Biowulf High Performance Computing at the NIH
Diamond on Biowulf

DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are:

References:

Documentation
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 -c 8 --mem 10g
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 diamond

[user@cn3144 ~]$ cp /usr/local/apps/diamond/TEST_DATA/reads.fna .

[user@cn3144 ~]$  diamond blastx -d /usr/local/apps/diamond/TEST_DATA/uniprot_sprot -q reads.fna -p $SLURM_CPUS_PER_TASK -o matches.m8

[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. diamond.sh). For example:

#!/bin/bash
set -e
module load diamond
diamond blastx -d /usr/local/apps/diamond/TEST_DATA/uniprot_sprot -q reads.fna -p $SLURM_CPUS_PER_TASK -o matches.m8 

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=8 --mem=10g diamond.sh
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. diamond.swarm). For example:

diamond blastx -d db_name -q read1.fna -p $SLURM_CPUS_PER_TASK -o out1
diamond blastx -d db_name -q read2.fna -p $SLURM_CPUS_PER_TASK -o out2
diamond blastx -d db_name -q read3.fna -p $SLURM_CPUS_PER_TASK -o out3

Submit this job using the swarm command.

swarm -f diamond.swarm -g 10 -t 8 --module diamond
where
-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 diamond Loads the diamond module for each subjob in the swarm