Pitt new user setup

Pittsburgh cluster - new user setup

Like our other clusters, the Pittsburgh cluster also runs Unix. If you're not familiar with using the Unix command line, please take a course. There are many available online.

Contact out admin Gengkon Lum ([email protected]) to request an account. For outside access you will also require a VPN account.

After connecting to the VPN, start an ssh session:

ssh [email protected]

Install clusterutil and micromamba

#Create directories for installed binaries and for downloaded git repos:
mkdir -p .local/bin/ bin/ repos/

#Install clusterutil:
cd repos/
git clone https://github.com/jweile/clusterUtil.git  
cd clusterUtil/  
./install.sh

#Install micromamba
# (A drop-in replacement for anaconda/miniconda that runs much faster)
cd
bash <(curl -L micro.mamba.pm/install.sh)
micromamba self-update
micromamba config set auto_activate_base true

Next we want to edit our .bashrc to add aliases for micromamba, the mm alias is just so we don't have to type out "micromamba" all the time. The conda alias is for backwards compatibility with scripts that rely on conda.

If you're nervous about editing dotfiles, you can make a backup copy first:

cp ~/.bashrc ~/.bashrc.backup

You can of course use your favourite editor to edit the file, but if you're new to Unix, you might prefer nano:

nano .bashrc

Add the following lines:

# User specific aliases and functions
alias mm=micromamba
alias conda=micromamba

Save and exit nano via Ctrl-S and Ctrl-X.

Setting up a github access token

Both at the LTRI and the Donnelly Centre a great number of people access Github on a daily basis all while sharing the same external IP address. From Github's perspective this can appear as a single IP address spamming it with access requests, thus throttling or temporarily banning access from our institutions. This is a problem when installing R packages directly from github, as this requires frequent access to it.

To get around those access limits, Github offers Personal Access Tokens (PATs), which looks like a string of random letters and numbers that serves as an application-specific password to your account. To learn how to create your PAT, refer to the relevant github help page.

Once you have generated a PAT, you can let R know to use it for future installations.

1. Go to your home directory and create a file called .Renviron

cd ~
nano .Renviron

2. Type GITHUB_PAT= and then copy-paste your PAT string after the = sign. Finally, press Enter to add a new line at the end
3. Save and exit nano (CTRL-S and CTRL-X)