[petsc-users] Accessing Vector's ghost values
Bojan Niceno
bojan.niceno at psi.ch
Thu Feb 23 13:33:19 CST 2012
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.
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
> <mailto: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 <mailto: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 <mailto: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
>> <mailto: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 <mailto: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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