Usage of the Linux Clusters at DESY Zeuthen

There are no dedicated parallel clusters available at the moment, but you can run parallel MPI jobs in the SGE farm. The documentation in Batch_System_Usage applies there.

Building Applications

Since SL5, all batch worker nodes have the openmpi implementation of the MPI standard installed.

There are MPI versions for the GCC, Intel and PGI compilers installed:

/opt/openmpi/gcc/bin/mpicc

/opt/openmpi/intel/bin/mpicc

/opt/openmpi/pgi/bin/mpicc

Compilers for C++ and Fortran are available as well.

Building applications

MPI Applications can be compiled on any 64 bit SL5 machine, e.g. sl5-64.ifh.de.

Batch System Access

A job script designated for a parallel job needs to specify the parallel environment and the number of required CPUs. The parameter looks like this:

#$ -pe multicore-mpi 4

Be sure to call the right mpirun version for your compiler. If you application was compiled with GCC, use

/opt/openmpi/gcc/bin/mpirun -np $NSLOTS yourapp

AFS Access

The application binary must be available to all nodes, that's why it should be placed in an AFS directory.

BLAS library

Both ATLAS ans GotoBLAS are available.

• ATLAS is in /opt/products/atlas
• libgoto is in /usr/lib or /usr/lib64 respectively.

Further documentation

HPC-Clusters at DESY Zeuthen , 11/22/06, technical seminar