Perun Cluster

Note - VPN is necessary for off campus access.

Connect to Perun

Please use a secure shell client to connect to perun.biochem.dal.ca.

X2go and XPRA are also available. The clients for X2go connection are available for download from X2go. X2go/XPRA access would be faster than X11 tunneling over secure shell connection when graphical user interfaces for Matlab or Maple, Plots using R etc are used from outside the University. Please see the X2go setup before using X2go. Cluster-nx.mathstat.dal.ca should be replaced by perun.biochem.dal.ca.

Use interactive queue

Interactive queues are retired. Please use perun.biochem.dal.ca for all interactive tasks.

Use batch queue

Batch jobs could be submitted like this

qsub -q <batch queue name> <submit.sh>

List running jobs in queues

Basic Submit Script Example

#!/bin/bash 
#$ -S /bin/bash 
. /etc/profile 
#$ -o job_output 
#$ -M <your email address> 
#$ -m be 
cd <path to the job> 
<The job to be submitted starts here>

MPI job submission example

#!/bin/bash 
#$ -S /bin/bash 
. /etc/profile 
#$ -o job_output 
#$ -M <your email address> 
#$ -m be 
#$ -pe openmpi <num cpus> 
cd <path to the job>  
mpirun -np <num cpus> <your compute job> 

OpenMP job submission example

#!/bin/bash 
#$ -S /bin/bash 
. /etc/profile 
#$ -o job_output 
#$ -M <your email address> 
#$ -m be 
#$ -pe threaded <num cpus> 
export OMP_NUM_THREADS=<num cpus> 
cd <path to the job>  
<your compute job starts here>

Threaded job submission example

#!/bin/bash 
#$ -S /bin/bash 
. /etc/profile 
#$ -o job_output 
#$ -M <your email address> 
#$ -m be 
#$ -pe threaded <num cpus> 
cd <path to the job>  
<your compute job starts here>