Biowulf High Performance Computing at the NIH
ctffind on Biowulf

CTFFIND and CTFTILT are two programs for finding CTFs of electron micrographs.

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. 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 ctffind
[user@cn3144 ~]$ ctffind --help

[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. ctffind.sh). For example:

#!/bin/bash
module load ctffind

time ctffind3.exe << eof
micrograph.mrc
montage.pow
2.0,200.0,0.07,60000,7.0                        !CS[mm],HT[kV],AmpCnst,XMAG,DStep[um]
128,200.0,8.0,5000.0,30000.0,1000.0,100.0       !Box,ResMin[A],ResMax[A],dFMin[A],dFMax[A],FStep[A],dAst[A]
eof

Submit this job using the Slurm sbatch command.

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