[petsc-users] Segmentation Violation in a very simple fortran code
Matthew Knepley
knepley at gmail.com
Fri Jun 18 00:01:09 CDT 2010
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]PETSCERROR: 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]PETSCERROR: 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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