Hello all,
i have a problem running the example program step-18 on more than one
processors by using mpirun with np > 1. I tried it on two different computers
(both 64 bit linux) and the problem occures on both of them, so the probability
is high that i have done something wrong. It seems like the same job has just
been sent to different processors.
I would appreciate any kind of hint.
Many thanks,
F.T.
This is my installation procedure:
1) i installed metis with mpicc as compiler
2) i configured and made petsc with these options:
--with-mpi=1 --with-shared=1 --with-clanguage=C++ --with-x=0
--with-mpi-dir=/etc/alternatives --download-c-blas-lapack=1
3) i commented out the lines void drand48(), double srand48(long), int
log2(int) in Lib/proto.h in metis
4) i configured deal.ii with the options:
--with-petsc=$PETSC_DIR --with-petsc-arch=linux-gnu-c-debug
--with-metis=$METIS_DIR --with-CC=mpicc --with-CXX=mpicxx
I made deal with "make 3dg" to see if the example works before i try "make all".
After everything was set up i compiled the program and ran it with "mpirun -np
1 ./step-18". Everything went fine. Running it with np set to anything higher
results in this error (the original error message is very long so i attached it
in a separate file):
Timestep 1 at time 1
Cycle 0:
Timestep 1 at time 1
Cycle 0:
Number of active cells: 3712 (by partition: 3712)
Number of active cells: 3712 (by partition: 3712)
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Nonconforming object sizes!
[0]PETSC ERROR: Sum of local lengths 34452 does not equal global length 17226,
my local length 17226
likely a call to VecSetSizes() or MatSetSizes() is wrong.
See
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#PetscSplitOwnership!
--------------------------------------------------------
A list of petsc error messages
--------------------------------------------------------
[Es:06059] *** Process received signal ***
[Es:06059] Signal: Aborted (6)
[Es:06059] Signal code: (-6)
[Es:06059] [ 0] /lib/libpthread.so.0 [0x7f0ab491d190]
[Es:06059] [ 1] /lib/libc.so.6(gsignal+0x35) [0x7f0ab2e884b5]
[Es:06059] [ 2] /lib/libc.so.6(abort+0x180) [0x7f0ab2e8bf50]
[Es:06059] [ 3]
/usr/lib/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x115)
[0x7f0ab3727cc5]
[Es:06059] [ 4] /usr/lib/libstdc++.so.6 [0x7f0ab37260f6]
[Es:06059] [ 5] /usr/lib/libstdc++.so.6 [0x7f0ab3724fe9]
[Es:06059] [ 6] /usr/lib/libstdc++.so.6(__gxx_personality_v0+0x261)
[0x7f0ab3725a91]
[Es:06059] [ 7] /lib/libgcc_s.so.1 [0x7f0ab31d46e3]
[Es:06059] [ 8] /lib/libgcc_s.so.1(_Unwind_Resume+0x68) [0x7f0ab31d47a8]
[Es:06059] [ 9] ./step-18(_ZN21QuasiStaticElasticity8TopLevelILi3EE3runEv+0)
[0x43e3ae]
[Es:06059] [10] ./step-18(main+0x95) [0x4340b6]
[Es:06059] [11] /lib/libc.so.6(__libc_start_main+0xfd) [0x7f0ab2e73abd]
[Es:06059] [12] ./step-18 [0x433819]
[Es:06059] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 6060 on node Es exited on signal 6
(Aborted).
--------------------------------------------------------------------------
2 total processes killed (some possibly by mpirun during cleanup)
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r...@es:~/workspace/zylinder# mpirun -np 2 ./step-18
Timestep 1 at time 1
Cycle 0:
Timestep 1 at time 1
Cycle 0:
Number of active cells: 3712 (by partition: 3712)
Number of active cells: 3712 (by partition: 3712)
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Nonconforming object sizes!
[0]PETSC ERROR: Sum of local lengths 34452 does not equal global length 17226,
my local length 17226
likely a call to VecSetSizes() or MatSetSizes() is wrong.
See
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#PetscSplitOwnership!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 11, Mon Feb 1 11:01:51 CST
2010
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: ./step-18 on a linux-gnu named Es by root Tue Feb 9 16:20:17
2010
[0]PETSC ERROR: Libraries linked from
/usr/numerics/petsc-3.0.0-p10/linux-gnu-c-debug/lib
[0]PETSC ERROR: Configure run at Mon Feb 8 13:34:45 2010
[0]PETSC ERROR: Configure options --with-mpi=1 --with-shared=1
--with-clanguage=C++ --with-x=0 --with-mpi-dir=/etc/alternatives
--download-c-blas-lapack=1 --download-c-blas-lapack=1
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: PetscSplitOwnership() line 94 in src/sys/utils/psplit.c
[0]PETSC ERROR: PetscMapSetUp() line 136 in src/vec/vec/impls/mpi/pmap.c
[0]PETSC ERROR: MatMPIAIJSetPreallocation_MPIAIJ() line 2697 in
src/mat/impls/aij/mpi/mpiaij.c
[0]PETSC ERROR: MatMPIAIJSetPreallocation() line 3402 in
src/mat/impls/aij/mpi/mpiaij.c
[0]PETSC ERROR: MatCreateMPIAIJ() line 3665 in src/mat/impls/aij/mpi/mpiaij.c
[1]PETSC ERROR: --------------------- Error Message
------------------------------------
[1]PETSC ERROR: Nonconforming object sizes!
[1]PETSC ERROR: Sum of local lengths 34452 does not equal global length 17226,
my local length 17226
likely a call to VecSetSizes() or MatSetSizes() is wrong.
See
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#PetscSplitOwnership!
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: Petsc Release Version 3.0.0, Patch 11, Mon Feb 1 11:01:51 CST
2010
[1]PETSC ERROR: See docs/changes/index.html for recent updates.
[1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[1]PETSC ERROR: See docs/index.html for manual pages.
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: ./step-18 on a linux-gnu named Es by root Tue Feb 9 16:20:17
2010
[1]PETSC ERROR: Libraries linked from
/usr/numerics/petsc-3.0.0-p10/linux-gnu-c-debug/lib
[1]PETSC ERROR: Configure run at Mon Feb 8 13:34:45 2010
[1]PETSC ERROR: Configure options --with-mpi=1 --with-shared=1
--with-clanguage=C++ --with-x=0 --with-mpi-dir=/etc/alternatives
--download-c-blas-lapack=1 --download-c-blas-lapack=1
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: PetscSplitOwnership() line 94 in src/sys/utils/psplit.c
[1]PETSC ERROR: PetscMapSetUp() line 136 in src/vec/vec/impls/mpi/pmap.c
[1]PETSC ERROR: MatMPIAIJSetPreallocation_MPIAIJ() line 2697 in
src/mat/impls/aij/mpi/mpiaij.c
[1]PETSC ERROR: MatMPIAIJSetPreallocation() line 3402 in
src/mat/impls/aij/mpi/mpiaij.c
[1]PETSC ERROR: MatCreateMPIAIJ() line 3665 in src/mat/impls/aij/mpi/mpiaij.c
[1]PETSC ERROR: --------------------- Error Message
------------------------------------
[1]PETSC ERROR: Nonconforming object sizes!
[1]PETSC ERROR: Sum of local lengths 34452 does not equal global length 17226,
my local length 17226
likely a call to VecSetSizes() or MatSetSizes() is wrong.
See
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#PetscSplitOwnership!
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: Petsc Release Version 3.0.0, Patch 11, Mon Feb 1 11:01:51 CST
2010
[1]PETSC ERROR: See docs/changes/index.html for recent updates.
[1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[1]PETSC ERROR: See docs/index.html for manual pages.
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: ./step-18 on a linux-gnu named Es by root Tue Feb 9 16:20:17
2010
[1]PETSC ERROR: Libraries linked from
/usr/numerics/petsc-3.0.0-p10/linux-gnu-c-debug/lib
[1]PETSC ERROR: Configure run at Mon Feb 8 13:34:45 2010
[1]PETSC ERROR: Configure options --with-mpi=1 --with-shared=1
--with-clanguage=C++ --with-x=0 --with-mpi-dir=/etc/alternatives
--download-c-blas-lapack=1 --download-c-blas-lapack=1
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: PetscSplitOwnership() line 94 in src/sys/utils/psplit.c
[1]PETSC ERROR: PetscMapSetUp() line 136 in src/vec/vec/impls/mpi/pmap.c
[1]PETSC ERROR: MatMPIAIJSetPreallocation_MPIAIJ() line 2697 in
src/mat/impls/aij/mpi/mpiaij.c
[1]PETSC ERROR: MatMPIAIJSetPreallocation() line 3402 in
src/mat/impls/aij/mpi/mpiaij.c
[1]PETSC ERROR: MatSetUpPreallocation_MPIAIJ() line 1757 in
src/mat/impls/aij/mpi/mpiaij.c
[1]PETSC ERROR: MatSetUpPreallocation() line 236 in src/mat/utils/gcreate.c
[1]PETSC ERROR: MatDestroy() line 801 in src/mat/interface/matrix.c
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Nonconforming object sizes!
[0]PETSC ERROR: Sum of local lengths 34452 does not equal global length 17226,
my local length 17226
likely a call to VecSetSizes() or MatSetSizes() is wrong.
See
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#PetscSplitOwnership!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 11, Mon Feb 1 11:01:51 CST
2010
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: ./step-18 on a linux-gnu named Es by root Tue Feb 9 16:20:17
2010
[0]PETSC ERROR: Libraries linked from
/usr/numerics/petsc-3.0.0-p10/linux-gnu-c-debug/lib
[0]PETSC ERROR: Configure run at Mon Feb 8 13:34:45 2010
[0]PETSC ERROR: Configure options --with-mpi=1 --with-shared=1
--with-clanguage=C++ --with-x=0 --with-mpi-dir=/etc/alternatives
--download-c-blas-lapack=1 --download-c-blas-lapack=1
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: PetscSplitOwnership() line 94 in src/sys/utils/psplit.c
[0]PETSC ERROR: PetscMapSetUp() line 136 in src/vec/vec/impls/mpi/pmap.c
[0]PETSC ERROR: MatMPIAIJSetPreallocation_MPIAIJ() line 2697 in
src/mat/impls/aij/mpi/mpiaij.c
[0]PETSC ERROR: MatMPIAIJSetPreallocation() line 3402 in
src/mat/impls/aij/mpi/mpiaij.c
[0]PETSC ERROR: MatSetUpPreallocation_MPIAIJ() line 1757 in
src/mat/impls/aij/mpi/mpiaij.c
[0]PETSC ERROR: MatSetUpPreallocation() line 236 in src/mat/utils/gcreate.c
[0]PETSC ERROR: MatDestroy() line 801 in src/mat/interface/matrix.c
terminate called after throwing an instance of
'dealii::PETScWrappers::MatrixBase::ExcPETScError'
terminate called after throwing an instance of
'dealii::PETScWrappers::MatrixBase::ExcPETScError'
what(): --------------------------------------------------------
An error occurred in line <95> of file <source/petsc_matrix_base.cc> in function
virtual dealii::PETScWrappers::MatrixBase::~MatrixBase()
The violated condition was:
ierr == 0
The name and call sequence of the exception was:
ExcPETScError(ierr)
Additional Information:
An error with error number 60 occured while calling a PETSc function
--------------------------------------------------------
[Es:06060] *** Process received signal ***
[Es:06060] Signal: Aborted (6)
[Es:06060] Signal code: (-6)
[Es:06060] [ 0] /lib/libpthread.so.0 [0x7f9bbf80b190]
[Es:06060] [ 1] /lib/libc.so.6(gsignal+0x35) [0x7f9bbdd764b5]
[Es:06060] [ 2] /lib/libc.so.6(abort+0x180) [0x7f9bbdd79f50]
[Es:06060] [ 3]
/usr/lib/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x115)
[0x7f9bbe615cc5]
[Es:06060] [ 4] /usr/lib/libstdc++.so.6 [0x7f9bbe6140f6]
[Es:06060] [ 5] /usr/lib/libstdc++.so.6 [0x7f9bbe612fe9]
[Es:06060] [ 6] /usr/lib/libstdc++.so.6(__gxx_personality_v0+0x261)
[0x7f9bbe613a91]
[Es:06060] [ 7] /lib/libgcc_s.so.1 [0x7f9bbe0c26e3]
[Es:06060] [ 8] /lib/libgcc_s.so.1(_Unwind_Resume+0x68) [0x7f9bbe0c27a8]
[Es:06060] [ 9] ./step-18(_ZN21QuasiStaticElasticity8TopLevelILi3EE3runEv+0)
[0x43e3ae]
[Es:06060] [10] ./step-18(main+0x95) [0x4340b6]
[Es:06060] [11] /lib/libc.so.6(__libc_start_main+0xfd) [0x7f9bbdd61abd]
[Es:06060] [12] ./step-18 [0x433819]
[Es:06060] *** End of error message ***
what(): --------------------------------------------------------
An error occurred in line <95> of file <source/petsc_matrix_base.cc> in function
virtual dealii::PETScWrappers::MatrixBase::~MatrixBase()
The violated condition was:
ierr == 0
The name and call sequence of the exception was:
ExcPETScError(ierr)
Additional Information:
An error with error number 60 occured while calling a PETSc function
--------------------------------------------------------
[Es:06059] *** Process received signal ***
[Es:06059] Signal: Aborted (6)
[Es:06059] Signal code: (-6)
[Es:06059] [ 0] /lib/libpthread.so.0 [0x7f0ab491d190]
[Es:06059] [ 1] /lib/libc.so.6(gsignal+0x35) [0x7f0ab2e884b5]
[Es:06059] [ 2] /lib/libc.so.6(abort+0x180) [0x7f0ab2e8bf50]
[Es:06059] [ 3]
/usr/lib/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x115)
[0x7f0ab3727cc5]
[Es:06059] [ 4] /usr/lib/libstdc++.so.6 [0x7f0ab37260f6]
[Es:06059] [ 5] /usr/lib/libstdc++.so.6 [0x7f0ab3724fe9]
[Es:06059] [ 6] /usr/lib/libstdc++.so.6(__gxx_personality_v0+0x261)
[0x7f0ab3725a91]
[Es:06059] [ 7] /lib/libgcc_s.so.1 [0x7f0ab31d46e3]
[Es:06059] [ 8] /lib/libgcc_s.so.1(_Unwind_Resume+0x68) [0x7f0ab31d47a8]
[Es:06059] [ 9] ./step-18(_ZN21QuasiStaticElasticity8TopLevelILi3EE3runEv+0)
[0x43e3ae]
[Es:06059] [10] ./step-18(main+0x95) [0x4340b6]
[Es:06059] [11] /lib/libc.so.6(__libc_start_main+0xfd) [0x7f0ab2e73abd]
[Es:06059] [12] ./step-18 [0x433819]
[Es:06059] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 6060 on node Es exited on signal 6
(Aborted).
--------------------------------------------------------------------------
2 total processes killed (some possibly by mpirun during cleanup)
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