Biowulf High Performance Computing at the NIH
OSPREY on Biowulf

OSPREY is a suite of programs for computational structure-based protein design. OSPREY is specifically designed to identify protein mutants that possess desired target properties (e.g., improved stability, switch of substrate specificity, etc.). OSPREY can also be used for predicting small-molecule drug inhibitors. Starting with version 2.0, OSPREY can now design protein-protein and protein-peptide interactions.

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, following Chapter 8 of the User Manual. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task 5 --mem 8g --gres lscratch:10
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 osprey
[+] Loading osprey, version 2.2~beta...
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn3144 46116226]$ cp -r  $OSPREY_HOME/example/ppi/* .
[user@cn3144 46116226]$ echo "dataDir $OSPREY_HOME/dataFiles" > KStar.cfg # use correct data file path on Biowulf
[user@cn3144 46116226]$ cat <<EOF > MutSearch.cfg
runName PDZexample
numMutations 3
doMinimize true
addWT true
addOrigRots true
resAllowed1_0 ALA VAL LEU ILE PHE TYR TRP CYS MET SER THR LYS ARG HIE HID ASP GLU ASN GLN GLY
resAllowed1_1 ALA VAL LEU ILE PHE TYR TRP CYS MET SER THR LYS ARG HIE HID ASP GLU ASN GLN GLY
resAllowed1_2 ALA VAL LEU ILE PHE TYR TRP CYS MET SER THR LYS ARG HIE HID ASP GLU ASN GLN GLY
iMinDEE true
Ival 0.5
initEw 0.2
approxMinGMEC true
lambda 1
algOption 1
EOF
[user@cn3144 46116226]$ java -Xmx${SLURM_MEM_PER_NODE}M KStar -t $SLURM_CPUS_PER_TASK -c KStar.cfg doDEE System.cfg MutSearch.cfg &> logDEE.out
[user@cn3144 46116226]$ 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. osprey.sh). For example:

#!/bin/sh
set -e
module load osprey
java -Xmx${SLURM_MEM_PER_NODE}M KStar -t $SLURM_CPUS_PER_TASK -c KStar.cfg doDEE System.cfg MutSearch.cfg &> logDEE.out

Submit this job using the Slurm sbatch command.

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

cd sample1 && java -Xmx${SLURM_MEM_PER_NODE}M KStar -t $SLURM_CPUS_PER_TASK -c KStar.cfg doDEE System.cfg MutSearch.cfg
cd sample2 && java -Xmx${SLURM_MEM_PER_NODE}M KStar -t $SLURM_CPUS_PER_TASK -c KStar.cfg doDEE System.cfg MutSearch.cfg
cd sample3 && java -Xmx${SLURM_MEM_PER_NODE}M KStar -t $SLURM_CPUS_PER_TASK -c KStar.cfg doDEE System.cfg MutSearch.cfg
cd sample4 && java -Xmx${SLURM_MEM_PER_NODE}M KStar -t $SLURM_CPUS_PER_TASK -c KStar.cfg doDEE System.cfg MutSearch.cfg

Submit this job using the swarm command.

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