Biowulf High Performance Computing at the NIH
Naccess on Biowulf

Briefly, the naccess program calculates the atomic accessible surface defined by rolling a probe of given size around a van der Waals surface. This program is an implimentation of the method of Lee and Richards (1971) J.Mol.Biol.55, 379-400. which does just that. The program is dimensioned for up to 20000 atoms, and allows the variation of the probe size and atomic radii by the user.

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 ~]$ ml naccess
[+] Loading naccess 2.1.1 ...
[user@cn3144 ~]$ zcat /pdb/pdb/cr/pdb1crn.ent.gz > 1crn.pdb
[user@cn3144 ~]$ naccess 1crn.pdb
naccess: using defualt vdw.radii
naccess: using default STD FILE

[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 naccess
naccess /path/to/blah.pdb

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. naccess.swarm). For example:

naccess 1pdb.pdb
naccess 2pdb.pdb
naccess 3pdb.pdb
naccess 4pdb.pdb

Submit this job using the swarm command.

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