Using Dedalus: Difference between revisions

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= Using Dedalus =


Dedalus is "A flexible framework for spectrally solving differential equations."[https://dedalus-project.org/]
Moved to https://kb.wisc.edu/math/internal/123324
 
Our research servers have version 3-beta(from the [https://github.com/DedalusProject/dedalus/ 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 ==
# Log in to a [https://kb.wisc.edu/math/internal/page.php?id=114567 research server] or Linux workstation.
# Run: '''source /usr/local/dedalus/setup'''
# You will see that the prompt is prefixed with '(main)'.
# Run: '''conda activate dedalus3'''
# You will see that the prompt is prefixed with '(dedalus3)'.
# You can now run Python3 code using the Dedalus modules.
 
== Notes ==
As per the [https://dedalus-project.readthedocs.io/en/latest/pages/performance_tips.html?highlight=NUMEXPR_MAX_THREADS#disable-multithreading 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'''

Latest revision as of 16:08, 9 January 2023

Moved to https://kb.wisc.edu/math/internal/123324

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