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<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US">Hello Barry,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US">I would like to better understand
</span><span style="font-size:11.0pt">pc_type redistribute usage. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I am plan to use pc_type <u>redistribute</u> in the context of adaptive mesh refinement on a structured grid in 2D. My base mesh (level 0) is indexed from 0 to N-1 elements and refined mesh (level 1) is indexed
from 0 to 4(N-1) elements. When I construct system matrix A on (level 1); I probably only use 20% of 4(N-1) elements, however the indexes are scattered in the range of 0 to 4(N-1). That leaves 80% of the rows and columns of the system matrix A on (level 1)
to be zero. From your earlier response, I believe this would be a use case for petsc_type redistribute.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Question (1)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">If N is really large, I would have to allocate memory of size 4(N-1) for the system matrix A on (level 1). How does pc_type redistribute<u>
</u>help? Because, I did end up allocating memory for a large system, where most of the rows and columns are zeros. Is most of the allotted memory not wasted?<u> Is this the correct usage?<o:p></o:p></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Question (2)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I tried using pc_type redistribute for a two level system.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I have <b><u>attached</u></b> the output only for (level 1)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">The solution converges to right solution but still petsc outputs some error messages.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[0]PETSC ERROR: WARNING! There are option(s) set that were not used! Could be the program crashed before they were used or a spelling mistake, etc!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[0]PETSC ERROR: Option left: name:-options_left (no value)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">But the there were no unused options<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">#PETSc Option Table entries:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">-ksp_type preonly<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">-options_left<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">-pc_type redistribute<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_converged_reason<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_monitor_true_residual<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_type cg<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_view<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_pc_type jacobi<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">#End of PETSc Option Table entries<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt">There are no unused options.<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Program ended with exit code: 0<o:p></o:p></span></p>
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Question (2)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">[0;39m[0;49m[0]PETSC ERROR: Object is in wrong state<o:p></o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">[0]PETSC ERROR: Matrix is missing diagonal entry in row 0 (65792)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">What does this error message imply? Given I only use 20% of 4(N-1) indexes, I can imagine most of the diagonal entrees are zero.
<u>Is my understanding correct?</u><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Question (3)<br>
<br>
<o:p></o:p></span></p>
<p class="p1">[0]PETSC ERROR: #5 MatZeroRowsColumnsIS() at /Users/karthikeyan.chockalingam/AMReX/SRC_PKG/petsc/src/mat/interface/matrix.c:6124</p>
<p class="p1"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I am using MatZeroRowsColumnsIS to set the homogenous Dirichelet boundary. I don’t follow why I get this error message as the linear system converges to the right solution.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thank you for your help.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Kind regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Karthik.<o:p></o:p></span></p>
<p class="p1"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Barry Smith <bsmith@petsc.dev><br>
<b>Date: </b>Tuesday, 10 January 2023 at 18:50<br>
<b>To: </b>Chockalingam, Karthikeyan (STFC,DL,HC) <karthikeyan.chockalingam@stfc.ac.uk><br>
<b>Cc: </b>petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov><br>
<b>Subject: </b>Re: [petsc-users] Eliminating rows and columns which are zeros<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> Yes, after the solve the x will contain correct values for ALL the locations including the (zeroed out rows). You use case is exactly what redistribute it for.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> Barry<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">On Jan 10, 2023, at 11:25 AM, Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam@stfc.ac.uk> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Thank you Barry. This is great!</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">I plan to solve using ‘-pc_type redistribute’ after applying the Dirichlet bc using</span></p>
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<p class="MsoNormal" style="background:white"><span class="s1"><span style="font-size:9.0pt;font-family:Menlo;color:#6C36A9">MatZeroRowsColumnsIS</span></span><span style="font-size:9.0pt;font-family:Menlo;color:black">(</span><span class="s2"><span style="font-size:9.0pt;font-family:Menlo;color:#326D74">A</span></span><span style="font-size:9.0pt;font-family:Menlo;color:black">,<span class="apple-converted-space"> </span></span><span class="s2"><span style="font-size:9.0pt;font-family:Menlo;color:#326D74">isout</span></span><span style="font-size:9.0pt;font-family:Menlo;color:black">,<span class="apple-converted-space"> </span></span><span class="s3"><span style="font-size:9.0pt;font-family:Menlo;color:#1C00CF">1</span></span><span style="font-size:9.0pt;font-family:Menlo;color:black">,<span class="apple-converted-space"> </span></span><span class="s2"><span style="font-size:9.0pt;font-family:Menlo;color:#326D74">x</span></span><span style="font-size:9.0pt;font-family:Menlo;color:black">,<span class="apple-converted-space"> </span></span><span class="s2"><span style="font-size:9.0pt;font-family:Menlo;color:#326D74">b)</span></span><span style="font-size:9.0pt;font-family:Menlo;color:black">;<span class="apple-converted-space"> </span></span><span style="font-size:9.0pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.0pt;font-family:Menlo;color:black"> </span><span style="font-size:9.0pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">While I retrieve the solution data from x (after the solve) – can I index them using the original ordering (if I may say that)?</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Kind regards,</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Karthik.</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt">From:<span class="apple-converted-space"> </span></span></b><span style="font-size:12.0pt">Barry Smith <</span><a href="mailto:bsmith@petsc.dev"><span style="font-size:12.0pt">bsmith@petsc.dev</span></a><span style="font-size:12.0pt">><br>
<b>Date:<span class="apple-converted-space"> </span></b>Tuesday, 10 January 2023 at 16:04<br>
<b>To:<span class="apple-converted-space"> </span></b>Chockalingam, Karthikeyan (STFC,DL,HC) <</span><a href="mailto:karthikeyan.chockalingam@stfc.ac.uk"><span style="font-size:12.0pt">karthikeyan.chockalingam@stfc.ac.uk</span></a><span style="font-size:12.0pt">><br>
<b>Cc:<span class="apple-converted-space"> </span></b></span><a href="mailto:petsc-users@mcs.anl.gov"><span style="font-size:12.0pt">petsc-users@mcs.anl.gov</span></a><span class="apple-converted-space"><span style="font-size:12.0pt"> </span></span><span style="font-size:12.0pt"><</span><a href="mailto:petsc-users@mcs.anl.gov"><span style="font-size:12.0pt">petsc-users@mcs.anl.gov</span></a><span style="font-size:12.0pt">><br>
<b>Subject:<span class="apple-converted-space"> </span></b>Re: [petsc-users] Eliminating rows and columns which are zeros</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><a href="https://petsc.org/release/docs/manualpages/PC/PCREDISTRIBUTE/#pcredistribute"><span style="font-size:11.0pt">https://petsc.org/release/docs/manualpages/PC/PCREDISTRIBUTE/#pcredistribute</span></a><span style="font-size:11.0pt">
-pc_type redistribute</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">It does everything for you. Note that if the right hand side for any of the "zero" rows is nonzero then the system is inconsistent and the system does not have a solution.</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Barry</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">On Jan 10, 2023, at 10:30 AM, Karthikeyan Chockalingam - STFC UKRI via petsc-users <</span><a href="mailto:petsc-users@mcs.anl.gov"><span style="font-size:11.0pt">petsc-users@mcs.anl.gov</span></a><span style="font-size:11.0pt">>
wrote:</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Hello,</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">I am assembling a MATIJ of size N, where a very large number of rows (and corresponding columns), are zeros. I would like to potentially eliminate them before the solve.</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">For instance say N=7</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.0pt;font-family:Menlo;color:#5D6C79">0 0<span class="apple-converted-space"> </span>0<span class="apple-converted-space"> </span>0 0 0 0</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.0pt;font-family:Menlo;color:#5D6C79">0 1 -1<span class="apple-converted-space"> </span>0 0 0 0</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.0pt;font-family:Menlo;color:#5D6C79">0 -1 2<span class="apple-converted-space"> </span>0 0 0 -1</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.0pt;font-family:Menlo;color:#5D6C79">0 0<span class="apple-converted-space"> </span>0<span class="apple-converted-space"> </span>0 0 0 0</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.0pt;font-family:Menlo;color:#5D6C79">0 0<span class="apple-converted-space"> </span>0<span class="apple-converted-space"> </span>0 0 0 0</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.0pt;font-family:Menlo;color:#5D6C79">0 0<span class="apple-converted-space"> </span>0<span class="apple-converted-space"> </span>0 0 0 0</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.0pt;font-family:Menlo;color:#5D6C79">0 0<span class="apple-converted-space"> </span>-1 0 0 0 1</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">I would like to reduce it to a 3x3</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">1 -1 0</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-1 2 -1</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">0 -1 1</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">I do know the size N.</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Q1) How do I do it?</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Q2) Is it better to eliminate them as it would save a lot of memory?</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Q3) At the moment, I don’t know which rows (and columns) have the zero entries but with some effort I probably can find them. Should I know which rows (and columns) I am eliminating?</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Thank you.</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Karthik.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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