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

Re: [petsc-dev] The problem about running an example in PETSc
by Jed Brown 30 Apr '13

30 Apr '13

Please always use "reply-all" so that your messages go to the list. Lulu Liu <lulu.liu(a)kaust.edu.sa> writes: > ierr = DMDACreate(comm, da);CHKERRQ(ierr); > ierr = DMDASetDim(*da, 3);CHKERRQ(ierr); // <-- fix this > line Why do we fix this line? Just pass 'dim' so that it works for any dimension. > ierr = DMDASetSizes(*da, M, N, P);CHKERRQ(ierr); I think that we should > fix this line... > > The error shown like: > > Partition in x direction is too fine! -6 1! Hmm, that error should only be able to occur before the DM is set up. M should be positive after setup. > ierr = DMDASetNumProcs(*da, m, n, p);CHKERRQ(ierr); > ierr = DMDASetBoundaryType(*da, bx, by, bz);CHKERRQ(ierr); > ierr = DMDASetDof(*da, dof);CHKERRQ(ierr); > ierr = DMDASetStencilType(*da, stencil_type);CHKERRQ(ierr); > ierr = DMDASetStencilWidth(*da, s);CHKERRQ(ierr); > ierr = DMDASetOwnershipRanges(*da, lx, ly, lz);CHKERRQ(ierr); > /* This violates the behavior for other classes, but right now users > expect negative dimensions to be handled this way */ > ierr = DMSetFromOptions(*da);CHKERRQ(ierr); // <--- delete > this > ierr = DMSetUp(*da);CHKERRQ(ierr); > ierr = DMViewFromOptions(*da,"-dm_view");CHKERRQ(ierr); // <--- delete > or set a prefix > > > On Tue, Apr 30, 2013 at 9:20 PM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > >> Lulu Liu <lulu.liu(a)kaust.edu.sa> writes: >> >> > src/ts/examples/tutorials/ex29.c I want domain partition is 1x2 >> > >> > mpiexec -n 2 ./ex29 -da_refine 4 -ts_max_steps 10 -ts_rtol 1e-3 -ts_atol >> > 1e-3 -ts_type arkimex -ts_monitor -snes_monitor -snes_type ngmres >> > -npc_snes_type nasm -npc_snes_nasm_type restrict -da_overlap 4 >> > -da_processors_x 1 -da_processors_y 2 >> >> Thanks for sending the command to reproduce. >> >> > 0 TS dt 0.05 time 0 >> > 0 SNES Function norm 1.762942085583e+01 >> > [0]PETSC ERROR: --------------------- Error Message >> > ------------------------------------ >> > [0]PETSC ERROR: Argument out of range! >> > [0]PETSC ERROR: Too many processors in Y direction: 2 1! >> > [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message >> > ------------------------------------ >> > [1]PETSC ERROR: Argument out of range! >> > [1]PETSC ERROR: Too many processors in Y direction: 2 1! >> > [1]PETSC ERROR: >> > ------------------------------------------------------------------------ >> > [1]PETSC ERROR: Petsc Development GIT revision: >> > bc51b945dfb4f1d1228fb677a132a806066a0f32 GIT Date: 2013-04-29 10:22:29 >> > -0500 >> > ------------------------------------------------------------------------ >> > [0]PETSC ERROR: Petsc Development GIT revision: >> > bc51b945dfb4f1d1228fb677a132a806066a0f32 GIT Date: 2013-04-29 10:22:29 >> > -0500 >> > [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: ./ex29 on a arch-basic named kl-12681.local by liul Tue >> Apr >> > 30 21:07:37 2013 >> > [0]PETSC ERROR: [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: ./ex29 on a arch-basic named kl-12681.local by liul Tue >> Apr >> > 30 21:07:37 2013 >> > [1]PETSC ERROR: Libraries linked from >> /Users/liul/soft/petsc/arch-basic/lib >> > [1]PETSC ERROR: Configure run at Tue Apr 30 15:46:16 2013 >> > [1]PETSC ERROR: Configure options --download-cmake >> --download-f-blas-lapack >> > --download-mpich --with-cc=gcc --with-fc=gfortran PETSC_ARCH=arch-basic >> > [1]PETSC ERROR: >> > ------------------------------------------------------------------------ >> > [1]PETSC ERROR: Libraries linked from >> /Users/liul/soft/petsc/arch-basic/lib >> > [0]PETSC ERROR: Configure run at Tue Apr 30 15:46:16 2013 >> > [0]PETSC ERROR: Configure options --download-cmake >> --download-f-blas-lapack >> > --download-mpich --with-cc=gcc --with-fc=gfortran PETSC_ARCH=arch-basic >> > [0]PETSC ERROR: >> > ------------------------------------------------------------------------ >> > [0]PETSC ERROR: DMSetUp_DA_2D() line 266 in >> > /Users/liul/soft/petsc/src/dm/impls/da/da2.c >> > DMSetUp_DA_2D() line 266 in /Users/liul/soft/petsc/src/dm/impls/da/da2.c >> > [1]PETSC ERROR: DMSetUp_DA() line 27 in >> > /Users/liul/soft/petsc/src/dm/impls/da/dareg.c >> > [1]PETSC ERROR: DMSetUp() line 469 in >> > /Users/liul/soft/petsc/src/dm/interface/dm.c >> > [1]PETSC ERROR: DMDACreate2d() line 888 in >> > /Users/liul/soft/petsc/src/dm/impls/da/da2.c >> > [1]PETSC ERROR: [0]PETSC ERROR: DMSetUp_DA() line 27 in >> > /Users/liul/soft/petsc/src/dm/impls/da/dareg.c >> > [0]PETSC ERROR: DMSetUp() line 469 in >> > /Users/liul/soft/petsc/src/dm/interface/dm.c >> > DMDAGetReducedDMDA() line 389 in >> > /Users/liul/soft/petsc/src/dm/impls/da/dacorn.c >> > [1]PETSC ERROR: CoefficientSubDomainRestrictHook() line 92 in >> > src/ts/examples/tutorials/ex29.c >> > [1]PETSC ERROR: DMCreateDomainDecomposition() line 1314 in >> > /Users/liul/soft/petsc/src/dm/interface/dm.c >> > [1]PETSC ERROR: SNESSetUp_NASM() line 112 in >> > /Users/liul/soft/petsc/src/snes/impls/nasm/nasm.c >> > [1]PETSC ERROR: SNESSetUp() line 2633 in >> > /Users/liul/soft/petsc/src/snes/interface/snes.c >> > [0]PETSC ERROR: DMDACreate2d() line 888 in >> > /Users/liul/soft/petsc/src/dm/impls/da/da2.c >> > [0]PETSC ERROR: DMDAGetReducedDMDA() line 389 in >> > /Users/liul/soft/petsc/src/dm/impls/da/dacorn.c >> >> if (dim == 1) { >> ierr = >> DMDACreate1d(PetscObjectComm((PetscObject)da),bx,M,nfields,s,dd->lx,nda);CHKERRQ(ierr); >> } else if (dim == 2) { >> ierr = >> DMDACreate2d(PetscObjectComm((PetscObject)da),bx,by,stencil_type,M,N,m,n,nfields,s,lx,ly,nda);CHKERRQ(ierr); >> } else if (dim == 3) { >> ierr = >> DMDACreate3d(PetscObjectComm((PetscObject)da),bx,by,bz,stencil_type,M,N,P,m,n,p,nfields,s,lx,ly,lz,nda);CHKERRQ(ierr); >> } >> >> This code should be fixed to use the precise API instead of the >> convenience routines DMDACreate*d(), so that it does NOT call >> DMSetFromOptions (or if it does, call it after setting a prefix). >> >> Lulu, would you be up for taking a crack at this and submitting a patch? >> Just take the sequence of calls found in DMDACreate3d: >> >> ierr = DMDACreate(comm, da);CHKERRQ(ierr); >> ierr = DMDASetDim(*da, 3);CHKERRQ(ierr); // <-- fix >> this line >> ierr = DMDASetSizes(*da, M, N, P);CHKERRQ(ierr); >> ierr = DMDASetNumProcs(*da, m, n, p);CHKERRQ(ierr); >> ierr = DMDASetBoundaryType(*da, bx, by, bz);CHKERRQ(ierr); >> ierr = DMDASetDof(*da, dof);CHKERRQ(ierr); >> ierr = DMDASetStencilType(*da, stencil_type);CHKERRQ(ierr); >> ierr = DMDASetStencilWidth(*da, s);CHKERRQ(ierr); >> ierr = DMDASetOwnershipRanges(*da, lx, ly, lz);CHKERRQ(ierr); >> /* This violates the behavior for other classes, but right now users >> expect negative dimensions to be handled this way */ >> ierr = DMSetFromOptions(*da);CHKERRQ(ierr); // <--- delete >> this >> ierr = DMSetUp(*da);CHKERRQ(ierr); >> ierr = DMViewFromOptions(*da,"-dm_view");CHKERRQ(ierr); // <--- delete >> or set a prefix >> >> I can help if you get stuck. >> >> https://bitbucket.org/petsc/petsc/wiki/Home >> > > > > -- > Best wishes, > Lulu Liu > Applied Mathematics and Computational Science > King Abdullah University of Science and Technology > Tel：＋966－0544701599 > > -- > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email.

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Re: [petsc-dev] The problem about running an example in PETSc
by Jed Brown 30 Apr '13

30 Apr '13

Lulu Liu <lulu.liu(a)kaust.edu.sa> writes: > src/ts/examples/tutorials/ex29.c I want domain partition is 1x2 > > mpiexec -n 2 ./ex29 -da_refine 4 -ts_max_steps 10 -ts_rtol 1e-3 -ts_atol > 1e-3 -ts_type arkimex -ts_monitor -snes_monitor -snes_type ngmres > -npc_snes_type nasm -npc_snes_nasm_type restrict -da_overlap 4 > -da_processors_x 1 -da_processors_y 2 Thanks for sending the command to reproduce. > 0 TS dt 0.05 time 0 > 0 SNES Function norm 1.762942085583e+01 > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Argument out of range! > [0]PETSC ERROR: Too many processors in Y direction: 2 1! > [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [1]PETSC ERROR: Argument out of range! > [1]PETSC ERROR: Too many processors in Y direction: 2 1! > [1]PETSC ERROR: > ------------------------------------------------------------------------ > [1]PETSC ERROR: Petsc Development GIT revision: > bc51b945dfb4f1d1228fb677a132a806066a0f32 GIT Date: 2013-04-29 10:22:29 > -0500 > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Development GIT revision: > bc51b945dfb4f1d1228fb677a132a806066a0f32 GIT Date: 2013-04-29 10:22:29 > -0500 > [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: ./ex29 on a arch-basic named kl-12681.local by liul Tue Apr > 30 21:07:37 2013 > [0]PETSC ERROR: [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: ./ex29 on a arch-basic named kl-12681.local by liul Tue Apr > 30 21:07:37 2013 > [1]PETSC ERROR: Libraries linked from /Users/liul/soft/petsc/arch-basic/lib > [1]PETSC ERROR: Configure run at Tue Apr 30 15:46:16 2013 > [1]PETSC ERROR: Configure options --download-cmake --download-f-blas-lapack > --download-mpich --with-cc=gcc --with-fc=gfortran PETSC_ARCH=arch-basic > [1]PETSC ERROR: > ------------------------------------------------------------------------ > [1]PETSC ERROR: Libraries linked from /Users/liul/soft/petsc/arch-basic/lib > [0]PETSC ERROR: Configure run at Tue Apr 30 15:46:16 2013 > [0]PETSC ERROR: Configure options --download-cmake --download-f-blas-lapack > --download-mpich --with-cc=gcc --with-fc=gfortran PETSC_ARCH=arch-basic > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: DMSetUp_DA_2D() line 266 in > /Users/liul/soft/petsc/src/dm/impls/da/da2.c > DMSetUp_DA_2D() line 266 in /Users/liul/soft/petsc/src/dm/impls/da/da2.c > [1]PETSC ERROR: DMSetUp_DA() line 27 in > /Users/liul/soft/petsc/src/dm/impls/da/dareg.c > [1]PETSC ERROR: DMSetUp() line 469 in > /Users/liul/soft/petsc/src/dm/interface/dm.c > [1]PETSC ERROR: DMDACreate2d() line 888 in > /Users/liul/soft/petsc/src/dm/impls/da/da2.c > [1]PETSC ERROR: [0]PETSC ERROR: DMSetUp_DA() line 27 in > /Users/liul/soft/petsc/src/dm/impls/da/dareg.c > [0]PETSC ERROR: DMSetUp() line 469 in > /Users/liul/soft/petsc/src/dm/interface/dm.c > DMDAGetReducedDMDA() line 389 in > /Users/liul/soft/petsc/src/dm/impls/da/dacorn.c > [1]PETSC ERROR: CoefficientSubDomainRestrictHook() line 92 in > src/ts/examples/tutorials/ex29.c > [1]PETSC ERROR: DMCreateDomainDecomposition() line 1314 in > /Users/liul/soft/petsc/src/dm/interface/dm.c > [1]PETSC ERROR: SNESSetUp_NASM() line 112 in > /Users/liul/soft/petsc/src/snes/impls/nasm/nasm.c > [1]PETSC ERROR: SNESSetUp() line 2633 in > /Users/liul/soft/petsc/src/snes/interface/snes.c > [0]PETSC ERROR: DMDACreate2d() line 888 in > /Users/liul/soft/petsc/src/dm/impls/da/da2.c > [0]PETSC ERROR: DMDAGetReducedDMDA() line 389 in > /Users/liul/soft/petsc/src/dm/impls/da/dacorn.c if (dim == 1) { ierr = DMDACreate1d(PetscObjectComm((PetscObject)da),bx,M,nfields,s,dd->lx,nda);CHKERRQ(ierr); } else if (dim == 2) { ierr = DMDACreate2d(PetscObjectComm((PetscObject)da),bx,by,stencil_type,M,N,m,n,nfields,s,lx,ly,nda);CHKERRQ(ierr); } else if (dim == 3) { ierr = DMDACreate3d(PetscObjectComm((PetscObject)da),bx,by,bz,stencil_type,M,N,P,m,n,p,nfields,s,lx,ly,lz,nda);CHKERRQ(ierr); } This code should be fixed to use the precise API instead of the convenience routines DMDACreate*d(), so that it does NOT call DMSetFromOptions (or if it does, call it after setting a prefix). Lulu, would you be up for taking a crack at this and submitting a patch? Just take the sequence of calls found in DMDACreate3d: ierr = DMDACreate(comm, da);CHKERRQ(ierr); ierr = DMDASetDim(*da, 3);CHKERRQ(ierr); // <-- fix this line ierr = DMDASetSizes(*da, M, N, P);CHKERRQ(ierr); ierr = DMDASetNumProcs(*da, m, n, p);CHKERRQ(ierr); ierr = DMDASetBoundaryType(*da, bx, by, bz);CHKERRQ(ierr); ierr = DMDASetDof(*da, dof);CHKERRQ(ierr); ierr = DMDASetStencilType(*da, stencil_type);CHKERRQ(ierr); ierr = DMDASetStencilWidth(*da, s);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(*da, lx, ly, lz);CHKERRQ(ierr); /* This violates the behavior for other classes, but right now users expect negative dimensions to be handled this way */ ierr = DMSetFromOptions(*da);CHKERRQ(ierr); // <--- delete this ierr = DMSetUp(*da);CHKERRQ(ierr); ierr = DMViewFromOptions(*da,"-dm_view");CHKERRQ(ierr); // <--- delete or set a prefix I can help if you get stuck. https://bitbucket.org/petsc/petsc/wiki/Home

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The problem about running an example in PETSc
by Lulu Liu 30 Apr '13

30 Apr '13

src/ts/examples/tutorials/ex29.c I want domain partition is 1x2 mpiexec -n 2 ./ex29 -da_refine 4 -ts_max_steps 10 -ts_rtol 1e-3 -ts_atol 1e-3 -ts_type arkimex -ts_monitor -snes_monitor -snes_type ngmres -npc_snes_type nasm -npc_snes_nasm_type restrict -da_overlap 4 -da_processors_x 1 -da_processors_y 2 0 TS dt 0.05 time 0 0 SNES Function norm 1.762942085583e+01 [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Argument out of range! [0]PETSC ERROR: Too many processors in Y direction: 2 1! [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message ------------------------------------ [1]PETSC ERROR: Argument out of range! [1]PETSC ERROR: Too many processors in Y direction: 2 1! [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: Petsc Development GIT revision: bc51b945dfb4f1d1228fb677a132a806066a0f32 GIT Date: 2013-04-29 10:22:29 -0500 ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Development GIT revision: bc51b945dfb4f1d1228fb677a132a806066a0f32 GIT Date: 2013-04-29 10:22:29 -0500 [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: ./ex29 on a arch-basic named kl-12681.local by liul Tue Apr 30 21:07:37 2013 [0]PETSC ERROR: [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: ./ex29 on a arch-basic named kl-12681.local by liul Tue Apr 30 21:07:37 2013 [1]PETSC ERROR: Libraries linked from /Users/liul/soft/petsc/arch-basic/lib [1]PETSC ERROR: Configure run at Tue Apr 30 15:46:16 2013 [1]PETSC ERROR: Configure options --download-cmake --download-f-blas-lapack --download-mpich --with-cc=gcc --with-fc=gfortran PETSC_ARCH=arch-basic [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: Libraries linked from /Users/liul/soft/petsc/arch-basic/lib [0]PETSC ERROR: Configure run at Tue Apr 30 15:46:16 2013 [0]PETSC ERROR: Configure options --download-cmake --download-f-blas-lapack --download-mpich --with-cc=gcc --with-fc=gfortran PETSC_ARCH=arch-basic [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: DMSetUp_DA_2D() line 266 in /Users/liul/soft/petsc/src/dm/impls/da/da2.c DMSetUp_DA_2D() line 266 in /Users/liul/soft/petsc/src/dm/impls/da/da2.c [1]PETSC ERROR: DMSetUp_DA() line 27 in /Users/liul/soft/petsc/src/dm/impls/da/dareg.c [1]PETSC ERROR: DMSetUp() line 469 in /Users/liul/soft/petsc/src/dm/interface/dm.c [1]PETSC ERROR: DMDACreate2d() line 888 in /Users/liul/soft/petsc/src/dm/impls/da/da2.c [1]PETSC ERROR: [0]PETSC ERROR: DMSetUp_DA() line 27 in /Users/liul/soft/petsc/src/dm/impls/da/dareg.c [0]PETSC ERROR: DMSetUp() line 469 in /Users/liul/soft/petsc/src/dm/interface/dm.c DMDAGetReducedDMDA() line 389 in /Users/liul/soft/petsc/src/dm/impls/da/dacorn.c [1]PETSC ERROR: CoefficientSubDomainRestrictHook() line 92 in src/ts/examples/tutorials/ex29.c [1]PETSC ERROR: DMCreateDomainDecomposition() line 1314 in /Users/liul/soft/petsc/src/dm/interface/dm.c [1]PETSC ERROR: SNESSetUp_NASM() line 112 in /Users/liul/soft/petsc/src/snes/impls/nasm/nasm.c [1]PETSC ERROR: SNESSetUp() line 2633 in /Users/liul/soft/petsc/src/snes/interface/snes.c [0]PETSC ERROR: DMDACreate2d() line 888 in /Users/liul/soft/petsc/src/dm/impls/da/da2.c [0]PETSC ERROR: DMDAGetReducedDMDA() line 389 in /Users/liul/soft/petsc/src/dm/impls/da/dacorn.c [0]PETSC ERROR: CoefficientSubDomainRestrictHook() line 92 in src/ts/examples/tutorials/ex29.c [0]PETSC ERROR: [1]PETSC ERROR: SNESSolve() line 3743 in /Users/liul/soft/petsc/src/snes/interface/snes.c [1]PETSC ERROR: SNESSolve_NGMRES() line 249 in /Users/liul/soft/petsc/src/snes/impls/ngmres/snesngmres.c [1]PETSC ERROR: SNESSolve() line 3755 in /Users/liul/soft/petsc/src/snes/interface/snes.c [1]PETSC ERROR: TSStep_ARKIMEX() line 765 in /Users/liul/soft/petsc/src/ts/impls/arkimex/arkimex.c [1]PETSC ERROR: TSStep() line 2457 in /Users/liul/soft/petsc/src/ts/interface/ts.c [1]PETSC ERROR: TSSolve() line 2584 in /Users/liul/soft/petsc/src/ts/interface/ts.c [1]PETSC ERROR: main() line 163 in src/ts/examples/tutorials/ex29.c DMCreateDomainDecomposition() line 1314 in /Users/liul/soft/petsc/src/dm/interface/dm.c [0]PETSC ERROR: SNESSetUp_NASM() line 112 in /Users/liul/soft/petsc/src/snes/impls/nasm/nasm.c [0]PETSC ERROR: SNESSetUp() line 2633 in /Users/liul/soft/petsc/src/snes/interface/snes.c [0]PETSC ERROR: SNESSolve() line 3743 in /Users/liul/soft/petsc/src/snes/interface/snes.c [0]PETSC ERROR: SNESSolve_NGMRES() line 249 in /Users/liul/soft/petsc/src/snes/impls/ngmres/snesngmres.c [0]PETSC ERROR: SNESSolve() line 3755 in /Users/liul/soft/petsc/src/snes/interface/snes.c [0]PETSC ERROR: application called MPI_Abort(MPI_COMM_WORLD, 63) - process 1 [cli_1]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 63) - process 1 TSStep_ARKIMEX() line 765 in /Users/liul/soft/petsc/src/ts/impls/arkimex/arkimex.c [0]PETSC ERROR: TSStep() line 2457 in /Users/liul/soft/petsc/src/ts/interface/ts.c [0]PETSC ERROR: TSSolve() line 2584 in /Users/liul/soft/petsc/src/ts/interface/ts.c [0]PETSC ERROR: main() line 163 in src/ts/examples/tutorials/ex29.c application called MPI_Abort(MPI_COMM_WORLD, 63) - process 0 [cli_0]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 63) - process 0 -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Re: [petsc-dev] Example src/snes/tutorials/examples/ex15.c
by Jed Brown 29 Apr '13

29 Apr '13

Travis Austin <austin(a)txcorp.com> writes: > Hi, > > I've been trying to build/link src/snes/tutorials/examples/ex15.c for src/snes/examples/tutorials/ex15.c > the case that I have defined 'clanguage' to be C++ on the configure > line. I get the following error: > > Undefined symbols for architecture x86_64: > "SNESPicardComputeFunction(_p_SNES*, _p_Vec*, _p_Vec*, void*)", > referenced from: > _main in ex15.o "SNESPicardComputeJacobian(_p_SNES*, _p_Vec*, > _p_Mat**, _p_Mat**, MatStructure*, void*)", referenced from: > _main in ex15.o ld: symbol(s) not found for architecture x86_64 > collect2: ld returned 1 exit status make: [ex15] Error 1 (ignored) > /bin/rm -f ex15.o Thanks for the report. The actual problem here is that we're not defining this interface in a header because we _don't_ want it to be used. The right fix is to clean up the implementation so that DMDASNESSetPicardLocal is all the user needs to call.

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Example src/snes/tutorials/examples/ex15.c
by Travis Austin 29 Apr '13

29 Apr '13

Hi, I've been trying to build/link src/snes/tutorials/examples/ex15.c for the case that I have defined 'clanguage' to be C++ on the configure line. I get the following error: Undefined symbols for architecture x86_64: "SNESPicardComputeFunction(_p_SNES*, _p_Vec*, _p_Vec*, void*)", referenced from: _main in ex15.o "SNESPicardComputeJacobian(_p_SNES*, _p_Vec*, _p_Mat**, _p_Mat**, MatStructure*, void*)", referenced from: _main in ex15.o ld: symbol(s) not found for architecture x86_64 collect2: ld returned 1 exit status make: [ex15] Error 1 (ignored) /bin/rm -f ex15.o The error appears related to name mangling and can be fixed if I add: extern "C" { extern PetscErrorCode SNESPicardComputeFunction(SNES,Vec,Vec,void*); extern PetscErrorCode SNESPicardComputeJacobian(SNES,Vec,Mat*,Mat*,MatStructure*,void*); } to the top of src/snes/tutorials/examples/ex15.c. Note that this error does not occur if building PETSc with default settings where the C compiler is used to build the library and the example. Thanks, Travis =============================== Travis Austin, Ph.D VP, Computational Mathematics Tech-X Corporation 5621 Arapahoe Ave Boulder, CO 80303 austin(a)txcorp.com ===============================

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Re: [petsc-dev] build problem with suitesparse 4.2
by Chaffra Affouda 26 Apr '13

26 Apr '13

On 04/24/2013 06:28 PM, Satish Balay wrote: > On Wed, 24 Apr 2013, Chaffra Affouda wrote: > >> Hello, >> >> I am getting the attached error when building with the latest suitesparse on >> ubuntu (suitesparse 4.2). I think umfpack examples must be linked with >> libcholmod.so but I might be mistaking. I am building on ubuntu precise > > --with-umfpack=1 --with-umfpack-include=/usr/include/suitesparse --with-umfpack-lib="[/usr/lib/libumfpack.so,/usr/lib/libamd.so]" --with-cholmod=1 --with-cholmod-include=/usr/include/suitesparse --with-cholmod-lib=/usr/lib/libcholmod.so > > --with-umfpack-lib=['/usr/lib/libumfpack.so', '/usr/lib/libamd.so'] and > --with-umfpack-include=['/usr/include/suitesparse'] did not work > <<< > > Possible ERROR while running linker: /usr/lib/libumfpack.so: undefined reference to `cholmod_l_print_common' > /usr/lib/libumfpack.so: undefined reference to `cholmod_l_analyze' > /usr/lib/libumfpack.so: undefined reference to `cholmod_l_finish' > /usr/lib/libumfpack.so: undefined reference to `cholmod_l_free_factor' > > > How about just using: --with-umfpack=1 --with-cholmod=1 [and not > specifying the includes/libs - and let configure figure this out from > its default configs] > > Satish > > That did not work because configure is asking for the path to the libraries. However I solved it by linking umfpack to cholmod. Thanks, Chaffra

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Re: [petsc-dev] MPI_UNSIGNED_LONG_LONG in mpiuni.h
by Satish Balay 25 Apr '13

25 Apr '13

On Thu, 25 Apr 2013, Chetan Jhurani wrote: > > -----Original Message----- > > From: Satish Balay [mailto:[email protected]] > > Sent: Thursday, April 25, 2013 8:50 PM > > To: Jed Brown > > Cc: Chetan Jhurani; 'For users of the development version of PETSc' > > Subject: Re: [petsc-dev] MPI_UNSIGNED_LONG_LONG in mpiuni.h > > > > On Thu, 25 Apr 2013, Jed Brown wrote: > > > > > Satish Balay <balay(a)mcs.anl.gov> writes: > > > > > > > It won't get used in PETSc unless PETSC_SIZEOF_LONG_LONG is defined > > > > [which is only for 64bit compilers that support 'long long' anyway. > > > > > > Yes, that sounds fine to me. > > > > Its in next now. > > > > https://bitbucket.org/petsc/petsc/commits/bc791515d821cb389576c2ca1dfa0b0e2… > > > > Satish > > Thanks! Also, thanks for preemptively fixing the strstr issue. > I was about to email about the crash. yeah - I saw that when testing the mpiuni fix on win64. Satish

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Re: [petsc-dev] MPI_UNSIGNED_LONG_LONG in mpiuni.h
by Chetan Jhurani 25 Apr '13

25 Apr '13

> -----Original Message----- > From: Satish Balay [mailto:[email protected]] > Sent: Thursday, April 25, 2013 8:50 PM > To: Jed Brown > Cc: Chetan Jhurani; 'For users of the development version of PETSc' > Subject: Re: [petsc-dev] MPI_UNSIGNED_LONG_LONG in mpiuni.h > > On Thu, 25 Apr 2013, Jed Brown wrote: > > > Satish Balay <balay(a)mcs.anl.gov> writes: > > > > > It won't get used in PETSc unless PETSC_SIZEOF_LONG_LONG is defined > > > [which is only for 64bit compilers that support 'long long' anyway. > > > > Yes, that sounds fine to me. > > Its in next now. > > https://bitbucket.org/petsc/petsc/commits/bc791515d821cb389576c2ca1dfa0b0e2… > > Satish Thanks! Also, thanks for preemptively fixing the strstr issue. I was about to email about the crash. Chetan

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Re: [petsc-dev] MPI_UNSIGNED_LONG_LONG in mpiuni.h
by Satish Balay 25 Apr '13

25 Apr '13

On Thu, 25 Apr 2013, Jed Brown wrote: > Satish Balay <balay(a)mcs.anl.gov> writes: > > > It won't get used in PETSc unless PETSC_SIZEOF_LONG_LONG is defined > > [which is only for 64bit compilers that support 'long long' anyway. > > Yes, that sounds fine to me. Its in next now. https://bitbucket.org/petsc/petsc/commits/bc791515d821cb389576c2ca1dfa0b0e2… satish

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Re: [petsc-dev] usage of string.h
by Satish Balay 25 Apr '13

25 Apr '13

pushed fix to next. https://bitbucket.org/petsc/petsc/commits/6ce87071a70dc571b20c8dec584cf34b3… satish On Thu, 25 Apr 2013, Satish Balay wrote: > I see the usage of string.h is removed from petsc sources. > > https://bitbucket.org/petsc/petsc/commits/b083e2b6e0be6f731fe9e787c55cf4647… > https://bitbucket.org/petsc/petsc/commits/573b0fb4b27458e353e9b121e629dc5c6… > > The remove of strings.h from str.c is added back in > https://bitbucket.org/petsc/petsc/commits/3964eb8815a373d98cd54ebd45324cfa2… > > Now I see a breakage in windows64 build with strstr() [usded in str.c] > - fixable by adding back string.h > > Is this the correct fix? Whats the intention of remove these includes? > > thanks, > Satish >

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