In my first program I have already set the name for the solution. Vec U has the name "pressure".
In my second program, how do I obtain and use/load "pressure"? Would I have to use PetscObjectQuery somehow? On Tue, Mar 31, 2015 at 6:00 PM, Matthew Knepley <[email protected]> wrote: > On Tue, Mar 31, 2015 at 5:54 PM, Justin Chang <[email protected]> wrote: > >> Matt thanks for the responses. I plan on loading the solution sol.h5 >> obtained from one program into another (as the auxiliary). So in my other >> program, I am solving a different problem but on the same mesh. I have the >> following lines in my other code: >> > > Yes, if you want to do this, you have to give these vectors proper names: > > PetscObjectSetName((PetscObject), U, "solution"); > > Thanks, > > Matt > > >> ierr = >> PetscViewerHDF5Open(PETSC_COMM_SELF,"sol.h5",FILE_MODE_READ,&viewer);CHKERRQ(ierr); >> ierr = VecLoad(auxVec,&viewer);CHKERRQ(ierr); >> ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); >> >> But when this program reaches VecLoad i get the following errors: >> >> HDF5-DIAG: Error detected in HDF5 (1.8.12) MPI-process 0: >> #000: H5D.c line 334 in H5Dopen2(): not found >> major: Dataset >> minor: Object not found >> #001: H5Gloc.c line 430 in H5G_loc_find(): can't find object >> major: Symbol table >> minor: Object not found >> #002: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal >> failed >> major: Symbol table >> minor: Object not found >> #003: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator >> failed >> major: Symbol table >> minor: Callback failed >> #004: H5Gloc.c line 385 in H5G_loc_find_cb(): object >> 'Vec_0x7f9831516fb0_0' doesn't exist >> major: Symbol table >> minor: Object not found >> [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> [0]PETSC ERROR: Error in external library >> [0]PETSC ERROR: Error in HDF5 call H5Dopen2() Status -1 >> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html >> for trouble shooting. >> [0]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2528-gbee642f GIT >> Date: 2015-03-29 20:36:38 -0500 >> [0]PETSC ERROR: ./trans on a arch-darwin-c-debug named >> CAML-03.CIVE.UH.EDU by jychang48 Tue Mar 31 17:45:38 2015 >> [0]PETSC ERROR: Configure options --download-chaco --download-exodusii >> --download-fblaslapack --download-hdf5 --download-metis --download-mumps >> --download-netcdf --download-openmpi --download-parmetis >> --download-scalapack --download-triangle --with-cc=gcc --with-cmake=cmake >> --with-cxx=g++ --with-debugging=1 --with-fc=gfortran --with-valgrind=1 >> CFLAGS= CXXFLAGS= PETSC_ARCH=arch-darwin-c-debug >> [0]PETSC ERROR: #1 VecLoad_HDF5() line 268 in >> /Users/jychang48/Software/petsc-dev/src/vec/vec/utils/vecio.c >> [0]PETSC ERROR: #2 VecLoad_Default() line 391 in >> /Users/jychang48/Software/petsc-dev/src/vec/vec/utils/vecio.c >> [0]PETSC ERROR: #3 VecLoad_Plex_Local() line 158 in >> /Users/jychang48/Software/petsc-dev/src/dm/impls/plex/plex.c >> [0]PETSC ERROR: #4 VecLoad() line 969 in >> /Users/jychang48/Software/petsc-dev/src/vec/vec/interface/vector.c >> [0]PETSC ERROR: #5 CreateMesh() line 265 in >> /Users/jychang48/Dropbox/Research_Topics/Code_PETSc/Nonneg/trans.c >> [0]PETSC ERROR: #6 main() line 381 in >> /Users/jychang48/Dropbox/Research_Topics/Code_PETSc/Nonneg/trans.c >> >> Any idea what's going on here? >> >> On Tue, Mar 31, 2015 at 5:46 PM, Matthew Knepley <[email protected]> >> wrote: >> >>> On Tue, Mar 31, 2015 at 5:29 PM, Justin Chang <[email protected]> wrote: >>> >>>> How do I invoke this command into my program? When I add "-vec_view >>>> hdf5:sol.h5" my program says this has been left out. >>>> >>> >>> You can call VecView() directly with an HDF5 Viewer, or I think its >>> easier to call >>> >>> VecViewFromOptions(U, NULL, "-vec_view"); >>> >>> Thanks, >>> >>> Matt >>> >>> >>>> On Tue, Mar 31, 2015 at 5:13 PM, Matthew Knepley <[email protected]> >>>> wrote: >>>> >>>>> On Tue, Mar 31, 2015 at 5:06 PM, Justin Chang <[email protected]> wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> So in my DMPlex FEM (serial) simulations, I want to output the >>>>>> solution U to a binary file. I have the following: >>>>>> >>>>>> ierr = >>>>>> PetscViewerBinaryOpen(PETSC_COMM_WORLD,"sol.dat",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr); >>>>>> ierr = VecView(U,viewer);CHKERRQ(ierr); >>>>>> ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); >>>>>> >>>>>> The mesh I am solving has 13368 nodes, and 404 of them are >>>>>> constrained using the DMPlexAddBoundary(...) function. However, when I >>>>>> output the vector I only get 12964 values, which I believe is leaving out >>>>>> the 404 constrained ones. How do I get all dofs in the vector U (both >>>>>> free >>>>>> and constrained) printed? >>>>>> >>>>> >>>>> I would use HDF5 which will do this automatically: >>>>> >>>>> -vec_view hdf5:sol.h5 >>>>> >>>>> Thanks, >>>>> >>>>> Matt >>>>> >>>>> >>>>>> Thanks, >>>>>> >>>>>> >>>>>> -- >>>>>> Justin Chang >>>>>> PhD Candidate, Civil Engineering - Computational Sciences >>>>>> University of Houston, Department of Civil and Environmental >>>>>> Engineering >>>>>> Houston, TX 77004 >>>>>> (512) 963-3262 >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> 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 >>>>> >>>> >>>> >>>> >>>> -- >>>> Justin Chang >>>> PhD Candidate, Civil Engineering - Computational Sciences >>>> University of Houston, Department of Civil and Environmental Engineering >>>> Houston, TX 77004 >>>> (512) 963-3262 >>>> >>> >>> >>> >>> -- >>> 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 >>> >> >> >> >> -- >> Justin Chang >> PhD Candidate, Civil Engineering - Computational Sciences >> University of Houston, Department of Civil and Environmental Engineering >> Houston, TX 77004 >> (512) 963-3262 >> > > > > -- > 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 > -- Justin Chang PhD Candidate, Civil Engineering - Computational Sciences University of Houston, Department of Civil and Environmental Engineering Houston, TX 77004 (512) 963-3262
