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<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US">Thank you very much for offering to debug.<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 built PETSc along with AMReX, so I tried to extract the PETSc code alone which would reproduce the same error on the smallest sized problem possible.<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 have attached three files:<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">petsc_amrex_error_redistribute.txt – The error message from amrex/petsc interface, but THE linear system solves and converges to a solution.<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">problem.c – A simple stand-alone petsc code, which produces almost the same error message.<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">petsc_ error_redistribute.txt – The error message from problem.c but strangely it does NOT solve – I am not sure why?<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">Please use problem.c to debug the issue.<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">Kind regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US">Karthik.<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>Saturday, 4 February 2023 at 00:22<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"> If you can help me reproduce the problem with a simple code I can debug the problem and fix it.<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">On Feb 3, 2023, at 6:42 PM, 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">I updated the main branch to the below commit but the same problem persists.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><b><span style="font-size:8.5pt;font-family:Menlo;color:black">[0]PETSC ERROR: Petsc Development GIT revision: v3.18.4-529-g995ec06f92<span class="apple-converted-space"> </span>GIT Date: 2023-02-03 18:41:48 +0000</span></b><span style="font-size:8.5pt;font-family:Menlo"><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">From:<span class="apple-converted-space"> </span></span></b><span style="font-size:12.0pt">Barry Smith <<a href="mailto:bsmith@petsc.dev">bsmith@petsc.dev</a>><br>
<b>Date:<span class="apple-converted-space"> </span></b>Friday, 3 February 2023 at 18:51<br>
<b>To:<span class="apple-converted-space"> </span></b>Chockalingam, Karthikeyan (STFC,DL,HC) <<a href="mailto:karthikeyan.chockalingam@stfc.ac.uk">karthikeyan.chockalingam@stfc.ac.uk</a>><br>
<b>Cc:<span class="apple-converted-space"> </span></b><a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a><span class="apple-converted-space"> </span><<a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>><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><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> If you switch to use the main branch of petsc <a href="https://petsc.org/release/install/download/#advanced-obtain-petsc-development-version-with-git">https://petsc.org/release/install/download/#advanced-obtain-petsc-development-version-with-git</a> you
will not have the problem below (previously we required that a row exist before we zeroed it but now we allow the row to initially have no entries and still be zeroed.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> Barry</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">On Feb 3, 2023, at 1:04 PM, Karthikeyan Chockalingam - STFC UKRI <<a href="mailto:karthikeyan.chockalingam@stfc.ac.uk">karthikeyan.chockalingam@stfc.ac.uk</a>> wrote:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Thank you. The entire error output was an attachment in my previous email. I am pasting here for your reference.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[1;31m[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[0;39m[0;49m[0]PETSC ERROR: Object is in wrong state</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[0]PETSC ERROR: Matrix is missing diagonal entry in row 0 (65792)</span><o:p></o:p></p>
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<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!</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[0]PETSC ERROR: Option left: name:-options_left (no value)</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[0]PETSC ERROR: See<span class="apple-converted-space"> </span><a href="https://petsc.org/release/faq/">https://petsc.org/release/faq/</a><span class="apple-converted-space"> </span>for trouble shooting.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[0]PETSC ERROR: Petsc Development GIT revision: v3.18.1-127-ga207d08eda GIT Date: 2022-10-30 11:03:25 -0500</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[0]PETSC ERROR: /Users/karthikeyan.chockalingam/AMReX/amrFEM/build/Debug/amrFEM on a named HC20210312 by karthikeyan.chockalingam Fri Feb 3 11:10:01 2023</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[0]PETSC ERROR: Configure options --with-debugging=0 --prefix=/Users/karthikeyan.chockalingam/AMReX/petsc --download-fblaslapack=yes --download-scalapack=yes --download-mumps=yes --with-hypre-dir=/Users/karthikeyan.chockalingam/AMReX/hypre/src/hypre</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[0]PETSC ERROR: #1 MatZeroRowsColumns_SeqAIJ() at /Users/karthikeyan.chockalingam/AMReX/SRC_PKG/petsc/src/mat/impls/aij/seq/aij.c:2218</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[0]PETSC ERROR: #2 MatZeroRowsColumns() at /Users/karthikeyan.chockalingam/AMReX/SRC_PKG/petsc/src/mat/interface/matrix.c:6085</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[0]PETSC ERROR: #3 MatZeroRowsColumns_MPIAIJ() at /Users/karthikeyan.chockalingam/AMReX/SRC_PKG/petsc/src/mat/impls/aij/mpi/mpiaij.c:879</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[0]PETSC ERROR: #4 MatZeroRowsColumns() at /Users/karthikeyan.chockalingam/AMReX/SRC_PKG/petsc/src/mat/interface/matrix.c:6085</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[0]PETSC ERROR: #5 MatZeroRowsColumnsIS() at /Users/karthikeyan.chockalingam/AMReX/SRC_PKG/petsc/src/mat/interface/matrix.c:6124</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[0]PETSC ERROR: #6 localAssembly() at /Users/karthikeyan.chockalingam/AMReX/amrFEM/src/FENodalPoisson.cpp:435</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> Residual norms for redistribute_ solve.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> 0 KSP preconditioned resid norm 5.182603110407e+00 true resid norm 1.382027496109e+01 ||r(i)||/||b|| 1.000000000000e+00</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> 1 KSP preconditioned resid norm 1.862430383976e+00 true resid norm 4.966481023937e+00 ||r(i)||/||b|| 3.593619546588e-01</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> 2 KSP preconditioned resid norm 2.132803507689e-01 true resid norm 5.687476020503e-01 ||r(i)||/||b|| 4.115313216645e-02</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> 3 KSP preconditioned resid norm 5.499797533437e-02 true resid norm 1.466612675583e-01 ||r(i)||/||b|| 1.061203687852e-02</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> 4 KSP preconditioned resid norm 2.829814271435e-02 true resid norm 7.546171390493e-02 ||r(i)||/||b|| 5.460217985345e-03</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> 5 KSP preconditioned resid norm 7.431048995318e-03 true resid norm 1.981613065418e-02 ||r(i)||/||b|| 1.433844891652e-03</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> 6 KSP preconditioned resid norm 3.182040728972e-03 true resid norm 8.485441943932e-03 ||r(i)||/||b|| 6.139850305312e-04</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> 7 KSP preconditioned resid norm 1.030867020459e-03 true resid norm 2.748978721225e-03 ||r(i)||/||b|| 1.989091193167e-04</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> 8 KSP preconditioned resid norm 4.469429300003e-04 true resid norm 1.191847813335e-03 ||r(i)||/||b|| 8.623908111021e-05</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> 9 KSP preconditioned resid norm 1.237303313796e-04 true resid norm 3.299475503456e-04 ||r(i)||/||b|| 2.387416685085e-05</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> 10 KSP preconditioned resid norm 5.822094326756e-05 true resid norm 1.552558487134e-04 ||r(i)||/||b|| 1.123391894522e-05</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> 11 KSP preconditioned resid norm 1.735776150969e-05 true resid norm 4.628736402585e-05 ||r(i)||/||b|| 3.349236115503e-06</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> Linear redistribute_ solve converged due to CONVERGED_RTOL iterations 11</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">KSP Object: (redistribute_) 1 MPI process</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> type: cg</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> maximum iterations=10000, initial guess is zero</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> tolerances: relative=1e-05, absolute=1e-50, divergence=10000.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> left preconditioning</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> using PRECONDITIONED norm type for convergence test</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">PC Object: (redistribute_) 1 MPI process</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> type: jacobi</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> type DIAGONAL</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> linear system matrix = precond matrix:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> Mat Object: 1 MPI process</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> type: mpiaij</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> rows=48896, cols=48896</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> total: nonzeros=307976, allocated nonzeros=307976</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> total number of mallocs used during MatSetValues calls=0</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> not using I-node (on process 0) routines</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">End of program</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> solve time 0.564714744 seconds</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Starting max value is: 0</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Min value of level 0 is: 0</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Interpolated min value is: 741.978761</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Unused ParmParse Variables:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> [TOP]::model.type(nvals = 1) :: [3]</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> [TOP]::ref_ratio(nvals = 1) :: [2]</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">AMReX (22.10-20-g3082028e4287) finalized</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">#PETSc Option Table entries:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-ksp_type preonly</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-options_left</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-pc_type redistribute</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_converged_reason</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_monitor_true_residual</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_type cg</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_view</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_pc_type jacobi</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">#End of PETSc Option Table entries</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">There are no unused options.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Program ended with exit code: 0</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Best,</span><o:p></o:p></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"> </span><o:p></o:p></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 <<a href="mailto:bsmith@petsc.dev">bsmith@petsc.dev</a>><br>
<b>Date:<span class="apple-converted-space"> </span></b>Friday, 3 February 2023 at 17:41<br>
<b>To:<span class="apple-converted-space"> </span></b>Chockalingam, Karthikeyan (STFC,DL,HC) <<a href="mailto:karthikeyan.chockalingam@stfc.ac.uk">karthikeyan.chockalingam@stfc.ac.uk</a>><br>
<b>Cc:<span class="apple-converted-space"> </span></b><a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a><span class="apple-converted-space"> </span><<a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>><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><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> We need all the error output for the errors you got below to understand why the errors are happening.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><br>
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<p class="MsoNormal"><span style="font-size:11.0pt">On Feb 3, 2023, at 11:41 AM, Karthikeyan Chockalingam - STFC UKRI <<a href="mailto:karthikeyan.chockalingam@stfc.ac.uk">karthikeyan.chockalingam@stfc.ac.uk</a>> wrote:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Hello Barry,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">I would like to better understand<span class="apple-converted-space"> </span>pc_type redistribute usage.<span class="apple-converted-space"> </span></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">I am plan to use pc_type<span class="apple-converted-space"> </span><u>redistribute</u><span class="apple-converted-space"> </span>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.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> Indeed the linear solve will be more efficient if you use the redistribute solver. </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> But I don't understand your plan. With adaptive refinement I would just create the two matrices, one for the initial grid on which you solve the system, this will be a smaller matrix and then create a new
larger matrix for the refined grid (and discard the previous matrix).<br>
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<p class="MsoNormal"><span style="font-size:11.0pt">Question (1)</span><o:p></o:p></p>
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<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<span class="apple-converted-space"><u> </u></span>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?<span class="apple-converted-space"><u> </u></span><u>Is this the correct usage?</u></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> See above<br>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Question (2)</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">I tried using pc_type redistribute for a two level system.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">I have<span class="apple-converted-space"> </span><b><u>attached</u></b><span class="apple-converted-space"> </span>the output only for (level 1)</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">The solution converges to right solution but still petsc outputs some error messages.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<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!</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">[0]PETSC ERROR: Option left: name:-options_left (no value)</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">But the there were no unused options</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">#PETSc Option Table entries:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-ksp_type preonly</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-options_left</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-pc_type redistribute</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_converged_reason</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_monitor_true_residual</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_type cg</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_view</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_pc_type jacobi</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">#End of PETSc Option Table entries</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt">There are no unused options.</span></b><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Program ended with exit code: 0</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">I cannot explain this<br>
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<p class="MsoNormal"><span style="font-size:11.0pt"><br>
Question (2)</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;color:black">[0;39m[0;49m[0]PETSC ERROR: Object is in wrong state</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;color:black">[0]PETSC ERROR: Matrix is missing diagonal entry in row 0 (65792)</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<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.<span class="apple-converted-space"> </span><u>Is my understanding correct?</u></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Question (3)<br>
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<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black">[0]PETSC ERROR: #5 MatZeroRowsColumnsIS() at /Users/karthikeyan.chockalingam/AMReX/SRC_PKG/petsc/src/mat/interface/matrix.c:6124</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black"> </span><o:p></o:p></p>
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<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.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Thank you for your help.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Kind regards,</span><o:p></o:p></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" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></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 <<a href="mailto:bsmith@petsc.dev">bsmith@petsc.dev</a>><br>
<b>Date:<span class="apple-converted-space"> </span></b>Tuesday, 10 January 2023 at 18:50<br>
<b>To:<span class="apple-converted-space"> </span></b>Chockalingam, Karthikeyan (STFC,DL,HC) <<a href="mailto:karthikeyan.chockalingam@stfc.ac.uk">karthikeyan.chockalingam@stfc.ac.uk</a>><br>
<b>Cc:<span class="apple-converted-space"> </span></b><a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a><span class="apple-converted-space"> </span><<a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>><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"> 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.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> Barry</span><o:p></o:p></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 <<a href="mailto:karthikeyan.chockalingam@stfc.ac.uk">karthikeyan.chockalingam@stfc.ac.uk</a>> wrote:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Thank you Barry. This is great!</span><o:p></o:p></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><o:p></o:p></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><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.0pt;font-family:Menlo;color:black"> </span><o:p></o:p></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><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Kind regards,</span><o:p></o:p></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" 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"><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><o:p></o:p></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><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Barry</span><o:p></o:p></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><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Hello,</span><o:p></o:p></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><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">For instance say N=7</span><o:p></o:p></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><o:p></o:p></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><o:p></o:p></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><o:p></o:p></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><o:p></o:p></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><o:p></o:p></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><o:p></o:p></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><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">I would like to reduce it to a 3x3</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">1 -1 0</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-1 2 -1</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">0 -1 1</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">I do know the size N.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Q1) How do I do it?</span><o:p></o:p></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><o:p></o:p></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><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Thank you.</span><o:p></o:p></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"><petsc_redistribute.txt></span><o:p></o:p></p>
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