Getting Started

The RCC cluster can be accessed using a web browser or the command line. Accessing RCC requires a Slurm account to be created for your user. See the “Project Sized” section of HPC Cost Model and Rates for rates and the Request HPC Services button to request a RCC Slurm account.

Requirements

To access RCC requires having a DHE Account and being on the DHTS VPN. Users can be sponsored for a DHE Account here: https://accounts.oit.duke.edu/sponsor. Article about sponsored accounts: https://duke.service-now.com/sp?id=kb_article&sys_id=bf006c174708755c763c4a88036d4386. See this article for how to connect to the DHTS VPN: https://duke.service-now.com/sp?id=kb_article&sys_id=dbe1c662971d4ed431b570b11153afa9.

Web Access

The RCC cluster is accessible using a web browser via the rcc-ondemand.dhe.duke.edu website. This website allows managing files, running Jupyter notebooks, and RStudio sessions.

SSH Access

Logging in to the RCC requires being connected to the Duke Health Virtual Private Network(VPN) with DHTS VPN Elevated Access.

Connecting to the cluster with SSH requires Elevated VPN Access due to an ISO requirement.

For help connecting to the VPN see this article https://duke.service-now.com/sp?id=kb_article&sys_id=dbe1c662971d4ed431b570b11153afa9.

For help requesting Elevated VPN access see https://duke.atlassian.net/wiki/spaces/somhpc/pages/196247828.

Once you are connected to the Duke Health VPN connect to the cluster by running the ssh command in a terminal:

ssh <NetID>@rcc-login.dhe.duke.edu

The first time you connect to the cluster you may be prompted to accept the finger print for the rcc-login server. Answer yes to this prompt:

Are you sure you want to continue connecting (yes/no/[fingerprint])? yes

See https://duke.atlassian.net/wiki/spaces/somhpc/pages/419430431 for common issues when connecting via ssh.

NOTE: The login node is not meant to be used for computational processing.

The login node should only be used for:

script and configuration file editing
job submission and monitoring
file transfers

To perform other tasks using either an interactive job or a background job.

Run a test job

Once you are connected to the login node it is a good idea to verify you can submit a job to the Slurm Cluster. Type the following command into your terminal replacing <GroupName> with the Slurm account assigned to your lab.

srun --account=<GroupName> echo 'Hello World!'

The expected output is as follows:

Hello World!

NOTE: All jobs on the RCC require a user to enter the account.

To list Slurm accounts for your user run:

sacctmgr show associations user=$USER format=account%20 -n

Training Courses

There are Slurm training courses offered by the Duke Compute Cluster: https://oit-rc.pages.oit.duke.edu/rcsupportdocs/help/training/. There are minor differences between RCC and DCC, but the process for running jobs on a Slurm cluster is the same.

Next: https://duke.atlassian.net/wiki/spaces/somhpc/pages/145916047