Biowulf High Performance Computing at the NIH
ResMap on Biowulf

ResMap (Resolution Map) is a Python (NumPy/SciPy) application with a Tkinter GUI and a command-line interface. It is a software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryo- EM).

References:

Documentation
Important Notes

This application requires an X-Windows connection. Users are encouraged to use NX or FastX as their X11 servers.

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 ~]$ module load ResMap
[user@cn3144 ~]$ ResMap

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

After typing 'ResMap' at the prompt, input is menu-driven.

ResMap window

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. ResMap.sh). For example:

#!/bin/bash
module load ResMap
ResMap --noguiSingle --vxSize=300 --minRes=2.0 --maxRes=10.0 ResMap.mrc

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] ResMap.sh