Hi Matthew, Thank you for your answer ! So I tried to add those steps, and I have the same behavior as the one described in this thread :
https://lists.mcs.anl.gov/pipermail/petsc-dev/2015-July/017978.html *[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------[0]PETSC ERROR: Object is in wrong state[0]PETSC ERROR: DM global to natural SF was not created.You must call DMSetUseNatural() before DMPlexDistribute().[0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html <https://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble shooting.[0]PETSC ERROR: Petsc Development GIT revision: v3.14.4-671-g707297fd510 GIT Date: 2021-02-24 22:50:05 +0000[0]PETSC ERROR: /ccc/work/cont001/ocre/bridelbert/EULERIAN2D/bin/eulerian2D on a named inti1401 by bridelbert Thu Jul 8 07:50:24 2021[0]PETSC ERROR: Configure options --with-clean=1 --prefix=/ccc/work/cont001/ocre/bridelbert/04-PETSC/build_uns3D_inti --with-make-np=8 --with-windows-graphics=0 --with-debugging=1 --download-mpich-shared=0 --with-x=0 --with-pthread=0 --with-valgrind=0 --PETSC_ARCH=INTI_UNS3D --with-fc=/ccc/products/openmpi-2.0.4/gcc--8.3.0/default/bin/mpifort --with-cc=/ccc/products/openmpi-2.0.4/gcc--8.3.0/default/bin/mpicc --with-cxx=/ccc/products/openmpi-2.0.4/gcc--8.3.0/default/bin/mpicxx --with-openmp=0 --download-sowing=/ccc/work/cont001/ocre/bridelbert/v1.1.26-p1.tar.gz --download-metis=/ccc/work/cont001/ocre/bridelbert/git.metis.tar.gz --download-parmetis=/ccc/work/cont001/ocre/bridelbert/git.parmetis.tar.gz --download-fblaslapack=/ccc/work/cont001/ocre/bridelbert/git.fblaslapack.tar.gz --with-cmake-dir=/ccc/products/cmake-3.13.3/system/default[0]PETSC ERROR: #1 DMPlexGlobalToNaturalBegin() line 247 in /ccc/work/cont001/ocre/bridelbert/04-PETSC/src/dm/impls/plex/plexnatural.c[0]PETSC ERROR: #2 User provided function() line 0 in User file* The creation of my DM is as follow : * ! Read mesh from file name 'meshname' call DMPlexCreateFromFile(PETSC_COMM_WORLD, meshname, PETSC_TRUE, dm, ierr); CHKERRA(ierr) ! Distribute on processors call DMSetUseNatural(dm, PETSC_TRUE, ierr) ; CHKERRA(ierr) ! Start with connectivity call DMSetBasicAdjacency(dm, PETSC_TRUE, PETSC_FALSE, ierr) ; CHKERRA(ierr) ! Distribute on processors call DMPlexDistribute(dm, overlap, PETSC_NULL_SF, dmDist, ierr) ; CHKERRA(ierr) ! Security check if (dmDist /= PETSC_NULL_DM) then ! Destroy previous dm call DMDestroy(dm, ierr) ; CHKERRA(ierr) ! Replace with dmDist dm = dmDist end if ! Finalize setup of the object call DMSetFromOptions(dm, ierr) ; CHKERRA(ierr) ! Boundary condition with ghost cells call DMPlexConstructGhostCells(dm, PETSC_NULL_CHARACTER, PETSC_NULL_INTEGER, dmGhost, ierr); CHKERRA(ierr) ! Security check if (dmGhost /= PETSC_NULL_DM) then ! Destroy previous dm call DMDestroy(dm, ierr) ; CHKERRA(ierr) ! Replace with dmGhost dm = dmGhost end if* And I write my vector as follow : * call DMCreateGlobalVector(dm, Xnat, ierr); CHKERRA(ierr) call PetscObjectSetName(Xnat, "NaturalSolution", ierr); CHKERRA(ierr) call DMPlexGlobalToNaturalBegin(dm, X, Xnat, ierr); CHKERRA(ierr) call DMPlexGlobalToNaturalEnd(dm, X, Xnat, ierr); CHKERRA(ierr) call DMGetOutputSequenceNumber(dm, save_seqnum, save_seqval, ierr); CHKERRA(ierr) call DMSetOutputSequenceNumber(dm, -1, 0.d0, ierr); CHKERRA(ierr) write(filename,'(A,I8.8,A)') "restart_", stepnum, ".bin" call PetscViewerCreate(PETSC_COMM_WORLD, binViewer, ierr); CHKERRA(ierr) call PetscViewerSetType(binViewer, PETSCVIEWERBINARY, ierr); CHKERRA(ierr) call PetscViewerFileSetMode(binViewer, FILE_MODE_WRITE, ierr); CHKERRA(ierr); call PetscViewerBinarySetUseMPIIO(binViewer, PETSC_TRUE, ierr); CHKERRA(ierr); call PetscViewerFileSetName(binViewer, trim(filename), ierr); CHKERRA(ierr) ! call VecView(X, binViewer, ierr); CHKERRA(ierr) call VecView(Xnat, binViewer, ierr); CHKERRA(ierr) call PetscViewerDestroy(binViewer, ierr); CHKERRA(ierr) call DMSetOutputSequenceNumber(dm, save_seqnum, save_seqval, ierr); CHKERRA(ierr)* Did you find the time to fix the bug you are mentioning in the thread above regarding the passing of the natural property when calling DMPlexConstructGhostCells ? Thanks !! Thibault Le mer. 7 juil. 2021 à 23:46, Matthew Knepley <[email protected]> a écrit : > On Wed, Jul 7, 2021 at 3:49 PM Thibault Bridel-Bertomeu < > [email protected]> wrote: > >> Hi Dave, >> >> Thank you for your fast answer. >> >> To postprocess the files in python, I use the PetscBinaryIO package that >> is provided with PETSc, yes. >> >> I load the file like this : >> >> >> >> >> >> >> >> >> *import numpy as npimport meshioimport PetscBinaryIO as pioimport >> matplotlib as mplimport matplotlib.pyplot as pltimport matplotlib.cm >> <http://matplotlib.cm> as cmmpl.use('Agg')* >> >> >> >> >> >> >> >> >> >> >> >> *restartname = "restart_00001001.bin"print("Reading {} >> ...".format(restartname))io = pio.PetscBinaryIO()fh = >> open(restartname)objecttype = io.readObjectType(fh)data = Noneif objecttype >> == 'Vec': data = io.readVec(fh)print("Size of data = ", >> data.size)print("Size of a single variable (4 variables) = ", data.size / >> 4)assert(np.isclose(data.size / 4.0, np.floor(data.size / 4.0)))* >> >> Then I load the mesh (it's from Gmsh so I use the meshio package) : >> >> >> >> >> >> *meshname = "ForwardFacing.msh"print("Reading {} >> ...".format(meshname))mesh = meshio.read(meshname)print("Number of vertices >> = ", mesh.points.shape[0])print("Number of cells = ", >> mesh.cells_dict['quad'].shape[0])* >> >> From the 'data' and the 'mesh' I use tricontourf from matplotlib to plot >> the figure. >> >> I removed the call to ...SetUseMPIIO... and it gives the same kind of >> data yes (I attached a figure of the data obtained with the binary viewer >> without MPI I/O). >> >> Maybe it's just a connectivity issue ? Maybe the way the Vec is written >> by the PETSc viewer somehow does not match the connectivity from the ori >> Gmsh file but some other connectivity of the partitionned DMPlex ? >> > > Yes, when you distribute the mesh, it gets permuted so that each piece is > contiguous. This happens on all meshes (DMDA, DMStag, DMPlex, DMForest). > When it is written out, it just concatenates that ordering, or what we > usually call the "global order" since it is the order of a global vector. > > >> If so, is there a way to get the latter ? >> > > If you call > > > https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMSetUseNatural.html > > before distribution, then a mapping back to the original ordering will be > saved. You can use > that mapping with a global vector and an original vector > > > https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DMPLEX/DMPlexGlobalToNaturalBegin.html > > to get a vector in the original ordering. However, you would also need to > understand how you want that output. > The ExodusII viewer uses this by default since people how use it (Blaise) > generally want that. Most people using > HDF5 (me) want the new order since it is faster. Plex ex15 and ex26 show > some manipulations using this mapping. > > >> I know the binary viewer does not work on DMPlex, >> > > You can output the Vec in native format, which will use the > GlobalToNatural reordering. It will not output the Plex, > but you will have the values in the order you expect. > > >> the VTK viewer yields a corrupted dataset >> > > VTK is not supported. We support Paraview through the Xdmf extension to > HDF5. > > >> and I have issues with HDF5 viewer with MPI (see another recent thread of >> mine) ... >> > > I have not been able to reproduce this yet. > > Thanks, > > Matt > > >> Thanks again for your help !! >> >> Thibault >> >> Le mer. 7 juil. 2021 à 20:54, Dave May <[email protected]> a >> écrit : >> >>> >>> >>> On Wed 7. Jul 2021 at 20:41, Thibault Bridel-Bertomeu < >>> [email protected]> wrote: >>> >>>> Dear all, >>>> >>>> I have been having issues with large Vec (based on DMPLex) and massive >>>> MPI I/O ... it looks like the data that is written by the Petsc Binary >>>> Viewer is gibberish for large meshes split on a high number of processes. >>>> For instance, I am using a mesh that has around 50 million cells, split on >>>> 1024 processors. >>>> The computation seems to run fine, the timestep computed from the data >>>> makes sense so I think internally everything is fine. But when I look at >>>> the solution (one example attached) it's noise - at this point it should >>>> show a bow shock developing on the left near the step. >>>> The piece of code I use is below for the output : >>>> >>>> call DMGetOutputSequenceNumber(dm, save_seqnum, >>>> save_seqval, ierr); CHKERRA(ierr) >>>> call DMSetOutputSequenceNumber(dm, -1, 0.d0, ierr); >>>> CHKERRA(ierr) >>>> write(filename,'(A,I8.8,A)') "restart_", stepnum, ".bin" >>>> call PetscViewerCreate(PETSC_COMM_WORLD, binViewer, >>>> ierr); CHKERRA(ierr) >>>> call PetscViewerSetType(binViewer, PETSCVIEWERBINARY, >>>> ierr); CHKERRA(ierr) >>>> call PetscViewerFileSetMode(binViewer, FILE_MODE_WRITE, >>>> ierr); CHKERRA(ierr); >>>> call PetscViewerBinarySetUseMPIIO(binViewer, >>>> PETSC_TRUE, ierr); CHKERRA(ierr); >>>> >>>> >>> >>> Do you get the correct output if you don’t call the function above (or >>> equivalently use PETSC_FALSE) >>> >>> >>> call PetscViewerFileSetName(binViewer, trim(filename), ierr); >>>> CHKERRA(ierr) >>>> call VecView(X, binViewer, ierr); CHKERRA(ierr) >>>> call PetscViewerDestroy(binViewer, ierr); CHKERRA(ierr) >>>> call DMSetOutputSequenceNumber(dm, save_seqnum, >>>> save_seqval, ierr); CHKERRA(ierr) >>>> >>>> I do not think there is anything wrong with it but of course I would be >>>> happy to hear your feedback. >>>> Nonetheless my question was : how far have you tested the binary mpi >>>> i/o of a Vec ? Does it make some sense that for a 50 million cell mesh >>>> split on 1024 processes, it could somehow fail ? >>>> Or is it my python drawing method that is completely incapable of >>>> handling this dataset ? (paraview displays the same thing though so I'm not >>>> sure ...) >>>> >>> >>> Are you using the python provided tools within petsc to load the Vec >>> from file? >>> >>> >>> Thanks, >>> Dave >>> >>> >>> >>>> Thank you very much for your advice and help !!! >>>> >>>> Thibault >>>> >>> > > -- > 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 > > https://www.cse.buffalo.edu/~knepley/ > <http://www.cse.buffalo.edu/~knepley/> >
