Biowulf High Performance Computing at the NIH
TINKER on Biowulf

TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special featuresf for biopolymers. It is designed to be an easily used and flexible system of progrms and routines for molecular mechanics and dynamics as well as other energy-based and structural manipulation calculations. TINKER provides a set of relatively small programs that interoperate to perform complex computations. New programs can be easily added by modelers with only limited programming experience.


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 TINKER
[+] Loading TINKER 8.4.3  ...

[user@cn3144 ~]$ newton molecule -k test a a 0.01

[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 tinnker
cd /data/$USER
newton molecule -k test a a 0.01

Submit this job using the Slurm sbatch command.

sbatch [--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. TINKER.swarm). For example:

newton molecule -k test a a 0.01
newton molecule -k test2 a a 0.01
newton molecule -k test3 a a 0.01
newton molecule -k test4 a a 0.01

Submit this job using the swarm command.

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