[petsc-users] Tutorials test case cannot run in parallel
袁煕
yuanxi at advancesoft.jp
Sat Oct 30 08:37:56 CDT 2021
Thank you for your reply.
I have solved the problem by modifying
----------------------------------------------------
call DMPlexCreateFromDAG(dm, depth, numPoints, coneSize,
cones,coneOrientations, vertexCoords, ierr);CHKERRA(ierr)
----------------------------------------------------
into
-----------------------------------------------------
numPoints1 = [0, 0, 0, 0]
if (rank == 0) then
call DMPlexCreateFromDAG(dm, depth, numPoints, coneSize,
cones,coneOrientations, vertexCoords, ierr);CHKERRA(ierr)
else
call DMPlexCreateFromDAG(dm, 3, numPoints1, PETSC_NULL_INTEGER,
PETSC_NULL_INTEGER,PETSC_NULL_INTEGER, PETSC_NULL_REAL, ierr)
endif
----------------------------------------------------
The result obtained as follows
DM Object: testplex 2 MPI processes
type: plex
testplex in 3 dimensions:
0-cells: 12 0
1-cells: 20 0
2-cells: 11 0
3-cells: 2 0
Labels:
celltype: 4 strata with value/size (0 (12), 7 (2), 4 (11), 1 (20))
depth: 4 strata with value/size (0 (12), 1 (20), 2 (11), 3 (2))
cell: 0 volume: 0.5000 centroid: -0.2500 0.5000 0.5000
cell: 1 volume: 0.5000 centroid: 0.2500 0.5000 0.5000
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 0 PID 15428 RUNNING AT DESKTOP-9ITFSBM
= KILLED BY SIGNAL: 9 (Killed)
===================================================================================
There is still problem left. I like it relevent
2021年10月30日(土) 21:51 Mark Adams <mfadams at lbl.gov>:
> Ah, I can reproduce this error with debugging turned on.
> This test is not a parallel test, but it does not say that serial is a
> requirement.
> So there is a problem here.
> Anyone?
>
> On Sat, Oct 30, 2021 at 8:29 AM Mark Adams <mfadams at lbl.gov> wrote:
>
>> 08:27 adams/pcksp-batch-kokkos *=
>> summit:/gpfs/alpine/csc314/scratch/adams/petsc/src/dm/impls/plex/tutorials$
>> make PETSC_ARCH=arch-summit-opt-gnu-kokkos-cuda ex3f90
>> mpifort -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O
>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O
>> -I/gpfs/alpine/csc314/scratch/adams/petsc/include
>> -I/gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-cuda/include
>> -I/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/gcc-9.1.0/hdf5-1.10.7-yxvwkhm4nhgezbl2mwzdruwoaiblt6q2/include
>> -I/sw/summit/cuda/11.0.3/include ex3f90.F90
>> -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-cuda/lib
>> -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-cuda/lib
>> -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-cuda/lib
>> -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-cuda/lib
>> -L/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/gcc-9.1.0/netlib-lapack-3.9.1-t2a6tcso5tkezcjmfrqvqi2cpary7kgx/lib64
>> -Wl,-rpath,/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/gcc-9.1.0/hdf5-1.10.7-yxvwkhm4nhgezbl2mwzdruwoaiblt6q2/lib
>> -L/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/gcc-9.1.0/hdf5-1.10.7-yxvwkhm4nhgezbl2mwzdruwoaiblt6q2/lib
>> -Wl,-rpath,/sw/summit/cuda/11.0.3/lib64 -L/sw/summit/cuda/11.0.3/lib64
>> -L/sw/summit/cuda/11.0.3/lib64/stubs
>> -Wl,-rpath,/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/gcc-9.1.0/spectrum-mpi-10.4.0.3-20210112-6jbupg3thjwhsabgevk6xmwhd2bbyxdc/lib
>> -L/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/gcc-9.1.0/spectrum-mpi-10.4.0.3-20210112-6jbupg3thjwhsabgevk6xmwhd2bbyxdc/lib
>> -Wl,-rpath,/autofs/nccs-svm1_sw/summit/gcc/9.1.0-alpha+20190716/lib/gcc/powerpc64le-unknown-linux-gnu/9.1.0
>> -L/autofs/nccs-svm1_sw/summit/gcc/9.1.0-alpha+20190716/lib/gcc/powerpc64le-unknown-linux-gnu/9.1.0
>> -Wl,-rpath,/autofs/nccs-svm1_sw/summit/gcc/9.1.0-alpha+20190716/lib/gcc
>> -L/autofs/nccs-svm1_sw/summit/gcc/9.1.0-alpha+20190716/lib/gcc
>> -Wl,-rpath,/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/gcc-9.1.0/netlib-lapack-3.9.1-t2a6tcso5tkezcjmfrqvqi2cpary7kgx/lib64
>> -Wl,-rpath,/autofs/nccs-svm1_sw/summit/gcc/9.1.0-alpha+20190716/lib64
>> -L/autofs/nccs-svm1_sw/summit/gcc/9.1.0-alpha+20190716/lib64
>> -Wl,-rpath,/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/gcc-8.3.1/darshan-runtime-3.3.0-mu6tnxlhxfplrq3srkkgi5dvly6wenwy/lib
>> -L/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/gcc-8.3.1/darshan-runtime-3.3.0-mu6tnxlhxfplrq3srkkgi5dvly6wenwy/lib
>> -Wl,-rpath,/autofs/nccs-svm1_sw/summit/gcc/9.1.0-alpha+20190716/lib
>> -L/autofs/nccs-svm1_sw/summit/gcc/9.1.0-alpha+20190716/lib -lpetsc
>> -lkokkoskernels -lkokkoscontainers -lkokkoscore -lp4est -lsc -lblas
>> -llapack -lhdf5_hl -lhdf5 -lm -lz -lcudart -lcufft -lcublas -lcusparse
>> -lcusolver -lcurand -lcuda -lstdc++ -ldl -lmpiprofilesupport
>> -lmpi_ibm_usempif08 -lmpi_ibm_usempi_ignore_tkr -lmpi_ibm_mpifh -lmpi_ibm
>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath
>> -lstdc++ -ldl -o ex3f90
>> 08:27 adams/pcksp-batch-kokkos *=
>> summit:/gpfs/alpine/csc314/scratch/adams/petsc/src/dm/impls/plex/tutorials$
>> jsrun -n 2 -g 1 ./ex3f90
>> DM Object: testplex 2 MPI processes
>> type: plex
>> testplex in 3 dimensions:
>> 0-cells: 12 12
>> 1-cells: 20 20
>> 2-cells: 11 11
>> 3-cells: 2 2
>> Labels:
>> celltype: 4 strata with value/size (0 (12), 7 (2), 4 (11), 1 (20))
>> depth: 4 strata with value/size (0 (12), 1 (20), 2 (11), 3 (2))
>> cell: 0 volume: 0.5000 centroid: -0.2500 0.5000 0.5000
>> cell: 1 volume: 0.5000 centroid: 0.2500 0.5000 0.5000
>> cell: 0 volume: 0.5000 centroid: -0.2500 0.5000 0.5000
>> cell: 1 volume: 0.5000 centroid: 0.2500 0.5000 0.5000
>> 08:28 adams/pcksp-batch-kokkos *=
>> summit:/gpfs/alpine/csc314/scratch/adams/pets
>>
>> On Fri, Oct 29, 2021 at 10:41 PM 袁煕 <yuanxi at advancesoft.jp> wrote:
>>
>>> Thanks, Mark.
>>>
>>> I do what you suggested but nothing changes. Besides, from your compile
>>> history and result,
>>>
>>> - you use gfortran with no MPI library, not mpif90
>>> - two CPUs gives exactly the same result
>>> - The first line of the DMView output should be "DM Object: testplex 2
>>> MPI processes", not "DM Object: testplex 1 MPI processes", when you use
>>> 2CPUs
>>>
>>> It seems like you did not use MPI but just two CPUs do exactly the same
>>> thing..
>>>
>>> Best regards,
>>>
>>> Yuan
>>>
>>>
>>> 2021年10月29日(金) 20:22 Mark Adams <mfadams at lbl.gov>:
>>>
>>>> This works for me (appended) using an up to date version of PETSc.
>>>>
>>>> I would delete the architecture director and reconfigure, and make all,
>>>> and try again.
>>>>
>>>> Next, you seem to be using git. Use the 'main' branch and try again.
>>>>
>>>> Mark
>>>>
>>>> (base) 07:09 adams/swarm-omp-pc *= ~/Codes/petsc$ cd
>>>> src/dm/impls/plex/tutorials/
>>>> (base) 07:16 adams/swarm-omp-pc *=
>>>> ~/Codes/petsc/src/dm/impls/plex/tutorials$ make
>>>> PETSC_DIR=/Users/markadams/Codes/petsc PETSC_ARCH=arch-macosx-gnu-g ex3f90
>>>> gfortran-11 -Wl,-bind_at_load -Wl,-multiply_defined,suppress
>>>> -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs
>>>> -Wl,-search_paths_first -Wl,-no_compact_unwind -fPIC -Wall
>>>> -ffree-line-length-0 -Wno-unused-dummy-argument -g -O -fPIC -Wall
>>>> -ffree-line-length-0 -Wno-unused-dummy-argument -g -O
>>>> -I/Users/markadams/Codes/petsc/include
>>>> -I/Users/markadams/Codes/petsc/arch-macosx-gnu-g/include ex3f90.F90
>>>> -Wl,-rpath,/Users/markadams/Codes/petsc/arch-macosx-gnu-g/lib
>>>> -L/Users/markadams/Codes/petsc/arch-macosx-gnu-g/lib
>>>> -Wl,-rpath,/Users/markadams/Codes/petsc/arch-macosx-gnu-g/lib
>>>> -L/Users/markadams/Codes/petsc/arch-macosx-gnu-g/lib
>>>> -Wl,-rpath,/usr/local/Cellar/gcc/11.2.0/lib/gcc/11/gcc/x86_64-apple-darwin20/11.2.0
>>>> -L/usr/local/Cellar/gcc/11.2.0/lib/gcc/11/gcc/x86_64-apple-darwin20/11.2.0
>>>> -Wl,-rpath,/usr/local/Cellar/gcc/11.2.0/lib/gcc/11
>>>> -L/usr/local/Cellar/gcc/11.2.0/lib/gcc/11 -lpetsc -lp4est -lsc -llapack
>>>> -lblas -lhdf5_hl -lhdf5 -lmetis -lz -lstdc++ -ldl -lgcc_s.1 -lgfortran
>>>> -lquadmath -lm -lquadmath -lstdc++ -ldl -lgcc_s.1 -o ex3f90
>>>> (base) 07:16 adams/swarm-omp-pc *=
>>>> ~/Codes/petsc/src/dm/impls/plex/tutorials$ mpirun -np 2 ./ex3f90
>>>> DM Object: testplex 1 MPI processes
>>>> type: plex
>>>> testplex in 3 dimensions:
>>>> 0-cells: 12
>>>> 1-cells: 20
>>>> 2-cells: 11
>>>> 3-cells: 2
>>>> Labels:
>>>> celltype: 4 strata with value/size (0 (12), 7 (2), 4 (11), 1 (20))
>>>> depth: 4 strata with value/size (0 (12), 1 (20), 2 (11), 3 (2))
>>>> DM Object: testplex 1 MPI processes
>>>> type: plex
>>>> testplex in 3 dimensions:
>>>> 0-cells: 12
>>>> 1-cells: 20
>>>> 2-cells: 11
>>>> 3-cells: 2
>>>> Labels:
>>>> celltype: 4 strata with value/size (0 (12), 7 (2), 4 (11), 1 (20))
>>>> depth: 4 strata with value/size (0 (12), 1 (20), 2 (11), 3 (2))
>>>> cell: 0 volume: 0.5000 centroid: -0.2500 0.5000 0.5000
>>>> cell: 1 volume: 0.5000 centroid: 0.2500 0.5000 0.5000
>>>> cell: 0 volume: 0.5000 centroid: -0.2500 0.5000 0.5000
>>>> cell: 1 volume: 0.5000 centroid: 0.2500 0.5000 0.5000
>>>>
>>>> On Fri, Oct 29, 2021 at 6:11 AM 袁煕 <yuanxi at advancesoft.jp> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I have tried the test case ex3f90 in the folder
>>>>> \src\dm\impls\plex\tutorials to run in parallel but found it fails. When I
>>>>> run it in 1 CPU by
>>>>>
>>>>> - mpirun -np 1 ./ex3f90
>>>>>
>>>>> Everything seems OK. But when run it in 2 CPU by
>>>>>
>>>>> - mpirun -np 2 ./ex3f90
>>>>>
>>>>> I got the following error message
>>>>>
>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>> --------------------------------------------------------------
>>>>> [0]PETSC ERROR: Object is in wrong state
>>>>> [0]PETSC ERROR: This DMPlex is distributed but its PointSF has no
>>>>> graph set
>>>>> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble
>>>>> shooting.
>>>>> [0]PETSC ERROR: Petsc Development GIT revision:
>>>>> v3.16.0-248-ge617e6467c GIT Date: 2021-10-19 23:11:25 -0500
>>>>> [0]PETSC ERROR: ./ex3f90 on a named pc-010-088 by Fri Oct 29
>>>>> 18:48:54 2021
>>>>> [0]PETSC ERROR: Configure options --with-cc=mpicc --with-cxx=mpicxx
>>>>> --with-fc=mpiifort --with-fortran-bindings=1 --with-debugging=0
>>>>> --with-blaslapack-dir=/opt/intel/oneapi/mkl/2021.4.0
>>>>> --with-mkl_pardiso-dir=/opt/intel/oneapi/mkl/2021.4.0 --download-metis=1
>>>>> --download-parmetis=1 --download-cmake --force --download-superlu_dist=1
>>>>> --download-mumps=1 --download-scalapack=1 --download-hypre=1
>>>>> --download-ml=1 --with-debugging=yes --prefix=/home/yuanxi
>>>>> [0]PETSC ERROR: #1 DMPlexCheckPointSF() at
>>>>> /home/yuanxi/myprograms/petsc/src/dm/impls/plex/plex.c:8626
>>>>> [0]PETSC ERROR: #2 DMPlexOrientInterface_Internal() at
>>>>> /home/yuanxi/myprograms/petsc/src/dm/impls/plex/plexinterpolate.c:595
>>>>> [0]PETSC ERROR: #3 DMPlexInterpolate() at
>>>>> /home/yuanxi/myprograms/petsc/src/dm/impls/plex/plexinterpolate.c:1357
>>>>> [0]PETSC ERROR: #4 User provided function() at User file:0
>>>>> Abort(73) on node 0 (rank 0 in comm 16): application called
>>>>> MPI_Abort(MPI_COMM_SELF, 73) - process 0
>>>>>
>>>>> ------------------------------------------------------------------------------------------------------------------------------------
>>>>>
>>>>> It fails in calling DMPlexInterpolate. Maybe this program is not
>>>>> considered to be run in parallel. But if I wish to do so, how should I
>>>>> modify it to let it run on multiple CPUs?
>>>>>
>>>>> Much thanks for your help
>>>>>
>>>>> Yuan
>>>>>
>>>>
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