<div dir="ltr">Hello everyone,<div><br></div><div>So i figured it out, and I got a work-around, but it's not pretty and I think there might be a nicer solution that you guys will see.</div><div><br></div><div>Here is the stack of calls for the VecLoad of a vector generated via a DMPlex :</div><div><br></div><div>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>CALLING PETSCVIEWERHDF5SETTIMESTEP FROM FORTRAN</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">TOTOTOTOTO :::>>> IN PETSCVIEWERHDF5SETTIMESTEP. <hdf5v.c></span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">TOTOTOTOTO :::>>> HDF5->TIMESTEP = 20. <hdf5v.c></span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>CALLING VECLOAD FROM FORTRAN</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">TOTOTOTOTO :::>>> INSIDE VECLOAD <vector.c></span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">TOTOTOTOTO :::>>> FORMAT = PETSC_VIEWER_RAW. <vector.c></span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">TOTOTOTOTO :::>>> IN VECLOAD_PLEX. <plex.c></span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">TOTOTOTOTO :::>>> IN VECLOAD_PLEX_HDF5_INTERNAL <plexhdf5.c></span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">TOTOTOTOTO :::>>> IN PETSCVIEWERHDF5SETTIMESTEP. <hdf5v.c></span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">TOTOTOTOTO :::>>> HDF5->TIMESTEP = 20. <hdf5v.c></span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">TOTOTOTOTO :::>>> IN VECLOAD_DEFAULT. <vecio.c></span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">TOTOTOTOTO :::>>> IN VECLOAD_HDF5 <vecio.c>.</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">TOTOTOTOTO :::>>> IN PETSCVIEWERHDF5LOAD. <hdf5io.c></span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">TOTOTOTOTO :::>>> IN PETSCVIEWERHDF5READINITIALIZE_PRIVATE. <hdf5io.c></span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">TOTOTOTOTO :::>>> TIMESTEP = 20. <hdf5io.c></span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(252,238,207)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">TOTOTOTOTO :::>>> LENIND = 1, TIMESTEP = 20. <hdf5io.c></span></p></div><div><br></div><div>Not everything is there, I just stopped at line 78 of hdf5io.c as Matt suggested.</div><div>The thing is, you can call </div><div><br></div><div><div style="color:rgb(212,212,212);background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;line-height:18px;white-space:pre"><div><span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerHDF5SetTimestep</span>(hdf5Viewer, restartiter, ierr); CHKERRA(ierr)</div></div></div><div><br></div><div>all you want before calling </div><div><br></div><div><div style="color:rgb(212,212,212);background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;line-height:18px;white-space:pre"><div><span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">VecLoad</span>(sol, hdf5Viewer, ierr); CHKERRA(ierr)</div></div></div><div><br></div><div>it won't have any effect.</div><div>The timestep that is set by the ..SetTimestep routine is overriden inside the </div><div><br></div><div><div style="color:rgb(212,212,212);background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;line-height:18px;white-space:pre"><div><span style="color:rgb(220,220,170)">VecLoad_Plex_HDF5_Internal</span></div></div></div><div><br></div><div>routine because of these lines :</div><div><br></div><div><div style="color:rgb(212,212,212);background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;line-height:18px;white-space:pre"><div> <span style="color:rgb(156,220,254)">ierr</span> = <span style="color:rgb(220,220,170)">DMGetOutputSequenceNumber</span>(<span style="color:rgb(156,220,254)">dm</span>, &<span style="color:rgb(156,220,254)">seqnum</span>, <span style="color:rgb(86,156,214)">NULL</span>);<span style="color:rgb(86,156,214)">CHKERRQ</span>(<span style="color:rgb(156,220,254)">ierr</span>);</div><div> <span style="color:rgb(156,220,254)">ierr</span> = <span style="color:rgb(220,220,170)">PetscViewerHDF5SetTimestep</span>(<span style="color:rgb(156,220,254)">viewer</span>, <span style="color:rgb(156,220,254)">seqnum</span>);<span style="color:rgb(86,156,214)">CHKERRQ</span>(<span style="color:rgb(156,220,254)">ierr</span>);</div></div></div><div><br></div><div>Since my point is to "restart" a computation from such a HDF5 file, when i read the file the DMPlex is brand new and has no idea what happened during another run of the program --> the "seqnum" is set to -1.</div><div>As a consequence, the viewer always sees its "timestep" variable as being -1 even if you try forcing it with</div><div><br></div><div><div><div style="color:rgb(212,212,212);background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;line-height:18px;white-space:pre"><div><span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerHDF5SetTimestep</span>(hdf5Viewer, restartiter, ierr); CHKERRA(ierr)</div></div></div><div></div></div><div><br></div><div>Anyways, one way to do it is then to add :</div><div><br></div><div><div style="color:rgb(212,212,212);background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;line-height:18px;white-space:pre"><div><span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">DMSetOutputSequenceNumber</span>(dm, restartiter, PETSC_NULL_REAL, ierr); CHKERRA(ierr)</div></div></div><div><br></div><div>to the code, that thus becomes :</div><div><br></div><div><div style="color:rgb(212,212,212);background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;line-height:18px;white-space:pre"><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">DMSetOutputSequenceNumber</span>(dm, restartiter, PETSC_NULL_REAL, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerHDF5Open</span>(PETSC_COMM_WORLD, <span style="color:rgb(220,220,170)">trim</span>(restartname), FILE_MODE_READ, hdf5Viewer, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerHDF5PushGroup</span>(hdf5Viewer, <span style="color:rgb(206,145,120)">"/fields"</span>, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerHDF5SetTimestep</span>(hdf5Viewer, restartiter, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">VecLoad</span>(sol, hdf5Viewer, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerDestroy</span>(hdf5Viewer, ierr); CHKERRA(ierr)</div></div></div><div><br></div><div>By the way, it even works if you remove the PushGroup(..., "/fields", ...) because this is also forced in VecLoad_Plex_HDF5_Internal.</div><div><br></div><div>Might be a better idea would be to do a DMLoad, what do you think ?</div><div><br></div><div>Thanks !!</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><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 jeu. 8 avr. 2021 à 13:35, Thibault Bridel-Bertomeu <<a href="mailto:thibault.bridelbertomeu@gmail.com">thibault.bridelbertomeu@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 dir="ltr"><div dir="ltr">Argh no I don't, I implemented it straight in a larger CFD code because everything is already there for setting-up the DM, DS, PetscFV etc...<div>Now that you guys gave me some more pointers I'll dig around with a debugger ..</div><div><br></div><div>Thanks !</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le jeu. 8 avr. 2021 à 13:25, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@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 dir="ltr">Do you have a self-contained thing I could run? This should be easy to clear up in the debugger.<div><br></div><div> Thanks,</div><div><br></div><div> Matt</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Apr 8, 2021 at 7:22 AM 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">Doesn't seem to be a Fortran stub problem, it's automatically generated and looks good to me ...<br clear="all"><div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div><div><div><div><div><br></div></div></div></div></div></div></div></div></div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le jeu. 8 avr. 2021 à 13:20, Thibault Bridel-Bertomeu <<a href="mailto:thibault.bridelbertomeu@gmail.com" target="_blank">thibault.bridelbertomeu@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 dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div><div><div><div>Well ... I cleaned everything and did a fresh compile just now with "print*, "foo"" here and there and it does print foo on the terminal ... So yes, I am running the changed code ! ;)</div></div></div></div></div><div><br></div><div><div style="color:rgb(212,212,212);background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;line-height:18px;white-space:pre-wrap"><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">DMCreateGlobalVector</span>(dm, sol, ierr); CHKERRA(ierr)</div><div style="line-height:18px"><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">VecZeroEntries</span>(sol, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscObjectSetName</span>(sol, <span style="color:rgb(206,145,120)">"Solution"</span>, ierr); CHKERRA(ierr)</div></div><div><span style="color:rgb(197,134,192)"> print</span>*, <span style="color:rgb(206,145,120)">"foo"</span></div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerCreate</span>(PETSC_COMM_WORLD, hdf5Viewer, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerSetType</span>(hdf5Viewer, PETSCVIEWERHDF5, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerFileSetMode</span>(hdf5Viewer, FILE_MODE_READ, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerFileSetName</span>(hdf5Viewer, <span style="color:rgb(220,220,170)">trim</span>(restartname), ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerHDF5SetTimestep</span>(hdf5Viewer, restartiter, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerHDF5PushGroup</span>(hdf5Viewer, <span style="color:rgb(206,145,120)">"/fields"</span>, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">VecLoad</span>(sol, hdf5Viewer, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerDestroy</span>(hdf5Viewer, ierr); CHKERRA(ierr)</div></div></div><div><br></div><div>In the snippet, restartiter is an integer equal to 20.</div><div>I agree with you the line you just sent me should fix the issue. Maybe it's a fortran stub problem, I'll double check the stubs.</div><div><br></div><div>Thanks !</div><div>Thibault<br><br></div></div></div></div></div></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le jeu. 8 avr. 2021 à 13:11, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@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 dir="ltr"><div dir="ltr">On Thu, Apr 8, 2021 at 4:08 AM Thibault Bridel-Bertomeu <<a href="mailto:thibault.bridelbertomeu@gmail.com" target="_blank">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 everyone, <div><br></div><div>Thank you for your answers.</div><div>Unfortunately, it does not work yet.</div><div><br></div><div>1/ I first tried just adding</div><div><br></div><div> <span style="background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;white-space:pre-wrap;color:rgb(197,134,192)">call</span><span style="background-color:rgb(30,30,30);color:rgb(212,212,212);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;white-space:pre-wrap"> </span><span style="background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;white-space:pre-wrap;color:rgb(220,220,170)">PetscViewerHDF5SetTimestep</span><span style="background-color:rgb(30,30,30);color:rgb(212,212,212);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;white-space:pre-wrap">(hdf5Viewer, 20, ierr); CHKERRA(ierr)</span></div><div><br></div><div>(the latest iteration in the *.hdf5 is iter 20) before the VecLoad, i.e.:</div><div><br></div><div><div style="color:rgb(212,212,212);background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;line-height:18px;white-space:pre-wrap"><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerCreate</span>(PETSC_COMM_WORLD, hdf5Viewer, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerSetType</span>(hdf5Viewer, PETSCVIEWERHDF5, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerFileSetMode</span>(hdf5Viewer, FILE_MODE_READ, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerFileSetName</span>(hdf5Viewer, <span style="color:rgb(220,220,170)">trim</span>(restartname), ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerHDF5SetTimestep</span>(hdf5Viewer, 20, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerHDF5PushGroup</span>(hdf5Viewer, <span style="color:rgb(206,145,120)">"/fields"</span>, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">VecLoad</span>(sol, hdf5Viewer, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerDestroy</span>(hdf5Viewer, ierr); CHKERRA(ierr)</div></div></div><div><br></div><div>but it does not change anything, the error is exactly the same as before (with or without the PushGroup by the way).</div></div></blockquote><div><br></div><div>This is the one I do not believe. If the Viewer has a non-negative timestep, it will increase the length index:</div><div><br></div><div> <a href="https://gitlab.com/petsc/petsc/-/blob/main/src/vec/is/utils/hdf5io.c#L78" target="_blank">https://gitlab.com/petsc/petsc/-/blob/main/src/vec/is/utils/hdf5io.c#L78</a></div><div><br></div><div>and we can see all the sizes in your HDF5 file. Are you sure you are running the one with the changed code?</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><br></div><div>2/ I then tried adding </div><div><br></div><div> <span style="background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;white-space:pre-wrap;color:rgb(197,134,192)">call</span><span style="background-color:rgb(30,30,30);color:rgb(212,212,212);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;white-space:pre-wrap"> </span><span style="background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;white-space:pre-wrap;color:rgb(220,220,170)">PetscViewerHDF5SetTimestep</span><span style="background-color:rgb(30,30,30);color:rgb(212,212,212);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;white-space:pre-wrap">(hdf5Viewer, -1, ierr); CHKERRA(ierr)</span><br></div><div><br></div><div>before the VecView to "prevent blocking with timesteps" as the doc says (<a href="https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Viewer/PetscViewerHDF5SetTimestep.html#PetscViewerHDF5SetTimestep" target="_blank">https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Viewer/PetscViewerHDF5SetTimestep.html#PetscViewerHDF5SetTimestep</a>), i.e. :</div><div><br></div><div><div style="color:rgb(212,212,212);background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;line-height:18px;white-space:pre-wrap"><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerCreate</span>(PETSC_COMM_WORLD, hdf5Viewer, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerSetType</span>(hdf5Viewer, PETSCVIEWERHDF5, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerFileSetMode</span>(hdf5Viewer, FILE_MODE_WRITE, ierr); CHKERRA(ierr);</div><div> <span style="color:rgb(197,134,192)">write</span>(filename,<span style="color:rgb(206,145,120)">'(A,I5.5,A)'</span>) <span style="color:rgb(206,145,120)">"restart_"</span>, stepnum, <span style="color:rgb(206,145,120)">".h5"</span></div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerFileSetName</span>(hdf5Viewer, <span style="color:rgb(220,220,170)">trim</span>(filename), ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerHDF5SetTimestep</span>(hdf5Viewer, -1, ierr); CHKERRA(ierr)<br></div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">VecView</span>(X, hdf5Viewer, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerDestroy</span>(hdf5Viewer, ierr); CHKERRA(ierr)</div></div></div><div><br></div><div>but the hdf5 files keep increasing in size and each one stores more data than the previous one ... can I not disable that "stacking" effect and just keep the iteration I want ?</div><div><br></div><div>3/ I tried adding </div><div><br></div><div> <span style="background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;white-space:pre-wrap;color:rgb(197,134,192)">call</span><span style="background-color:rgb(30,30,30);color:rgb(212,212,212);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;white-space:pre-wrap"> </span><span style="background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;white-space:pre-wrap;color:rgb(220,220,170)">PetscViewerHDF5SetTimestep</span><span style="background-color:rgb(30,30,30);color:rgb(212,212,212);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;white-space:pre-wrap">(hdf5Viewer, stepnum, ierr); CHKERRA(ierr)</span><br></div><div><br></div><div>before the VecView to try and just keep one iteration in the file, i.e. :</div><div><br></div><div><div><div style="color:rgb(212,212,212);background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;line-height:18px;white-space:pre-wrap"><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerCreate</span>(PETSC_COMM_WORLD, hdf5Viewer, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerSetType</span>(hdf5Viewer, PETSCVIEWERHDF5, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerFileSetMode</span>(hdf5Viewer, FILE_MODE_WRITE, ierr); CHKERRA(ierr);</div><div> <span style="color:rgb(197,134,192)">write</span>(filename,<span style="color:rgb(206,145,120)">'(A,I5.5,A)'</span>) <span style="color:rgb(206,145,120)">"restart_"</span>, stepnum, <span style="color:rgb(206,145,120)">".h5"</span></div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerFileSetName</span>(hdf5Viewer, <span style="color:rgb(220,220,170)">trim</span>(filename), ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerHDF5SetTimestep</span>(hdf5Viewer, stepnum, ierr); CHKERRA(ierr)<br></div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">VecView</span>(X, hdf5Viewer, ierr); CHKERRA(ierr)</div><div> <span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerDestroy</span>(hdf5Viewer, ierr); CHKERRA(ierr)</div></div></div><div></div></div><div><br></div><div>but it has no effect whatsoever on the hdf5 files that are written ... they still store several timesteps, and then I cannot VecLoad what I want, i still get the same error.</div><div><br></div><div>Any more idea ? I keep reading the doc on the HDF5 viewer and thinking that this or that function could solve the issue but either it has zero effect or does not solve the issue ...</div><div><br></div><div>Thanks !!!</div><div><br></div><div>Thibault</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le jeu. 8 avr. 2021 à 02:42, Barry Smith <<a href="mailto:bsmith@petsc.dev" target="_blank">bsmith@petsc.dev</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><div><br></div> Matt,<div><br></div><div> Is there anyway to provide this "extra meta-data" inside the generated HDF file? Then when a fresh viewer opens the file it uses this meta-data to know that the file contains "time-steps" and allows processing of them? The simplest thing would be to have the viewer generate an error if the file has time-steps but the user does not "request a (or more) time-steps" instead of getting confused about the vector sizes.</div><div><br></div><div> Barry</div><div><br></div><div><br><div><br><blockquote type="cite"><div>On Apr 7, 2021, at 6:32 PM, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:</div><br><div><div dir="ltr"><div dir="ltr">On Wed, Apr 7, 2021 at 4:10 PM Thibault Bridel-Bertomeu <<a href="mailto:thibault.bridelbertomeu@gmail.com" target="_blank">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">Hello Vaclav,<div><br></div><div>Thank you for your quick answer !!</div><div>OK so, if I need to push the group, I added :</div><div><br></div><div><div style="color:rgb(212,212,212);background-color:rgb(30,30,30);font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;line-height:18px;white-space:pre-wrap"><div><span style="color:rgb(197,134,192)">call</span> <span style="color:rgb(220,220,170)">PetscViewerHDF5PushGroup</span>(hdf5Viewer, <span style="color:rgb(206,145,120)">"/fields"</span>, ierr); CHKERRA(ierr)</div></div></div><div><br></div><div>right after the call to PetscViewerFileSetName.</div><div>The result is the same, it produces the following error :</div><div><br></div><div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(172,31,22);background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures"><b>[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</b></span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: Unexpected data in file</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: Global size of array in file is 105, not 25300 as expected</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: See <a href="https://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank">https://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: Petsc Development GIT revision: v3.14.4-671-g707297fd510<span> </span>GIT Date: 2021-02-24 22:50:05 +0000</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: ../../../bin/eulerian3D on a<span> </span>named macbook-pro-de-thibault.home by tbridel Wed Apr<span> </span>7 22:05:14 2021</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: Configure options --with-clean=1 --prefix=/Users/tbridel/Documents/1-CODES/04-PETSC/build_uns3D --with-make-np=2 --with-windows-graphics=0 --with-debugging=0 --download-fblaslapack --download-mpich-shared=0 --with-x=0 --with-pthread=0 --with-valgrind=0 --PETSC_ARCH=macosx_uns3D --with-fc=/usr/local/bin/mpifort --with-cc=/usr/local/bin/mpicc --with-cxx=/usr/local/bin/mpic++ --with-openmp=0 --download-hypre=yes --download-sowing=yes --download-metis=yes --download-parmetis=yes --download-triangle=yes --download-tetgen=yes --download-ctetgen=yes --download-p4est=yes --download-zlib=yes --download-c2html=yes --download-eigen=yes --download-pragmatic=yes --with-hdf5-dir=/usr/local/opt/hdf5-mpi --with-cmake-dir=/usr/local/opt/cmake --with-libtoolize=/usr/local/bin/glibtoolize --with-autoreconf=/usr/local/bin/autoreconf</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: #1 PetscViewerHDF5ReadSizes_Private() line 114 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/vec/is/utils/hdf5io.c</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: #2 PetscViewerHDF5Load() line 208 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/vec/is/utils/hdf5io.c</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: #3 VecLoad_HDF5() line 132 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/vec/vec/utils/vecio.c</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: #4 VecLoad_Default() line 257 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/vec/vec/utils/vecio.c</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: #5 VecLoad_Plex_Local() line 474 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/dm/impls/plex/plex.c</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: #6 VecLoad_Plex_HDF5_Internal() line 295 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/dm/impls/plex/plexhdf5.c</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: #7 VecLoad_Plex() line 496 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/dm/impls/plex/plex.c</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: #8 VecLoad() line 953 in /Users/tbridel/Documents/1-CODES/04-PETSC/src/vec/vec/interface/vector.c</span></div><div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(252,238,207)"><span style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: #9 User provided function() line 0 in User file</span></div></div><div><br></div><div><div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div><div><div><div><div>Do you know where it could come from ?</div></div></div></div></div></div></div></div></div></div></div></div></div></blockquote><div><br></div><div>I think I understand this. PETSc tries to be clever to allow you to store timesteps. It gives the HDF5 array an extra dimension. Somehow</div><div>the Viewer has to know this. The TS does this automatically, so you have an array</div><div><br></div><div> <span style="font-variant-ligatures:no-common-ligatures;font-size:11px">GROUP "fields" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> DATASET "Solution" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> DATATYPE H5T_IEEE_F64LE</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> DATASPACE SIMPLE { ( 21, 5060, 5 ) / ( H5S_UNLIMITED, 5060, 5 ) }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> }</span></div><div><br></div><div>which has 21 timesteps. However, when you create a brand new Viewer, it does not know, and mistakenly thinks there is a single vector</div><div>of length 21 * 5 = 105. You can tell your reader which timestep you want to extract using</div><div><br></div><div> <a href="https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Viewer/PetscViewerHDF5SetTimestep.html" target="_blank">https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Viewer/PetscViewerHDF5SetTimestep.html</a><br></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><div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div><div><div><div><div>As for what I am doing exactly : i am using the DMPlex with a PetscFV to solve the fluid mechanics Euler equations in 3D. The PetscFV linked to the DS of the DMPlex might be why there is a /fields before the /Solution maybe .. ?</div><div><br></div><div>Cheers and thank you again for your help !!</div><div><br></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 avr. 2021 à 10:07, Hapla Vaclav <<a href="mailto:vaclav.hapla@erdw.ethz.ch" target="_blank">vaclav.hapla@erdw.ethz.ch</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>
<div><span>Dear Thibault</span></div>
<div><br>
</div>
<div>
<div>
<blockquote type="cite">
<div>On 7 Apr 2021, at 08:18, Thibault Bridel-Bertomeu <<a href="mailto:thibault.bridelbertomeu@gmail.com" target="_blank">thibault.bridelbertomeu@gmail.com</a>> wrote:</div>
<br>
<div>
<div dir="ltr">
<div>Dear all, <br>
</div>
<div><br>
</div>
<div>I have been facing a problem with VecLoad recently, even though it seems to me I did exactly like in the examples/tutorials.</div>
<div><br>
</div>
<div>Basically, a program writes a vector with the HDF5 writer like this :</div>
<div></div>
<div>
<pre lang="fortran"><span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC45" lang="fortran"><span> </span><span> call</span><span> </span><span>DMCreateGlobalVector</span><span>(</span><span>dm</span><span>,</span><span> </span><span>sol</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span>
<span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC46" lang="fortran"><span> </span><span> call</span><span> </span><span>VecZeroEntries</span><span>(X</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span>
<span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC47" lang="fortran"><span> </span><span> call</span><span> </span><span>PetscObjectSetName</span><span>(X</span><span>,</span><span> </span><span>"Solution"</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span><span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC65" lang="fortran"><span> <br></span></span></pre>
<pre lang="fortran"><span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC65" lang="fortran"><span> < do something with X to fill it up with relevant data ><br></span></span></pre>
<pre lang="fortran"><span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC65" lang="fortran"><span> </span><span>call</span><span> </span><span>PetscViewerCreate</span><span>(</span><span>PETSC_COMM_WORLD</span><span>,</span><span> </span><span>hdf5Viewer</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span>
<span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC66" lang="fortran"><span> </span><span>call</span><span> </span><span>PetscViewerSetType</span><span>(</span><span>hdf5Viewer</span><span>,</span><span> </span><span>PETSCVIEWERHDF5</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span>
<span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC67" lang="fortran"><span> </span><span>call</span><span> </span><span>PetscViewerFileSetMode</span><span>(</span><span>hdf5Viewer</span><span>,</span><span> </span><span>FILE_MODE_WRITE</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>);</span></span>
<span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC68" lang="fortran"><span> </span><span>write</span><span>(</span><span>filename</span><span>,</span><span>'(A,I5.5,A)'</span><span>)</span><span> </span><span>"restart_"</span><span>,</span><span> </span><span>stepnum</span><span>,</span><span> </span><span>".h5"</span></span>
<span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC69" lang="fortran"><span> </span><span>call</span><span> </span><span>PetscViewerFileSetName</span><span>(</span><span>hdf5Viewer</span><span>,</span><span> </span><span>trim</span><span>(</span><span>filename</span><span>),</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span>
<span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC70" lang="fortran"><span> </span><span>call</span><span> </span><span>VecView</span><span>(</span><span>X</span><span>,</span><span> </span><span>hdf5Viewer</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span>
<span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC71" lang="fortran"><span> </span><span>call</span><span> </span><span>PetscViewerDestroy</span><span>(</span><span>hdf5Viewer</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span>
</pre>
</div>
<div>and the same program (but with different start-up options, say) re-reads such a file like this :</div>
<div><br>
</div>
<div>
<pre lang="fortran"><span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC64" lang="fortran"><span><span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC45" lang="fortran"><span> </span><span> call</span><span> </span><span>DMCreateGlobalVector</span><span>(</span><span>dm</span><span>,</span><span> </span><span>sol</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span>
<span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC46" lang="fortran"><span> </span><span> call</span><span> </span><span>VecZeroEntries</span><span>(</span><span>sol</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span>
<span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC47" lang="fortran"><span> </span><span> call</span><span> </span><span>PetscObjectSetName</span><span>(</span><span>sol</span><span>,</span><span> </span><span>"Solution"</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span> <br> </span><span>call</span><span> </span><span>PetscViewerCreate</span><span>(</span><span>PETSC_COMM_WORLD</span><span>,</span><span> </span><span>hdf5Viewer</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span>
<span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC65" lang="fortran"><span> </span><span>call</span><span> </span><span>PetscViewerSetType</span><span>(</span><span>hdf5Viewer</span><span>,</span><span> </span><span>PETSCVIEWERHDF5</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span>
<span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC66" lang="fortran"><span> </span><span>call</span><span> </span><span>PetscViewerFileSetMode</span><span>(</span><span>hdf5Viewer</span><span>,</span><span> </span><span>FILE_MODE_READ</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span>
<span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC67" lang="fortran"><span> </span><span>call</span><span> </span><span>PetscViewerFileSetName</span><span>(</span><span>hdf5Viewer</span><span>,</span><span> </span><span>trim</span><span>(</span><span>restartname</span><span>),</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span>
<span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC68" lang="fortran"><span> </span><span>call</span><span> </span><span>VecLoad</span><span>(</span><span>sol</span><span>,</span><span> </span><span>hdf5Viewer</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span>
<span id="gmail-m_4634622126182048306gmail-m_2871988643623181545gmail-m_-3627241083550638964gmail-m_-8877699833071185355gmail-m_-1795475030234232808gmail-m_1441798517920077622gmail-m_4982510822038283072gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC69" lang="fortran"><span> </span><span>call</span><span> </span><span>PetscViewerDestroy</span><span>(</span><span>hdf5Viewer</span><span>,</span><span> </span><span>ierr</span><span>);</span><span> </span><span>CHKERRA</span><span>(</span><span>ierr</span><span>)</span></span>
</pre>
</div>
<div><br>
</div>
<div>Such a dataset can be found under this link : <a href="https://drive.google.com/file/d/1owLAx5vknNhj61_5ieAwnWOR9cmkTseL/view?usp=sharing" target="_blank">
https://drive.google.com/file/d/1owLAx5vknNhj61_5ieAwnWOR9cmkTseL/view?usp=sharing</a></div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>
<div>I'm just looking at the HDF5 file. The structure is like this</div>
<div><br>
</div>
<div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures">> $PETSC_DIR/$PETSC_ARCH/bin/h5dump -H restart_00020.h5</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> </span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures">HDF5 "restart_00020.h5" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures">GROUP "/" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> GROUP "cell_fields" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> DATASET "Solution_FV solver" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> DATATYPE H5T_IEEE_F64LE</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> DATASPACE SIMPLE { ( 21, 3884, 5 ) / ( H5S_UNLIMITED, 3884, 5 ) }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> ATTRIBUTE "vector_field_type" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> DATATYPE H5T_STRING {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> STRSIZE 7;</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> STRPAD H5T_STR_NULLTERM;</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> CSET H5T_CSET_ASCII;</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> CTYPE H5T_C_S1;</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> DATASPACE SCALAR</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> GROUP "fields" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> DATASET "Solution" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> DATATYPE H5T_IEEE_F64LE</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> DATASPACE SIMPLE { ( 21, 5060, 5 ) / ( H5S_UNLIMITED, 5060, 5 ) }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> DATASET "time" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> DATATYPE H5T_IEEE_F64LE</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> DATASPACE SIMPLE { ( 21, 1 ) / ( H5S_UNLIMITED, 1 ) }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures"> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures">}</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal">
<span style="font-variant-ligatures:no-common-ligatures">}</span></div>
</div>
</div>
<br>
<blockquote type="cite">
<div>
<div dir="ltr">
<div><br>
</div>
<div>I would like the reader to read the /fields/Solution group basically, but I am not even sure it tries to do that.</div>
<div>Anyhow, I got an error, saying that the size found in the file (105) does not match the expected size (25300). If I look at the shape of /fields/Solution it is given as (21, 5030, 5). First, it is weird, cause the 21 seems to be 1 + current iteration
number ... but anyways we find the 5 variables and the 5030 cells. Only the reader seems to do 21 * 5 when it should be doing 5030 * 5 ...</div>
<div>I tried adding 'PetscViewerHDF5PushGroup(hdf5Viewer, "/fields/Solution", ierr)' to force it to read that group, but it does not change anything.</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>You definitely need to push the group, unless it's the root group "/". There is no way the reader would guess the correct group if it's not the root one [and I don't think it would be a good idea to implement such searching].</div>
<div><br>
</div>
<div>If you tried adding</div>
<div> PetscViewerHDF5PushGroup(hdf5Viewer, "/fields/Solution", ierr)</div>
<div>you likely pushed a wrong group. If the Vec name was set to "Solution" like in your snippet [using PetscObjectSetName()], the absolute dataset name to look up would be "/fields/Solution/Solution".</div>
<div><br>
</div>
<div>But in your file, there's just a dataset "/fields/Solution", so its parent group is just "/fields". So please try pushing this.</div>
<div><br>
</div>
<div>I would gladly try to reproduce your case - perhaps the error handling should be improved so that it would guide you into the right direction. But it would be helpful to know exactly what you're doing - the snippet with VecView() above should produce "/Solution"
dataset but in the file you're sending, there's "/fields/Solution".</div>
<div><br>
</div>
<div>Note also you don't need to do VecZeroEntries() before loading because VecLoad() fully rewrites the Vec data in memory anyway.</div>
<br>
<blockquote type="cite">
<div>
<div dir="ltr">
<div><br>
</div>
<div>I would appreciate it if anyone could give me pointers on this issue ...
<br>
</div>
<div><br>
</div>
<div>Thank you very much in advance !!</div>
<div><br>
</div>
<div>Thibault<br>
</div>
</div>
</div>
</blockquote>
<br>
</div>
<div>Thanks,</div>
<div>Vaclav</div>
<br>
</div>
</div>
</blockquote></div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><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>
</div></blockquote></div><br></div></div></blockquote></div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><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>
</blockquote></div></div>
</blockquote></div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><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>
</blockquote></div></div>
</blockquote></div>