Biowulf High Performance Computing at the NIH
usearch on Biowulf

USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than 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@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 usearch
[user@cn3144 ~]$ cp -R $USEARCH_EXAMPLES/hmptut .
[user@cn3144 ~]$ cd hmptut/scripts
[user@cn3144 ~]$ bash run.bash

[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:

# --- This file is --
module load usearch
usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.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. usearch.swarm). For example:

usearch -cluster_fast seqs.fasta.1 -id 0.9 -centroids nr.fasta
usearch -cluster_fast seqs.fasta.2 -id 0.9 -centroids nr.fasta
usearch -cluster_fast seqs.fasta.3 -id 0.9 -centroids nr.fasta
usearch -cluster_fast seqs.fasta.4 -id 0.9 -centroids nr.fasta

Submit this job using the swarm command.

swarm -f usearch.swarm [-g #] [-t #] --module usearch
-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 usearch Loads the usearch module for each subjob in the swarm