Biowulf High Performance Computing at the NIH
PEET on Biowulf

PEET is a set of programs, separate from but typically used in conjunction with IMOD, to align and average particles / subvolumes extracted from 3D volumes.

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 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 PEET

[user@cn3144 ~]$   averageAll
Starting averageAll_mce ...
This is PEET Version 1.12.0 5-March-2018.
Copyright 2000-2018 The Regents of the University of Colorado.
MATLAB. Copyright 1984-2018 The Mathworks, Inc.
[...]

[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. PEET.sh). For example:

#!/bin/bash
set -e
module load PEET
PEET < PEET.in > PEET.out

Submit this job using the Slurm sbatch command.

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

PEET < PEET.in > PEET.out
PEET < PEET.in > PEET.out
PEET < PEET.in > PEET.out
PEET < PEET.in > PEET.out

Submit this job using the swarm command.

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