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Ok, I will try to implement your suggestions. <br>
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Thank you very much for your help, <br>
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Pantelis<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Barry Smith <bsmith@petsc.dev><br>
<b>Sent:</b> Tuesday, March 14, 2023 5:21 PM<br>
<b>To:</b> Pantelis Moschopoulos <pmoschopoulos@outlook.com><br>
<b>Cc:</b> Dave May <dave.mayhem23@gmail.com>; petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov><br>
<b>Subject:</b> Re: [petsc-users] Memory Usage in Matrix Assembly.</font>
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Yes, you should partition the elements and redistribute them for optimal parallelism.
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<div> You can use the MatPartitioning object to partition the graph of the elements which will tell you what elements should be assigned to each MPI process. But then you need to move the element information to the correct process. At that point your code
will remain pretty much as it is now.</div>
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<div> Barry</div>
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<div>On Mar 14, 2023, at 10:59 AM, Pantelis Moschopoulos <pmoschopoulos@outlook.com> wrote:</div>
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Dear Dave,<span class="x_Apple-converted-space"> </span><br>
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Yes, I observe this in parallel runs. How I can change the parallel layout of the matrix? In my implementation, I read the mesh file, and the I split the domain where the first rank gets the first N elements, the second rank gets the next N elements etc. Should
I use metis to distribute elements? Note that I use continuous finite elements, which means that some values will be cached in a temporary buffer.</div>
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Thank you very much,<span class="x_Apple-converted-space"> </span><br>
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Pantelis<br>
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<font face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b><span class="x_Apple-converted-space"> </span>Dave May <dave.mayhem23@gmail.com><br>
<b>Sent:</b><span class="x_Apple-converted-space"> </span>Tuesday, March 14, 2023 4:40 PM<br>
<b>To:</b><span class="x_Apple-converted-space"> </span>Pantelis Moschopoulos <pmoschopoulos@outlook.com><br>
<b>Cc:</b><span class="x_Apple-converted-space"> </span>petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov><br>
<b>Subject:</b><span class="x_Apple-converted-space"> </span>Re: [petsc-users] Memory Usage in Matrix Assembly.</font>
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<div dir="ltr" class="x_x_gmail_attr">On Tue 14. Mar 2023 at 07:15, Pantelis Moschopoulos <<a href="mailto:pmoschopoulos@outlook.com">pmoschopoulos@outlook.com</a>> wrote:<br>
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Hi everyone,<span class="x_Apple-converted-space"> </span><br>
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I am a new Petsc user that incorporates Petsc for FEM in a Fortran code. <br>
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My question concerns the sudden increase of the memory that Petsc needs during the assembly of the jacobian matrix. After this point, memory is freed. It seems to me like Petsc performs memory allocations and the deallocations during assembly.<span class="x_Apple-converted-space"> </span><br>
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I have used the following commands with no success:<span class="x_Apple-converted-space"> </span><br>
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CALL MatSetOption(petsc_A, MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE,ier)
<div>CALL MatSetOption(petsc_A, MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE,ier)</div>
CALL MatSetOption(petsc_A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE,ier).</div>
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CALL MatSetOption(petsc_A, MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE,ier)</div>
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The structure of the matrix does not change during my simulation, just the values. I am expecting this behavior the first time that I create this matrix because the preallocation instructions that I use are not very accurate but this continues every time I
assemble the matrix.</div>
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What I am missing here?</div>
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<div dir="auto">I am guessing this observation is seen when you run a parallel job.</div>
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<div dir="auto">MatSetValues() will cache values in a temporary memory buffer if the values are to be sent to a different MPI rank.<br>
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<div dir="auto">Hence if the parallel layout of your matrix doesn’t closely match the layout of the DOFs on each mesh sub-domain, then a huge number of values can potentially be cached. After you call MatAssemblyBegin(), MatAssemblyEnd() this cache will be
freed.<br>
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<div dir="auto">Thanks,</div>
<div dir="auto">Dave</div>
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Thank you very much,<span class="x_Apple-converted-space"> </span><br>
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Pantelis<span class="x_Apple-converted-space"> </span></div>
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