LAFTER on Biowulf
LAFTER is a local filter for single particle TEM reconstructions
Documentation
Important Notes
- Module Name: lafter (see the modules page for more information)
- Multithreaded
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 lafter [user@cn3144 ~]$ lafter --v1 half_map1.mrc --v2 half_map2.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. lafter.sh). For example:
#!/bin/bash set -e module load lafter lafter --v1 half_map1.mrc --v2 half_map2.mrc
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] lafter.sh