The CHMI server, nicknamed ‘Acadia’, is a powerful Linux workstation running Ubuntu 23.10 It has 2Tb of RAM, and two 26-core Intel Xeon 5320 'Ice Lake-SP' 2.2 GHz CPUs (total of 52 CPU cores, or 104 threads). This machine is also equipped with two NVIDIA RTX6000 GPUs with ‘Ada Lovelace’ architecture, each with 48GB of memory. You can read more about these GPUs here.
Software available on this machine changes from time to time, but you can always view a relatively up-to-date listing of informatics tools we have installed here. In addition to this software, we also host RStudio Server Pro on this machine, which allows anyone with an account on the server to run RStudio in their browser with full access to this machine's compute capabilities. We also have Geneious Prime installed and accessible remotely through a desktop sharing protocol.
Our Linux server is equipped with roughly 100Tb of storage. There are two main directories you will need to be familiar with:
/home - this is where everyone’s home directories live. Each user will have a folder with their name in
/home. This directory resides on a single 8Tb NVMe solid-state drive (SSD) with read/write speeds of > 3000 MB/s. Roughly 5Tb of this drive are devoted to
/home. There is no back-up for this drive, which means that you should never use this drive for storing important data. There are situations in which you may want to temporarily store data on
/home, particularly when fast read/writes speeds are needed. For example, during basecalling for Oxford Nanopore data.
/data - this is where you should store raw data. Each user will have a folder with their name in
/data. This directory lives on an array of 6 separate 20Tb drives formatted as a single RAID5, giving us ~90Tb of total storage! RAID5 arrays can tolerate a single drive failure without any data loss. Despite the large size and RAID format of this drive array, it is not designed for long-term data storage. You should contact PennVet IT support to get access to the school’s archival storage server.
Use of the server is free-of-charge to approved PennVet labs. However, to protect the machine from abuse and prevent issues with storage, we have a few rules all users must follow. Failure to adhere to these rules will result in a warning. Additional violations will result in suspension of your account. Here are the rules:
/home/[USERNAME] on the server, you will also be given a data folder that is located on
/data/[USERNAME]. All data must be stored in this directory not your
<aside> 📌 Accounts on our Linux server will only be granted to labs at PennVet. Contact Dan Beiting if you're at PennVet and would like to request an account.