From HP-SEE Wiki

Contents 1 Message passing model 1.1 MPICH implementations 1.2 Open MPI 1.3 Porting between MPI implementations 2 Shared memory model 2.1 OpenMP 2.2 Pthreads 3 Hybrid programming 4 CUDA

Message passing model

MPICH implementations

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.

• MPICH1

• MVAPICH

• MPICH-MX

• MPICH2

• Intel MPI
• MPIX (IBM)

Open MPI

CMSLTM @IMBB (NEURON ParallelContext)

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.

Porting between MPI implementations

Shared memory model

OpenMP

Pthreads

Hybrid programming

CUDA