[petsc-users] Scaling of the Petsc Binary Viewer
Matthew Knepley
knepley at gmail.com
Thu Jul 8 16:05:48 CDT 2021
On Thu, Jul 8, 2021 at 7:35 AM Thibault Bridel-Bertomeu <
thibault.bridelbertomeu at gmail.com> 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
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> *[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 :
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> * ! 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 :
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> * 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 <knepley at gmail.com> a
> écrit :
>
>> On Wed, Jul 7, 2021 at 3:49 PM Thibault Bridel-Bertomeu <
>> thibault.bridelbertomeu at gmail.com> 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 <dave.mayhem23 at gmail.com> a
>>> écrit :
>>>
>>>>
>>>>
>>>> On Wed 7. Jul 2021 at 20:41, Thibault Bridel-Bertomeu <
>>>> thibault.bridelbertomeu at gmail.com> 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/>
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