Update and clean up configuration. Set defaults to Run 3 real pp data. (#516)

Author: vkucera

README.md

@@ -38,7 +38,7 @@ The validation framework is a general configurable platform that gives user the
 Its flexibility is enabled by strict separation of its specialised components into a system of Bash scripts.
 Configuration is separate from execution code, input configuration is separate from task configuration, execution steps are separate from the main steering code.
 
-* The steering script [`runtest.sh`](exec/runtest.sh) provides control parameters and interface to the machinery for task execution.
+* The steering script [`run_analysis.sh`](exec/run_analysis.sh) provides control parameters and interface to the machinery for task execution.
 * User provides configuration Bash scripts which:
   * modify control parameters,
   * produce modified configuration files,
@@ -50,7 +50,7 @@ Execution code can be found in the [`exec`](exec) directory.
 
 **The user should not touch anything in this directory!**
 
-The steering script [`runtest.sh`](exec/runtest.sh) performs the following execution steps:
+The steering script [`run_analysis.sh`](exec/run_analysis.sh) performs the following execution steps:
 
 * Load input specification.
 * Load tasks configuration.
@@ -85,10 +85,10 @@ All steps are activated by default and some can be disabled individually by sett
 
 ## Configuration
 
-The steering script [`runtest.sh`](exec/runtest.sh) can be executed with the following optional arguments:
+The steering script [`run_analysis.sh`](exec/run_analysis.sh) can be executed with the following optional arguments:
 
 ```bash
-bash [<path>/]runtest.sh [-h] [-i <input-configuration>] [-t <task-configuration>] [-d]
+[<path>/]run_analysis.sh [-h] [-i <input-configuration>] [-t <task-configuration>] [-d]
 ```
 
 `<input-configuration>` Input specification script. See [Input specification](#input-specification).
@@ -227,7 +227,7 @@ Now you are ready to run the validation code.
 **Make sure that your Bash environment is clean!
 Do not load ROOT, AliPhysics, O<sup>2</sup>, O<sup>2</sup>Physics or any other aliBuild package environment before running the framework!**
 
-Enter any directory and execute the steering script `runtest.sh`.
+Enter any directory and execute the steering script `run_analysis.sh`.
 (You can create a symlink for convenience.)
 All the processing will take place in the current directory.
 
@@ -264,7 +264,7 @@ which can help you figure out what went wrong, where and why.
 You can execute the script from the current working directory using the following syntax (options can be combined):
 
 ```bash
-bash [<path>/]debug.sh [-h] [-t TYPE] [-b [-u]] [-f] [-w] [-e]
+[<path>/]debug.sh [-h] [-t TYPE] [-b [-u]] [-f] [-w] [-e]
 ```
 
 `-h` Print out the usage help.
@@ -306,7 +306,7 @@ as well as re-building your AliPhysics and O<sup>2</sup>(Physics) installations
 You can execute the script from any directory on your system using the following syntax:
 
 ```bash
-python [<path>/]exec/update_packages.py [-h] [-d] [-l] [-c] database
+[<path>/]exec/update_packages.py [-h] [-d] [-l] [-c] database
 ```
 
 optional arguments:
@@ -353,7 +353,7 @@ It is possible to check your code locally (before even committing or pushing):
 ### Space checker
 
 ```bash
-bash [<path>/]exec/check_spaces.sh
+[<path>/]exec/check_spaces.sh
 ```
 
 ### [ClangFormat](https://clang.llvm.org/docs/ClangFormat.html)

codeHF/README.md

@@ -45,9 +45,7 @@ You can use the [`download_from_grid.sh`](../exec/download_from_grid.sh) script
 Enter the `codeHF` directory and execute the steering script:
 
 ```bash
-bash runtest.sh
+./run_analysis.sh
 ```
 
-Running all the steps with `INPUT_CASE=2` takes about 40 seconds in total.
-
 The postprocessing step produces several plots `comparison_histos_(...).pdf`, `MC_(...).pdf`.

codeHF/clean.sh

@@ -1,10 +1,10 @@
 #!/bin/bash
 # shellcheck disable=SC2034 # Ignore unused parameters.
 
-# Input specification for runtest.sh
+# Input specification for run_analysis.sh
 # (Modifies input parameters.)
 
-INPUT_CASE=2            # Input case
+INPUT_CASE=7            # Input case
 
 NFILESMAX=1             # Maximum number of processed input files. (Set to -0 to process all; to -N to process all but the last N files.)
 
@@ -19,144 +19,127 @@ NJOBSPARALLEL_O2=$(python3 -c "print(min(10, round($(nproc) / 2)))")
 # Default settings:
 # INPUT_LABEL="nothing"           # Input description
 # INPUT_DIR="$PWD"                # Input directory
-# INPUT_FILES="AliESDs.root"      # Input file pattern
+# INPUT_FILES="AO2D.root"         # Input file pattern
 # INPUT_SYS="pp"                  # Collision system ("pp", "PbPb")
-# INPUT_RUN=2                     # LHC Run (2, 3, 5)
-# INPUT_IS_O2=0                   # Input files are in O2 format.
+# INPUT_RUN=3                     # LHC Run (2, 3, 5)
+# INPUT_IS_O2=1                   # Input files are in O2 format.
 # INPUT_IS_MC=0                   # Input files are MC data.
 # INPUT_PARENT_MASK=""            # Path replacement mask for the input directory of parent files in case of linked derived O2 input. Set to ";" if no replacement needed. Syntax: "alien:///path/in/alien;/local/path"
 # INPUT_TASK_CONFIG=""            # Input-specific task configuration (e.g. enabling converters), overriding the task configuration in CONFIG_TASKS. String of space-separated commands.
 # JSON="dpl-config.json"          # O2 device configuration
 
-# O2 device configuration
-JSONRUN3="dpl-config_run3.json"              # Run 3
-# JSONRUN5_HF="dpl-config_run5_hf.json"        # Run 5, open HF
-# JSONRUN5_ONIAX="dpl-config_run5_oniaX.json"  # Run 5, onia (J/psi and X), (higher pt cut on 2-prong decay tracks and no DCA cut on single track)
-JSON="$JSONRUN3"
-
 INPUT_BASE="/data2/data" # alicecerno2
 
 case $INPUT_CASE in
   1)
     INPUT_LABEL="Run 2, p-p 5.02 TeV LHC17p, real"
     INPUT_DIR="$INPUT_BASE/Run2/pp_5.02TeV/real/LHC17p_pass1_CENT_woSDD"
+    INPUT_FILES="AliESDs.root"
+    INPUT_RUN=2
+    INPUT_IS_O2=0
     ;;
   2) # reference
     INPUT_LABEL="Run 2, p-p 5.02 TeV LHC17p, MC LHC18a4a2_cent"
     INPUT_DIR="$INPUT_BASE/Run2/pp_5.02TeV/sim/LHC18a4a2_cent/282099"
+    INPUT_FILES="AliESDs.root"
+    INPUT_RUN=2
+    INPUT_IS_O2=0
     INPUT_IS_MC=1
     ;;
   3)
     INPUT_LABEL="Run 2, p-p 5.02 TeV LHC17p, MC LHC18a4a2_cent"
     INPUT_DIR="$INPUT_BASE/Run2/pp_5.02TeV/sim/LHC18a4a2_cent/282341"
+    INPUT_FILES="AliESDs.root"
+    INPUT_RUN=2
+    INPUT_IS_O2=0
     INPUT_IS_MC=1
     ;;
   4)
     INPUT_LABEL="Run 2, Pb-Pb 5.02 TeV LHC15o, real"
     INPUT_DIR="$INPUT_BASE/Run2/PbPb_5.02TeV/real/LHC15o"
+    INPUT_FILES="AliESDs.root"
     INPUT_SYS="PbPb"
+    INPUT_RUN=2
+    INPUT_IS_O2=0
     INPUT_TASK_CONFIG="DOO2_CONV_BC=1"
     ;;
   5)
     INPUT_LABEL="Run 2, Pb-Pb 5.02 TeV LHC15o, MC LHC15k1a3"
     INPUT_DIR="$INPUT_BASE/Run2/PbPb_5.02TeV/sim/LHC15k1a3"
+    INPUT_FILES="AliESDs.root"
     INPUT_SYS="PbPb"
+    INPUT_RUN=2
+    INPUT_IS_O2=0
     INPUT_IS_MC=1
     INPUT_TASK_CONFIG="DOO2_CONV_BC=1"
     ;;
   6)
     INPUT_LABEL="Run 2, p-p 13 TeV LHC16p, MC LHC19g6f3, dedicated Ξc"
     INPUT_DIR="$INPUT_BASE/Run2/pp_13TeV/sim/LHC19g6f3"
+    INPUT_FILES="AliESDs.root"
+    INPUT_RUN=2
+    INPUT_IS_O2=0
     INPUT_IS_MC=1
     ;;
   7)
     INPUT_LABEL="Run 3, p-p 13.6 TeV, LHC22o_pass4, real"
     INPUT_DIR="$INPUT_BASE/Run3/pp_13.6TeV/real/LHC22o_pass4_minBias_small"
-    INPUT_FILES="AO2D.root"
-    INPUT_RUN=3
-    INPUT_IS_O2=1
     INPUT_TASK_CONFIG="DOO2_CONV_BC=1 DOO2_CONV_MCCOLL=1 DOO2_CONV_TRKEX_0_2=1 DOO2_CONV_V0=1 DOO2_CONV_MFT=1"
     ;;
   8)
     INPUT_LABEL="Run 3, p-p 13.6 TeV, LHC22r, real, low interaction rate (100 kHz)"
     INPUT_DIR="$INPUT_BASE/Run3/pp_13.6TeV/real/LHC22r"
-    INPUT_FILES="AO2D.root"
-    INPUT_RUN=3
-    INPUT_IS_O2=1
     INPUT_TASK_CONFIG="DOO2_CONV_ZDC=1 DOO2_CONV_BC=1 DOO2_CONV_MCCOLL=1 DOO2_CONV_TRKEX_0_2=1 DOO2_CONV_COLL=1 DOO2_CONV_V0=1"
     ;;
   9)
     INPUT_LABEL="Run 3, p-p 13.6 TeV, MC LHC21k6, general purpose"
     INPUT_DIR="$INPUT_BASE/Run3/pp_13.6TeV/sim/LHC21k6"
-    INPUT_FILES="AO2D.root"
-    INPUT_RUN=3
-    INPUT_IS_O2=1
     INPUT_IS_MC=1
     INPUT_TASK_CONFIG="DOO2_CONV_ZDC=1 DOO2_CONV_BC=1 DOO2_CONV_MCCOLL=1 DOO2_CONV_TRKEX_0_2=1 DOO2_CONV_COLL=1 DOO2_CONV_V0=1"
     ;;
   10)
     INPUT_LABEL="Run 2, p-p 13 TeV LHC18f, MC LHC20f4a (ESD)"
     INPUT_DIR="$INPUT_BASE/Run2/pp_13TeV/sim/LHC20f4a"
+    INPUT_FILES="AliESDs.root"
+    INPUT_RUN=2
+    INPUT_IS_O2=0
     INPUT_IS_MC=1
     ;;
   11)
     INPUT_LABEL="Run 2, p-p 13 TeV LHC18f, MC LHC20f4a (AO2D)"
     INPUT_DIR="$INPUT_BASE/Run2/pp_13TeV/sim_converted/LHC20f4a"
-    INPUT_FILES="AO2D.root"
-    INPUT_IS_O2=1
+    INPUT_RUN=2
     INPUT_IS_MC=1
     INPUT_TASK_CONFIG="DOO2_CONV_ZDC=1 DOO2_CONV_BC=1 DOO2_CONV_BCINFO=1 DOO2_CONV_MCCOLL=1 DOO2_CONV_TRKEX_0_2=1 DOO2_CONV_COLL=1 DOO2_CONV_V0=1"
     ;;
   12)
     INPUT_LABEL="Run 2, p-p 13 TeV, LHC17j (AO2D)"
     INPUT_DIR="$INPUT_BASE/Run2/pp_13TeV/real_converted/LHC17j_20220601" # converted good AO2Ds
-    INPUT_FILES="AO2D.root"
-    INPUT_IS_O2=1
+    INPUT_RUN=2
     INPUT_TASK_CONFIG="DOO2_CONV_ZDC=1 DOO2_CONV_BC=1 DOO2_CONV_BCINFO=1 DOO2_CONV_TRKEX_0_2=1 DOO2_CONV_COLL=1 DOO2_CONV_V0=1"
     ;;
   13)
     INPUT_LABEL="Run 3, p-p 13.6 TeV, MC LHC22b1b, D2H enriched"
     INPUT_DIR="$INPUT_BASE/Run3/pp_13.6TeV/sim/LHC22b1b"
-    INPUT_FILES="AO2D.root"
-    INPUT_RUN=3
-    INPUT_IS_O2=1
     INPUT_IS_MC=1
     INPUT_TASK_CONFIG="DOO2_CONV_ZDC=1 DOO2_CONV_BC=1 DOO2_CONV_MCCOLL=1 DOO2_CONV_TRKEX_0_2=1 DOO2_CONV_V0=1"
     ;;
   14)
     INPUT_LABEL="Run 3, p-p 13.6 TeV, MC LHC23f4b2, general purpose"
     INPUT_DIR="$INPUT_BASE/Run3/pp_13.6TeV/sim/LHC23f4b2"
-    INPUT_FILES="AO2D.root"
-    INPUT_RUN=3
-    INPUT_IS_O2=1
     INPUT_IS_MC=1
     INPUT_TASK_CONFIG="DOO2_CONV_BC=1 DOO2_CONV_MCCOLL=1 DOO2_CONV_TRKEX_0_2=1 DOO2_CONV_V0=1"
     ;;
   15)
     INPUT_LABEL="Run 3, Pb-Pb 5.36 TeV LHC23zzi_pass2"
     INPUT_DIR="$INPUT_BASE/Run3/PbPb_5.36TeV/real/LHC23zzi"
-    INPUT_FILES="AO2D.root"
     INPUT_SYS="PbPb"
-    INPUT_RUN=3
-    INPUT_IS_O2=1
     INPUT_TASK_CONFIG="DOO2_CONV_TRKEX_1_2=1"
     ;;
   16)
     INPUT_LABEL="Run 3, p-p 13.6 TeV, MC LHC24d3, anchored"
     INPUT_DIR="$INPUT_BASE/Run3/pp_13.6TeV/sim/LHC24d3"
-    INPUT_FILES="AO2D.root"
-    INPUT_RUN=3
-    INPUT_IS_O2=1
     INPUT_IS_MC=1
     INPUT_TASK_CONFIG="DOO2_CONV_MCCOLL=1 DOO2_CONV_TRKEX_1_2=1"
     ;;
-  17)
-    INPUT_LABEL="Run 3, p-p 13.6 TeV, LHC22o_pass4_minBias_small"
-    INPUT_DIR="$INPUT_BASE/Run3/pp_13.6TeV/real/LHC22o_pass4_minBias_small"
-    INPUT_FILES="AO2D.root"
-    INPUT_RUN=3
-    INPUT_IS_O2=1
-    INPUT_IS_MC=0
-    INPUT_TASK_CONFIG="DOO2_CONV_MCCOLL=1 DOO2_CONV_BC=1 DOO2_CONV_TRKEX_0_2=1 DOO2_CONV_V0=1"
-    ;;
   esac