OpenMP

Compiling OpenMP code on zcluster

The compilers installed on zcluster support shared memory applications using OpenMP. Here are the compiler options to include when using OpenMP:

Compiler	Commands	Option
PGI	pgcc, pgCC, pgf90, etc.	-mp
Intel	icc, ifort	-openmp
GNU	gcc, gfortran, g++, gcc44, etc.	-fopenmp

Defining number of OpenMP threads

The number of OpenMP threads can be specified using the environment variable OMP_NUM_THREADS. For example, to define 4 threads:

For bash/sh:

export OMP_NUM_THREADS=4

For csh/tcsh:

setenv OMP_NUM_THREADS 4

Sample script to run a shared memory job using OpenMP

Sample script (sub.sh) to run a program that uses 4 OpenMP threads:

#!/bin/bash
cd working_directory
export OMP_NUM_THREADS=4
time ./myprog

Sample job submission command on zcluster

To submit a shared memory job that uses 4 OpenMP threads to the rcc-30d queue:

qsub -q rcc-30d -pe thread 4 sub.sh