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

[Quentin Chevalier]

@Lawrence, thanks for the details, but point 7 fails with :

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.

Just like @wence's tentative command. I've changed the dockerfile of
dolfinx to add the --with-hdf5 flag and I'm trying to build a new optimised
docker image with :

echo '{ "cffi_extra_compile_args" : ["-O2", "-march=native" ] }' >
dolfinx_jit_parameters.json
docker build --target dolfinx --file Dockerfile --build-arg
PETSC_SLEPC_OPTFLAGS="-O2 -march=native" --build-arg
DOLFINX_CMAKE_CXX_FLAGS="-march=native" .

It's slowgoing, but it might eventually do the trick I guess.

@bsmith, the --with-petsc4py flag changes nothing.

MWE is unchanged :
* Run this docker container <https://hub.docker.com/r/dolfinx/dolfinx>
* Do : python3 -c "from petsc4py import PETSc;
PETSc.Viewer().createHDF5('dummy.h5')"

Updated attempt at a fix :
* cd /usr/local/petsc/
* ./configure --with-hdf5 --with-petsc4py --force (turns out the container
sets PETSC_ARCH and PETSC_DIR as environment variables by default)
* make all

This still produces the same error :

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

Quentin




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

Quentin CHEVALIER – IA parcours recherche

LadHyX - Ecole polytechnique

__________


On Tue, 7 Dec 2021 at 16:52, Barry Smith <bsmith at petsc.dev> wrote:

>
>   You can also just add --with-petsc4py to your PETSc configure command
> and it will manage automatically the petsc4py install. So
>
> ./configure --with-hdf5 --any-other --configure-flags --you-want
> --with-petsc4py
>
>
>  Some people don't like this approach, I don't understand exactly why not;
> it should be equivalent (if it is not equivalent then perhaps it could be
> fixed?).
>
> On Dec 7, 2021, at 10:18 AM, Lawrence Mitchell <wence at gmx.li> wrote:
>
> Comments inline below:
>
> On 7 Dec 2021, at 14:43, 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
>
> @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 downloads petsc4py from pypi. It is not guaranteed to give you a
> version that matches the PETSc version you have installed (which is the
> source of your error below)
>
>
> This
> gives rise to a different error :
>
> [...]
>
> 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.
>
>
> The steps to build PETSc with HDF5 support and then get a compatible
> petsc4py are:
>
> 1. Download the PETSc source somehow (https://petsc.org/release/download/)
>
> I now assume that this source tree lives in .../petsc
>
> 2. cd .../petsc
>
> 3. ./configure --with-hdf5 --any-other --configure-flags --you-want
>
> 4. Run the appropriate "make" command as suggested by configure
>
> 5. Run the appropriate "make check" command as suggested by configure
>
> 6. Set PETSC_DIR and PETSC_ARCH appropriately
>
> 7. pip install src/binding/petsc4py
>
> If you are working the docker container from dolfinx/dolfinx, you can see
> the commands that are run to install PETSc, and then petsc4py, here
> https://github.com/FEniCS/dolfinx/blob/main/docker/Dockerfile#L243
>
> If you want to reproduce these versions of PETSc but with the addition of
> HDF5 support, just add --with-hdf5 to all of the relevant configure lines.
>
> Lawrence
>
>
>
>
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