Biowulf High Performance Computing at the NIH
PSIPRED on Biowulf

PSIPRED generates secondary structure predictions using up to four feed-forward neural networks and output from PSI-BLAST.


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 --cpus-per-task=4
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 PSIPRED
[user@cn3144 ~]$ cp $PSIPRED_EXAMPLES/example.fasta .
[user@cn3144 ~]$ runpsipredplus example.fasta
Running PSI-BLAST with sequence example.fasta ...
Predicting secondary structure...
Pass1 ...
Pass2 ...
Cleaning up ...
Final output files: example.ss2 example.horiz
[user@cn3144 ~]$ ls
example.fasta  example.horiz  example.ss2

[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:

module load PSIPRED
runpsipredplus my.fasta

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#]
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. PSIPRED.swarm). For example:

runpsipredplus file1.fasta > run1.out
runpsipredplus file2.fasta > run2.out
runpsipredplus file3.fasta > run3.out
runpsipredplus file4.fasta > run4.out

Submit this job using the swarm command.

swarm -f PSIPRED.swarm [-g #] [-t #] --module PSIPRED
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module PSIPRED Loads the PSIPRED module for each subjob in the swarm