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![Parameter file? Excuse me?
Basically a name <-> parameter pair
dt = 0.05 # Dt for the integration
tstop = 10 # [ms]
Not obligatory, but it's very handy because:
• Sumatra can store your parameters in the record
• If Sumatra understand them then You can change
parameter on the fly
$ smt run default.param tstop=20 dt=0.01](https://image.slidesharecdn.com/sumatraandgit-100421074654-phpapp01/85/Sumatra-and-git-11-320.jpg)
Uploaded byMichele Mattioni
Sumatra and git
Sumatra is an electronic lab book designed to streamline the documentation of simulations and experiments by automatically tracking details such as parameters and outcomes. It integrates with version control systems like Git, Mercurial, and Subversion, enabling users to organize, search, and rerun their simulations easily. Additionally, Sumatra helps researchers manage their work efficiently and offers tools to recover from errors, ensuring consistent and focused scientific efforts.
Sumatra and git
- 1. Sumatra: an electroniclabook. Git it right Michele Mattioni Computational Neurobiology group mattioni@ebi.ac.uk EBI is an Outstation of the European Molecular Biology Laboratory.
- 3. Open questions whichI had no answer: • Where are my results? • Which parameters I used on that simulation? http://www.flickr.com/photos/valeriebb/3006348550/ • Which one was that simulation? • Why it worked yesterday and not today? From Valerie Everett's photostream • At exactly which point it worked yesterday? • Where is my mind stuff?
- 4. How the experimentalpeople solve that? • Write down on a labbook everything they do : • reagents • times • protocols why! http://www.flickr.com/photos/mwichary/3249202959/ • • what worked, what didn't • ... Marcin Wichary's photostream
- 5. We need anelectronic labbook • Able to track (automatically) our 'experiments' details: • script launched • parameters used • reason • outcome • But we can also: • search them • organize them • Rerun them!
- 6. Say hello toSumatra http://neuralensemble.org/trac/sumatra Slide from Andrew Davison (main developer), http://neuralensemble.org/meetings/talks/CodeJam3_Davison_Sumatra.pdf
- 7. Sumatra: what Ineed to use it • Code under version control • Accepted version control: • Mercurial (hg) • Subversion (svn) • Git (git) (I patched it! Power of the opensource..) • your choice (exstensible architeture) • Scripts organized as Main class and parameter_file
- 8. smt Usage $ cd myproject $ smt init MyProject Normal way you launched the script: $ python main.py default.param New way using Sumatra: $ smt run simulator=python main=main.py default.param
- 9. Shorter cmdline tolaunch the job From $ smt run simulator=python main=main.py default.param Configure it (it has to be done once.) $ smt configure simulator=python main=main.py To $ smt run default.param
- 10. What if Iuse java? $ java main default.param $ smt run simulator=java main=main default.param
- 11. Parameter file? Excuseme? Basically a name <-> parameter pair dt = 0.05 # Dt for the integration tstop = 10 # [ms] Not obligatory, but it's very handy because: • Sumatra can store your parameters in the record • If Sumatra understand them then You can change parameter on the fly $ smt run default.param tstop=20 dt=0.01
- 12. Where is mystuff? smt monitor a directory (default Data). • Any new file/image saved there is automatically added to the simulation record You save the results Sumatra remembers where is it My way: I create a dir for each day and then save all my stuff in dedicated folder • Data/19042010/Sim_1/, Data/19042010/Sim_2/ • Data/20042010/Sim_1/, Data20042010/Sim_2/
- 13. Access the results:smt $ smt list default_20100407163228 default_20100407171249 $ smt list l Label : default_20100420170241 Reason : Testing the tagging from the cmdline Outcome : It works! Duration : 4.38211798668 Repository : GitRepository at /home/mattions/Work/model/MSN/TimeScales Main_File : spineIntegration.py Version : 8a61ecdd999e30d25c29620a87d9f4536aa67e9e Executable : Python (version: 2.6.4) at /usr/bin/python Timestamp : 20100420 17:02:41.445588 Tags : test, test2
- 14. Access the results:smtweb
- 15. Access the results:smtweb
- 16. Accessing the plotfrom the link
- 17. How to install ATM:Git support only available from the latest code: hg clone https://neuralensemble.org/hg/sumatra git clone http://github.com/mattions/sumatra_on_github
- 18. How sumatra savedthe day (yesterday) Scenario: • Made some massive restructuring/refactoring on neuronvisio • Get lost on the way • Nothing worked anymore. But ...
- 19. Searched the lastsimulation where it worked
- 20. Selected the latestworking, and neuronvisio ver.
- 21. Find that commiton neuronvisio repo
- 22.
- 23. Merged restart backinto master kind of apply twice the same patch, but you know it was worth it.
- 24. Summary • Sumatra canhelp you to: • keep your stuff organized • not lose your work • speed up the recovery time when somethig get wrong • remember what you used ages ago, to make that figure • be more focus on your science. • You can help sumatra • Using it • Asking for request (ok, send a patch. It's quicker and easier)
- 25. Acknowledgement • Andrew Davison (main sumatra developer) • people got the picture from (link on each picture) • Nicolas Le Novère (to let me work on this) • Computational Neurobiology group @ EBI.
- 26. Got questions? http://neuralensemble.org/trac/sumatra