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

Fri Jun 18 00:23:39 CDT 2010

You are right, that was a leftover of a previous test made with a viewer. 
Commenting that line I get the previous result 

SEGV: Segmentation Violation   

Sorry for the previous mistake... 
Thanks
Valerio

On 2010-06-18, at 1:01 AM, Matthew Knepley wrote:

> This is obviously not the whole code because you are calling PetscViewerDestroy()
> somewhere with a bad viewer. Please check the return codes of all PETSc calls.
> 
>   THanks,
> 
>     Matt
> 
> On Thu, Jun 17, 2010 at 11:43 PM, Valerio Grazioso <graziosov at me.queensu.ca> wrote:
> Ok... but adding it I get in the same position a different error:
> 
> [0]PETSC ERROR: --------------------- Error Message ------------------------------------
> [1]PETSC ERROR: [0]PETSC ERROR: Invalid argument!
> [0]PETSC ERROR: Wrong type of object: Parameter # 1!
> [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: --------------------- Error Message ------------------------------------
> [1]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 Fri Jun 18 00:34:57 2010
> [0]PETSC ERROR: Libraries linked from /home/hpc2231/lib/petsc-3.1-p3/linux-gnu-c-debug/lib
> Invalid argument!
> [1]PETSC ERROR: Wrong type of object: Parameter # 1!
> [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 Fri Jun 18 00:34:57 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: PetscViewerDestroy() line 99 in src/sys/viewer/interface/view.c
> [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: PetscViewerDestroy() line 99 in src/sys/viewer/interface/view.c
> 
> 
> Valerio
> 
> 
> On 2010-06-18, at 12:30 AM, Matthew Knepley wrote:
> 
>> The VecView() has no 'err' argument.
>> 
>>    Matt
>> 
>> On Thu, Jun 17, 2010 at 11:19 PM, Valerio Grazioso <graziosov at me.queensu.ca> 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 
>> 
>> 
>> 
>> 
>> 
>> 
>>  
>> 
>> 
>> 
>> -- 
>> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
>> -- Norbert Wiener
> 
> 
> 
> 
> -- 
> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
> -- Norbert Wiener

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