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| == OpenMPI example == | | === OpenMPI === |
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| To use OpenMPI with intel Compiler, create a .modulerc in your home
| | see [[Open MPI]] |
| with this contents:
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| #%Module1.0#
| | === Intel MPI === |
| set version 1.0
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| module load compiler/intel/11.0
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| module load mpi/openmpi/1.3-intel-11.0
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| For compilationuse the mpi wrapper scripts like mpicc/mpic++/mpif90.
| | see [[Intel MPI]] |
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| The following example is for a pure MPI job, using 16 nodes (128 processes).
| | === MVAPICH2 === |
| For Illustration, this is done using an interactvie session (-I option)
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| First step: Batch submit to get the nodes
| | see [[MVAPICH2]] |
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| qsub -l nodes=16:nehalem:ppn=8,walltime=6:00:00 -I # get the 16 nodes
| | === MPI I/O === |
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| In the session you will get after some time, the application is started with
| | see [[MPI-IO]] |
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| mpirun -np 128 PathToYourApp
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| == Intel MPI example ==
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| As Nehalem system is a two socket system with local attached ccNUMA memory,
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| memory and process placmeent can be crucial.
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| Here is an example that shows a 16 node Job, using 1 process per socket and 4 threads
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| per socket and optimum NUMA placement of processes and memory.
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| Prerequiste: Use intel MPI and best intel compiler
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| To setup environment for this, use this .modulerc file in your home:
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| #%Module1.0#
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| set version 1.0
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| module load compiler/intel/11.0
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| module load mpi/impi/intel-11.0.074-impi-3.2.0.011
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| And compile your application using mpicc/mpif90.
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| First step: Batch submit to get the nodes
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| qsub -l nodes=16:nehalem:ppn=8,walltime=6:00:00 -I # get the 16 nodes
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| Second step: make a hostlist
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| sort -u $PBS_NODEFILE > m
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| Third step: make a process ring to be used by MPI later
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| mpdboot -n 16 -f m -r ssh
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| Fourth step: start MPI application
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| mpiexec -perhost 2 -genv I_MPI_PIN 0 -np 32 ./wrapper.sh ./yourGloriousApp
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| With wrapper.sh looking like this
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| #!/bin/bash
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| export KMP_AFFINITY=verbose,scatter
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| export OMP_NUM_THREADS=4
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| if [ $(expr $PMI_RANK % 2) = 0 ]
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| then
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| export GOMP_CPU_AFFINITY=0-3
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| numactl --preferred=0 --cpunodebind=0 $@
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| else
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| export GOMP_CPU_AFFINITY=4-7
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| numactl --preferred=1 --cpunodebind=1 $@
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| fi
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| Result is an application running on 16 nodes, using 32 processes spawning
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| 128 threads. One set of 4 therads is pinned to the one socket, the other set of 4 threads to the other socket.
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