<div dir="ltr">The PETSC_DIR exactly corresponds to the previous one, so I guess that rules option b) out, except if a specific option is required to overwrite a previous installation of PETSc. As for a), well I thought reconfiguring pretty direct, you're welcome to give me a hint as to what could be wrong in the following process.<br><div><br>Steps to reproduce this behaviour are as follows :<br>* Run <a href="https://hub.docker.com/r/dolfinx/dolfinx" target="_blank">this docker container</a>
<br></div><div>* Do : python3 -c<span id="gmail-m_7701977338169516942gmail-LC1" lang="python"><span> "from petsc4py import PETSc</span>; <span>PETSc</span><span>.</span><span>Viewer</span><span>().</span><span>createHDF5</span><span>(</span><span>'dummy.h5')"</span></span></div><div><span id="gmail-m_7701977338169516942gmail-LC1" lang="python"><span><br></span></span></div><div><span id="gmail-m_7701977338169516942gmail-LC1" lang="python"><span>After you get the error Unknown PetscViewer type, feel free to try :</span></span></div><div><span id="gmail-m_7701977338169516942gmail-LC1" lang="python"><span><br></span></span></div><div><span id="gmail-m_7701977338169516942gmail-LC1" lang="python"><span>* cd /usr/local/petsc/</span></span></div><div><span id="gmail-m_7701977338169516942gmail-LC1" lang="python"><span>* ./configure --with-hfd5</span></span></div><div><span id="gmail-m_7701977338169516942gmail-LC1" lang="python"><span>*
make
PETSC_DIR=/usr/local/petsc PETSC-ARCH=linux-gnu-real-32 all</span></span></div><div><span id="gmail-m_7701977338169516942gmail-LC1" lang="python"><span><br></span></span></div><div><span id="gmail-m_7701977338169516942gmail-LC1" lang="python"><span>Then repeat the MWE and observe absolutely no behavioural change whatsoever. I'm afraid I don't know PETSc well enough to be surprised by that.<br></span></span></div><div><span id="gmail-m_7701977338169516942gmail-LC1" lang="python"><span></span></span></div><div><br>Quentin<br></div></div><br clear="all"><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><span style="font-family:"Arial",sans-serif;color:black"> </span>
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<span style="font-size:11pt;font-family:"Berlin Sans FB",sans-serif;color:rgb(127,127,127)">Quentin CHEVALIER – IA parcours recherche</span></p>
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<span style="font-size:11pt;font-family:"Berlin Sans FB",sans-serif;color:rgb(127,127,127)">LadHyX - Ecole polytechnique</span></p>
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<span style="font-size:11pt;font-family:"Berlin Sans FB",sans-serif;color:rgb(127,127,127)">__________</span></p></td></tr></tbody></table></div></div></div></div><br><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 6 Dec 2021 at 19:24, Matthew Knepley <<a href="mailto:knepley@gmail.com">knepley@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"><div dir="ltr">On Mon, Dec 6, 2021 at 1:22 PM Quentin Chevalier <<a href="mailto:quentin.chevalier@polytechnique.edu" target="_blank">quentin.chevalier@polytechnique.edu</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">It failed all of the tests included in `make<br>
PETSC_DIR=/usr/local/petsc PETSC-ARCH=linux-gnu-real-32 check`, with<br>
the error `/usr/bin/bash: line 1: cd: src/snes/tutorials: No such file<br>
or directory`<br>
<br>
I am therefore fairly confident this a "file absence" problem, and not<br>
a compilation problem.<br>
<br>
I repeat that there was no error at compilation stage. The final stage<br>
did present `gmake[3]: Nothing to be done for 'libs'.` but that's all.<br>
<br>
Again, running `./configure --with-hdf5` followed by a `make<br>
PETSC_DIR=/usr/local/petsc PETSC-ARCH=linux-gnu-real-32 all` does not<br>
change the problem. I get the same error at the same position as<br>
before.<br></blockquote><div><br></div><div>If you reconfigured and rebuilt, it is impossible to get the same error, so</div><div><br></div><div> a) You did not reconfigure</div><div><br></div><div> b) Your new build is somewhere else on the machine</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">
I will comment I am running on OpenSUSE.<br>
<br>
Quentin<br>
<br>
On Mon, 6 Dec 2021 at 19:09, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:<br>
><br>
> On Mon, Dec 6, 2021 at 1:08 PM Quentin Chevalier <<a href="mailto:quentin.chevalier@polytechnique.edu" target="_blank">quentin.chevalier@polytechnique.edu</a>> wrote:<br>
>><br>
>> Hello Matthew and thanks for your quick response.<br>
>><br>
>> I'm afraid I did try to snoop around the container and rerun PETSc's<br>
>> configure with the --with-hdf5 option, to absolutely no avail.<br>
>><br>
>> I didn't see any errors during config or make, but it failed the tests<br>
>> (which aren't included in the minimal container I suppose)<br>
><br>
><br>
> Failed which tests? What was the error?<br>
><br>
> Thanks,<br>
><br>
> Matt<br>
><br>
>><br>
>> Quentin<br>
>><br>
>><br>
>><br>
>> Quentin CHEVALIER – IA parcours recherche<br>
>><br>
>> LadHyX - Ecole polytechnique<br>
>><br>
>> __________<br>
>><br>
>><br>
>><br>
>> On Mon, 6 Dec 2021 at 19:02, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:<br>
>> ><br>
>> > On Mon, Dec 6, 2021 at 11:28 AM Quentin Chevalier <<a href="mailto:quentin.chevalier@polytechnique.edu" target="_blank">quentin.chevalier@polytechnique.edu</a>> wrote:<br>
>> >><br>
>> >> Hello PETSc users,<br>
>> >><br>
>> >> This email is a duplicata of this gitlab issue, sorry for any inconvenience caused.<br>
>> >><br>
>> >> I want to compute a PETSc vector in real mode, than perform calculations with it in complex mode. I want as much of this process to be parallel as possible. Right now, I compile PETSc in real mode, compute my vector and save it to a file, then switch to complex mode, read it, and move on.<br>
>> >><br>
>> >> This creates unexpected behaviour using MPIIO, so on Lisandro Dalcinl's advice I'm moving to HDF5 format. My code is as follows (taking inspiration from petsc4py doc, a bitbucket example and another one, all top Google results for 'petsc hdf5') :<br>
>> >>><br>
>> >>> viewer = PETSc.Viewer().createHDF5(file_name, 'r', COMM_WORLD)<br>
>> >>> q.load(viewer)<br>
>> >>> q.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)<br>
>> >><br>
>> >><br>
>> >> This crashes my code. I obtain traceback :<br>
>> >>><br>
>> >>> File "/home/shared/code.py", line 121, in Load<br>
>> >>> viewer = PETSc.Viewer().createHDF5(file_name, 'r', COMM_WORLD)<br>
>> >>> File "PETSc/Viewer.pyx", line 182, in petsc4py.PETSc.Viewer.createHDF5<br>
>> >>> petsc4py.PETSc.Error: error code 86<br>
>> >>> [0] PetscViewerSetType() at /usr/local/petsc/src/sys/classes/viewer/interface/viewreg.c:442<br>
>> >>> [0] Unknown type. Check for miss-spelling or missing package: <a href="https://petsc.org/release/install/install/#external-packages" rel="noreferrer" target="_blank">https://petsc.org/release/install/install/#external-packages</a><br>
>> >>> [0] Unknown PetscViewer type given: hdf5<br>
>> ><br>
>> > This means that PETSc has not been configured with HDF5 (--with-hdf5 or --download-hdf5), so the container should be updated.<br>
>> ><br>
>> > THanks,<br>
>> ><br>
>> > Matt<br>
>> ><br>
>> >><br>
>> >> I have petsc4py 3.16 from this docker container (list of dependencies include PETSc and petsc4py).<br>
>> >><br>
>> >> I'm pretty sure this is not intended behaviour. Any insight as to how to fix this issue (I tried running ./configure --with-hdf5 to no avail) or more generally to perform this jiggling between real and complex would be much appreciated,<br>
>> >><br>
>> >> Kind regards.<br>
>> >><br>
>> >> Quentin<br>
>> ><br>
>> ><br>
>> ><br>
>> > --<br>
>> > 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<br>
>> ><br>
>> > <a href="https://www.cse.buffalo.edu/~knepley/" rel="noreferrer" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br>
><br>
><br>
><br>
> --<br>
> 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<br>
><br>
> <a href="https://www.cse.buffalo.edu/~knepley/" rel="noreferrer" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br>
</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>