Hands-On: Interactive jobs

In the previous Data Storage hands-on section, you should have copied the class scripts to your /data area. If you skipped or missed that section, type

hpc-classes biowulf

In the following session, you will submit a batch job for Freebayes, a a Bayesian genetic variant detector . If you're not familiar with this program, don't worry -- this is just an example. The basic principles of job submission are not specific for Freebayes.

sinteractive

# once you are logged into a node
cd /data/$USER/hpc-classes/biowulf/freebayes

# load the freebayes module
module load freebayes

# run the program
freebayes -f genome.fasta input.bam

# exit your interactive session (IMPORTANT!)
exit

How do you know if you are on the Biowulf login node or in an interactive session on a compute node?

Answer

The terminal prompt will tell you. On the login node it will show:

[user@biowulf]

On a compute node it will show

[user@cn1232]

Of course, this assumes you have not modified your prompt.

How many CPUs and how much memory is allocated to this interactive session?

Answer

No CPUs or memory were specified, therefore this job would have been allocated the default 2 CPUs and 4 GB of memory.

How would you get more CPUs or memory allocated?

Answer

Use --cpus-per-task and --mem to allocate a specific number of CPUs or memory. e.g.

sinteractive --cpus-per-task=8
sinteractive --mem=10g

You were planning to run a GUI program in an interactive session. What does this error message indicate?

Error: Can't open display: localhost:19.0

Answer

You did not set up an Xwindows connection to Biowulf, or your Xwindows session is not working correctly. See the How to Connect webpage.