HPC Resources: Poseidon - AlexanderLabWHOI/LabWiki GitHub Wiki
Poseidon
When you start at WHOI you should be automatically assigned a username that will grant you access to WHOI's shared HPC resource: Poseidon. When you arrive check with Harriet to make sure that you get properly added to the Alexander Lab shared directory. More information on Poseidon can be found here: https://whoi-it.whoi.edu/resources/.
To access Poseidon you need to be either connected to a WHOI network (e.g. Arctic or LAN) or, if you are off campus, you will need to set up a remote access through VPN prior to logging onto Poseidon. To setup VPN and DUO account follow this guide.
If you have problems setting up your remote access or logging on to Poseidon contact the helpdesk (x2439).
Logging onto Poseidon
Once you have been assigned your username and are connected to the WHOI network (either locally or through VPN) you can connect to Poseidon. To connect, open your terminal app of choice and then type:
ssh [email protected]
You should then see a welcome message like this:
Last login: Tue Apr 16 09:23:46 2019 from dyn-128
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| _ \___ ___ ___(_)__| |___ _ _ / __| |_ _ __| |_ ___ _ _
| _/ _ (_-</ -_) / _` / _ \ ' \ | (__| | || (_-< _/ -_) '_|
|_| \___/__/\___|_\__,_\___/_||_| \___|_|\_,_/__/\__\___|_|
Welcome to the Poseidon Cluster at WHOI!
You might consider adding the login to an alias in your local .bash_profile that allows you to login automatically by typing whoi.
alias whoi="ssh [email protected]"
A note: there are two log in nodes:
poseidon-l1andposeidon-l2. If you ssh into@poseidon.whoi.eduyou will be randomly logged into one or the other. If you care (for any reason) which node you login to you can specify it in your login like the above alias example.
Another note, setting up a ssh-key login will save you having to type your password each time you log on. A nice tutorial on how to set this up can be found here.
Navigating Poseidon
When you first log on you should will automatically be logged into your home directory ($HOME or /vortexfs1/home/username). You should have 1Tb of storage in your home directory and you should be the only person who can access this directory. You can store and do whatever you want in this directory.
All of your computation and active writing to disk should be done in your scratch directory. This can be found at $SCRATCH or /vortexfs1/scratch/username.
Additionally, members of the Alexander Lab will have access to a lab space /vortexfs1/omics/alexander. This directory has 16Tb of space and is shared. When you first join please make yourself a directory that is the same as your username. This will be your space, where you can test out code, and store analysis pipelines, etc.. Please do not write or edit other peoples directories (you shouldn't be able to...).
There is also a data directory for the Alexander Lab (/vortexfs1/omics/alexander/data), here we keep data sets that were generated in the lab and datasets of shared interest. Please make sure to make all raw data read only (chmod 0444). You should not copy files from this directory into your directory in the Alexander Lab space. Rather, please create symbolic links (ln -fs file .) into your directory.
In addition to the Alexander Lab data directory there is also a general biology data directory (/vortexfs1/omics/data) that stores some larger datasets (e.g. Tara, MMETSP, NCBI nr/nt for blast). You will not have write access to these data, but again, can use symbolic links to put the data in a convenient location for your analysis. If you have a dataset that you would like to have added to this directory, please talk to Harriet.