[petsc-users] Segmentation Violation in a very simple fortran code

Fri Jun 18 09:01:40 CDT 2010

> call PetscFinalize(PETSC_NULL_CHARACTER,err)

  PetscFinalize() does not take a string argument, you should have 

> call PetscFinalize(err)

On Jun 17, 2010, at 11:19 PM, Valerio Grazioso wrote:

> 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 
> 
> 
> 
> 
> 
> 
>  

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