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

[Barry Smith]

  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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