Biowulf High Performance Computing at the NIH
NovaCTF on Biowulf

Description

References:

Documentation
Important Notes

This app requires the clip command from IMOD.

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 novactf IMOD

[user@cn3144 ~]$ clip flipyz input.ali output.ali

[user@cn3144 ~]$ novaCTF -Algorithm defocus -InputProjections input_stack.st -FULLIMAGE 464,464 -THICKNESS 140 -TILTFILE angles.tlt -SHIFT 0.0,0.0 -CorrectionType phaseflip -DefocusFileFormat ctffind4 -CorrectAstigmatism 1 -DefocusFile defocus_file.txt -PixelSize 0.135 -DefocusStep 15 -DefocusShiftFile file_with_additional_defocus.txt

[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. novactf.sh). For example:

#!/bin/bash
set -e
module load novactf IMOD
novaCTF -Algorithm defocus -InputProjections input_stack.st -FULLIMAGE 464,464 -THICKNESS 140 -TILTFILE angles.tlt -SHIFT 0.0,0.0 -CorrectionType phaseflip -DefocusFileFormat ctffind4 -CorrectAstigmatism 1 -DefocusFile defocus_file.txt -PixelSize 0.135 -DefocusStep 15 -DefocusShiftFile file_with_additional_defocus.txt

Submit this job using the Slurm sbatch command.

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