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<div class="">Dear Matthew,</div>
<div class=""><br class="">
</div>
<div class="">Thanks for your email. I have attached the python code that reproduces the following error in my computer:</div>
<div class=""><br class="">
</div>
<div class="">
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">(.pydev) </span><span class="" style="color:rgb(255,99,85)">➜
</span><span class="" style="color:rgb(93,253,255)">dmplex_fem</span><span class="" style=""> mpirun -np 2 python Cpp2Python.py</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">Traceback (most recent call last):</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> File "Cpp2Python.py", line 383, in <module></span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> sys.exit(Cpp2Python())</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> File "Cpp2Python.py", line 357, in Cpp2Python</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> dm = createfields(dm)</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> File "Cpp2Python.py", line 62, in createfields</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> section.setFieldName(0, "u")</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> File "PETSc/Section.pyx", line 59, in petsc4py.PETSc.Section.setFieldName</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">petsc4py.PETSc.Error: error code 63</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">[1] PetscSectionSetFieldName() line 427 in /private/tmp/pip-install-laf1l3br/petsc/src/vec/is/section/interface/section.c</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">[1] Argument out of range</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">[1] Section field 0 should be in [0, 0)</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">Traceback (most recent call last):</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> File "Cpp2Python.py", line 383, in <module></span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> sys.exit(Cpp2Python())</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> File "Cpp2Python.py", line 357, in Cpp2Python</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> dm = createfields(dm)</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> File "Cpp2Python.py", line 62, in createfields</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> section.setFieldName(0, "u")</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> File "PETSc/Section.pyx", line 59, in petsc4py.PETSc.Section.setFieldName</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">petsc4py.PETSc.Error: error code 63</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">[0] PetscSectionSetFieldName() line 427 in /private/tmp/pip-install-laf1l3br/petsc/src/vec/is/section/interface/section.c</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">[0] Argument out of range</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">[0] Section field 0 should be in [0, 0)</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">-------------------------------------------------------</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">Primary job terminated normally, but 1 process returned</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">a non-zero exit code.. Per user-direction, the job has been aborted.</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">-------------------------------------------------------</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">--------------------------------------------------------------------------</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">mpirun detected that one or more processes exited with non-zero status, thus causing</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">the job to be terminated. The first process to do so was:</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16); min-height:25px">
<span class="" style=""></span><br class="">
</div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> Process name: [[23972,1],0]</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style=""> Exit code: 1</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">--------------------------------------------------------------------------</span></div>
</div>
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<div class="">I’m using Python 3.8 and this is the output of ‘pip freeze'</div>
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<div class="">
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">(.pydev) </span><span class="" style="color:rgb(255,99,85)">➜
</span><span class="" style="color:rgb(93,253,255)">dmplex_fem</span><span class="" style=""> pip freeze</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">cachetools==4.0.0</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">cycler==0.10.0</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">kiwisolver==1.1.0</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">llvmlite==0.31.0</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">matplotlib==3.2.1</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">mpi4py==3.0.3</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">numba==0.48.0</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">numpy==1.18.2</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">petsc==3.12.4</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">petsc4py==3.12.0</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">plexus==0.1.0</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">pyparsing==2.4.6</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">python-dateutil==2.8.1</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">scipy==1.4.1</span></div>
<div class="" style="margin:0px; font-size:13px; line-height:normal; font-family:Inconsolata-dz; color:rgb(16,16,16)">
<span class="" style="">six==1.14.0</span></div>
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</div>
<div class="">I’m looking forward to getting your insight on the issue.</div>
<div class="">Best regards,</div>
<br class="">
<div class="">
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— Alejandro</div>
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<blockquote type="cite" class="">
<div class="">On 25 Mar 2020, at 17:37, Matthew Knepley <<a href="mailto:knepley@gmail.com" class="">knepley@gmail.com</a>> wrote:</div>
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<div dir="ltr" class="">
<div dir="ltr" class="">On Wed, Mar 25, 2020 at 12:29 PM Alejandro Aragon - 3ME <<a href="mailto:A.M.Aragon@tudelft.nl" class="">A.M.Aragon@tudelft.nl</a>> wrote:<br class="">
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<blockquote class="x_gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
<div class="" style="word-wrap:break-word">
<div class="">Dear everyone,</div>
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<div class="">
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">(.pydev) </span><span class="" style="color:rgb(180,36,25)">➜
</span><span class="" style="color:rgb(46,174,187)">testmodule</span><span class="" style="">
</span><span class="" style="color:rgb(64,11,217)">git:(</span><span class="" style="color:rgb(180,36,25)">e0bc9ae</span><span class="" style="color:rgb(64,11,217)">)
</span><span class="" style="color:rgb(159,160,28)">✗</span><span class="" style=""> mpirun -np 2 python testmodule/__main__.py</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">{3: <testmodule.constitutive.elastic.Elastic object at 0x10feea520>}</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">{3: <testmodule.constitutive.elastic.Elastic object at 0x10d96d520>}</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">Traceback (most recent call last):</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style=""> File "testmodule/__main__.py", line 32, in <module></span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style=""> sys.exit(main(sys.argv))</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style=""> File "testmodule/__main__.py", line 29, in main</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style=""> step.solve(m)</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style=""> File "/Users/aaragon/Local/testmodule/testmodule/fem/analysis/static.py", line 33, in solve</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style=""> self.Amat.assemblyBegin(assembly=0) # FINAL_ASSEMBLY = 0</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style=""> File "PETSc/Mat.pyx", line 1039, in petsc4py.PETSc.Mat.assemblyBegin</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">petsc4py.PETSc.Error: error code 63</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">[1] MatAssemblyBegin() line 5182 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/interface/matrix.c</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">[1] MatAssemblyBegin_MPIAIJ() line 810 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/impls/aij/mpi/mpiaij.c</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">[1] MatStashScatterBegin_Private() line 462 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/utils/matstash.c</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">[1] MatStashScatterBegin_BTS() line 931 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/utils/matstash.c</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">[1] PetscCommBuildTwoSidedFReq() line 555 in /private/tmp/pip-install-zurcx_6k/petsc/src/sys/utils/mpits.c</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">[1] Argument out of range</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">[1] toranks[0] 2 not in comm size 2</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">Traceback (most recent call last):</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style=""> File "testmodule/__main__.py", line 32, in <module></span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style=""> sys.exit(main(sys.argv))</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style=""> File "testmodule/__main__.py", line 29, in main</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style=""> step.solve(m)</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style=""> File "/Users/aaragon/Local/testmodule/testmodule/fem/analysis/static.py", line 33, in solve</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style=""> self.Amat.assemblyBegin(assembly=0) # FINAL_ASSEMBLY = 0</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style=""> File "PETSc/Mat.pyx", line 1039, in petsc4py.PETSc.Mat.assemblyBegin</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">petsc4py.PETSc.Error: error code 63</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">[0] MatAssemblyBegin() line 5182 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/interface/matrix.c</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">[0] MatAssemblyBegin_MPIAIJ() line 810 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/impls/aij/mpi/mpiaij.c</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">[0] MatStashScatterBegin_Private() line 462 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/utils/matstash.c</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">[0] MatStashScatterBegin_BTS() line 931 in /private/tmp/pip-install-zurcx_6k/petsc/src/mat/utils/matstash.c</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">[0] PetscCommBuildTwoSidedFReq() line 555 in /private/tmp/pip-install-zurcx_6k/petsc/src/sys/utils/mpits.c</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">[0] Argument out of range</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">[0] toranks[0] 2 not in comm size 2</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">-------------------------------------------------------</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">Primary job terminated normally, but 1 process returned</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">a non-zero exit code.. Per user-direction, the job has been aborted.</span></div>
<div class="" style="margin:0px; line-height:normal; font-family:Inconsolata-dz; color:rgb(242,242,242); font-size:13px">
<span class="" style="">-------------------------------------------------------</span></div>
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<span class="" style="">--------------------------------------------------------------------------</span></div>
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<span class="" style="">mpirun detected that one or more processes exited with non-zero status, thus causing</span></div>
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<span class="" style="">the job to be terminated. The first process to do so was:</span></div>
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<span class="" style=""> Process name: [[46994,1],0]</span></div>
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<span class="" style=""> Exit code: 1</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 class="" style="background-color:rgb(255,255,255); color:rgb(74,92,110); font-family:Menlo; font-size:15px"><span class="" style="color:rgb(159,159,159)"># Begins assembling the matrix. This routine should be called after completing all calls to MatSetValues().<br class=""></span><span class="" style="color:rgb(218,139,209)">self</span>.Amat.assemblyBegin(<span class="" style="color:rgb(255,140,96)">assembly</span>=<span class="" style="color:rgb(93,151,196)">0</span>) <span class="" style="color:rgb(159,159,159)"># FINAL_ASSEMBLY = 0<br class=""></span><span class="" style="color:rgb(159,159,159)"># Completes assembling the matrix. This routine should be called after MatAssemblyBegin().<br class=""></span><span class="" style="color:rgb(218,139,209)">self</span>.Amat.assemblyEnd(<span class="" style="color:rgb(255,140,96)">assembly</span>=<span class="" style="color:rgb(93,151,196)">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="">It looks like you have an inconsistent build, or a memory overwrite. Since you are in Python, I suspect the former. Can you build</div>
<div class="">PETSc from scratch and try this? Does it work in serial? Can you send a small code that reproduces this?</div>
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<div class=""> Thanks,</div>
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<div class=""> Matt</div>
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<div class="">Best regards,</div>
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-- Norbert Wiener</div>
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