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PyLith is a finite element code for the solution of dynamic and quasi-static tectonic deformation problems.
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[REPLACE THIS WITH AN APPROPRIATE TITLE FOR YOUR DEBUGGING HELP REQUEST] #773

Open Evelyn0416 opened 4 weeks ago

Evelyn0416 commented 4 weeks ago

When I run step06.cfg in pylith 2.2.2, after creating the model via trelisr, the error shows as below:

Fatal error. Calling MPI_Abort() to abort PyLith application. Traceback (most recent call last): File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 74, in onComputeNodes self.main(*args, **kwds) File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/apps/PyLithApp.py", line 126, in main self.problem.verifyConfiguration() File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/problems/TimeDependent.py", line 104, in verifyConfiguration Problem.verifyConfiguration(self) File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/problems/Problem.py", line 189, in verifyConfiguration self.mesh().checkMaterialIds(idValues) File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/topology/Mesh.py", line 68, in checkMaterialIds MeshOps_checkMaterialIds(self, materialIds) RuntimeError: Material id '10' for cell '0' does not match the id of any available materials or interfaces. application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0 /home/swjtu/pylith/1/bin/nemesis: mpirun: exit 255 /home/swjtu/pylith/1/bin/pylith: /home/swjtu/pylith/1/bin/nemesis: exit 1

So what should I do to solve this problem.

knepley commented 4 weeks ago

It appears that your mesh labels do not match the label values in the .cfg file. Here is says that cell 0 has label value 10 in your mesh, but this value is not associated to a material in the .cfg file.

Thanks,

 Matt

On Tue, Sep 24, 2024 at 5:14 AM Evelyn0416 @.***> wrote:

When I run step06.cfg in pylith 2.2.2, after creating the model via trelisr, the error shows as below:

Fatal error. Calling MPI_Abort() to abort PyLith application. Traceback (most recent call last): File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 74, in onComputeNodes self.main(*args, **kwds) File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/apps/PyLithApp.py", line 126, in main self.problem.verifyConfiguration() File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/problems/TimeDependent.py", line 104, in verifyConfiguration Problem.verifyConfiguration(self) File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/problems/Problem.py", line 189, in verifyConfiguration self.mesh().checkMaterialIds(idValues) File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/topology/Mesh.py", line 68, in checkMaterialIds MeshOps_checkMaterialIds(self, materialIds) RuntimeError: Material id '10' for cell '0' does not match the id of any available materials or interfaces. application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0 /home/swjtu/pylith/1/bin/nemesis: mpirun: exit 255 /home/swjtu/pylith/1/bin/pylith: /home/swjtu/pylith/1/bin/nemesis: exit 1

So what should I do to solve this problem.

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Evelyn0416 commented 3 weeks ago

It appears that your mesh labels do not match the label values in the .cfg file. Here is says that cell 0 has label value 10 in your mesh, but this value is not associated to a material in the .cfg file. Thanks, Matt … On Tue, Sep 24, 2024 at 5:14 AM Evelyn0416 @.> wrote: When I run step06.cfg in pylith 2.2.2, after creating the model via trelisr, the error shows as below: Fatal error. Calling MPI_Abort() to abort PyLith application. Traceback (most recent call last): File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 74, in onComputeNodes self.main(args, kwds) File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/apps/PyLithApp.py", line 126, in main self.problem.verifyConfiguration() File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/problems/TimeDependent.py", line 104, in verifyConfiguration Problem.verifyConfiguration(self) File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/problems/Problem.py", line 189, in verifyConfiguration self.mesh().checkMaterialIds(idValues) File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/topology/Mesh.py", line 68, in checkMaterialIds MeshOps_checkMaterialIds(self, materialIds) RuntimeError: Material id '10' for cell '0' does not match the id of any available materials or interfaces. application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0 /home/swjtu/pylith/1/bin/nemesis: mpirun: exit 255 /home/swjtu/pylith/1/bin/pylith: /home/swjtu/pylith/1/bin/nemesis: exit 1 So what should I do to solve this problem. — Reply to this email directly, view it on GitHub <#773>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEORCIHMLDCZUSQE3AFXC3ZYEUQFAVCNFSM6AAAAABOX2SA36VHI2DSMVQWIX3LMV43ASLTON2WKOZSGU2DIOBSG4ZTINY . You are receiving this because you are subscribed to this thread.Message ID: @.***> -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ http://www.cse.buffalo.edu/~knepley/

I am glad for your answer. Now a new question arises as follows:

[0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Petsc has generated inconsistent data [0]PETSC ERROR: Point 1280838 not found in support of cone point 1753945 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.10.2, Jul, 01, 2019 [0]PETSC ERROR: /home/swjtu/pylith/pylith-2.2.2-linux-x86_64/bin/mpinemesis on a named DESKTOP-CT7EFOQ by root Wed Sep 25 23:07:35 2024 [0]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0 --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/brad/pylitFatal error. Calling MPI_Abort() to abort PyLith application. h-binary/dist/include -I/home/brad/pylith-binary/dist/include " LDFLAGS="-L/home/brad/pylith-binary/dist/lib -L/home/brad/pylith-binary/dist/lib64 -L/home/brad/pylith-binary/dist/lib -L/home/brad/pylith-binary/dist/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith PETSC_ARCH=arch-pylith [0]PETSC ERROR: #1 DMPlexCheckSymmetry() line 6600 in /home/brad/pylith-binary/build/petsc-pylith/src/dm/impls/plex/plex.c [0]PETSC ERROR: #2 static void pylith::topology::MeshOps::checkTopology(const pylith::topology::Mesh&)() line 100 in ../../../pylith-2.2.2/libsrc/pylith/topology/MeshOps.cc Traceback (most recent call last): File "/home/swjtu/pylith/pylith-2.2.2-linux-x86_64/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 74, in onComputeNodes self.main(*args, **kwds) File "/home/swjtu/pylith/pylith-2.2.2-linux-x86_64/lib/python2.7/site-packages/

Does it mean that something is wrong with the model somewhere, right? I don’t know how to solve it. Any suggestions or help will be greatly appreciated.

knepley commented 3 weeks ago

On Wed, Sep 25, 2024 at 11:09 AM Evelyn0416 @.***> wrote:

It appears that your mesh labels do not match the label values in the .cfg file. Here is says that cell 0 has label value 10 in your mesh, but this value is not associated to a material in the .cfg file. Thanks, Matt … <#m556926534767188244> On Tue, Sep 24, 2024 at 5:14 AM Evelyn0416 @.**> wrote: When I run step06.cfg in pylith 2.2.2, after creating the model via trelisr, the error shows as below: Fatal error. Calling MPI_Abort() to abort PyLith application. Traceback (most recent call last): File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 74, in onComputeNodes self.main(args, kwds) File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/apps/PyLithApp.py", line 126, in main self.problem.verifyConfiguration() File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/problems/TimeDependent.py", line 104, in verifyConfiguration Problem.verifyConfiguration(self) File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/problems/Problem.py", line 189, in verifyConfiguration self.mesh().checkMaterialIds(idValues) File "/home/swjtu/pylith/1/lib/python2.7/site-packages/pylith/topology/Mesh.py", line 68, in checkMaterialIds MeshOps_checkMaterialIds(self, materialIds) RuntimeError: Material id '10' for cell '0' does not match the id of any available materials or interfaces. application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0 /home/swjtu/pylith/1/bin/nemesis: mpirun: exit 255 /home/swjtu/pylith/1/bin/pylith: /home/swjtu/pylith/1/bin/nemesis: exit 1 So what should I do to solve this problem. — Reply to this email directly, view it on GitHub <#773 https://github.com/geodynamics/pylith/issues/773>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEORCIHMLDCZUSQE3AFXC3ZYEUQFAVCNFSM6AAAAABOX2SA36VHI2DSMVQWIX3LMV43ASLTON2WKOZSGU2DIOBSG4ZTINY https://github.com/notifications/unsubscribe-auth/AAEORCIHMLDCZUSQE3AFXC3ZYEUQFAVCNFSM6AAAAABOX2SA36VHI2DSMVQWIX3LMV43ASLTON2WKOZSGU2DIOBSG4ZTINY . You are receiving this because you are subscribed to this thread.Message ID: @.*> -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ http://www.cse.buffalo.edu/~knepley/

I am glad for your answer. Now a new question arises as follows:

[0]PETSC ERROR: --------------------- Error Message

[0]PETSC ERROR: Petsc has generated inconsistent data [0]PETSC ERROR: Point 1280838 not found in support of cone point 1753945 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.10.2, Jul, 01, 2019 [0]PETSC ERROR: /home/swjtu/pylith/pylith-2.2.2-linux-x86_64/bin/mpinemesis on a named DESKTOP-CT7EFOQ by root Wed Sep 25 23:07:35 2024 [0]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0 --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/brad/pylitFatal error. Calling MPI_Abort() to abort PyLith application. h-binary/dist/include -I/home/brad/pylith-binary/dist/include " LDFLAGS="-L/home/brad/pylith-binary/dist/lib -L/home/brad/pylith-binary/dist/lib64 -L/home/brad/pylith-binary/dist/lib -L/home/brad/pylith-binary/dist/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith PETSC_ARCH=arch-pylith [0]PETSC ERROR: #1 https://github.com/geodynamics/pylith/issues/1 DMPlexCheckSymmetry() line 6600 in /home/brad/pylith-binary/build/petsc-pylith/src/dm/impls/plex/plex.c [0]PETSC ERROR: #2 https://github.com/geodynamics/pylith/issues/2 static void pylith::topology::MeshOps::checkTopology(const pylith::topology::Mesh&)() line 100 in ../../../pylith-2.2.2/libsrc/pylith/topology/MeshOps.cc Traceback (most recent call last): File "/home/swjtu/pylith/pylith-2.2.2-linux-x86_64/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 74, in onComputeNodes self.main(*args, **kwds) File "/home/swjtu/pylith/pylith-2.2.2-linux-x86_64/lib/python2.7/site-packages/

Does it mean that something is wrong with the model somewhere, right? I don’t know how to solve it. Any suggestions or help will be greatly appreciated.

Yes, the mesh is invalid. I am not sure how this happened. It should not be possible to produce this kind of invalid mesh, but it might mean that something about the fault specification is wrong. Can you turn off all faults and retry?

Thanks,

Matt

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-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener

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