ModelAngelo on Biowulf

ModelAngelo is an automatic atomic model building program for cryo-EM maps.


Important Notes

Some features of ModelAngelo require the hhblits command of hhsuite.

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 --gres=gpu:a100:1
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 model-angelo

[user@cn3144 ~]$ model_angelo build -v map.mrc -f sequence.fasta -o output

[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:

set -e
module load model-angelo
model_angelo build_no_seq -v map.mrc -o output
hhblits -i output/hmm_profiles/A.hhm -d PATH_TO_DB -o A.hhr -oa3m A.a3m -M first

Submit this job using the Slurm sbatch command.

sbatch --gres=gpu:a100:1 --partition=gpu [--cpus-per-task=#] [--mem=#]