Usage of the Linux Clusters at DESY Zeuthen
At Zeuthen a cluster of 16 dual opteron machines is available. It is integrated into the SGE batch system. The documentation in ["Batch System Usage"] applies to it.
Building Applications
Applications for the cluster must be compiled on a 64 bit machine, at the moment, this means either lx64 or linfini. There are MPI versions for the GCC, Intel and PGI compilers installed:
/usr/local/ibgd/mpi/osu/gcc/mvapich-0.9.5/bin/mpicc
/usr/local/ibgd/mpi/osu/intel/mvapich-0.9.5/bin/mpicc
/usr/local/ibgd/mpi/osu/pgi/mvapich-0.9.5/bin/mpicc
Compilers for C++ and Fortran are available as well.
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 mpich-ppn2 4
It is important to request the right limit for memory with the parameter h_vmem. The machines have 3673204k of RAM and by default two jobs are executed on one node, so the maximal amount of memory is 1650M per process.
AFS Access
The application binary must be available to all nodes, that's why it should be placed in an AFS directory.
Be aware that the batch system renews the AFS token, but only on the node that starts the first process (node 0). That's why you should access the AFS from that node. An example scenario looks like this:
- Copy data from AFS to node 0.
- Copy it with scp to the nodes that need it to the directory $TMPDIR, the machine names are in $TMPDIR/machines
- Run your MPI job.
- Copy the results with scp from the local discs to node 0.
- Copy the data from node 0 to AFS.