[petsc-users] [petsc4py] Assembly fails
Matthew Knepley
knepley at gmail.com
Sat Mar 28 14:09:35 CDT 2020
On Sat, Mar 28, 2020 at 1:30 PM Alejandro Aragon - 3ME <
A.M.Aragon at tudelft.nl> wrote:
> Dear Matthew,
>
> Thanks for your email. I tried first what you suggested and it didn’t
> work. However, I actually tried also commenting the same function in
> Section and worked! This is the working code:
>
I do not understand what you mean above.
Thanks,
Matt
> def createfields(dm):
> """Set up the solution field"""
>
> dim = dm.getDimension()
> # The number of solution fields
> numFields = 1
> dm.setNumFields(numFields)
> # numComp - An array of size numFields that holds the number of components for each field
> numComp = np.array([dim], dtype=np.int32)
> # numDof - An array of size numFields*(dim+1) which holds
> # the number of dof for each field on a mesh piece of dimension d
> numDof = np.zeros(numFields*(dim+1), dtype=np.int32)
> numDof[0] = dim # u is defined on vertices
>
> # Create a PetscSection based upon the dof layout specification provided
> # PetscSection: Mapping from integers in a designated range to contiguous sets of integers
> section = dm.createSection(numComp, numDof)
> # Sets the name of a field in the PetscSection, 0 is the field number and "u" is the field name
> section.setFieldName(0, "u")
> # Set the PetscSection encoding the local data layout for the DM
> dm.setDefaultSection(section)
>
> return dm
>
>
> The question I now have is whether PETSc 3.13 and the matching petsc4py
> will change functionality to the point that this code will no longer work.
> Would that be the case?
>
> Best regards,
>
> — Alejandro
>
> On 28 Mar 2020, at 18:14, Matthew Knepley <knepley at gmail.com> wrote:
>
> On Fri, Mar 27, 2020 at 10:09 AM Matthew Knepley <knepley at gmail.com>
> wrote:
>
>> 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)
>>
>
> So Nicolas Barral found a much better way to do this. You only need
>
> dm.setNumFields(1)
>
> Thanks,
>
> Matt
>
>
>> from
>> https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMAddField.html
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mcs.anl.gov_petsc_petsc-2Dcurrent_docs_manualpages_DM_DMAddField.html&d=DwMFaQ&c=XYzUhXBD2cD-CornpT4QE19xOJBbRy-TBPLK0X9U2o8&r=U1Pry6bTDByPujjSnTcPY6KNXqrym6APfmtom-lIPFA&m=UZjBC-wnFeOXp0s_J1LfjZeUVWAtsWXRKX6gZQ64z7Q&s=ICc46rZbM067ZBpFcy0TKivavc07pbkZe1e8Bu4SmIA&e=>
>> 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/
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cse.buffalo.edu_-7Eknepley_&d=DwMFaQ&c=XYzUhXBD2cD-CornpT4QE19xOJBbRy-TBPLK0X9U2o8&r=U1Pry6bTDByPujjSnTcPY6KNXqrym6APfmtom-lIPFA&m=UZjBC-wnFeOXp0s_J1LfjZeUVWAtsWXRKX6gZQ64z7Q&s=pgBjejAN8aAlWZNjhIiXXP8IhXJrAr2HeI7cLhj0wlM&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/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cse.buffalo.edu_-7Eknepley_&d=DwMFaQ&c=XYzUhXBD2cD-CornpT4QE19xOJBbRy-TBPLK0X9U2o8&r=U1Pry6bTDByPujjSnTcPY6KNXqrym6APfmtom-lIPFA&m=UZjBC-wnFeOXp0s_J1LfjZeUVWAtsWXRKX6gZQ64z7Q&s=pgBjejAN8aAlWZNjhIiXXP8IhXJrAr2HeI7cLhj0wlM&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/>
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