<div dir="ltr"><div dir="ltr">On Wed, Jul 7, 2021 at 3:49 PM Thibault Bridel-Bertomeu <<a href="mailto:thibault.bridelbertomeu@gmail.com">thibault.bridelbertomeu@gmail.com</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi Dave,<div><br></div><div>Thank you for your fast answer.</div><div><br></div><div>To postprocess the files in python, I use the PetscBinaryIO package that is provided with PETSc, yes.</div><div><br></div><div>I load the file like this :</div><div><br></div><div><i>import numpy as np<br>import meshio<br>import PetscBinaryIO as pio<br>import matplotlib as mpl<br>import matplotlib.pyplot as plt<br>import <a href="http://matplotlib.cm" target="_blank">matplotlib.cm</a> as cm<br><br>mpl.use('Agg')</i><br></div><div><br></div><div><i>restartname = "restart_00001001.bin"<br>print("Reading {} ...".format(restartname))<br>io = pio.PetscBinaryIO()<br>fh = open(restartname)<br>objecttype = io.readObjectType(fh)<br>data = None<br>if objecttype == 'Vec':<br> data = io.readVec(fh)<br>print("Size of data = ", data.size)<br>print("Size of a single variable (4 variables) = ", data.size / 4)<br>assert(np.isclose(data.size / 4.0, np.floor(data.size / 4.0)))</i><br></div><div><br></div><div>Then I load the mesh (it's from Gmsh so I use the meshio package) :</div><div><br></div><div><i>meshname = "ForwardFacing.msh"<br>print("Reading {} ...".format(meshname))<br>mesh = meshio.read(meshname)<br>print("Number of vertices = ", mesh.points.shape[0])<br>print("Number of cells = ", mesh.cells_dict['quad'].shape[0])</i><br></div><div><br></div><div>From the 'data' and the 'mesh' I use tricontourf from matplotlib to plot the figure.</div><div><br></div><div>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).</div><div><br></div><div>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 ?</div></div></blockquote><div><br></div><div>Yes, when you distribute the mesh, it gets permuted so that each piece is contiguous. This happens on all meshes (DMDA, DMStag, DMPlex, DMForest).</div><div>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.</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div> If so, is there a way to get the latter ?</div></div></blockquote><div><br></div><div>If you call</div><div><br></div><div> <a href="https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMSetUseNatural.html">https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMSetUseNatural.html</a></div><div><br></div><div>before distribution, then a mapping back to the original ordering will be saved. You can use</div><div>that mapping with a global vector and an original vector</div><div><br></div><div> <a href="https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DMPLEX/DMPlexGlobalToNaturalBegin.html">https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DMPLEX/DMPlexGlobalToNaturalBegin.html</a></div><div><br></div><div>to get a vector in the original ordering. However, you would also need to understand how you want that output.</div><div>The ExodusII viewer uses this by default since people how use it (Blaise) generally want that. Most people using</div><div>HDF5 (me) want the new order since it is faster. Plex ex15 and ex26 show some manipulations using this mapping.</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div> I know the binary viewer does not work on DMPlex,</div></div></blockquote><div><br></div><div>You can output the Vec in native format, which will use the GlobalToNatural reordering. It will not output the Plex,</div><div>but you will have the values in the order you expect.</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div> the VTK viewer yields a corrupted dataset</div></div></blockquote><div><br></div><div>VTK is not supported. We support Paraview through the Xdmf extension to HDF5.</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div> and I have issues with HDF5 viewer with MPI (see another recent thread of mine) ...</div></div></blockquote><div><br></div><div>I have not been able to reproduce this yet.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Thanks again for your help !!</div><div><br clear="all"><div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div><div><div><div><div>Thibault </div></div></div></div></div></div></div></div></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le mer. 7 juil. 2021 à 20:54, Dave May <<a href="mailto:dave.mayhem23@gmail.com" target="_blank">dave.mayhem23@gmail.com</a>> a écrit :<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><br></div><div><br><div class="gmail_quote"><div dir="ltr">On Wed 7. Jul 2021 at 20:41, Thibault Bridel-Bertomeu <<a href="mailto:thibault.bridelbertomeu@gmail.com" target="_blank">thibault.bridelbertomeu@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Dear all, <div><br></div><div>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.</div><div>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.</div><div>The piece of code I use is below for the output :</div><div><br></div><div> call DMGetOutputSequenceNumber(dm, save_seqnum, save_seqval, ierr); CHKERRA(ierr)<br> call DMSetOutputSequenceNumber(dm, -1, 0.d0, ierr); CHKERRA(ierr)<br> write(filename,'(A,I8.8,A)') "restart_", stepnum, ".bin"<br> call PetscViewerCreate(PETSC_COMM_WORLD, binViewer, ierr); CHKERRA(ierr)<br> call PetscViewerSetType(binViewer, PETSCVIEWERBINARY, ierr); CHKERRA(ierr)<br> call PetscViewerFileSetMode(binViewer, FILE_MODE_WRITE, ierr); CHKERRA(ierr);<br> call PetscViewerBinarySetUseMPIIO(binViewer, PETSC_TRUE, ierr); CHKERRA(ierr);<br> </div></div></blockquote><div dir="auto"><br></div><div dir="auto">Do you get the correct output if you don’t call the function above (or equivalently use PETSC_FALSE)</div><div dir="auto"><br></div><div dir="auto"><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>call PetscViewerFileSetName(binViewer, trim(filename), ierr); CHKERRA(ierr)<br> call VecView(X, binViewer, ierr); CHKERRA(ierr)<br> call PetscViewerDestroy(binViewer, ierr); CHKERRA(ierr)<br> call DMSetOutputSequenceNumber(dm, save_seqnum, save_seqval, ierr); CHKERRA(ierr)<br></div><div><br></div><div>I do not think there is anything wrong with it but of course I would be happy to hear your feedback.</div><div>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 ?</div><div>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 ...)</div></div></blockquote><div dir="auto"><br></div><div dir="auto">Are you using the python provided tools within petsc to load the Vec from file?</div><div dir="auto"><br></div><div dir="auto"><br></div><div dir="auto">Thanks,</div><div dir="auto">Dave</div><div dir="auto"><br></div><div dir="auto"><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div></div><div><br></div><div>Thank you very much for your advice and help !!!</div></div><div dir="ltr"><div><br></div><div><div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div><div><div><div><div>Thibault </div></div></div></div></div></div></div></div></div></div></div></div></div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>