Sumatra and git
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Sumatra is a System Management Tool to keep track of your simulation results. Now it has also git support.
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Sumatra and git
- 1. Sumatra: an electronic labook. 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 which I 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 experimental people 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 an electronic 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 to Sumatra http://neuralensemble.org/trac/sumatra Slide from Andrew Davison (main developer), http://neuralensemble.org/meetings/talks/CodeJam3_Davison_Sumatra.pdf
- 7. Sumatra: what I need 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 to launch 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 I use java? $ java main default.param $ smt run simulator=java main=main default.param
- 11. 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
- 12. Where is my stuff? 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 plot from 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 saved the day (yesterday) Scenario: • Made some massive restructuring/refactoring on neuronvisio • Get lost on the way • Nothing worked anymore. But ...
- 19. Searched the last simulation where it worked
- 20. Selected the latest working, and neuronvisio ver.
- 21. Find that commit on neuronvisio repo
- 22. Branched it
- 23. Merged restart back into master kind of apply twice the same patch, but you know it was worth it.
- 24. Summary • Sumatra can help 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