Logging In

Navigate to the Cluster

To get the Tufts HPC cluster you’ll first need an account. If you haven’t already done so please request an account with Research Technology. You will also need to either be on a Tufts network or be connected to the VPN. Once you have an account and are connected to the VPN/Tufts Network, navigate to the OnDemand Website and log in with your tufts credentials. Once you are logged in you’ll notice a few navigation options:

Open an Interactive Session

Now that we are logged in let’s use the cluster! To start click on Clusters > Tufts HPC Shell Access. You’ll notice the following:

Where:

• tutln01 is your username
• @login-prod-01 is the node you are on

Now it is IMPORTANT to note that when you log in you are on the login node. This is a shared node, sort of like a waiting room. You can’t run anything from this login node. For that you’ll need to request compute resources so type and enter this into your terminal:

srun --time=0-24:00:00 --partition=batch -n 1 --mem=8Gb --reservation=bioworkshop --pty bash

So what did you do? Well you just used what is called a SLURM command. SLURM is what is known as a job scheduler and it is used to organize how jobs are run on the HPC. Let’s break down what you did above:

• srun runs a parallel job on the cluster
• --time How long do we want to use this resource? The format is in day-hour:minute:second, so here we requested 0 day, 24 hours, 0 minutes and 0 seconds
• --partition identifies the partition you want to use - here we use the batch parition
• -n How many CPU cores do we want to use? Here we asked for 1
• --mem How much memory do we want to use? Here we asked for 8 gigabytes
• --pty What kind of terminal do we want? Here we asked for a bash terminal
• --reservation what reservation do we want to use? sometimes nodes are “reserved” for a special use case like this workshop. Here we ask for the bioworkshop reservation

Now you’ll notice that the node has changed:

[tutln01@i2cmp008 ~]$ 

Now let’s create a directory for our workshop with mkdir and change into it with cd :

mkdir hpcDay2
cd hpcDay2

In our workshop directory we will set up a directory structure to organize our inputs/outputs:

mkdir data
mkdir results
mkdir scripts

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