Parallel code
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Message Passing Model
Section contributed by IFIN-HH
In most distributed memory systems parallelization is achieved by using various implementations of the widely adopted Message Passing Interface (MPI) standard [mpis]. MPI presents a set of specifications for writing message-passing programs, that is parallel programs in which one assumes the interprocess communication through messages. There are two versions of the MPI standard currently in use, MPI-1 and MPI-2, and various library implementations of these which are particularly tuned for specific target platforms.
The standard specifications, and its implementations that are used in the framework of the HP-SEE ecosystem have been shortly exposed in D8.1 [D8.1].
Here a detailed discussion is presented on the message passing issues that are relevant for the migration, adaption and optimization of parallel applications into the HPC infrastructure, together with examples drawn from the developers’ experience.
The topics is restricted to the libraries that are effectively in use in HP-SEE: implementations of the MPI-1 version (MPICH1 and its derivatives MPICH-MX, MVAPICH), Open MPI (which implements MPI-2), and MPICH2 (together with its derivatives MVAPICH2, MPIX, and Intel MPI) - which implements both versions MPI-1 and MPI-2.
REFERENCES
[mpis] MPI standard, http://www.mcs.anl.gov/research/projects/mpi/
[D8.1] HP-SEE deliverable D8.1, Software Scalability Analysis and Interoperability Issues Assessment
MPICH implementations
Section contributed by IFIN-HH
Proposed as a freely available and portable implementation of the MPI standard, MPICH has evolved along with it, from the MPICH1 implementation [mpc1] (fulfilling MPI-1 specifications and partially supporting some MPI-2 features like the parallel I/O), to MPICH2 [mpc2], which is moreover fully compatible with the MPI-2 version of the standard. Although the development of the MPICH1 was frozen since 2005 to the 1.2.7p1 version, with the intention to be replaced with MPICH2, it continues to be the most used MPI implementation worldwide.
REFERENCES
[mpc1] MPICH1, http://www.mcs.anl.gov/research/projects/mpi/mpich1-old/
[mpc2] MPICH2, http://www.mcs.anl.gov/research/projects/mpich2/
Open MPI
Introduction Implementations of OpenMPI are used in the HP-SEE infrastructure by ...
NEURON ParallelContext
Section contributed by IMBB-FORTH (CMSLTM application)
Preferred MPI environment is OpenMPI (openmpi_gcc-1.4.3). NEURON was compiled with parallel support (MPI) using the gcc compiler:
./configure --without-iv --with-paranrn --prefix=/home/gkastel/src/nrn-7.1
We used NEURON's ParallelContext to distribute the simulation of each neuron to different nodes evenly.
