1. Introduction to Ganga Karl Harrison (University of Cambridge) ATLAS Distributed Analysis Tutorial Milano, 5-6 February 2007 http://cern.ch/ganga

2. 6 February 20072/18 Ganga basics Ganga is an easy-to-use frontend for job definition and management –Allows simple switching between testing on a local batch system and large-scale data processing on distributed resources (Grid) –Developed in the context of ATLAS and LHCb For ATLAS, have built-in support for applications based on Athena framework, for JobTransforms, and for DQ2 data-management system –Component architecture readily allows extension –Implemented in Python Strong development team, meaning strong user support –F.Brochu (Cambridge), U.Egede (Imperial), J.Elmsheuser (München), K.Harrison (Cambridge), H.C.Lee (ASCC), D.Liko (CERN), A.Maier (CERN), J.T.Moscicki (CERN), A.Muraru (Bucharest), V.Romanovsky (IHEP), A.Soroko (Oxford), C.L.Tan (Birmingham) Contributions past and present from many others

3. 6 February 20073/18 Ganga job abstraction A job in Ganga is constructed from a set of building blocks, not all required for every job Merger Application Backend Input Dataset Output Dataset Splitter Data read by application Data written by application Rule for dividing into subjobs Rule for combining outputs Where to run What to run Job

4. 6 February 20074/18 Framework for plugin handling Athena GangaObject IApplication IBackendIDataset ISplitterIMerger LCG -CE -requirements -jobtype -middleware -id -status -reason -actualCE -exitcode -atlas_release -max_events -options -option_file -user_setupfile -user_area User System Plugin Interfaces Example plugins and schemas Ganga provides a framework for handling different types of Application, Backend, Dataset, Splitter and Merger, implemented as plugin classes Each plugin class has its own schema

5. 6 February 20075/18 Applications and Backends Running of a particular Application on a given Backend is enabled by implementing an appropriate adapter component or Runtime Handler –Can often use same Runtime Handler for several Backend: less coding PBSOSGNorduGridLocalLSFPANDA US-ATLAS WMS LHCb WMS Executable Athena (Simulation/Digitisation/ Reconstruction/Analysis) AthenaMC (Production) Gauss/Boole/Brunel/DaVinci (Simulation/Digitisation/ Reconstruction/Analysis) LHCbExperiment neutralATLAS Implemented Coming soon

6. 6 February 20076/18 LHCb applications ATLAS applications Other applications Applications Experiment-specific workload-management systems Local batch systemsDistributed (Grid) systems Processing systems (backends) Metadata catalogues Data storage and retrieval File catalogues Tools for data management Local repository Remote repository Ganga job archives Ganga monitoring loop User interface for job definition and management Ganga has built-in support for ATLAS and LHCb Component architecture allows customisation for other user groups Ganga: how the pieces fit together

7. 6 February 20077/18 Help with using Ganga Ganga documentation can be found in the User Guides section of the Ganga web side: http://cern.ch/ganga/http://cern.ch/ganga/ –Most relevant items are: Installation Working with Ganga - general introduction to functionality GUI manual - introduction to graphical interface Link to ATLAS Wiki page for distributed analysis using Ganga –https://twiki.cern.ch/twiki/bin/view/Atlas/GangaTutorial427https://twiki.cern.ch/twiki/bin/view/Atlas/GangaTutorial427 –Today’s tutorial borrows heavily from this For problems or feature requests, do any of the following: –Use hypernews forum for Ganga users and developers: https://hypernews.cern.ch/HyperNews/Atlas/get/GANGAUserDeveloper.html https://hypernews.cern.ch/HyperNews/Atlas/get/GANGAUserDeveloper.html –Send e-mail to hn-atlas-GANGAUserDeveloper@cern.chhn-atlas-GANGAUserDeveloper@cern.ch –Submit a report via Ganga’s bug-submission page in Savannah: https://savannah.cern.ch/bugs/?func=additem&group=ganga https://savannah.cern.ch/bugs/?func=additem&group=ganga Should either login to Savannah first, or give e-mail address

8. 6 February 20078/18 Setting up to run Athena jobs with Ganga Setup sequence for account on lxplus is as follows –Ensure that you have a Grid certificate installed, and that you are registered with the ATLAS Virtual Organisation –Setup environment for Athena, then checkout and build UserAnalysis package –Setup the environment for using LCG client tools –Setup the environment for using DQ2 –Setup the environment for using Ganga Can work from an account on a different machine, but this implies installing Ganga, an ATLAS release, LCG client and DQ2 tools –Not difficult on a supported platform, but takes time Detailed setup instructions given as part of hands-on exercises source /afs/cern.ch/sw/ganga/install/etc/setup-atlas.sh Optional, but sometimes useful

9. 6 February 20079/18 Using Ganga Command Line Interface in Python (CLIP) provides interactive job definition and submission from an enhanced Python shell (IPython) –Especially good for trying things out, and seeing how the system works Scripts, which may contain any Python/IPython or CLIP commands, allow automation of repetitive tasks Scripts included in distribution enable kind of approach traditionally used when submitting jobs to a local batch system Graphical User Interface (GUI) allows job management based on mouse selections and field completion –Lots of configuration possibilities Ganga allows users to work in a variety of ways CLIP and scripts covered now GUI dealt with in separate session

10. 6 February 200710/18 Ganga startup and configuration files A Ganga CLIP session is started by giving the command: –If the user doesn’t have a valid proxy then his/her Grid passphrase is requested When Ganga is first run, a configuration file.gangarc is created in the user’s home directory –The file includes comments on the configuration possibilities –The latest default configuration file can always be obtained with: Before processing.gangarc Ganga processes, in the order they are specified, any configuration files pointed to by the environment variable GANGA_CONFIG_PATH –This makes possible the use of group configuration files, but allows settings to be overridden on a user-by-user basis ganga ganga -g

11. 6 February 200711/18 Ganga workspace Ganga creates a directory gangadir in your home directory and uses this for storing job-related files and information –You can’t move this directory, but before running Ganga, you can create ~/gangadir as a link to another location gangadir repository input Local templates output workspace Remote gui jobs6667

12. 6 February 200712/18 Python commands Ganga is developed in Python, making use of IPython extensions All Python/IPython commands can be used at the prompt in a Ganga CLIP session, and the syntax for CLIP and Python commands is the same Information about Python can be found at: http://www.python.org/http://www.python.org/ –If you’re new to Python, the on-line tutorial is extremely helpful The following are often useful # A hash (#) marks the start of a comment # A slash (\) at the end of a line indicates that # the following line is a continuation dir() # List currently available objects help() # Give help help( item ) # Give help on specified item x = 5 # Assign value to variable print x # Print value of variable ctrl-D # Exit from session

13. 6 February 200713/18 IPython commands Information about IPython extensions can be found at: http://ipython.scipy.org/ http://ipython.scipy.org/ One useful extension is the possibility to use shell commands from Python, together with both shell variables and Python variables # Use ! before shell commands # Use $ before Python variables # Use $$ before shell variables here = ‘where the heart is’ !echo $$HOME is $here !ls $$HOME/mySubdir !emacs # Start emacs session, but don’t try adding & Exit # Exit from session

14. 6 February 200714/18 Ganga CLIP commands (1) Ganga commands are explained in the guide Working with Ganga: http://cern.ch/ganga/user/html/GangaIntroduction http://cern.ch/ganga/user/html/GangaIntroduction From a CLIP session, available classes, objects and functions may be listed, and help can be requested for each Useful commands include the following plugins( ‘type’) # List plugins of specified type: # ‘applications’, ‘backends’, etc j1 = Job( backend =LSF() ) # Create a new job for LSF a1 = Executable() # Create Executable application j1.application = a1 # Set value for job’s application j1.backend = LCG() # Change job’s backend to LCG export( j1, ‘myJob.py’ ) # Write job to specified file load( ‘myJob.py’ ) # Load job(s) from specified file j2 = j1.copy() # Create j2 as a copy of job j1 jobs # List jobs jobs[ i ].subjobs # List subjobs for split job i

15. 6 February 200715/18 Ganga CLIP commands (2) When a job j has been defined, the following methods can be used Once a job has been submitted, it can no longer be modified, and it cannot be resubmitted, but the job can be copied and the copy can be modified/submitted Ganga supports use of templates, which can be used as the basis of a job definition j.submit() # Submit the job j.kill() # Kill the job (if running) j.remove() # Kill the job and delete associated files j.peek() # List files in job’s output directory t = JobTemplate() # Create template templates # List templates j3 = Job( templates[ i ] ) # Create job from template i

16. 6 February 200716/18 CLIP: “Hello World” example From a Ganga CLIP session, a job that writes “Hello World” can be created, and then submitted to LCG, as follows app = Executable() app.exe = ‘/bin/echo’ app.env = {} app.args = [‘Hello World’ ] # Property values set above are in fact the defaults # for Executable application j = Job( application = app, backend = LCG() ) j.submit() # Check on job progress jobs # When job has completed, check the output j.peek( ‘stdout’ )

17. 6 February 200717/18 Using Ganga commands from a Linux shell Ganga includes scripts that can be used from a Linux shell (i.e. outside of CLIP) # Create a job for submitting Executable to LCG ganga make_job Executable LCG test.py [ Edit test.py to set Executable and/or LCG properties ] # Submit job ganga submit test.py # Query status, triggering output retrieval if job is completed ganga query # Kill job ganga kill id # Remove job from Ganga repository and workspace ganga remove id For ATLAS users, Ganga also includes athena script for running Athena jobs Given job name or id as returned by query, also have possibilities such as Same syntax can be used from inside CLIP, with no overheads for startup

18. 6 February 200718/18 Hands-on exercises Set of 11 exercises attached to course agenda –You should aim to complete at least the first 8 Exercises 1-5: deal with setup for using Ganga with ATLAS release 12.0.4 Exercises 5-8: introduce basic CLIP functionality Exercise 9: shows how to use Ganga for job submission from the Linux shell Exercises 10-11: provide minimal examples of how to use Python and IPython –Can be left for later if you don’t have time now, or can be omitted altogether if you’re already an expert