Tutorials

Preamble

This is a list of tutorials with step-by-step actions to do several tasks that might be required during your Master/PhD/Internship.
Be aware that they (but should not) contain typos. Moreover, it is always based on an example scenario, you have to understand and adapt the tutorial to your case.
Be aware that these tutorials have been written ages ago by one or several students that might not be around anymore and that might not be aware of changes that the group did to the processes and scripts.
Do not copy/paste the command without understanding what you’re doing. If you don’t understand, ask. You’ll do yourself more harm by copy/pasting and then fixing the issues than asking first.

All documents are automatically accessible from a UofA Google account. If you don’t have access, Nathan will have to give you permission individually. If I don’t do that fast enough, send him an email.

Linux

  • Beginner guide
  • Access our linux servers via windows
  • NEMO

  • Setting up NEMO on Graham for a new user
  • Setting up a new NEMO 3.6 experiment on Graham
  • Setting up a new NEMO 3.6 experiment on Graham (step by step version)
  • Setting up a new NEMO 3.6 experiment on Graham with passive tracers
  • Optimizing NEMO 3.6 decomposition
  • UofA NEMO FAQ
  • Rotating Velocity Components
  • Rotating to Obtain Across and Along Section Velocities
  • Ariane Guide
  • Running Ariane
  • Setting up high frequency output XIOS nests
  • Building a weight file for an atmospheric forcing
  • Perpertual year forcing
  • What to do when NEMO's job timed out but the run finished
  • Inge's hints and suggestions for debugging NEMO
  • CDFTOOLS Usage
  • Setting up Globus
  • Linux softwares and script

  • ImageMagick: Image Manipulator
  • FFmpeg: Make movies
  • vim editor: Command line text editor
  • Mathematical explanation on how work several tools

  • Volume flux calculation with NEMO output
  • How to calculate eddy kinetic energy
  • Analysis Tools

  • CDFTOOLS
  • Ariane
  • Ferret
  • Sectionplot package: get a 2D representation of a given section
  • SectionFlux package: get a time serie of several transport at a given section
  • General NEMO output visualization in batch mode:
  • Evaluation Package
  • Outdated tutorials

  • NEMO 3.4 directory layout on jasper
  • Run NEMO step by step on jasper
  • System Environment Setting on Local Servers (edit ~/.bashrc)

  • Add defaut paths for running programs:
  • Our version of Matlab: version 2016a is set by default; to use version 2014a, run matlab2014 instead