Using Dedalus

Using Dedalus

*** Note that the Dedalus setup is still being finalized. It is not recommended that you use it for anything important yet. ***

Dedalus is "A flexible framework for spectrally solving differential equations."[1]

Our research servers have version 3-beta(from the Git master branch of 19 May 2020).

More information is available here:

• https://dedalus-project.org/
• https://dedalus-project.readthedocs.io/en/latest/
• https://github.com/DedalusProject/dedalus/

Using

1. Log in to a research server or Linux workstation.
2. Run: source /usr/local/dedalus/setup
3. You will see that the prompt is prefixed with '(main)'.
4. Run: conda activate dedalus3
5. You will see that the prompt is prefixed with '(dedalus3)'.
6. You can now run Python3 code using the Dedalus modules.

Notes

As per the Dedalus documentation the following environment variables will be set when the Dedalus environment is activated:

   OMP_NUM_THREADS=1
   NUMEXPR_MAX_THREADS=1

See:

• https://www.openmp.org/spec-html/5.0/openmpse50.html
• https://numexpr.readthedocs.io/projects/NumExpr3/en/latest/user_guide.html#threadpool-configuration

This could have an effect on other code/applications you might run from the Dedalus environment.

FAQ

When I try to run conda it says command not found

If your prompt is not prefixed with '(main)' then Conda is not initialized. Depending on how your account is configured(Bash login scripts to be speciic) you may need to do one of the following:

• A temporary fix is to run Bash again: bash
• A permanent fix is to copy the "conda initialize" block of code from ~/.bashrc to the end of ~/.profile. If you do not have a .profile file then check if you have a .bash_profile file.

I think there is a problem with the installation

The first thing you should do is to run the regression tests that are built in to Dedalus. Depending on the outcome you may want to contact IT to investigate.

To run the tests do this: python3 -m dedalus test