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On Wed, May 1, 2024 at 4: 23 PM Ferrand, Jesus A. <FERRANJ2@ 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
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<div dir="ltr"><div dir="ltr">On Wed, May 1, 2024 at 4:23 PM Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu">FERRANJ2@my.erau.edu</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg478286811837034506">
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Matt:<br>
<br>
My bad again, I need to clarify something that I just realized doesn't make sense.</div>
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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></div></div></blockquote><div><br></div><div>You know the number of cells if you can read connectivity. Do you mean that the format does not tell you</div><div>the number of vertices?</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg478286811837034506"><div dir="ltr">
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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" target="_blank">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" target="_blank">knepley@gmail.com</a>><br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a> <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">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!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbEGErkJ-$" id="m_478286811837034506OWA584aa1d4-edb6-60bd-5deb-f91144368942" target="_blank">PetscErrorCode</a> <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DMSetUp/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbHlKVRsv$" id="m_478286811837034506OWAee8ffec2-b719-bd5e-caba-518db51191f5" target="_blank">DMSetUp</a>(<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/DM/DM/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbLTlKr33$" id="m_478286811837034506OWA3616444b-12cb-5c6e-4bc4-2ed41a565772" target="_blank">DM</a> dm)</b>
817: {
818: <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionBegin/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbO3Lr_yl$" id="m_478286811837034506OWAc4311b67-9870-d0e2-1ee4-91bbb4af9897" target="_blank">PetscFunctionBegin</a>;
820: if (dm->setupcalled) <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbIQ_4i0Z$" id="m_478286811837034506OWAd6efe15d-f606-32e3-e6d1-cd6019950f9d" target="_blank">PetscFunctionReturn</a>(<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbEGErkJ-$" id="m_478286811837034506OWAefa8868d-743e-61c6-0199-4a6232bbd97a" target="_blank">PETSC_SUCCESS</a>);
821: <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscTryTypeMethod/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbAvZ6cYM$" id="m_478286811837034506OWAef63a750-3ca0-e48e-c615-5d8e140b643f" target="_blank">PetscTryTypeMethod</a>(dm, setup);
822: dm->setupcalled = <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PETSC_TRUE/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbDXZdzLl$" id="m_478286811837034506OWA0a74d419-3406-eb21-730c-249b244d24ef" target="_blank">PETSC_TRUE</a>;
823: <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscFunctionReturn/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbIQ_4i0Z$" id="m_478286811837034506OWA077d38f2-b064-f5f4-70e9-ddec399435dc" target="_blank">PetscFunctionReturn</a>(<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscErrorCode/__;!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbEGErkJ-$" id="m_478286811837034506OWA291d9c37-9b72-4bca-2be4-d92dcb362ddc" target="_blank">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" target="_blank">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" target="_blank">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" target="_blank">FERRANJ2@my.erau.edu</a>><br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a> <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">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="m_478286811837034506OWAcff6ba0e-2d0c-2d92-3a16-57020f9a3f3a" target="_blank">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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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="m_478286811837034506OWAed1a4422-632a-2bc9-7d0c-fdd8cbb84892" style="margin-top:0px;margin-bottom:0px" target="_blank">ferranj2@my.erau.edu</a></span></p>
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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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<div style="direction:ltr"><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbKClgWhj$" id="m_478286811837034506OWAc1da9e97-cc12-a51c-de50-3b7e7cacebc2" target="_blank">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" target="_blank">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" target="_blank">FERRANJ2@my.erau.edu</a>><br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a> <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">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="m_478286811837034506OWAd202a882-da56-cf44-cb6d-00d21c8fbd5b" target="_blank">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="m_478286811837034506OWA41fc8cd1-1810-77b6-926b-326591846547" style="margin-top:0px;margin-bottom:0px" target="_blank">ferranj2@my.erau.edu</a></span></p>
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jesus.ferrand@gmail.com</a></span></p>
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</div></blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>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><br></div><div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dYZsj6bNyjrW3n2ZUHSK0N1eCUS5ylIPHxjjS0SQT-DSlMCOeipzRVmuuasQCL9GHi7tXPQbRftLbKClgWhj$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>