[petsc-users] Accessing Vector's ghost values

Thu Feb 23 12:44:18 CST 2012

On Thu, Feb 23, 2012 at 12:28 PM, Bojan Niceno <bojan.niceno at psi.ch> wrote:

>  On 2/23/2012 7:24 PM, Matthew Knepley wrote:
>
> On Thu, Feb 23, 2012 at 12:05 PM, Bojan Niceno <bojan.niceno at psi.ch>wrote:
>
>>  Dear Matthew,
>>
>>
>> thank you for your response.  When I use VecCreateGhost, I get the
>> following:
>>
>
>  It appears that you passed a bad communicator. Did you not initialize a
> 'comm' variable?
>
>
> I pass PETSC_COMM_WORLD to VecCreateGhost.
>
> I don't know what you mean by 'comm' variable :-(  I called all the
> routines to initialize PETSc.
>

Send your code to petsc-maint at mcs.anl.gov.

   Matt

>
>     Cheers,
>
>
>     Bojan
>
>
>     Matt
>
>
>>  [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [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/faq.html#valgrind[0]PETSC
>> ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to
>> find memory corruption errors
>> [0]PETSC ERROR: 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: [0] PetscCommDuplicate line 140 src/sys/objects/tagm.c
>> [0]PETSC ERROR: [0] PetscHeaderCreate_Private line 30
>> src/sys/objects/inherit.c
>> [0]PETSC ERROR: [0] VecCreate line 32 src/vec/vec/interface/veccreate.c
>> [0]PETSC ERROR: [0] VecCreateGhostWithArray line 567
>> src/vec/vec/impls/mpi/pbvec.c
>> [0]PETSC ERROR: [0] VecCreateGhost line 647 src/vec/vec/impls/mpi/pbvec.c
>> [0]PETSC ERROR: --------------------- Error Message
>> ------------------------------------
>> [0]PETSC ERROR: Signal received!
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 6, Wed Jan 11 09:28:45
>> CST 2012
>> [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: ./PSI-Flow on a arch-linu named lccfd06 by niceno Thu Feb
>> 23 19:02:45 2012
>> [0]PETSC ERROR: Libraries linked from
>> /homecfd/niceno/PETSc-3.2-p6/arch-linux2-c-debug/lib
>> [0]PETSC ERROR: Configure run at Fri Feb 10 10:24:13 2012
>> [0]PETSC ERROR: Configure options
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR: User provided function() line 0 in unknown directory
>> unknown file
>>
>> I don't understand what could be causing it.  I took very good care to
>> match the global numbers of ghost cells when calling VecCreateGhost
>>
>>
>>     Kind regards,
>>
>>
>>     Bojan
>>
>>
>> On 2/23/2012 5:53 PM, Matthew Knepley wrote:
>>
>> On Thu, Feb 23, 2012 at 10:46 AM, Bojan Niceno <bojan.niceno at psi.ch>wrote:
>>
>>> Hi all,
>>>
>>> I've never used a mailing list before, so I hope this message will reach
>>> PETSc users and experts and someone might be willing to help me.  I am also
>>> novice in PETSc.
>>>
>>> I have developed an unstructured finite volume solver on top of PETSc
>>> libraries.  In sequential, it works like a charm.  For the parallel
>>> version, I do domain decomposition externally with Metis, and work out
>>> local and global numberings, as well as communication patterns between
>>> processor.  (The latter don't seem to be needed for PETSc, though.)  When I
>>> run my program in parallel, it also works, but I miss values in vectors'
>>> ghost points.
>>>
>>> I create vectors with command: VecCreate(PETSC_COMM_WORLD, &x);
>>>
>>> Is it possible to get the ghost values if a vector is created like this?
>>>
>>
>>  I do not understand this question. By definition, "ghost values" are
>> those not stored in the global vector.
>>
>>
>>> I have tried to use VecCreateGhost, but for some reason which is beyond
>>> my comprehension, PETSc goes berserk when it reaches the command:
>>> VecCreateGhost(PETSC_COMM_WORLD, n, PETSC_DECIDE, nghost, ifrom, &x)
>>>
>>
>>  I think you can understand that "berserk" tells me absolutely nothing.
>> Error message? Stack trace? Did you try to run an
>> example which uses VecGhost?
>>
>>    Thanks,
>>
>>       Matt
>>
>>
>>> Can anyone help me?  Either how to reach ghost values for vector created
>>> by VecCreate, or how to use VecCreateGhost properly?
>>>
>>>
>>>   Kind regards,
>>>
>>>   Bojan
>>>
>>
>>
>>
>>  --
>> 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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