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May 2024 Maintenance Details

Kristen Finch

Kristen Finch

HPC Staff Scientist

Hello HYAK Community,

Thanks again for your patience with our monthly scheduled maintenance, there are some notable improvements we implemented today.

KLONE node image: Over the past few weeks, you may have noticed some KLONE instability. This was a result of some behind the scenes storage upgrades that inadvertently introduced wider impacts to the existing cluster automation. At the time, we introduced a temporary fix to get the cluster back online but with today’s maintenance we implemented a more comprehensive fix.

Infiniband firmware: The KLONE cluster is built on the infiniband HPC interconnect for node-to-node communication. While KLONE originally launched with the HDR generation of infiniband, we have since upgraded mid-KLONE to have a HDR-NDR hybrid interconnect. NDR infiniband is required to support the latest compute slices we offer. We updated the firmware on our NDR switches following vendor recommendations for increased stability.

Apptainer on MOX: Apptainer (formerly Singularity) is the root-less containerization solution we provide on both HYAK clusters. Apptainer version 1.3.1 was deployed on both KLONE and MOX. As a reminder, on KLONE Apptainer is accessed through a module and is only available on compute nodes after module load apptainer. On MOX, Apptainer is default software and can be accessed with Apptainer commands directly after starting an interactive job for example, apptainer --version.

Training Opportunities: COMPLECS (San Diego Supercomputer) is hosting an Intermediate Linux Shell Scripting online workshop on Thursday May, 16 at 11:00 am Pacific Time. Register here.

Our next scheduled maintenance will be Tuesday June, 11, 2024. Stay informed by joining our mailing list. Sign up here.

Questions? If you have any questions for us, please reach out to the team by emailing help@uw.edu with Hyak in the subject line.

Migrating from MOX to KLONE

Nam Pho

Nam Pho

Director for Research Computing

If you were previously a proficient MOX user and now find yourself on KLONE, what's new / different? This is a high-level summary, please consult the documentation [link] for more details.


Updated August 10, 2021 to include additional information specific for GPU users.


  • Logging in was previously to mox.hyak.uw.edu now it's klone.hyak.uw.edu.
  • As a reminder login nodes are only to connect to the cluster, navigate the cluster file system, and submit jobs. This applies to both KLONE and MOX. Do not compile codes on the login node or run any programs that require significant compute (get a session with SLURM).

Data Transfer#

  • Only use the login node to transfer data on KLONE. On MOX you'd have used a build node or could have used the login node if it wasn't very computationally heavy.


  • The path to lab storage is still /gscratch/mylab on both KLONE and MOX. You'll need to copy over the data from MOX to KLONE you want to continue using.
  • Home directories are still 10GB per user, same on both clusters.
  • Scrubbed exists on KLONE just as it did on MOX at /gscratch/scrubbed this is a free-for-all space on both clusters where files are automatically deleted after 21 days.
  • Some new benefits of the KLONE storage compared to MOX:
    • There are snapshots for gscratch! Look inside the /gscratch/mylab/.snapshots folder for a copy of your lab folder once an hour, every hour, for 24 hours. This is not a backup copy nor a replacement for version management (e.g., git) but useful for retrieving recent versions or something accidentally deleted. This is currently disabled.
    • More storage! Previously you received 500GB or 0.5TB of gscratch quota per node (or pair of GPUs) contributed to MOX. Now on KLONE we've doubled your associated storage quota! For example, 2 nodes on MOX would mean 1TB of gscratch but 2 nodes on KLONE now means 2TB of gscratch. If you had an 8 x GPU node on MOX you would have received 2TB of gscratch but an 8 x GPU node on KLONE now means 4TB of gscratch.
    • It's faster! We've had reports of performance that's averaging a 30% speed up all else being equal, nothing you need to do aside from use KLONE instead of MOX.
    • It's faster than fast! While KLONE storage is faster than MOX storage overall, gscratch on KLONE is further turbo charged with a NVMe flash based tier. NVMe flash is among the fastest storage mediums you can get and further differentiating benefit if you use gscratch vs scrubbed on KLONE.


  1. When submitting a SLURM job, whether interactive (i.e., salloc) or batch (i.e., sbatch) you'll want to first decide which account to use. This is the group you're part of. You can run the command groups to see your affiliated accounts and run hyakalloc to see all the resources (e.g., compute cores, memory, GPUs) used and available associated with each affiliated account.
  2. Then decide if you want to run this job to count under your resource allocation by submitting to the compute partition (i.e., -p compute) or if you want this job to use idle resources from other groups across the cluster using the checkpoint partition (i.e., -p ckpt).
  • Non-standard partitions. Run sinfo to see the list of all possible partitions, this is only if your group contributed non-standard nodes (e.g., high memory, GPUs) and need to idenitify the appropriate partition names to get immediate use. Otherwise, you'd only be able to get them in a checkpoint capacity. For GPU users this is currently either the gpu-2080ti or the gpu-rtx6k partitions for 11GB and 24GB of GPU memory cards, respectively.
  • There is no build node on KLONE. Get an interactive session (e.g., salloc) under an existing account and partition combination you have access to.
  • All nodes have internet now on KLONE. Do all data transfers to and from KLONE on the KLONE login nodes, the login nodes on KLONE have dual 40 Gbps uplinks to the internet. While the compute nodes on KLONE have internet routing now, they are bottlenecked at 1 Gbps so not suitable for big data transfers.


  • Singularity containers work the same on both clusters, we encourage this when possible. Refer to our container documentation [link].
  • Modules is updated to the latest versions of the most core parts that the HYAK team maintains (e.g., gcc, Intel, Matlab). Refresh yourself about modules [link].
  • If neither Singularity nor existing modules works for you, you may have to re-compile your codes on KLONE. "contrib" modules works different now on KLONE vs MOX, please check out the details [link].