<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:0 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Menlo;
panose-1:2 11 6 9 3 8 4 2 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
font-size:10.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
span.apple-converted-space
{mso-style-name:apple-converted-space;}
span.s1
{mso-style-name:s1;}
span.s2
{mso-style-name:s2;}
span.s3
{mso-style-name:s3;}
span.EmailStyle23
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:302393684;
mso-list-type:hybrid;
mso-list-template-ids:424939324 461153474 134807577 134807579 134807567 134807577 134807579 134807567 134807577 134807579;}
@list l0:level1
{mso-level-number-format:roman-lower;
mso-level-text:"\(%1\)";
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:54.0pt;
text-indent:-36.0pt;}
@list l0:level2
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level3
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level4
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level5
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level6
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level7
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level8
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level9
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
ol
{margin-bottom:0cm;}
ul
{margin-bottom:0cm;}
--></style>
</head>
<body lang="EN-GB" link="blue" vlink="purple" style="word-wrap:break-word;overflow-wrap: break-word;-webkit-nbsp-mode: space;line-break:after-white-space">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US">No problem. I don’t completely follow.<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">(Q1) I have used MATMPIAJI but not sure what is MatZero* (star) and what it does? And its relevance to my problem.<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">(Q2) Since I am creating a MATMPIAJI system– what would be the best way to insert 0.0 in to ALL diagonals (both active and inactive rows) to begin with?<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">(Q3) If I have to insert 0.0 only into diagonals of “inactive” rows after I have
</span><span style="font-size:11.0pt">put values into the matrix</span><span style="font-size:11.0pt;mso-fareast-language:EN-US"> would be an effort. Unless there is a straight forward to do it in PETSc.<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">(Q4) For my problem do I need to use PCREDISTIBUTE or any linear solve would eliminate those rows?
<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">Best,<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>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<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>Monday, 6 February 2023 at 20:18<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>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"> Sorry, I had a mistake in my thinking, PCREDISTRIBUTE supports completely empty rows but MatZero* does not.<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> When you put values into the matrix you will need to insert a 0.0 on the diagonal of each "inactive" row; all of this will be eliminated during the linear solve process. It would be a major project to change
the MatZero* functions to handle empty rows. <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> Barry<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">On Feb 4, 2023, at 12:06 PM, Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam@stfc.ac.uk> wrote:<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Thank you very much for offering to debug.</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">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.</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">I have attached three files:</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">petsc_amrex_error_redistribute.txt – The error message from amrex/petsc interface, but THE linear system solves and converges to a solution.</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">problem.c – A simple stand-alone petsc code, which produces almost the same error message.</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">petsc_ error_redistribute.txt – The error message from problem.c but strangely it does NOT solve – I am not sure why?</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Please use problem.c to debug the issue.</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Kind regards,</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Karthik.</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<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>Saturday, 4 February 2023 at 00:22<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>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
<div>
<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.</span><o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> Barry</span><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br>
<br>
<br>
</span><o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">On Feb 3, 2023, at 6:42 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>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
<div>
<div>
<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><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<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>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> Barry</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">[1;31m[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> Residual norms for redistribute_ solve.</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">KSP Object: (redistribute_) 1 MPI process</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> type: cg</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> maximum iterations=10000, initial guess is zero</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> tolerances: relative=1e-05, absolute=1e-50, divergence=10000.</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> left preconditioning</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> using PRECONDITIONED norm type for convergence test</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">PC Object: (redistribute_) 1 MPI process</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> type: jacobi</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> type DIAGONAL</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> linear system matrix = precond matrix:</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> Mat Object: 1 MPI process</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> type: mpiaij</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> rows=48896, cols=48896</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> total: nonzeros=307976, allocated nonzeros=307976</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> total number of mallocs used during MatSetValues calls=0</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> not using I-node (on process 0) routines</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">End of program</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> solve time 0.564714744 seconds</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Starting max value is: 0</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Min value of level 0 is: 0</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Interpolated min value is: 741.978761</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Unused ParmParse Variables:</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> [TOP]::model.type(nvals = 1) :: [3]</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> [TOP]::ref_ratio(nvals = 1) :: [2]</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">AMReX (22.10-20-g3082028e4287) finalized</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">#PETSc Option Table entries:</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-ksp_type preonly</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-options_left</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-pc_type redistribute</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_converged_reason</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_monitor_true_residual</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_type cg</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_view</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_pc_type jacobi</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">#End of PETSc Option Table entries</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">There are no unused options.</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Program ended with exit code: 0</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Best,</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Karthik.</span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<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>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br>
<br>
<br>
<br>
<br>
</span><o:p></o:p></p>
</div>
</div>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Hello Barry,</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
<br>
<br>
<br>
<br>
</span><o:p></o:p></p>
</div>
</div>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Question (1)</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> See above<br>
<br>
<br>
<br>
<br>
</span><o:p></o:p></p>
</div>
</div>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Question (2)</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">But the there were no unused options</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">#PETSc Option Table entries:</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-ksp_type preonly</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-options_left</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-pc_type redistribute</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_converged_reason</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_monitor_true_residual</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_type cg</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_ksp_view</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-redistribute_pc_type jacobi</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">#End of PETSc Option Table entries</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><b><span style="font-size:11.0pt">There are no unused options.</span></b><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Program ended with exit code: 0</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">I cannot explain this<br>
<br>
<br>
<br>
<br>
</span><o:p></o:p></p>
</div>
</div>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br>
Question (2)</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Question (3)<br>
<br>
<br>
<br>
<br>
<br>
</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Thank you for your help.</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Kind regards,</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Karthik.</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<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>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> Barry</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br>
<br>
<br>
<br>
<br>
<br>
</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Thank you Barry. This is great!</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:9.0pt;font-family:Menlo;color:black"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Kind regards,</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Karthik.</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<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>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Barry</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:11.0pt"><br>
<br>
<br>
<br>
<br>
</span><o:p></o:p></p>
</div>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Hello,</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">For instance say N=7</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">I would like to reduce it to a 3x3</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">1 -1 0</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">-1 2 -1</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">0 -1 1</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">I do know the size N.</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Q1) How do I do it?</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Thank you.</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Karthik.</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<p style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;text-align:start;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:6.0pt;font-family:Helvetica">This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments<span class="apple-converted-space"> </span>and
should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry
out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses. </span><span style="font-size:13.5pt;font-family:Helvetica"><o:p></o:p></span></p>
</div>
</blockquote>
</div>
</div>
</div>
</blockquote>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><petsc_redistribute.txt></span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</div>
</blockquote>
</div>
</div>
</blockquote>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><petsc_error_redistribute.txt><petsc_amrex_error_redistribute.txt><problem.c><o:p></o:p></span></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
</div>
</body>
</html>