The Octopus HPC uses slurm. There are many online resources for using slurm on HPC, including
In this document we discuss where differences may occur. For one, Octopus is one of the busiest HPCs in the world, no kidding, because of the large scale pangenome effort at UTHSC.
As a user you will likely notice that. When you plan to fire up large jobs please discuss this on our matrix channel, otherwise jobs may get banned. Also Octopus is run by its users, pretty much in the form of a do-ocracy. Please respect our efforts.
Important warning: Octopus is non-HIPAA. Octopus is not designed to handle sensitive data. Running clinical data without the right permissions is punishable by law. Use designated HIPAA systems for that type of data and analysis.
sinfo tells you about the slurm nodes:
export PATH=$PATH:/usr/local/bin sinfo -a sinfo -R # show node state scontrol show node octopus10
squeue gives info about the job queue
squeue -l
sbatch allows you to submit a batch job
sbatch
To get a shell prompt on one of the nodes (useful for testing your environment)
srun -N 1 --mem=32G --pty /bin/bash
scontrol show node octopus10 Reason=Kill task failed [root@2026-04-23T15:01:19]
"Kill task failed" — this means Slurm tried to kill a job/task on the node (likely at job completion or cancellation) and the kill didn't succeed within the expected time. Slurm then drained the node as a precaution, since it can't guarantee the node is in a clean state.
What to check on the node:
ps aux | grep -E 'D|Z' journalctl -u slurmd --since "2026-04-23 14:55" tail -100 /var/log/slurmd.log cat /proc/mounts dmesg | tail -50
To put it back into service (once you're satisfied the node is clean): bash
scontrol update NodeName=octopus10 State=resume
No modules: Octopus does not use the venerable module system to support deployment. In contrast it uses the modern Guix packaging system. In the future we may add Nix support too.
An example of using R with guix is described here:
If you choose, you can still use conda, brew, spack, Python virtualenv, and what not. Userland tools will work. Even Docker or singularity may work as they work from Guix.