[petsc-users] Issues Compiling petsc4py with Cython

[maitri ksh]

It was a version incompatibility issue, resolved by configuring it with
petsc. Thank you stefano & satish.

On Wed, Jun 26, 2024 at 12:34 AM Satish Balay <balay.anl at fastmail.org>
wrote:

> Best to get latest petsc and build petsc4py along with petsc:
>
> For example:
>
> balay at petsc-gpu-02:/scratch/balay$ wget -q
> https://urldefense.us/v3/__https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-3.21.2.tar.gz__;!!G_uCfscf7eWS!ZtQZK7hSb7b0O7qL1NxuDxYo3aNcfvkMEs6i_bMC-NNUYojWqG8zVItjnY-Kvihf1GDSMdRoUuj7yOs32AUG7ysB$ 
> balay at petsc-gpu-02:/scratch/balay$ tar -xf petsc-3.21.2.tar.gz
> balay at petsc-gpu-02:/scratch/balay$ cd petsc-3.21.2/
> balay at petsc-gpu-02:/scratch/balay/petsc-3.21.2$ ./configure
> --download-mpich --download-fblaslapack --download-mpi4py --with-petsc4py=1
> && make && make check && make petsc4pytest
>
> =============================================================================================
>                          Configuring PETSc to compile on your system
>
> =============================================================================================
> <snip>
> testPlaceArray (test_vec.TestVecShared) ... ok
> testPlaceArray (test_vec.TestVecShared) ... ok
> <snip>
> Ran 6154 tests in 134.314s
> OK
> =====================================
> balay at petsc-gpu-02:/scratch/balay/petsc-3.21.2$
>
>
> Satish
>
> On Tue, 25 Jun 2024, Stefano Zampini wrote:
>
> > Which version of petsc4py is it?
> >
> > Il giorno mar 25 giu 2024 alle ore 20:35 maitri ksh <
> maitri.ksh at gmail.com>
> > ha scritto:
> >
> > > I am currently working on integrating petsc4py, but I am encountering
> > > persistent compilation issues related to Cython. Below are the details
> of
> > > my setup and the errors I am facing. I would greatly appreciate any
> > > assistance or guidance on how
> > > ZjQcmQRYFpfptBannerStart
> > > This Message Is From an External Sender
> > > This message came from outside your organization.
> > >
> > > ZjQcmQRYFpfptBannerEnd
> > >
> > > I am currently working on integrating petsc4py, but I am encountering
> > > persistent compilation issues related to Cython. Below are the details
> of
> > > my setup and the errors I am facing. I would greatly appreciate any
> > > assistance or guidance on how to resolve these issues.
> > > System Configuration:
> > >
> > >    - *PETSc Architecture*: linux-gnu-c-debug
> > >    - *Python Environment*: Python 3.6 (virtual environment)
> > >    - *Cython Version*: 3.0.10
> > >    - *Compiler*: /gcc11.2/bin/gcc
> > >
> > >  During the build process, I received multiple warnings and errors
> related
> > > to the use of noexcept, nogil, and except in function declarations.
> Here
> > > are some of the specific errors:
> > >
> > > cythonizing 'petsc4py.PETSc.pyx' -> 'petsc4py.PETSc.c'
> > > warning: petsc4py.PETSc.pyx:1:0: Dotted filenames
> ('petsc4py.PETSc.pyx')
> > > are deprecated. Please use the normal Python package directory layout.
> > >
> /home/maitri.ksh/Maitri/petsc/petsc4py/myenv/lib64/python3.6/site-packages/Cython/Compiler/Main.py:381:
> > > FutureWarning: Cython directive 'language_level' not set, using '3str'
> for
> > > now (Py3). This has changed from earlier releases! File:
> > > include/petsc4py/PETSc.pxd
> > >   tree = Parsing.p_module(s, pxd, full_module_name)
> > > warning: PETSc/PETSc.pyx:53:48: The keyword 'nogil' should appear at
> the
> > > end of the function signature line. Placing it before 'except' or
> > > 'noexcept' will be disallowed in a future version of Cython.
> > > warning: PETSc/petscvec.pxi:406:79: The keyword 'nogil' should appear
> at
> > > the end of the function signature line. Placing it before 'except' or
> > > 'noexcept' will be disallowed in a future version of Cython.
> > > warning: PETSc/petscvec.pxi:411:79: The keyword 'nogil' should appear
> at
> > > the end of the function signature line. Placing it before 'except' or
> > > 'noexcept' will be disallowed in a future version of Cython.
> > > ...
> > >
> > > Error compiling Cython file:
> > > ...
> > > PETSc/petscobj.pxi:91:29: Cannot assign type 'int (void *) except? -1
> > > nogil' to 'int (*)(void *) noexcept'. Exception values are
> incompatible.
> > > Suggest adding 'noexcept' to the type of 'PetscDelPyDict'.
> > > ...
> > > PETSc/cyclicgc.pxi:34:20: Cannot assign type 'int (PyObject *,
> visitproc,
> > > void *) except? -1' to 'traverseproc *'. Exception values are
> incompatible.
> > > Suggest adding 'noexcept' to the type of 'tp_traverse'.
> > > ...
> > > PETSc/cyclicgc.pxi:35:20: Cannot assign type 'int (PyObject *) except?
> -1'
> > > to 'inquiry *'. Exception values are incompatible. Suggest adding
> > > 'noexcept' to the type of 'tp_clear'.
> > > ...
> > > PETSc/PETSc.pyx:351:17: Cannot assign type 'void (void) except *
> nogil' to
> > > 'void (*)(void) noexcept'. Exception values are incompatible. Suggest
> > > adding 'noexcept' to the type of 'finalize'.
> > > error: Cython failure: 'petsc4py.PETSc.pyx' -> 'petsc4py.PETSc.c'
> > >
> > > Any advice on building petsc4py in environments similar to mine would
> be
> > > greatly appreciated.
> > > Thanks,
> > > Maitri
> > >
> >
> >
> >
>
>
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