[petsc-users] [EXTERNAL] Re: Is there anything like a "DMPlexSetCones()" ?
Matthew Knepley
knepley at gmail.com
Mon May 6 09:55:31 CDT 2024
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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWoiqoBkl$ > DMSetUp <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DMSetUp/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWiHpYbys$ >(DM <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DM/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWms3JV3i$ > dm)*
> 817: {
> 818: PetscFunctionBegin <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionBegin/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWnKFkf_9$ >;
> 820: if (dm->setupcalled) PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWgYBYkMz$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWoiqoBkl$ >);
> 821: PetscTryTypeMethod <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscTryTypeMethod/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWjbXkgtI$ >(dm, setup);
> 822: dm->setupcalled = PETSC_TRUE <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PETSC_TRUE/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWkJC5LJt$ >;
> 823: PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWgYBYkMz$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWoiqoBkl$ >);
> 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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
>
> ------------------------------
> *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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
>
>
>
> --
> 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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
>
> ------------------------------
> *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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWoiqoBkl$ > DMSetUp <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DMSetUp/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWiHpYbys$ >(DM <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DM/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWms3JV3i$ > dm)*
> 817: {
> 818: PetscFunctionBegin <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionBegin/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWnKFkf_9$ >;
> 820: if (dm->setupcalled) PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWgYBYkMz$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWoiqoBkl$ >);
> 821: PetscTryTypeMethod <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscTryTypeMethod/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWjbXkgtI$ >(dm, setup);
> 822: dm->setupcalled = PETSC_TRUE <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PETSC_TRUE/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWkJC5LJt$ >;
> 823: PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWgYBYkMz$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWoiqoBkl$ >);
> 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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
>
> ------------------------------
> *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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
>
>
>
> --
> 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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
>
>
>
> --
> 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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
>
> ------------------------------
> *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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWoiqoBkl$ > DMSetUp <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DMSetUp/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWiHpYbys$ >(DM <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DM/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWms3JV3i$ > dm)*
> 817: {
> 818: PetscFunctionBegin <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionBegin/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWnKFkf_9$ >;
> 820: if (dm->setupcalled) PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWgYBYkMz$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWoiqoBkl$ >);
> 821: PetscTryTypeMethod <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscTryTypeMethod/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWjbXkgtI$ >(dm, setup);
> 822: dm->setupcalled = PETSC_TRUE <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PETSC_TRUE/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWkJC5LJt$ >;
> 823: PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWgYBYkMz$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWoiqoBkl$ >);
> 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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
>
> ------------------------------
> *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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
>
>
>
> --
> 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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
>
> ------------------------------
> *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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWoiqoBkl$ > DMSetUp <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DMSetUp/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWiHpYbys$ >(DM <https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DM/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWms3JV3i$ > dm)*
> 817: {
> 818: PetscFunctionBegin <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionBegin/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWnKFkf_9$ >;
> 820: if (dm->setupcalled) PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWgYBYkMz$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWoiqoBkl$ >);
> 821: PetscTryTypeMethod <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscTryTypeMethod/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWjbXkgtI$ >(dm, setup);
> 822: dm->setupcalled = PETSC_TRUE <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PETSC_TRUE/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWkJC5LJt$ >;
> 823: PetscFunctionReturn <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWgYBYkMz$ >(PETSC_SUCCESS <https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWoiqoBkl$ >);
> 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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
>
> ------------------------------
> *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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
>
>
>
> --
> 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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
>
>
>
> --
> 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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
>
>
>
> --
> 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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
>
--
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!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWihF3ryu$ <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cfVoObgiLc90zIrUaHVMSXqAJtv69Ufe3A1lF0j0zEtULlt1kmKQ7ywA6tGfxdvxMMGDSlHe66KyWlvTXVNW$ >
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