Experiments

Functionality Test

A simple functionality test is provided here. Please follow the instructions there.

Prepare Experiments

To prepare the execution of the experiments:

1. Set your NFS server's IP and username in experiment/nfsConnection.txt; this will be used to adjust the network speed of the server.
2. Set NFS server's IP in experiment/nfs.yaml.
3. Create a file experiment/nfsPassword.txt and insert your NFS password; this will be used to adjust the network speed of the server.
4. Change the Kubernetes namespace in experiment/namespace.txt and in experiment/accounts.yaml, experiment/nfsClaim.yaml, setup/dowload-pod.yaml, maybe adjust your storage classes.
5. Label your Kubernetes nodes and adjust experiment/nextflow_usedby.config and setup/download-pod.yaml accordingly.
6. Configure the NFS Server for Kubernetes: kubectl apply -f experiment/nfs.yaml and kubectl apply -f experiment/nfsClaim.yaml

Setup Inputs

Go into the setup directory.

Placing all the inputs for a workflow into the PVC just takes two steps now:

Start the download pod (the image is built from the Dockerfile provided):

kubectl create -f download-pod.yaml

As soon as the task is ready you execute the script for one workflow:

bash setup-inputs.sh <workflow-name>

Or, alternatively, setup all the workflow inputs at once:

bash setup-all-inputs.sh

Rangeland Setup

For Rangeland, you need to download input data according to the Rangeland README. The inputdata directory in the Rangeland repository corresponds to the /nfs/rangeland/input directory.

Execute

Go into the experiment directory.

To run the experiments: bash runExperimentFromRemote.sh <strategy> <network speed> where strategy is nfs, ceph, orig-nfs, or orig-ceph. The network speed is an integer.