I am new to PETSc. What MPI and What compiler ? If it is Intel compiler, add -mcmodel=medium to the compile line and see that helps.
Logan From: petsc-users-bounces at mcs.anl.gov [mailto:[email protected]] On Behalf Of Valerio Grazioso Sent: Thursday, June 17, 2010 11:20 PM To: petsc-users at mcs.anl.gov Subject: [petsc-users] Segmentation Violation in a very simple fortran code Hi, I'm stuck with an implementation of a 3D Poisson solver with PETSc in fortran90. I was getting strange Segmentation Violation and after some debugging I realized that the the problem was in the vector created with DACreateGlobalVector() So I've written a simple code: **************************************************************************** program PetscTest implicit none Vec q PetscScalar alpha DA da PetscErrorCode err PetscInt i3,i1 i3=4 i1=1 call DACreate3d(PETSC_COMM_WORLD,DA_NONPERIODIC,DA_STENCIL_STAR,i3,i3,i3,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,i1,i1, & PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,da,err) call DACreateGlobalVector(da,q,err) alpha=1.0 call VecSet(q,alpha,err) call vecView(q,PETSC_VIEWER_STDOUT_WORLD) call VecDestroy(q,err); call PetscFinalize(PETSC_NULL_CHARACTER,err) end program **************************************************************************** And this is the output that i get if I run the executable with mpirun -n 2 ./PetscTest -da_view **************************************************************************** Processor [0] M 4 N 4 P 4 m 1 n 1 p 2 w 1 s 1 X range of indices: 0 4, Y range of indices: 0 4, Z range of indices: 0 2 Processor [1] M 4 N 4 P 4 m 1 n 1 p 2 w 1 s 1 X range of indices: 0 4, Y range of indices: 0 4, Z range of indices: 2 4 Process [0] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Process [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [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/petsc-as/documentation/troubleshooting.html#Signal[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: [0]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: --------------------- Error Message ------------------------------------ [1]PETSC ERROR: Signal received! [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: Petsc Release Version 3.1.0, Patch 3, Fri Jun 4 15:34:52 CDT 2010 [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: ./PetscTest on a linux-gnu named up0001 by hpc2231 Thu Jun 17 23:58:50 2010 [1]PETSC ERROR: Libraries linked from /home/hpc2231/lib/petsc-3.1-p3/linux-gnu-c-debug/lib [1]PETSC ERROR: Configure run at Thu Jun 17 23:00:54 2010 [1]PETSC ERROR: Configure options LIBS="-limf -lm" --download-hypre=1 --with-fortran-interfaces=1 [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [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/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors [0]PETSC ERROR: -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 59. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- 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: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 3, Fri Jun 4 15:34:52 CDT 2010 [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: ./PetscTest on a linux-gnu named up0001 by hpc2231 Thu Jun 17 23:58:50 2010 [0]PETSC ERROR: Libraries linked from /home/hpc2231/lib/petsc-3.1-p3/linux-gnu-c-debug/lib [0]PETSC ERROR: Configure run at Thu Jun 17 23:00:54 2010 [0]PETSC ERROR: Configure options LIBS="-limf -lm" --download-hypre=1 --with-fortran-interfaces=1 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file -------------------------------------------------------------------------- mpirun has exited due to process rank 1 with PID 10883 on node up0001 exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------- [up0001:10881] 1 more process has sent help message help-mpi-api.txt / mpi-abort [up0001:10881] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages **************************************************************************** If been looking trough the troubleshooting and FAQ with no success and now I'm stuck .... Any ideas or suggestions Thanks Valerio -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20100618/19026999/attachment-0001.htm>
