[petsc-dev] Error when calling PETSc
Satish Balay
balay at mcs.anl.gov
Fri Jun 19 12:57:59 CDT 2015
As the message says:
> [0]PETSC ERROR: New nonzero at (0,20) caused a malloc
> Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to turn off this check
Note: mallocs make the code slow - so its up to you to do a proper
preallocation of memory - or disable the check as the above message
indicadtes [and ignore the performance penalty for now.].
Satish
On Fri, 19 Jun 2015, Hector E Barrios Molano wrote:
> Hi PETSc Experts,
>
> I'm compiling a Windows program using petsc-dev, this program
> previously used petsc-3.1 the only change performed was:
>
> MatCreateMPIBAIJ --> MatCreateBAIJ
>
> As the PETSc documentation suggested.
>
> I only changed the name of the function.
>
> I got to a problem when the program is launched and PETSc is called by
> the program:
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Argument out of range
> [0]PETSC ERROR: New nonzero at (0,20) caused a malloc
> Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to
> turn off this check
> [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
> shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.6-34-gc9ff9ea GIT
> Date: 2015-06-17 23:52:21 -0500
> [0]PETSC ERROR: F:\prog_win\prog\Debug\prog.exe on a windows-intel
> named HECTOR-PC by hector Thu Jun 18 18:31:42 2015
> [0]PETSC ERROR: Configure options --with-cc="win32fe cl"
> --with-fc="win32fe ifort" --prefix=/cygdrive/c/Installed/petsc/
> --PETSC_ARCH=windows-intel
> --with-parmetis-include=/cygdrive/c/Installed/parmetis/include
> --with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib
> --with-metis-include=/cygdrive/c/Installed/parmetis/include
> --with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib
> --with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]"
> --with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]"
> --with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]"
> --with-scalapack-include=/cygdrive/c/Installed/mkl/include
> --with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_lp64.lib]"
> [0]PETSC ERROR: #1 MatSetValues_SeqBAIJ() line 2192 in
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: #2 MatSetValues() line 1175 in
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Argument out of range
> [0]PETSC ERROR: New nonzero at (1,21) caused a malloc
> Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to
> turn off this check
> [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
> shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.6-34-gc9ff9ea GIT
> Date: 2015-06-17 23:52:21 -0500
> [0]PETSC ERROR: F:\prog_win\prog\Debug\prog.exe on a windows-intel
> named HECTOR-PC by hector Thu Jun 18 18:31:42 2015
> [0]PETSC ERROR: Configure options --with-cc="win32fe cl"
> --with-fc="win32fe ifort" --prefix=/cygdrive/c/Installed/petsc/
> --PETSC_ARCH=windows-intel
> --with-parmetis-include=/cygdrive/c/Installed/parmetis/include
> --with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib
> --with-metis-include=/cygdrive/c/Installed/parmetis/include
> --with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib
> --with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]"
> --with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]"
> --with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]"
> --with-scalapack-include=/cygdrive/c/Installed/mkl/include
> --with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_lp64.lib]"
> [0]PETSC ERROR: #3 MatSetValues_SeqBAIJ() line 2192 in
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: #4 MatSetValues() line 1175 in
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> .
> .
> .
> [0]PETSC ERROR: #3599 MatSetValues_SeqBAIJ() line 2192 in
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: #3600 MatSetValues() line 1175 in
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [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: 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] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c
> [0]PETSC ERROR: [0] MatSetValues line 1142
> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Signal received
> [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
> shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.6-34-gc9ff9ea GIT
> Date: 2015-06-17 23:52:21 -0500
> [0]PETSC ERROR: F:\prog_win\prog\Debug\prog.exe on a windows-intel
> named HECTOR-PC by hector Fri Jun 19 12:43:06 2015
> [0]PETSC ERROR: Configure options --with-cc="win32fe cl"
> --with-fc="win32fe ifort" --prefix=/cygdrive/c/Installed/petsc/
> --PETSC_ARCH=windows-intel
> --with-parmetis-include=/cygdrive/c/Installed/parmetis/include
> --with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib
> --with-metis-include=/cygdrive/c/Installed/parmetis/include
> --with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib
> --with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]"
> --with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]"
> --with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]"
> --with-scalapack-include=/cygdrive/c/Installed/mkl/include
> --with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_lp64.lib]"
> [0]PETSC ERROR: #3601 User provided function() line 0 in unknown file
>
> job aborted:
> [ranks] message
>
> [0] application aborted
> aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0
>
>
> I'm compiling the program on Visual Studio, what could be the problem?
>
> Thanks for your help,
>
> Hector
>
More information about the petsc-dev
mailing list