[firedrake] Calling PETSc within PyOP2 kernels

[Justin Chang]

Strange, I had no issue running this on my Ubuntu system, it only happened
with my MacOSX (El Capitan).

Perhaps I need to reinstall firedrake on my MacOSX and will holler if I get
the same error again

On Thu, Nov 12, 2015 at 2:46 AM, Justin Chang <jychang48 at gmail.com> wrote:

> 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:
>
>> -----BEGIN PGP SIGNED MESSAGE-----
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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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>
>
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