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<div class="">Dear everyone,</div>
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<div class="">I’m new to petsc4py and I’m trying to run a simple finite element code that uses DMPLEX to load a .msh file (created by Gmsh). In version 3.10 the code was working but I recently upgraded to 3.12 and I get the following error:</div>
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<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">(.pydev) </span>
<span style="font-variant-ligatures: no-common-ligatures; color: #b42419" class="">➜
</span><span style="font-variant-ligatures: no-common-ligatures; color: #2eaebb" class="">testmodule</span><span style="font-variant-ligatures: no-common-ligatures" class="">
</span><span style="font-variant-ligatures: no-common-ligatures; color: #400bd9" class="">git:(</span><span style="font-variant-ligatures: no-common-ligatures; color: #b42419" class="">e0bc9ae</span><span style="font-variant-ligatures: no-common-ligatures; color: #400bd9" class="">)
</span><span style="font-variant-ligatures: no-common-ligatures; color: #9fa01c" class="">✗</span><span style="font-variant-ligatures: no-common-ligatures" class=""> mpirun -np 2 python testmodule/__main__.py</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">{3: <testmodule.constitutive.elastic.Elastic object at 0x10feea520>}</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">{3: <testmodule.constitutive.elastic.Elastic object at 0x10d96d520>}</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">Traceback (most recent call last):</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> File "testmodule/__main__.py", line 32, in <module></span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> sys.exit(main(sys.argv))</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> File "testmodule/__main__.py", line 29, in main</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> step.solve(m)</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> File "/Users/aaragon/Local/testmodule/testmodule/fem/analysis/static.py", line 33, in solve</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> self.Amat.assemblyBegin(assembly=0) # FINAL_ASSEMBLY = 0</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> File "PETSc/Mat.pyx", line 1039, in petsc4py.PETSc.Mat.assemblyBegin</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">petsc4py.PETSc.Error: error code 63</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">[1] MatAssemblyBegin() line 5182 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/interface/matrix.c</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">[1] MatAssemblyBegin_MPIAIJ() line 810 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/impls/aij/mpi/mpiaij.c</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">[1] MatStashScatterBegin_Private() line 462 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/utils/matstash.c</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">[1] MatStashScatterBegin_BTS() line 931 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/utils/matstash.c</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">[1] PetscCommBuildTwoSidedFReq() line 555 in /private/tmp/pip-install-zurcx_6k/petsc/src/sys/utils/mpits.c</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">[1] Argument out of range</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">[1] toranks[0] 2 not in comm size 2</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">Traceback (most recent call last):</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> File "testmodule/__main__.py", line 32, in <module></span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> sys.exit(main(sys.argv))</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> File "testmodule/__main__.py", line 29, in main</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> step.solve(m)</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> File "/Users/aaragon/Local/testmodule/testmodule/fem/analysis/static.py", line 33, in solve</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> self.Amat.assemblyBegin(assembly=0) # FINAL_ASSEMBLY = 0</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> File "PETSc/Mat.pyx", line 1039, in petsc4py.PETSc.Mat.assemblyBegin</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">petsc4py.PETSc.Error: error code 63</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">[0] MatAssemblyBegin() line 5182 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/interface/matrix.c</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">[0] MatAssemblyBegin_MPIAIJ() line 810 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/impls/aij/mpi/mpiaij.c</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">[0] MatStashScatterBegin_Private() line 462 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/utils/matstash.c</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">[0] MatStashScatterBegin_BTS() line 931 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/utils/matstash.c</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">[0] PetscCommBuildTwoSidedFReq() line 555 in /private/tmp/pip-install-zurcx_6k/petsc/src/sys/utils/mpits.c</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">[0] Argument out of range</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">[0] toranks[0] 2 not in comm size 2</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">-------------------------------------------------------</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">Primary job terminated normally, but 1 process returned</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">a non-zero exit code.. Per user-direction, the job has been aborted.</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">-------------------------------------------------------</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">--------------------------------------------------------------------------</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">mpirun detected that one or more processes exited with non-zero status, thus causing</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">the job to be terminated. The first process to do so was:</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); min-height: 25px; font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class="">
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<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> Process name: [[46994,1],0]</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> Exit code: 1</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Inconsolata-dz; color: rgb(242, 242, 242); background-color: rgba(0, 0, 0, 0.85098); font-size: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">--------------------------------------------------------------------------</span></div>
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<div class="">This is in the call to assembly, which looks like this:</div>
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<pre style="background-color: rgb(255, 255, 255); color: rgb(74, 92, 110); font-family: Menlo; font-size: 15px;" class=""><span style="color: rgb(159, 159, 159);" class=""># Begins assembling the matrix. This routine should be called after completing all calls to MatSetValues().<br class=""></span><span style="color: rgb(218, 139, 209);" class="">self</span>.Amat.assemblyBegin(<span style="color: rgb(255, 140, 96);" class="">assembly</span>=<span style="color: rgb(93, 151, 196);" class="">0</span>) <span style="color: rgb(159, 159, 159);" class=""># FINAL_ASSEMBLY = 0<br class=""></span><span style="color: rgb(159, 159, 159);" class=""># Completes assembling the matrix. This routine should be called after MatAssemblyBegin().<br class=""></span><span style="color: rgb(218, 139, 209);" class="">self</span>.Amat.assemblyEnd(<span style="color: rgb(255, 140, 96);" class="">assembly</span>=<span style="color: rgb(93, 151, 196);" class="">0</span>)<br class=""></pre>
<div class="">I would appreciate if someone can give me some insight on what has changed in the new version of petsc4py (or petsc for that matter) to make this code work again.</div>
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<div class="">Best regards,</div>
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— Alejandro</div>
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