<div dir="ltr">Try adding -mat_block_size 3<div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Dec 13, 2021 at 11:57 AM Karthikeyan Chockalingam - STFC UKRI <<a href="mailto:karthikeyan.chockalingam@stfc.ac.uk">karthikeyan.chockalingam@stfc.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<p class="gmail-m_-1073648265619177122p1"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:10pt;color:black">I tried to run the problem using -pc_type hypre but it errored out:<u></u><u></u></span></span></p>
<p class="gmail-m_-1073648265619177122p1"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:10pt;color:black"><u></u> <u></u></span></span></p>
<p class="MsoNormal"><span style="font-size:10pt;font-family:Menlo;color:black">./ex56 -cells 4,4,2 -max_conv_its 1 -lx 1. -alpha .01 -petscspace_degree 1 -ksp_type cg -ksp_monitor -ksp_rtol 1.e-8
</span><span style="font-size:10pt;font-family:Menlo;color:black">-pc_type hypre -pc_hypre_type<b>
</b>boomeramg </span><span style="font-size:10pt;font-family:Menlo;color:black">-snes_monitor -use_mat_nearnullspace true -snes_rtol 1.e-10 -ex56_dm_view -log_view -ex56_dm_vec_type cuda
</span><b><span style="font-size:10pt;font-family:Menlo;color:red">-ex56_dm_mat_type hypre</span></b><span style="font-size:10pt;font-family:Menlo;color:red">
</span><span style="font-size:10pt;font-family:Menlo;color:black">-options_left<u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p1"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:10pt;color:black"><u></u> <u></u></span></span></p>
<p class="gmail-m_-1073648265619177122p1"><span class="gmail-m_-1073648265619177122s1"><b><span style="font-size:8pt"><u></u> <u></u></span></b></span></p>
<p class="gmail-m_-1073648265619177122p1"><span class="gmail-m_-1073648265619177122s1"><b><span style="font-size:8pt"><u></u> <u></u></span></b></span></p>
<p class="gmail-m_-1073648265619177122p1"><span class="gmail-m_-1073648265619177122s1"><b><span style="font-size:8pt">[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</span></b></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: Petsc has generated inconsistent data</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: Blocksize of layout 1 must match that of mapping 3 (or the latter must be 1)</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a> for trouble shooting.</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: Petsc Development GIT revision: v3.16.1-353-g887dddf386</span></span><span class="gmail-m_-1073648265619177122apple-converted-space"><span style="font-size:8pt">
</span></span><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">GIT Date: 2021-11-19 20:24:41 +0000</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: ./ex56 on a arch-linux2-c-opt named sqg2b13.bullx by kxc07-lxm25 Mon Dec 13 16:50:02 2021</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: Configure options --with-debugging=0 --with-blaslapack-dir=/lustre/scafellpike/local/apps/intel/intel_cs/2018.0.128/mkl --with-cuda=1 --with-cuda-arch=70 --download-hypre=yes --download-hypre-configure-arguments="--with-cuda=yes
--enable-gpu-profiling=yes --enable-cusparse=yes --enable-cublas=yes --enable-curand=yes</span></span><span class="gmail-m_-1073648265619177122apple-converted-space"><span style="font-size:8pt">
</span></span><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">--enable-unified-memory=yes HYPRE_CUDA_SM=70" --with-shared-libraries=1 --known-mpi-shared-libraries=1 --with-cc=mpicc --with-cxx=mpicxx -with-fc=mpif90</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: #1 PetscLayoutSetISLocalToGlobalMapping() at /lustre/scafellpike/local/HT04048/lxm25/kxc07-lxm25/petsc-main/petsc/src/vec/is/utils/pmap.c:371</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: #2 MatSetLocalToGlobalMapping() at /lustre/scafellpike/local/HT04048/lxm25/kxc07-lxm25/petsc-main/petsc/src/mat/interface/matrix.c:2089</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: #3 DMCreateMatrix_Plex() at /lustre/scafellpike/local/HT04048/lxm25/kxc07-lxm25/petsc-main/petsc/src/dm/impls/plex/plex.c:2460</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: #4 DMCreateMatrix() at /lustre/scafellpike/local/HT04048/lxm25/kxc07-lxm25/petsc-main/petsc/src/dm/interface/dm.c:1445</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: #5 main() at ex56.c:439</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: PETSc Option Table entries:</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -alpha .01</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -cells 4,4,2</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -ex56_dm_mat_type hypre</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -ex56_dm_vec_type cuda</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -ex56_dm_view</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -ksp_monitor</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -ksp_rtol 1.e-8</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -ksp_type cg</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -log_view</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -lx 1.</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -max_conv_its 1</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -options_left</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -pc_hypre_type boomeramg</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -pc_type hypre</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -petscspace_degree 1</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -snes_monitor</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -snes_rtol 1.e-10</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -use_gpu_aware_mpi 0</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">[0]PETSC ERROR: -use_mat_nearnullspace true</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p1"><span class="gmail-m_-1073648265619177122s1"><b><span style="font-size:8pt">[0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint@mcs.anl.gov----------</span></b></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">--------------------------------------------------------------------------</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">with errorcode 77.</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p3"><span style="font-size:8pt"><u></u> <u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">You may or may not see output from other processes, depending on</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">exactly when Open MPI kills them.</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="gmail-m_-1073648265619177122p2"><span class="gmail-m_-1073648265619177122s1"><span style="font-size:8pt">--------------------------------------------------------------------------</span></span><span style="font-size:8pt"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:8pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span><u></u> <u></u></span></p>
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<p class="MsoNormal"><b><span style="font-size:12pt;color:black">From: </span></b><span style="font-size:12pt;color:black">Mark Adams <<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>><br>
<b>Date: </b>Monday, 13 December 2021 at 13:58<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>Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</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] Unstructured mesh<u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">On Mon, Dec 13, 2021 at 8:35 AM Karthikeyan Chockalingam - STFC UKRI <<a href="mailto:karthikeyan.chockalingam@stfc.ac.uk" target="_blank">karthikeyan.chockalingam@stfc.ac.uk</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal">Thanks Matt. Couple of weeks back you mentioned<u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10pt;font-family:Menlo">“<span style="color:black">There are many unstructured grid examples, e.g. SNES ex13, ex17, ex56. The solver can run on the GPU,
but the vector/matrix FEM assembly does not. I am working on that now.”</span></span><u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">I am able to run other examples in ksp/tutorials on gpus. I complied ex56 in snes/tutorials no differently. The only difference being I didn’t specify _dm_vec_type and _dm_vec_type
(as you mentioned they are not assembled on gpus anyways plus I am working on an unstructured grid thought _dm is not right type for this problem). I was hoping to see gpu flops recorded for KSPSolve, which I didn’t.
<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Okay, I will wait for Mark to comment.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">This (DM) example works like any other, with a prefix, as far as GPU: -ex56_dm_vec_type cuda and -ex56_dm_mat_type cusparse, or aijkokkos/kokkos, etc.<u></u><u></u></p>
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<p class="MsoNormal">Run with -options_left to verify that these are used. <u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Kind regards,<u></u><u></u></p>
<p class="MsoNormal">Karthik.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"><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>Monday, 13 December 2021 at 13:17<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] Unstructured mesh</span><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">On Mon, Dec 13, 2021 at 7:15 AM Karthikeyan Chockalingam - STFC UKRI <<a href="mailto:karthikeyan.chockalingam@stfc.ac.uk" target="_blank">karthikeyan.chockalingam@stfc.ac.uk</a>>
wrote:<u></u><u></u></p>
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<p class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431p1"><span class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431apple-converted-space"><span style="font-size:10pt">Thank you. I was able to confirm both the below options produced the same
mesh</span></span><u></u><u></u></p>
<p class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431p1"><span class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431apple-converted-space"><span style="font-size:10pt"> </span></span><u></u><u></u></p>
<p class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431p1"><span class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431apple-converted-space"><span style="font-size:10pt"> </span></span><span class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431s1"><span style="font-size:10pt">./ex56
-cells 2,2,1 -max_conv_its 2</span></span><u></u><u></u></p>
<p class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431p1"><span class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431s1"><span style="font-size:10pt">./ex56 -cells 4,4,2 -max_conv_its 1</span></span><u></u><u></u></p>
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<p class="MsoNormal">Good <u></u><u></u></p>
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<p class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431p1"><span class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431s1"><span style="font-size:10pt">But I didn’t get how is
</span></span><span style="font-size:10pt">-cells i,j,k <1,1,1><span class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431s1"> is related to the number of MPI processes.</span></span><u></u><u></u></p>
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<p class="MsoNormal">It is not. The number of processes is specified independently using 'mpiexec -n <p>' or when using the test system NP=<p>. <u></u><u></u></p>
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<p class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431msolistparagraph" style="margin-left:54pt">
<span class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431s1"><span style="font-size:10pt;font-family:Menlo">(i)</span></span><span class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431s1"><span style="font-size:7pt;font-family:"Times New Roman",serif">
</span></span><span style="font-size:10pt;font-family:Menlo">Say I start with -cells 1,1,1 -max_conv its<span class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431s1"> 7; that would eventually leave all refinement on level 7 running on 1 MPI process?</span></span><u></u><u></u></p>
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<span style="font-size:10pt;font-family:Menlo">(ii)</span><span style="font-size:7pt;font-family:"Times New Roman",serif">
</span><span style="font-size:10pt;font-family:Menlo">Say I start with -cells 2,2,1 -max_conv its<span class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431s1"> n</span>; is it recommended to run on 4 MPI processes?</span><u></u><u></u></p>
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<p class="MsoNormal">No, those options do not influence the number of processes.<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">I am running ex56 on gpu; I am looking at KSPSolve (or any other event) but no gpu flops are recorded in the -log_view?<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">I do not think you are running on the GPU then. Mark can comment, but we usually specify GPU execution using the Vec and Mat types<u></u><u></u></p>
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<p class="MsoNormal">through -dm_vec_type and -dm_mat_type.<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"> Thanks,<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"> Matt<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">For your reference I used the below flags:<u></u><u></u></p>
<p class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431p1"><span class="gmail-m_-1073648265619177122gmail-m-743708965511543589gmail-m4613828314074599431s1"><span style="font-size:10pt">./ex56 -cells 1,1,1 -max_conv_its 3 -lx 1. -alpha .01 -petscspace_degree 1 -ksp_type cg -ksp_monitor
-ksp_rtol 1.e-8 -pc_type asm -snes_monitor -use_mat_nearnullspace true -snes_rtol 1.e-10 -ex56_dm_view -log_view</span></span><u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Kind regards,<u></u><u></u></p>
<p class="MsoNormal">Karthik.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:12pt;color:black">From:
</span></b><span style="font-size:12pt;color:black">Mark Adams <<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>><br>
<b>Date: </b>Sunday, 12 December 2021 at 23:00<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>Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</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] Unstructured mesh</span><u></u><u></u></p>
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<p class="MsoNormal">On Sun, Dec 12, 2021 at 3:19 PM Karthikeyan Chockalingam - STFC UKRI <<a href="mailto:karthikeyan.chockalingam@stfc.ac.uk" target="_blank">karthikeyan.chockalingam@stfc.ac.uk</a>>
wrote:<u></u><u></u></p>
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<p class="MsoNormal">Thank for your response that was helpful. I have a couple of questions:<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p style="margin-left:54pt">(i)<span style="font-size:7pt;font-family:"Times New Roman",serif">
</span>How can I control the level of refinement? I tried to pass the flag “-ex56_dm_refine 0” but that didn’t stop the refinement from 8 giving 32 cubes.<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">I answered this question recently but ex56 clobbers ex56_dm_refine in the convergence loop. I have an MR that prints a warning if you provide a ex56_dm_refine. <u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">* snes/ex56 runs a convergence study and confusingly sets the options manually, thus erasing your -ex56_dm_refine.<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">* To refine, use -max_conv_its N <3>, this sets the number of steps of refinement. That is, the length of the convergence study<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">* You can adjust where it starts from with -cells i,j,k <1,1,1><u></u><u></u></p>
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<p class="MsoNormal">You do want to set this if you have multiple MPI processes so that the size of this mesh is the number of processes. That way it starts with one cell per process and refines from
there.<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p style="margin-left:54pt">(ii)<span style="font-size:7pt;font-family:"Times New Roman",serif">
</span>What does -cell 2,2,1 correspond to? <u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">The initial mesh or mesh_0. The convergence test uniformly refines this mesh. So if you want to refine this twice you could use -cells 8,8,4<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p style="margin-left:54pt">How can I determine the total number of dofs? <u></u>
<u></u></p>
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<p class="MsoNormal">Unfortunately, that is not printed but you can calculate from the initial cell grid, the order of the element and the refinement in each iteration of the convergence tests.<u></u><u></u></p>
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<p style="margin-left:54pt">So that I can perform a scaling study by changing the input of the flag -cells.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">You can and the convergence test gives you data for a strong speedup study in one run. Each solve is put in its own "stage" of the output and you want to look at KSPSolve lines
in the log_view output. <u></u><u></u></p>
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<p class="MsoNormal"><br clear="all">
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">--
<u></u><u></u></p>
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<p class="MsoNormal">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></p>
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<p class="MsoNormal"><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><u></u><u></u></p>
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