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| === OpenMPI example === | | === OpenMPI === |
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| ==== simple example ====
| | see [[Open MPI]] |
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| To use OpenMPI with intel Compiler, create a .modulerc in your home
| | === Intel MPI === |
| with this contents:
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| #%Module1.0#
| | see [[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 compilation use the mpi wrapper scripts like mpicc/mpic++/mpif90.
| | === MVAPICH2 === |
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| The following example is for a pure MPI job, using 16 nodes (128 processes).
| | see [[MVAPICH2]] |
| For Illustration, this is done using an interactvie session (-I option)
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| First step: Batch submit to get the nodes
| | === MPI I/O === |
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| qsub -l nodes=16:nehalem:ppn=8,walltime=6:00:00 -I # get the 16 nodes
| | see [[MPI-IO]] |
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| In the session you will get after some time, the application is started with
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| mpirun -np 128 PathToYourApp
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| ==== more complex examples ====
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| Open MPI divides resources in something called 'slots'. By specifying <code>ppn:X</code> to the batchsystem, the number of slots per node is specified.
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| So for a simple MPI job with 8 process per node (=1 process per core) <code>ppn:8</code> is best choice, as in above example. Details can be specified on <code>mpirun</code> command line. PBS setup is adjusted for ppn:8, please do not use other values.
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| If you want to use less processes per node e.g. because you are restricted by memory per process, or you have a hybrid parallel application using OpenMP and MPI, MPI would always put the first 8 processes on the first node, second 8 on second and so on. To avoid this, you can use the <code>-npernode</code> option.
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| {{Command
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| | command = mpirun -np X -npernode 2 your_app
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| }}
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| This would start 2 processes per node. Like this, you can use a larger number of nodes
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| with a smaller number of processes, or you can e.g. start threads out of the processes.
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| If you want to pin your processes to a CPU (and enable NUMA memory affinity) use
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| {{Command
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| | command = mpirun -np X --mca mpi_paffinity_alone 1 your_app
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| }}
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| {{Warning
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| | text = This will not behave as expected for hybrid multithreaded applications, as the threads will be pinned to a single CPU as well! Use this only in case of one process per core, no extra threads.
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| }}
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| For pinning of hybrid OpenMP/MPI, you can use the wrapper from the intel MPI example,
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| and do not use mpi_paffinity_alone switch, but
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| {{Command
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| | command = mpirun -np X -npernode 2 /path/to/wrapper.sh /path/to/app
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| }}
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| === Intel MPI example ===
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| ==== simple example ====
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| Load the necessary modules
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| {{Command
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| | command = module load mpi/impi
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| }}
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| Run your application with
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| {{Command
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| | command = mpirun -r ssh -np 8 your_app
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| }}
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| ==== more complex 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 placement 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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| Prerequisite: 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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| {{File
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| | filename = .modulerc
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| | content = <pre>
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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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| </pre>
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| }}
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| And compile your application using mpicc/mpicxx/mpif90 (GNU compiler) or mpiicc/mpiicpc/mpiifort (Intel compiler).
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| First step: Batch submit to get the nodes
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| {{Command
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| | command = qsub -l nodes=16:nehalem:ppn=8,walltime=6:00:00 -I # get the 16 nodes
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| }}
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| Second step: make a hostlist
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| {{Command
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| | command = sort -u $PBS_NODEFILE > m
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| }}
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| Third step: make a process ring to be used by MPI later
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| {{Command
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| | command = mpdboot -n 16 -f m -r ssh
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| }}
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| Fourth step: start MPI application
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| {{Command
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| | command = mpiexec -perhost 2 -genv I_MPI_PIN 0 -np 32 ./wrapper.sh ./yourGloriousApp
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| }}
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| With wrapper.sh looking like this
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| {{File
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| | filename = wrapper.sh
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| | content =<pre>
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| #!/bin/bash
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| export KMP_AFFINITY=verbose,scatter
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| export OMP_NUM_THREADS=4
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| RANK=${OMPI_COMM_WORLD_RANK:=$PMI_RANK}
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| if [ $(expr $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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| </pre>
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| }}
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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 threads is pinned to the one socket, the other set of 4 threads to the other socket.
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| === MVAPICH2 example ===
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| ==== simple example ====
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| Load the necessary module
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| {{Command
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| | command = module load mpi/mvapich2
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| }}
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| Run your application with
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| {{Command
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| | command = mpirun_rsh -np 8 -hostfile $PBS_NODEFILE your_app
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| }}
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