[petsc-users] Superlu_dist error
Jose David Bermeol
jbermeol at purdue.edu
Sun Oct 6 12:52:00 CDT 2013
Hi again, now I'm getting the error again. The problem happens when I'm using the flag -O3 for the compiler. So what should I do next to solve this??
Attached is my code, and for tis example I'm creating the matrix in the code.
Thanks
Nonzeros in L 10
Nonzeros in U 10
nonzeros in L+U 10
nonzeros in LSUB 10
NUMfact space (MB) sum(procs): L\U 0.00 all 0.03
Total highmark (MB): All 0.03 Avg 0.02 Max 0.02
Mat conversion(PETSc->SuperLU_DIST) time (max/min/avg):
0.000124216 / 4.81606e-05 / 8.61883e-05
EQUIL time 0.00
ROWPERM time 0.00
COLPERM time 0.00
SYMBFACT time 0.00
DISTRIBUTE time 0.00
FACTOR time 0.00
Factor flops 1.000000e+02 Mflops 0.31
SOLVE time 0.00
[1]PETSC ERROR: ------------------------------------------------------------------------
[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[1]PETSC ERROR: likely location of problem given in stack below
[1]PETSC ERROR: --------------------- Stack Frames ------------------------------------
[1]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[1]PETSC ERROR: INSTEAD the line number of the start of the function
[1]PETSC ERROR: is given.
[1]PETSC ERROR: [1] SuperLU_DIST:pzgssvx line 234 /home/jbermeol/petsc/petsc_superlu_dist/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c
[1]PETSC ERROR: [1] MatMatSolve_SuperLU_DIST line 198 /home/jbermeol/petsc/petsc_superlu_dist/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c
[1]PETSC ERROR: [1] MatMatSolve line 3207 /home/jbermeol/petsc/petsc_superlu_dist/src/mat/interface/matrix.c
[1]PETSC ERROR: --------------------- Error Message ------------------------------------
[1]PETSC ERROR: Signal received!
[1]PETSC ERROR: ------------------------------------------------------------------------
[1]PETSC ERROR: Petsc Release Version 3.4.2, Jul, 02, 2013
[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: ./test_solver on a arch-linux2-c-debug named carter-fe00.rcac.purdue.edu by jbermeol Sun Oct 6 13:43:00 2013
[1]PETSC ERROR: Libraries linked from /home/jbermeol/petsc/petsc_superlu_dist/arch-linux2-c-debug/lib
[1]PETSC ERROR: Configure run at Sun Oct 6 13:38:20 2013
[1]PETSC ERROR: Configure options --with-cc=mpiicc --with-cxx=mpiicpc --with-fc=mpiifort --with-scalar-type=complex --with-shared-libraries=1 --with-debugging=1 --download-f-blas-lapack --download-superlu_dist=yes --download-superlu=yes --download-parmetis=yes --download-metis COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[1]PETSC ERROR: ------------------------------------------------------------------------
[1]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1
Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[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] SuperLU_DIST:pzgssvx line 234 /home/jbermeol/petsc/petsc_superlu_dist/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c
[0]PETSC ERROR: [0] MatMatSolve_SuperLU_DIST line 198 /home/jbermeol/petsc/petsc_superlu_dist/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c
[0]PETSC ERROR: [0] MatMatSolve line 3207 /home/jbermeol/petsc/petsc_superlu_dist/src/mat/interface/matrix.c
[0]PETSC ERROR: --------------------- Error Message ------------------------------------
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.4.2, Jul, 02, 2013
[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: ./test_solver on a arch-linux2-c-debug named carter-fe00.rcac.purdue.edu by jbermeol Sun Oct 6 13:43:00 2013
[0]PETSC ERROR: Libraries linked from /home/jbermeol/petsc/petsc_superlu_dist/arch-linux2-c-debug/lib
[0]PETSC ERROR: Configure run at Sun Oct 6 13:38:20 2013
[0]PETSC ERROR: Configure options --with-cc=mpiicc --with-cxx=mpiicpc --with-fc=mpiifort --with-scalar-type=complex --with-shared-libraries=1 --with-debugging=1 --download-f-blas-lapack --download-superlu_dist=yes --download-superlu=yes --download-parmetis=yes --download-metis COPTFLAGS=-03 CXXOPTFLAGS=-03 FOPTFLAGS=-03
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
----- Original Message -----
From: "Matthew Knepley" <knepley at gmail.com>
To: "Jose David Bermeol" <jbermeol at purdue.edu>
Cc: "For users of the development version of PETSc" <petsc-dev at mcs.anl.gov>, petsc-users at mcs.anl.gov
Sent: Sunday, October 6, 2013 8:19:30 AM
Subject: Re: [petsc-users] Superlu_dist error
On Sun, Oct 6, 2013 at 12:10 AM, Jose David Bermeol < jbermeol at purdue.edu > wrote:
Hi again, I compile with the following configuration:
--with-cc=mpiicc --with-cxx=mpiicpc --with-fc=mpiifort --with-scalar-type=complex --with-shared-libraries=1 --with-debugging=1 --with-pic=1 --with-clanguage=C++ --with-fortran=1 --with-fortran-kernels=0 --download-f-blas-lapack --download-superlu_dist=yes --download-superlu=yes --download-parmetis=yes --download-metis
Get rid of:
--with-pic=1 --with-fortran=1 --with-fortran-kernels=0
since they do not really do anything, and just put back MKL. I suspect you will get a crash, and then
it sounds like an MKL bug, or a bizarre incompatibility between SuperLU and MKL. If not, we explore further.
Thanks,
Matt
And my code run perfec, so that means is a MKL problem or a mismatch between versions, so how to test what is the problem??
Thanks
----- Original Message -----
From: "Matthew Knepley" < knepley at gmail.com >
To: "Jose David Bermeol" < jbermeol at purdue.edu >
Cc: "For users of the development version of PETSc" < petsc-dev at mcs.anl.gov >, petsc-users at mcs.anl.gov
Sent: Saturday, October 5, 2013 11:55:24 PM
Subject: Re: [petsc-users] Superlu_dist error
On Sat, Oct 5, 2013 at 10:49 PM, Jose David Bermeol < jbermeol at purdue.edu > wrote:
Hi I'm runnig petsc trying to solve a linear system with superlu_dist. However i have a memory violation, atached is the code, and here is the output. Email me if you need something else to figured out what is happening.
So it looks like SuperLU_Dist is bombing during an LAPACK operation. It could be an MKL problem, or a SuperLU_Dist problem, or our problem,
or a mismatch between versions. I would try to simplify the configuration in order to cut down on the possibilities. Eliminate everything that is not
necessary for SuperLU_dist first. Then change to --download-f-blas-lapack. If you still have a crash, send us the matrix since that should be
reproducible and we can report a SuperLU_dist bug or fix our code.
Thanks,
Matt
Thanks
mpiexec -n 2 ./test_solver -mat_superlu_dist_statprint -mat_superlu_dist_matinput distributed
Nonzeros in L 10
Nonzeros in U 10
nonzeros in L+U 10
nonzeros in LSUB 10
NUMfact space (MB) sum(procs): L\U 0.00 all 0.03
Total highmark (MB): All 0.03 Avg 0.02 Max 0.02
Mat conversion(PETSc->SuperLU_DIST) time (max/min/avg):
0.000146866 / 0.000145912 / 0.000146389
EQUIL time 0.00
ROWPERM time 0.00
COLPERM time 0.00
SYMBFACT time 0.00
DISTRIBUTE time 0.00
FACTOR time 0.00
Factor flops 1.000000e+02 Mflops 0.31
SOLVE time 0.00
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[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: [1]PETSC ERROR: ------------------------------------------------------------------------
[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
Try option -start_in_debugger or -on_error_attach_debugger
[1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]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
[1]PETSC ERROR: likely location of problem given in stack below
[1]PETSC ERROR: --------------------- Stack Frames ------------------------------------
[1]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR: [1]PETSC ERROR: INSTEAD the line number of the start of the function
[1]PETSC ERROR: is given.
[1]PETSC ERROR: [1] SuperLU_DIST:pzgssvx line 234 /home/jbermeol/Nemo5/libs/petsc/build-cplx/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c
[1]PETSC ERROR: [1] MatMatSolve_SuperLU_DIST line 198 /home/jbermeol/Nemo5/libs/petsc/build-cplx/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c
[1]PETSC ERROR: INSTEAD the line number of the start of the function
[0]PETSC ERROR: is given.
[0]PETSC ERROR: [0] SuperLU_DIST:pzgssvx line 234 /home/jbermeol/Nemo5/libs/petsc/build-cplx/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c
[0]PETSC ERROR: [1] MatMatSolve line 3207 /home/jbermeol/Nemo5/libs/petsc/build-cplx/src/mat/interface/matrix.c
[1]PETSC ERROR: --------------------- Error Message ------------------------------------
[1]PETSC ERROR: [0] MatMatSolve_SuperLU_DIST line 198 /home/jbermeol/Nemo5/libs/petsc/build-cplx/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c
[0]PETSC ERROR: [0] MatMatSolve line 3207 /home/jbermeol/Nemo5/libs/petsc/build-cplx/src/mat/interface/matrix.c
Signal received!
[1]PETSC ERROR: ------------------------------------------------------------------------
[1]PETSC ERROR: Petsc Release Version 3.4.2, Jul, 02, 2013
[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: ./test_solver on a linux-complex named carter-fe02.rcac.purdue.edu by jbermeol Sat Oct 5 23:45:21 2013
[1]PETSC ERROR: [0]PETSC ERROR: --------------------- Error Message ------------------------------------
[0]PETSC ERROR: Libraries linked from /home/jbermeol/Nemo5/libs/petsc/build-cplx/linux-complex/lib
[1]PETSC ERROR: Configure run at Sat Oct 5 11:19:36 2013
[1]PETSC ERROR: Configure options --with-cc=mpiicc --with-cxx=mpiicpc --with-fc=mpiifort --with-scalar-type=complex --with-shared-libraries=1 --with-debugging=1 --with-pic=1 --with-clanguage=C++ --with-fortran=1 --with-fortran-kernels=0 --with-blas-lapack-dir=/apps/rhel6/intel/composer_xe_2013.3.163/mkl --with-blacs-lib=/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so --with-blacs-include=/apps/rhel6/intel/composer_xe_2013.3.163/mkl/include --with-scalapack-lib="-L/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" --with-scalapack-include=/apps/rhel6/intel/composer_xe_2013.3.163/mkl/include --with-valgrind-dir=/apps/rhel6/valgrind/3.8.1 --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --with-mkl-include=/apps/rhel6/intel/composer_xe_2013.3.163/mkl/include --with-mkl-lib="[/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_intel_lp64.so,/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_intel_thread.so,/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_core.so,/apps/rhel6/intel/composer_xe_2013.3.163/mkl/../compiler/lib/intel64/libiomp5.so]" --with-cpardiso-dir=/home/jbermeol/testPetscSolvers/intel_mkl_cpardiso --with-hdf5 --download-hdf5=yes --download-metis=yes --download-parmetis=yes --download-superlu_dist=yes --download-superlu=yes --download-mumps=yes --download-spooles=yes --download-pastix=yes --download-ptscotch=yes --download-umfpack=yes --download-sowing
Signal received!
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.4.2, Jul, 02, 2013
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: [1]PETSC ERROR: ------------------------------------------------------------------------
[1]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
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: ./test_solver on a linux-complex named carter-fe02.rcac.purdue.edu by jbermeol Sat Oct 5 23:45:21 2013
[0]PETSC ERROR: Libraries linked from /home/jbermeol/Nemo5/libs/petsc/build-cplx/linux-complex/lib
[0]PETSC ERROR: Configure run at Sat Oct 5 11:19:36 2013
[0]PETSC ERROR: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1
Configure options --with-cc=mpiicc --with-cxx=mpiicpc --with-fc=mpiifort --with-scalar-type=complex --with-shared-libraries=1 --with-debugging=1 --with-pic=1 --with-clanguage=C++ --with-fortran=1 --with-fortran-kernels=0 --with-blas-lapack-dir=/apps/rhel6/intel/composer_xe_2013.3.163/mkl --with-blacs-lib=/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so --with-blacs-include=/apps/rhel6/intel/composer_xe_2013.3.163/mkl/include --with-scalapack-lib="-L/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" --with-scalapack-include=/apps/rhel6/intel/composer_xe_2013.3.163/mkl/include --with-valgrind-dir=/apps/rhel6/valgrind/3.8.1 --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --with-mkl-include=/apps/rhel6/intel/composer_xe_2013.3.163/mkl/include --with-mkl-lib="[/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_intel_lp64.so,/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_intel_thread.so,/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_core.so,/apps/rhel6/intel/composer_xe_2013.3.163/mkl/../compiler/lib/intel64/libiomp5.so]" --with-cpardiso-dir=/home/jbermeol/testPetscSolvers/intel_mkl_cpardiso --with-hdf5 --download-hdf5=yes --download-metis=yes --download-parmetis=yes --download-superlu_dist=yes --download-superlu=yes --download-mumps=yes --download-spooles=yes --download-pastix=yes --download-ptscotch=yes --download-umfpack=yes --download-sowing
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
--
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
--
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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