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"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
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"You know the number of cells if you can read connectivity. Do you mean that the format does not tell you</div>
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the number of vertices?"</div>
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<br>
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Sort of...</div>
<div style="direction: ltr; margin: 0px 40px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
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.</div>
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Which prevents me from knowing the chart a priori.<br>
I figured out the number of vertices using PetscHashSetI to determine the number of unique entries in the connectivity list.</div>
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<br>
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<span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Matthew Knepley <knepley@gmail.com><br>
<b>Sent:</b> Wednesday, May 1, 2024 8:52 PM<br>
<b>To:</b> Ferrand, Jesus A. <FERRANJ2@my.erau.edu><br>
<b>Cc:</b> petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov><br>
<b>Subject:</b> Re: [EXTERNAL] Re: [petsc-users] Is there anything like a "DMPlexSetCones()" ?</span>
<div> </div>
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<div style="direction: ltr;">On Wed, May 1, 2024 at 4:23 PM Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu" id="OWAa34ad222-41ef-8ebb-d63e-45b26a990ee9" class="OWAAutoLink" data-loopstyle="linkonly">FERRANJ2@my.erau.edu</a>> wrote:</div>
<blockquote style="margin: 0px 0px 0px 0.8ex; padding-left: 1ex; border-left: 1px solid rgb(204, 204, 204);">
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Matt:<br>
<br>
My bad again, I need to clarify something that I just realized doesn't make sense.</div>
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
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."</div>
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Scratch that, obviously, if I can read the connectivity, I know the buffer sizes.</div>
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<br>
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What I should have said is that I cannot know the "chart" that one sets in DMPlexSetChart() a priori like in most cases.</div>
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I need to determine the chart from the connectivity lists.</div>
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<div style="direction: ltr;">You know the number of cells if you can read connectivity. Do you mean that the format does not tell you</div>
<div style="direction: ltr;">the number of vertices?</div>
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<div style="direction: ltr;"> Thanks,</div>
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<div style="direction: ltr;"> Matt</div>
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<span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu" id="OWA5b453a06-77d5-ad4d-a4fe-540a37763109" class="OWAAutoLink" data-loopstyle="linkonly">FERRANJ2@my.erau.edu</a>><br>
<b>Sent:</b> Wednesday, May 1, 2024 8:17 PM<br>
<b>To:</b> Matthew Knepley <<a href="mailto:knepley@gmail.com" id="OWA8451e849-2418-9b01-f21a-f872b4eda520" class="OWAAutoLink" data-loopstyle="linkonly">knepley@gmail.com</a>><br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" id="OWAd08a3383-dd03-26aa-feed-526798c12261" class="OWAAutoLink" data-loopstyle="linkonly">petsc-users@mcs.anl.gov</a> <<a href="mailto:petsc-users@mcs.anl.gov" id="OWAde234459-3bc4-3862-f03e-69e083396cb2" class="OWAAutoLink" data-loopstyle="linkonly">petsc-users@mcs.anl.gov</a>><br>
<b>Subject:</b> Re: [EXTERNAL] Re: [petsc-users] Is there anything like a "DMPlexSetCones()" ?</span>
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Matt:</div>
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<br>
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"I do not understand the "flag check". What is that?"</div>
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<br>
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My bad, I should have referred to the "dm->setupcalled".<br>
I believe this PetscBool is checked by the other DM (not just DMPlex) APIs.</div>
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The subsequent checks for dm->setupcalled == PETSC_TRUE is what I meant to say.</div>
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Here's a copy of DMSetUp().</div>
<pre style="width: 80px;"><div style="direction: ltr; margin-right: 80px; margin-left: 80px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);"><b><a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVa4H8D00$" id="OWAdcdf9a24-6408-217f-ed17-fbc1d98cd596" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PetscErrorCode</a> <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DMSetUp/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDV8IM749Q$" id="OWA3a92438a-c0d1-5cab-91bd-2c778db594c1" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">DMSetUp</a>(<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DM/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVgDhrMSM$" id="OWA9f596d1a-5c0d-4e06-2336-dc4379ff7c9d" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">DM</a> dm)</b>
817: {
818: <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionBegin/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVnUPckbQ$" id="OWAe5ac62da-4614-0e2e-eef8-b47c8a183a25" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PetscFunctionBegin</a>;
820: if (dm->setupcalled) <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVA6jIYzM$" id="OWA7f17161a-ebbc-6b13-0e44-7e5530888927" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PetscFunctionReturn</a>(<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVa4H8D00$" id="OWA089d7ae3-758b-5511-6b90-23ba25ec69b2" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PETSC_SUCCESS</a>);
821: <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscTryTypeMethod/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVj0O9HKI$" id="OWA50871ab1-54bc-5b4e-7cfa-a56b53acbbb9" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PetscTryTypeMethod</a>(dm, setup);
822: dm->setupcalled = <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PETSC_TRUE/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVmrWLiyw$" id="OWA8e67be08-f22d-0744-00b1-2cfd27dd72cb" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PETSC_TRUE</a>;
823: <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVA6jIYzM$" id="OWA36ec5552-682d-ba97-5459-c0c5c6a17360" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PetscFunctionReturn</a>(<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVa4H8D00$" id="OWA548bba14-0528-33cb-edb8-cf0bf2d0e111" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PETSC_SUCCESS</a>);
824: }</div></pre>
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"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?"</div>
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It's a memory that I myself allocate based on a file's contents.</div>
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
The nature of the I/O makes it so that I need to read the connectivity before I get a semblance of buffer sizes.<br>
Otherwise, I would stick to the tried and tested way.<br>
<br>
Also, when replying to the PETSc developers, users must reply to <a href="mailto:petsc-users@mcs.anl.gov" id="OWA987e206d-175d-4151-552b-c47b499aaa51" class="OWAAutoLink" data-loopstyle="linkonly">
petsc-users@mcs.anl.gov</a> and not just to the individual email accounts of the developers, right?</div>
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<br>
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<br>
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<br>
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<br>
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<div id="x_m_478286811837034506x_divRplyFwdMsg" dir="ltr" style="color: inherit; background-color: inherit;">
<span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Matthew Knepley <<a href="mailto:knepley@gmail.com" id="OWA7ff217b3-e4cb-c19c-db5f-fb49846fd868" class="OWAAutoLink" data-loopstyle="linkonly">knepley@gmail.com</a>><br>
<b>Sent:</b> Wednesday, May 1, 2024 8:07 PM<br>
<b>To:</b> Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu" id="OWA6fa0d1ff-8ca4-9ca2-ec11-d7fd566a31ca" class="OWAAutoLink" data-loopstyle="linkonly">FERRANJ2@my.erau.edu</a>><br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" id="OWA819daf86-0770-0632-e70c-21b121e8ec28" class="OWAAutoLink" data-loopstyle="linkonly">petsc-users@mcs.anl.gov</a> <<a href="mailto:petsc-users@mcs.anl.gov" id="OWA5bffea7c-f3eb-e407-ab96-b6695aa564db" class="OWAAutoLink" data-loopstyle="linkonly">petsc-users@mcs.anl.gov</a>><br>
<b>Subject:</b> [EXTERNAL] Re: [petsc-users] Is there anything like a "DMPlexSetCones()" ?</span>
<div> </div>
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<span style="color: rgb(214, 0, 0);"><b>CAUTION:</b></span><span style="color: black;"> 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.</span></div>
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<div style="direction: ltr;">On Wed, May 1, 2024 at 3:34 PM Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu" id="OWA686272c1-974c-79a2-5a7d-093821d8f29b" class="OWAAutoLink" data-loopstyle="linkonly">FERRANJ2@my.erau.edu</a>> wrote:</div>
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This Message Is From an External Sender</div>
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This message came from outside your organization.</div>
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Dear PETSc team:<br>
<br>
For a project that I'm working on, I need to manually build a DMPlex.</div>
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>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:</div>
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<br>
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<ol style="direction: ltr; margin-top: 0px; margin-bottom: 0px;" data-listchain="__List_Chain_1635" start="1">
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<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
DMPlexSetChart() <-- Input nCells + nVerts</div>
</li><li style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); list-style-type: "2) ";">
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
DMPlexSetConeSize() <-- Input ConeSize for each point in [0,nCells)</div>
</li><li style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); list-style-type: "3) ";">
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
DMSetUp() – Allocates memory internally.</div>
</li><li style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); list-style-type: "4) ";">
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
DMPlexGetCones() --> Gives you the memory onto which to write the cell connectivity.</div>
</li><li style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); list-style-type: "5) ";">
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
*Write connectivity*</div>
</li><li style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); list-style-type: "6) ";">
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
DMPlexReorderCell() <-- For each point in [0,nCells)</div>
</li></ol>
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
I'm in a situation where the memory given by step (4) is available a-priori.</div>
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
I was hoping to skip steps 2, 3 , and 4 with something like a "DMPlexSetCones()", but such an API does not exist.</div>
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
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).</div>
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
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().</div>
</blockquote>
<div style="direction: ltr;"><br>
</div>
<div style="direction: ltr;">I do not understand the "flag check". What is that?</div>
<div style="direction: ltr;"><br>
</div>
<div style="direction: ltr;">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?</div>
<div style="direction: ltr;"><br>
</div>
<div style="direction: ltr;"> Thanks,</div>
<div style="direction: ltr;"><br>
</div>
<div style="direction: ltr;"> Matt</div>
<div style="direction: ltr;"> </div>
<blockquote style="margin: 0px 0px 0px 0.8ex; padding-left: 1ex; border-left: 1px solid rgb(204, 204, 204);">
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<p style="line-height: normal; background-color: white; margin: 0px 0px 11px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">Sincerely:</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Courier New", monospace; font-size: 14pt; color: red;"><b><u>J.A. Ferrand</u></b></span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">Embry-Riddle Aeronautical University - Daytona Beach - FL<br>
Ph.D. Candidate, Aerospace Engineering</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">M.Sc. Aerospace Engineering</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">B.Sc. Aerospace Engineering</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">B.Sc. Computational Mathematics</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);"><br>
</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;"><u>Phone:</u> (386)-843-1829</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;"><u>Email(s):</u> <a href="mailto:ferranj2@my.erau.edu" id="OWA8faa330b-6e0f-2880-3fd8-efb5ff4edcef" class="OWAAutoLink" style="margin-top: 0px; margin-bottom: 0px;" data-loopstyle="linkonly">ferranj2@my.erau.edu</a></span></p>
<p style="text-indent: 0.5in; line-height: normal; background-color: white; margin: 0px;">
<span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">
<a href="mailto:jesus.ferrand@gmail.com" id="OWAf553f1ad-bd14-ca87-84a0-5920067e7250" class="OWAAutoLink" style="margin-top: 0px; margin-bottom: 0px;" data-loopstyle="linkonly">
jesus.ferrand@gmail.com</a></span></p>
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</div>
</blockquote>
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</div>
<div style="direction: ltr;"><br>
</div>
<div style="direction: ltr;">--</div>
<div style="direction: ltr;">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener</div>
<div style="direction: ltr;"><br>
</div>
<div style="direction: ltr;"><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVu0P9fBI$" id="OWA14d2e185-712c-935d-4b10-76850ee49d7a" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">https://www.cse.buffalo.edu/~knepley/</a></div>
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<span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Matthew Knepley <<a href="mailto:knepley@gmail.com" id="OWA513c6de5-fdbd-f146-b489-2733230de447" class="OWAAutoLink" data-loopstyle="linkonly">knepley@gmail.com</a>><br>
<b>Sent:</b> Wednesday, May 1, 2024 8:07 PM<br>
<b>To:</b> Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu" id="OWAbf5867b0-c3f6-ce5b-7c3a-98f66b7405dd" class="OWAAutoLink" data-loopstyle="linkonly">FERRANJ2@my.erau.edu</a>><br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" id="OWAf92d5b1c-7a59-da27-6007-9d9754649686" class="OWAAutoLink" data-loopstyle="linkonly">petsc-users@mcs.anl.gov</a> <<a href="mailto:petsc-users@mcs.anl.gov" id="OWA310f90a4-b30c-0354-8970-3b6dfce56477" class="OWAAutoLink" data-loopstyle="linkonly">petsc-users@mcs.anl.gov</a>><br>
<b>Subject:</b> [EXTERNAL] Re: [petsc-users] Is there anything like a "DMPlexSetCones()" ?</span>
<div> </div>
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<span style="color: rgb(214, 0, 0);"><b>CAUTION:</b></span><span style="color: black;"> 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.</span></div>
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<div style="direction: ltr;">On Wed, May 1, 2024 at 3:34 PM Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu" id="OWA8198e914-06a6-d8be-c49a-ca762d8d8685" class="OWAAutoLink" data-loopstyle="linkonly">FERRANJ2@my.erau.edu</a>> wrote:</div>
<blockquote style="margin: 0px 0px 0px 0.8ex; padding-left: 1ex; border-left: 1px solid rgb(204, 204, 204);">
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This Message Is From an External Sender</div>
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This message came from outside your organization.</div>
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<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
Dear PETSc team:<br>
<br>
For a project that I'm working on, I need to manually build a DMPlex.</div>
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
>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:</div>
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<ol style="direction: ltr; margin-top: 0px; margin-bottom: 0px;" data-listchain="__List_Chain_1636" start="1">
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<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
DMPlexSetChart() <-- Input nCells + nVerts</div>
</li><li style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); list-style-type: "2) ";">
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
DMPlexSetConeSize() <-- Input ConeSize for each point in [0,nCells)</div>
</li><li style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); list-style-type: "3) ";">
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
DMSetUp() – Allocates memory internally.</div>
</li><li style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); list-style-type: "4) ";">
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
DMPlexGetCones() --> Gives you the memory onto which to write the cell connectivity.</div>
</li><li style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); list-style-type: "5) ";">
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
*Write connectivity*</div>
</li><li style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); list-style-type: "6) ";">
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
DMPlexReorderCell() <-- For each point in [0,nCells)</div>
</li></ol>
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
I'm in a situation where the memory given by step (4) is available a-priori.</div>
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
I was hoping to skip steps 2, 3 , and 4 with something like a "DMPlexSetCones()", but such an API does not exist.</div>
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
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).</div>
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
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().</div>
</blockquote>
<div style="direction: ltr;"><br>
</div>
<div style="direction: ltr;">I do not understand the "flag check". What is that?</div>
<div style="direction: ltr;"><br>
</div>
<div style="direction: ltr;">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?</div>
<div style="direction: ltr;"><br>
</div>
<div style="direction: ltr;"> Thanks,</div>
<div style="direction: ltr;"><br>
</div>
<div style="direction: ltr;"> Matt</div>
<div style="direction: ltr;"> </div>
<blockquote style="margin: 0px 0px 0px 0.8ex; padding-left: 1ex; border-left: 1px solid rgb(204, 204, 204);">
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<div style="background-color: rgb(255, 255, 255); font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
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<p style="line-height: normal; background-color: white; margin: 0px 0px 11px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">Sincerely:</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Courier New", monospace; font-size: 14pt; color: red;"><b><u>J.A. Ferrand</u></b></span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">Embry-Riddle Aeronautical University - Daytona Beach - FL<br>
Ph.D. Candidate, Aerospace Engineering</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">M.Sc. Aerospace Engineering</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">B.Sc. Aerospace Engineering</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">B.Sc. Computational Mathematics</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);"><br>
</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;"><u>Phone:</u> (386)-843-1829</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;"><u>Email(s):</u> <a href="mailto:ferranj2@my.erau.edu" id="OWA3a2eab63-ee7c-8153-259b-19dff0dcff01" class="OWAAutoLink" style="margin-top: 0px; margin-bottom: 0px;" data-loopstyle="linkonly">ferranj2@my.erau.edu</a></span></p>
<p style="text-indent: 0.5in; line-height: normal; background-color: white; margin: 0px;">
<span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">
<a href="mailto:jesus.ferrand@gmail.com" id="OWAb39c1933-7cee-b9f0-a733-73213238632a" class="OWAAutoLink" style="margin-top: 0px; margin-bottom: 0px;" data-loopstyle="linkonly">
jesus.ferrand@gmail.com</a></span></p>
</div>
</div>
</blockquote>
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</div>
<div style="direction: ltr;"><br>
</div>
<div style="direction: ltr;">--</div>
<div style="direction: ltr;">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener</div>
<div style="direction: ltr;"><br>
</div>
<div style="direction: ltr;"><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVu0P9fBI$" id="OWA37e9868e-7d5d-1428-c057-fd60e407105a" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">https://www.cse.buffalo.edu/~knepley/</a></div>
</blockquote>
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</div>
<div style="direction: ltr;"><br>
</div>
<div style="direction: ltr;">--</div>
<div style="direction: ltr;">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener</div>
<div style="direction: ltr;"><br>
</div>
<div style="direction: ltr;"><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVu0P9fBI$" id="OWA2545c66d-816d-63b9-757f-3be2337e9222" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">https://www.cse.buffalo.edu/~knepley/</a></div>
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<span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Matthew Knepley <knepley@gmail.com><br>
<b>Sent:</b> Wednesday, May 1, 2024 8:52 PM<br>
<b>To:</b> Ferrand, Jesus A. <FERRANJ2@my.erau.edu><br>
<b>Cc:</b> petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov><br>
<b>Subject:</b> Re: [EXTERNAL] Re: [petsc-users] Is there anything like a "DMPlexSetCones()" ?</span>
<div> </div>
</div>
<div style="direction: ltr;">On Wed, May 1, 2024 at 4:23 PM Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu" id="OWAbae7a098-4c6f-5008-bfb9-7a173cda274f" class="OWAAutoLink" data-loopstyle="linkonly">FERRANJ2@my.erau.edu</a>> wrote:</div>
<blockquote style="margin: 0px 0px 0px 0.8ex; padding-left: 1ex; border-left: 1px solid rgb(204, 204, 204);">
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
Matt:<br>
<br>
My bad again, I need to clarify something that I just realized doesn't make sense.</div>
<div style="direction: ltr; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
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."</div>
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Scratch that, obviously, if I can read the connectivity, I know the buffer sizes.</div>
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What I should have said is that I cannot know the "chart" that one sets in DMPlexSetChart() a priori like in most cases.</div>
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I need to determine the chart from the connectivity lists.</div>
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<div style="direction: ltr;">You know the number of cells if you can read connectivity. Do you mean that the format does not tell you</div>
<div style="direction: ltr;">the number of vertices?</div>
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<div style="direction: ltr;"> Thanks,</div>
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<span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu" id="OWA9aadafab-c6e2-466e-ceda-0c9b25b999a7" class="OWAAutoLink" data-loopstyle="linkonly">FERRANJ2@my.erau.edu</a>><br>
<b>Sent:</b> Wednesday, May 1, 2024 8:17 PM<br>
<b>To:</b> Matthew Knepley <<a href="mailto:knepley@gmail.com" id="OWAd2a1129e-c76a-5f33-b7ae-e9f0147540c2" class="OWAAutoLink" data-loopstyle="linkonly">knepley@gmail.com</a>><br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" id="OWA5b70e2ff-3a09-145d-0953-77d59d5a65be" class="OWAAutoLink" data-loopstyle="linkonly">petsc-users@mcs.anl.gov</a> <<a href="mailto:petsc-users@mcs.anl.gov" id="OWA1701cb67-d7c5-5514-ae4c-5de8f6cd1dd8" class="OWAAutoLink" data-loopstyle="linkonly">petsc-users@mcs.anl.gov</a>><br>
<b>Subject:</b> Re: [EXTERNAL] Re: [petsc-users] Is there anything like a "DMPlexSetCones()" ?</span>
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Matt:</div>
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"I do not understand the "flag check". What is that?"</div>
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My bad, I should have referred to the "dm->setupcalled".<br>
I believe this PetscBool is checked by the other DM (not just DMPlex) APIs.</div>
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The subsequent checks for dm->setupcalled == PETSC_TRUE is what I meant to say.</div>
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Here's a copy of DMSetUp().</div>
<pre style="width: 80px;"><div style="direction: ltr; margin-right: 80px; margin-left: 80px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);"><b><a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVa4H8D00$" id="OWAb91cbd99-2679-bc8b-0953-84120ba52a95" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PetscErrorCode</a> <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DMSetUp/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDV8IM749Q$" id="OWA9ca16e63-d615-cd91-58a0-0cabfab7706d" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">DMSetUp</a>(<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DM/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVgDhrMSM$" id="OWA27e17768-5be6-6fb4-70b0-764b9b1ad8af" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">DM</a> dm)</b>
817: {
818: <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionBegin/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVnUPckbQ$" id="OWA27dcabe7-e220-5818-6476-b5c03828fdcc" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PetscFunctionBegin</a>;
820: if (dm->setupcalled) <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVA6jIYzM$" id="OWA77b93fee-6e88-c5d8-a844-775fb2aaa1e3" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PetscFunctionReturn</a>(<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVa4H8D00$" id="OWAbc8923dd-b93c-7c79-ccf8-34dff27ae997" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PETSC_SUCCESS</a>);
821: <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscTryTypeMethod/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVj0O9HKI$" id="OWA4fbdab8a-44a4-237e-d2a6-2478d092526f" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PetscTryTypeMethod</a>(dm, setup);
822: dm->setupcalled = <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PETSC_TRUE/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVmrWLiyw$" id="OWA084e0dcf-c5be-ed8a-f9b3-726561cb4a43" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PETSC_TRUE</a>;
823: <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVA6jIYzM$" id="OWA6e8093f0-c27d-a394-5936-a0fdde5e9c56" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PetscFunctionReturn</a>(<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!bg9QrJhAkKOSNFt840OnuOpmX_IlSabDICy99_9tMp9uABL-2lhCm_LG2Fj8rwdySPMiK7rnfMLSIPxs3jDVa4H8D00$" id="OWA7d46889a-8b6d-4b10-0953-c3f76f69f4c0" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PETSC_SUCCESS</a>);
824: }</div></pre>
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"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?"</div>
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It's a memory that I myself allocate based on a file's contents.</div>
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The nature of the I/O makes it so that I need to read the connectivity before I get a semblance of buffer sizes.<br>
Otherwise, I would stick to the tried and tested way.<br>
<br>
Also, when replying to the PETSc developers, users must reply to <a href="mailto:petsc-users@mcs.anl.gov" id="OWA339594d1-e339-8a55-9ebb-5cd0bae29f05" class="OWAAutoLink" data-loopstyle="linkonly">
petsc-users@mcs.anl.gov</a> and not just to the individual email accounts of the developers, right?</div>
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<span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Matthew Knepley <<a href="mailto:knepley@gmail.com" id="OWAe968c95f-4a27-8020-c5ff-982cf264c054" class="OWAAutoLink" data-loopstyle="linkonly">knepley@gmail.com</a>><br>
<b>Sent:</b> Wednesday, May 1, 2024 8:07 PM<br>
<b>To:</b> Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu" id="OWAce540ff9-0219-c249-4bfb-159aa501b174" class="OWAAutoLink" data-loopstyle="linkonly">FERRANJ2@my.erau.edu</a>><br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" id="OWA1cb5fa76-732c-2da4-6a2c-9351519482f3" class="OWAAutoLink" data-loopstyle="linkonly">petsc-users@mcs.anl.gov</a> <<a href="mailto:petsc-users@mcs.anl.gov" id="OWA75d90c20-73e5-652b-bf68-067304c00584" class="OWAAutoLink" data-loopstyle="linkonly">petsc-users@mcs.anl.gov</a>><br>
<b>Subject:</b> [EXTERNAL] Re: [petsc-users] Is there anything like a "DMPlexSetCones()" ?</span>
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<span style="color: rgb(214, 0, 0);"><b>CAUTION:</b></span><span style="color: black;"> 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.</span></div>
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<div style="direction: ltr;">On Wed, May 1, 2024 at 3:34 PM Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu" id="OWAe7f4bcdd-5a0f-f2da-0675-f70677ee9c1e" class="OWAAutoLink" data-loopstyle="linkonly">FERRANJ2@my.erau.edu</a>> wrote:</div>
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This Message Is From an External Sender</div>
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Dear PETSc team:<br>
<br>
For a project that I'm working on, I need to manually build a DMPlex.</div>
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>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:</div>
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<ol style="direction: ltr; margin-top: 0px; margin-bottom: 0px;" data-listchain="__List_Chain_1637" start="1">
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DMPlexSetChart() <-- Input nCells + nVerts</div>
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DMPlexSetConeSize() <-- Input ConeSize for each point in [0,nCells)</div>
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DMSetUp() – Allocates memory internally.</div>
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DMPlexGetCones() --> Gives you the memory onto which to write the cell connectivity.</div>
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*Write connectivity*</div>
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DMPlexReorderCell() <-- For each point in [0,nCells)</div>
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I'm in a situation where the memory given by step (4) is available a-priori.</div>
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I was hoping to skip steps 2, 3 , and 4 with something like a "DMPlexSetCones()", but such an API does not exist.</div>
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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).</div>
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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().</div>
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<div style="direction: ltr;">I do not understand the "flag check". What is that?</div>
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<div style="direction: ltr;">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?</div>
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<div style="direction: ltr;"> Thanks,</div>
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<div style="direction: ltr;"> Matt</div>
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<p style="line-height: normal; background-color: white; margin: 0px 0px 11px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">Sincerely:</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Courier New", monospace; font-size: 14pt; color: red;"><b><u>J.A. Ferrand</u></b></span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">Embry-Riddle Aeronautical University - Daytona Beach - FL<br>
Ph.D. Candidate, Aerospace Engineering</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">M.Sc. Aerospace Engineering</span></p>
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<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;"><u>Phone:</u> (386)-843-1829</span></p>
<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;"><u>Email(s):</u> <a href="mailto:ferranj2@my.erau.edu" id="OWA10dfda44-db14-5791-4b4c-f66aa929406b" class="OWAAutoLink" style="margin-top: 0px; margin-bottom: 0px;" data-loopstyle="linkonly">ferranj2@my.erau.edu</a></span></p>
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<span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">
<a href="mailto:jesus.ferrand@gmail.com" id="OWA7a99b8ad-8961-852f-8abe-e15037c374e1" class="OWAAutoLink" style="margin-top: 0px; margin-bottom: 0px;" data-loopstyle="linkonly">
jesus.ferrand@gmail.com</a></span></p>
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<div style="direction: ltr;">--</div>
<div style="direction: ltr;">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener</div>
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<span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Matthew Knepley <<a href="mailto:knepley@gmail.com" id="OWAc6404b52-5c53-a92a-0546-de24f2e4c799" class="OWAAutoLink" data-loopstyle="linkonly">knepley@gmail.com</a>><br>
<b>Sent:</b> Wednesday, May 1, 2024 8:07 PM<br>
<b>To:</b> Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu" id="OWAb310d2eb-d412-07b6-98c1-c85ed99c74f8" class="OWAAutoLink" data-loopstyle="linkonly">FERRANJ2@my.erau.edu</a>><br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" id="OWA60dcfb09-a0d6-4c39-eaa3-2675ae5d7f2d" class="OWAAutoLink" data-loopstyle="linkonly">petsc-users@mcs.anl.gov</a> <<a href="mailto:petsc-users@mcs.anl.gov" id="OWA36724de3-66bf-71c9-7d73-e9eba39860b0" class="OWAAutoLink" data-loopstyle="linkonly">petsc-users@mcs.anl.gov</a>><br>
<b>Subject:</b> [EXTERNAL] Re: [petsc-users] Is there anything like a "DMPlexSetCones()" ?</span>
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<div style="direction: ltr;">On Wed, May 1, 2024 at 3:34 PM Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu" id="OWA6eda1f9c-1443-7e09-0b6e-ec89ba398926" class="OWAAutoLink" data-loopstyle="linkonly">FERRANJ2@my.erau.edu</a>> wrote:</div>
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Dear PETSc team:<br>
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For a project that I'm working on, I need to manually build a DMPlex.</div>
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>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:</div>
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DMPlexSetChart() <-- Input nCells + nVerts</div>
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DMPlexSetConeSize() <-- Input ConeSize for each point in [0,nCells)</div>
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DMSetUp() – Allocates memory internally.</div>
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DMPlexGetCones() --> Gives you the memory onto which to write the cell connectivity.</div>
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*Write connectivity*</div>
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DMPlexReorderCell() <-- For each point in [0,nCells)</div>
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I'm in a situation where the memory given by step (4) is available a-priori.</div>
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I was hoping to skip steps 2, 3 , and 4 with something like a "DMPlexSetCones()", but such an API does not exist.</div>
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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).</div>
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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().</div>
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<div style="direction: ltr;">I do not understand the "flag check". What is that?</div>
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<div style="direction: ltr;">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?</div>
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<div style="direction: ltr;"> Thanks,</div>
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<div style="direction: ltr;"> Matt</div>
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<p style="line-height: normal; background-color: white; margin: 0px;"><span style="font-family: "Courier New", monospace; font-size: 14pt; color: red;"><b><u>J.A. Ferrand</u></b></span></p>
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<div style="direction: ltr;">--</div>
<div style="direction: ltr;">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener</div>
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<div style="direction: ltr;">--</div>
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