Biowulf High Performance Computing at the NIH
Gctf on Biowulf

Gctf provides accurate estimation of the contrast transfer function (CTF) for near-atomic resolution cryo electron microscopy (cryoEM) reconstruction using GPUs. The main target of Gctf is to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction.


Important Notes

Gctf can utilize GPUs. This requires the user load the proper CUDA library for the executables. For example, the executable Gctf-v1.06_sm_30_cu7.5_x86_64 requires module load CUDA/7.5 prior to use.

Alternatively, a wrapper script which automatically loads the correct CUDA library can be used: Gctf

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session, along with at least one GPU, and run the program. Sample session:

[user@biowulf]$ sinteractive --constraint=gpup100 --gres=gpu:p100:1
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 Gctf CUDA/7.5
[user@cn3144 ~]$ Gctf-v1.06_sm_30_cu7.5_x86_64 --apix 1.07  --kV 300 --Cs 2.7 --ac 0.1  Micrographs/Falcon*.mrc

[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 Gctf
Gctf --apix 1.07 --kV 300 --Cs 2.7 --ac 0.1 Micrographs/Falcon*.mrc

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] --gres=gpu:p100:1 --partition=gpu