Computational Infrastructure

Welcome to our Bioinformatics Computational Infrastructure

Bioinformatics Sannio in collaboration with Biogem offers comprehensive and integrated high-performance services that cover the range of computationally-based research, but with a focus in computational biology and bioinformatics. The infrastructure includes 2 CPU computational Nodes respectively with 64 and 32 cores and over 512GB ram each, 1 GPU based computational node equipped with 2 NVIDIA Tesla K20 boards, and 1 NAS server with over 40TB of storage capacity.

Getting started

To gain access to our system, you first need to send an email to ceccarelli (at) unisannio.it and lcerulo (at) unisannio.it to get a user account. Then you need to setup a VPN connection from your client. (Users from the Bioinformatics laboratory at Biogem don’t need a VPN connection as they are part of the bioinformatics.biogem.it local network)

Connecting from MAC OSX

Download and install Tunnel blik (https://code.google.com/p/tunnelblick/) an open source graphic user interface for OpenVPN on OS X. Download and unzip in a local folder the OpenVPN configuration package (biogem-vpn) for MacOS. Rename the folder as biogem-vpn.tblk, create a new tblk connection, and connect with your user account.

Connecting from Windows

Download and unzip the following OpenVPN portable package (OpenVPNPortable). Double click on OpenVPNPortable.exe. This will install the openVPN GUI client in your taskbar. Launch the openVPN GUI with administrator privileges and login with your user account to connect. If your windows don’t let you to change the dns you can add the following in the hosts file located in c:\WINDOWS\system32\drivers\etc\hosts

172.16.17.10 bioblade bioblade.bioinformatics.biogem.it
172.16.17.11 simone simone.bioinformatics.biogem.it
172.16.17.12 samantha samantha.bioinformatics.biogem.it

Connecting from Unix/Linux

Download and Install the openvpn package following instructions depending on you Unix/Linux distribution (yum install openvpn in Centos/Redhat or apt-get install openvpn on Ubuntu/Debian). Download and unzip in a local folder the openVPN configuration package (biogem-vpn-linux) for Linux and connect with the following command:

sudo openvpn client.conf

When your client is connected you will be part of the local bioinformatics network (bioinformatics.biogem.it)

Available Hostnames
  1. bioblade 32 core CPU node (alias cpunode0.bioinformatics.biogem.it)
  2. samantha 64 core CPU node (alias cpunode1.bioinformatics.biogem.it)
  3. simone GPU node (alias gpunode1.bioifnormatics.biogem.it)

why such names? BiobladeSamanthaSimone

Connect to Rstudio server

Each computational node is equipped with the latest versions of R and Rstudio. To connect to Rstudio you can use the host name followed by the 8181 port number. For example:

http://samantha:8181
Connect with ssh

You can connect to each computational node with an ssh client as follows:

ssh userid@hostname

where userid is your user account and hostname is one among bioblade, samantha, or simone. The ssh client is available by default for Unix/Linux/MacOS users. Windows users can adopt the putty client.

Setting up SSH public/private keys (optional)

Step 1:

% ssh-keygen -t dsa
Generating public/private dsa key pair.
Enter file in which to save the key (~/.ssh/id_dsa): (just type return)
Enter passphrase (empty for no passphrase): (just type return)
Enter same passphrase again: (just type return)
Your identification has been saved in ~/.ssh/id_dsa
Your public key has been saved in ~/.ssh/id_dsa.pub
The key fingerprint is:
Some really long string

Step 2:

Then, paste the content of the local ~/.ssh/id_dsa.pub file into the file ~/.ssh/authorized_keys on the remote host.

Local folder organisation

Your local folder is organised with two symbolic links, public-storage and private-storage, pointing respectively to a public and a private storage area.

./
./public-storage
./private-storage

The public area is used to share data among research groups working on common projects. The private area should be to store no more used personal data (i.e. closed/suspended projects). To get the maximum disk speed access you should use the local host space. Please employ the local disk space only for current open projects.