[petsc-users] Accessing Vector's ghost values
Bojan Niceno
bojan.niceno at psi.ch
Thu Feb 23 12:51:04 CST 2012
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?
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
--
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120223/5e4ec54f/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/png
Size: 6515 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120223/5e4ec54f/attachment-0003.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/png
Size: 6515 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120223/5e4ec54f/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Signature.png
Type: image/png
Size: 6515 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120223/5e4ec54f/attachment-0005.png>
More information about the petsc-users
mailing list