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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,
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<div class="elementToProof" style="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 class="elementToProof" style="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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<span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Ferrand, Jesus A. <FERRANJ2@my.erau.edu><br>
<b>Sent:</b> Wednesday, May 1, 2024 8:17 PM<br>
<b>To:</b> Matthew Knepley <knepley@gmail.com><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>
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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!Y59qV_AfccorvDZ2Ux5zlODn2plUGK9DDK2MadlAOvbh7uPhFCvfhWkUgJ_4ncaI6RxBeDbsKAPuyB-H6hOIvmDOx14$" id="OWA584aa1d4-edb6-60bd-5deb-f91144368942" class="x_OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PetscErrorCode</a> <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DMSetUp/__;!!G_uCfscf7eWS!Y59qV_AfccorvDZ2Ux5zlODn2plUGK9DDK2MadlAOvbh7uPhFCvfhWkUgJ_4ncaI6RxBeDbsKAPuyB-H6hOIOSy-UaQ$" id="OWAee8ffec2-b719-bd5e-caba-518db51191f5" class="x_OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">DMSetUp</a>(<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DM/__;!!G_uCfscf7eWS!Y59qV_AfccorvDZ2Ux5zlODn2plUGK9DDK2MadlAOvbh7uPhFCvfhWkUgJ_4ncaI6RxBeDbsKAPuyB-H6hOIQUtSyT4$" id="OWA3616444b-12cb-5c6e-4bc4-2ed41a565772" class="x_OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">DM</a> dm)</b>
817: {
818: <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionBegin/__;!!G_uCfscf7eWS!Y59qV_AfccorvDZ2Ux5zlODn2plUGK9DDK2MadlAOvbh7uPhFCvfhWkUgJ_4ncaI6RxBeDbsKAPuyB-H6hOIthWKl2Y$" id="OWAc4311b67-9870-d0e2-1ee4-91bbb4af9897" class="x_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!Y59qV_AfccorvDZ2Ux5zlODn2plUGK9DDK2MadlAOvbh7uPhFCvfhWkUgJ_4ncaI6RxBeDbsKAPuyB-H6hOIA9zrkn4$" id="OWAd6efe15d-f606-32e3-e6d1-cd6019950f9d" class="x_OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PetscFunctionReturn</a>(<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!Y59qV_AfccorvDZ2Ux5zlODn2plUGK9DDK2MadlAOvbh7uPhFCvfhWkUgJ_4ncaI6RxBeDbsKAPuyB-H6hOIvmDOx14$" id="OWAefa8868d-743e-61c6-0199-4a6232bbd97a" class="x_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!Y59qV_AfccorvDZ2Ux5zlODn2plUGK9DDK2MadlAOvbh7uPhFCvfhWkUgJ_4ncaI6RxBeDbsKAPuyB-H6hOIFSJZYG4$" id="OWAef63a750-3ca0-e48e-c615-5d8e140b643f" class="x_OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PetscTryTypeMethod</a>(dm, setup);
822: dm->setupcalled = <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PETSC_TRUE/__;!!G_uCfscf7eWS!Y59qV_AfccorvDZ2Ux5zlODn2plUGK9DDK2MadlAOvbh7uPhFCvfhWkUgJ_4ncaI6RxBeDbsKAPuyB-H6hOIQcJ2U-8$" id="OWA0a74d419-3406-eb21-730c-249b244d24ef" class="x_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!Y59qV_AfccorvDZ2Ux5zlODn2plUGK9DDK2MadlAOvbh7uPhFCvfhWkUgJ_4ncaI6RxBeDbsKAPuyB-H6hOIA9zrkn4$" id="OWA077d38f2-b064-f5f4-70e9-ddec399435dc" class="x_OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly">PetscFunctionReturn</a>(<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!Y59qV_AfccorvDZ2Ux5zlODn2plUGK9DDK2MadlAOvbh7uPhFCvfhWkUgJ_4ncaI6RxBeDbsKAPuyB-H6hOIvmDOx14$" id="OWA291d9c37-9b72-4bca-2be4-d92dcb362ddc" class="x_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 petsc-users@mcs.anl.gov 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 <knepley@gmail.com><br>
<b>Sent:</b> Wednesday, May 1, 2024 8:07 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> [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="OWAcff6ba0e-2d0c-2d92-3a16-57020f9a3f3a" class="x_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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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>
<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>
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</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="OWAed1a4422-632a-2bc9-7d0c-fdd8cbb84892" class="x_OWAAutoLink" style="margin-top: 0px; margin-bottom: 0px;" data-loopstyle="linkonly">ferranj2@my.erau.edu</a></span></p>
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<a href="mailto:jesus.ferrand@gmail.com" id="OWA3aa21571-8401-c879-4848-2621bbe0465a" class="x_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;">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 <knepley@gmail.com><br>
<b>Sent:</b> Wednesday, May 1, 2024 8:07 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> [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="OWAd202a882-da56-cf44-cb6d-00d21c8fbd5b" class="x_OWAAutoLink" data-loopstyle="linkonly">FERRANJ2@my.erau.edu</a>> wrote:</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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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>
<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>
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</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="OWA41fc8cd1-1810-77b6-926b-326591846547" class="x_OWAAutoLink" style="margin-top: 0px; margin-bottom: 0px;" data-loopstyle="linkonly">ferranj2@my.erau.edu</a></span></p>
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<a href="mailto:jesus.ferrand@gmail.com" id="OWA304e1462-e04c-b5c5-bed1-78b0133bc708" class="x_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>
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-- Norbert Wiener</div>
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