About our server

hardware

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

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.

drives and filesystem

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.

General rules

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:

• We will set-up your account and install any software you may need. Please do not install software yourself unless you’ve cleared it with me (Dan Beiting) first. You can find a full list of of all the software installed system-wide here.
• In addition to your home account which is located at /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 /home/[USERNAME] folder.
• Data storage space is limited, so we periodically monitor storage space and may request that data not currently in use be moved off the server.
• Please be courteous and clean up after yourself. Delete files that aren't needed (e.g. .gz/.tar/.zip files that have been uncompressed).
• We require a strong password for each account. We will set this password for you, and ask that you do not change it. Please do not share this password with anyone outside of your lab. If you need to send this password to a lab mate, please do so using a secure method. We use password pusher for this.
• We are not responsible for backing up your raw data or analysis scripts and files. You should use the PennVet storage server for secure backup (contact PennVet IT for more info). See below for more information on how to transfer data from our Linux server to your account on the PennVet Storage server.

Connect to CHMI linux server via SSH

<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.

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