[petsc-users] Accessing Vector's ghost values

Matthew Knepley knepley at gmail.com
Thu Feb 23 13:36:17 CST 2012 

On Thu, Feb 23, 2012 at 1:33 PM, Bojan Niceno <bojan.niceno at psi.ch> wrote:

>  Dear Matt,
>
>
> I sent the code as an attached tarball.  I sent it with case I run, so is
> 2 MB big.  It is now in the cue for moderator's approval.
>

No, you HAVE to send it to petsc-maint at mcs.anl.gov, as I said last time,
for exactly this reason.

  Matt


> Thanks.
>
>
>     Kind regards,
>
>
>     Bojan
>
>
> On 2/23/2012 8:04 PM, Matthew Knepley wrote:
>
> 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
>
>
>
> --
>



-- 
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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