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The following is a quick start guide on access Viking and running a basic job.  Please refer to the documentation for more in depth examples.

Viking Account Creation

  1. Before logging into Viking please ensure your project supervisor fills in this form to request a project code.
  2. The user then needs to fill in this form to request an account once they have a project code. 
  3. Accounts should take no longer than 24 hours to be created. You will receive an email on creation of your account.

See VK1) How to access Viking for more information

Login into Viking

Viking has a Linux Operating system therefore how you access Viking will depend on what your operating system is on your local machine.

Before You Login

If you have not changed your IT Services password since August 2013 then you must do so before you will be able to login. All user password changes are manage via the My IT Account  web page. Click on the Password Management (IDM) link in the Manage Your Password field to change your password. You may be given the option to 'synchronise' your password; please use this option if you do not want to change your password. The password change (or synchronisation) may take a few minutes before it is visible to the servers.

Accessing Viking off campus

To access the Viking off campus you can either use the Virtual Private Network - VPN or the SSH gateway service (registration required). The instructions below should work if you log on through the VPN; the SSH service works slightly differently.

Access from a Windows desktop

Command-line access using PuTTY

PuTTY is available on all IT Services Managed Windows systems. It is pre-installed on Classroom PCs; on Office PCs you can install it from Run Advertised Programs / Software Center. It appears under "Internet Tools" on the start menu.

On unmanaged PCs you can download the installer from the PuTTY Website.

Configuring PuTTY to connect to Viking

Open PuTTY and configure it to connect to Viking:

  1. Add the name "viking.york.ac.uk" to the 'Host Name' field
  2. Check the 'Connection Type' to SSH
  3. Type the name "Viking"  in 'Saved Sessions'
  4. Click 'Save'

  1. Expand the 'SSH' tab from the 'Category' list
  2. Choose 'X11' from 'SSH' list
  3. Check 'Enable X11 Forwarding'

Connecting to Viking

  1. Start PuTTY
  2. Select 'Viking' from the 'Saved Sessions'
  3. Click 'Open'

A terminal window should appear. Log in with your university username and password.  The first time you connect you will get a security alert showing the fingerprint of the server, labeled as 'ssh-rsa' or 'ssh-ed25519'.

If you are successful this is what you will see:

Whilst it is possible to configure X11 forwarding through PuTTY, X11 forwarding will only work on the Viking login nodes, which means that you won't be able to run graphical applications e.g. MATLAB on the Viking compute nodes using X11 forwarding. Details about virtual desktop sessions on Viking are provided in the Virtual Desktop section of this document.

Access from a Mac

Go to the Finder on your Mac, find Applications, open the Utilities folder in Applications and then start the Terminal app from the Utilities folder. (You may wish to add Terminal to your Dock.) Then type the following, using your university username (abc123). You do not need to type the $; this is an example of a prompt, which tells us the terminal is ready for us to type something. You should see something similar when you open Terminal, though it may be a bit longer (it may show your username for example). Just type anything from after the $.

[bash-4.1]$ ssh -X abc123@viking.york.ac.uk

Access from a UNIX server or desktop

To log in from a terminal emulator, use the following command: 

[bash-4.1]$ ssh abc123@viking.york.ac.uk

where abc123 is your IT Services username. You will be prompted for your IT Services password. Please note, X11 forwarding will only work on the Viking login nodes, which means that you won't be able to run graphical applications e.g. MATLAB on the Viking compute nodes using X11 forwarding. Details about virtual desktop sessions on Viking are provided in the Virtual Desktop section of this document.

 If you require X forwarding, type:

[bash-4.1]$ ssh -X abc123@viking.york.ac.uk

See How to log in to Viking for more information

Storing your data and programs

When you first login to Viking this is what you should see

Viking uses a Linux operating system  there you will need to navigate using the Linux command line.  

If you are new to Linux command line I recommend running through the examples in An Introduction to Research Computing at York wiki course to get you started.

Storing data

There are two areas you have access to.  Your home folder where you land on first logging in and your scratch folder.

Here is a breakdown on the different areas and what they provide.

Homescratch
50GB space limit3TB initial quota more on request
Backed upNot backed up
Slower performance

Lustre High performance filesystem.

We recommend running all jobs from your scratch folder.  Any data you need to keep long term should be moved to a backed up storage area. Further details on storage options can be found here.

Loading software

We have an entire suite of software available on Viking.  We use Easybuild to install the software and a module system to help you navigate what is available.

To view all available software run

[abc123@login1(viking) ~]$ module avail

If you want to see the versions of a particular software run:

[abc123@login1(viking) ~]$ module avail Kraken2

The module spider string command allows you to search for modules matching the string.

[abc123@login1(viking) ~]$ module spider Kraken2

To load a module type module load <module name>. You can append a version number to load a specific instance of a package. Note the <tab> key can be used to complete the command.

[abc123@login1(viking) ~]$ module load lang/Bison <tab> <tab>
lang/Bison Bison/3.0.4-GCCcore-8.1.0
lang/Bison/3.0.4
[abc123@login1(viking) ~]$ module load lang/Bison/3.0.4-GCCcore-8.1.0

To list currently loaded modules type module list

[abc123@login1(viking) ~]$ module list

Run module purge to unload all loaded modules.

[abc123@login1(viking) ~]$ module purge

To unload a specific module use

[abc123@login1(viking) ~]$ module unload

If you need to have a program installed on Viking please email itsupport@york.ac.uk with the details.

See VK2) Modules and the user environment for more information.

Running a basic Job

Viking uses a queuing system called Slurm to ensure that your jobs are fairly scheduled to run on Viking. 

To submit a job to the queue you will need to create a submit script. 

#!/bin/bash
#SBATCH --job-name=simple                # Job name
#SBATCH --mail-type=BEGIN,END,FAIL       # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=abc123@york.ac.uk    # Where to send mail  
#SBATCH --ntasks=1                       # Run on a single CPU
#SBATCH --mem=1gb                        # Job memory request
#SBATCH --time=00:01:00                  # Time limit hrs:min:sec
#SBATCH --output=basic_job_%j.log        # Standard output and error log
#SBATCH --partition=nodes				 # Job queue
#SBATCH --account=PROJECTCODE            # Project account
 

module purge							 # purge any loaded modules
module load lang/Python/3.7.0-foss-2018b # Load a module within a job script

echo My working directory is `pwd`
echo Running job on host:
echo -e '\t'`hostname` at `date`
echo
echo
echo Job completed at `date`

To Submit a job run

[abc123@login1(viking) ~]$ sbatch simple.job

To see your job in the queue run the squeue commnd.  The job running below has a  jobid of 147875

[abc123@login1(viking) scratch]$ squeue -u abc123
JOBID  PARTITION NAME     USER ST TIME NODES NODELIST(REASON)
147875 nodes     simple.j abc123 R  0:04 1     node170

To delete a job from the queue use the scancel [options] <jobid> command, where jobid is a number referring to the specified job (available from squeue).

[abc123@login1(viking) scratch]$ scancel 147876

A user can delete all their jobs from the batch queues with the -u option:

$ scancel -u=<userid>

To look at your job history run sacct -j jobid

[abc123@login1(viking) scratch]$ sacct -j 147876
JobID        JobName    Partition  Account    AllocCPUS  State      ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
147876       simple.job nodes      dept-proj+ 1          CANCELLED+ 0:0
147876.batch batch                 dept-proj+ 1          CANCELLED  0:15

See VK3) Submitting Jobs to Viking and VK4) Job script configuration for more information.

Copying your data to and from Viking

You may have data stored elsewhere that you wish to copy to Viking.  There are different ways to do this

There are different ways to copy your data  dependent on which operating system you use on your local machine.

Copying Files To/From a Windows Desktop

WinSCP is an open source free SFTP client, SCP client, FTPS client and FTP client for Windows. Its main function is file transfer between a local and a remote computer. WinSCP is available on IT Services supported desktops or can be downloaded from http://winscp.net/eng/index.php.

Run WinSCP  from the Start menu or double clicking on the icon on the desktop;


A login window will appear. Fill in the hostname and your username:

Running WinSCP

You can click the "Save" button to save the session details for future use:

Return to the login window and click the "Login" button. Some hosts may present you with an information window:

You will then be prompted for your password:

The file manager window will be displayed:

The drag-and-drop interface is a similar to Windows file manager and its use should be intuitive.

Copying Files To/From a Linux/MacOS desktop

There are a number of ways to copying files and directories using Linux command line.

you can copy your data from any Linux device to Viking using the following commands 

  • scp
  • rsync

Here are a couple of examples.  

scp 

This is recommended for a small number of files.

You wish to copy your data from local machine to your scratch area on Viking.  Run the following commands on your local machine in the terminal. 

[bash-4.1]$ #For an individual file
[bash-4.1]$ scp afile abc123@viking.york.ac.uk:~/scratch 

[bash-4.1]$ #For a folder with lots of files
[bash-4.1]$ scp -r adir abc123@viking.york.ac.uk:~/scratch

What if you want to copy files from your scratch area on Viking to your local machine?  Run the following commands on your local machine.

[bash-4.1]$ #For an individual file
[bash-4.1]$ scp abc123@viking.york.ac.uk:~/scratch/afile . 

[bash-4.1]$ #For a folder with lots of files
[bash-4.1]$ scp -r abc123@viking.york.ac.uk:~/scratch/adir .

There are many options you can use with scp.  To view these options either run

man scp 

on the device you are using scp on or have a look at this scp wiki page.

RSYNC

Rsync is another command that will let you copy files and folders to the Viking.  If you have a large number of files it is always best to use Rsync. 

To copy a folder adir from your local machine to your scratch area on Viking, run the following command on your local machine.

[bash-4.1]$ rsync -avz adir abc123@viking.york.ac.uk:~/scratch

There are many options you can use with rsync.  To view these options either run

man rsync 

on the device you are using rsync on or consult the rsync webpage.

See VK7) Copying and moving your data to Viking. for more information.

Help and support

In the first instance check our wiki pages or email itsupport@york.ac.uk where one of our team will be in touch.























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