Production Reco Scripts

Control/CalypsoExample/Reconstruction/CMakeLists.txt

+################################################################################
+# Package: Reconstruction
+################################################################################
+
+# Declare the package name:
+atlas_subdir( Reconstruction )
+
+# Component(s) in the package:
+#atlas_add_component( GeoModelTest
+#                     src/GeoModelTestAlg.cxx
+#                     src/components/GeoModelTest_entries.cxx
+#                     INCLUDE_DIRS ${GEOMODEL_INCLUDE_DIRS}
+#                     LINK_LIBRARIES ${GEOMODEL_LIBRARIES} AthenaBaseComps GeoModelFaserUtilities ScintReadoutGeometry TrackerReadoutGeometry MagFieldInterfaces MagFieldElements MagFieldConditions )
+
+#atlas_add_test( ReconstructionTest
+#                SCRIPT python ${CMAKE_CURRENT_SOURCE_DIR}/python/GeoModelTestConfig.py
+#                PROPERTIES WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+#                PROPERTIES TIMEOUT 300 )
+
+# Install files from the package:
+#atlas_install_joboptions( share/*.py )
+#atlas_install_python_modules( python/*.py )
+atlas_install_scripts( scripts/*.sh scripts/*.py )

Control/CalypsoExample/Reconstruction/README.md

+This package stores the production reconstruction scripts.
+
+The following scripts run production reconstruction jobs:
+* `faser_reco.py` - this is the python script for the main reconstruction job.
+
+* `submit_faser_reco.sh` - bash script to set up the environment and run the faser_reco job.  This can be called from condor or other batch scheduling systems.
+
+
+Production reco is intended to be run from a specific git tag.
+
+To see the available tags, use
+```
+git tag -l "reco/*"
+```
+and to check out a tag simply use the tag name in the checkout command
+```
+git checkout reco/r0001
+```
+
+To make a production reco tag, the easiest is to just tag a commit
+```
+git tag -a reco/r0001 9fceb02 -m "tag message"
+```
+
+This needs to be pushed to the upstream master
+```
+git push origin reco/r0001
+git push upstream reco/r0001
+```
+If you need to delete a tag from the repository
+```
+git push origin --delete reco/r0001
+```
+
+To checkout a branch based on a tag (to be able to make fixes):
+```
+git checkout -b mybranch reco/r0001
+```
+
+To find the updated files between two tags, and the changes in those files
+```
+git diff tag1 tag2 --stat
+git diff tag1 tag2 -- filename
+```

Control/CalypsoExample/Reconstruction/scripts/faser_reco.py

+#!/usr/bin/env python
+#
+# Copyright (C) 2002-2017 CERN for the benefit of the ATLAS collaboration
+# Run with:
+# ./faser_reco.py filepath [runtype]
+# 
+# filepath - fully qualified path, including url if needed, to the input raw data file
+#   example: "root://hepatl30//atlas/local/torrence/faser/commissioning/TestBeamData/Run-004150/Faser-Physics-004150-00000.raw"
+# 
+# runtype - optional flag to specify the data type (TI12Data or TestBeamData).
+#   In a normal file system location, this will be extracted from the directory name,
+#   but runtype will override this assignment. 
+#
+import sys
+import argparse
+
+parser = argparse.ArgumentParser(description="Run FASER reconstruction")
+
+parser.add_argument("file_path",
+                    help="Fully qualified path of the raw input file")
+parser.add_argument("run_type", nargs="?", default="",
+                    help="Specify run type (if it can't be parsed from path)")
+parser.add_argument("-r", "--reco", default="",
+                    help="Specify reco tag (to append to output filename)")
+parser.add_argument("-n", "--nevents", type=int, default=-1,
+                    help="Specify number of events to process (default: all)")
+
+args = parser.parse_args()
+
+from pathlib import Path
+
+filepath=Path(args.file_path)
+
+# runtype has been provided
+if len(args.run_type) > 0:
+    runtype=args.run_type
+
+# Extract runtype from path
+# Should be directory above run
+# i.e.: TestBeamData/Run-004150/Faser-Physics-004150-00000.raw"
+else:
+    if len(filepath.parts) < 3:
+        print("Can't determine run type from path - specify on command line instead")
+        sys.exit(-1)
+
+    runtype = filepath.parts[-3]
+
+print(f"Starting reconstruction of {filepath.name} with type {runtype}")
+if args.nevents > 0:
+    print(f"Reconstructing {args.nevents} events by command-line option")
+
+# Start reconstruction
+
+from AthenaConfiguration.ComponentAccumulator import ComponentAccumulator
+from AthenaConfiguration.ComponentFactory import CompFactory
+from AthenaCommon.Constants import VERBOSE, INFO
+
+from AthenaCommon.Configurable import Configurable
+from CalypsoConfiguration.AllConfigFlags import ConfigFlags
+
+Configurable.configurableRun3Behavior = True
+    
+# Flags for this job
+ConfigFlags.Input.isMC = False                               # Needed to bypass autoconfig
+ConfigFlags.IOVDb.DatabaseInstance = "OFLP200"               # Use MC conditions for now
+
+ConfigFlags.Input.ProjectName = "data20"
+ConfigFlags.GeoModel.Align.Dynamic    = False
+
+# TI12 Cosmics geometry
+if runtype == "TI12Data":
+    ConfigFlags.GeoModel.FaserVersion = "FASER-01" 
+    ConfigFlags.IOVDb.GlobalTag = "OFLCOND-FASER-01"
+
+# Testbeam setup 
+elif runtype == "TestBeamData":
+    ConfigFlags.GeoModel.FaserVersion = "FASER-TB00" 
+    ConfigFlags.IOVDb.GlobalTag = "OFLCOND-FASER-02"
+
+else:
+    print("Invalid run type found:", runtype)
+    print("Specify correct type or update list")
+    sys.exit(-1)
+
+
+# Must use original input string here, as pathlib mangles double // in path names
+ConfigFlags.Input.Files = [ args.file_path ]
+
+filestem = filepath.stem
+if len(args.reco) > 0:
+    filestem += f"-{args.reco}"
+
+ConfigFlags.addFlag("Output.xAODFileName", f"{filestem}-xAOD.root")
+ConfigFlags.Output.ESDFileName = f"{filestem}-ESD.root"
+
+#
+# Play around with this?
+# ConfigFlags.Concurrency.NumThreads = 2
+# ConfigFlags.Concurrency.NumConcurrentEvents = 2
+ConfigFlags.lock()
+
+#
+# Configure components
+from CalypsoConfiguration.MainServicesConfig import MainServicesCfg
+from AthenaPoolCnvSvc.PoolWriteConfig import PoolWriteCfg
+    
+acc = MainServicesCfg(ConfigFlags)
+acc.merge(PoolWriteCfg(ConfigFlags))
+
+#
+# Set up RAW data access
+from FaserByteStreamCnvSvc.FaserByteStreamCnvSvcConfig import FaserByteStreamCnvSvcCfg
+acc.merge(FaserByteStreamCnvSvcCfg(ConfigFlags))
+
+#
+# Needed, or move to MainServicesCfg?
+from FaserGeoModel.FaserGeoModelConfig import FaserGeometryCfg
+acc.merge(FaserGeometryCfg(ConfigFlags))
+
+# Set up algorithms
+from WaveRecAlgs.WaveRecAlgsConfig import WaveformReconstructionCfg    
+acc.merge(WaveformReconstructionCfg(ConfigFlags))
+
+# Tracker clusters
+from TrackerPrepRawDataFormation.TrackerPrepRawDataFormationConfig import FaserSCT_ClusterizationCfg
+acc.merge(FaserSCT_ClusterizationCfg(ConfigFlags))
+
+# ... try SpacePoints
+#from TrackerSpacePointFormation.TrackerSpacePointFormationConfig import TrackerSpacePointFinderCfg
+#acc.merge(TrackerSpacePointFinderCfg(ConfigFlags))
+
+# Try Dave's fitter
+from TrackerClusterFit.TrackerClusterFitConfig import ClusterFitAlgCfg
+acc.merge(ClusterFitAlgCfg(ConfigFlags))
+
+#
+# Configure output
+from OutputStreamAthenaPool.OutputStreamConfig import OutputStreamCfg
+itemList = [ "xAOD::EventInfo#*"
+             , "xAOD::EventAuxInfo#*"
+             , "xAOD::FaserTriggerData#*"
+             , "xAOD::FaserTriggerDataAux#*"
+             , "FaserSCT_RDO_Container#*"
+             , "Tracker::FaserSCT_ClusterContainer#*"
+             #, "Tracker::SCT_SpacePointContainer#*"
+             #, "Tracker::SCT_SpacePointOverlapCollection#*"
+             , "TrackCollection#*"
+]
+acc.merge(OutputStreamCfg(ConfigFlags, "xAOD", itemList))
+
+# Waveform reconstruction
+from WaveRecAlgs.WaveRecAlgsConfig import WaveformReconstructionOutputCfg    
+acc.merge(WaveformReconstructionOutputCfg(ConfigFlags))
+
+# Check what we have
+print( "Writing out xAOD objects:" )
+print( acc.getEventAlgo("OutputStreamxAOD").ItemList )
+
+# Configure verbosity    
+# ConfigFlags.dump()
+# logging.getLogger('forcomps').setLevel(VERBOSE)
+# acc.foreach_component("*").OutputLevel = VERBOSE
+acc.foreach_component("*").OutputLevel = INFO
+acc.foreach_component("*ClassID*").OutputLevel = INFO
+# log.setLevel(VERBOSE)
+
+#acc.getService("FaserByteStreamInputSvc").DumpFlag = True
+#acc.getService("FaserEventSelector").OutputLevel = VERBOSE
+#acc.getService("FaserByteStreamInputSvc").OutputLevel = VERBOSE
+#acc.getService("FaserByteStreamCnvSvc").OutputLevel = VERBOSE
+#acc.getService("FaserByteStreamAddressProviderSvc").OutputLevel = VERBOSE
+acc.getService("MessageSvc").Format = "% F%40W%S%7W%R%T %0W%M"
+
+# Execute and finish
+sys.exit(int(acc.run(maxEvents=args.nevents).isFailure()))

Control/CalypsoExample/Reconstruction/scripts/submit_faser_reco.sh

+#!/bin/bash
+# Used with a condor file to submit to vanilla universe
+#
+# Usage:
+# submit_faser_reco.sh file_path [release_directory] [working_directory]
+# 
+# file_path - full file name (with path)
+# release_directory - optional path to release install directory (default pwd)
+# working_directory - optional path to output directory location (default pwd)
+#
+# The release directory must already be set up 
+# (so an unqualified asetup can set up the release properly)
+#
+# Script will use git describe to find the release tag.  
+# If this matches reco/r???? it will be passed to the reco job
+#
+#----------------------------------------
+#
+# Parse command-line options
+file_path=${1}
+release_directory=${2}
+working_directory=${3}
+#
+# Set defaults if arguments aren't provided
+if [ -z "$file_path" ]
+then
+  echo "No file_path specified!"
+  exit 1
+fi
+#
+if [ -z "$release_directory" ]
+then
+  release_directory=`pwd`
+fi
+#
+if [ -z "$working_directory" ]
+then
+  working_directory=`pwd`
+fi
+starting_directory=`pwd`
+#
+# Now extract the run number and file stem
+#
+# First, get the filename
+file_name=$(basename "$file_path")
+# 
+# Now split based on '.' to get stem
+defaultIFS=$IFS
+IFS='.'
+read file_stem ext <<< "$file_name"
+#
+# Finally extract the run number
+IFS='-'
+# Read the split words into an array based on delimiter
+read faser type run_number segment <<< "$file_stem"
+#
+# Set the IFS delimeter back or else echo doesn't work...
+IFS=$defaultIFS
+#
+# Make output directory if needed
+output_directory="$working_directory/Run-$run_number"
+mkdir -p "$output_directory"
+#
+# This magic redirects everything in this script to our log file
+exec >& "$output_directory/$file_stem.log"
+echo `date` - $HOSTNAME
+echo "File: $file_name"
+echo "Release: $release_directory"
+echo "Output: $output_directory"
+echo "Starting: $starting_directory"
+#
+# Set up the release (do this automatically)?
+export ATLAS_LOCAL_ROOT_BASE=/cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase
+source $ATLAS_LOCAL_ROOT_BASE/user/atlasLocalSetup.sh 
+#
+# Try automatic
+# Always go back to the starting directory in case paths are relative
+cd "$starting_directory"
+cd "$release_directory"
+asetup
+source build/x8*/setup.sh
+#
+# Do this by hand
+# asetup --input="$release_directory/calypso/asetup.faser" Athena,22.0.40
+# source "$release_directory/build/x8*/setup.sh"
+#
+#
+# Try to find a release tag
+cd calypso
+recotag=`git describe`
+if [[ "$recotag" == "reco/r"???? ]]; then
+  rtag=`echo "$recotag" | cut -c 6-11`
+  echo "Found reco tag: $rtag"
+fi
+#
+# Move to the run directory
+cd "$starting_directory"
+cd "$output_directory"
+#
+# Remove any previous directory if it exists
+if [[ -e "$file_stem" ]]; then
+    echo "Remove previous directory $file_stem"
+    rm -rf "$file_stem"
+fi
+#
+# Make run directory
+mkdir "$file_stem"
+cd "$file_stem"
+#
+# Run job
+if [ -z "$rtag" ]
+then
+    faser_reco.py "$file_path"
+else
+    faser_reco.py "--reco=$rtag" "$file_path"
+fi
+#
+# Print out ending time
+date