On Thu, Jul 8, 2021 at 7:35 AM Thibault Bridel-Bertomeu < [email protected]> wrote:
> 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 ? > No, thanks for reminding me. I coded up what I think is a fix, but I do not have a test yet. Maybe you can help me make one. Here is the branch https://gitlab.com/petsc/petsc/-/commits/knepley/fix-plex-natural-fvghost Can you run and see if it fixes that error? Then we can figure out the best way to do your output. Thanks, Matt > 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/> >> > -- 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/>
