setup on lxplus

    * your account should be able to run athena "hello world" as discribed in the workbook [[https://twiki.cern.ch/twiki/bin/view/Atlas/WorkBookRunAthenaHelloWorld]]
    * login to lxplus
    * start athena 

 >  source ~/cmthome/setup.sh -tag=12.0.4 

    * start the grid 

 >  source /afs/cern.ch/project/gd/LCG-share/sl3/etc/profile.d/grid_env.sh

 >  source /afs/cern.ch/project/gd/LCG-share/sl3/etc/profile.d/grid_env.sh

 >  export LFC_HOST=lfc-atlas.cern.ch 

 >  export LCG_CATALOG_TYPE=lfc

 >  voms-proxy-init

    * create a long term proxy (recommended for mc production, default 1 week) 

 >  myproxy-init

    * check with 

 >  myproxy-info

    * the long term proxy lies on "myproxy.cern.ch" and is automatically used by ganga
    * start dq2 (dataset mangagement) 

 >  source /afs/usatlas.bnl.gov/Grid/Don-Quijote/dq2_user_client/setup.sh.CERN 

    * start ganga (4.2.7) as atlas user in graphical user interface with 

 >  /afs/cern.ch/sw/ganga/install/slc3_gcc323/4.2.7/bin/ganga --config-path=GangaAtlas/Atlas.ini --gui

 >  /afs/cern.ch/sw/ganga/install/slc3_gcc323/4.2.7/bin/ganga --config-path=GangaAtlas/Atlas.ini --gui

    * type "y" to create a default ganga config file ".gangarc"
    * ganga should start 

    * open a second shell, and type 

 >  source ~/cmthome/setup.sh -tag=12.0.4 

 >  source /afs/cern.ch/project/gd/LCG-share/sl3/etc/profile.d/grid_env.sh

 >  source /afs/cern.ch/project/gd/LCG-share/sl3/etc/profile.d/grid_env.sh

 >  export LFC_HOST=lfc-atlas.cern.ch 

 >  export LCG_CATALOG_TYPE=lfc

 >  voms-proxy-init

 >  source /afs/usatlas.bnl.gov/Grid/Don-Quijote/dq2_user_client/setup.sh.CERN 

 >  source /afs/usatlas.bnl.gov/Grid/Don-Quijote/dq2_user_client/setup.sh.CERN 

    * change into a run directotory 

 >  cd testarea/12.0.4/PhysicsAnalysis/AnalysisCommon/UserAnalysis/run 

setup at DESY Zeuthen

    * start athena 

 >  source /usr1/scratch/userscratch/USERNAME/cmthome/setup.sh -tag=12.0.3

    * start the grid 

 >  source /afs/desy.de/group/grid/UI/GLITE-3_0_4/etc/profile.d/grid_env.sh

 >  export LFC_HOST=lfc-atlas.cern.ch 

 >  export LCG_CATALOG_TYPE=lfc

 >  voms-proxy-init

    * log with another shell into lxplus and create a long term proxy with "myproxy-init" as described above (myproxy-init at atlhltX fails)
    * start dq2 

 >  source /afs/ifh.de/project/grid/dq2/setup.sh

    * start ganga

 >  ini ganga

 >  ganga --config-path=GangaAtlas/Atlas.ini --gui 


hello world with Ganga in graphical user interface

    * you should contain "HelloWorldOptions.py" in your run directory
    * click on "new" in the ganga window to create a new job
    * click on application and change from "Executable" to "Athena" in the drop down box on the right side
    * expand the application menu
    * click on "option file" and browse on your disk to "HelloWorldOptions.py" to load it into ganga
    * click on "max events" and write "10"
    * click on "backend" and change from "local" to "LCG"
    * click on "submit" button
    * inspect the status of the job from "submitted", "running" to "completed", hopefully not to "failed"
    * retrieve the output by clicking on the job with the right button and choose "retrieve output", click on the file you want to read
    * you can also inspect input/output directly in ~/gangadir/workspace/... 

generating events (1. step in the chain)

    * the normal way would be to download in the second shell the atlas production transform archive, actual releases can be found here 

 >  wget http://cern.ch/atlas-computing/links/kitsDirectory/Production/kits/AtlasProduction_12_0_31_08_noarch.tar.gz

    * by default you have to create minimum 5000 events, but for educational test and to save time, we create 3 events,
    * creating more than 3 is simple and strait forward (but takes longer time)
    * you can change the default of 5000 events as discribed here
    * to save time download a file already changed down to 3 events (default is only changed for 1 example: "DC3.005711.PythiaB_bbmu6mu4X.py") 

 >  cp "/afs/cern.ch/user/v/volkmann/public/AtlasProduction_12_0_31_8_noarch.tar.gz" .

    * click on new in the ganga window
    * change "application" to "AthenaMC"
    * type into atlas release "12.0.31"
    * type into eventgen_job_option "DC3.005711.PythiaB_bbmu6mu4X.py"
    * type into firstevent "1"
    * make sure that mode is "evgen"
    * type into number_events_job "3"
    * type into process_name something meaningful like "bbmu6mu4X"
    * type into production_name another meaningful thing like "bphys"
    * change the random seed to a 9 digit number
    * type in a 6-digit run number like "000001"
    * browse the transform script "AtlasProduction_12_0_31_8_noarch.tar.gz" into ganga
    * type into transform_script "csc_evgen_trf.py"
    * click on backend and choose "LCG"
    * expand LCG and choose one of the following computing elements 

** tbn20.nikhef.nl:2119/jobmanager-pbs-qlong

** lcg-ce0.ifh.de:2119/jobmanager-lcgpbs-atlas

** grid-ce1.desy.de:2119/jobmanager-lcgpbs-atlas

    * (you find all by typing "lcg-infosites --vo atlas ce" into the shell)
    * click on outputdata and select "DQOutputDataset"
    * click on splitter and choose "AthenaMCSplitterJob"
    * click on numsubjobs and type "3"
    * click on nsubjobs_inputfile and type also "3"
    * submit the job
    * inspect the output in the other open shell with dq2 if the 3 jobs reach "completed" (sometimes dq2 doesn't work at atlhltX)
    * you find the output datasetname in ganga

 >  dq2_ls -g datasetname

    * you should see the three root files (each has 1 event in this example) 

simulating and digitizing events (2. and 3. step in the chain)

    * create a new job, and choose again "AthenaMC" in the application form
    * type into the form the atlas_release, prozess_name, production_name and run_number of the previous generation job
    * type into first_event "1"
    * type into number_events_job "1"
    * choose a 9-digit random seed
    * browse the job transform archieve again into the job "AtlasProduction_12_0_31_8_noarch.tar.gz"
    * type into transform_skript "csc_simul_trf.py"
    * choose in backend "LCG" and type a ce into it (as previously mentioned)
    * click on inputdata and choose "DQ2OutputDataset" and expand the menu
    * type into datasetname the name of the dataset from the previous job
    * click on outputdata and choose "DQ2OutputDataset"
    * choose in Splitter "AthenaMCSplitterJob" and expand
    * type into n_subjobs_inputfile "1"
    * type into number_input_jobs "3"
    * type into numsubjobs "3"
    * submit the job and inspect the result with dq2_ls -g datasetname 

reconstructing events (4. step in the chain)

    * everything remais the same to simulation exept:
    * change mode to "recon"
    * type into transform_skript "csc_reco_trf.py"
    * type into the inputdata the corresponding name of your simulation dataset
    * check the output dataset with "dq2_ls -g datasetname"
    * download the dataset with "dq2_get datasetname" and inspect with root 

links

    * http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/BPHYSICS/underlying/grid/gangainstructions.htm
    * http://gridui02.usatlas.bnl.gov:25880/server/pandamon/query?overview=dslist
    * https://twiki.cern.ch/twiki/bin/view/Atlas/AtlasEvgenTrf
    * http://www.cern.ch/ganga