If you install with -O instead of -O3 (use a different PETSC_ARCH so it doesn't overwrite) does the problem go away?
Barry On Oct 6, 2013, at 12:52 PM, Jose David Bermeol <[email protected]> wrote: > 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" <[email protected]> > To: "Jose David Bermeol" <[email protected]> > Cc: "For users of the development version of PETSc" <[email protected]>, > [email protected] > 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 < [email protected] > > 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" < [email protected] > > To: "Jose David Bermeol" < [email protected] > > Cc: "For users of the development version of PETSc" < [email protected] > >, [email protected] > 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 < [email protected] > > 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<test_superlu_dist.c>
