MPI Libraries

On the HPC cluster, we have two different kinds of MPI libraries: OpenMPI and intel MPI (impi)

The OpenMPI library is an open source implementation for the MPI protocol. The Intel MPI library is an optimized implementation for the MPI protocol. Different versions compiled with different compilers are available. A list is given by typing

module avail openmpi
module avail impi

For performance reasons the latest release of OpenMPI / impi should be used.

Compiling with OpenMPI

Before compiling load the actual module of OpenMPI, e.g.

module load openmpi/1.8.4/gcc

for using the GNU compiler.

The compilation can be done by following wrappers of OpenMPI:

Name	Description
mpicc	C compiler
mpic++, mpiCC or mpicxx	C++ compiler
mpif77	Fortran 77 compiler
mpif90	Fortran 90 compiler

These programs are only wrappers which means that the scripts sets additional flags for OpenMPI (e.g. include path, flags for linking OpenMPI libraries, ...). For using the Intel Compiler please use the module

module load openmpi/1.8.4/intel

Below there is a list of all environment variables for setting other compiler.

Environment variable	Description
OMPI_CC	Set the C compiler
OMPI_CXX	Sets the C++ compiler
OMPI_F77	Sets the Fortran 77 compiler
OMPI_FC	Sets the Fortran 90 compiler

Run parallel programs

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

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

Please don't forget to load the correct OpenMPI module before (the same OpenMPI module which was used for compilation)!

On FLOW the communication will be done over InfiniBand (automatically). Due to new virtual nodes without InfiniBand the explicit setting of InfiniBand usage by setting the environment variable OMPI_MCA_btl by

 export OMPI_MCA_btl="openib,sm,self"

or by using the mpirun or mpiexec command line option

mpirun -mca btl "openib,sm,self" ...

is depricated and can causes problems on the vx* nodes!

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/gcc

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