Intel MPI

The Intel MPI library is an optimized implementation for the MPI protocol. Up to now two different releases are available. A list is given by typing

module avail intel/impi

For always the latest release of Intel MPI should be used.

Note: The release 4.0.1.007 is depricated!

Compiling with Intel MPI

Before compiling load the actual module of Intel MPI by

module load impi/5.0.0.028/32/intel

for Intel and

module load impi/5.0.0.028/64/intel

for the GNU compiler. The compilation can be done by following wrappers of Intel MPI:

Name	Description
mpicc	C compiler
mpicxx	C++ compiler
mpifc	Fortran compiler
mpif77	Fortran 77 compiler
mpif90	Fortran 90 compiler

These programs are only wrappers which means that the scripts sets additional flags for Intel MPI (e.g. include path, flags for linking Intel MPI libraries, ...) use other compilers (e.g. GNU compiler, Intel Compiler). The compilers can be choosen by setting environment variables, e.g.

 export I_MPI_CC=icc

for using the Intel C compiler. Below there is a list of all environment variables for setting the compiler.

Environment variable	Description
I_MPI_CC	Set the C compiler for the mpicc script
I_MPI_CXX	Sets the C++ compiler for the mpicxx script
I_MPI_FC	Sets the Fortran for the mpifc script
I_MPI_F77	Sets the Fortran 77 compiler for the mpif77 script
I_MPI_F90	Sets the Fortran 90 compiler for the mpif90 script

Alternatively for GNU compilers and Intel Compilers there exists following wrapper scripts which needs no special environment variables settings.

Wrapper for Intel Compiler	Wrapper for GNU Compiler	Description
mpiicc	mpigcc	C compiler
mpiicpc	mpigxx	C++ compiler
mpiifort		Fortran 77 compiler

Run parallel programs

The typical call to launch a MPI program within an SGE script is

 mpirun <MPI_program> <MPI_program_options>

Since Intel MPI 4.1 the number of processes should be determined automatically. Please don't forget to load the correct Intel MPI module before (the same Intel MPI module which was used for compilation)! Note: The command mpiexec is depricated because it doesn't support the SGE queuing system and can cause problems.

Only for legacy reasons: For the depricated Intel MPI release 4.0.1.007 the command has to be

 mpirun -machinefile $TMPDIR/machines -np $NSLOTS <MPI_program> <MPI_program_options>

On FLOW it is important to use the InfiniyBand network to increase the performance (up to 30 time faster communication!) of your MPI application. Usually this should be set automatically.

To check if InfinyBand was used one can set the environment variable

 export I_MPI_DEBUG=2

or alternatively by the command line parameter

mpirun env I_MPI_DEBUG 2 ...

SGE script options

To submit MPI programs by SGE you have to set a parallel environment. The the parallel environment for the Intel MPI 4.1 must be specified by

 #$ -pe impi41 NUM_OF_CORES
 #$ -R y
 

For the depricated release 4.0 the parallel environment is specified by

 #$ -pe impi NUM_OF_CORES
 #$ -R y
 

Useful environment variables

During the execution of a program called by mpirun following useful environment variables are set

Environment variable	Description
PMI_SIZE	Total number of parallel processes.
PMI_RANK	MPI rank of the current process.

External links

• Intel MPI homepage
• Reference manual