[petsc-users] errors when repeatedly using MatSetValues and MatAssembly in a loop

[Jed Brown]

Shaohao Chen <shchen at www.phys.lsu.edu> writes:

> Dear writers and users of PETSc,
>
> I received errors as attached. It seems that I over allocated memory, so that the system killed my 
> job. I repeatedly used MatSetValues and MatAssembly in a big loop. This error massage appears 
> during this loop. The structure of my codes is as following. Could you please give me some hints 
> where I could over allocate memory? Thanks!
>
> Structure of my codes:
> Mat A;
> MatCreate(A);
> MatSetSizes(A);
> MatSetUp(A);
> MatSetValues(A);     // set initio values
> MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
> MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
> MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);   // fix nonzero structure for all 
> uses below
> ------ begin loop -----
> 
...
> MatSetValues(A);  // update values of some parts of the matrix
> MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);      // the error massage appears here, after tens of 
> steps of the loop. 
> MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
> 


> KSPSolve(A,...);
> 

.
> ------ end loop -----
>
>
> ==== attached errors =====
>
> [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] MatStashScatterGetMesg_Private line 617 src/mat/utils/matstash.c
> [0]PETSC ERROR: [0] MatAssemblyEnd_MPIAIJ line 673 src/mat/impls/aij/mpi/mpiaij.c
> [0]PETSC ERROR: [0] MatAssemblyEnd line 4930 src/mat/interface/matrix.c

I suspect other memory corruption.  Please try valgrind.  If you don't
figure it out, send a reduced test case so that we can reproduce.

> [0]PETSC ERROR: --------------------- Error Message -----------------------------------
> -
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR: ---------------------------------------------------------------------
> ---
> [0]PETSC ERROR: Petsc Release Version 3.4.0, May, 13, 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: /home/shaohao/program-basis/ais/ais-tdse on a arch-linux2-c-debug named 
> qb002 by shaohao Thu May 16 10:55:09 2013
> [0]PETSC ERROR: Libraries linked from /usr/local/packages/petsc/3.4.0/intel-11.1-mvapich-
> 1.1/lib
> [0]PETSC ERROR: Configure run at Tue May 14 14:20:15 2013
> [0]PETSC ERROR: Configure options --prefix=/usr/local/packages/petsc/3.4.0/intel-11.1-
> mvapich-1.1 --with-mpi=1 --with-mpi-compilers=1 --with-c-support=1 --with-fortran=1 --
> with-c++-support=1 --with-lapack-lib=/usr/local/packages/lapack/3.4.2/intel-
> 11.1/lib/liblapack.a --with-blas-lib=/usr/local/packages/lapack/3.4.2/intel-11.1/lib/libblas.a --
> with-expat=1 --with-expat-dir=/usr
> [0]PETSC ERROR: ---------------------------------------------------------------------
> ---
> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
> [0] [MPI Abort by user] Aborting Program!
> Abort signaled by rank 0: MPI Abort by user Aborting program !
> Exit code -3 signaled from qb002
> Killing remote processes...MPI process terminated unexpectedly
> DONE
>
>
> --
> Shaohao Chen
> Department of Physics & Astronomy, 
> Louisiana State University, 
> Baton Rouge, LA