DeepAb on Biowulf

DeepAb is antibody structure prediction using interpretable deep learning.


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 input in bold):

[user@biowulf]$ sinteractive --gres=gpu:p100:1 -c 8 --mem=20g
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 deepab

[user@cn3144 ~]$ --decoys 4 --num_procs $SLURM_CPUS_ON_NODE --use_gpu --renumber \
--pred_dir $(pwd)/preds --model_dir $DEEPAB_HOME/trained_models/ensemble_abresnet \

[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 deepab --decoys 4 --num_procs $SLURM_CPUS_ON_NODE --use_gpu --renumber --pred_dir $(pwd)/preds --model_dir $DEEPAB_HOME/trained_models/ensemble_abresnet $DEEPAB_HOME/data/sample_files/4h0h.fasta

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=8 --mem=20g --gres=gpu:p100:1
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. deepab.swarm). For example: --renumber --cdr_loop h3 --model_file $DEEPAB_HOME/trained_models/ensemble_abresnet/ --out_file output_1.pdb sample_1.pdb --renumber --cdr_loop h3 --model_file $DEEPAB_HOME/trained_models/ensemble_abresnet/ --out_file output_2.pdb sample_2.pdb --renumber --cdr_loop h3 --model_file $DEEPAB_HOME/trained_models/ensemble_abresnet/ --out_file output_3.pdb sample_3.pdb --renumber --cdr_loop h3 --model_file $DEEPAB_HOME/trained_models/ensemble_abresnet/ --out_file output_4.pdb sample_4.pdb

Submit this job using the swarm command.

swarm -f deepab.swarm -g 10g -t 2 --module deepab
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file).
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module deepab Loads the deepab module for each subjob in the swarm