Cluster usage

Useful resources for using the OHSU Exacloud cluster

An exceptionally good tutorial is available at https://laderast.github.io/exacloud_tutorial/

Another good tutorial is available at http://docplayer.net/152843431-The-command-line-without-tears-exacloud-for-big-or-medium-tasks.html that has a lot of information on things like setting up your bash environment

The exacloud cluster uses SLURM to run jobs on the nodes. SLURM is pretty widely supported, and lots of Googleable information on it.

The first tutorial above describes how to interact with it. Any program or code you want to run on the cluster needs to go through SLURM.

exacloud: Main partition. Many nodes, with anywhere from 28 to 44 CPUs/node. Generally not a long wait time.
gpu: Partition with fewer nodes, but they have GPUs. Depending on how many GPUs you request, the wait time can stack up on this partition.

Exacloud has 3 main places you can store files.

RDS, accessible at /home/groups/ZuckermanLab: General storage for data. We have a fairly large storage allocation here, so any data you're holding on to long-term should go in here.
gscratch, accessible at /home/exacloud/gscratch/ZuckermanLab: High-performance storage. If you're actively working with files you're loading data in or out of, you'll get the best performance by putting them here. In some cases, it can be a striking difference (I've benchmarked a 30% speedup in some simulations just by moving them from the RDS to gscratch.)

NOTE: This filesystem has been acting up a little lately. At time of writing, this will likely be sorted out by Nov. 21 2021 or so, so I maintain you should use it for data you're actively working with whenever possible.
home, at /home/users/<your username>: Generally, you shouldn't be using this to store data or anything. It's got a quite small amount of space available, and it's not high performance. However, it can be convenient to temporarily throw stuff in here when you're copying files on/off, or for putting things like shell scripts.