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.
Documentation
Important Notes
- Module Name: PyRosetta (see the modules page for more information)
- Singlethreaded
- Environment variables set
- PYROSETTA_HOME
- Example files in $PYROSETTA_HOME/demo
- Reference data in /pdb/pdb
Many aspects of PyRosetta require an X11 connection. Please see https://hpc.nih.gov/docs/connect.html for graphical methods of connecting.
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ 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 ... quit() [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 D010_Pose_structure.py ... 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. PyRosetta.sh). For example:
#!/bin/bash module load PyRosetta python your_python_code.py
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] PyRosetta.sh