HPC High Performance Computing: 1. System Access

System Access

It’s important to remember that to access the cluster from outside the campus, a VPN connection must be used for security reasons. Here you have the instructions to configure the VPN.

To ensure a secure login session, users must connect to the login node using the secure shell SSH protocol.

Before any login sessions can be initiated using ssh, a working SSH client needs to be present in the local machine. Wikipedia is a good source of information on SSH in general and provides information on the various clients available for your particular operating system, but here we'll cover common examples for Windows 7, Ubuntu Linux and Mac OS Mavericks.

You must remember that the login node is not a calculation node. In order to load modules and execute your applications, you must connect to any of the calculation nodes through interactive or salloc command (ssh to nodes have been disabled to avoid the interactive use of them without going through slurm) 

test@login01:~$ module load MATLAB/2017a
-bash: module: command not found
test@login01:~$ interactive
salloc: Granted job allocation 391355
test@node001:~$ module load MATLAB/2017a
test@node001:~$ module list

Currently Loaded Modules:
  1) Java/1.8.0_121   2) MATLAB/2017a


 

When you are connected in the login node, you can send jobs to the scheduler through the "sbatch" command. What is inside the script will be executed in the node assigned by the scheduler, not in the login node.

 

test@login01:~/Scripts/Matlab$ sbatch matlab.sh 
Submitted batch job 391235
test@login01:~/Scripts/Matlab$ squeue -u test
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
            391235     short matlab_t  test  R       0:09      1 node007

 

Connecting to SNOW from a Windows client

You need to install on your workstation a set of free tools to interact with the cluster:

  • Putty

www.putty.org

Purpose: Free SSH client

  • XShell 5

http://www.netsarang.com/download/free_license.html

Purpose: Free SSH client

 

In this tutorial, we'll work with Putty and XShell. 

Putty:

  • Download and install the Putty client. It's a single .exe file, place it on some folder on your hard disk
  • Execute putty, and configure X forwarding options

PuTTY Configuration

Open a ssh connection to the server hpc.s.upf.edu. The first time, you'll geta warning for the SSL signature key coming from hpc.s. Accept it permanently to avoid this window coming out every time:

PuTTY Security Alert

Use your DTIC username and password to get access to the server. 

login as: test
test@hpc.s.upf.edu's password:
Last login: Tue Dec 12 19:39:51 2017 from 10.60.84.200
test@login01:~$

Connecting to SNOW from a Linux client

Connecting to SNOW from a linux machine is pretty easy, as everything is built in by default in every distribution. Simply open a terminal and type 'ssh -X username@hpc.s.upf.edu', where:

username is your DTIC user, in the usual form userrname

-X tells your Linux client to forward and manage the graphical X sessions you eventually need to open over hpc.s.upf.edu

Connecting to SNOW from a Mac OS client

Simply using the terminal application we can connect to the slurm cluster:

Connecting to SNOW from a Mac OS client