Using Slurm

submitting jobs: sbatch

Consider this simple python3 script that should calculate Pi up to 1 million digits: <source lang='python'> from decimal import * D=Decimal getcontext().prec=10000000 p=sum(D(1)/16**k*(D(4)/(8*k+1)-D(2)/(8*k+4)-D(1)/(8*k+5)-D(1)/(8*k+6))for k in range(411)) print(str(p)[:10000002]) </source>

In order for this script to run, the first thing that is needed is that Python3, which is not the default Python version on the cluster, is load into your environment. Availability of (different versions of) software can be checked by the following command:

 module avail

In the list you should note that python3 is indeed available to be loaded, which then can be loaded with the following command:

 module load python/3.3.3

The following shell/slurm script can then be used to schedule the job using the sbatch command: <source lang='bash'>

1. !/bin/bash
2. #SBATCH --time=100
3. SBATCH --ntasks=1
4. SBATCH --output=output_%j.txt
5. SBATCH --error=error_output_%j.txt
6. SBATCH --job-name=calc_pi.py
7. SBATCH --partition=research

time python3 calc_pi.py </source>

The script, assuming it was named 'run_calc_pi.sh', can then be posted using the following command:

<source lang='bash'> sbatch run_calc_pi.sh </source>

monitoring submitted jobs: squeue

Once a job is submitted, the status can be monitored using the 'squeue' command:

 squeue

You should then get a list of jobs that are running at that time on the cluster, for the example on how to submit using the 'sbatch' command, it may look like so:

 JOBID PARTITION     NAME     USER  ST       TIME  NODES NODELIST(REASON)
  3347  research calc_pi. megen002   R       0:03      1 node049

removing jobs from a list: scancel

If for some reason you want to delete a job that is either in the queue or already running, you can remove it using the 'scancel' command. The 'scancel' command takes the jobid as a parameter. The For the example above, this would be done using the following code: <source lang='bash'> scancel 3347 </source>

other

 PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
 student*     up   infinite     12  down* node[043-048,055-060]
 student*     up   infinite     50   idle fat[001-002],node[001-042,049-054]
 research     up   infinite     12  down* node[043-048,055-060]
 research     up   infinite     50   idle fat[001-002],node[001-042,049-054]
 ABGC         up   infinite     12  down* node[043-048,055-060]
 ABGC         up   infinite     50   idle fat[001-002],node[001-042,049-054]