Biowulf High Performance Computing at the NIH
netOglyc on Biowulf

NetOglyc produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load netOglyc
[user@cn3144 ~]$ netOglyc $NETOGLYC_EXAMPLES/GLP_MACFU.fsa

[user@cn3144 ~]$  

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. For example:

set -e
module load netOglyc
netOglyc my_fasta_file.fasta > my_fasta_file.out

Submit this job using the Slurm sbatch command.

Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. netOglyc.swarm). For example:

netOglyc < 1.fasta > 1.out
netOglyc < 2.fasta > 2.out
netOglyc < 3.fasta > 3.out
netOglyc < 4.fasta > 4.out

Submit this job using the swarm command.

swarm -f netOglyc.swarm --module netOglyc
--module netOglyc Loads the netOglyc module for each subjob in the swarm