September 2007 - petsc-dev - mailman3.cels.anl.gov

Re: [PETSC #16801] petsc-dev make test breaks with 2 processes?
by Matthew Knepley 26 Sep '07

26 Sep '07

I pushed a fix. Matt On 9/26/07, Matthew Knepley <petsc-maint(a)mcs.anl.gov> wrote: > Cool, I can reproduce the failure. Satish just put code in to check this, so > the error makes sense. I will find it after my run. > > Matt > > On 9/25/07, mspieg <mspieg(a)ldeo.columbia.edu> wrote: > > Hi all, > > I just pulled, reconfigured and rebuilt petsc-dev (changeset: > > 11135:7c2e5fab809d) and the 2 processor test failed with an error from > > PetscLogFlops (see error message below). The same configuration file works > > fine in the the latest release 2.3.3-p6. Not immediately critical, but I > > need petsc-dev for the PCDMMGDM routines (of which I'm still tracking down a > > pernicous bug, but am getting close). > > All help greatly appreciated > > cheers > > marc > > p.s. system is MacOSX 10.4.10, mpich2-1.0.5p4 > > > > -------------output of make test---------------------- > > Running test examples to verify correct installation > > C/C++ example src/snes/examples/tutorials/ex19 run > > successfully with 1 MPI process > > Possible error running C/C++ > > src/snes/examples/tutorials/ex19 with 2 MPI processes > > See > > http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html > > lid velocity = 0.0016, prandtl # = 1, grashof # = 1 > > [0]PETSC ERROR: --------------------- Error Message > > ------------------------------------ > > [0]PETSC ERROR: Argument out of range! > > [0]PETSC ERROR: PetscLogFlops: flop-count given is neagitive: -32.00! > > [0]PETSC ERROR: > > ------------------------------------------------------------------------ > > [0]PETSC ERROR: Petsc Development Version 2.3.3, Patch 6, unknown HG > > revision: unknown > > [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: ./ex19 on a macosx-gn named mingus.home by mspieg Tue Sep 25 > > 23:34:58 2007 > > [0]PETSC ERROR: Libraries linked from > > /Applications/petsc/petsc-dev/lib > > [0]PETSC ERROR: Configure run at Tue Sep 25 23:12:21 2007 > > [0]PETSC ERROR: Configure options CC=gcc FC=gfortran --with-python > > --with-shared=1 --with-dynamic=1 > > --with-mpi-dir=/Applications/mpich/mpich2-1.0.5p4 --do > > [1]PETSC ERROR: --------------------- Error Message > > ------------------------------------ > > [1]PETSC ERROR: Argument out of range! > > [1]PETSC ERROR: PetscLogFlops: flop-count given is neagitive: -84.00! > > [1]PETSC ERROR: > > ------------------------------------------------------------------------ > > [1]PETSC ERROR: Petsc Development Version 2.3.3, Patch 6, unknown HG > > revision: unknown > > [1]PETSC ERROR: See docs/changes/index.html for recent updates. > > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [1]PETSC ERROR: See docs/index.html for manual pages. > > [1]PETSC ERROR: > > ------------------------------------------------------------------------ > > [1]PETSC ERROR: ./ex19 on a macosx-gn named mingus.home by mspieg Tue Sep 25 > > 23:34:58 2007 > > [1]PETSC ERROR: Libraries linked from > > /Applications/petsc/petsc-dev/lib > > [1]PETSC ERROR: Configure run at Tue Sep 25 23:12:21 2007 > > [1]PETSC ERROR: Configure options CC=gcc FC=gfortran --with-python > > --with-shared=1 --with-dynamic=1 > > --with-mpi-dir=/Applications/mpich/mpich2-1.0.5p4 > > --download-mpich-pm=gforker --with-debugging=1 PETSC_ARCH=macosx-gnu-local-g > > [0]PETSC ERROR: > > ------------------------------------------------------------------------ > > [0]PETSC ERROR: MatMultAdd_SeqMAIJ_4() line 585 in src/mat/impls/maij/maij.c > > [0]PETSC ERROR: MatMult_MPIMAIJ_dof() line 2118 in src/mat/impls/maij/maij.c > > [0]PETSC ERROR: MatMult() line 1670 in src/mat/interface/matrix.c > > [0]PETSC ERROR: MatInterpolate() line 5925 in src/mat/interface/matrix.c > > [0]PETSC ERROR: PCMGFCycle_Private() line 28 in src/ksp/pc/impls/mg/fmg.c > > [0]PETSC ERROR: PCApply_MG() line 207 in src/ksp/pc/impls/mg/mg.c > > [0]PETSC ERROR: PCApply() line 356 in src/ksp/pc/interface/precon.c > > [0]PETSC ERROR: FGMREScycle() line 232 in > > src/ksp/ksp/impls/gmres/fgmres/fgmres.c > > [0]PETSC ERROR: KSPSolve_FGMRES() line 358 in > > src/ksp/ksp/impls/gmres/fgmres/fgmres.c > > [0]PETSC ERROR: KSPSolve() line 378 in src/ksp/ksp/interface/itfunc.c > > [0]PETSC ERROR: SNES_KSPSolve() line 2539 in src/snes/interface/snes.c > > [0]PETSC ERROR: SNESSolve_LS() line 184 in > > src/snes/wnload-mpich-pm=gforker --with-debugging=1 > > PETSC_ARCH=macosx-gnu-local-g > > [1]PETSC ERROR: > > ------------------------------------------------------------------------ > > [1]PETSC ERROR: MatMultAdd_SeqMAIJ_4() line 585 in src/mat/impls/maij/maij.c > > [1]PETSC ERROR: MatMult_MPIMAIJ_dof() line 2118 in src/mat/impls/maij/maij.c > > [1]PETSC ERROR: MatMult() line 1670 in src/mat/interface/matrix.c > > [1]PETSC ERROR: MatInterpolate() line 5925 in src/mat/interface/matrix.c > > [1]PETSC ERROR: PCMGFCycle_Private() line 28 in src/ksp/pc/impls/mg/fmg.c > > [1]PETSC ERROR: PCApply_MG() line 207 in src/ksp/pc/impls/mg/mg.c > > [1]PETSC ERROR: PCApply() line 356 in src/ksp/pc/interface/precon.c > > [1]PETSC ERROR: FGMREScycle() line 232 in > > src/ksp/ksp/impls/gmres/fgmres/fgmres.c > > [1]PETSC ERROR: KSPSolve_FGMRES() line 358 in > > src/ksp/ksp/impls/gmres/fgmres/fgmres.c > > [1]PETSC ERROR: KSPSolve() line 378 in src/ksp/ksp/interface/itfunc.c > > [1]PETSC ERROR: SNES_KSPSolve() line 2539 in src/snes/interface/snes.c > > [1]PETSC ERROR: SNESSolve_LS() line 184 in src/snes/impls/ls/ls.c > > [0]PETSC ERROR: SNESSolve() line 1867 in src/snes/interface/snes.c > > [0]PETSC ERROR: DMMGSolveSNES() line 510 in src/snes/utils/damgsnes.c > > [0]PETSC ERROR: DMMGSolve() line 393 in src/snes/utils/damg.c > > [0]PETSC ERROR: main() line 154 in > > src/snes/examples/tutorials/ex19.c > > [cli_0]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > > impls/ls/ls.c > > [1]PETSC ERROR: SNESSolve() line 1867 in src/snes/interface/snes.c > > [1]PETSC ERROR: DMMGSolveSNES() line 510 in src/snes/utils/damgsnes.c > > [1]PETSC ERROR: DMMGSolve() line 393 in src/snes/utils/damg.c > > [1]PETSC ERROR: main() line 154 in > > src/snes/examples/tutorials/ex19.c > > [cli_1]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1 > > Graphics example src/snes/examples/tutorials/ex19 run > > successfully with 1 MPI process > > Fortran example src/snes/examples/tutorials/ex5f run > > successfully with 1 MPI process > > Completed test examples > > > > > > > > ---------------------------------------------------- > > Marc Spiegelman > > Lamont-Doherty Earth Observatory > > Dept. of Applied Physics/Applied Math > > Columbia University > > http://www.ldeo.columbia.edu/~mspieg > > ---------------------------------------------------- > > > > > > > -- > 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

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Re: [PETSC #16801] petsc-dev make test breaks with 2 processes?
by Matthew Knepley 26 Sep '07

26 Sep '07

Cool, I can reproduce the failure. Satish just put code in to check this, so the error makes sense. I will find it after my run. Matt On 9/25/07, mspieg <mspieg(a)ldeo.columbia.edu> wrote: > Hi all, > I just pulled, reconfigured and rebuilt petsc-dev (changeset: > 11135:7c2e5fab809d) and the 2 processor test failed with an error from > PetscLogFlops (see error message below). The same configuration file works > fine in the the latest release 2.3.3-p6. Not immediately critical, but I > need petsc-dev for the PCDMMGDM routines (of which I'm still tracking down a > pernicous bug, but am getting close). > All help greatly appreciated > cheers > marc > p.s. system is MacOSX 10.4.10, mpich2-1.0.5p4 > > -------------output of make test---------------------- > Running test examples to verify correct installation > C/C++ example src/snes/examples/tutorials/ex19 run > successfully with 1 MPI process > Possible error running C/C++ > src/snes/examples/tutorials/ex19 with 2 MPI processes > See > http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html > lid velocity = 0.0016, prandtl # = 1, grashof # = 1 > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Argument out of range! > [0]PETSC ERROR: PetscLogFlops: flop-count given is neagitive: -32.00! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Development Version 2.3.3, Patch 6, unknown HG > revision: unknown > [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: ./ex19 on a macosx-gn named mingus.home by mspieg Tue Sep 25 > 23:34:58 2007 > [0]PETSC ERROR: Libraries linked from > /Applications/petsc/petsc-dev/lib > [0]PETSC ERROR: Configure run at Tue Sep 25 23:12:21 2007 > [0]PETSC ERROR: Configure options CC=gcc FC=gfortran --with-python > --with-shared=1 --with-dynamic=1 > --with-mpi-dir=/Applications/mpich/mpich2-1.0.5p4 --do > [1]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [1]PETSC ERROR: Argument out of range! > [1]PETSC ERROR: PetscLogFlops: flop-count given is neagitive: -84.00! > [1]PETSC ERROR: > ------------------------------------------------------------------------ > [1]PETSC ERROR: Petsc Development Version 2.3.3, Patch 6, unknown HG > revision: unknown > [1]PETSC ERROR: See docs/changes/index.html for recent updates. > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [1]PETSC ERROR: See docs/index.html for manual pages. > [1]PETSC ERROR: > ------------------------------------------------------------------------ > [1]PETSC ERROR: ./ex19 on a macosx-gn named mingus.home by mspieg Tue Sep 25 > 23:34:58 2007 > [1]PETSC ERROR: Libraries linked from > /Applications/petsc/petsc-dev/lib > [1]PETSC ERROR: Configure run at Tue Sep 25 23:12:21 2007 > [1]PETSC ERROR: Configure options CC=gcc FC=gfortran --with-python > --with-shared=1 --with-dynamic=1 > --with-mpi-dir=/Applications/mpich/mpich2-1.0.5p4 > --download-mpich-pm=gforker --with-debugging=1 PETSC_ARCH=macosx-gnu-local-g > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: MatMultAdd_SeqMAIJ_4() line 585 in src/mat/impls/maij/maij.c > [0]PETSC ERROR: MatMult_MPIMAIJ_dof() line 2118 in src/mat/impls/maij/maij.c > [0]PETSC ERROR: MatMult() line 1670 in src/mat/interface/matrix.c > [0]PETSC ERROR: MatInterpolate() line 5925 in src/mat/interface/matrix.c > [0]PETSC ERROR: PCMGFCycle_Private() line 28 in src/ksp/pc/impls/mg/fmg.c > [0]PETSC ERROR: PCApply_MG() line 207 in src/ksp/pc/impls/mg/mg.c > [0]PETSC ERROR: PCApply() line 356 in src/ksp/pc/interface/precon.c > [0]PETSC ERROR: FGMREScycle() line 232 in > src/ksp/ksp/impls/gmres/fgmres/fgmres.c > [0]PETSC ERROR: KSPSolve_FGMRES() line 358 in > src/ksp/ksp/impls/gmres/fgmres/fgmres.c > [0]PETSC ERROR: KSPSolve() line 378 in src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: SNES_KSPSolve() line 2539 in src/snes/interface/snes.c > [0]PETSC ERROR: SNESSolve_LS() line 184 in > src/snes/wnload-mpich-pm=gforker --with-debugging=1 > PETSC_ARCH=macosx-gnu-local-g > [1]PETSC ERROR: > ------------------------------------------------------------------------ > [1]PETSC ERROR: MatMultAdd_SeqMAIJ_4() line 585 in src/mat/impls/maij/maij.c > [1]PETSC ERROR: MatMult_MPIMAIJ_dof() line 2118 in src/mat/impls/maij/maij.c > [1]PETSC ERROR: MatMult() line 1670 in src/mat/interface/matrix.c > [1]PETSC ERROR: MatInterpolate() line 5925 in src/mat/interface/matrix.c > [1]PETSC ERROR: PCMGFCycle_Private() line 28 in src/ksp/pc/impls/mg/fmg.c > [1]PETSC ERROR: PCApply_MG() line 207 in src/ksp/pc/impls/mg/mg.c > [1]PETSC ERROR: PCApply() line 356 in src/ksp/pc/interface/precon.c > [1]PETSC ERROR: FGMREScycle() line 232 in > src/ksp/ksp/impls/gmres/fgmres/fgmres.c > [1]PETSC ERROR: KSPSolve_FGMRES() line 358 in > src/ksp/ksp/impls/gmres/fgmres/fgmres.c > [1]PETSC ERROR: KSPSolve() line 378 in src/ksp/ksp/interface/itfunc.c > [1]PETSC ERROR: SNES_KSPSolve() line 2539 in src/snes/interface/snes.c > [1]PETSC ERROR: SNESSolve_LS() line 184 in src/snes/impls/ls/ls.c > [0]PETSC ERROR: SNESSolve() line 1867 in src/snes/interface/snes.c > [0]PETSC ERROR: DMMGSolveSNES() line 510 in src/snes/utils/damgsnes.c > [0]PETSC ERROR: DMMGSolve() line 393 in src/snes/utils/damg.c > [0]PETSC ERROR: main() line 154 in > src/snes/examples/tutorials/ex19.c > [cli_0]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > impls/ls/ls.c > [1]PETSC ERROR: SNESSolve() line 1867 in src/snes/interface/snes.c > [1]PETSC ERROR: DMMGSolveSNES() line 510 in src/snes/utils/damgsnes.c > [1]PETSC ERROR: DMMGSolve() line 393 in src/snes/utils/damg.c > [1]PETSC ERROR: main() line 154 in > src/snes/examples/tutorials/ex19.c > [cli_1]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1 > Graphics example src/snes/examples/tutorials/ex19 run > successfully with 1 MPI process > Fortran example src/snes/examples/tutorials/ex5f run > successfully with 1 MPI process > Completed test examples > > > > ---------------------------------------------------- > Marc Spiegelman > Lamont-Doherty Earth Observatory > Dept. of Applied Physics/Applied Math > Columbia University > http://www.ldeo.columbia.edu/~mspieg > ---------------------------------------------------- > > -- 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

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petsc-dev make test breaks with 2 processes?
by mspieg 25 Sep '07

25 Sep '07

Hi all, I just pulled, reconfigured and rebuilt petsc-dev (changeset: 11135:7c2e5fab809d) and the 2 processor test failed with an error from PetscLogFlops (see error message below). The same configuration file works fine in the the latest release 2.3.3-p6. Not immediately critical, but I need petsc-dev for the PCDMMGDM routines (of which I'm still tracking down a pernicous bug, but am getting close). All help greatly appreciated cheers marc p.s. system is MacOSX 10.4.10, mpich2-1.0.5p4 -------------output of make test---------------------- Running test examples to verify correct installation C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 MPI processes See http://www.mcs.anl.gov/petsc/petsc-as/documentation/ troubleshooting.html lid velocity = 0.0016, prandtl # = 1, grashof # = 1 [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Argument out of range! [0]PETSC ERROR: PetscLogFlops: flop-count given is neagitive: -32.00! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Development Version 2.3.3, Patch 6, unknown HG revision: unknown [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: ./ex19 on a macosx-gn named mingus.home by mspieg Tue Sep 25 23:34:58 2007 [0]PETSC ERROR: Libraries linked from /Applications/petsc/petsc-dev/lib [0]PETSC ERROR: Configure run at Tue Sep 25 23:12:21 2007 [0]PETSC ERROR: Configure options CC=gcc FC=gfortran --with-python -- with-shared=1 --with-dynamic=1 --with-mpi-dir=/Applications/mpich/ mpich2-1.0.5p4 --do [1]PETSC ERROR: --------------------- Error Message ------------------------------------ [1]PETSC ERROR: Argument out of range! [1]PETSC ERROR: PetscLogFlops: flop-count given is neagitive: -84.00! [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: Petsc Development Version 2.3.3, Patch 6, unknown HG revision: unknown [1]PETSC ERROR: See docs/changes/index.html for recent updates. [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [1]PETSC ERROR: See docs/index.html for manual pages. [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: ./ex19 on a macosx-gn named mingus.home by mspieg Tue Sep 25 23:34:58 2007 [1]PETSC ERROR: Libraries linked from /Applications/petsc/petsc-dev/lib [1]PETSC ERROR: Configure run at Tue Sep 25 23:12:21 2007 [1]PETSC ERROR: Configure options CC=gcc FC=gfortran --with-python -- with-shared=1 --with-dynamic=1 --with-mpi-dir=/Applications/mpich/ mpich2-1.0.5p4 --download-mpich-pm=gforker --with-debugging=1 PETSC_ARCH=macosx-gnu-local-g [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: MatMultAdd_SeqMAIJ_4() line 585 in src/mat/impls/maij/ maij.c [0]PETSC ERROR: MatMult_MPIMAIJ_dof() line 2118 in src/mat/impls/maij/ maij.c [0]PETSC ERROR: MatMult() line 1670 in src/mat/interface/matrix.c [0]PETSC ERROR: MatInterpolate() line 5925 in src/mat/interface/matrix.c [0]PETSC ERROR: PCMGFCycle_Private() line 28 in src/ksp/pc/impls/mg/ fmg.c [0]PETSC ERROR: PCApply_MG() line 207 in src/ksp/pc/impls/mg/mg.c [0]PETSC ERROR: PCApply() line 356 in src/ksp/pc/interface/precon.c [0]PETSC ERROR: FGMREScycle() line 232 in src/ksp/ksp/impls/gmres/ fgmres/fgmres.c [0]PETSC ERROR: KSPSolve_FGMRES() line 358 in src/ksp/ksp/impls/gmres/ fgmres/fgmres.c [0]PETSC ERROR: KSPSolve() line 378 in src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: SNES_KSPSolve() line 2539 in src/snes/interface/snes.c [0]PETSC ERROR: SNESSolve_LS() line 184 in src/snes/wnload-mpich- pm=gforker --with-debugging=1 PETSC_ARCH=macosx-gnu-local-g [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: MatMultAdd_SeqMAIJ_4() line 585 in src/mat/impls/maij/ maij.c [1]PETSC ERROR: MatMult_MPIMAIJ_dof() line 2118 in src/mat/impls/maij/ maij.c [1]PETSC ERROR: MatMult() line 1670 in src/mat/interface/matrix.c [1]PETSC ERROR: MatInterpolate() line 5925 in src/mat/interface/matrix.c [1]PETSC ERROR: PCMGFCycle_Private() line 28 in src/ksp/pc/impls/mg/ fmg.c [1]PETSC ERROR: PCApply_MG() line 207 in src/ksp/pc/impls/mg/mg.c [1]PETSC ERROR: PCApply() line 356 in src/ksp/pc/interface/precon.c [1]PETSC ERROR: FGMREScycle() line 232 in src/ksp/ksp/impls/gmres/ fgmres/fgmres.c [1]PETSC ERROR: KSPSolve_FGMRES() line 358 in src/ksp/ksp/impls/gmres/ fgmres/fgmres.c [1]PETSC ERROR: KSPSolve() line 378 in src/ksp/ksp/interface/itfunc.c [1]PETSC ERROR: SNES_KSPSolve() line 2539 in src/snes/interface/snes.c [1]PETSC ERROR: SNESSolve_LS() line 184 in src/snes/impls/ls/ls.c [0]PETSC ERROR: SNESSolve() line 1867 in src/snes/interface/snes.c [0]PETSC ERROR: DMMGSolveSNES() line 510 in src/snes/utils/damgsnes.c [0]PETSC ERROR: DMMGSolve() line 393 in src/snes/utils/damg.c [0]PETSC ERROR: main() line 154 in src/snes/examples/tutorials/ex19.c [cli_0]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 impls/ls/ls.c [1]PETSC ERROR: SNESSolve() line 1867 in src/snes/interface/snes.c [1]PETSC ERROR: DMMGSolveSNES() line 510 in src/snes/utils/damgsnes.c [1]PETSC ERROR: DMMGSolve() line 393 in src/snes/utils/damg.c [1]PETSC ERROR: main() line 154 in src/snes/examples/tutorials/ex19.c [cli_1]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1 Graphics example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process Fortran example src/snes/examples/tutorials/ex5f run successfully with 1 MPI process Completed test examples ---------------------------------------------------- Marc Spiegelman Lamont-Doherty Earth Observatory Dept. of Applied Physics/Applied Math Columbia University http://www.ldeo.columbia.edu/~mspieg ----------------------------------------------------

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Re: Release
by Barry Smith 25 Sep '07

25 Sep '07

On Tue, 25 Sep 2007, Lisandro Dalcin wrote: > On 9/22/07, Matthew Knepley <knepley(a)gmail.com> wrote: > > What do you think about 2.4 in October? I really want to get the new > > install out there.' > > I'm experimenting at home about a way to compile petsc with > '-fstrict-aliasing', in order to follow C99 strict aliasing rules. > However, If I am right, this requiered a new layout for PetscObect's > structure (I basically followed the approach being used for Python > 3.0). As a side effect, some very commonly used struct members (like > 'comm', 'type_name', and 'prefix') have to be accessed by casting > derived objecs as PetscObject, i.e.: Vec v; ((PetscObject)v)->comm. > Please explain in detail. > I have also some problems when calling PetscObjectQueryFunction, as > the compiler complains about strict aliasing rules, and I need to > define an additional function pointer, get the function, and next cast > to the a actual func. pointer to do the call. Not suure yet if this > can be improved, perhaps a macro can help. Yes this function pointer casting stuff is a royal pain and ugly. > > Is there any interest in this be completed? It's a nonsense? Might be easier to just rewrite everything in C++. :-) Barry > In case > you want me to continue this work, I will need a bit of help in a few > places related to low-level calls related to sockets and sys calls. > >

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Re: Release
by Lisandro Dalcin 25 Sep '07

25 Sep '07

On 9/22/07, Matthew Knepley <knepley(a)gmail.com> wrote: > What do you think about 2.4 in October? I really want to get the new > install out there.' I'm experimenting at home about a way to compile petsc with '-fstrict-aliasing', in order to follow C99 strict aliasing rules. However, If I am right, this requiered a new layout for PetscObect's structure (I basically followed the approach being used for Python 3.0). As a side effect, some very commonly used struct members (like 'comm', 'type_name', and 'prefix') have to be accessed by casting derived objecs as PetscObject, i.e.: Vec v; ((PetscObject)v)->comm. I have also some problems when calling PetscObjectQueryFunction, as the compiler complains about strict aliasing rules, and I need to define an additional function pointer, get the function, and next cast to the a actual func. pointer to do the call. Not suure yet if this can be improved, perhaps a macro can help. Is there any interest in this be completed? It's a nonsense? In case you want me to continue this work, I will need a bit of help in a few places related to low-level calls related to sockets and sys calls. -- Lisandro Dalcï¿½n --------------- Centro Internacional de Mï¿½todos Computacionales en Ingenierï¿½a (CIMEC) Instituto de Desarrollo Tecnolï¿½gico para la Industria Quï¿½mica (INTEC) Consejo Nacional de Investigaciones Cientï¿½ficas y Tï¿½cnicas (CONICET) PTLC - Gï¿½emes 3450, (3000) Santa Fe, Argentina Tel/Fax: +54-(0)342-451.1594

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Release
by Matthew Knepley 22 Sep '07

22 Sep '07

What do you think about 2.4 in October? I really want to get the new install out there.' Matt -- 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

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Re: flexible TS implementation for user-defined timestepping
by Lisandro Dalcin 19 Sep '07

19 Sep '07

On 9/18/07, Matthew Knepley <knepley(a)gmail.com> wrote: > I can accept that the user might have to change the function. However, if we > cannot swap methods in the way we can swap KSP or SNES, what is the value > for the user? For me, having a consistent, generic TS interface that just save me to write the time-step loop, and where I can set 'hooks' for pre/post solve/step and make timestep control, it really great. I already have the code completelly defining the complete function/Jacobian (derivative term/mass matrix all included in the inner FEM computation), but then current TS implementations does not support my code, as it is forcing me to setup my problem as it where dU/dt=F(U), and that just does not fit my formulation. I believe other PETSc users solving transient problems have the same problem, and then never used TS and wrote his/her own time-loop. > That is the point I am trying to make. I can see how to do many > FD methods if I have the identity, but see no approach to FEM. So maybe we > can be more specific about: > > a) What class of methods we can support interchangably Perhaps very few, or even none. In specialized FEM formulations, you have to think your time-step problem as a algebraic nonlinear problem, where you need to solve for U^{n+1}, and some space operators are influenced by the time discretization. There are other problems where you just cannot easy guess the way to alleviate the user. Pressure-splitting methods in incompressible CFD have to be solved at each time level with SNES/KSP combinations for momentum and pressure updating. And those formulations are really different to a monolithic, saddle-point like, formulation. So I really doubt we can be able to alleviate all users from having to write the code for advancing solution in each timestep. But TS can provide the time-looping management in a consistent way. > b) What interface is necessary to support these methods At the very high-level, TS would be in charge of doing the time-looping. Particular type implementations should just have to deal on how to update the solution at each time step (not sure if this is possible with some external packages like sundials). Perhaps TS will also need a new inner object (like KSP has PC, or SNES has KSP) to deal with the more low-level details of particular time/space discretizations. As you can see, I do not have (like you) a clear idea of who to define a inteface for this. -- Lisandro Dalcï¿½n --------------- Centro Internacional de Mï¿½todos Computacionales en Ingenierï¿½a (CIMEC) Instituto de Desarrollo Tecnolï¿½gico para la Industria Quï¿½mica (INTEC) Consejo Nacional de Investigaciones Cientï¿½ficas y Tï¿½cnicas (CONICET) PTLC - Gï¿½emes 3450, (3000) Santa Fe, Argentina Tel/Fax: +54-(0)342-451.1594

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Re: flexible TS implementation for user-defined timestepping
by Matthew Knepley 18 Sep '07

18 Sep '07

On 9/18/07, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > > On Tue, 18 Sep 2007, Matthew Knepley wrote: > > > On 9/18/07, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > > > > > I do not see why 1,2, and 3 are incompatiable with an "algebra based" > > > TS level. It just requires a smart design. > > > > 1) I put this in before as TSSetIdentityMatrix() which was the only way I could > > see doing it. That led to problem 2). > > > > 2) If the user gives me some arbitrary matrix, I do not see how to effectively > > combine operations. I have to do everything in series. This is not optimal, > > but might be not bad. However, we through away that method so I thought > > people disapproved. > > > > 3) This requires changing the discretization that the user has in his SNES > > functions. > > Hmmm, maybe this is the key point in our disconnect. I did not envision that > the user could simply take a function they use for SNES and pop it into TS > (somehow) to get a time-stepping algorithm. Nor do I see this is a useful goal. > If the user is doing A nonlinear equation they should use SNES, if they are > solving a differential/algebraic equation they should use TS and never the twain > should meet. (That is one does not graduate up to TS from SNES, in the way > one does not graduate up from KSP to SNES.) I can accept that the user might have to change the function. However, if we cannot swap methods in the way we can swap KSP or SNES, what is the value for the user? That is the point I am trying to make. I can see how to do many FD methods if I have the identity, but see no approach to FEM. So maybe we can be more specific about: a) What class of methods we can support interchangably b) What interface is necessary to support these methods Matt Matt > Barry > > Of course the TS implementations should generally use SNES when possible. > > > > I do not see how to do this without an independent idea of both > > a) his equations and b) his discretization. > > > > I really believe this is not jsut an issue of smart algebraic design, > > and moreover > > I believe that this is exactly why TS has never been written. > > > > Matt > > > > > Barry > > > > > > > > > On Tue, 18 Sep 2007, Matthew Knepley wrote: > > > > > > > On 9/17/07, Matthew Knepley <knepley(a)gmail.com> wrote: > > > > > I think this example demonstrates my major problem with the current TS > > > > > implementation. I have had this problem since I was in grad school. We > > > > > would like to abstract different "methods" like CN for timestepping. This > > > > > is really abstracting the process of temporal discretization, and so far we > > > > > choose finite difference type discretizations. When these are combined > > > > > with FEM in space, this becomes difficult since we have no prescription for > > > > > constructing the operators we might need (like the identity in the FEM > > > > > space). Moreover, even when I added methods allowing the user to specify > > > > > these, the computation is not optimal since the parts are distended. > > > > > > > > Okay "algebra only" crowd, I agree this would be great. However, please address > > > > the two problems I identify in the above paragraph, namely: > > > > > > > > 1) How can you handle user-discretized operators, like the identity, which are > > > > necessary for any of these schemes? > > > > > > > > 2) Even if you get these from the user, how can you efficiently implement the > > > > scheme, since what we really want is assembly of the entire F() at each > > > > timestep (in method of lines)? > > > > > > > > 3) Moreover, how can this scheme ever do spacetime formulations, which are > > > > much better for many problems? > > > > > > > > Matt > > > > > > > > > Matt > > > > > > > > > > On 9/17/07, Lisandro Dalcin <dalcinl(a)gmail.com> wrote: > > > > > > Current TS implementations never fited my needs. Why? My target > > > > > > application is solving incompressible NS equations with FEM and fully > > > > > > implicit schemes (trapezoidal rule with theta in [0.5, 1.0] ) and > > > > > > residual-based stabilization (SUPG/PSPG). Then I need to solve at each > > > > > > time step a nonlinear problem like F(t, u, t0, u0), where F is > > > > > > nonlinear in u. I'm surelly naive, and I could not accomodate my > > > > > > function and Jacobian code for the beuler/cn TS implementations. > > > > > > > > > > > > Futhermore, I've recently convinced some coworkers to take advance of > > > > > > SNES/TS features and my Python wrappers (petsc4py) to manage the the > > > > > > time evolution of some problems related to fluid-structure interaction > > > > > > and mesh movement (formulated as an optimization problem, only nodal > > > > > > positions change, not remeshing needed for many timesteps). > > > > > > > > > > > > In order to support those applications setups, I've wrote a new TS > > > > > > implemetation, which enables users to (almost) completely define the > > > > > > temporal evolution of their problems, with pre/post solve/step > > > > > > methods and support for accept/reject steps and implementing timestep > > > > > > size control. Some of these features are available in some TS types, > > > > > > but not all-in-one. > > > > > > > > > > > > This code is available for review in petsc4py SVN repo (link below), > > > > > > an python example of this in action (very simple, just for testing all > > > > > > is working) is attached. Currently it only support implicit schemes > > > > > > and nonlinear problems, but I believe it can be extended to support > > > > > > explicit schemes and linear problems. > > > > > > > > > > > > http://petsc4py.googlecode.com/svn/trunk/petsc/lib/ext/src/ts/impls/implici… > > > > > > > > > > > > I want to know the opinion of PETSc core developers and potential > > > > > > users ot this, and I hope anyone can provide suggestions for > > > > > > improvements. After that, I can push this to petsc-dev for general > > > > > > availability (in fact, the code is almost ready to be integrated in > > > > > > petsc). > > > > > > > > > > > > Perhaps in the long term, all this can be integrated in the generic TS > > > > > > interface if that is appropriate. Of course, this would require some > > > > > > (I hope minor) changes in TS interface, some additions, and a > > > > > > reimplementation of some default TS types > > > > > > > > > > > > Regards, and I'm waiting for your comments. > > > > > > > > > > > > > > > > > > -- > > > > > > Lisandro Dalcï¿½n > > > > > > --------------- > > > > > > Centro Internacional de Mï¿½todos Computacionales en Ingenierï¿½a (CIMEC) > > > > > > Instituto de Desarrollo Tecnolï¿½gico para la Industria Quï¿½mica (INTEC) > > > > > > Consejo Nacional de Investigaciones Cientï¿½ficas y Tï¿½cnicas (CONICET) > > > > > > PTLC - Gï¿½emes 3450, (3000) Santa Fe, Argentina > > > > > > Tel/Fax: +54-(0)342-451.1594 > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > 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

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Re: flexible TS implementation for user-defined timestepping
by Barry Smith 18 Sep '07

18 Sep '07

On Tue, 18 Sep 2007, Matthew Knepley wrote: > On 9/18/07, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > > > I do not see why 1,2, and 3 are incompatiable with an "algebra based" > > TS level. It just requires a smart design. > > 1) I put this in before as TSSetIdentityMatrix() which was the only way I could > see doing it. That led to problem 2). > > 2) If the user gives me some arbitrary matrix, I do not see how to effectively > combine operations. I have to do everything in series. This is not optimal, > but might be not bad. However, we through away that method so I thought > people disapproved. > > 3) This requires changing the discretization that the user has in his SNES > functions. Hmmm, maybe this is the key point in our disconnect. I did not envision that the user could simply take a function they use for SNES and pop it into TS (somehow) to get a time-stepping algorithm. Nor do I see this is a useful goal. If the user is doing A nonlinear equation they should use SNES, if they are solving a differential/algebraic equation they should use TS and never the twain should meet. (That is one does not graduate up to TS from SNES, in the way one does not graduate up from KSP to SNES.) Barry Of course the TS implementations should generally use SNES when possible. > I do not see how to do this without an independent idea of both > a) his equations and b) his discretization. > > I really believe this is not jsut an issue of smart algebraic design, > and moreover > I believe that this is exactly why TS has never been written. > > Matt > > > Barry > > > > > > On Tue, 18 Sep 2007, Matthew Knepley wrote: > > > > > On 9/17/07, Matthew Knepley <knepley(a)gmail.com> wrote: > > > > I think this example demonstrates my major problem with the current TS > > > > implementation. I have had this problem since I was in grad school. We > > > > would like to abstract different "methods" like CN for timestepping. This > > > > is really abstracting the process of temporal discretization, and so far we > > > > choose finite difference type discretizations. When these are combined > > > > with FEM in space, this becomes difficult since we have no prescription for > > > > constructing the operators we might need (like the identity in the FEM > > > > space). Moreover, even when I added methods allowing the user to specify > > > > these, the computation is not optimal since the parts are distended. > > > > > > Okay "algebra only" crowd, I agree this would be great. However, please address > > > the two problems I identify in the above paragraph, namely: > > > > > > 1) How can you handle user-discretized operators, like the identity, which are > > > necessary for any of these schemes? > > > > > > 2) Even if you get these from the user, how can you efficiently implement the > > > scheme, since what we really want is assembly of the entire F() at each > > > timestep (in method of lines)? > > > > > > 3) Moreover, how can this scheme ever do spacetime formulations, which are > > > much better for many problems? > > > > > > Matt > > > > > > > Matt > > > > > > > > On 9/17/07, Lisandro Dalcin <dalcinl(a)gmail.com> wrote: > > > > > Current TS implementations never fited my needs. Why? My target > > > > > application is solving incompressible NS equations with FEM and fully > > > > > implicit schemes (trapezoidal rule with theta in [0.5, 1.0] ) and > > > > > residual-based stabilization (SUPG/PSPG). Then I need to solve at each > > > > > time step a nonlinear problem like F(t, u, t0, u0), where F is > > > > > nonlinear in u. I'm surelly naive, and I could not accomodate my > > > > > function and Jacobian code for the beuler/cn TS implementations. > > > > > > > > > > Futhermore, I've recently convinced some coworkers to take advance of > > > > > SNES/TS features and my Python wrappers (petsc4py) to manage the the > > > > > time evolution of some problems related to fluid-structure interaction > > > > > and mesh movement (formulated as an optimization problem, only nodal > > > > > positions change, not remeshing needed for many timesteps). > > > > > > > > > > In order to support those applications setups, I've wrote a new TS > > > > > implemetation, which enables users to (almost) completely define the > > > > > temporal evolution of their problems, with pre/post solve/step > > > > > methods and support for accept/reject steps and implementing timestep > > > > > size control. Some of these features are available in some TS types, > > > > > but not all-in-one. > > > > > > > > > > This code is available for review in petsc4py SVN repo (link below), > > > > > an python example of this in action (very simple, just for testing all > > > > > is working) is attached. Currently it only support implicit schemes > > > > > and nonlinear problems, but I believe it can be extended to support > > > > > explicit schemes and linear problems. > > > > > > > > > > http://petsc4py.googlecode.com/svn/trunk/petsc/lib/ext/src/ts/impls/implici… > > > > > > > > > > I want to know the opinion of PETSc core developers and potential > > > > > users ot this, and I hope anyone can provide suggestions for > > > > > improvements. After that, I can push this to petsc-dev for general > > > > > availability (in fact, the code is almost ready to be integrated in > > > > > petsc). > > > > > > > > > > Perhaps in the long term, all this can be integrated in the generic TS > > > > > interface if that is appropriate. Of course, this would require some > > > > > (I hope minor) changes in TS interface, some additions, and a > > > > > reimplementation of some default TS types > > > > > > > > > > Regards, and I'm waiting for your comments. > > > > > > > > > > > > > > > -- > > > > > Lisandro Dalcín > > > > > --------------- > > > > > Centro Internacional de Métodos Computacionales en Ingeniería (CIMEC) > > > > > Instituto de Desarrollo Tecnológico para la Industria Química (INTEC) > > > > > Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) > > > > > PTLC - Güemes 3450, (3000) Santa Fe, Argentina > > > > > Tel/Fax: +54-(0)342-451.1594 > > > > > > > > > > > > > > > > > > > > > > -- > > > > 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 > > > > > > > > > > > > > > > >

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Re: flexible TS implementation for user-defined timestepping
by Matthew Knepley 18 Sep '07

18 Sep '07

On 9/18/07, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > I do not see why 1,2, and 3 are incompatiable with an "algebra based" > TS level. It just requires a smart design. 1) I put this in before as TSSetIdentityMatrix() which was the only way I could see doing it. That led to problem 2). 2) If the user gives me some arbitrary matrix, I do not see how to effectively combine operations. I have to do everything in series. This is not optimal, but might be not bad. However, we through away that method so I thought people disapproved. 3) This requires changing the discretization that the user has in his SNES functions. I do not see how to do this without an independent idea of both a) his equations and b) his discretization. I really believe this is not jsut an issue of smart algebraic design, and moreover I believe that this is exactly why TS has never been written. Matt > Barry > > > On Tue, 18 Sep 2007, Matthew Knepley wrote: > > > On 9/17/07, Matthew Knepley <knepley(a)gmail.com> wrote: > > > I think this example demonstrates my major problem with the current TS > > > implementation. I have had this problem since I was in grad school. We > > > would like to abstract different "methods" like CN for timestepping. This > > > is really abstracting the process of temporal discretization, and so far we > > > choose finite difference type discretizations. When these are combined > > > with FEM in space, this becomes difficult since we have no prescription for > > > constructing the operators we might need (like the identity in the FEM > > > space). Moreover, even when I added methods allowing the user to specify > > > these, the computation is not optimal since the parts are distended. > > > > Okay "algebra only" crowd, I agree this would be great. However, please address > > the two problems I identify in the above paragraph, namely: > > > > 1) How can you handle user-discretized operators, like the identity, which are > > necessary for any of these schemes? > > > > 2) Even if you get these from the user, how can you efficiently implement the > > scheme, since what we really want is assembly of the entire F() at each > > timestep (in method of lines)? > > > > 3) Moreover, how can this scheme ever do spacetime formulations, which are > > much better for many problems? > > > > Matt > > > > > Matt > > > > > > On 9/17/07, Lisandro Dalcin <dalcinl(a)gmail.com> wrote: > > > > Current TS implementations never fited my needs. Why? My target > > > > application is solving incompressible NS equations with FEM and fully > > > > implicit schemes (trapezoidal rule with theta in [0.5, 1.0] ) and > > > > residual-based stabilization (SUPG/PSPG). Then I need to solve at each > > > > time step a nonlinear problem like F(t, u, t0, u0), where F is > > > > nonlinear in u. I'm surelly naive, and I could not accomodate my > > > > function and Jacobian code for the beuler/cn TS implementations. > > > > > > > > Futhermore, I've recently convinced some coworkers to take advance of > > > > SNES/TS features and my Python wrappers (petsc4py) to manage the the > > > > time evolution of some problems related to fluid-structure interaction > > > > and mesh movement (formulated as an optimization problem, only nodal > > > > positions change, not remeshing needed for many timesteps). > > > > > > > > In order to support those applications setups, I've wrote a new TS > > > > implemetation, which enables users to (almost) completely define the > > > > temporal evolution of their problems, with pre/post solve/step > > > > methods and support for accept/reject steps and implementing timestep > > > > size control. Some of these features are available in some TS types, > > > > but not all-in-one. > > > > > > > > This code is available for review in petsc4py SVN repo (link below), > > > > an python example of this in action (very simple, just for testing all > > > > is working) is attached. Currently it only support implicit schemes > > > > and nonlinear problems, but I believe it can be extended to support > > > > explicit schemes and linear problems. > > > > > > > > http://petsc4py.googlecode.com/svn/trunk/petsc/lib/ext/src/ts/impls/implici… > > > > > > > > I want to know the opinion of PETSc core developers and potential > > > > users ot this, and I hope anyone can provide suggestions for > > > > improvements. After that, I can push this to petsc-dev for general > > > > availability (in fact, the code is almost ready to be integrated in > > > > petsc). > > > > > > > > Perhaps in the long term, all this can be integrated in the generic TS > > > > interface if that is appropriate. Of course, this would require some > > > > (I hope minor) changes in TS interface, some additions, and a > > > > reimplementation of some default TS types > > > > > > > > Regards, and I'm waiting for your comments. > > > > > > > > > > > > -- > > > > Lisandro Dalcï¿½n > > > > --------------- > > > > Centro Internacional de Mï¿½todos Computacionales en Ingenierï¿½a (CIMEC) > > > > Instituto de Desarrollo Tecnolï¿½gico para la Industria Quï¿½mica (INTEC) > > > > Consejo Nacional de Investigaciones Cientï¿½ficas y Tï¿½cnicas (CONICET) > > > > PTLC - Gï¿½emes 3450, (3000) Santa Fe, Argentina > > > > Tel/Fax: +54-(0)342-451.1594 > > > > > > > > > > > > > > > > > -- > > > 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

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