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/DMSetUseNatu...
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/DMPlexGl...
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/>