Using GANGA with AMAAthena

Introduction

This guide gives an step-by-step instruction for running AMAAthena within GANGA on a NIKHEF desktop (e.g. ribble.nikhef.nl). AMAAthena is an Athena package providing a framework for modular analysis. GANGA is an official ATLAS grid utility for distributed data analysis.

Preparation

Please follow the AMAAthena guide to setup CMT and checkout AMAAthena package.

Starting GANGA

Typing the following commands within the directory: PhysicsAnalysis/AnalysisCommon/AMA/AMAAthena/cmt in a clean shell environment (i.e. no environment setup for Athena and CMT).

% source /project/atlas/nikhef/dq2/dq2_setup.sh.NIKHEF
% export DPNS_HOST=tbn18.nikhef.nl
% export LFC_HOST=lfc-atlas.grid.sara.nl
% source /project/atlas/nikhef/ganga/etc/setup.[c]sh
% ganga --config-path=/project/atlas/nikhef/ganga/config/Atlas.ini.nikhef

GANGA magic functions for cmtsetup

Inside GANGA, one could deal with the complex CMT setup with two magic functions.

The following example shows how to setup the CMT environment for Athena 14.2.0 in 32 bit mode.

In [n]: config.Athena.CMTHOME = '/path/to/your/cmthome'
In [n]: cmtsetup 14.2.0,32
In [n]: setup

Running AMAAthena in GANGA

The example below assumes:

Users have the following Athena job option files in the run directory of the AMAAthena package
AMAAthena_jobOptions.py
Trigger_jobOptions.py
Users have the following AMA driver configuration files in the run directory of the AMAAthena package
exampleaod.conf
reader.conf
Analysis is performed on dataset: fdr08_run2.0052280.physics_Muon.merge.AOD.o3_f8_m10

Creating new GANGA job

In [n]: j = Job()

Setting application

In [n]: j.application = AMAAthena()
In [n]: j.application.option_file += [ File('../run/AMAAthena_jobOptions.py'), File('../run/Trigger_jobOptions.py') ]
In [n]: j.application.driver_config.config_file = File('../run/exampleaod.conf')
In [n]: j.application.driver_config.include_file += [ File('../run/reader.conf') ]
In [n]: j.application.prepare()

Setting input data

StagerDataset When using the StagerDataset, the AMAAthena job will use the Athena FileStager to copy dataset files from a grid storage.

In [n]: j.inputdata = StagerDataset()
In [n]: j.inputdata.dataset += [ 'fdr08_run2.0052280.physics_Muon.merge.AOD.o3_f8_m10' ]

DQ2Dataset When using the DQ2Dataset, GANGA will handle the file access externally from Athena.

In [n]: j.inputdata = DQ2Dataset()
In [n]: j.inputdata.dataset += [ 'fdr08_run2.0052280.physics_Muon.merge.AOD.o3_f8_m10' ]
In [n]: j.inputdata.type = 'DQ2_DOWNLOAD'

Setting job splitter (optional)

The examples below ask each subjob to process on 2 files in maximum.

using StagerJobSplitter with StagerDataset

In [n]: j.splitter = StagerJobSplitter()
In [n]: j.splitter.numfiles = 2

using DQ2JobSplitter with DQ2Dataset for jobs running on LCG

In [n]: j.splitter = DQ2JobSplitter()
In [n]: j.splitter.numfiles = 2

Setting computing backend

using Stoomboot cluster

In [n]: j.backend = PBS()

using LCG

In [n]: j.backend = LCG()

StagerDataset is not yet supported for jobs on LCG. Please using DQ2Dataset instead.

Submitting job

In [n]: j.submit()

After job submission

Checking job status

GANGA automatically polls the up-to-date status of your jobs and updates local repository accordingly. A notification will pop up to the user when the job status is changed.

In addition, you can get a job summary table by:

In [n]: jobs

or a summary table for subjobs:

In [n]: j.subjobs

Result and output merging

For the moment, the completed (sub-)job returns an root summary file. The file is stored in the summary sub-directory in the job's output directory.

For jobs using StagerJobSplitter, the RootMerger is automatically assigned to the job so that when the whole job is completed, the summary root files from subjobs are merged together.

For jobs using DQ2Dataset, the merging process can be done manually when the whole job is completed. For example, assuming each subjob produces a root summary file called summary/summary_mySample_confFile_exampleaod.conf_nEvts_1000.root. To merge them, one can do:

In [n]: merger = RootMerger()
In [n]: merger.files += ['summary/summary_mySample_confFile_exampleaod.conf_nEvts_1000.root']
In [n]: merger.overwrite = True
In [n]: merger.ignorefailed = True
In [n]: merger.merge(j)

The merged root file with the same name will be created in the job's outputdir.

Killing and removing jobs

You can kill a job by calling

In [n]: j.kill()

or remove a job by

In [n]: j.remove()

Advanced usage

Restricting max. number of events

In [n]: j.application.max_events = '1000'

Dealing with failed sub-jobs

It's very possible to have some failed sub-jobs. In this case, GANGA reports the whole job as failed. There is no necessary to resubmit the whole job, you can just resubmit the failed subjobs. Assuming you have a failed job, j:

In [n]:for sj in j.subjobs:
   ...:     if sj.status == 'failed':
   ...:         sj.resubmit()
   ...:         

More information

GANGA workbook
GANGA tutorials for ATLAS users

Known issues/ToDo items

StagerDataset not supported for jobs on LCG

--Hclee 16:17, 13 Aug 2008 (MET DST)