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Subject: Re: [OMPI users] Using openmpi within python and crashes
From: Lisandro Dalcin (dalcinl_at_[hidden])
Date: 2009-07-10 01:03:26


What Python version are you using?

I would use 'ctypes' modules (available in recent Python's stdlib) in
order do open the MPI shared library, next call MPI_Init() from Python
code... Of couse, I'm assuming you Fortran code can manage the case of
MPI being initialized (by using MPI_Initialized()).

Regarding argc,argv, you just should pass NULL. OpenMPI is MPI-2
compiant, so it does not require the actuall cmd line args.

BTW, you should use ctypes.RTLD_GLOBAL flag when opening libmpi.so.

If you have trouble, feel free to mail me directly for futher help.

BTW: Do you know about mpi4py http://mpi4py.scipy.org/ ? It has
support for interoperate with Fortran codes. You can even use dynamic
process management, and build a python script that "chats" with a
Fortran program lauched by using MPI_Comm_spawn()... See for example
the master/worker Mandelbrot example at
http://mpi4py.googlecode.com/svn/trunk/demo/mandelbrot/

On Thu, Jul 9, 2009 at 2:53 PM, John R. Cary<cary_at_[hidden]> wrote:
> Our scenario is that we are running python, then importing a module written
> in Fortran.
> We run via:
>
> mpiexec -n 8 -x PYTHONPATH -x SIDL_DLL_PATH python tokHsmNP8.py
>
> where the script calls into Fortran to call MPI_Init.
>
> On 8 procs (but not one) we get hangs in the code (on some machines but not
> others!). Hard to tell precisely where, because it is in a PETSc method.
>
> Running with valgrind
>
> mpiexec -n 8 -x PYTHONPATH -x SIDL_DLL_PATH valgrind python tokHsmNP8.py
>
> gives a crash, with some salient output:
>
> ==936==
> ==936== Syscall param sched_setaffinity(mask) points to unaddressable
> byte(s)
> ==936==    at 0x39336DAA79: syscall (in /lib64/libc-2.10.1.so)
> ==936==    by 0x10BCBD58: opal_paffinity_linux_plpa_api_probe_init (in
> /usr/local/openmpi-1.3.2-notorque/lib/libopen-pal.so.0.0.0)
> ==936==    by 0x10BCE054: opal_paffinity_linux_plpa_init (in
> /usr/local/openmpi-1.3.2-notorque/lib/libopen-pal.so.0.0.0)
> ==936==    by 0x10BCC9F9:
> opal_paffinity_linux_plpa_have_topology_information (in
> /usr/local/openmpi-1.3.2-notorque/lib/libopen-pal.so.0.0.0)
> ==936==    by 0x10BCBBFF: linux_module_init (in
> /usr/local/openmpi-1.3.2-notorque/lib/libopen-pal.so.0.0.0)
> ==936==    by 0x10BC99C3: opal_paffinity_base_select (in
> /usr/local/openmpi-1.3.2-notorque/lib/libopen-pal.so.0.0.0)
> ==936==    by 0x10B9DB83: opal_init (in
> /usr/local/openmpi-1.3.2-notorque/lib/libopen-pal.so.0.0.0)
> ==936==    by 0x10920C6C: orte_init (in
> /usr/local/openmpi-1.3.2-notorque/lib/libopen-rte.so.0.0.0)
> ==936==    by 0x10579D06: ompi_mpi_init (in
> /usr/local/openmpi-1.3.2-notorque/lib/libmpi.so.0.0.0)
> ==936==    by 0x10599175: PMPI_Init (in
> /usr/local/openmpi-1.3.2-notorque/lib/libmpi.so.0.0.0)
> ==936==    by 0x10E2BDF4: mpi_init (in
> /usr/local/openmpi-1.3.2-notorque/lib/libmpi_f77.so.0.0.0)
> ==936==    by 0xDF30A1F: uedge_mpiinit_ (in
> /home/research/cary/projects/facetsall-iter/physics/uedge/par/build/uedgeC.so)
> ==936==  Address 0x0 is not stack'd, malloc'd or (recently) free'd
>
> This makes me think that our call to mpi_init is wrong.  At
>
>  http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Init.html
>
> it says
>
>  Because the Fortran and C versions of MPI_Init
> <http://www.mpi-forum.org/docs/mpi-11-html/node151.html#node151> are
> different, there is a restriction on who can call MPI_Init
> <http://www.mpi-forum.org/docs/mpi-11-html/node151.html#node151>. The
> version (Fortran or C) must match the main
>  program. That is, if the main program is in C, then the C version of
> MPI_Init <http://www.mpi-forum.org/docs/mpi-11-html/node151.html#node151>
> must be called. If the main program is in Fortran, the Fortran version must
> be called.
>
> Should I infer from this that since python is a C code, one must call the C
> version of MPI_Init (with argc, argv)?
>
> Or since the module is written mostly in Fortran with mpi calls of only the
> Fortran variety, I can initialize
> with the Fortran MPI_Init?
>
> Thanks.....John Cary
>
>
>
>
>
>
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> http://www.open-mpi.org/mailman/listinfo.cgi/users
>

-- 
Lisandro Dalcín
---------------
Centro Internacional de Métodos Computacionales en Ingeniería (CIMEC)
Instituto de Desarrollo Tecnológico para la Industria Química (INTEC)
Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
PTLC - Güemes 3450, (3000) Santa Fe, Argentina
Tel/Fax: +54-(0)342-451.1594