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Batch System PBSPro (Hawk): Difference between revisions

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The ''omplace'' command helps with the placement of OpenMP threads within an MPI program.
The ''omplace'' command helps with the placement of OpenMP threads within an MPI program.
In above example, the threads in a 64-process MPI program with two threads per process are placed as follows:
In the above example, the threads in a 64-process MPI program with two threads per process are placed as follows:


* Rank 0, thread 0 on CPU 0 of compute node 1
* Rank 0, thread 0 on CPU 0 of compute node 1

Revision as of 12:37, 26 September 2019

The batch system on Hawk TDS is PBSPro 19.2.1. For general usage see the PBS User Guide (19.2.3)

At the moment the setup is basic and it works for the TDS only. More features, testing and productive like setup will be done in July.

Examples

Single node

Here is an example for a job using a single node:

qsub -l nodes=2,walltime=1:00:00


The basic commands to build and run a MPI program are:

module load mpt

mpicc hi.hpe.c -o hi.hpe

mpirun ./hi.hpe


simple batch script

Here is a simple pbs job script:

File: Job.hi.hpe.pbs
#!/bin/bash

#PBS -N Hi_Thomas
#PBS -l select=16:mpiprocs=64
#PBS -l walltime=00:20:00
 
module load mpt
mpirun ./hi.hpe


To submit the job script execute

qsub Job.hi.hpe.pbs


simple batch script for Hybrid MPI/OpenMP application

To run an MPI application with 64 Processes and two OpenMP threads per process on two compute nodes, include the following in the pbs job script:

File: Job.hi.mpiomp.hpe.pbs
#!/bin/bash

#PBS -N Hi_MPI_OpenMP
#PBS -l select=2:ncpus=64:mpiprocs=32:ompthreads=2
#PBS -l walltime=00:20:00
 
module load mpt
export OMP_NUM_THREADS=2
mpirun -np 64 omplace  -nt 2 [-vv] ./hi.mpiomp


The omplace command helps with the placement of OpenMP threads within an MPI program. In the above example, the threads in a 64-process MPI program with two threads per process are placed as follows:

  • Rank 0, thread 0 on CPU 0 of compute node 1
  • Rank 0, thread 1 on CPU 1 of compute node 1
  • ...
  • Rank 31, thread 1 on CPU 33 of compute node 1
  • Rank 32, thread 0 on CPU 0 of compute node 2
  • ...
  • Rank 63, thread 0 on CPU 32 of compute node 2
  • Rank 63, thread 1 on CPU 33 of compute node 2

The optional -vv parameter print out the placement of the processes and threads to standard output.
Warning: Due to the limited scaling of the standard output, you should not use the optional parameter -vv for medium and large jobs.