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 [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
