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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.

Sumatra is a System Management Tool to keep track of your simulation results. Now it has also git support.

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  • 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.
  • 2. 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?
  • 3. 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
  • 4. 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!
  • 5. Say hello to Sumatra http://neuralensemble.org/trac/sumatra Slide from Andrew Davison (main developer), http://neuralensemble.org/meetings/talks/CodeJam3_Davison_Sumatra.pdf
  • 6. 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
  • 7. 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
  • 8. 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
  • 9. What if I use java? $ java main default.param $ smt run ­­simulator=java ­­main=main default.param
  • 10. 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
  • 11. 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/
  • 12. 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
  • 13. Access the results: smtweb
  • 14. Access the results: smtweb
  • 15. Accessing the plot from the link
  • 16. 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
  • 17. How sumatra saved the day (yesterday) Scenario: • Made some massive restructuring/refactoring on neuronvisio • Get lost on the way • Nothing worked anymore. But ...
  • 18. Searched the last simulation where it worked
  • 19. Selected the latest working, and neuronvisio ver.
  • 20. Find that commit on neuronvisio repo
  • 21. Branched it
  • 22. Merged restart back into master kind of apply twice the same patch, but you know it was worth it.
  • 23. 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)
  • 24. 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.
  • 25. Got questions? http://neuralensemble.org/trac/sumatra