Connecting to Cineca

To open a ssh connection to the computer cluster GALILEO on CINECA. If you have a Mac or a PC running Linux, start the terminal (black screen icon) and type:

ssh username@login.galileo.cineca.it

and give your password when prompted. Now you get a welcoming message from CINECA to inform you that you have successfully logged in.

Now follow the tutor instructions and have a look to the GALILEO file system

Clone software repository

Clone the scripts on your personal SCRATCH AREA:

cd $CINECA_SCRATCH
git clone https://gitlab.com/andrea.franzetti/icme9.git

Install software and dependencies:

cd icme9
./built_deps.sh

Install MEGAN tools:

module load jre
chmod a+x ./deps/megan/MEGAN_Community_unix_6_12_3.sh
./deps/megan/MEGAN_Community_unix_6_12_3.sh

and follow teacher instructions.

Start an interactive session on a node of your own

Now you need to start an interactive session and reserve 12 cores in a single node on the GALILEO server to run your analyses. One GALILEO node contains 36 cores and 120 Gb of RAM.

To start an interactive session type:

srun -p gll_usr_prod --account train_embo2018 --reservation=s_tra_embo2018 --time 08:00:00 --mem=28000 -N 1 -n 12 --pty /bin/bash
cd $CINECA_SCRATCH/icme9

Setting variables

In the file “conf_cluster.conf” you can set environment variables and bioinformatic parameters for the analysis.

Open the file with an editor:

nano conf_cluster.conf

and modify it following the instructions of the instructor.

To make the changes active source the file:

source conf_cluster.conf