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| At Zeuthen, two clusters are available, one with 16 dual Opteron machines connected by Infiniband and one with 8 dual Xeons and Myrinet. They are integrated into the SGE batch system. The documentation in [[Batch_System_Usage]] applies to them. | 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. |
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| Since the upgrade to SL5, both clusters use the openmpi implementation of the MPI standard. | Since SL5, all batch worker nodes have the openmpi implementation of the MPI standard installed. |
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| === Infiniband === Applications for the plejade cluster must be compiled on a 64 bit SL5 machine, e.g. sl5-64.ifh.de. === Myrinet === Applications for the geminide cluster must be compiled on a 32 bit SL5 machine, e.g. sl5.ifh.de. |
=== Building applications === MPI Applications can be compiled on any 64 bit SL5 machine, e.g. sl5-64.ifh.de. |
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| 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 the Infiniband cluster: | 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: |
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| #$ -pe mpich-ppn2 4 On the Myrinet cluster, it is similar: #$ -pe mpichgm-ppn2 4 It is important to request the right limit for memory with the parameter h_vmem. The Opteron machines have 3.3G of RAM and by default two jobs are executed on one node, so the maximal amount of memory is 1650M per process: #$ -l h_vmem=1650M The Xeons have 922.5M of RAM. If your application is using threads, it is recommended to set the value of h_stack (by default the same as h_vmem) to a sane value, e.g. 10M. |
#$ -pe multicore-mpi 4 |
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