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Christopher J. Steele edited this page Apr 25, 2023 · 21 revisions

Welcome to the documentation wiki! This page provides access to all documentation for processes and software used within NeuralABC.

Essential resources

Useful code snippets and descriptions

Resources for New Students

Experimental setups, code, and instructions

Data manipulation and storage

Working with the machines in the lab

Using the VPN

A comprehensive overview

  1. Intro Guide: Welcome
  2. Intro Guide: Python
  3. Intro Guide: Additional Resources

Running processes while logged out

2022 Update: The tmux mitigation steps listed below are no longer required. Legacy details listed below for posterity, will be removed in future versions of this document.

  • Running multiple persistent terminal sessions with tmux: (What is tmux?)
  • See here for a lab-based overview of tmux

We previously ran KDE Neon for the lab machines, which comes with loads of benefits and a few drawbacks. One drawback is that the current implementation of systemd does not play very well with our logins and logouts and, without going into any details, it means that running processes and analyses when you are not physically logged in is more difficult than just running it inside a tmux session (what is tmux?). See here for a lab-based overview of tmux.

As of now, existing users need to add an alias to their .bashrc file. After logging out and back in, the tmux command should work as expected, including setting up tunnels for jupyter lab / notebook!.

Edit the file /home/.bashrc with your favourite editor, e.g.,: kwrite ~/.bashrc or nano .bashrc and add the following line to the end:

alias tmux="loginctl enable-linger; systemd-run --user --scope tmux"

This may not be necessary on some systems (as they get updated) and is in a bit of flux. If, after adding the alias, logging out, and logging back in, you receive the following error:

tmux
Failed to create bus connection: No such file or directory

then you can use which tmux to identify the location of tmux and run it directly. Or, you can comment out the line in your .bashrc by placing a # as the first character.

If neither of these approaches results in a persistent tmux session, please:

  1. contact your friendly support staff, since you won't be able to do this without root access!
  2. do a quick check of /etc/systemd/logind.conf and set KillUserProcesses=no
  3. restart systemd-logind.service sudo systemctl restart systemd-logind

Applying ANTs Transforms

https://github.com/neuralabc/documentation/wiki/antsApplyTransforms----Forward-and-inverse-warps-for-warping-images

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