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PETSC ERROR when simulating flow past cylinder using mpirun

Open noirchen opened this issue 3 months ago • 0 comments

Hello, I am running into a PETSC error when I run the ns-code2 example. I convert the notebook to a python script and execute mpiexec -np 8 python ns-code2.py. All the test figures are correctly generated, but a petsc error of signal number 11 occurs. I installed fenicsx using conda on a linux machine with 16 cores.

The output is

Info    : [ 30%] Difference - Performing Face-Face intersection                                                         Info    : [ 70%] Difference - Performing intersection of shapes                                                         Info    : [ 80%] Difference - Making faces                                                                              Info    : [ 90%] Difference - Adding holes                                                                              Info    : Meshing 1D...
Info    : [  0%] Meshing curve 5 (Ellipse)
Info    : [ 30%] Meshing curve 6 (Line)
Info    : [ 50%] Meshing curve 7 (Line)
Info    : [ 70%] Meshing curve 8 (Line)
Info    : [ 90%] Meshing curve 9 (Line)
Info    : Done meshing 1D (Wall 0.0156927s, CPU 0.015616s)
Info    : Meshing 2D...
Info    : Meshing surface 1 (Plane, Frontal-Delaunay for Quads)
Info    : Simple recombination completed (Wall 0.00590733s, CPU 0.005909s): 103 quads, 16 triangles, 0 invalid quads, 0 quads with Q < 0.1, avg Q = 0.82361, min Q = 0.425555
Info    : Simple recombination completed (Wall 0.00678814s, CPU 0.006789s): 460 quads, 0 triangles, 0 invalid quads, 0 quads with Q < 0.1, avg Q = 0.865979, min Q = 0.499255
Info    : Done meshing 2D (Wall 0.0214993s, CPU 0.0215s)
Info    : Refining mesh...
Info    : Meshing order 2 (curvilinear on)...
Info    : [  0%] Meshing curve 5 order 2
Info    : [ 20%] Meshing curve 6 order 2
Info    : [ 40%] Meshing curve 7 order 2
Info    : [ 60%] Meshing curve 8 order 2
Info    : [ 70%] Meshing curve 9 order 2
Info    : [ 90%] Meshing surface 1 order 2
Info    : Done meshing order 2 (Wall 0.00653468s, CPU 0.005628s)
Info    : Done refining mesh (Wall 0.00710949s, CPU 0.006142s)
Info    : 1952 nodes 2069 elements
Info    : Meshing order 2 (curvilinear on)...
Info    : [  0%] Meshing curve 5 order 2
Info    : [ 20%] Meshing curve 6 order 2
Info    : [ 40%] Meshing curve 7 order 2
Info    : [ 60%] Meshing curve 8 order 2
Info    : [ 70%] Meshing curve 9 order 2
Info    : [ 90%] Meshing surface 1 order 2
Info    : Done meshing order 2 (Wall 0.0258181s, CPU 0.024792s)
Info    : Optimizing mesh (Netgen)...
Info    : Done optimizing mesh (Wall 2.12e-06s, CPU 3e-06s)
Solving PDE: 100%|██████████| 12800/12800 [07:17<00:00, 28.90it/s][4]PETSC ERROR: ------------------------------------------------------------------------
[4]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[4]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[4]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[4]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[4]PETSC ERROR: to get more information on the crash.
[4]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash.
Abort(59) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 4

noirchen avatar Oct 30 '24 07:10 noirchen