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.
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#include <petscmat.h>
#include <petscvec.h>
#include <petsctime.h>
#include <petscsnes.h>
#include <petscdmda.h>
#include "petscsys.h"
#include <stdio.h>
void create_matrix(MPI_Comm comm, Mat* mat, PetscInt Nrow, PetscInt Ncol, MatType type){
MatCreate(comm, mat);
MatSetSizes(*mat,PETSC_DECIDE,PETSC_DECIDE,Nrow,Ncol);
MatSetType(*mat,type);
MatSetUp(*mat);
}
void create_vector(MPI_Comm comm, Vec* mat, PetscInt N, VecType type){
VecCreate(comm, mat);
VecSetSizes(*mat, PETSC_DECIDE, N);
VecSetType(*mat,type);
VecSetUp(*mat);
}
void destroy_matrix(Mat* mat){
MatDestroy(mat);
}
void destroy_vector(Vec* mat){
VecDestroy(mat);
}
Mat create_identity_matrix(MPI_Comm comm,
PetscMPIInt size,
PetscMPIInt rank,
PetscInt Nrow,
PetscInt Ncol,
PetscScalar a){
PetscInt i, j;
PetscScalar val;
Mat X;
MatType matType;
if(size == 1) matType = MATSEQAIJ;
else matType = MATMPIAIJ;
create_matrix(comm, &X, Nrow, Ncol, matType);
MatAssemblyBegin(X,MAT_FINAL_ASSEMBLY);
MatZeroEntries(X);
MatAssemblyEnd(X,MAT_FINAL_ASSEMBLY);
MatShift(X, a);
return X;
}
Mat create_dense_matrix(MPI_Comm comm,
PetscMPIInt size,
PetscMPIInt rank,
PetscInt Nrow,
PetscInt Ncol,
PetscScalar a){
PetscInt i, j;
PetscScalar val;
Mat X;
MatType matType;
if(size == 1) matType = MATSEQDENSE;
else matType = MATMPIDENSE;
create_matrix(comm, &X, Nrow, Ncol, matType);
if(rank == 0)
for(i = 0; i < Nrow; i++)
for(j = 0; j < Ncol; j++){
val = a*(i + 1);
MatSetValues(X, 1, &i, 1, &j, &val, INSERT_VALUES);
}
MatAssemblyBegin(X,MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(X,MAT_FINAL_ASSEMBLY);
return X;
}
PetscReal check_error_matrix(Mat* real_solution, Mat* solution, NormType normType){
Mat w;
PetscErrorCode ierr;
MatType type;
ierr = MatGetType(*real_solution, &type);CHKERRQ(ierr);
MPI_Comm comm;
ierr = PetscObjectGetComm((PetscObject)*real_solution,&comm);CHKERRQ(ierr);
PetscInt Nrow, Ncol;
MatGetSize(*real_solution,&Nrow,&Ncol);CHKERRQ(ierr);
create_matrix(comm, &w, Nrow, Ncol, type);
PetscReal diff;
ierr = MatCopy(*real_solution,w,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatAYPX(w,-1.0,*solution,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatNorm(w,normType,&diff);CHKERRQ(ierr);
destroy_matrix(&w);
return diff;
}
int main(int argc,char **argv){
PetscInt A_size, number_rhs, i;
PetscErrorCode ierr;
PetscBool allowd_MatMatSolve, multiple_systems;
Mat A, B, X, real_X;
Vec x,b;
VecType vecType;
PetscMPIInt rank, size;
PetscInitialize(&argc,&argv,0,NULL);
A_size = 10;
number_rhs = 2;
ierr = MPI_Comm_rank(MPI_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(MPI_COMM_WORLD,&size);CHKERRQ(ierr);
A = create_identity_matrix(MPI_COMM_WORLD, size, rank, A_size, A_size, 1);
real_X = create_dense_matrix(MPI_COMM_WORLD, size, rank, A_size, number_rhs, 2);
ierr = MatMatMult(A, real_X, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &B);CHKERRQ(ierr);
MatType matType;
if(size == 1) matType = MATSEQDENSE;
else matType = MATMPIDENSE;
create_matrix(MPI_COMM_WORLD, &X, A_size, number_rhs, matType);
if(size == 1) vecType = VECSEQ;
else vecType = VECMPI;
PetscLogDouble time1, time2;
ierr = PetscTime(&time1);CHKERRQ(ierr);
KSP ksp;
PC pc;
Mat F;
ierr = KSPCreate(MPI_COMM_WORLD, &ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp, A, A, SAME_PRECONDITIONER);CHKERRQ(ierr);
ierr = KSPSetType(ksp, KSPPREONLY);CHKERRQ(ierr);
ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr);
ierr = PCSetType(pc, PCLU);CHKERRQ(ierr);
ierr = PCFactorSetMatSolverPackage(pc, MATSOLVERSUPERLU_DIST);CHKERRQ(ierr);
ierr = KSPSetUp(ksp);
ierr = PCFactorGetMatrix(pc, &F);CHKERRQ(ierr);
ierr = MatMatSolve(F, B, X);CHKERRQ(ierr);
KSPDestroy(&ksp);
ierr = PetscTime(&time2);CHKERRQ(ierr);
PetscReal error;
error = check_error_matrix(&real_X, &X, NORM_INFINITY);
time1 = time2 - time1;
if(size > 1){
ierr = MPI_Reduce(&time1, &time2, 1, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
} else {
time2 = time1;
}
if(rank == 0){
printf("Test: %s\n", "superlu_dist");
printf("Error: %f\n", (double)error);
printf("Time: %f\n", (double)time2);
}
destroy_matrix(&A);
destroy_matrix(&B);
destroy_matrix(&real_X);
destroy_matrix(&X);
ierr = PetscFinalize();
return 0;
}
