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README.md
consul_config
general_config
generate_openstack
manager_config
node_config

README.md

Deploying Workflow on OpenStack

We have tested and deployed this workflow using NCSA's Nebula, an OpenStack based configuration.

The general layout is to run

Base images and deployment

We're currently using Ubuntu 16.04-based images. To deploy them, do the following steps:

  1. Create an ssh key pair (or use an existing one) which you will use to log into the images. ssh-keygen -t rsa -f nebula_key will generate an RSA key, and you can then add the contents of nebula_key.pub to the "key pairs" pane of the "Access and Security" section of the "Compute menu" in OpenStack.
  2. Get the OpenStack RC file from the "API Access" pane of the "Access and Security" section mentioned above, source it in your shell, and enter your password.
  3. Write your ssh_keys_config file which contains the ssh keys that should be allowed to log into the system, and also the ca.pem which will be trusted by the swarm (once we actually have TLS working).
  4. Run ./generate_openstack in this directory and wait for the VMs to be generated
  5. When they have completed, you can log into one of the two manager nodes to start jobs on the docker swarm. (See Running jobs using docker below).

Installing nextflow

Running jobs using docker

To run a job using docker, ssh into one of the manager nodes. You can do this using:

nova ssh -i ssh_identity manager0 --login ubuntu --extra-opts='-o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no'

which will log into the manager node manager0.

You can then run docker containers like the following, which starts a busybox shell, while mounting the /srv/imputation directory which is shared between all nodes:

docker -H :4000 run -i -u 1000 -P -v /srv/imputation:/srv/imputation:Z busybox sh

Running the imputation workflow

You can also run our imputation workflow using nextflow:

 NXF_EXECUTOR_CPUS=100 /srv/imputation/nextflow/nextflow run \
 -qs 1000 -ps 1000 run.nf -with-docker 'quay.io/dondelelcaro/impute2:latest' \
 -c ../docker_nextflow

The environmental variable NXF_EXECUTOR_CPUS=100 tells nextflow that we have 100 available CPUs so that the local executor will schedule more than a single job on the available docker swarm. This value may need to be tuned for a particular workflow depending on how many swarms you have running.