OpenMPI
The OpenMPI library is an open source implementation for the MPI protocol. Different versions compiled with different compilers are available. A list is given by typing
module avail openmpi
For performance reasons the latest release of OpenMPI should be used.
Compiling with OpenMPI
Before compiling load the actual module of OpenMPI, e.g.
module load openmpi/1.6.2/gcc/64/4.7.1
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, ...) use other compilers (e.g. GNU compiler, Intel Compiler). The compilers can be choosen by setting environment variables, e.g.
export OMPI_CC=icc
for using the Intel C compiler. Below there is a list of all environment variables for setting the 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 $NSLOTS <MPI_program> <MPI_program_options>
Please don't forget to load the correct OpenMPI module before (the same OpenMPI module which was used for compilation)!
For performance reasons it is important to use the InfiniyBand connectors on FLOW. The InfinyBand will be used by setting the environment variable OMPI_MCA_btl by
export OMPI_MCA_btl="openib,sm,self"
or by using the mpirun or mpiexec command line option
mpirun -mca btl "openib,sm,self" ...
If this setting is not correct the MPI will communicate over the GigaBit Ethernet which is about 30 times slower!
To check if InfinyBand was used one can set the environment variable
export OMPI_MCA_mca_verbose=1
SGE script options
To submit MPI programs by SGE you have to set a parallel environment. The the parallel environment for HERO must be specified by
#$ -pe openmpi NUM_OF_CORES #$ -R y
For the FLOW the parallel environment is specified by
#$ -pe openmpi_ib 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 |
|---|---|
| OMPI_COMM_WORLD_SIZE | Total number of parallel processes. |
| OMPI_COMM_WORLD_RANK | MPI rank of the current process. |
