> On 6 Dec 2021, at 7:42 PM, Quentin Chevalier > <quentin.cheval...@polytechnique.edu> wrote: > > 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. > > Steps to reproduce this behaviour are as follows : > * Run this docker container <https://hub.docker.com/r/dolfinx/dolfinx> > * Do : python3 -c "from petsc4py import PETSc; > PETSc.Viewer().createHDF5('dummy.h5')" > > After you get the error Unknown PetscViewer type, feel free to try : > > * cd /usr/local/petsc/ > * ./configure --with-hfd5
It’s hdf5, not hfd5. It’s PETSC_ARCH, not PETSC-ARCH. PETSC_ARCH is missing from your configure line. Thanks, Pierre > * make PETSC_DIR=/usr/local/petsc PETSC-ARCH=linux-gnu-real-32 all > > 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. > > Quentin > > > > > Quentin CHEVALIER – IA parcours recherche > LadHyX - Ecole polytechnique > > __________ > > > > On Mon, 6 Dec 2021 at 19:24, Matthew Knepley <knep...@gmail.com > <mailto:knep...@gmail.com>> wrote: > On Mon, Dec 6, 2021 at 1:22 PM Quentin Chevalier > <quentin.cheval...@polytechnique.edu > <mailto:quentin.cheval...@polytechnique.edu>> wrote: > It failed all of the tests included in `make > PETSC_DIR=/usr/local/petsc PETSC-ARCH=linux-gnu-real-32 check`, with > the error `/usr/bin/bash: line 1: cd: src/snes/tutorials: No such file > or directory` > > I am therefore fairly confident this a "file absence" problem, and not > a compilation problem. > > I repeat that there was no error at compilation stage. The final stage > did present `gmake[3]: Nothing to be done for 'libs'.` but that's all. > > Again, running `./configure --with-hdf5` followed by a `make > PETSC_DIR=/usr/local/petsc PETSC-ARCH=linux-gnu-real-32 all` does not > change the problem. I get the same error at the same position as > before. > > If you reconfigured and rebuilt, it is impossible to get the same error, so > > a) You did not reconfigure > > b) Your new build is somewhere else on the machine > > Thanks, > > Matt > > I will comment I am running on OpenSUSE. > > Quentin > > On Mon, 6 Dec 2021 at 19:09, Matthew Knepley <knep...@gmail.com > <mailto:knep...@gmail.com>> wrote: > > > > On Mon, Dec 6, 2021 at 1:08 PM Quentin Chevalier > > <quentin.cheval...@polytechnique.edu > > <mailto:quentin.cheval...@polytechnique.edu>> wrote: > >> > >> Hello Matthew and thanks for your quick response. > >> > >> I'm afraid I did try to snoop around the container and rerun PETSc's > >> configure with the --with-hdf5 option, to absolutely no avail. > >> > >> I didn't see any errors during config or make, but it failed the tests > >> (which aren't included in the minimal container I suppose) > > > > > > Failed which tests? What was the error? > > > > Thanks, > > > > Matt > > > >> > >> Quentin > >> > >> > >> > >> Quentin CHEVALIER – IA parcours recherche > >> > >> LadHyX - Ecole polytechnique > >> > >> __________ > >> > >> > >> > >> On Mon, 6 Dec 2021 at 19:02, Matthew Knepley <knep...@gmail.com > >> <mailto:knep...@gmail.com>> wrote: > >> > > >> > On Mon, Dec 6, 2021 at 11:28 AM Quentin Chevalier > >> > <quentin.cheval...@polytechnique.edu > >> > <mailto:quentin.cheval...@polytechnique.edu>> wrote: > >> >> > >> >> Hello PETSc users, > >> >> > >> >> This email is a duplicata of this gitlab issue, sorry for any > >> >> inconvenience caused. > >> >> > >> >> 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. > >> >> > >> >> 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') : > >> >>> > >> >>> viewer = PETSc.Viewer().createHDF5(file_name, 'r', COMM_WORLD) > >> >>> q.load(viewer) > >> >>> q.ghostUpdate(addv=PETSc.InsertMode.INSERT, > >> >>> mode=PETSc.ScatterMode.FORWARD) > >> >> > >> >> > >> >> This crashes my code. I obtain traceback : > >> >>> > >> >>> File "/home/shared/code.py", line 121, in Load > >> >>> viewer = PETSc.Viewer().createHDF5(file_name, 'r', COMM_WORLD) > >> >>> File "PETSc/Viewer.pyx", line 182, in > >> >>> petsc4py.PETSc.Viewer.createHDF5 > >> >>> petsc4py.PETSc.Error: error code 86 > >> >>> [0] PetscViewerSetType() at > >> >>> /usr/local/petsc/src/sys/classes/viewer/interface/viewreg.c:442 > >> >>> [0] Unknown type. Check for miss-spelling or missing package: > >> >>> https://petsc.org/release/install/install/#external-packages > >> >>> <https://petsc.org/release/install/install/#external-packages> > >> >>> [0] Unknown PetscViewer type given: hdf5 > >> > > >> > This means that PETSc has not been configured with HDF5 (--with-hdf5 or > >> > --download-hdf5), so the container should be updated. > >> > > >> > THanks, > >> > > >> > Matt > >> > > >> >> > >> >> I have petsc4py 3.16 from this docker container (list of dependencies > >> >> include PETSc and petsc4py). > >> >> > >> >> 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, > >> >> > >> >> Kind regards. > >> >> > >> >> Quentin > >> > > >> > > >> > > >> > -- > >> > What most experimenters take for granted before they begin their > >> > experiments is infinitely more interesting than any results to which > >> > their experiments lead. > >> > -- Norbert Wiener > >> > > >> > https://www.cse.buffalo.edu/~knepley/ > >> > <https://www.cse.buffalo.edu/~knepley/> > > > > > > > > -- > > What most experimenters take for granted before they begin their > > experiments is infinitely more interesting than any results to which their > > experiments lead. > > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > <https://www.cse.buffalo.edu/~knepley/> > > > -- > What most experimenters take for granted before they begin their experiments > is infinitely more interesting than any results to which their experiments > lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/> > <image003.jpg>
