= Usage of the Linux Clusters at DESY Zeuthen =

There are 4 dedicated parallel clusters (blade centers) in testing mode, but you can also run parallel MPI jobs in the SGE farm. The documentation in [[Batch_System_Usage]] applies there.

== Building Applications ==

=== Openmpi ===
Since SL5, all batch worker nodes have the openmpi implementation of the MPI standard installed. Recently the machines were upgraded to the default SL5.4 packages of openmpi. For 64 bit applications use the installation in /usr/lib64/openmpi/1.3.2-gcc/bin, for 32 bit use 
the binaries from /usr/lib/openmpi/1.3.2-gcc/bin .

Additional openmpi versions are installed to support the Intel and PGI compilers:
{{{
/usr/lib64/openmpi-1.3.2-intel/bin
/usr/lib64/openmpi-1.3.2-pgi/bin
}}}

If you don't want to specify the full path to your preferred MPI implementation, configure a default by using the ini command or running mpi-selector-menu on a build machine.

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

=== Mvapich / Mvapich2 ===
Two additional mpi implementations are installed on all pax machines:
{{{
/usr/lib64/mvapich/1.1.0-gcc/bin
/usr/lib64/mvapich2/1.2-gcc/bin
}}} 
To use mvapich, add one of those versions to your path, compile your application with that mpi compiler and run it as specified here:
http://mvapich.cse.ohio-state.edu/support/user_guide_mvapich2-1.4.html#x1-160005.2
== 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 for up to 8 slots on a single node:

#$ -pe multicore-mpi 8

For more MPI processes, use -pe mpi.


Be sure to call the right mpirun version for your architecture. If you application was compiled for 64 bit, use

/usr/lib64/openmpi/1.3.2-gcc/bin/mpirun --mca btl "^udapl" -np $NSLOTS yourapp

The mca option is needed to disable the udapl btl plugin that currently does not work.

== 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