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Difference between revisions of "NEC Cluster Using MPI"

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Here is an example that shows a 16 node Job, using 1 process per socket and 4 threads
 
Here is an example that shows a 16 node Job, using 1 process per socket and 4 threads
 
per socket and optimum NUMA placement of processes and memory.
 
per socket and optimum NUMA placement of processes and memory.
 +
 +
Prerequiste: Use intel MPI and best intel compiler
 +
To setup environment for this, use this .modulerc file in your home:
 +
 +
#%Module1.0#
 +
set version 1.0
 +
module load compiler/intel/11.0
 +
module load mpi/impi/intel-11.0.074-impi-3.2.0.011
 +
 +
And compile your application using mpicc/mpif90.
  
 
First step: Batch submit to get the nodes
 
First step: Batch submit to get the nodes

Revision as of 19:43, 17 July 2009

Intel MPI example

As Nehalem system is a twosocket system with local attached ccNUMA memory, memory and process placmeent can be crucial.

Here is an example that shows a 16 node Job, using 1 process per socket and 4 threads per socket and optimum NUMA placement of processes and memory.

Prerequiste: Use intel MPI and best intel compiler To setup environment for this, use this .modulerc file in your home:

#%Module1.0#
set version 1.0
module load compiler/intel/11.0
module load mpi/impi/intel-11.0.074-impi-3.2.0.011

And compile your application using mpicc/mpif90.

First step: Batch submit to get the nodes

 qsub -l nodes=16:nehalem:ppn=8,walltime=6:00:00 -I           # get the 16 nodes

Second step: make a hostlist

 sort -u  $PBS_NODEFILE  > m

Third step: make a process ring to be used by MPI later

mpdboot  -n 16 -f m -r ssh  

Fourth step: start MPI application

mpiexec -perhost 2 -genv I_MPI_PIN 0  -np 32 ./wrapper.sh ./yourGloriousApp

With wrapper.sh looking like this

#!/bin/bash
export KMP_AFFINITY=verbose,scatter
export OMP_NUM_THREADS=4
if [ $(expr $PMI_RANK % 2) = 0  ]
then
       export GOMP_CPU_AFFINITY=0-3
       numactl --preferred=0 --cpunodebind=0 $@
else
       export GOMP_CPU_AFFINITY=4-7
       numactl --preferred=1 --cpunodebind=1 $@
fi


Result is an application running on 16 nodes, using 32 processes spawning 128 threads. One set of 4 therads is pinned to the one socket, the other set of 4 threads to the other socket.