Bielawski Group

Connect to Awarnach

Please use a secure shell client to connect to awarnach.mathstat.dal.ca.

NX is also available as an alternative. The clients for NX connection are available for download from X2go. NX 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 NX. Cluster-nx.mathstat.dal.ca should be replaced by awarnach.mathstat.dal.ca.

Use interactive queue

Please type qrsh to get an ssh session to the least loaded compute node. If you would like to get an interactive session with one of the specific queues, please type

qrsh -q <queue name>

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>