Ok I have done that, please have a look. It's a really weird problem. 2010/9/6 Barry Smith <bsmith at mcs.anl.gov>
> > This should not happen. Send the code to petsc-maint at mcs.anl.gov > > Barry > > On Sep 6, 2010, at 10:54 AM, Leo van Kampenhout wrote: > > Hello Barry, Matt, > About this error I am having: > > [2]PETSC ERROR: Nonconforming object sizes! > [2]PETSC ERROR: Mat mat,Vec y: local dim 700536 697068! > > > I am creating my RHS and initial vector from the same DA as the matrix is > from (see below). I even tried with setting RHS==1 instead of loading from > file, to no avail. I found out the error occurs when #PROC=3,5,7,...,8+ but > NOT when #PROC=2,4,8. It might have something to do with differences in > partitioning strategies of Mat and Vec? As you know my gridsize has a rather > unusual value (number of gridpoints is 2101608). > > Leo > > ** > > call DACreateGlobalVector(da,x,ierr) > call VecDuplicate(x,b,ierr) > (...) > call DAGetMatrix(da,MATMPIAIJ,A,ierr) > (...) > call VecSet(b,one,ierr) > call KSPCreate(MPI_COMM_WORLD,ksp,ierr) > call KSPSetOperators(ksp,A,A,SAME_NONZERO_PATTERN,ierr) > (...) > call KSPSolve(ksp,b,x,ierr) > > > > > 2010/9/3 Barry Smith <bsmith at mcs.anl.gov> > >> >> You initial vectors must be created with the same DA that is >> associated with the Matrix for the layout to be automatically correct. Use >> DACreateGlobalVector() instead of VecCreate(). You may already be doing this >> and then the problem is more subtle. Let us know. >> >> Barry >> >> Something may be going wrong with the copy header >> >> On Sep 3, 2010, at 11:35 AM, Matthew Knepley wrote: >> >> On Fri, Sep 3, 2010 at 5:50 PM, Leo van Kampenhout < >> lvankampenhout at gmail.com> wrote: >> >>> Thanks. Following this conversation closely, i have already built petsc >>> with --with-debugging=0 and found that then thing work better there. Until >>> there is a ultimate fix I'm perfectly happy with that. >>> >>> Even on my cluster, I can now run the program for 2,4,8 cores. But there >>> is always a catch... with 10 cores, GMRES breaks down! (see below) Sorry to >>> bother you with this, it seems unrelated at first sight. Should I issue a >>> new thread for this? >>> >> >> This is almost certainly somewhere you are not careful about constructing >> a Vec with the proper layout (as the message says). In fact, from the >> trace >> it looks like the rhs Vec passed in is not compatible with the matrix. >> >> Matt >> >> >>> Regards, Leo >>> >>> [5]PETSC ERROR: --------------------- Error Message >>> ------------------------------------ >>> [5]PETSC ERROR: Nonconforming object sizes! >>> [5]PETSC ERROR: Mat mat,Vec y: local dim 210161 213282! >>> [5]PETSC ERROR: >>> ------------------------------------------------------------------------ >>> [5]PETSC ERROR: Petsc Development HG revision: >>> 6da7d8c5aaa81099861622f4e6bf1087652253a7 HG Date: Fri Sep 03 15:06:40 2010 >>> +0200 >>> [5]PETSC ERROR: See docs/changes/index.html for recent updates. >>> [5]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >>> [5]PETSC ERROR: See docs/index.html for manual pages. >>> [5]PETSC ERROR: >>> ------------------------------------------------------------------------ >>> [5]PETSC ERROR: ./main on a linux-opt named node164 by s1459295 Fri >>> Sep 3 17:44:26 2010 >>> [5]PETSC ERROR: Libraries linked from >>> /home/s1459295/install/petsc-dev/linux-optimized/lib >>> [5]PETSC ERROR: Configure run at Fri Sep 3 15:28:20 2010 >>> [5]PETSC ERROR: Configure options --with-debugging=0 >>> [5]PETSC ERROR: >>> ------------------------------------------------------------------------ >>> [5]PETSC ERROR: MatMult() line 1976 in src/mat/interface/matrix.c >>> [5]PETSC ERROR: KSPInitialResidual() line 55 in >>> src/ksp/ksp/interface/itres.c >>> [5]PETSC ERROR: KSPSolve_GMRES() line 236 in >>> src/ksp/ksp/impls/gmres/gmres.c >>> [5]PETSC ERROR: KSPSolve() line 427 in src/ksp/ksp/interface/itfunc.c >>> >>> >>> >>> >>> >>> 2010/9/3 Jed Brown <jed at 59a2.org> >>> >>> On Fri, 3 Sep 2010 09:15:09 -0600 (GMT-06:00), Shri <abhyshr at mcs.anl.gov> >>>> wrote: >>>> > Leo, >>>> > Jed and I both tried running a MatLoad example (see >>>> src/dm/da/examples/tests/ex35.c) with petsc configured in debug mode and >>>> had >>>> issues running it with your grid size 202 X 102 X 102. This example runs in >>>> a reasonable amount of time with the optimized petsc build. >>>> > I suggest running your code on a smaller grid (100 X100 X 100 seems to >>>> work fine in the debug mode) for now, get it working and then using the >>>> optimized petsc build (--debugging=0) for the large grid size. >>>> >>>> I wrote an improved sort that doesn't have this bad behavior, but I'm >>>> trying to figure out why the old one is okay in optimized mode. See >>>> here: >>>> >>>> http://gist.github.com/563948 >>>> >>>> The MEDIAN macro chooses the median of the first, last, and middle >>>> element in the segment. Performance looks like >>>> >>>> FAST -O1: 2.0 seconds >>>> FAST -O0: 5 seconds >>>> SLOW -O1: 2.3 seconds >>>> SLOW -O0: more than an hour >>>> >>>> SLOW, which is basically the old implementation does a lot of shuffling >>>> with the array and ends up hitting a bad case for quicksort (even with >>>> the median choice). What I don't understand, is that apparently >>>> building SLOW with -O1 transforms the algorithm into something >>>> asymptotically faster. The assembly is a few hundred lines, and it's >>>> not obvious to me what this transform would be. >>>> >>>> Jed >>>> >>> >>> >> >> >> -- >> 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-dev/attachments/20100907/7aca954a/attachment.html>
