umx!

Parallel Execution

Parallel execution in OpenMx can be on mulitple cores, or distributed across distinct machines. Single models can be processed using parallel resrouces, and multiple models can be run and results combined.

Modern CPUs contain multiple cores (processing units that share memory), and machines may contain more than one CPU. Some chips also implement “virtual” cores which help allow the compiler to keep the hardware working while one process is data limited.

You can see total number of cores on your machine with detectCores() (on my 2016 iMac, the answer is 8 (4 real, with hyperthreading).

Out of the box, OpenMx uses detectCores() - 1 to execute in parallel on supported OS’s.

Set cores with umx

umx allows you to get and set the number of cores OpenMx will use with:

umx_set_cores()  # See many cores are currently requested?
umx_set_cores(3) # Request use of 3 cores

Under the hood, this is getting or setting an mxOption:

mxOption(NULL, "Number of Threads") # get current value

mxOption(NULL, "Number of Threads", n) # set value to n

So this

umx_set_cores(detectCores())

is equivalent to:

mxOption(NULL, "Number of Threads", detectCores())

Now you don’t need to remember or type this long option string!

Support for multiple cores is expected on all R platforms during 2016, and will dramatically speed up model runtime, e,g,CIs.

top tip: Use R’s tab-function completion (just type umx_ and tab to see the list…): top tip: TextMate OpenMx bundle contains snippets for many of umx’s features.

OpenMP on unix clusters

If you’re trying to use mulitple cores on a managed cluster, you might need to request these in the control script that schedules your jobs.

Here’s an example for edinburgh’s cluster. The key is -pe OpenMP 12

#!/bin/sh
# This is a simple example of a batch script
# call me as
# qsub -P ppls_psychology -cwd  -o ~/bin/makeOpenMx.out -e ~/bin/makeOpenMx.err ~/bin/makeOpenMx.sh
# Grid Engine options 
#$ -cwd
# Set the maximum run time to 30 minutes, 0 seconds:
#$ -l h_rt=00:30:00
#$ -N parallel_example
#$ -pe OpenMP 12
 
# initiallise environment module 
. /etc/profile.d/modules.sh
 
# use Intel compilers (icc,ifort)
# Load R
module load R/3.2.2
module load gcc/4.8.3
module load intel
 
# set number of threads
 
export OMP_NUM_THREADS=$NSLOTS
echo OMP_NUM_THREADS=$OMP_NUM_THREADS

R CMD BATCH my.R my.out