<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><br class=""></div> Matt,<div class=""><br class=""></div><div class=""> 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 class=""><br class=""></div><div class=""> Barry</div><div class=""><br class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 7, 2021, at 6:32 PM, Matthew Knepley <<a href="mailto:knepley@gmail.com" class="">knepley@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class="">On Wed, Apr 7, 2021 at 4:10 PM Thibault Bridel-Bertomeu <<a href="mailto:thibault.bridelbertomeu@gmail.com" class="">thibault.bridelbertomeu@gmail.com</a>> wrote:<br class=""></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" class="">Hello Vaclav,<div class=""><br class=""></div><div class="">Thank you for your quick answer !!</div><div class="">OK so, if I need to push the group, I added :</div><div class=""><br class=""></div><div class=""><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" class=""><div class=""><span style="color:rgb(197,134,192)" class="">call</span> <span style="color:rgb(220,220,170)" class="">PetscViewerHDF5PushGroup</span>(hdf5Viewer, <span style="color:rgb(206,145,120)" class="">"/fields"</span>, ierr); CHKERRA(ierr)</div></div></div><div class=""><br class=""></div><div class="">right after the call to PetscViewerFileSetName.</div><div class="">The result is the same, it produces the following error :</div><div class=""><br class=""></div><div class=""><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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><b class="">[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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[0]PETSC ERROR: See <a href="https://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank" class="">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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[0]PETSC ERROR: Petsc Development GIT revision: v3.14.4-671-g707297fd510<span class=""> </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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[0]PETSC ERROR: ../../../bin/eulerian3D on a<span class=""> </span>named macbook-pro-de-thibault.home by tbridel Wed Apr<span class=""> </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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[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);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[0]PETSC ERROR: #9 User provided function() line 0 in User file</span></div></div><div class=""><br class=""></div><div class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class=""><div class="">Do you know where it could come from ?</div></div></div></div></div></div></div></div></div></div></div></div></div></blockquote><div class=""><br class=""></div><div class="">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 class="">the Viewer has to know this. The TS does this automatically, so you have an array</div><div class=""><br class=""></div><div class=""> <span style="font-variant-ligatures:no-common-ligatures;font-size:11px" class="">GROUP "fields" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> DATASET "Solution" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> DATATYPE H5T_IEEE_F64LE</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> DATASPACE SIMPLE { ( 21, 5060, 5 ) / ( H5S_UNLIMITED, 5060, 5 ) }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> }</span></div><div class=""><br class=""></div><div class="">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 class="">of length 21 * 5 = 105. You can tell your reader which timestep you want to extract using</div><div class=""><br class=""></div><div class=""> <a href="https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Viewer/PetscViewerHDF5SetTimestep.html" class="">https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Viewer/PetscViewerHDF5SetTimestep.html</a><br class=""></div><div class=""><br class=""></div><div class=""> Thanks,</div><div class=""><br class=""></div><div class=""> Matt</div><div class=""> </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" class=""><div class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class=""><div class="">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 class=""><br class=""></div><div class="">Cheers and thank you again for your help !!</div><div class=""><br class=""></div><div class="">Thibault</div></div></div></div></div></div></div></div></div></div></div></div></div><br class=""><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" class="">vaclav.hapla@erdw.ethz.ch</a>> a écrit :<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="">
<div class=""><span style="" class="">Dear Thibault</span></div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 7 Apr 2021, at 08:18, Thibault Bridel-Bertomeu <<a href="mailto:thibault.bridelbertomeu@gmail.com" target="_blank" class="">thibault.bridelbertomeu@gmail.com</a>> wrote:</div>
<br class="">
<div class="">
<div dir="ltr" class="">
<div class="">Dear all, <br class="">
</div>
<div class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
<div class="">Basically, a program writes a vector with the HDF5 writer like this :</div>
<div class=""></div>
<div class="">
<pre lang="fortran" class=""><span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC45" lang="fortran" class=""><span class=""> </span><span class=""> call</span><span class=""> </span><span class="">DMCreateGlobalVector</span><span class="">(</span><span class="">dm</span><span class="">,</span><span class=""> </span><span class="">sol</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span>
<span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC46" lang="fortran" class=""><span class=""> </span><span class=""> call</span><span class=""> </span><span class="">VecZeroEntries</span><span class="">(X</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span>
<span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC47" lang="fortran" class=""><span class=""> </span><span class=""> call</span><span class=""> </span><span class="">PetscObjectSetName</span><span class="">(X</span><span class="">,</span><span class=""> </span><span class="">"Solution"</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span><span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC65" lang="fortran" class=""><span class=""> <br class=""></span></span></pre>
<pre lang="fortran" class=""><span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC65" lang="fortran" class=""><span class=""> < do something with X to fill it up with relevant data ><br class=""></span></span></pre>
<pre lang="fortran" class=""><span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC65" lang="fortran" class=""><span class=""> </span><span class="">call</span><span class=""> </span><span class="">PetscViewerCreate</span><span class="">(</span><span class="">PETSC_COMM_WORLD</span><span class="">,</span><span class=""> </span><span class="">hdf5Viewer</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span>
<span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC66" lang="fortran" class=""><span class=""> </span><span class="">call</span><span class=""> </span><span class="">PetscViewerSetType</span><span class="">(</span><span class="">hdf5Viewer</span><span class="">,</span><span class=""> </span><span class="">PETSCVIEWERHDF5</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span>
<span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC67" lang="fortran" class=""><span class=""> </span><span class="">call</span><span class=""> </span><span class="">PetscViewerFileSetMode</span><span class="">(</span><span class="">hdf5Viewer</span><span class="">,</span><span class=""> </span><span class="">FILE_MODE_WRITE</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">);</span></span>
<span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC68" lang="fortran" class=""><span class=""> </span><span class="">write</span><span class="">(</span><span class="">filename</span><span class="">,</span><span class="">'(A,I5.5,A)'</span><span class="">)</span><span class=""> </span><span class="">"restart_"</span><span class="">,</span><span class=""> </span><span class="">stepnum</span><span class="">,</span><span class=""> </span><span class="">".h5"</span></span>
<span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC69" lang="fortran" class=""><span class=""> </span><span class="">call</span><span class=""> </span><span class="">PetscViewerFileSetName</span><span class="">(</span><span class="">hdf5Viewer</span><span class="">,</span><span class=""> </span><span class="">trim</span><span class="">(</span><span class="">filename</span><span class="">),</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span>
<span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC70" lang="fortran" class=""><span class=""> </span><span class="">call</span><span class=""> </span><span class="">VecView</span><span class="">(</span><span class="">X</span><span class="">,</span><span class=""> </span><span class="">hdf5Viewer</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span>
<span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC71" lang="fortran" class=""><span class=""> </span><span class="">call</span><span class=""> </span><span class="">PetscViewerDestroy</span><span class="">(</span><span class="">hdf5Viewer</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span>
</pre>
</div>
<div class="">and the same program (but with different start-up options, say) re-reads such a file like this :</div>
<div class=""><br class="">
</div>
<div class="">
<pre lang="fortran" class=""><span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC64" lang="fortran" class=""><span class=""><span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC45" lang="fortran" class=""><span class=""> </span><span class=""> call</span><span class=""> </span><span class="">DMCreateGlobalVector</span><span class="">(</span><span class="">dm</span><span class="">,</span><span class=""> </span><span class="">sol</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span>
<span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC46" lang="fortran" class=""><span class=""> </span><span class=""> call</span><span class=""> </span><span class="">VecZeroEntries</span><span class="">(</span><span class="">sol</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span>
<span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC47" lang="fortran" class=""><span class=""> </span><span class=""> call</span><span class=""> </span><span class="">PetscObjectSetName</span><span class="">(</span><span class="">sol</span><span class="">,</span><span class=""> </span><span class="">"Solution"</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span> <br class=""> </span><span class="">call</span><span class=""> </span><span class="">PetscViewerCreate</span><span class="">(</span><span class="">PETSC_COMM_WORLD</span><span class="">,</span><span class=""> </span><span class="">hdf5Viewer</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span>
<span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC65" lang="fortran" class=""><span class=""> </span><span class="">call</span><span class=""> </span><span class="">PetscViewerSetType</span><span class="">(</span><span class="">hdf5Viewer</span><span class="">,</span><span class=""> </span><span class="">PETSCVIEWERHDF5</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span>
<span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC66" lang="fortran" class=""><span class=""> </span><span class="">call</span><span class=""> </span><span class="">PetscViewerFileSetMode</span><span class="">(</span><span class="">hdf5Viewer</span><span class="">,</span><span class=""> </span><span class="">FILE_MODE_READ</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span>
<span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC67" lang="fortran" class=""><span class=""> </span><span class="">call</span><span class=""> </span><span class="">PetscViewerFileSetName</span><span class="">(</span><span class="">hdf5Viewer</span><span class="">,</span><span class=""> </span><span class="">trim</span><span class="">(</span><span class="">restartname</span><span class="">),</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span>
<span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC68" lang="fortran" class=""><span class=""> </span><span class="">call</span><span class=""> </span><span class="">VecLoad</span><span class="">(</span><span class="">sol</span><span class="">,</span><span class=""> </span><span class="">hdf5Viewer</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span>
<span id="gmail-m_3416988461638334820gmail-m_6621939839129280338gmail-LC69" lang="fortran" class=""><span class=""> </span><span class="">call</span><span class=""> </span><span class="">PetscViewerDestroy</span><span class="">(</span><span class="">hdf5Viewer</span><span class="">,</span><span class=""> </span><span class="">ierr</span><span class="">);</span><span class=""> </span><span class="">CHKERRA</span><span class="">(</span><span class="">ierr</span><span class="">)</span></span>
</pre>
</div>
<div class=""><br class="">
</div>
<div class="">Such a dataset can be found under this link : <a href="https://drive.google.com/file/d/1owLAx5vknNhj61_5ieAwnWOR9cmkTseL/view?usp=sharing" target="_blank" class="">
https://drive.google.com/file/d/1owLAx5vknNhj61_5ieAwnWOR9cmkTseL/view?usp=sharing</a></div>
</div>
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</blockquote>
<div class=""><br class="">
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<div class="">
<div style="" class="">I'm just looking at the HDF5 file. The structure is like this</div>
<div style="" class=""><br class="">
</div>
<div style="" class="">
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">> $PETSC_DIR/$PETSC_ARCH/bin/h5dump -H restart_00020.h5</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> </span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">HDF5 "restart_00020.h5" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">GROUP "/" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> GROUP "cell_fields" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> DATASET "Solution_FV solver" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> DATATYPE H5T_IEEE_F64LE</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> DATASPACE SIMPLE { ( 21, 3884, 5 ) / ( H5S_UNLIMITED, 3884, 5 ) }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> ATTRIBUTE "vector_field_type" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> DATATYPE H5T_STRING {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> STRSIZE 7;</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> STRPAD H5T_STR_NULLTERM;</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> CSET H5T_CSET_ASCII;</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> CTYPE H5T_C_S1;</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> DATASPACE SCALAR</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> GROUP "fields" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> DATASET "Solution" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> DATATYPE H5T_IEEE_F64LE</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> DATASPACE SIMPLE { ( 21, 5060, 5 ) / ( H5S_UNLIMITED, 5060, 5 ) }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> DATASET "time" {</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> DATATYPE H5T_IEEE_F64LE</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> DATASPACE SIMPLE { ( 21, 1 ) / ( H5S_UNLIMITED, 1 ) }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> }</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">}</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">}</span></div>
</div>
</div>
<br class="">
<blockquote type="cite" class="">
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<div class="">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 class="">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 class="">I tried adding 'PetscViewerHDF5PushGroup(hdf5Viewer, "/fields/Solution", ierr)' to force it to read that group, but it does not change anything.</div>
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</blockquote>
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</div>
<div class="">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 class=""><br class="">
</div>
<div class="">If you tried adding</div>
<div class=""> PetscViewerHDF5PushGroup(hdf5Viewer, "/fields/Solution", ierr)</div>
<div class="">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 class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
<div class="">Note also you don't need to do VecZeroEntries() before loading because VecLoad() fully rewrites the Vec data in memory anyway.</div>
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<blockquote type="cite" class="">
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<div class="">I would appreciate it if anyone could give me pointers on this issue ...
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</div>
<div class="">Thank you very much in advance !!</div>
<div class=""><br class="">
</div>
<div class="">Thibault<br class="">
</div>
</div>
</div>
</blockquote>
<br class="">
</div>
<div class="">Thanks,</div>
<div class="">Vaclav</div>
<br class="">
</div>
</div>
</blockquote></div>
</blockquote></div><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br class="">-- Norbert Wiener</div><div class=""><br class=""></div><div class=""><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank" class="">https://www.cse.buffalo.edu/~knepley/</a><br class=""></div></div></div></div></div></div></div></div>
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