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newton_cheatsheet.md

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Logging in

Replace USERNAME with your user name

Via ssh

ssh [email protected]

Via X2GO

  • Install x2go client
  • Create new session
Setting Value
Session name newton
host newton.bioeng.ru
login USERNAME
session type custom desktop: vglrun startxfce4
  • Double click created session
  • On a first login wait until question about default panel settings arizes. Select default panels.

Important X2GO Info:

You can run multiple sessions detach and resume them later.

  • To detach from a session just close X2GO window.
  • To resume a session, choose it during login
  • To finish session, click your user name (top right panel) and choose "Log out"

Troubleshooting

  • If there are no desktop panels and icons open terminal (right click on a desktop, 'Open Terminal Here') and run this line: xfce4-panel --quit ; pkill xfconfd ; rm -rf ~/.config/xfce4/panel ~/.config/xfce4/xfconf/xfce-perchannel-xml/xfce4-panel.xml ; xfce4-panel

Then select default panel settings.

Via JupyterHub

Open https://newton.bioeng.ru/jupyter and log in.

JupyterHub and conda

Firstly see info about conda environments and conda cheatcheet.

In jupyter you can select different kernels. There are a couple of preinstalled kernels that contain different conda environments (see 'conda' tab in jupyter), those environments are located at /opt/miniconda3 and can not be chaneged by user. To add a new kernel for your project you have to install ipykernel package to the environment:

  1. Create or clone conda environment (skip it, if you already done that): conda create -n YOUR_ENV_NAME
  2. source activate YOUR_ENV_NAME
  3. conda install ipykernel

JupyterHub and JupyterLab

Currently jupyter notebooks are lunched by default.

To open JupyterLab change the last word in the link from /tree to /lab

Conda

To load conda use module load conda3