Using the HPC Scheduler

The HPC has migrated from LSF to Slurm for scheduling jobs.

To use Slurm,

Load the module

• module load slurm

Run the job

• From the command line:

srun -J myjobname -c #CORE -e ERROR_FILE -o OUTPUT_FILE -q PQ_dcnlab -p investor my_command_line_arguments

• Using a script:

#!/bin/bash
#---Number of core 
#SBATCH -c 1

#---Job's name in LSF system
#SBATCH -J example_job

#---Error file
#SBATCH -e example_job_err

#---Output file
#SBATCH -o example_job_out

#---Queue name
#SBATCH -q PQ_nbc

#---Partition
#SBATCH -p investor

##########################################################
# Setup envrionmental variable.
##########################################################
export NPROCS=`echo $LSB_HOSTS | wc -w`
export OMP_NUM_THREADS=$NPROCS

. $MODULESHOME/../global/profile.modules
module load fsl
module load afni

##########################################################
##########################################################

echo "hello world!">