[firedrake] Calling PETSc within PyOP2 kernels

[Justin Chang]

Lawrence,

So I did what you said, but still got the same error:

PETSC ERROR: Logging has not been enabled.

You might have forgotten to call PetscInitialize().

--------------------------------------------------------------------------

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD

with errorcode 56.


NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.

You may or may not see output from other processes, depending on

exactly when Open MPI kills them.

--------------------------------------------------------------------------

Any ideas why this is happening?

Justin

On Thu, Nov 12, 2015 at 2:37 AM, Lawrence Mitchell <
lawrence.mitchell at imperial.ac.uk> wrote:

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> Hi Justin,
>
> On 12/11/15 09:22, Justin Chang wrote:
> > Hi Lawrence,
> >
> > So I had a nice working code where it runs point-wise SNES in
> > pyop2, and it ran decently fast. However, with the latest firedrake
> > update, it forced me to make a few additional changes to the pyop2
> > kernel, namely adding PetcInitialize(....) and PetscFinalize(), and
> > my code now runs really slow after  I run it after several time
> > steps on a Unit Interval of 100 elements.
>
> So you shouldn't have to do this, something is definitely not right here
> .
>
> > Attached is the code as well as the supplemental 1D analytical
> > expressions and pyop2 reactions kernel. Run the code as "python
> > 1D_OS_analytical_ex1.py 100 0 0".
>
> I tried this with firedrake commit 6134b86, PyOP2 commit 64db689 (i.e.
> current master for both).  And didn't run into this problem.  Could it
> be that the compiled code from before the update was explicitly linked
> (with a baked-in rpath) against a different petsc to the one you have
> now?  To assuage my fears, can you run
> firedrake/scripts/firedrake-clean to clear out the compiled kernel
> cache?  And then run again without calling PetscInitialize/Finalize
> inside your kernel.
>
>
> Cheers,
>
> Lawrence
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