CHMI maintains a custom configured compute server that runs Linux Ubuntu 18.04 LTS. This machine has two 6-core Intel Xeon E5-2643v4 CPUs (12 cores total), 512 Gb of RAM and 18Tb of RAID1 storage. If you are a PennVet lab and wish to use this machine, please contact Dan Beiting (beiting@upenn.edu) for more information.
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General rules

Use of the server is free-of-charge to approved 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 rule 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.
  • 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 (18Tb goes quickly!), so we periodically montior storage space and may request that data not currently in use be moved off the server.
  • We require a strong password for each account. We will set this password for you, and ask that you do not change it.

Creating and managing user accounts (CHMI only)

Add a new user

First, add a new user to the home directory

sudo adduser [username]

Then give the new user sudo priveleges

usermod -aG sudo username

Delete a user

sudo deluser --remove-home [username]

Installing software (CHMI only)

  • All software must be installed only in /usr/local/bin/
  • Once installed, you’ll need to add the path to the executable to your PATH variable. To do this, open the system profile (a text document, so it can be opened with either the nano or vim text editors, both of which are built into the linux system) 
    sudo nano /etc/profile
  • scroll to the bottom of the /etc/profile file and add the path to the new software. For example, if you had downloaded the program kallisto, you would add export PATH=$PATH:/usr/local/bin/kallisto to the bottom of the /etc/profile document.
  • now your program will be available to any user, regardless of the directory in which they are working. Changes to /etc/profile may not take effect until you start a new session.

Connecting to the Linux server

ssh username@130.91.255.137
#you'll be prompted to enter your password and then you'll be connected
#once connected you'll see a new prompt with username@ubuntu1604

command line tips

If you’re new to the command-line in Linux, there are lots of online resoures for learning, but here are a few of the commands that will help you move around and carry out basic tasks. Note that many of these may only work if run as sudo.

typing this at the prompt does this
tar -xvzf <fileName.tar.gz> unzip a .tar file
ls -l list all files and folders in your working diretory with info on permissions
du -a -h --max-depth=1 | sort -hr lists all files and folders in your working directory sorted by size
du -sh * simpler version of the command above. lists all files in a folder and shows their file size
ls -l | wc -l counts files in a directory
tree -d lists all files and folders in your working directory as a tree structure
pressing up arrow recalls previous command
cd / takes you to the root directory
cd ~ takes you to your home directory
cd .. takes you up one level in your file directory
cd ../.. takes you up two levels in your file directory
chmod u+x <fileName> edits permissions on file
chown <yourUserName> <fileName> makes you the owner of a file
chgrp <yourUserName> <fileName> assigns you as the group for the file
rm -rf <directoryName> removes a folder and all of its contents
wget <URLtoFile> downloads a file from a website
defaults write com.apple.finder AppleShowAllFiles YES show all hidden files in the finder (Mac only)
Tags: bioinformatics