[petsc-users] Accessing Vector's ghost values

Matthew Knepley knepley at gmail.com
Thu Feb 23 13:04:45 CST 2012 

On Thu, Feb 23, 2012 at 12:51 PM, Bojan Niceno <bojan.niceno at psi.ch> wrote:

>  Dear Matt,
>
>
> are you sure?  It is almost 4000 lines long!  Shall I send only the
> function which bother me?
>
> If the entire code is what you need, shall I make a tarball and attach it?
>

Send something the builds and runs. Don't care how long it is.

   Matt


>     Kind regards,
>
>
>     Bojan
>
> On 2/23/2012 7:44 PM, Matthew Knepley wrote:
>
> 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
>
>
>
> --
>



-- 
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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