Abacus - Part 1

Bernat Bramon & Fernando Cagua

December 15, 2017

The cluster is just another computer

Basic unix commands

Open a terminal and play with these commands:

mkdir new_directory
touch new_file

cd new_directory
cd ..
ls -l 
cp new_file new_directory/
ls -l new_directory

rm -r new_directory new_file

Try exploring your own computer using the terminal. For example, navigate to your last project’s directory.

Accessing the cluster

Log into your account

ssh usr123@abacus

Create a new directory in your home directory. It’s just the same as in your computer.

mkdir ~/workshop

Change your password


To exit the cluster use Ctlr + D

Moving files to the cluster

Start by making an R script by typing the following:

message("my first job in the cluster")

Now let’s move it to the cluster

In your computer’s terminal type:

scp ~/path_to_sript/r_script_name.R usr123@abacus:~/workshop 

We can also modify the R script in Abacus

In the abacus terminal type:

cd ~/workshop
nano r_script_name.R

Besides nano you can also use other text editors like vim or vi in case you need/want to modify files directly in the cluster

Pulling files from Github

Visit the GitHub repository on http://github.com/efcaguab/sge-workshop

We can downloading from GitHub to the cluster.

But first we need to enable internet in Abacus.

telnet ienabler 259

On the Abacus terminal:

cd ~/
git clone git@github.com:efcaguab/sge-workshop.git

Now you have all the workshop materials in abacus. Try to modify script-2.R from Abaucs using nano

Abacus basics

  • A high performance computer (HPC) is not a faster computer. It’s several computers connected together.

  • Each of these computers is called node. Each node can have multiple cores

  • Every core can run one job

  • One node acts as a master which distributes jobs across the other nodes

  • To distribute those jobs, the master node uses queues. We’ll look into that in Part 2

  • When you log-in, as we did before, you access the master node


  • Abacus has 22 nodes total. 15 of them are available for computing at the School of Biology

  • Nodes available have between 8 and 48 cores each. Total of 432 cores

  • You can explore this yourself by going to http://abacus/ganglia/ on your browser

Have a look at the file structure

ls /

When you log-in you’re actually in /home/usr123

  • Usually you store your scripts and raw data in you home directory

  • The output files, especially if they’re heavy, should go to /data/people/usr123

  • Create your own directory in /data/people

Best practices

In your computer you would run an R script using

Rscript script.R

☢ Never do that in the cluster ☢

cause you could break it…

  • Make sure that your script runs well in your computer before sending it to the cluster.

  • Troubleshooting in the cluster can be a nightmare.

  • Abacus is a shared resource. Be nice to other people. Don’t use it all unless you really need it.

  • Don’t be afraid to use it though. It’s there for us.