[petsc-users] How to read/write a HDF5 file using petsc4py ?

Quentin Chevalier quentin.chevalier at polytechnique.edu
Wed Dec 8 03:07:33 CST 2021 

@all thanks for your time it's heartening to see a lively community.

@Barry I've restarted the container and grabbed the .log file directly
after the docker magic. I've tried a make check, it unsurprisingly spews
the same answer as before :

Running check examples to verify correct installation
Using PETSC_DIR=/usr/local/petsc and PETSC_ARCH=linux-gnu-real-32
/usr/bin/bash: line 1: cd: src/snes/tutorials: No such file or directory
/usr/bin/bash: line 1: cd: src/snes/tutorials: No such file or directory
gmake[3]: *** No rule to make target 'testex19'.  Stop.
gmake[2]: *** [makefile:155: check_build] Error 2


@Matthew ok will do, but I think @Lawrence has already provided that
answer. It's possible to change the dockerfile and recompute the dolfinx
image with hdf5, only it is a time-consuming process.

Quentin



[image: cid:image003.jpg at 01D690CB.3B3FDC10]

Quentin CHEVALIER – IA parcours recherche

LadHyX - Ecole polytechnique

__________


On Tue, 7 Dec 2021 at 19:16, Matthew Knepley <knepley at gmail.com> wrote:

> On Tue, Dec 7, 2021 at 9:43 AM Quentin Chevalier <
> quentin.chevalier at polytechnique.edu> wrote:
>
>> @Matthew, as stated before, error output is unchanged, i.e.the python
>> command below produces the same traceback :
>>
>> # python3 -c "from petsc4py import PETSc;
>> PETSc.Viewer().createHDF5('d.h5')"
>> Traceback (most recent call last):
>>   File "<string>", line 1, in <module>
>>   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
>> [0] Unknown PetscViewer type given: hdf5
>>
>
> The reason I wanted the output was that the C output shows the configure
> options that the PETSc library
> was built with, However, Python seems to be eating this, so I cannot check.
>
> It seems like using this container is counter-productive. If it was built
> correctly, making these changes would be trivial.
> Send mail to FEniCS (I am guessing Chris Richardson maintains this), and
> ask how they intend people to change these
> options.
>
>   Thanks,
>
>      Matt.
>
>
>> @Wence that makes sense. I'd assumed that the original PETSc had been
>> overwritten, and if the linking has gone wrong I'm surprised anything
>> happens with petsc4py at all.
>>
>> Your tentative command gave :
>>
>> ERROR: Invalid requirement: '/usr/local/petsc/src/binding/petsc4py'
>> Hint: It looks like a path. File
>> '/usr/local/petsc/src/binding/petsc4py' does not exist.
>>
>> So I tested that global variables PETSC_ARCH & PETSC_DIR were correct
>> then ran "pip install petsc4py" to restart petsc4py from scratch. This
>> gives rise to a different error :
>> # python3 -c "from petsc4py import PETSc"
>> Traceback (most recent call last):
>>   File "<string>", line 1, in <module>
>>   File "/usr/local/lib/python3.9/dist-packages/petsc4py/PETSc.py",
>> line 3, in <module>
>>     PETSc = ImportPETSc(ARCH)
>>   File "/usr/local/lib/python3.9/dist-packages/petsc4py/lib/__init__.py",
>> line 29, in ImportPETSc
>>     return Import('petsc4py', 'PETSc', path, arch)
>>   File "/usr/local/lib/python3.9/dist-packages/petsc4py/lib/__init__.py",
>> line 73, in Import
>>     module = import_module(pkg, name, path, arch)
>>   File "/usr/local/lib/python3.9/dist-packages/petsc4py/lib/__init__.py",
>> line 58, in import_module
>>     with f: return imp.load_module(fullname, f, fn, info)
>>   File "/usr/lib/python3.9/imp.py", line 242, in load_module
>>     return load_dynamic(name, filename, file)
>>   File "/usr/lib/python3.9/imp.py", line 342, in load_dynamic
>>     return _load(spec)
>> ImportError:
>> /usr/local/lib/python3.9/dist-packages/petsc4py/lib/linux-gnu-real-32/
>> PETSc.cpython-39-x86_64-linux-gnu.so:
>> undefined symbol: petscstack
>>
>> Not sure that it a step forward ; looks like petsc4py is broken now.
>>
>> Quentin
>>
>> On Tue, 7 Dec 2021 at 14:58, Matthew Knepley <knepley at gmail.com> wrote:
>> >
>> > On Tue, Dec 7, 2021 at 8:26 AM Quentin Chevalier <
>> quentin.chevalier at polytechnique.edu> wrote:
>> >>
>> >> Ok my bad, that log corresponded to a tentative --download-hdf5. This
>> >> log corresponds to the commands given above and has --with-hdf5 in its
>> >> options.
>> >
>> >
>> > Okay, this configure was successful and found HDF5
>> >
>> >>
>> >> The whole process still results in the same error.
>> >
>> >
>> > Now send me the complete error output with this PETSc.
>> >
>> >   Thanks,
>> >
>> >      Matt
>> >
>> >>
>> >> Quentin
>> >>
>> >>
>> >>
>> >> Quentin CHEVALIER – IA parcours recherche
>> >>
>> >> LadHyX - Ecole polytechnique
>> >>
>> >> __________
>> >>
>> >>
>> >>
>> >> On Tue, 7 Dec 2021 at 13:59, Matthew Knepley <knepley at gmail.com>
>> wrote:
>> >> >
>> >> > On Tue, Dec 7, 2021 at 3:55 AM Quentin Chevalier <
>> quentin.chevalier at polytechnique.edu> wrote:
>> >> >>
>> >> >> Hello Matthew,
>> >> >>
>> >> >> That would indeed make sense.
>> >> >>
>> >> >> Full log is attached, I grepped hdf5 in there and didn't find
>> anything alarming.
>> >> >
>> >> >
>> >> > At the top of this log:
>> >> >
>> >> > Configure Options: --configModules=PETSc.Configure
>> --optionsModule=config.compilerOptions PETSC_ARCH=linux-gnu-complex-64
>> --COPTFLAGS=-O2 --CXXOPTFLAGS=-O2 --FOPTFLAGS=-O2 --with-make-np=2
>> --with-64-bit-indices=yes --with-debugging=no --with-fortran-bindings=no
>> --with-shared-libraries --download-hypre --download-mumps
>> --download-ptscotch --download-scalapack --download-suitesparse
>> --download-superlu_dist --with-scalar-type=complex
>> >> >
>> >> >
>> >> > So the HDF5 option is not being specified.
>> >> >
>> >> >   Thanks,
>> >> >
>> >> >      Matt
>> >> >
>> >> >> Cheers,
>> >> >>
>> >> >> Quentin
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> Quentin CHEVALIER – IA parcours recherche
>> >> >>
>> >> >> LadHyX - Ecole polytechnique
>> >> >>
>> >> >> __________
>> >> >>
>> >> >>
>> >> >>
>> >> >> On Mon, 6 Dec 2021 at 21:39, Matthew Knepley <knepley at gmail.com>
>> wrote:
>> >> >>>
>> >> >>> On Mon, Dec 6, 2021 at 3:27 PM Quentin Chevalier <
>> quentin.chevalier at polytechnique.edu> wrote:
>> >> >>>>
>> >> >>>> Fine. MWE is unchanged :
>> >> >>>> * Run this docker container
>> >> >>>> * Do : python3 -c "from petsc4py import PETSc;
>> PETSc.Viewer().createHDF5('dummy.h5')"
>> >> >>>>
>> >> >>>> Updated attempt at a fix :
>> >> >>>> * cd /usr/local/petsc/
>> >> >>>> * ./configure PETSC_ARCH= linux-gnu-real-32
>> PETSC_DIR=/usr/local/petsc --with-hdf5 --force
>> >> >>>
>> >> >>>
>> >> >>> Did it find HDF5? If not, it will shut it off. You need to send us
>> >> >>>
>> >> >>>   $PETSC_DIR/configure.log
>> >> >>>
>> >> >>> so we can see what happened in the configure run.
>> >> >>>
>> >> >>>   Thanks,
>> >> >>>
>> >> >>>       Matt
>> >> >>>
>> >> >>>>
>> >> >>>> * make PETSC_DIR=/usr/local/petsc PETSC-ARCH= linux-gnu-real-32
>> all
>> >> >>>>
>> >> >>>> Still no joy. The same error remains.
>> >> >>>>
>> >> >>>> Quentin
>> >> >>>>
>> >> >>>>
>> >> >>>>
>> >> >>>> On Mon, 6 Dec 2021 at 20:04, Pierre Jolivet <pierre at joliv.et>
>> wrote:
>> >> >>>> >
>> >> >>>> >
>> >> >>>> >
>> >> >>>> > On 6 Dec 2021, at 7:42 PM, Quentin Chevalier <
>> quentin.chevalier at 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
>> >> >>>> > * 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 <knepley at gmail.com>
>> wrote:
>> >> >>>> >>
>> >> >>>> >> On Mon, Dec 6, 2021 at 1:22 PM Quentin Chevalier <
>> quentin.chevalier at 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 <
>> knepley at gmail.com> wrote:
>> >> >>>> >>> >
>> >> >>>> >>> > On Mon, Dec 6, 2021 at 1:08 PM Quentin Chevalier <
>> quentin.chevalier at 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 <
>> knepley at gmail.com> wrote:
>> >> >>>> >>> >> >
>> >> >>>> >>> >> > On Mon, Dec 6, 2021 at 11:28 AM Quentin Chevalier <
>> quentin.chevalier at 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
>> >> >>>> >>> >> >>> [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/
>> >> >>>> >>> >
>> >> >>>> >>> >
>> >> >>>> >>> >
>> >> >>>> >>> > --
>> >> >>>> >>> > 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/
>> >> >>>> >>
>> >> >>>> >>
>> >> >>>> >>
>> >> >>>> >> --
>> >> >>>> >> 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/
>> >> >>>> >
>> >> >>>> > <image003.jpg>
>> >> >>>> >
>> >> >>>> >
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> --
>> >> >>> 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/
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > 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/
>> >
>> >
>> >
>> > --
>> > 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/
>>
>
>
> --
> 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/>
>
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