Distributed memory parallelization
Message Passing Interface (MPI) is a standardized and portable message-passing standard designed by a group of researchers from academia and industry to function on a wide variety of parallel computing architectures. MPI is a communication protocol for programming parallel computers. Both point-to-point and collective communication are supported. "MPI's goals are high performance, scalability, and portability. MPI remains the dominant model used in high-performance computing today. MPI is not sanctioned by any major standards body; nevertheless, it has become a de facto standard for communication among processes that model a parallel program running on a distributed memory system. Actual distributed memory supercomputers such as computer clusters often run such programs. Most MPI implementations consist of a specific set of routines directly callable from C, C++, Fortran (i.e., an API) and any language able to interface with such libraries, including C#, Java or Python.
MPI on our clusters
Two kinds of MPI libraries are available on our cluster: Open MPI (recommended) and MVAPICH2. Before you can submit and execute an MPI job, you must load the corresponding modules (compiler + MPI, in that order):
module load compiler module load mpi_library
The command used to launch an MPI application is mpirun.
Let's assume for example that hello_world was compiled with GCC 4.8.2 and linked with Open MPI 1.6.5. The command to execute this job on 4 processors is:
module load gcc/4.8.2 module load open_mpi/1.6.5 bsub -n 4 mpirun ./hello_world
Note that mpirun automatically uses all processors allocated to the job by LSF.
bsub -n 4 mpirun -np 4 ./hello_world ← "-np 4" not needed!
It is therefore not necessary to indicate this number again to the mpirun command itself: