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? 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20100903/030d5351/attachment.html>