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Hello Matt, Thanks for the help. I believe the problem is coming from an incorrect linking with MPI and PETSc. I tried running with petscmpiexec from $PETSC_DIR/lib/petsc/bin/petscmpiexec. This gave me the error Error build location not found!
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Hello Matt,
<div><br>
</div>
<div>Thanks for the help. I believe the problem is coming from an incorrect linking with MPI and PETSc. </div>
<div><br>
</div>
<div>I tried running with petscmpiexec from <span style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px;">$PETSC_DIR/lib/petsc/bin/petscmpiexec.</span><font color="#000000"><span style="caret-color: rgb(0, 0, 0);"> This gave me the error </span></font></div>
<div><span style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px;"><br>
</span></div>
<div><span style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px;">Error build location not found! Please set PETSC_DIR and PETSC_ARCH correctly for this build.</span>
<div><br>
</div>
<div><br>
</div>
<div>Naturally I have set these two values and echo $PETSC_DIR gives the path I expect, so it seems like I am running my programs with a different version of MPI than petsc expects which could explain the memory usage.</div>
<div><br>
</div>
<div>Do you have any ideas how to fix this?</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Matt</div>
<div><br>
<blockquote type="cite">
<div>On 24 Jul 2024, at 8:41 PM, Matthew Knepley <knepley@gmail.com> wrote:</div>
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<div>You don't often get email from<span class="Apple-converted-space"> </span><a href="mailto:knepley@gmail.com">knepley@gmail.com</a>.<span class="Apple-converted-space"> </span><a href="https://urldefense.us/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!G_uCfscf7eWS!epHRik2gEGTbxUIxHTZA8CUffEfzhhzq27rzxfOcoDlVKKH1y-WhrMjjMMlcrPTnLioR4wetiSo-dP3RtNApVyMi1iL0g-561B0$">Learn why this is important</a></div>
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<div dir="ltr">
<div dir="ltr">On Tue, Jul 23, 2024 at 8:02 PM Matthew Thomas <<a href="mailto:matthew.thomas1@anu.edu.au">matthew.thomas1@anu.edu.au</a>> wrote:<br>
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<div>Hello Matt,
<div><br>
</div>
<div>I have attached the output with mat_view for 8 and 40 processors.</div>
<div><br>
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<div>I am unsure what is meant by the matrix communicator and the partitioning. I am using the default behaviour in every case. How can I find this information?</div>
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</div>
<div>This shows that the matrix is taking the same amount of memory for 8 and 40 procs, so that is not your problem. Also,</div>
<div>it is a very small amount of memory:</div>
<div><br>
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<div> 100K rows x 3 nz/row x 8 bytes/nz = 2.4 MB</div>
<div><br>
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<div>and 50% overhead for indexing, so something under 4MB. I am not sure what is taking up the rest of the memory, but I do not</div>
<div>think it is PETSc from the log you included.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
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<div>I have attached the log view as well if that helps.</div>
<div><br>
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<div>Thanks,</div>
<div>Matt</div>
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<div>On 23 Jul 2024, at 9:24 PM, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:</div>
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<div>You don't often get email from<span> </span><a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>.<span> </span><a href="https://urldefense.us/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!G_uCfscf7eWS!epHRik2gEGTbxUIxHTZA8CUffEfzhhzq27rzxfOcoDlVKKH1y-WhrMjjMMlcrPTnLioR4wetiSo-dP3RtNApVyMi1iL0g-561B0$" target="_blank">Learn why this is important</a></div>
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<div dir="ltr">Also, you could run with
<div><br>
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<div> -mat_view ::ascii_info_detail</div>
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<div>and send the output for both cases. The storage of matrix values is not redundant, so something else is</div>
<div>going on. First, what communicator do you use for the matrix, and what partitioning?</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
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<div>
<div dir="ltr">On Mon, Jul 22, 2024 at 10:27 PM Barry Smith <<a href="mailto:bsmith@petsc.dev" target="_blank">bsmith@petsc.dev</a>> wrote:<br>
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<div>On Jul 22, 2024, at 9:18 PM, Matthew Thomas via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>> wrote:</div>
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<pre style="font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; text-decoration: none; font-family: sans-serif; white-space: pre-wrap;">Hello,
I am using petsc and slepc to solve an eigenvalue problem for sparse matrices. When I run my code with double the number of processors, the memory usage also doubles.
I am able to reproduce this behaviour with ex1 of slepc’s hands on exercises.
The issue is occurring with petsc not with slepc as this still occurs when I remove the solve step and just create and assemble the petsc matrix.
With n=100000, this uses ~1Gb with 8 processors, but ~5Gb with 40 processors.
This was done with petsc 3.21.3, on linux compiled with Intel using Intel-MPI
Is this the expected behaviour? If not, how can I bug fix this?
Thanks,
Matt</pre>
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<span>--<span> </span></span><br>
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<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>
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<div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!epHRik2gEGTbxUIxHTZA8CUffEfzhhzq27rzxfOcoDlVKKH1y-WhrMjjMMlcrPTnLioR4wetiSo-dP3RtNApVyMi1iL0TD7Xv-0$" originalsrc="http://www.cse.buffalo.edu/~knepley/" shash="KCFokSmsh5ps56NWzr6DeOebwPUkHMRQzXUhsV5KycoeaMS+6J+aCJqvz2cu1zt+C3XhoQLnVty+z3DovVW+WI3cbgrHNaCkaQ+L5uutEpRMGxAJFjDZnopxNgE43S2ukVpS3jiLsx8yKU/KXrvKZ23CzA6bH2nQWBKAoBOHe7M=" target="_blank">https://www.cse.buffalo.edu/~knepley/</a></div>
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<span class="gmail_signature_prefix">--<span class="Apple-converted-space"> </span></span><br>
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<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>
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<div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!epHRik2gEGTbxUIxHTZA8CUffEfzhhzq27rzxfOcoDlVKKH1y-WhrMjjMMlcrPTnLioR4wetiSo-dP3RtNApVyMi1iL0TD7Xv-0$" originalsrc="http://www.cse.buffalo.edu/~knepley/" shash="ajhm7fkmi2PMxDwpKsVMZPpa/NcsBu28dQWC4ldonJyS2OOEXXLP3rR6P899ZdP9V57YyoIfboJLcqLtml4TJz8ZpMaR81DZnFcEiGl8FuIaJugSlDqaJmDvHTnUFbgoQWzU48Z1dps8a2iZoVJHF5XaIyIvqu+wzcZYUTlmimw=" target="_blank">https://www.cse.buffalo.edu/~knepley/</a></div>
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