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Slurm Docker Cluster

This is a multi-container Slurm cluster using Kubernetes. The Helm chart creates a named volume for persistent storage of MySQL data files as well as an NFS volume for shared storage.

Dependencies

Requires:

  • A Kubernetes cluster
  • Local installations of
    • Helm
    • kubectl

Containers and Volumes

The Helm chart will run the following containers:

  • login
  • mysql
  • slurmdbd
  • slurmctld
  • slurmd (2 replicas by default)

The Helm chart will create the following named volumes:

  • var_lib_mysql ( -> /var/lib/mysql )

A named ReadWriteMany (RWX) volume mounted to /home is also expected, this can be external or can be deployed using the scripts in the /nfs directory (See "Deploying the Cluster")

Configuring the Cluster

All config files in slurm-cluster-chart/files will be mounted into the container to configure their respective services on startup. Note that changes to these files will not all be propagated to existing deployments (see "Reconfiguring the Cluster"). Additional parameters can be found in the values.yaml file, which will be applied on a Helm chart deployment. Note that some of these values will also not propagate until the cluster is restarted (see "Reconfiguring the Cluster").

Deploying the Cluster

Generating Cluster Secrets

On initial deployment ONLY, run

./generate-secrets.sh

This generates a set of secrets. If these need to be regenerated, see "Reconfiguring the Cluster"

Connecting RWX Volume

A ReadWriteMany (RWX) volume is required, if a named volume exists, set nfs.claimName in the values.yaml file to its name. If not, manifests to deploy a Rook NFS volume are provided in the /nfs directory. You can deploy this by running

./nfs/deploy-nfs.sh

and leaving nfs.claimName as the provided value.

Supplying Public Keys

To access the cluster via ssh, you will need to make your public keys available. All your public keys from localhost can be added by running

./publish-keys.sh

Deploying with Helm

After configuring kubectl with the appropriate kubeconfig file, deploy the cluster using the Helm chart:

helm install <deployment-name> slurm-cluster-chart

Subsequent releases can be deployed using:

helm upgrade <deployment-name> slurm-cluster-chart

Note: When updating the cluster with helm upgrade, a pre-upgrade hook will prevent upgrades if there are running jobs in the Slurm queue. Attempting to upgrade will set all Slurm nodes to DRAINED state. If an upgrade fails due to running jobs, you can undrain the nodes either by waiting for running jobs to complete and then retrying the upgrade or by manually undraining them by accessing the cluster as a privileged user. Alternatively you can bypass the hook by running helm upgrade with the --no-hooks flag (may result in running jobs being lost)

Accessing the Cluster

Retrieve the external IP address of the login node using:

LOGIN=$(kubectl get service login -o jsonpath="{.status.loadBalancer.ingress[0].ip}")

and connect to the cluster as the rocky user with

ssh rocky@$LOGIN

From the shell, execute slurm commands, for example:

[root@slurmctld /]# sinfo
PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
normal*      up 5-00:00:00      2   idle c[1-2]

Running MPI Benchmarks

The Intel MPI Benchmarks are included in the containers. These can be run both with mpirun and srun. They can also be run as a containerised workload using apptainer.

Example job scripts:

  • srun:
#!/usr/bin/env bash

#SBATCH -N 2
#SBATCH --ntasks-per-node=1

echo $SLURM_JOB_ID: $SLURM_JOB_NODELIST
srun /usr/lib64/openmpi/bin/mpitests-IMB-MPI1 pingpong
  • mpirun
#!/usr/bin/env bash

#SBATCH -N 2
#SBATCH --ntasks-per-node=1

echo $SLURM_JOB_ID: $SLURM_JOB_NODELIST
/usr/lib64/openmpi/bin/mpirun --prefix /usr/lib64/openmpi mpitests-IMB-MPI1 pingpong
  • apptainer
#!/usr/bin/env bash
#SBATCH -N2
#SBATCH --ntasks-per-node=1
MPI_CONTAINER_TAG="main"
echo SLURM_JOB_NAME: $SLURM_JOB_NAME
echo $SLURM_JOB_ID: $SLURM_JOB_NODELIST
srun singularity exec docker://ghcr.io/stackhpc/mpitests-container:${MPI_CONTAINER_TAG} /usr/lib64/openmpi/bin/mpitests-IMB-MPI1 pingpong

Note: The mpirun script assumes you are running as user 'rocky'. If you are running as root, you will need to include the --allow-run-as-root argument

Reconfiguring the Cluster

Changes to config files

To guarantee changes to config files are propagated to the cluster, use

kubectl rollout restart deployment <deployment-names>

Generally restarts to slurmd, slurmctld, login and slurmdbd will be required

Changes to secrets

Regenerate secrets by rerunning

./generate-secrets.sh

Some secrets are persisted in volumes, so cycling them requires a full teardown and reboot of the volumes and pods which these volumes are mounted on. Run

kubectl delete deployment mysql
kubectl delete pvc var-lib-mysql
helm upgrade <deployment-name> slurm-cluster-chart

and then restart the other dependent deployments to propagate changes:

kubectl rollout restart deployment slurmd slurmctld login slurmdbd