Ok thank you very much yet again! Adoni
On 11 November 2013 12:49, Matthew Knepley <[email protected]> wrote: > On Mon, Nov 11, 2013 at 6:47 AM, Anthony Vergottis > <[email protected]>wrote: > >> I would also like to ask as I have some confusion. Are the DM objects >> capable of handling all aspects of the parallel computations within a given >> problem? >> >> Let me elaborate - for example if I am passing a mesh structure >> (triangular 3 node elements) as the following: >> >> Elem 0: N1 N5 N6 >> etc..... >> where N# is the node tag. >> >> into a DM object and then perform a decomposition for as many processes I >> required. When the mesh partitions are distributed to their processes do I >> then have the ability by using DM objects or something else built into >> PETSc to compute specific calculations on each process without the need to >> hardcode any MPI? >> > > I believe the answer is yes. I could be more specific with a concrete > example. For instance, the DM can > calculate a parallel residual without the user ever seeing MPI. > > Matt > > >> I hope I have explained this well. >> >> Thanks again. >> Adoni >> >> >> On 11 November 2013 12:33, Anthony Vergottis <[email protected]>wrote: >> >>> Thanks mate that worked! >>> >>> Thanks. >>> Adoni >>> >>> >>> >>> On 11 November 2013 12:29, Matthew Knepley <[email protected]> wrote: >>> >>>> On Mon, Nov 11, 2013 at 6:25 AM, Anthony Vergottis < >>>> [email protected]> wrote: >>>> >>>>> I compile ex12 but when I run the program I get this in the terminal. >>>>> >>>> >>>> I guess I should make better defaults. Here are the runs I use for ex12: >>>> >>>> >>>> https://bitbucket.org/petsc/petsc/src/a965ca046084fa53248a41da989a0a62cb6266ea/config/builder.py?at=master#cl-180 >>>> >>>> You can see that the problem here is that the -petscspace_order has not >>>> been set. So to test P_1 I use >>>> >>>> -run_type test -refinement_limit 0.0 -bc_type dirichlet -interpolate >>>> 0 -petscspace_order 1 -show_initial -dm_plex_print_fem 1 >>>> >>>> and then take away run_type (or use full) to solve the problem. SNES >>>> ex62 is the Stokes problem, and run parameters are >>>> in the same place. >>>> >>>> Thanks, >>>> >>>> Matt >>>> >>>> >>>>> adoni@Adoni:~/Desktop/petsc-lat/src/snes/examples/tutorials$ make ex12 >>>>> /home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/bin/mpicxx -o ex12.o >>>>> -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g >>>>> -fPIC -I/home/adoni/Desktop/petsc-lat/include >>>>> -I/home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/include >>>>> /home/adoni/Desktop/petsc-lat/src/snes/examples/tutorials/ex12.c >>>>> /home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/bin/mpicxx -Wall >>>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -o ex12 >>>>> ex12.o -Wl,-rpath,/home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/lib >>>>> -L/home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/lib -lpetsc >>>>> -Wl,-rpath,/home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/lib -lflapack >>>>> -lfblas -ltriangle -lX11 -lparmetis -lmetis -lpthread -lchaco -lctetgen >>>>> -lm >>>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.6 >>>>> -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>> -L/lib/x86_64-linux-gnu -lmpichf90 -lgfortran -lm -lgfortran -lm >>>>> -lquadmath >>>>> -lm -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s >>>>> -ldl >>>>> /bin/rm -f ex12.o >>>>> adoni@Adoni:~/Desktop/petsc-lat/src/snes/examples/tutorials$ mpiexec >>>>> -np 2 ./ex12 >>>>> [0]PETSC ERROR: --------------------- Error Message >>>>> ------------------------------------ >>>>> [0]PETSC ERROR: Invalid argument! >>>>> [0]PETSC ERROR: The section cell closure size 0 != dual space >>>>> dimension 1! >>>>> [0]PETSC ERROR: >>>>> ------------------------------------------------------------------------ >>>>> [0]PETSC ERROR: Petsc Development GIT revision: unknown GIT Date: >>>>> 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: ./ex12 on a arch-linux2-c-debug named Adoni by adoni >>>>> Mon Nov 11 12:21:49 2013 >>>>> [0]PETSC ERROR: Libraries linked from >>>>> /home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/lib >>>>> [0]PETSC ERROR: Configure run at Fri Nov 8 20:03:26 2013 >>>>> [0]PETSC ERROR: Configure options --with-clanguage=c++ >>>>> --with-shared-libraries=1 --download-f-blas-lapack --download-mpich >>>>> --download-boost --download-triangle --download-ctetgen --download-chaco >>>>> --download-metis --download-parmetis >>>>> [0]PETSC ERROR: >>>>> ------------------------------------------------------------------------ >>>>> [0]PETSC ERROR: DMPlexProjectFunctionLocal() line 207 in >>>>> src/dm/impls/plex/plexfem.c >>>>> [0]PETSC ERROR: DMPlexProjectFunction() line 258 in >>>>> src/dm/impls/plex/plexfem.c >>>>> [0]PETSC ERROR: main() line 686 in >>>>> /home/adoni/Desktop/petsc-lat/src/snes/examples/tutorials/ex12.c >>>>> [0]PETSC ERROR: --------------------- Error Message >>>>> ------------------------------------ >>>>> [0]PETSC ERROR: Invalid argument! >>>>> [0]PETSC ERROR: The section cell closure size 0 != dual space >>>>> dimension 1! >>>>> [0]PETSC ERROR: >>>>> ------------------------------------------------------------------------ >>>>> [0]PETSC ERROR: Petsc Development GIT revision: unknown GIT Date: >>>>> 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: ./ex12 on a arch-linux2-c-debug named Adoni by adoni >>>>> Mon Nov 11 12:21:49 2013 >>>>> [0]PETSC ERROR: Libraries linked from >>>>> /home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/lib >>>>> [0]PETSC ERROR: Configure run at Fri Nov 8 20:03:26 2013 >>>>> [0]PETSC ERROR: Configure options --with-clanguage=c++ >>>>> --with-shared-libraries=1 --download-f-blas-lapack --download-mpich >>>>> --download-boost --download-triangle --download-ctetgen --download-chaco >>>>> --download-metis --download-parmetis >>>>> [0]PETSC ERROR: >>>>> ------------------------------------------------------------------------ >>>>> [0]PETSC ERROR: DMPlexProjectFunctionLocal() line 207 in >>>>> src/dm/impls/plex/plexfem.c >>>>> [0]PETSC ERROR: DMPlexProjectFunction() line 258 in >>>>> src/dm/impls/plex/plexfem.c >>>>> [0]PETSC ERROR: main() line 686 in >>>>> /home/adoni/Desktop/petsc-lat/src/snes/examples/tutorials/ex12.c >>>>> application called MPI_Abort(MPI_COMM_WORLD, 62) - process 0 >>>>> [unset]: aborting job: >>>>> application called MPI_Abort(MPI_COMM_WORLD, 62) - process 0 >>>>> application called MPI_Abort(MPI_COMM_WORLD, 62) - process 0 >>>>> [unset]: aborting job: >>>>> application called MPI_Abort(MPI_COMM_WORLD, 62) - process 0 >>>>> >>>>> This occurs for all process counts. >>>>> >>>>> Thanks. >>>>> >>>>> Adoni >>>>> >>>>> >>>>> On 11 November 2013 12:19, Matthew Knepley <[email protected]> wrote: >>>>> >>>>>> On Mon, Nov 11, 2013 at 6:10 AM, Anthony Vergottis < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> Dear All, >>>>>>> >>>>>>> I am trying to find a good example within PETSc that examples with >>>>>>> some detail the use of DM objects within a parallel and FEM framework. I >>>>>>> have looked at most of the example and have not found anything like >>>>>>> this. >>>>>>> Is there any other material available on the subject from any other >>>>>>> source >>>>>>> or maybe I missed something within the PETSc full download file? >>>>>>> >>>>>> >>>>>> Did you look at SNES ex12? Is it not understandable? >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Matt >>>>>> >>>>>> >>>>>>> Thanks in advance. >>>>>>> >>>>>>> Regards, >>>>>>> Adonis >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> 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 >>>> >>> >>> >> > > > -- > 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 >
