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Ganga Tutorial

Ganga Tutorial. Hurng-Chun Lee. Agenda. Part I: Ganga introduction Part II: Ganga hands-on Part III: More about Ganga. Part I: Ganga Introduction. Ganga overview. PBS. PBS. LocalPC. SGE. LHCb Users. PANDA. LSF. Atlas Users. Motivation.

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Ganga Tutorial

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  1. Ganga Tutorial Hurng-Chun Lee

  2. Agenda • Part I: Ganga introduction • Part II: Ganga hands-on • Part III: More about Ganga EGEE Tutorial, Manchester

  3. Part I: Ganga Introduction Ganga overview

  4. PBS PBS LocalPC SGE LHCb Users PANDA LSF Atlas Users Motivation • In practice users deal with multiple computing backends Biomed,... EGEE Tutorial, Manchester

  5. PBS PBS Motivation • FAQ: running applications on multiple computing backends I must learnmany interfaces LocalPC SGE PANDA How to configuremy applications? LSF Do I get a consistent viewon all my jobs? EGEE Tutorial, Manchester

  6. Ganga User requirements • User requirements • interact with all backend systems in a very similar way • submit, kill, monitor jobs • configure the applications easily and transparently across desired backends • organize work • job history: keep track of what user did • save job outputs in a consistent way • reuse configuration of previously submitted jobs EGEE Tutorial, Manchester

  7. Ganga Wish list • Wish list • easy to learn and use • powerful: not limiting the features of the backends • close to the application (which is typically compiled locally) • not imposing single working style: scripts, command line, GUI,... EGEE Tutorial, Manchester

  8. Considerations of scientific application development • Realities • Computing environment is heterogeneous • Computing technology is evolving • User requirement is also evolving • Requirement • Application users prefer to learn as few as possible the tools which are light-weight, handy and well-integrated with each other. • Ganga tries to answer the questions: • How to minimize developer’s effort in building applications? • How to minimize user’s effort in running applications? EGEE Tutorial, Manchester

  9. GangaFramework Application Plugins Ganga Application Software LSF ClientLCG UI Backend Plugins .... Ganga • Ganga: Job Management Interface • a utility which you download to your computer • or it is already installed in your institute in a shared area • for example: /nfs/sw/ganga/install/4.2.14 • it is an add-on to installed software • comes with a set of plugins for Atlas and LHCb • open- other applications and backend may be easily added • even by users EGEE Tutorial, Manchester

  10. Mandatory Optional Ganga Job Where the Ganga journey starts … EGEE Tutorial, Manchester

  11. Plug-in based design • Ease user’s experience in switching between different technologies • Concentrate developer’s effort in specific domain Common interface Specific implementation EGEE Tutorial, Manchester

  12. Applications & backends EGEE Tutorial, Manchester

  13. The Ganga development team • Ganga is an ATLAS/LHCb joint project • Support for development work • Core team: • F.Brochu (Cambridge), U.Egede (Imperial), J. Elmsheuser (Munich), K.Harrison (Cambridge), H.C.Lee (ASGC Taipei), D.Liko (CERN), A.Maier (CERN), J.T.Moscicki (CERN), A.Muraru (Bucharest), W.Reece (Imperial), A.Soroko (Oxford), CL.Tan (Birmingham) EGEE Tutorial, Manchester

  14. Part I: Introduction to Ganga Using Ganga

  15. Download & Install wget http://ganga.web.cern.ch/ganga/download/ganga-install python ganga-install \ --prefix=~/opt/ganga \ --extern=GangaAtlas,GangaGUI,GangaPlotter \ 4.2.8 download installer First Launch export PATH $HOME/opt/ganga/install/slc3_gcc323/4.2.8/bin:$PATH ganga -o’[LCG]ENABLE_EDG=False’ -o’[LCG]ENABLE_GLITE=False’ *** Welcome to Ganga *** Version: Ganga-4-2-8 Documentation and support: http://cern.ch/ganga Type help() or help('index') for online help. In [1]: Do you really want to exit ([y]/n)? start Ganga with inline configurations Ganga CLIP Download, Install, First launch installation prefix Installation of external modules Ganga version <ctrl>-D to exit Ganga CLIP EGEE Tutorial, Manchester

  16. Get your hands dirty ... • Job().submit() submit and run a test job on local machine • Job(backend=LCG()).submit() submit and run a a test job on LCG • jobs browse the created jobs (job history) • j = jobs[1] get the first job from the job history • j print the details of the job and see what you can set for a job • j.copy().submit() make a copy of the job and submit the new job • j.<tab> see what you can do with the job EGEE Tutorial, Manchester

  17. Syntax [Configuration] TextShell = IPython ... ... [LCG] EDG_ENABLE = True ... ... How to set configurations Hardcoded configurations export GANGA_CONFIG_PATH = /some/physics/subgroup.ini:GangaLHCb/LHCb.ini ganga --config-path=/some/pyhsycis/subgroup.ini:GangaLHCb/LHCb.ini ~/.gangarc ganga -o Override sequence user config > site config > release config site config user config Configurations Python ConfigParser standard release config EGEE Tutorial, Manchester

  18. Metadata of jobs Data of jobs The ‘gangadir’ • created at the first launch within $HOME directory • To locate it in different directory: • [DefaultJobRepository] local_root = /alternative/gangadir/repository • [FileWorkspace] topdir = /alternative/gangadir/workspace EGEE Tutorial, Manchester

  19. *** Welcome to Ganga *** Version: Ganga-4-2-8 Documentation and support: http://cern.ch/ganga Type help() or help('index') for online help. In [1]: jobs Out[1]: Statistics: 1 jobs -------------- # id status name subjobs application backend backend.actualCE # 1 completed Executable LCG lcg-compute.hpc.unimelb.edu.au:2119/jobmanage CLIP GUI #!/usr/bin/env ganga #-*-python-*- import time j = Job() j.backend = LCG() j.submit() while not j.status in [‘completed’,’failed’]: print(‘job still running’) time.sleep(30) ./myjob.exec ganga ./myjob.exec In [1]:execfile(“myjob.exec”) GPI & Scripting User interfaces EGEE Tutorial, Manchester

  20. Some handy functions • <tab> completion • <page up/down> for cmd history • system command integration • Job template • In[1]: plugins() • plugins(‘backends’) • In[2]: help() • etc. In[1]: j = jobs[1] In[2]: cat $j.outputdir/stdout Hello World In[1]: t = JobTemplate(name=’lcg_simple’) In[2]: t.backend = LCG(middleware=’EDG’) In[3]: templates Out[3]: Statistics: 1 templates -------------- # id status name subjobs application backend backend.actualCE # 3 template lcg_simple Executable LCG In[4]: j = Job(templates[3]) In[5]: j.submit() EGEE Tutorial, Manchester

  21. j = Job() j.application = Athena() j.application.option_file = ‘myOpts.py’ j.application.prepare(athena_compile = False) j.inputdata = DQ2Dataset() j.inputdata.dataset = ‘interestingDataset.AOD.v12003104’ j.inputdata.type = ‘DQ2_Local’ j.outputdata = AthenaOutputDataset() j.outputdata.outputdata = ‘myOutput.root’ j.splitter = AthenaSplitterJob(numsubjobs=2) j.merger = AthenaOutputMerger() j.backend = LCG( CE=’ce102.cern.ch:2119/jobmanager-lcglsf-grid_2nh_atlas’ ) j.submit() CLIP mode application inputdata Outputdata Splitter & Merger Scripting mode Real Application: the ATLAS data analysis application EGEE Tutorial, Manchester

  22. Behind the scene ... EGEE Tutorial, Manchester

  23. Application plugin specific backend binding generic logic Splitter Merger Datasets Application plugin A good example: python/GangaTutorial/Lib/*.py EGEE Tutorial, Manchester

  24. Summary • What is Ganga? • An easy-to-use front-end for job definition and management • A generic framework extensible for specific applications • A light-weight application component fully implemented in Python • What Ganga can help in application development? • Ganga provides a set of ready-to-use APIs for high-level job management • It simplifies developers’ effort in developing applications • End-users can easily extend Ganga for their own purpose EGEE Tutorial, Manchester

  25. Part II: Ganga hands-on

  26. Step 0: launch Ganga CLIP https://twiki.cern.ch/twiki/bin/view/ArdaGrid/EGEETutorialPackage • Skip the installation step • Start your Ganga CLIP session using the commands: shell> ganga --config-path=GangaTutorial/Tutorial.ini \ --option=‘[LCG]VirtualOrganisation=gilda’ EGEE Tutorial, Manchester

  27. Step 1: Your first Ganga job - an arbitrary shell script In [1]: !vi myscript.sh In [2]: !chmod +x myscript.sh In [2]: j = Job() In [3]: j.application = Executable() In [4]: j.application.exe = File(‘myscript.sh’) In [5]: j.application.args = [‘ganga’] In [6]: j.backend = Local() In [7]: j.submit() In [8]: jobs In [9]: j.peek() In [10]:cat $j.outputdir/stdout #!/bin/sh echo "hello! ${1}” echo $HOSTNAME cat /proc/cpuinfo | grep 'model name’ cat /proc/meminfo | grep 'MemTotal' ./myscript.sh ganga EGEE Tutorial, Manchester

  28. Step 2: your first Ganga job on the Grid In [11]:j = j.copy() In [12]:j.backend = LCG() In [13]:j.application.args = [‘grid’] In [14]:j.submit() In [15]:j In [16]:cat $j.backend.loginfo(verbosity=1) In [17]:jobs EGEE Tutorial, Manchester

  29. Exercise: Prime number lookup • Hints of the exercise • Create a Ganga job • Application specification • Input dataset specification • Splitter specification • Backend specification • Submit the job • Using the following Ganga components for this exercise: • Application: PrimeFactorizer() • Dataset: PrimeTableDataset() • Splitter: PrimeFactorizerSplitter() EGEE Tutorial, Manchester

  30. Part III: More about Ganga

  31. Job statistics on 2580 grid jobs from Ganga Integration with frameworks EGEE Tutorial, Manchester

  32. Web portal for biologists • Interface created by biologists (Model-View-Controller design pattern) • The Model makes use of Ganga as a submission tool and DIANE to better handle docking jobs on the Grid • The Controller organizes a set of actions to perform the virtual screening pipeline; The View represents biological aspects EGEE Tutorial, Manchester

  33. GANGA Activities • Main Users • Other activities Garfield HARP EGEE Tutorial, Manchester

  34. submission tool More than job submission: Monitoring & Accounting EGEE Tutorial, Manchester

  35. More than 500 unique Users ~ 550 different users, ~100 users weeklythe monitoring started end 2006 ~60% Atlas ~25% LHCb ~15% others Easter EGEE Tutorial, Manchester

  36. Ganga usage over 50 local sites CLIP and scripts most popular EGEE Tutorial, Manchester

  37. More info. • Ganga Home: http://cern.ch/ganga • Official Ganga User’s Guide: http://ganga.web.cern.ch/ganga/user/html/GangaIntroduction/ • Tutorial for ATLAS data analysis using Ganga: https://twiki.cern.ch/twiki/bin/view/Atlas/DistributedAnalysisUsingGanga • Looking for helps: • ATLAS user support: hn-atlas-GANGAUserDeveloper@cern.ch • direct support from developers: project-ganga-developers@cern.ch EGEE Tutorial, Manchester

  38. Working with Ganga … • Your applications developed in testbed environments can be smoothly migrated to production environments • Your jobs are managed in a systematic way • Your grid jobs benefit from a hidden job wrapper instrumented for • advanced input/output control • runtime progress monitoring • New technologies will be transparent for you without changing your way of running applications EGEE Tutorial, Manchester

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