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| 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. | 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. |
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=== Openmpi === |
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| === Building applications === | ==== Building applications ==== |
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| === 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 |
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| The mca option is needed to disable the udapl btl plugin that currently does not work. |
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 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