Biowulf High Performance Computing at the NIH
pyDockRMSD on Biowulf

Description

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 pydockrmsd

[user@cn3144 ~]$  

[user@cn3144 ~]$ mkdir test && cd test
[user@cn3144 ~]$ cp -Rp ../github/pyDockRMSD/examples/data .
[user@cn3144 ~]$ cat << EOF > z.py
from pydockrmsd.dockrmsd import PyDockRMSD
import pydockrmsd.hungarian as hungarian
dockrmsd = PyDockRMSD("./data/targets/1a8i/crystal.mol2",
                      "./data/targets/1a8i/vina1.mol2")
print(dockrmsd.rmsd)
print(dockrmsd.total_of_possible_mappings)
print(dockrmsd.optimal_mapping)
print(dockrmsd.error)
print(hungarian("./data/targets/1a8i/crystal.mol2",
                "./data/targets/1a8i/vina1.mol2"))
EOF
[user@cn3144 ~]$ python z.py
0.692337048145839
108.0
Optimal mapping (First file -> Second file, * indicates correspondence is not one-to-one):
C  1 -> C  1
C  2 -> C  2
O  3 -> O 15 *
C  4 -> C  3 *
O  5 -> O 17 *
C  6 -> C  4 *
O  7 -> O 22 *
C  8 -> C  5 *
C  9 -> C 19 *
O 10 -> O 20 *
O 11 -> O  6 *
N 12 -> N  7 *
C 13 -> C  8 *
O 14 -> O  9 *
N 15 -> N 10 *
C 16 -> C 11 *
O 17 -> O 12 *

0.6923022121452281

[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. pydockrmsd.sh). For example:

#!/bin/bash
set -e
module load pydockrmsd
python my_pydockrmsd_script.py

Submit this job using the Slurm sbatch command.

sbatch pydockrmsd.sh