[petsc-users] Segmentation Violation in a very simple fortran code
Matthew Knepley
knepley at gmail.com
Fri Jun 18 07:32:04 CDT 2010
I suspect that
a) Not all arguments are correct, Fortran does not checking
b) Some object was not created
Use the debugger, -start_in_debugger, to investigate the SEGV
Matt
On Fri, Jun 18, 2010 at 12:23 AM, Valerio Grazioso
<graziosov at me.queensu.ca>wrote:
> 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]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
>
>
>
--
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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