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README-setting-up-storage.md

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Setting up Storage

The LSF cluster needs storage configured for:

  1. Storing the LSF configuration
  2. Running jobs

In both cases the LSF cluster will mount pre-created Persistent Volume Claims (PVC)s to access the storage. Dynamic storage is not recommended for LSF configuration. Deleting the LSF cluster will also remove the LSF job data. Dynamic storage should only be used for initial testing were job data loss is okay.

More commonly users home directories, data and application binaries will be hosted on NFS servers. In this case a Persistent Volume (PV) and PVC can be created to access NFS filesystems.

Using Dynamic Storage for LSF Configuration

If you choose to use dynamic storage for LSF configuration and work data, use the following to create the PVC:

  1. Create a file called lsfpvc.yaml with the following contents:
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
  name: mylsfpvc
  namespace: lsf
spec:
  accessModes:
  - ReadWriteMany
  resources:
    requests:
      storage: 20G
  storageClassName: {Provide the StorageClassName of the dynamic storage}
  volumeMode: Filesystem
  1. Create the PVC with:
kubectl create -f lsfpvc.yaml
  1. Verify that the PVC has been created with:
kubectl get pvc -n lsf

You should see the mylsfpvc pvc.

Creating a NFS Hosted PV and PVC for LSF

Kubernetes pods can access NFS servers provied the worker nodes can mount the NFS filesystem. Use the following proceedure to create a PV and PVC for LSF configuration and work directories:

  1. Create the PV spec file mylsfpv.yaml with the following contents:
apiVersion: v1
kind: PersistentVolume
metadata:
  name: mylsfpv
spec:
  accessModes:
  - ReadWriteMany             # Has to be this for failover
  capacity:
    storage: 10Gi             # Specify the amount of storage to provide
  nfs:
    path: /some/export        # Use you exported filesystem from the NFS server
    server: 11.22.33.44       # Use the IP address of your NFS server
  persistentVolumeReclaimPolicy: Retain
  volumeMode: Filesystem
  claimRef:
    name: mylsfpvc            # We are pre-binding the PVC to ensure that the correct PVC uses this PV
    namespace: lsf
  1. Create the PV:
kubectl create -f mylsfpv.yaml
  1. Create the PVC spec file mylsfpvc.yaml with the following contents:
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
  name: mylsfpvc
  namespace: lsf
spec:
  accessModes:
  - ReadWriteMany
  resources:
    requests:
      storage: 10G
  volumeMode: Filesystem
  storageClassName: ""
  1. Create the PV:
kubectl create -f mylsfpvc.yaml
  1. Check that the PVC has been created and is bound to the PV
kubectl get pvc -n lsf mylsfpvc

You should see something like:

NAME         STATUS   VOLUME              CAPACITY   ACCESS MODES   STORAGECLASS          AGE
mylsfpvc     Bound    mylsfpv             10Gi       RWX                                  4s

The PVC is ready for use. Remember to set the lsfpvcname in the LSF cluster yaml file.

Creating a NFS Hosted PV and PVC for Home, Data and Applications

The process to create PV's and PVC's for other volumes is the same as for the LSF configuration and work directory.

  1. Create copies of the mylsfpv.yaml and mylsfpvc.yaml files for each filesystem you want to access in the LSF pods.
cp mylsfpv.yaml myhomepv.yaml
cp mylsfpvc.yaml myhomepvc.yaml
  1. Edit the files and change the names of the PV and PVCs.
apiVersion: v1
kind: PersistentVolume
metadata:
  name: myhomepv           <---- Change the name
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
  name: myhomepvc           <---- Change the name
  1. In the PV file set the NFS server and exported path to want to mount in the PV file.
kind: PersistentVolume
metadata:
  name: myhomepv
spec:
  nfs:
    path: /some/export        # Use you exported filesystem from the NFS server
    server: 11.22.33.44       # Use the IP address of your NFS server
  1. Change the PV access mode if needed:
spec:
  accessModes:
  - ReadWriteMany             # You may use ReadOnlyMany to prevent write access
  1. Update the PV claimReference in the PV to bind it to the PVC.
spec:
  claimRef:
    name: mylsfpvc            # We are pre-binding the PVC to ensure that the correct PVC uses this PV
    namespace: lsf
  1. Repeat these steps to prepare additional PV's and PVC's needed by the LSF jobs.

Remember to update the LSF cluster yaml file with the names of the PVCs just created.

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