Deprecated

This page is now only of historical interest. For up to date ganga and pathena instructions, please see the information in the ATLAS Software Tutorial.

  source /afs/cern.ch/sw/ganga/install/etc/setup-atlas.sh

  source ~/cmthome/setup.sh -tag=14.5.2.6,32,AtlasProduction

  cd $TESTAREA/14.5.2.6/PhysicsAnalysis/AnalysisCommon/UserAnalysis/cmt
  source setup.sh

   cd ../run
   ganga

globalflags.ConditionsTag.set_Value_and_Lock('COMCOND-REPC-002-13')

    execfile('pandaBackend_test.py') 

source /afs/cern.ch/atlas/offline/external/GRID/ddm/DQ2Clients/setup.sh
   dq2-get "your_dataset_name"

1    j = Job()

    execfile('pandaBackend_test.py') 

run% ganga pandaBackend_test.py

Reusing the environment

First you need to find the name of the previous library. Say we want to reuse the library built in ganga job 323: given a job ID:

Either: in ganga:

In [19]:jobs(323).backend.libds

Out[19]: user.nedwards.20100610.323.lib

or use dq2:

$ dq2-ls %nedwards%323*

user.nedwards.20100610.323

user.nedwards.20100610.323.lib

user.nedwards.20100610.323_sub07797849

The library is user.nedwards.20100610.323.lib. In subsequent job options you can set:

Running Executable on panda Backend

This has been said to work on panda backend. It has not been tested. If found to be successful please UPDATE!

______________________________________________________________________________

j = Job()
j.application=Executable()
j.application.exe='myscript.sh'
j.backend=Panda()
j.backend.site='ANALY_FZK'
j.inputsandbox=['/path/to/myscript.sh']
j.submit()

_____________________________________________________________________________

Also for the LCG() backend, a site can be specified:
j.backend.requirements.other=['other.GlueSiteUniqueID=="UKI-SCOTGRID-GLASGOW"']

The Ganga output looks something like this (Note the output is a dataset: Output dataset user09.chriscollins.ganga.2.20091210 ):

run% ganga pandaBackend_test.py

*** Welcome to Ganga ***
Version: Ganga-5-4-3
Documentation and support: http://cern.ch/ganga
Type help() or help('index') for online help.

This is free software (GPL), and you are welcome to redistribute it
under certain conditions; type license() for details.


For help visit the ATLAS Distributed Analysis Help eGroup:
  https://groups.cern.ch/group/hn-atlas-dist-analysis-help/

GangaAtlas                         : INFO     Found 0 tasks
Ganga.GPIDev.Lib.JobRegistry       : INFO     Found 2 jobs in "jobs", completed in 0 seconds
Ganga.GPIDev.Lib.JobRegistry       : INFO     Found 0 jobs in "templates", completed in 0 seconds

********************************************************************
New in 5.2.0: Change the configuration order w.r.t. Athena.prepare()
              New Panda backend schema - not backwards compatible
For details see the release notes or the wiki tutorials
********************************************************************

GangaAtlas.Lib.Athena              : WARNING  New prepare() method has been called. The old prepare method is c   alled now prepare_old()
GangaAtlas.Lib.Athena              : INFO     Found Working Directory /home/chrisc/atlas/GANGA-TEST-15.3.0.1/15   .3.0.1
GangaAtlas.Lib.Athena              : INFO     Found ATLAS Release 15.3.0
GangaAtlas.Lib.Athena              : INFO     Found ATLAS Production Release 15.3.0.1
GangaAtlas.Lib.Athena              : INFO     Found ATLAS Project AtlasProduction
GangaAtlas.Lib.Athena              : INFO     Found ATLAS CMTCONFIG i686-slc4-gcc34-opt
GangaAtlas.Lib.Athena              : INFO     Using run directory: PhysicsAnalysis/HiggsPhys/HiggsAssocTop/TtHH   bbDPDBasedAnalysis/run/
GangaAtlas.Lib.Athena              : INFO     Extracting athena run configuration ...
GangaAtlas.Lib.Athena              : INFO     Detected Athena run configuration: {'input': {'noInput': True}, '   other': {}, 'output': {'outNtuple': ['FILE1'], 'alloutputs': ['D3PD.root']}}
GangaAtlas.Lib.Athena              : INFO     Creating /tmp/chrisc/sources.f3f6d811-f7cd-42d3-8d50-47c47f58ae78   .tar ...
GangaAtlas.Lib.Athena              : INFO     Option athena_compile=False. Adding InstallArea to /tmp/chrisc/so   urces.f3f6d811-f7cd-42d3-8d50-47c47f58ae78.tar ...
Ganga.GPIDev.Lib.Job               : INFO     submitting job 2
Ganga.GPIDev.Lib.Job               : INFO     job 2 status changed to "submitting"
GangaPanda.Lib.Panda               : INFO     Panda brokerage results: cloud UK, site ANALY_GLASGOW
GangaAtlas.Lib.ATLASDataset        : WARNING  Dataset mc08.106314.Pythia_ttH120_2l2nu4b.merge.AOD.e364_s462_r63   5_t53_tid065132 has 8 locations
GangaAtlas.Lib.ATLASDataset        : WARNING  Please be patient - waiting for site-index update at site UKI-SCO   TGRID-GLASGOW_LOCALGROUPDISK ...
GangaAtlas.Lib.Athena              : WARNING  You are using DQ2JobSplitter.filesize or the backend used support   s only a maximum dataset size of 10000 MB per subjob - job splitting has been adjusted accordingly.
GangaPanda.Lib.Athena              : INFO     Input dataset(s) ['mc08.106314.Pythia_ttH120_2l2nu4b.merge.AOD.e3   64_s462_r635_t53_tid065132']
GangaPanda.Lib.Athena              : INFO     Output dataset user09.chriscollins.ganga.2.20091210
GangaPanda.Lib.Athena              : INFO     Running job options: TtAnalysis-ttHSignalSMALL-GRID.py
GangaPanda.Lib.Panda               : INFO     Uploading source tarball sources.f3f6d811-f7cd-42d3-8d50-47c47f58   ae78.tar.gz in /tmp/chrisc to Panda...
Ganga.GPIDev.Lib.Job               : INFO     job 2.0 status changed to "submitting"
Ganga.GPIDev.Lib.Job               : INFO     job 2.0 status changed to "submitted"
Ganga.GPIDev.Lib.Job               : INFO     job 2 status changed to "submitted"

Helpful commands inside Ganga:
jobs lists your jobs
jobs(1) lists the content of job 1
help() goes into help mode ( quit to leave help)
j=jobs(1) and j.kill() will kill job 1.

Your output will be in the dq2 registered dataset. For me this was user09.chriscollins.ganga.2.20091210 Again this is available from jobs(x)

Using Ganga to submit jobs to the Panda backend on lxplus

cp ../share/AnalysisSkeleton_topOptions.py .

BUT to prepare your code for running on the Grid there are some changes needed for this Athena JO - please add these lines:

______________________________________________________________________________

include("RecExCommission/RecExCommissionFlags_jobOptions.py" )
ATLASCosmicFlags.useLocalCOOL  = True
# setup DBReplicaSvc to choose closest Oracle replica, configurables style
from AthenaCommon.AppMgr import ServiceMgr
from PoolSvc.PoolSvcConf import PoolSvc
ServiceMgr+=PoolSvc(SortReplicas=True)
from DBReplicaSvc.DBReplicaSvcConf import DBReplicaSvc
ServiceMgr+=DBReplicaSvc(UseCOOLSQLite=False) 

here

globalflags.ConditionsTag.set_Value_and_Lock('COMCOND-REPC-002-13')

file

    execfile('pandaBackend_test.py') 

4. Go to run directory and start ganga (once the code is compiled).

    ganga pandaBackend_test.py

this

1026613035

The Ganga JO 'pandaBackend_test.py' could look like this (without line numbers):

Line 5 is set to False because we have already compiled the packages locally if you want your job to compile 
your checked out code before submitting then simply change this to True

here

  source ~/cmthome/setup.sh -tag=14.5.2.6,32,AtlasProduction

  cd $TESTAREA/14.5.2.6/PhysicsAnalysis/AnalysisCommon/UserAnalysis/cmt

here

here

  cd $TEST/PhysicsAnalysis/AnalysisCommon/UserAnalysis/cmt
  source setup.sh

   cd ../run
   ganga

5. Execute your Ganga job script while Ganga is running (where an example of what the 'pandaBackend_test.py' would look like is below in other words have this file in your run directory) and type:

    execfile('pandaBackend_test.py')

          
source /afs/cern.ch/atlas/offline/external/GRID/ddm/DQ2Clients/setup.sh
   dq2-get "your_dataset_name"

1    j = Job()

NOTE: Line 3 is overriding the database release to match the one needed to read ESD/DPD. In the case of the spring cosmic reprocessing,the DB release is 6.6.1.1. If the database releases don't match the jobs fail on the Grid. Line 4 corresponds to your Athena jobOptions. You can use the top job options copied from your UserAnalysis packages share directory.

cp ../share/AnalysisSkeleton_topOptions.py .

______________________________________________________________________________

here

globalflags.ConditionsTag.set_Value_and_Lock('COMCOND-REPC-002-13')

Line 5 is set to False because we have already compiled the packages locally.
Line 6 tells Ganga to tar your user area and send it with the job.
Line 10 specifies the backend to which you are sending your job. There are three options: LCG, 
Panda and NorduGrid. I chose Panda because my data existed only in BNLPANDA, a site in the US cloud. 
Line 12 corresponds to the number of subjobs you want to split your job into. 
Finally in Line 13 you submit your job.

here

  source cmthome/setup.sh -tag=14.5.2.6,32,AtlasProduction

  cd $TEST/PhysicsAnalysis/AnalysisCommon/UserAnalysis/cmt

4. Go to run directory and start ganga.

Using Ganga to submit jobs to the Panda backend

References:

Full Ganga Atlas Tutorial

Data preparation reporocessing - using Ganga

1. In a clean shell, setup Ganga. It is important to setup Ganga before Athena.

  source /afs/cern.ch/sw/ganga/install/etc/setup-atlas.sh

2. Setup the athena release.

   
> source cmthome/setup.sh -tag=14.5.2.6,AtlasProduction

3. Setup any checked out packages you use in your code.
   > cd $TEST/PhysicsAnalysis/AnalysisCommon/UserAnalysis/cmt
   > source setup.sh
4. Go to run directory and start ganga.
   > cd ../run
   > ganga
5. Execute your job script.
   In[0]: execfile('cbarrera_test2.py')
6. You can monitor your job's progress by typing *jobs* inside Ganga or, if you submitted to the Panda backend by http://panda.cern.ch:25880/server/pandamon/query.
7. Once your job has finished you can copy the output data using the dq2 tools.
   > source /afs/cern.ch/atlas/offline/external/GRID/ddm/DQ2Clients/setup.sh
   > dq2-get 

yourData

Obviously it's not as simple as that... 

Here is the job file I submitted using ganga:

1    j = Job()
2    j.application = Athena()
3    j.application.atlas_dbrelease = 'ddo.000001.Atlas.Ideal.DBRelease.v06060101:DBRelease-6.6.1.1.tar.gz'
4    j.application.option_file = 'Data_jobOptions_cosmic.py'
5    j.application.athena_compile = False
6    j.application.prepare()
7    j.inputdata = DQ2Dataset()
8    j.inputdata.dataset = "data08_cos.00092051.physics_IDCosmic.recon.ESD.o4_r653/"
9    j.outputdata = DQ2OutputDataset()
10   j.backend = Panda()
11   j.splitter = DQ2JobSplitter()
12   j.splitter.numsubjobs = 20
13   j.submit()

A few comments on some of these lines. Line 3 is overriding the database release to match the one needed to read ESD/DPD. In the case of the spring cosmic reprocessing, 
the DB release is 6.6.1.1. If the database releases don't match the jobs fail on the Grid. I don't understand why it works locally though (maybe a question for Graeme). 
Line 4 corresponds to your jobOptions. There were some changes I needed to do in mine as well, to prepare my code for running on the Grid:

______________________________________________________________________________

include("RecExCommission/RecExCommissionFlags_jobOptions.py" )
ATLASCosmicFlags.useLocalCOOL  = True
# setup DBReplicaSvc to choose closest Oracle replica, configurables style
from AthenaCommon.AppMgr import ServiceMgr
from PoolSvc.PoolSvcConf import PoolSvc
ServiceMgr+=PoolSvc(SortReplicas=True)
from DBReplicaSvc.DBReplicaSvcConf import DBReplicaSvc
ServiceMgr+=DBReplicaSvc(UseCOOLSQLite=False) 

globalflags.ConditionsTag.set_Value_and_Lock('COMCOND-REPC-002-13')
______________________________________________________________________________

Also remember to remove the input data line in the original JO's (from second Reference webpage). Line 5 is set to False because we have already compiled the packages 
locally. Line 6 tells Ganga to tar your user area and send it with the job. Line 10 specifies the backend to which you are sending your job. There are three options: LCG, 
Panda and NorduGrid. I chose Panda because my data existed only in BNLPANDA, a site in the US cloud. And apparently, as Graeme told us yesterday, that's the way to go: 
prepare your jobs with Ganga and then submit to PanDa. Line 12 corresponds to the number of subjobs you want to split your job into. I read in this page 
https://twiki.cern.ch/twiki/bin/view/Atlas/DAGangaFAQ#DQ2JobSplitter_won_t_submit_when that if you are using DQ2Splitter you should not specify a site, that you should let 
it decide. But I believe specifying a cloud is permitted. Finally in Line 13 you submit your job.

This instructions are just guidance. I am sure unexpected things will emerge when dealing with different cases.