Quick Start Guide (v2)

Logging into Kamiak

Okta is used when logging into Kamiak

Okta is used for authentication when logging into Kamiak over ssh and scp, which are used for job submission and file transfer, respectively. Your username and password will be your WSU network ID (NID) and its associated password.

You will need to install a client-side program on your laptop or endpoint, called opkssh, to launch the authentication into Okta. You will only need to authenticate once every 24 hours. You then use ssh and scp as normal. Under the hood opkssh uses short-lived ssh certificates to log into Kamiak. Below are the instructions to install opkssh, and use it to log into Kamiak.

Install opkssh on your laptop or endpoint.

Run the below installation scripts as the user who will be logging into Kamiak. You do not need to be an administrator to install or use opkssh.

Use opkssh to log into Kamiak.

  1. Authenticate using Okta.
    You only need to do this once every 24 hours.
    • opkssh login kamiak
  2. Run ssh or scp as normal.
    ssh as many times as you wish. You will not be prompted to authenticate again.
    • ssh your.name@kamiak.wsu.edu

Partitions and job queues

Kamiak is an HPC cluster housing compute nodes which are purchased by investors and colleges. The nodes are grouped into partitions named after their lab group or college. Jobs submitted to a partition are placed into a “queue” of the same name, and will wait to run until resources requested by the job are available, using fairshare scheduling. The allocation of resources and running of jobs is performed by the Slurm job scheduler.

In addition to the investor and college partitions, there is an overarching backfill partition named “kamiak” that contains all nodes, and is available for use by the entire research community. The “kamiak” partition allows users to utilize idle compute resources regardless of ownership.

Investors have priority access to the nodes they own. Any backfill job running on an investor node will be preempted if the investor’s job needs its cores in order to be able to run. Preempted means the job will be canceled and automatically resubmitted to the backfill queue.

For information on the queues currently set up on Kamiak see the queue list.

Job submission

Kamiak uses the Slurm job scheduler to coordinate the use of resources on Kamiak. To run a job on Kamiak you will first need to create a Slurm job submission script describing the job’s resource requirements. Jobs are then submitted using the sbatch command. Alternatively, you can launch an interactive session on a compute node using idev, and see bash commands executed as you type them. The status of your job can be monitored using the squeue command. Submitted jobs can be killed using the command scancel followed by the Job ID. For more information on job submissions see the Job Submission section of the Kamiak users guide.

Storage

Home storage

Each user on Kamiak has a home directory, accessible at /home/myWSU.netid

Lab storage

Each faculty lab account has a folder at /data/lab/myLabName, with a default amount of storage. Additional storage can be rented through the CIRC service center.

Scratch storage

Users who need temporary storage may take advantage of scratch space.
 
For information of default storage sizes see the Storage section in the Kamiak user guide.

Software

Modules

Kamiak uses environment modules to control the Linux software environment. Users can run the module avail command to see a list of available software modules. Software can be added to the linux environment using the command module load <package name>. For more information see environment modules in the Kamiak users guide.

Conda

Conda is also used to manage software environments and install packages. Kamiak provides both anaconda3 and miniconda3 modules, which can be used to create and manage conda environments. For more information see python_and_conda in the Kamiak users guide.