It doesn't work outside the debug mode... I still get the same error:

(firedrake) [mmfg@login1.arc3 3D_code]$ firedrake-clean

Removing cached TSFC kernels from /home/ufaserv1_i/mmfg/firedrake/firedrake/.cache/tsfc

Removing cached PyOP2 code from /home/ufaserv1_i/mmfg/firedrake/firedrake/.cache/pyop2

(firedrake) [mmfg@login1.arc3 3D_code]$ unset PYOP2_DEBUG

(firedrake) [mmfg@login1.arc3 3D_code]$ python TOC2.py

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

A process has executed an operation involving a call to the

"fork()" system call to create a child process. Open MPI is currently

operating in a condition that could result in memory corruption or

other system errors; your job may hang, crash, or produce silent

data corruption. The use of fork() (or system() or other calls that

create child processes) is strongly discouraged.

The process that invoked fork was:

Local host: [[32797,1],0] (PID 77567)

If you are *absolutely sure* that your application will successfully

and correctly survive a call to fork(), you may disable this warning

by setting the mpi_warn_on_fork MCA parameter to 0.

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

[0]PETSC ERROR: ------------------------------------------------------------------------

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind

[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors

[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run

[0]PETSC ERROR: to get more information on the crash.

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

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD

with errorcode 59.

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.

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

De : firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> de la part de Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk>
Envoyé : jeudi 8 février 2018 11:48
À : firedrake@imperial.ac.uk
Objet : Re: [firedrake] .at() PETSC error

On 08/02/18 11:38, Floriane Gidel [RPG] wrote:
> Hi Lawrence,
>
>
> with
>
> $ firedrake-clean
> $ export PYOP2_DEBUG=1
> $ gdb --args python TOC2.py
>
> (gdb) break PetsError
>
> (gdb) run
>
>
> I have no error anymore. So it seems that it fixed the issue! Should I
> try to run it with
>
> $ python TOC2.py
>
>
> to make sure that it's fixed ? What was the issue then?

So it might be that by compiling in debug mode, a bug no longer
appears. But let's try in non-debug mode:

so do:

$ firedrake-clean
$ unset PYOP2_DEBUG
$ python TOC2.py

And see if you get an error.

If not, it's possible just that somehow some compiled code was wrongly
cached?

Lawrence

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