QuickStart Guide

Get an Account

The use of Garnatxa is constrained to I2SysBio’s members and external collaborations. If you are member of a I2SysBio’s research group then your main researcher has to create a ticket requesting for a new account.

Attention

Only main researchers (IP) are allowed to request a new account in Garnatxa.

Visit: https://garnatxadoc.uv.es/support and open a new ticket.

Sign in using the same credentials in Garnatxa (username or email and password)

Choose the help topic: Garnatxa HPC / New Account Requests and fill in information about yourself (main researcher) and the new user.

After we will review all the data you will then shortly receive an email with your credentials and some information to connect to Garnatxa.

All users of Garnatxa are automatically subscribed to the mailing-list i2sysbio-hpcusers@uv.es where we will distribute announcements regarding the operation of Garnatxa.

If you don’t receive the email then contact with us in order to figure out what occurred.

Prerequisites to connect to Garnatxa

The access to the cluster Garnatxa is closed to the external connections except if you are connecting from inside the domain of the University of Valencia (UV).

If you connect from external placements then you will have to start setting up a VPN connection. To do this read the configuring the VPN section.

Set up the VPN connection

Connect to Garnatxa by SSH

Once you have a user account, you can connect to garnatxa.uv.es using ssh ( secure shell protocol). If you are running Linux or Mac OSX, open a terminal and type: ssh USERNAME@garnatxa.uv.es, where USERNAME is the login name that you received by mail. The enter the password that you were given.

For Windows computers there is a built-in SSH client that can be enabled on Windows 10 from 2018. First enable WSL and then you have to open a command window and type the ssh command. If your Windows version is older than 2018 you will need to download and use a SSH client as PuTTY or similar.

$ [USERNAME@master ~]$ ssh USERNAME@garnatxa.uv.es

USERNAME@garnatxa.uv.es's password:
#############################################################
##                                                         ##
##                   Welcome to I2SysBio                   ##
##        _____                        _                   ##
##       / ____|                      | |                  ##
##      | |  __  __ _ _ __ _ __   __ _| |___  ____ _       ##
##      | | |_ |/ _` | '__| '_ \ / _` | __\ \/ / _` |      ##
##      | |__| | (_| | |  | | | | (_| | |_ >  < (_| |      ##
##       \_____|\__,_|_|  |_| |_|\__,_|\__/_/\_\__,_|      ##
##                                                         ##
##                 Supercomputing facility                 ##
##       for bioinformatics & computational biology        ##
##                                                         ##
#############################################################

Basic guide about using garnatxa: /doc/garnatxa_guide.txt
Usage statistics: /doc/statistics
$

Note

The first time you access to Garnatxa you might warnings about changed host keys from your SSH client (see below). Type ‘yes’ in order to accept public key of Garnatxa and continue connecting.

The authenticity of host ‘garnatxa ‘ can’t be established. ECDSA key fingerprint is SHA256:7fUYLmRdI6b1TMMz92ln3bGFCw8J9mJOv3jniz7Xt8c. Are you sure you want to continue connecting (yes/no)?

Change your password

The first thing you must to do when enter to Garnatxa is to change your password. Type the command: passwd and enter your old password (sent via email) then enter your new password.

$ passwd
Changing password for user USERNAME.
Current Password: ********
New password: ********
Retype new password: ********
passwd: all authentication tokens updated successfully.

Attention

The new password must have a minimum length of 8 characters, one special character (i.e: ! % @ #) and one number.

Attention

When you change the password in Garnatxa you must use that new password in the VPN connection. Close your VPN connection and try using the changed password. If you can’t find where to change the password in the VPN, you will have to delete the VPN configuration and add it again (using the new password).

Training course and additional documentation

Now you have access to Garnatxa we strongly recommend to continue with a brief training course. The course aims to give an introductory overview of High Performance Computing (HPC) in general, and of the facilities of the Garnatxa HPC Cluster in particular.

Also if your knowledge about Linux environments and other computer languages is low, you can a serial of basic lessons here: https://software-carpentry.org/lessons/