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README.md

Submitting HADDOCK 3 Jobs Through Slurm

Prepare Singularity Image and Test

  1. Make a Singularity image from the HADDOCKer image.
module load singularity

singularity pull haddock3.sif docker://cford38/haddock:3
  1. Running Numerous Experiments

The submit_dist.sh script reads in a .csv file that lists the desired experiment IDs to be run. Then, it loops through each ID and spins off jobs for each experiment using the submit_iter.sh script. This uses the pulled HADDOCK 3 Docker container that has been converted to a Singularity image.

bash submit_dist.sh

Testing in Docker

## Pull the image and retag it
docker pull cford38/haddock:3.0.0-beta.5
docker image tag cford38/haddock:3.0.0-beta.5 haddock3

## Run the container
docker run -v .:/data --name haddock3 -it haddock3 /bin/bash

## Once inside the container
cd /data/data/experiments/<YOUR EXPERIMENT>
haddock3 config.cfg

Testing in Singularity

  • Note: You should ssh into an interactive node: ssh sth-i3
singularity run haddock3.sif /bin/bash

haddock3 config.cfg