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 -------------- next part -------------- An HTML attachment was scrubbed... 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