Running CCM jobs on Big Red II

Since moving to Indiana University with my advisor, I have made frequent use of the HPC resources made available to grad students, staff, and faculty here. I have made particularly frequent use of the Mason cluster, which has 16 machines, each with 500 GB available memory and 32 processors.

However, over this last weekend I wanted to make use of IU’s new Big Red II. This is your much more typical HPC environment designed for distributed-memory MPI jobs utilizing processors on different machines in parallel. I occasionally run MPI jobs, so I am familiar with the likes of mpirun and mpiexec (Big Red II uses aprun). These particular jobs, however, were not MPI jobs, and therefore needed to be run in “cluster compatibility mode”, or CCM for short. Below is a simple example launch script that will execute a BLAST job in CCM mode on Big Red II.

#!/bin/bash

#PBS -N NameOfYourBlastJob   # a name for the job
#PBS -l nodes=1:ppn=32       # request a single machine with 32 processors for this job
#PBS -l walltime=12:00:00    # request a 12-hour time slot for this job
#PBS -q cpu                  # use the 'cpu' queue
#PBS -l gres=ccm             # use Cluster Compatibility Mode
#PBS -M username@indiana.edu # email address to which notifications will be sent
#PBS -m bea                  # send email notifications when the job begins, ends, and/or aborts

# Place 'module load ccm' in your ~/.modules file
WD=/N/dc2/scratch/username/working-directory

ccmrun blastx -query $WD/sequences.fna \
       -db $WD/reference-proteins.faa \
       -out $WD/blast-results.xml \
       -evalue 1e-15 \
       -outfmt 5 \
       -show_gis \
       -num_alignments 10 \
       -num_threads 32

Then as usual, the job can be launched by running qsub your-launch-script.sh.

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s