------------------
> *From:* Matthew Knepley <knepley at gmail.com>
> *Sent:* Wednesday, May 1, 2024 8:52 PM
> *To:* Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
> *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()" ?
>
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEKC-qu2V$ > DMSetUp <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DMSetUp/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEFRaFnFP$ >(DM <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DM/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOsMzn8I$ > dm)*
> 817: {
> 818: PetscFunctionBegin <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionBegin/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYECLIvlTF$ >;
> 820: if (dm->setupcalled) PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEPMSYHRs$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEKC-qu2V$ >);
> 821: PetscTryTypeMethod <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscTryTypeMethod/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEMNOEPZO$ >(dm, setup);
> 822: dm->setupcalled = PETSC_TRUE <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PETSC_TRUE/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEEwtC_Xx$ >;
> 823: PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEPMSYHRs$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEKC-qu2V$ >);
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
> ------------------------------
> *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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
>
>
> --
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
>
>
> --
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
> ------------------------------
> *From:* Matthew Knepley <knepley at gmail.com>
> *Sent:* Friday, May 3, 2024 6:45 PM
> *To:* Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
> *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()" ?
>
> On Wed, May 1, 2024 at 6:30 PM Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
> wrote:
>
> "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?"
>
> Sort of...
> So, the format does provide the number of vertices, however, due to the
> way I read the data in parallel I don't know immediately how many local
> vertices there will be.
> Which prevents me from knowing the chart a priori.
> I figured out the number of vertices using PetscHashSetI to determine the
> number of unique entries in the connectivity list.
>
>
> Right, but that means that the connectivity you read in is not in local
> numbering. You will have to renumber it, so making a copy is probably
> necessary anyway. This is the same sort of processing I do for the parallel
> read.
>
> Thanks,
>
> Matt
>
>
> ------------------------------
> *From:* Matthew Knepley <knepley at gmail.com>
> *Sent:* Wednesday, May 1, 2024 8:52 PM
> *To:* Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
> *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()" ?
>
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEKC-qu2V$ > DMSetUp <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DMSetUp/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEFRaFnFP$ >(DM <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DM/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOsMzn8I$ > dm)*
> 817: {
> 818: PetscFunctionBegin <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionBegin/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYECLIvlTF$ >;
> 820: if (dm->setupcalled) PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEPMSYHRs$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEKC-qu2V$ >);
> 821: PetscTryTypeMethod <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscTryTypeMethod/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEMNOEPZO$ >(dm, setup);
> 822: dm->setupcalled = PETSC_TRUE <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PETSC_TRUE/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEEwtC_Xx$ >;
> 823: PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEPMSYHRs$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEKC-qu2V$ >);
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
> ------------------------------
> *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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
>
>
> --
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
> ------------------------------
> *From:* Matthew Knepley <knepley at gmail.com>
> *Sent:* Wednesday, May 1, 2024 8:52 PM
> *To:* Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
> *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()" ?
>
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEKC-qu2V$ > DMSetUp <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DMSetUp/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEFRaFnFP$ >(DM <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DM/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOsMzn8I$ > dm)*
> 817: {
> 818: PetscFunctionBegin <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionBegin/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYECLIvlTF$ >;
> 820: if (dm->setupcalled) PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEPMSYHRs$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEKC-qu2V$ >);
> 821: PetscTryTypeMethod <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscTryTypeMethod/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEMNOEPZO$ >(dm, setup);
> 822: dm->setupcalled = PETSC_TRUE <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PETSC_TRUE/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEEwtC_Xx$ >;
> 823: PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEPMSYHRs$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEKC-qu2V$ >);
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
> ------------------------------
> *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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
>
>
> --
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
>
>
> --
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
>
>
> --
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
>
>
> --
> 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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
>
--
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!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEOhAg41j$ <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!e9WPKXONc0pLYPYlljjUQFKHdYCzY9jNdMc8ArfhWOkp0rNjus9LqI5q44BmF41a_NqGuSVzGofYEDpqhdq6$ >
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