= 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 Goto``BLAS are available. 

 * ATLAS is in /opt/products/atlas

 * libgoto is in /usr/lib or /usr/lib64 respectively. 

== Further documentation ==

[[http://www-zeuthen.desy.de/technisches_seminar/texte/Technisches_Seminar_Waschk.pdf|HPC-Clusters at DESY Zeuthen]] , 11/22/06, technical seminar