<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">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>
<p 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></p>
<p 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 style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: Unexpected data in file</span></p>
<p 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 style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: Global size of array in file is 105, not 25300 as expected</span></p>
<p 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 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></p>
<p 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 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></p>
<p 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 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></p>
<p 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 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></p>
<p 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 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></p>
<p 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 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></p>
<p 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 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></p>
<p 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 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></p>
<p 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 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></p>
<p 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 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></p>
<p 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 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></p>
<p 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 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></p>
<p 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 style="font-variant-ligatures:no-common-ligatures">[0]PETSC ERROR: #9 User provided function() line 0 in User file</span></p></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">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 style="color:rgb(0,0,0)">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_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_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_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_3416988461638334820gmail-m_6621939839129280338gmail-LC65" lang="fortran"><span> <br></span></span></pre>
<pre lang="fortran"><span id="gmail-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_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_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_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_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_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_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_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_3416988461638334820gmail-m_6621939839129280338gmail-LC64" lang="fortran"><span><span id="gmail-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_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_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_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_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_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_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_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 style="color:rgb(0,0,0)">I'm just looking at the HDF5 file. The structure is like this</div>
<div style="color:rgb(0,0,0)"><br>
</div>
<div style="color:rgb(0,0,0)">
<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<div>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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<div>I would appreciate it if anyone could give me pointers on this issue ...
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<div>Thank you very much in advance !!</div>
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<div>Thibault<br>
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<div>Thanks,</div>
<div>Vaclav</div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>