[petsc-users] [petsc4py] Assembly fails
Matthew Knepley
knepley at gmail.com
Fri Mar 27 09:09:11 CDT 2020
On Fri, Mar 27, 2020 at 3:31 AM Alejandro Aragon - 3ME <
A.M.Aragon at tudelft.nl> wrote:
> Dear Matthew,
>
> Thanks for your email. I have attached the python code that reproduces the
> following error in my computer:
>
I think I see the problem. There were changes in DM in order to support
fields which only occupy part of the domain.
Now you need to tell the DM about the fields before it builds a Section. I
think in your code, you only need
f = PetscContainer()
f.setName("potential")
dm.addField(field = f)
from
https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMAddField.html
before the createSection().
My Python may not be correct since I never use that interface.
Thanks,
Matt
> (.pydev) ➜ dmplex_fem mpirun -np 2 python Cpp2Python.py
> Traceback (most recent call last):
> File "Cpp2Python.py", line 383, in <module>
> sys.exit(Cpp2Python())
> File "Cpp2Python.py", line 357, in Cpp2Python
> dm = createfields(dm)
> File "Cpp2Python.py", line 62, in createfields
> section.setFieldName(0, "u")
> File "PETSc/Section.pyx", line 59, in petsc4py.PETSc.Section.setFieldName
> petsc4py.PETSc.Error: error code 63
> [1] PetscSectionSetFieldName() line 427 in
> /private/tmp/pip-install-laf1l3br/petsc/src/vec/is/section/interface/section.c
> [1] Argument out of range
> [1] Section field 0 should be in [0, 0)
> Traceback (most recent call last):
> File "Cpp2Python.py", line 383, in <module>
> sys.exit(Cpp2Python())
> File "Cpp2Python.py", line 357, in Cpp2Python
> dm = createfields(dm)
> File "Cpp2Python.py", line 62, in createfields
> section.setFieldName(0, "u")
> File "PETSc/Section.pyx", line 59, in petsc4py.PETSc.Section.setFieldName
> petsc4py.PETSc.Error: error code 63
> [0] PetscSectionSetFieldName() line 427 in
> /private/tmp/pip-install-laf1l3br/petsc/src/vec/is/section/interface/section.c
> [0] Argument out of range
> [0] Section field 0 should be in [0, 0)
> -------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code.. Per user-direction, the job has been aborted.
> -------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun detected that one or more processes exited with non-zero status,
> thus causing
> the job to be terminated. The first process to do so was:
>
> Process name: [[23972,1],0]
> Exit code: 1
> --------------------------------------------------------------------------
>
> I’m using Python 3.8 and this is the output of ‘pip freeze'
>
> (.pydev) ➜ dmplex_fem pip freeze
> cachetools==4.0.0
> cycler==0.10.0
> kiwisolver==1.1.0
> llvmlite==0.31.0
> matplotlib==3.2.1
> mpi4py==3.0.3
> numba==0.48.0
> numpy==1.18.2
> petsc==3.12.4
> petsc4py==3.12.0
> plexus==0.1.0
> pyparsing==2.4.6
> python-dateutil==2.8.1
> scipy==1.4.1
> six==1.14.0
>
> I’m looking forward to getting your insight on the issue.
> Best regards,
>
> — Alejandro
>
>
>
> On 25 Mar 2020, at 17:37, Matthew Knepley <knepley at gmail.com> wrote:
>
> On Wed, Mar 25, 2020 at 12:29 PM Alejandro Aragon - 3ME <
> A.M.Aragon at tudelft.nl> wrote:
>
> Dear everyone,
>
> 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:
>
> (.pydev) ➜ testmodule git:(e0bc9ae) ✗ mpirun -np 2 python
> testmodule/__main__.py
> {3: <testmodule.constitutive.elastic.Elastic object at 0x10feea520>}
> {3: <testmodule.constitutive.elastic.Elastic object at 0x10d96d520>}
> Traceback (most recent call last):
> File "testmodule/__main__.py", line 32, in <module>
> sys.exit(main(sys.argv))
> File "testmodule/__main__.py", line 29, in main
> step.solve(m)
> File
> "/Users/aaragon/Local/testmodule/testmodule/fem/analysis/static.py", line
> 33, in solve
> self.Amat.assemblyBegin(assembly=0) # FINAL_ASSEMBLY = 0
> File "PETSc/Mat.pyx", line 1039, in petsc4py.PETSc.Mat.assemblyBegin
> petsc4py.PETSc.Error: error code 63
> [1] MatAssemblyBegin() line 5182 in
> /private/tmp/pip-install-zurcx_6k/petsc/src/mat/interface/matrix.c
> [1] MatAssemblyBegin_MPIAIJ() line 810 in
> /private/tmp/pip-install-zurcx_6k/petsc/src/mat/impls/aij/mpi/mpiaij.c
> [1] MatStashScatterBegin_Private() line 462 in
> /private/tmp/pip-install-zurcx_6k/petsc/src/mat/utils/matstash.c
> [1] MatStashScatterBegin_BTS() line 931 in
> /private/tmp/pip-install-zurcx_6k/petsc/src/mat/utils/matstash.c
> [1] PetscCommBuildTwoSidedFReq() line 555 in
> /private/tmp/pip-install-zurcx_6k/petsc/src/sys/utils/mpits.c
> [1] Argument out of range
> [1] toranks[0] 2 not in comm size 2
> Traceback (most recent call last):
> File "testmodule/__main__.py", line 32, in <module>
> sys.exit(main(sys.argv))
> File "testmodule/__main__.py", line 29, in main
> step.solve(m)
> File
> "/Users/aaragon/Local/testmodule/testmodule/fem/analysis/static.py", line
> 33, in solve
> self.Amat.assemblyBegin(assembly=0) # FINAL_ASSEMBLY = 0
> File "PETSc/Mat.pyx", line 1039, in petsc4py.PETSc.Mat.assemblyBegin
> petsc4py.PETSc.Error: error code 63
> [0] MatAssemblyBegin() line 5182 in
> /private/tmp/pip-install-zurcx_6k/petsc/src/mat/interface/matrix.c
> [0] MatAssemblyBegin_MPIAIJ() line 810 in
> /private/tmp/pip-install-zurcx_6k/petsc/src/mat/impls/aij/mpi/mpiaij.c
> [0] MatStashScatterBegin_Private() line 462 in
> /private/tmp/pip-install-zurcx_6k/petsc/src/mat/utils/matstash.c
> [0] MatStashScatterBegin_BTS() line 931 in
> /private/tmp/pip-install-zurcx_6k/petsc/src/mat/utils/matstash.c
> [0] PetscCommBuildTwoSidedFReq() line 555 in
> /private/tmp/pip-install-zurcx_6k/petsc/src/sys/utils/mpits.c
> [0] Argument out of range
> [0] toranks[0] 2 not in comm size 2
> -------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code.. Per user-direction, the job has been aborted.
> -------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun detected that one or more processes exited with non-zero status,
> thus causing
> the job to be terminated. The first process to do so was:
>
> Process name: [[46994,1],0]
> Exit code: 1
> --------------------------------------------------------------------------
>
>
> This is in the call to assembly, which looks like this:
>
> # Begins assembling the matrix. This routine should be called after completing all calls to MatSetValues().
> self.Amat.assemblyBegin(assembly=0) # FINAL_ASSEMBLY = 0
> # Completes assembling the matrix. This routine should be called after MatAssemblyBegin().
> self.Amat.assemblyEnd(assembly=0)
>
> 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.
>
>
> It looks like you have an inconsistent build, or a memory overwrite. Since
> you are in Python, I suspect the former. Can you build
> PETSc from scratch and try this? Does it work in serial? Can you send a
> small code that reproduces this?
>
> Thanks,
>
> Matt
>
>
> Best regards,
>
> — Alejandro
>
>
>
> --
> 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/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cse.buffalo.edu_-7Eknepley_&d=DwMFaQ&c=XYzUhXBD2cD-CornpT4QE19xOJBbRy-TBPLK0X9U2o8&r=U1Pry6bTDByPujjSnTcPY6KNXqrym6APfmtom-lIPFA&m=WPJk3cZzX4wkA5n5wceeOf2wjrRxHYug5Gs78b9WHlc&s=vuuUnGL1h2Bfv_uY7e5cMSfiF1btYPrvwf5vKy1JoN0&e=>
>
>
>
--
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/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20200327/51dc8c22/attachment.html>
More information about the petsc-users
mailing list