February 2013 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] Error with ML preconditioner
by Jed Brown 18 Feb '13

18 Feb '13

Hmm, this debugging check was added by Mark here. https://bitbucket.org/petsc/petsc-dev/commits/fb7e4343253b73d3fb40857991a8c… Barry touched the code a bit earlier to add this case: https://bitbucket.org/petsc/petsc-dev/commits/c997baff1558fd165412be034e812… Prior to that, Mark had reversed the meaning of that bit of code: https://bitbucket.org/petsc/petsc-dev/commits/a85625d104df12863d7d1735f9fdb… Even in Barry's original code, I don't understand why we can expect this check to be producing a collective result. Surely there can be some ranks that see everything evenly divide and others that do not. It seems to me that we should either (a) explicitly disallow matrices with a block size to be built when the blocks are not filled or (b) when the user requests blocks, pad blocks so that we can always use an ISBlock. On Mon, Feb 18, 2013 at 2:35 PM, Garth N. Wells <gnw20(a)cam.ac.uk> wrote: > I have some code using ML as a preconditioner, and it works fines > with PETSc 3.3 but crashes with PETSc dev. I'm not setting any of the > ML parameters. Hopefully someone will recognise the error (below) and > save me having to bisect the changesets, which is hard because changes > in PETSc dev make it hard for me to compile against earlier PETSc dev > revisions. > > Garth > > > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Petsc has generated inconsistent data! > [0]PETSC ERROR: Use of blocked not consistant (I am usning blocked)! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Development HG revision: > 96a09d6a701823d69aede247ed949c1dd4e7c8ff HG Date: Mon Feb 18 11:08:29 > 2013 -0600 > [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: Unknown Name on a arch-linux2-c-debug named ....... > Mon Feb 18 19:25:17 2013 > [0]PETSC ERROR: Libraries linked from /home/garth/local/gcc/petsc-dev/lib > [0]PETSC ERROR: > [3]PETSC ERROR: See docs/index.html for manual pages. >

1 0

Re: [petsc-dev] Error with ML preconditioner
by Garth N. Wells 18 Feb '13

18 Feb '13

On 18 February 2013 20:56, Mark F. Adams <mark.adams(a)columbia.edu> wrote: > Do you have more of a stack in the error output? > Below is the rest of it. > The ML interface has had some additions to make it more consistent with blocked matrices. Do you block all of your matrices? > No. Can you give me a hint around which changesets I should test to find what broke? Garth > [2]PETSC ERROR: ------------------------------------------------------------------------ [2]PETSC ERROR: MatSetUpMultiply_MPIAIJ() line 129 in /home/garth/local/src/petsc-dev/src/mat/impls/aij/mpi/mmaij.c Unknown Name on a arch-linux2-c-debug named gnw-tech by garth Mon Feb 18 20:10:41 2013 [3]PETSC ERROR: Libraries linked from /home/garth/local/gcc/petsc-dev/lib [3]PETSC ERROR: Configure run at Mon Feb 18 19:55:45 2013 [3]PETSC ERROR: Configure options --with-shared-libraries=1 --download-hypre=yes --download-umfpack=yes --download-mumps=yes --download-scalapack=yes --download-blacs=yes --with-mpi-dir=/home/garth/local/gcc/mpich --with-parmetis --with-parmetis-dir=/home/garth/local/gcc/parmetis-4.0.2 --with-metis --with-metis-dir=/home/garth/local/gcc/metis-5.0.2 --with-ml-include=/home/garth/local/gcc/trilinos-11.0.3/include --with-ml-lib="[/home/garth/local/gcc/trilinos-11.0.3/lib/libml,/home/garth/local/gcc/parmetis-4.0.2/lib/libparmetis.so,libz]" --prefix=/home/garth/local/gcc/petsc-dev --with-ptscotch-include=/home/garth/local/gcc/scotch-6.0.0/include --with-ptscotch-lib="[/home/garth/local/gcc/scotch-6.0.0/lib/libptscotch,/home/garth/local/gcc/scotch-6.0.0/lib/lib/libptesmumps,/home/garth/local/gcc/scotch-6.0.0/lib/libscotch,/home/garth/local/gcc/scotch-6.0.0/lib/libptscotcherr]" --with-blas-lib="[/home/garth/local/gcc/atlas-latest/lib/libf77blas.a,/home/garth/local/gcc/atlas-latest/lib/libatlas.a]" --with-lapack-lib="[/home/garth/local/gcc/lapack-latest/lib/liblapack.a]" --download-superlu --download-superlu_dist [3]PETSC ERROR: ------------------------------------------------------------------------ [3]PETSC ERROR: MatSetUpMultiply_MPIAIJ() line 129 in /home/garth/local/src/petsc-dev/src/mat/impls/aij/mpi/mmaij.c Configure run at Mon Feb 18 19:55:45 2013 [4]PETSC ERROR: Configure options --with-shared-libraries=1 --download-hypre=yes --download-umfpack=yes --download-mumps=yes --download-scalapack=yes --download-blacs=yes --with-mpi-dir=/home/garth/local/gcc/mpich --with-parmetis --with-parmetis-dir=/home/garth/local/gcc/parmetis-4.0.2 --with-metis --with-metis-dir=/home/garth/local/gcc/metis-5.0.2 --with-ml-include=/home/garth/local/gcc/trilinos-11.0.3/include --with-ml-lib="[/home/garth/local/gcc/trilinos-11.0.3/lib/libml,/home/garth/local/gcc/parmetis-4.0.2/lib/libparmetis.so,libz]" --prefix=/home/garth/local/gcc/petsc-dev --with-ptscotch-include=/home/garth/local/gcc/scotch-6.0.0/include --with-ptscotch-lib="[/home/garth/local/gcc/scotch-6.0.0/lib/libptscotch,/home/garth/local/gcc/scotch-6.0.0/lib/lib/libptesmumps,/home/garth/local/gcc/scotch-6.0.0/lib/libscotch,/home/garth/local/gcc/scotch-6.0.0/lib/libptscotcherr]" --with-blas-lib="[/home/garth/local/gcc/atlas-latest/lib/libf77blas.a,/home/garth/local/gcc/atlas-latest/lib/libatlas.a]" --with-lapack-lib="[/home/garth/local/gcc/lapack-latest/lib/liblapack.a]" --download-superlu --download-superlu_dist [4]PETSC ERROR: ------------------------------------------------------------------------ [4]PETSC ERROR: MatSetUpMultiply_MPIAIJ() line 129 in /home/garth/local/src/petsc-dev/src/mat/impls/aij/mpi/mmaij.c [4]PETSC ERROR: [2]PETSC ERROR: MatAssemblyEnd_MPIAIJ() line 702 in /home/garth/local/src/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c [3]PETSC ERROR: MatAssemblyEnd_MPIAIJ() line 702 in /home/garth/local/src/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c [3]PETSC ERROR: MatAssemblyEnd() line 4896 in /home/garth/local/src/petsc-dev/src/mat/interface/matrix.c MatAssemblyEnd_MPIAIJ() line 702 in /home/garth/local/src/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c [4]PETSC ERROR: MatAssemblyEnd() line 4896 in /home/garth/local/src/petsc-dev/src/mat/interface/matrix.c [4]PETSC ERROR: [2]PETSC ERROR: MatAssemblyEnd() line 4896 in /home/garth/local/src/petsc-dev/src/mat/interface/matrix.c [2]PETSC ERROR: MatWrapML_MPIAIJ() line 446 in /home/garth/local/src/petsc-dev/src/ksp/pc/impls/ml/ml.c [3]PETSC ERROR: MatWrapML_MPIAIJ() line 446 in /home/garth/local/src/petsc-dev/src/ksp/pc/impls/ml/ml.c [3]PETSC ERROR: PCSetUp_ML() line 916 in /home/garth/local/src/petsc-dev/src/ksp/pc/impls/ml/ml.c MatWrapML_MPIAIJ() line 446 in /home/garth/local/src/petsc-dev/src/ksp/pc/impls/ml/ml.c [4]PETSC ERROR: PCSetUp_ML() line 916 in /home/garth/local/src/petsc-dev/src/ksp/pc/impls/ml/ml.c [2]PETSC ERROR: PCSetUp_ML() line 916 in /home/garth/local/src/petsc-dev/src/ksp/pc/impls/ml/ml.c [2]PETSC ERROR: PCSetUp() line 832 in /home/garth/local/src/petsc-dev/src/ksp/pc/interface/precon.c [3]PETSC ERROR: PCSetUp() line 832 in /home/garth/local/src/petsc-dev/src/ksp/pc/interface/precon.c [4]PETSC ERROR: PCSetUp() line 832 in /home/garth/local/src/petsc-dev/src/ksp/pc/interface/precon.c --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Petsc has generated inconsistent data! [0]PETSC ERROR: Use of blocked not consistant (I am usning blocked)! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Development HG revision: 96a09d6a701823d69aede247ed949c1dd4e7c8ff HG Date: Mon Feb 18 11:08:29 2013 -0600 [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: Unknown Name on a arch-linux2-c-debug named gnw-tech by garth Mon Feb 18 20:10:41 2013 [0]PETSC ERROR: Libraries linked from /home/garth/local/gcc/petsc-dev/lib [5]PETSC ERROR: ------------------------------------------------------------------------ [5]PETSC ERROR: Unknown Name on a arch-linux2-c-debug named gnw-tech by garth Mon Feb 18 20:10:41 2013 [5]PETSC ERROR: Libraries linked from /home/garth/local/gcc/petsc-dev/lib [5]PETSC ERROR: Configure run at Mon Feb 18 19:55:45 2013 [5]PETSC ERROR: Configure options --with-shared-libraries=1 --download-hypre=yes --download-umfpack=yes --download-mumps=yes --download-scalapack=yes --download-blacs=yes --with-mpi-dir=/home/garth/local/gcc/mpich --with-parmetis --with-parmetis-dir=/home/garth/local/gcc/parmetis-4.0.2 --with-metis --with-metis-dir=/home/garth/local/gcc/metis-5.0.2 --with-ml-include=/home/garth/local/gcc/trilinos-11.0.3/include --with-ml-lib="[/home/garth/local/gcc/trilinos-11.0.3/lib/libml,/home/garth/local/gcc/parmetis-4.0.2/lib/libparmetis.so,libz]" --prefix=/home/garth/local/gcc/petsc-dev --with-ptscotch-include=/home/garth/local/gcc/scotch-6.0.0/include --with-ptscotch-lib="[/home/garth/local/gcc/scotch-6.0.0/lib/libptscotch,/home/garth/local/gcc/scotch-6.0.0/lib/lib/libptesmumps,/home/garth/local/gcc/scotch-6.0.0/lib/libscotch,/home/garth/local/gcc/scotch-6.0.0/lib/libptscotcherr]" --with-blas-lib="[/home/garth/local/gcc/atlas-latest/lib/libf77blas.a,/home/garth/local/gcc/atlas-latest/lib/libatlas.a]" --with-lapack-lib="[/home/garth/local/gcc/lapack-latest/lib/liblapack.a]" --download-superlu --download-superlu_dist [5]PETSC ERROR: ------------------------------------------------------------------------ [5]PETSC ERROR: MatSetUpMultiply_MPIAIJ() line 129 in /home/garth/local/src/petsc-dev/src/mat/impls/aij/mpi/mmaij.c [5]PETSC ERROR: MatAssemblyEnd_MPIAIJ() line 702 in /home/garth/local/src/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c [5]PETSC ERROR: MatAssemblyEnd() line 4896 in /home/garth/local/src/petsc-dev/src/mat/interface/matrix.c [5]PETSC ERROR: MatWrapML_MPIAIJ() line 446 in /home/garth/local/src/petsc-dev/src/ksp/pc/impls/ml/ml.c [5]PETSC ERROR: PCSetUp_ML() line 916 in /home/garth/local/src/petsc-dev/src/ksp/pc/impls/ml/ml.c [5]PETSC ERROR: PCSetUp() line 832 in /home/garth/local/src/petsc-dev/src/ksp/pc/interface/precon.c [0]PETSC ERROR: Configure run at Mon Feb 18 19:55:45 2013 [0]PETSC ERROR: Configure options --with-shared-libraries=1 --download-hypre=yes --download-umfpack=yes --download-mumps=yes --download-scalapack=yes --download-blacs=yes --with-mpi-dir=/home/garth/local/gcc/mpich --with-parmetis --with-parmetis-dir=/home/garth/local/gcc/parmetis-4.0.2 --with-metis --with-metis-dir=/home/garth/local/gcc/metis-5.0.2 --with-ml-include=/home/garth/local/gcc/trilinos-11.0.3/include --with-ml-lib="[/home/garth/local/gcc/trilinos-11.0.3/lib/libml,/home/garth/local/gcc/parmetis-4.0.2/lib/libparmetis.so,libz]" --prefix=/home/garth/local/gcc/petsc-dev --with-ptscotch-include=/home/garth/local/gcc/scotch-6.0.0/include --with-ptscotch-lib="[/home/garth/local/gcc/scotch-6.0.0/lib/libptscotch,/home/garth/local/gcc/scotch-6.0.0/lib/lib/libptesmumps,/home/garth/local/gcc/scotch-6.0.0/lib/libscotch,/home/garth/local/gcc/scotch-6.0.0/lib/libptscotcherr]" --with-blas-lib="[/home/garth/local/gcc/atlas-latest/lib/libf77blas.a,/home/garth/local/gcc/atlas-latest/lib/libatlas.a]" --with-lapack-lib="[/home/garth/local/gcc/lapack-latest/lib/liblapack.a]" --download-superlu --download-superlu_dist [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: MatSetUpMultiply_MPIAIJ() line 129 in /home/garth/local/src/petsc-dev/src/mat/impls/aij/mpi/mmaij.c [0]PETSC ERROR: MatAssemblyEnd_MPIAIJ() line 702 in /home/garth/local/src/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c [0]PETSC ERROR: MatAssemblyEnd() line 4896 in /home/garth/local/src/petsc-dev/src/mat/interface/matrix.c [0]PETSC ERROR: MatWrapML_MPIAIJ() line 446 in /home/garth/local/src/petsc-dev/src/ksp/pc/impls/ml/ml.c [0]PETSC ERROR: PCSetUp_ML() line 916 in /home/garth/local/src/petsc-dev/src/ksp/pc/impls/ml/ml.c [0]PETSC ERROR: PCSetUp() line 832 in /home/garth/local/src/petsc-dev/src/ksp/pc/interface/precon.c > On Feb 18, 2013, at 3:35 PM, Garth N. Wells <gnw20(a)cam.ac.uk> wrote: > >> I have some code using ML as a preconditioner, and it works fines >> with PETSc 3.3 but crashes with PETSc dev. I'm not setting any of the >> ML parameters. Hopefully someone will recognise the error (below) and >> save me having to bisect the changesets, which is hard because changes >> in PETSc dev make it hard for me to compile against earlier PETSc dev >> revisions. >> >> Garth >> >> >> [0]PETSC ERROR: --------------------- Error Message >> ------------------------------------ >> [0]PETSC ERROR: Petsc has generated inconsistent data! >> [0]PETSC ERROR: Use of blocked not consistant (I am usning blocked)! >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: Petsc Development HG revision: >> 96a09d6a701823d69aede247ed949c1dd4e7c8ff HG Date: Mon Feb 18 11:08:29 >> 2013 -0600 >> [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: Unknown Name on a arch-linux2-c-debug named ....... >> Mon Feb 18 19:25:17 2013 >> [0]PETSC ERROR: Libraries linked from /home/garth/local/gcc/petsc-dev/lib >> [0]PETSC ERROR: >> [3]PETSC ERROR: See docs/index.html for manual pages. >> >

1 0

Re: [petsc-dev] Error with ML preconditioner
by Mark F. Adams 18 Feb '13

18 Feb '13

Do you have more of a stack in the error output? The ML interface has had some additions to make it more consistent with blocked matrices. Do you block all of your matrices? On Feb 18, 2013, at 3:35 PM, Garth N. Wells <gnw20(a)cam.ac.uk> wrote: > I have some code using ML as a preconditioner, and it works fines > with PETSc 3.3 but crashes with PETSc dev. I'm not setting any of the > ML parameters. Hopefully someone will recognise the error (below) and > save me having to bisect the changesets, which is hard because changes > in PETSc dev make it hard for me to compile against earlier PETSc dev > revisions. > > Garth > > > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Petsc has generated inconsistent data! > [0]PETSC ERROR: Use of blocked not consistant (I am usning blocked)! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Development HG revision: > 96a09d6a701823d69aede247ed949c1dd4e7c8ff HG Date: Mon Feb 18 11:08:29 > 2013 -0600 > [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: Unknown Name on a arch-linux2-c-debug named ....... > Mon Feb 18 19:25:17 2013 > [0]PETSC ERROR: Libraries linked from /home/garth/local/gcc/petsc-dev/lib > [0]PETSC ERROR: > [3]PETSC ERROR: See docs/index.html for manual pages. >

1 0

Error with ML preconditioner
by Garth N. Wells 18 Feb '13

18 Feb '13

I have some code using ML as a preconditioner, and it works fines with PETSc 3.3 but crashes with PETSc dev. I'm not setting any of the ML parameters. Hopefully someone will recognise the error (below) and save me having to bisect the changesets, which is hard because changes in PETSc dev make it hard for me to compile against earlier PETSc dev revisions. Garth [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Petsc has generated inconsistent data! [0]PETSC ERROR: Use of blocked not consistant (I am usning blocked)! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Development HG revision: 96a09d6a701823d69aede247ed949c1dd4e7c8ff HG Date: Mon Feb 18 11:08:29 2013 -0600 [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: Unknown Name on a arch-linux2-c-debug named ....... Mon Feb 18 19:25:17 2013 [0]PETSC ERROR: Libraries linked from /home/garth/local/gcc/petsc-dev/lib [0]PETSC ERROR: [3]PETSC ERROR: See docs/index.html for manual pages.

1 0

Re: [petsc-dev] Google Summer of Code
by Jed Brown 18 Feb '13

18 Feb '13

On Mon, Feb 18, 2013 at 1:56 PM, Karl Rupp <rupp(a)mcs.anl.gov> wrote: > > But is this any different from other summer students and contributions > from outside throughout the past ~20 years? > Not really, just potentially different student background and visibility in a different venue.

1 0

Re: [petsc-dev] Google Summer of Code
by Karl Rupp 18 Feb '13

18 Feb '13

Hi, > The crux with documentation is that it is not explicitly allowed as > a separate project for GSoC, so it really needs to be a Summer of > *Code*. You can reasonably expect that the student takes care of > documentation for the code he/she writes, but you won't get much > additional documentation work done. > > > No, no. I meant that it forces _us_ to improve the documentation since > it gives a us a consumer of that material asking questions about > anything that is unclear. But is this any different from other summer students and contributions from outside throughout the past ~20 years? Best regards, Karli

1 0

Re: [petsc-dev] Google Summer of Code
by Jed Brown 18 Feb '13

18 Feb '13

On Mon, Feb 18, 2013 at 1:48 PM, Karl Rupp <rupp(a)mcs.anl.gov> wrote: > The crux with documentation is that it is not explicitly allowed as a > separate project for GSoC, so it really needs to be a Summer of *Code*. You > can reasonably expect that the student takes care of documentation for the > code he/she writes, but you won't get much additional documentation work > done. > No, no. I meant that it forces _us_ to improve the documentation since it gives a us a consumer of that material asking questions about anything that is unclear.

1 0

Re: [petsc-dev] Google Summer of Code
by Karl Rupp 18 Feb '13

18 Feb '13

Hi Jed, > I've been org admin for TU Wien and mentored a couple of students in > 2011 and 2012. It's a nice thing to make PETSc known in the FOSS > community. > > In terms of raw code/functionality output, however, expect that *on > average* you need to invest more time in the student than what you > would come up with by coding it yourself. > > > This is the nature of teaching. The goal would be to improve workflow > and developer docs to make such contributions easier, and hopefully to > catch the interest of people that might later become more regular > contributors. I don't doubt that you are aware of that, but others might not ;-) The crux with documentation is that it is not explicitly allowed as a separate project for GSoC, so it really needs to be a Summer of *Code*. You can reasonably expect that the student takes care of documentation for the code he/she writes, but you won't get much additional documentation work done. Best regards, Karli

1 0

Re: [petsc-dev] Google Summer of Code
by Jed Brown 18 Feb '13

18 Feb '13

On Mon, Feb 18, 2013 at 1:29 PM, Karl Rupp <rupp(a)mcs.anl.gov> wrote: > Hi, > > I've been org admin for TU Wien and mentored a couple of students in 2011 > and 2012. It's a nice thing to make PETSc known in the FOSS community. > > In terms of raw code/functionality output, however, expect that *on > average* you need to invest more time in the student than what you would > come up with by coding it yourself. This is the nature of teaching. The goal would be to improve workflow and developer docs to make such contributions easier, and hopefully to catch the interest of people that might later become more regular contributors.

1 0

Re: [petsc-dev] Google Summer of Code
by Karl Rupp 18 Feb '13

18 Feb '13

Hi, I've been org admin for TU Wien and mentored a couple of students in 2011 and 2012. It's a nice thing to make PETSc known in the FOSS community. In terms of raw code/functionality output, however, expect that *on average* you need to invest more time in the student than what you would come up with by coding it yourself. As a new organization, one must not expect to get more than two, maybe three, slots. Best regards, Karli On 02/18/2013 01:21 PM, Jed Brown wrote: > This year's program was recently announced. > > http://www.google-melange.com/gsoc/events/google/gsoc2013 > > Applications from mentoring organizations have to be received between > March 18 and March 29. If we would like PETSc to be a mentoring > organization, we should start by sketching a few project ideas. There > are a few such projects on this page, but we'd need to collect a few > that would be interesting and feasible as a summer project. > > https://bitbucket.org/petsc/petsc-dev/issues?status=new&status=open

1 0