<div dir="ltr"><div dir="ltr">On Mon, Sep 7, 2020 at 9:58 AM Berend van Wachem <<a href="mailto:berend.vanwachem@ovgu.de">berend.vanwachem@ovgu.de</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">Dear Jed,<br>
<br>
Thanks for the suggestion. I've tried writing to .vtu (see attached <br>
code), but that doesn't seem to work for a section containing multiple <br>
fields? Upon running the attached code, I get the error:<br></blockquote><div><br></div><div>Yes, Jed removed that error check today. It should make it to master is a few days. You can just delete that line I think.</div><div>I still prefer to use HDF5 and XDMF since it is much more flexible, and easier to store many things in. I put lots of fields</div><div>in the HDF5 file (and hopefully will get time to support many meshes in it), and also support timesteps. I recognize that</div><div>VTU is familiar, which is a plus for that format.</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">
$ mpirun -np 1 visualizemesh<br>
[0]PETSC ERROR: --------------------- Error Message <br>
--------------------------------------------------------------<br>
[0]PETSC ERROR: Petsc has generated inconsistent data<br>
[0]PETSC ERROR: Total number of field components 1 != block size 4<br>
[0]PETSC ERROR: See <a href="https://www.mcs.anl.gov/petsc/documentation/faq.html" rel="noreferrer" target="_blank">https://www.mcs.anl.gov/petsc/documentation/faq.html</a> <br>
for trouble shooting.<br>
[0]PETSC ERROR: Petsc Release Version 3.13.3, Jul 01, 2020<br>
[0]PETSC ERROR: visualizemesh on a linux-gcc-opt named <br>
<a href="http://ivt14.mb.uni-magdeburg.de" rel="noreferrer" target="_blank">ivt14.mb.uni-magdeburg.de</a> by berend Mon Sep 7 15:55:10 2020<br>
[0]PETSC ERROR: Configure options --with-debugging=0 COPTFLAGS="-O3 <br>
-march=native -mtune=native" CXXOPTFLAGS="-O3 -march=native <br>
-mtune=native" FOPTFLAGS="-O3 -march=native -mtune=native" --with-clean <br>
--download-metis=yes --download-parmetis=yes --download-hdf5 <br>
--download-p4est --download-triangle --download-tetgen <br>
--with-zlib-lib=/usr/lib64/libz.a --with-zlib-include=/usr/include<br>
[0]PETSC ERROR: #1 DMPlexVTKWriteAll_VTU() line 334 in <br>
/usr/local/petsc-3.13.3/src/dm/impls/plex/plexvtu.c<br>
[0]PETSC ERROR: #2 DMPlexVTKWriteAll() line 688 in <br>
/usr/local/petsc-3.13.3/src/dm/impls/plex/plexvtk.c<br>
[0]PETSC ERROR: #3 PetscViewerFlush_VTK() line 100 in <br>
/usr/local/petsc-3.13.3/src/sys/classes/viewer/impls/vtk/vtkv.c<br>
[0]PETSC ERROR: #4 PetscViewerFlush() line 26 in <br>
/usr/local/petsc-3.13.3/src/sys/classes/viewer/interface/flush.c<br>
[0]PETSC ERROR: #5 PetscViewerDestroy() line 113 in <br>
/usr/local/petsc-3.13.3/src/sys/classes/viewer/interface/view.c<br>
[0]PETSC ERROR: #6 main() line 102 in visualizemesh.c<br>
[0]PETSC ERROR: No PETSc Option Table entries<br>
[0]PETSC ERROR: ----------------End of Error Message -------send entire <br>
error message to petsc-maint@mcs.anl.gov----------<br>
application called MPI_Abort(MPI_COMM_SELF, 102077) - process 0<br>
<br>
<br>
Or am I making a mistake?<br>
<br>
Thanks, best wishes, Berend.<br>
<br>
<br>
<br>
<br>
On 2020-09-03 16:53, Jed Brown wrote:<br>
> Use the xml format (not the legacy format) by naming your file.vtu <br>
> instead of file.vtk<br>
> <br>
> On Thu, Sep 3, 2020, at 8:17 AM, Berend van Wachem wrote:<br>
>> Dear PETSc,<br>
>><br>
>> What is the best way to write data from a DMPLEX vector to file, so it<br>
>> can be viewed with paraview?<br>
>> I've found that the standard VTK format works for a serial job, but if<br>
>> there is more than 1 processor, the geometry data gets messed up.<br>
>> I've attached a small working example for a cylinder and the visualised<br>
>> geometry with paraview for 1 processors and 4 processors.<br>
>> Any pointers or "best practice" very much appreciated.<br>
>><br>
>> Best regards,<br>
>><br>
>> Berend.<br>
>><br>
>><br>
>><br>
>><br>
>> *Attachments:*<br>
>><br>
>> * visualisemesh-1proc.png<br>
>> * visualisemesh-4proc.png<br>
>> * visualizemesh.c<br>
</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>