<div dir="ltr"><div dir="ltr">On Mon, Dec 12, 2022 at 10:00 AM Karthikeyan Chockalingam - STFC UKRI <<a href="mailto:karthikeyan.chockalingam@stfc.ac.uk">karthikeyan.chockalingam@stfc.ac.uk</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg2346674789063525718">
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<p class="MsoNormal"><span style="font-size:11pt">Thank you Matt and Blaise.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">I will try out IS (though I have not it before)<u></u><u></u></span></p>
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<u></u><span class="m_7482898405322785891apple-converted-space"><span style="font-size:11pt"><span>(i)<span style="font:7pt "Times New Roman"">
</span></span></span></span><u></u><span class="m_7482898405322785891apple-converted-space"><span style="font-size:11pt">Can IS be of different size, on different processors, and still call ISALLGather?</span></span></p></div></div></div></blockquote><div>Yes.</div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg2346674789063525718"><div lang="EN-GB" style="overflow-wrap: break-word;"><div class="m_7482898405322785891WordSection1"><p class="m_7482898405322785891MsoListParagraph" style="margin-left:54pt"><span class="m_7482898405322785891apple-converted-space"><span style="font-size:11pt"><u></u><u></u></span></span></p>
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<u></u><span class="m_7482898405322785891apple-converted-space"><span style="font-size:11pt"><span>(ii)<span style="font:7pt "Times New Roman"">
</span></span></span></span><u></u><span class="m_7482898405322785891apple-converted-space"><span style="font-size:11pt">Can IS be passed as row indices to MatZeroRowsColumns?</span></span></p></div></div></div></blockquote><div><br></div><div><a href="https://petsc.org/main/docs/manualpages/Mat/MatZeroRowsColumnsIS/">https://petsc.org/main/docs/manualpages/Mat/MatZeroRowsColumnsIS/</a><br></div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg2346674789063525718"><div lang="EN-GB" style="overflow-wrap: break-word;"><div class="m_7482898405322785891WordSection1">
<p class="MsoNormal"><span class="m_7482898405322785891apple-converted-space"><span style="font-size:11pt">I will look into DMlabels and start a different thread if needed.<u></u><u></u></span></span></p>
<p class="MsoNormal"><span class="m_7482898405322785891apple-converted-space"><span style="font-size:11pt"><u></u> <u></u></span></span></p>
<p class="MsoNormal"><span class="m_7482898405322785891apple-converted-space"><span style="font-size:11pt">Best,<u></u><u></u></span></span></p>
<p class="MsoNormal"><span class="m_7482898405322785891apple-converted-space"><span style="font-size:11pt">Karthik.<u></u><u></u></span></span></p>
<p class="MsoNormal"><span class="m_7482898405322785891apple-converted-space"><span style="font-size:13.5pt;color:black"><u></u> <u></u></span></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="font-size:12pt;color:black">From:
</span></b><span style="font-size:12pt;color:black">Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>><br>
<b>Date: </b>Saturday, 10 December 2022 at 02:20<br>
<b>To: </b>Chockalingam, Karthikeyan (STFC,DL,HC) <<a href="mailto:karthikeyan.chockalingam@stfc.ac.uk" target="_blank">karthikeyan.chockalingam@stfc.ac.uk</a>><br>
<b>Cc: </b>Mark Adams <<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>>, <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a> <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>><br>
<b>Subject: </b>Re: [petsc-users] Union of sequential vecs<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">On Fri, Dec 9, 2022 at 6:50 PM Karthikeyan Chockalingam - STFC UKRI via petsc-users <</span><a href="mailto:petsc-users@mcs.anl.gov" target="_blank"><span style="font-size:11pt">petsc-users@mcs.anl.gov</span></a><span style="font-size:11pt">>
wrote:<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Thank you Mark and Barry.
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
<p class="MsoNormal"><a href="mailto:mfadams@lbl.gov" target="_blank"><span style="font-size:11pt;text-decoration:none">@Mark Adams</span></a><span style="font-size:11pt"> I follow you for the most
part. Shouldn’t R be an MPI Vector?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">Here it goes:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">Q[Vec[i]] for all "i" in my local (sequential) "Vec".<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">Compute number of local nonzeros in Q, call it n.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">//Create a MPI Vector R, with local size n<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
<p class="m_7482898405322785891m9063915685637258561p1">VecCreate(PETSC_COMM_WORLD, &R); </p>
<p class="m_7482898405322785891m9063915685637258561p1">VecSetType(R, VECMPI); </p>
<p class="m_7482898405322785891m9063915685637258561p1">VecSetSizes(R, <b>n</b>, PETSC_DECIDE); </p>
<p class="m_7482898405322785891m9063915685637258561p1"> </p>
<p class="MsoNormal"><span style="font-size:11pt">//Populate MPI Vector R with local (sequential) "Vec".<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
<p class="m_7482898405322785891m9063915685637258561p1">VecGetOwnershipRange(R, &istart, &iend); </p>
<p class="m_7482898405322785891m9063915685637258561p1">local_size = iend - istart; //The local_size should be ‘<b>n</b>’ right?</p>
<p class="m_7482898405322785891m9063915685637258561p1">VecGetArray(R, &values); </p>
<p class="m_7482898405322785891m9063915685637258561p1"><span class="m_7482898405322785891m9063915685637258561apple-converted-space">
</span><span class="m_7482898405322785891m9063915685637258561s1"><b>for</b></span> (i = <span class="m_7482898405322785891m9063915685637258561s2">
0</span>; i < local_size; i++) {</p>
<p class="m_7482898405322785891m9063915685637258561p1"><span class="m_7482898405322785891m9063915685637258561apple-converted-space">
</span>values[i] = Vec[i];</p>
<p class="m_7482898405322785891m9063915685637258561p1"><span class="m_7482898405322785891m9063915685637258561apple-converted-space">
</span>}</p>
<p class="m_7482898405322785891m9063915685637258561p1">VecRestoreArray(R, &values); </p>
<p class="m_7482898405322785891m9063915685637258561p1"> </p>
<p class="MsoNormal"><span style="font-size:11pt">//Scatter R to all processors
<u></u><u></u></span></p>
<p class="m_7482898405322785891m9063915685637258561p1"> </p>
<p class="MsoNormal" style="background:white">
<span style="font-size:9pt;font-family:Menlo;color:black">Vec V_SEQ;</span><span style="font-size:11pt"><u></u><u></u></span></p>
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<span style="font-size:9pt;font-family:Menlo;color:black">VecScatter ctx;</span><span style="font-size:11pt"><u></u><u></u></span></p>
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<span style="font-size:9pt;font-family:Menlo;color:black"> </span><span style="font-size:11pt"><u></u><u></u></span></p>
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<span style="font-size:9pt;font-family:Menlo;color:black">VecScatterCreateToAll(R,&ctx,&V_SEQ);</span><span style="font-size:11pt"><u></u><u></u></span></p>
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<span style="font-size:9pt;font-family:Menlo;color:black"> </span><span style="font-size:11pt"><u></u><u></u></span></p>
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<span style="font-size:9pt;font-family:Menlo;color:black">//Remove duplicates in V_SEQ</span><span style="font-size:11pt"><u></u><u></u></span></p>
<p class="MsoNormal" style="background:white">
<span style="font-size:9pt;font-family:Menlo;color:black">How can I use PetscSortRemoveDupsInt to remove duplicates in V_SEQ?</span><span style="font-size:11pt"><u></u><u></u></span></p>
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<span style="font-size:9pt;font-family:Menlo;color:black"> </span><span style="font-size:11pt"><u></u><u></u></span></p>
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<span style="font-size:9pt;font-family:Menlo;color:black"> </span><span style="font-size:11pt"><u></u><u></u></span></p>
<p class="MsoNormal" style="background:white">
<span style="font-size:9pt;font-family:Menlo;color:black">Physics behind:</span><span style="font-size:11pt"><u></u><u></u></span></p>
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<span style="font-size:9pt;font-family:Menlo;color:black">I am reading a parallel mesh, and want to mark all the boundary nodes. I use a local (sequential) Vec to store the boundary nodes for each parallel partition. Hence, local Vecs can end up with duplicate
node index among them, which I would like to get rid of when I combine all of them together.</span><span style="font-size:11pt"><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">1) Blaise is right you should use an IS, not a Vec, to hold node indices. His solution is only a few lines, so I would use it.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">2) I would not recommend doing things this way in the first place. PETSc can manage parallel meshes scalably, marking boundaries using DMLabel objects.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> Thanks,<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> Matt<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<span style="font-size:9pt;font-family:Menlo;color:black">Best,</span><span style="font-size:11pt"><u></u><u></u></span></p>
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<span style="font-size:9pt;font-family:Menlo;color:black">Karthik.</span><span style="font-size:11pt"><u></u><u></u></span></p>
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<span style="font-size:9pt;font-family:Menlo;color:black"> </span><span style="font-size:11pt"><u></u><u></u></span></p>
<p class="m_7482898405322785891m9063915685637258561p1"> </p>
<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="font-size:12pt;color:black">From:
</span></b><span style="font-size:12pt;color:black">Mark Adams <</span><a href="mailto:mfadams@lbl.gov" target="_blank"><span style="font-size:12pt">mfadams@lbl.gov</span></a><span style="font-size:12pt;color:black">><br>
<b>Date: </b>Friday, 9 December 2022 at 21:08<br>
<b>To: </b>Chockalingam, Karthikeyan (STFC,DL,HC) <</span><a href="mailto:karthikeyan.chockalingam@stfc.ac.uk" target="_blank"><span style="font-size:12pt">karthikeyan.chockalingam@stfc.ac.uk</span></a><span style="font-size:12pt;color:black">><br>
<b>Cc: </b>Barry Smith <</span><a href="mailto:bsmith@petsc.dev" target="_blank"><span style="font-size:12pt">bsmith@petsc.dev</span></a><span style="font-size:12pt;color:black">>,
</span><a href="mailto:petsc-users@mcs.anl.gov" target="_blank"><span style="font-size:12pt">petsc-users@mcs.anl.gov</span></a><span style="font-size:12pt;color:black"> <</span><a href="mailto:petsc-users@mcs.anl.gov" target="_blank"><span style="font-size:12pt">petsc-users@mcs.anl.gov</span></a><span style="font-size:12pt;color:black">><br>
<b>Subject: </b>Re: [petsc-users] Union of sequential vecs</span><span style="font-size:11pt"><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">If your space is pretty compact, eg, (0,12), you could create an MPI vector Q of size 13, say, and each processor can add 1.0 to Q[Vec[i]], for all
"i" in my local "Vec".<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Then each processor can count the number of local nonzeros in Q, call it n, create a new vector, R, with local size n, then set R[i] = global index
of the nonzero for each nonzero in Q, i=0:n.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Do some sort of vec-scatter-to-all with R to get what you want.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Does that work?<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Mark<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">On Fri, Dec 9, 2022 at 3:25 PM Karthikeyan Chockalingam - STFC UKRI via petsc-users <</span><a href="mailto:petsc-users@mcs.anl.gov" target="_blank"><span style="font-size:11pt">petsc-users@mcs.anl.gov</span></a><span style="font-size:11pt">>
wrote:<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">That is where I am stuck,
<u>I don’t know</u> who to combine them to get Vec = {2,5,7,8,10,11,12}.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">I just want them in an MPI vector.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">I finally plan to call VecScatterCreateToAll so that all processor gets a copy.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">Thank you.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">Kind regards,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">Karthik.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="font-size:12pt;color:black">From:
</span></b><span style="font-size:12pt;color:black">Barry Smith <</span><a href="mailto:bsmith@petsc.dev" target="_blank"><span style="font-size:12pt">bsmith@petsc.dev</span></a><span style="font-size:12pt;color:black">><br>
<b>Date: </b>Friday, 9 December 2022 at 20:04<br>
<b>To: </b>Chockalingam, Karthikeyan (STFC,DL,HC) <</span><a href="mailto:karthikeyan.chockalingam@stfc.ac.uk" target="_blank"><span style="font-size:12pt">karthikeyan.chockalingam@stfc.ac.uk</span></a><span style="font-size:12pt;color:black">><br>
<b>Cc: </b></span><a href="mailto:petsc-users@mcs.anl.gov" target="_blank"><span style="font-size:12pt">petsc-users@mcs.anl.gov</span></a><span style="font-size:12pt;color:black"> <</span><a href="mailto:petsc-users@mcs.anl.gov" target="_blank"><span style="font-size:12pt">petsc-users@mcs.anl.gov</span></a><span style="font-size:12pt;color:black">><br>
<b>Subject: </b>Re: [petsc-users] Union of sequential vecs</span><span style="font-size:11pt"><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> How are you combining them to get Vec = {2,5,7,8,10,11,12}?<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> Do you want the values to remain on the same MPI rank as before, just in an MPI vector?<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">On Dec 9, 2022, at 2:28 PM, Karthikeyan Chockalingam - STFC UKRI via petsc-users <</span><a href="mailto:petsc-users@mcs.anl.gov" target="_blank"><span style="font-size:11pt">petsc-users@mcs.anl.gov</span></a><span style="font-size:11pt">>
wrote:<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Hi,<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">I want to take the union of a set of sequential vectors, each living in a different processor.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Say,<span class="m_7482898405322785891m9063915685637258561m5796220908723221417apple-converted-space"> </span><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Vec_Seq1 = {2,5,7}<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Vec_Seq2 = {5,8,10,11}<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Vec_Seq3 = {5,2,12}.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Finally, get the union of all them Vec = {2,5,7,8,10,11,12}.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">I initially wanted to create a parallel vector and insert the (sequential vector) values but I do not know, to which index to insert the values to.
But I do know the total size of Vec (which in this case is 7).<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Any help is much appreciated.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Kind regards,<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Karthik.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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</blockquote>
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<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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</blockquote>
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</blockquote>
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<p class="MsoNormal"><span style="font-size:11pt"><br clear="all">
<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">-- <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank"><span style="font-size:11pt">https://www.cse.buffalo.edu/~knepley/</span></a><span style="font-size:11pt"><u></u><u></u></span></p>
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</div></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>