[petsc-users] A question about DMPlexDistribute
leejearl
leejearl at 126.com
Thu Aug 11 20:00:17 CDT 2016
Thank you for your reply. I have attached the code, grid and the error
message.
cavity.c is the code file, cavity.exo is the grid, and error.dat is the
error message.
The command is "mpirun -n 2 ./cavity"
On 2016年08月11日 23:29, Matthew Knepley wrote:
> On Thu, Aug 11, 2016 at 3:14 AM, leejearl <leejearl at 126.com
> <mailto:leejearl at 126.com>> wrote:
>
> Hi,
> Thank you for your reply. It help me very much.
> But, for "/petsc-3.7.2/src/ts/examples/tutorials/ex11.c", when
> I set the overlap to 2 levels, the command is
> "mpirun -n 3 ./ex11 -f annulus-20.exo -ufv_mesh_overlap 2 -physics
> sw", it suffers a error.
> It seems to me that setting overlap to 2 is very common. Are
> there issues that I have not take into consideration?
> Any help are appreciated.
>
> I will check this out. I have not tested an overlap of 2 here since I
> generally use nearest neighbor FV methods for
> unstructured stuff. I have test examples that run fine for overlap >
> 1. Can you send the entire error message?
>
> If the error is not in the distribution, but rather in the analytics,
> that is understandable because this example is only
> intended to be run using a nearest neighbor FV method, and thus might
> be confused if we give it two layers of ghost
> cells.
>
> Matt
>
>
> leejearl
>
>
> On 2016年08月11日 14:57, Julian Andrej wrote:
>> Hi,
>>
>> take a look at slide 10 of [1], there is visually explained what
>> the overlap between partitions is.
>>
>> [1]
>> https://www.archer.ac.uk/training/virtual/files/2015/06-PETSc/slides.pdf
>> <https://www.archer.ac.uk/training/virtual/files/2015/06-PETSc/slides.pdf>
>>
>> On Thu, Aug 11, 2016 at 8:48 AM, leejearl <leejearl at 126.com
>> <mailto:leejearl at 126.com>> wrote:
>>
>> Hi, all:
>> I want to use PETSc to build my FVM code. Now, I have a
>> question about
>> the function DMPlexDistribute(DM dm, PetscInt overlap,
>> PetscSF *sf, DM *dmOverlap) .
>>
>> In the example
>> "/petsc-3.7.2/src/ts/examples/tutorials/ex11.c". When I set
>> the overlap
>> as 0 or 1, it works well. But, if I set the overlap as 2, it
>> suffers a problem.
>> I am confused about the value of overlap. Can it be set
>> as 2? What is the meaning of
>> the parameter overlap?
>> Any helps are appreciated!
>>
>> leejearl
>>
>>
>>
>>
>
>
>
>
> --
> 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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[1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[1]PETSC ERROR: Argument out of range
[1]PETSC ERROR: key 1633 is greater than largest key allowed 2
[1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[1]PETSC ERROR: Petsc Release Version 3.7.2, Jun, 05, 2016
[1]PETSC ERROR: ./cavity on a arch-linux2-c-debug named leejearl by leejearl Fri Aug 12 08:51:51 2016
[1]PETSC ERROR: Configure options --prefix=/home/leejearl/Install/petsc-openmpi --with-mpi=/home/leejearl/Install/openmpi/gnu/1.8.4 --download-exodusii=yes --download-netcdf --with-hdf5-dir=/home/leejearl/Install/hdf5-1.8.14 --download-metis=yes
[1]PETSC ERROR: #1 PetscTableAdd() line 46 in /home/leejearl/Software/petsc/petsc-3.7.2/include/petscctable.h
[1]PETSC ERROR: #2 PetscSFSetGraph() line 347 in /home/leejearl/Software/petsc/petsc-3.7.2/src/vec/is/sf/interface/sf.c
[1]PETSC ERROR: #3 DMLabelGather() line 1092 in /home/leejearl/Software/petsc/petsc-3.7.2/src/dm/label/dmlabel.c
[1]PETSC ERROR: #4 DMPlexPartitionLabelPropagate() line 1633 in /home/leejearl/Software/petsc/petsc-3.7.2/src/dm/impls/plex/plexpartition.c
[1]PETSC ERROR: #5 DMPlexCreateOverlap() line 615 in /home/leejearl/Software/petsc/petsc-3.7.2/src/dm/impls/plex/plexdistribute.c
[1]PETSC ERROR: #6 DMPlexDistributeOverlap() line 1729 in /home/leejearl/Software/petsc/petsc-3.7.2/src/dm/impls/plex/plexdistribute.c
[1]PETSC ERROR: #7 DMPlexDistribute() line 1635 in /home/leejearl/Software/petsc/petsc-3.7.2/src/dm/impls/plex/plexdistribute.c
[1]PETSC ERROR: #8 main() line 54 in /home/leejearl/Desktop/PETSc/gks_cavity/cavity.c
[1]PETSC ERROR: No PETSc Option Table entries
[1]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 63.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: likely location of problem given in stack below
[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR: INSTEAD the line number of the start of the function
[0]PETSC ERROR: is given.
[0]PETSC ERROR: [0] PetscCommDuplicate line 136 /home/leejearl/Software/petsc/petsc-3.7.2/src/sys/objects/tagm.c
[0]PETSC ERROR: [0] PetscHeaderCreate_Private line 36 /home/leejearl/Software/petsc/petsc-3.7.2/src/sys/objects/inherit.c
[0]PETSC ERROR: [0] PetscSectionCreate line 42 /home/leejearl/Software/petsc/petsc-3.7.2/src/vec/is/utils/vsectionis.c
[0]PETSC ERROR: [0] DMLabelDistribute_Internal line 898 /home/leejearl/Software/petsc/petsc-3.7.2/src/dm/label/dmlabel.c
[0]PETSC ERROR: [0] DMLabelGather line 1063 /home/leejearl/Software/petsc/petsc-3.7.2/src/dm/label/dmlabel.c
[0]PETSC ERROR: [0] DMPlexPartitionLabelPropagate line 1628 /home/leejearl/Software/petsc/petsc-3.7.2/src/dm/impls/plex/plexpartition.c
[0]PETSC ERROR: [0] DMPlexCreateOverlap line 561 /home/leejearl/Software/petsc/petsc-3.7.2/src/dm/impls/plex/plexdistribute.c
[0]PETSC ERROR: [0] DMPlexDistributeOverlap line 1715 /home/leejearl/Software/petsc/petsc-3.7.2/src/dm/impls/plex/plexdistribute.c
[0]PETSC ERROR: [0] DMPlexDistribute line 1555 /home/leejearl/Software/petsc/petsc-3.7.2/src/dm/impls/plex/plexdistribute.c
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.7.2, Jun, 05, 2016
[0]PETSC ERROR: ./cavity on a arch-linux2-c-debug named leejearl by leejearl Fri Aug 12 08:51:51 2016
[0]PETSC ERROR: Configure options --prefix=/home/leejearl/Install/petsc-openmpi --with-mpi=/home/leejearl/Install/openmpi/gnu/1.8.4 --download-exodusii=yes --download-netcdf --with-hdf5-dir=/home/leejearl/Install/hdf5-1.8.14 --download-metis=yes
[0]PETSC ERROR: #1 User provided function() line 0 in unknown file
[leejearl:22730] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[leejearl:22730] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
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ALL: cavity
CFLAGS =
FFLAGS =
CPPFLAGS =
FPPFLAGS =
CLEANFILES = cavity
include ${PETSC_DIR}/lib/petsc/conf/variables
include ${PETSC_DIR}/lib/petsc/conf/rules
cavity: cavity.o chkopts
${CLINKER}$ -o cavity cavity.o ${PETSC_LIB}$
${RM} cavity.o
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