How to use thinlinc to login to Arrhenius¶
Introduction¶
Interactive HPC enables scientific users to run scientific computations interactively using remote desktop environment and interactive job launcher.
What is ThinLinc?¶
ThinLinc is a remote desktop program developed by Cendio which allows users to connect to a remote server using a ThinLinc Client. It uses ssh for authentication and VNC for graphics. ThinLinc has two main components, Server and Client. Thinlinc server is setup by NAISS admins to enable remote desktop environment. ThinLinc client which is available for Linux, Mac and windows can be installed by users on their laptop or desktop.
How ThinLinc can help in my computation?¶
A user connecting to ThinLinc server is presented with a remote desktop graphical environment where they have access to graphical applications, utilities, terminal etc. Users can create or update their files on Lustre file system, Submit interactive jobs to SLURM and can use interactive job launcher ‘gfxlauncher’ to start various graphical applications e.g. Matlab, RStudio, Mathemtica etc. and Jupyter Labs/Notebooks.
What is gfxlauncher?¶
Gfxlauncher is an application written in Python which provides users an interactive way to launch GUI applications and submit SLURM jobs. It is developed at LUNARC, Lund University Sweden. Gfxlauncher runs on top of ThinLinc to assist users in launching interactive jobs such as Jupyter Notebooks, Matlab, RStudio etc.
Getting started with interactive HPC¶
Users should download ThinLinc client (tlclient) which is required to connect to remote ThinLinc server. Depending upon which operating system you are using, you can download relevant installation media from Cendio download page. Once downloaded, run the installation and follow the installation dialog box.
Authentication in ThinLinc Client using password and TOTP¶
After starting the thinlinc client enter...
In the field Server you should enter tl.hpc.arrhenius.naiss.se
and then fill in your username and Password.
After you press Connect, you will get a new window asking for Verification code. Enter the 6 digits from your TOTP app, and you will be logged into Thinlinc.
If your Thinlinc client is set to the public key mode (i.e it shows Server, Username and Key prompts), you need to switch it to password mode...
- Click
Advancedif option button is not visible - Click the
Optionsbutton - Go to the
Securitytab - Choose
Password.
Unfortunately the Thinlinc client does not support combining an SSH public key with TOTP1. It may become possible to use SSH public key + TOTP in a future version of the Thinlinc client.
Launching Interactive jobs from Menu¶
GUI applications available on integrated in Remote Desktop Menu system. Users can launch Graphical applications and Jupyter Notebooks/Lab interactively.
Graphical application¶
Applications which have a graphical interface such as Matlab, Mathematica etc. can be launched interactively using gfxlauncher.
* gfxlauncher menu will appear where you can choose various options for this application
* Click on three dots to choose resources e.g. Jobname, Tasks per node and memory
* View logs for gfxlauncher by clicking ‘More’
* View Job Script which will be submitted for this interactive job
* Start job by clicking ‘Start’ button and review progress in log tab.
Launching Jupyter Lab and Jupyter Notebook¶
You can interactively launch Jupyter Lab and Notebook by following the steps as below;
Step 01: Click on Applications -> Jupyter -> Jupyter Lab or Jupyter Notebook
Step 02: Configure your job parameters in the dialog box.
Step 03: Click Start, wait for the job to start and in few seconds a firefox browser will open with Jupyter Lab or Notebook session. If you close the firefox browser, you can connect to same Jupyter session again by clicking ‘Reconnect to Lab’.
Launching interactive jobs from Terminal¶
If your application is not integrated in menu system, you can still run such application interactively via terminal in Remote desktop environment.
- Request for node allocation and note down the allocated nid number e.g. nid00xx
- Login to allocated node
- Load application module and launch
How to exit from ThinLinc Session¶
Disconnect or Logout¶
If you don’t have application running in remote desktop environment, please logout from current sesssion by selecting Logout as shown below to free up ThinLinc licenses for someone else.
If you simply close your ThinLinc client, your session will continue to run on server. You can then reconnect via ThinLinc client and same session will resume. This however is not recommended if you don’t have any active application running on the ThinLinc node since this uses up ThinLinc licenses.
FAQ s¶
- Menu structure in ThinLinc client is not working as expected, what should I do?
When you connect to ThinLinc, a special script runs and generates up to date menu entries under your home directory. These menu entries may become outdated. You can simply issue following commands in terminal to clear up current menu entries and log out / log in again to ThinLinc session to recreate updated menu structure.
- How can I request to add additional applications in Menu Integration?
You can always open a service request for additional applications to be intergrated in menu system. 1. What will happen if I close ThinLinc session?
You current session and applications will continue to run. 1. I am getting license error, what should I do?
We currently have 30 ThinLinc client licenses. This means 11th user connecting to ThinLinc will get License error. You can reconnect after sometime to see if license becomes available. If this happens quiet often, you can send in a support request for us to consider increasing ThinLinc client licenses. 1. How to use custom anaconda environment for Jupyter Notebooks with gfxlauncher?
This is currently work in progress and will be implemented soon.
Source repository