<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=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 6 Dec 2021, at 7:42 PM, Quentin Chevalier <<a href="mailto:quentin.chevalier@polytechnique.edu" class="">quentin.chevalier@polytechnique.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">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 class=""><div class=""><br class="">Steps to reproduce this behaviour are as follows :<br class="">* Run <a href="https://hub.docker.com/r/dolfinx/dolfinx" target="_blank" class="">this docker container</a>
<br class=""></div><div class="">* Do : python3 -c<span id="gmail-m_7701977338169516942gmail-LC1" lang="python" class=""><span class=""> "from petsc4py import PETSc</span>; <span class="">PETSc</span><span class="">.</span><span class="">Viewer</span><span class="">().</span><span class="">createHDF5</span><span class="">(</span><span class="">'dummy.h5')"</span></span></div><div class=""><span id="gmail-m_7701977338169516942gmail-LC1" lang="python" class=""><span class=""><br class=""></span></span></div><div class=""><span id="gmail-m_7701977338169516942gmail-LC1" lang="python" class=""><span class="">After you get the error Unknown PetscViewer type, feel free to try :</span></span></div><div class=""><span id="gmail-m_7701977338169516942gmail-LC1" lang="python" class=""><span class=""><br class=""></span></span></div><div class=""><span id="gmail-m_7701977338169516942gmail-LC1" lang="python" class=""><span class="">* cd /usr/local/petsc/</span></span></div><div class=""><span id="gmail-m_7701977338169516942gmail-LC1" lang="python" class=""><span class="">* ./configure --with-hfd5</span></span></div></div></div></blockquote><div><br class=""></div><div>It’s hdf5, not hfd5.</div><div>It’s PETSC_ARCH, not PETSC-ARCH.</div><div>PETSC_ARCH is missing from your configure line.</div><div><br class=""></div><div>Thanks,</div><div>Pierre</div><div><br class=""></div><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class=""><span id="gmail-m_7701977338169516942gmail-LC1" lang="python" class=""><span class="">*
make
PETSC_DIR=/usr/local/petsc PETSC-ARCH=linux-gnu-real-32 all</span></span></div><div class=""><span id="gmail-m_7701977338169516942gmail-LC1" lang="python" class=""><span class=""><br class=""></span></span></div><div class=""><span id="gmail-m_7701977338169516942gmail-LC1" lang="python" class=""><span class="">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 class=""></span></span></div><div class=""><span id="gmail-m_7701977338169516942gmail-LC1" lang="python" class=""><span class=""></span></span></div><div class=""><br class="">Quentin<br class=""></div></div><br clear="all" class=""><div class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><span style="font-family: Arial, sans-serif;" class=""> </span>
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<span style="font-size:11pt;font-family:"Berlin Sans FB",sans-serif;color:rgb(127,127,127)" class="">Quentin CHEVALIER – IA parcours recherche</span></p><p class="MsoNormal" style="margin-left:0.9pt;line-height:12pt;break-after:avoid">
<span style="font-size:11pt;font-family:"Berlin Sans FB",sans-serif;color:rgb(127,127,127)" class="">LadHyX - Ecole polytechnique</span></p><p class="MsoNormal" style="margin-left:0.9pt;line-height:12pt;break-after:avoid">
<span style="font-size:11pt;font-family:"Berlin Sans FB",sans-serif;color:rgb(127,127,127)" class="">__________</span></p></td></tr></tbody></table></div></div></div></div><br class=""><br class=""><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" class="">knepley@gmail.com</a>> wrote:<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 dir="ltr" class=""><div dir="ltr" class="">On Mon, Dec 6, 2021 at 1:22 PM Quentin Chevalier <<a href="mailto:quentin.chevalier@polytechnique.edu" target="_blank" class="">quentin.chevalier@polytechnique.edu</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">It failed all of the tests included in `make<br class="">
PETSC_DIR=/usr/local/petsc PETSC-ARCH=linux-gnu-real-32 check`, with<br class="">
the error `/usr/bin/bash: line 1: cd: src/snes/tutorials: No such file<br class="">
or directory`<br class="">
<br class="">
I am therefore fairly confident this a "file absence" problem, and not<br class="">
a compilation problem.<br class="">
<br class="">
I repeat that there was no error at compilation stage. The final stage<br class="">
did present `gmake[3]: Nothing to be done for 'libs'.` but that's all.<br class="">
<br class="">
Again, running `./configure --with-hdf5` followed by a `make<br class="">
PETSC_DIR=/usr/local/petsc PETSC-ARCH=linux-gnu-real-32 all` does not<br class="">
change the problem. I get the same error at the same position as<br class="">
before.<br class=""></blockquote><div class=""><br class=""></div><div class="">If you reconfigured and rebuilt, it is impossible to get the same error, so</div><div class=""><br class=""></div><div class=""> a) You did not reconfigure</div><div class=""><br class=""></div><div class=""> b) Your new build is somewhere else on the machine</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">
I will comment I am running on OpenSUSE.<br class="">
<br class="">
Quentin<br class="">
<br class="">
On Mon, 6 Dec 2021 at 19:09, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank" class="">knepley@gmail.com</a>> wrote:<br class="">
><br class="">
> On Mon, Dec 6, 2021 at 1:08 PM Quentin Chevalier <<a href="mailto:quentin.chevalier@polytechnique.edu" target="_blank" class="">quentin.chevalier@polytechnique.edu</a>> wrote:<br class="">
>><br class="">
>> Hello Matthew and thanks for your quick response.<br class="">
>><br class="">
>> I'm afraid I did try to snoop around the container and rerun PETSc's<br class="">
>> configure with the --with-hdf5 option, to absolutely no avail.<br class="">
>><br class="">
>> I didn't see any errors during config or make, but it failed the tests<br class="">
>> (which aren't included in the minimal container I suppose)<br class="">
><br class="">
><br class="">
> Failed which tests? What was the error?<br class="">
><br class="">
> Thanks,<br class="">
><br class="">
> Matt<br class="">
><br class="">
>><br class="">
>> Quentin<br class="">
>><br class="">
>><br class="">
>><br class="">
>> Quentin CHEVALIER – IA parcours recherche<br class="">
>><br class="">
>> LadHyX - Ecole polytechnique<br class="">
>><br class="">
>> __________<br class="">
>><br class="">
>><br class="">
>><br class="">
>> On Mon, 6 Dec 2021 at 19:02, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank" class="">knepley@gmail.com</a>> wrote:<br class="">
>> ><br class="">
>> > On Mon, Dec 6, 2021 at 11:28 AM Quentin Chevalier <<a href="mailto:quentin.chevalier@polytechnique.edu" target="_blank" class="">quentin.chevalier@polytechnique.edu</a>> wrote:<br class="">
>> >><br class="">
>> >> Hello PETSc users,<br class="">
>> >><br class="">
>> >> This email is a duplicata of this gitlab issue, sorry for any inconvenience caused.<br class="">
>> >><br class="">
>> >> 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 class="">
>> >><br class="">
>> >> 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 class="">
>> >>><br class="">
>> >>> viewer = PETSc.Viewer().createHDF5(file_name, 'r', COMM_WORLD)<br class="">
>> >>> q.load(viewer)<br class="">
>> >>> q.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)<br class="">
>> >><br class="">
>> >><br class="">
>> >> This crashes my code. I obtain traceback :<br class="">
>> >>><br class="">
>> >>> File "/home/shared/code.py", line 121, in Load<br class="">
>> >>> viewer = PETSc.Viewer().createHDF5(file_name, 'r', COMM_WORLD)<br class="">
>> >>> File "PETSc/Viewer.pyx", line 182, in petsc4py.PETSc.Viewer.createHDF5<br class="">
>> >>> petsc4py.PETSc.Error: error code 86<br class="">
>> >>> [0] PetscViewerSetType() at /usr/local/petsc/src/sys/classes/viewer/interface/viewreg.c:442<br class="">
>> >>> [0] Unknown type. Check for miss-spelling or missing package: <a href="https://petsc.org/release/install/install/#external-packages" rel="noreferrer" target="_blank" class="">https://petsc.org/release/install/install/#external-packages</a><br class="">
>> >>> [0] Unknown PetscViewer type given: hdf5<br class="">
>> ><br class="">
>> > This means that PETSc has not been configured with HDF5 (--with-hdf5 or --download-hdf5), so the container should be updated.<br class="">
>> ><br class="">
>> > THanks,<br class="">
>> ><br class="">
>> > Matt<br class="">
>> ><br class="">
>> >><br class="">
>> >> I have petsc4py 3.16 from this docker container (list of dependencies include PETSc and petsc4py).<br class="">
>> >><br class="">
>> >> 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 class="">
>> >><br class="">
>> >> Kind regards.<br class="">
>> >><br class="">
>> >> Quentin<br class="">
>> ><br class="">
>> ><br class="">
>> ><br class="">
>> > --<br 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<br class="">
>> ><br class="">
>> > <a href="https://www.cse.buffalo.edu/~knepley/" rel="noreferrer" target="_blank" class="">https://www.cse.buffalo.edu/~knepley/</a><br class="">
><br class="">
><br class="">
><br class="">
> --<br 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<br class="">
><br class="">
> <a href="https://www.cse.buffalo.edu/~knepley/" rel="noreferrer" target="_blank" class="">https://www.cse.buffalo.edu/~knepley/</a><br class="">
</blockquote></div><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class=""><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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