Biowulf High Performance Computing at the NIH
PyRosetta on Biowulf

PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.

PyRosetta was created at Johns Hopkins University by Jeffrey J. Gray, Sergey Lyskov, and the PyRosetta Team.

Important Notes

Many aspects of PyRosetta require an X11 connection. Please see for graphical methods of connecting.

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 --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 PyRosetta
[user@cn3144 ~]$ python
Python 2.7.15 |Anaconda, Inc.| (default, Oct 23 2018, 18:31:10) 
[GCC 7.3.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyrosetta
>>> pyrosetta.init()

... your code here ...

[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144 ~]$ cp -r $PYROSETTA_HOME/demo .
[user@cn3144 ~]$ cd demo
[user@cn3144 ~]$ cp -r $PYROSETTA_HOME/test .
[user@cn3144 ~]$ mkdir .test.output
[user@cn3144 ~]$ python

... pyrosetta output here ...

[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 PyRosetta

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#]