Introduction of full config.json sim chain including shell scripts

New folder created: macro/PWG/common/production. All files related to config.json chain moved there. run_reco_config_json.C and run_analysis_tree_maker_json_config.C added. run_json.sh and run_sim_json.sh added. Full chain currently runs during CI.

Introduction of full config.json sim chain including shell scripts
New folder created: macro/PWG/common/production. All files related to config.json chain moved there. run_reco_config_json.C and run_analysis_tree_maker_json_config.C added. run_json.sh and run_sim_json.sh added. Full chain currently runs during CI.
98c73a16 · Frederic Julian Linz · Florian Uhlig · 4d96e6ae · 98c73a16 · 98c73a16
Commit 98c73a16 authored 2 years ago by Frederic Julian Linz Committed by Florian Uhlig 2 years ago
--- a/macro/CMakeLists.txt
+++ b/macro/CMakeLists.txt
@@ -14,9 +14,12 @@ If(NOT ${CBM_TEST_MODEL} MATCHES Experimental)
  Message("Additional Nightly tests")
 EndIf()

+  add_subdirectory(PWG)
+
 #--- Additional tests for weekly builds
 If(${CBM_TEST_MODEL} MATCHES Weekly)
  add_subdirectory(KF)
+  add_subdirectory(PWG)
  Message("Additional long running Weekly tests")
 EndIf()

@@ -35,6 +38,17 @@ Install(FILES ${CBMROOT_SOURCE_DIR}/scripts/loadlib.C
        DESTINATION share/cbmroot/macro/
       )

+Install(FILES ${CBMROOT_SOURCE_DIR}/macro/PWG/common/production/run_json.sh 
+              ${CBMROOT_SOURCE_DIR}/macro/PWG/common/production/run_sim_reco_json.sh
+              ${CBMROOT_SOURCE_DIR}/macro/PWG/common/production/run_transport_json_config.C
+              ${CBMROOT_SOURCE_DIR}/macro/PWG/common/production/run_digi_json_config.C
+              ${CBMROOT_SOURCE_DIR}/macro/PWG/common/production/run_reco_json_config.C
+              ${CBMROOT_SOURCE_DIR}/macro/PWG/common/production/run_analysis_tree_maker_json_config.C
+              ${CBMROOT_SOURCE_DIR}/macro/PWG/common/production/config.json
+        DESTINATION share/cbmroot/macro/PWG/common/production
+        )
+Install(CODE "FILE(MAKE_DIRECTORY ${CMAKE_INSTALL_PREFIX}/share/cbmroot/macro/PWG/common/production)")
+
 Install(FILES KF/DecayConfig.C KF/registerGeantDecays.C KF/registerLightIons.C KF/registerPythiaDecays.C
              KF/kf_kfparticle.C KF/kf_thermal_signal_generator.C  KF/kf_transport.C
        DESTINATION share/cbmroot/macro/KF

--- a/macro/PWG/CMakeLists.txt
+++ b/macro/PWG/CMakeLists.txt
+add_subdirectory(common)
--- a/macro/PWG/common/CMakeLists.txt
+++ b/macro/PWG/common/CMakeLists.txt
+add_subdirectory(production)
--- a/macro/PWG/common/production/CMakeLists.txt
+++ b/macro/PWG/common/production/CMakeLists.txt
+# Check if Python is installed and excute test only if python is available
+
+find_package(Python)
+
+if (Python_FOUND)
+  set(production_macro_events 2)
+
+  GENERATE_TEST_SCRIPT(${CBMROOT_SOURCE_DIR}/macro/PWG/common/production/run_json.sh)
+
+  # copy the configuration to the build directory and replace variables
+  configure_file(${CBMROOT_SOURCE_DIR}/macro/PWG/common/production/config_ci.json.in
+                 ${CBMROOT_BINARY_DIR}/macro/PWG/common/production/config_ci.json
+                 @ONLY
+                )
+
+  File(COPY ${CBMROOT_SOURCE_DIR}/macro/include/.rootrc DESTINATION ${CBMROOT_BINARY_DIR}/macro/PWG/common/production)
+
+  Set(testname PWG_common_production_run_json)
+
+  Add_Test(${testname} ${CMAKE_CURRENT_BINARY_DIR}/run_json.sh ${CMAKE_CURRENT_BINARY_DIR}/config_ci.json)
+  Set_Tests_Properties(${testname} PROPERTIES TIMEOUT 600)
+endif()
--- a/macro/run/config.json
+++ b/macro/run/config.json
 {
+  "accessory": {
+    "batch": true,
+    "nEvents": 10,
+    "jobName": "cbmsim",
+    "jobRange": "1-10",
+    "account": "cbm",
+    "ram": "4G",
+    "partition": "main",
+    "time": "3:00:00",
+    "excludeNodes": "",
+    "logDir": "/lustre/cbm/users/${USER}/mc/out/log",
+    "cbmRoot": "/lustre/cbm/users/fkornas/soft/cbmroot/MR_master22_fr_v18.6.7_fs_apr21p2/bin/CbmRootConfig.sh",
+    "jobScript": "${PWD}/run_sim_reco.sh",
+    "transport": {
+      "run": true,
+      "plutoShift": 0,
+      "macro": "${VMCWORKDIR}/macro/PWG/common/production/run_transport_json_config.C"},
+    "digitization": {
+      "run": true,
+      "macro": "${VMCWORKDIR}/macro/PWG/common/production/run_digi_json_config.C"},
+    "reconstruction": {
+      "run": true,
+      "macro": "${VMCWORKDIR}/macro/PWG/common/production/run_reco_json_config.C"},
+    "AT": { 
+      "run": true,
+      "macro": "${VMCWORKDIR}/macro/PWG/common/production/run_analysis_tree_maker_json_config.C"}
+  },
  "logScreenLevel": "INFO",
  "logVerbosityLevel": "LOW",
  "transport": {
    "input": [
      {"generator": "unigen",
-       "file": "${VMCWORKDIR}/input/urqmd.auau.10gev.centr.root"},
+       "file": "/lustre/cbm/users/ogolosov/mc/generators/dcmqgsm_smm/auau/pbeam12agev/mbias/root/dcmqgsm_${taskId}.root"},
      {"generator": "pluto",
-       "file": "${VMCWORKDIR}/input/pluto.auau.8gev.omega.mpmm.0001.root",
+       "file": "/lustre/cbm/users/ogolosov/mc/generators/pluto/auau/pbeam12agev/w/w.zip#w_${plutoFileId}.root",
       "plutoPdg": 0},
-      {"generator": "beam",
+      {"#generator": "beam",
       "beamA": 197,
       "beamZ": 79,
       "beamQ": 79,
       "beamP": 12.0,
-       "beamStartZ": -1.0}
+       "beamStartZ": -45.0}
    ],
-    "output": {
-      "path": "test",
+    "output": { 
+      "path": "/lustre/cbm/users/${USER}/mc/out/tra/${taskId}/${taskId}",
      "overwrite": false
    },
    "target": {
@@ -26,7 +53,7 @@
      "position": {
        "x": 0.0,
        "y": 0.0,
-        "z": 0.0
+        "z": -44.0
      },
      "rotation.y": 0.0
    },
@@ -34,7 +61,7 @@
      "position": {
        "x": 0.0,
        "y": 0.0,
-        "zFocus": 0.0,
+        "zFocus": -44.0,
        "sigmaX": 0.1,
        "sigmaY": 0.1
      },
@@ -55,25 +82,25 @@
    },
    "geometry": {
      "baseSetup": "sis100_electron",
-      "magneticField": {
+      "#magneticField": {
        "tag": "v18a",
        "scale": 1.0,
        "position": {
          "x": 0.0,
          "y": 0.0,
-          "z": 0.0
+          "z": 40.0
        }
      },
      "subsystems": {
        "magnet":   "v21a",
-        "pipe":     "v16e_1e",
-        "mvd":      "v20c_tr",
-        "sts":      "v20a",
+        "pipe":     "v21d",
+	"mvd":      "v20d_tr",
+        "sts":      "v21e",
        "rich":     "v21a",
-        "trd":      "v20c_1e",
-        "tof":      "v20c_1e",
-        "psd":      "v20c",
-        "platform": "v13a"
+        "trd":      "v20b_1e",
+        "tof":      "v21a_1e",
+        "psd":      "v22a",
+        "platform": "v22b"
      }
    },
    "stackFilter": {
@@ -86,16 +113,16 @@
  "digitization": {
    "generateRunInfo": false,
    "eventMode": false,
-    "timeSliceLength": -1.0,
+    "timeSliceLength": 1e5,
    "storeAllTimeSlices": false,
    "startTime": 1000,
-    "produceNoise": true,
+    "produceNoise": false,
    "input": [
      {"id": 0,
-       "path": "test",
-       "rate": "1.e7",
+       "path": "/lustre/cbm/users/${USER}/mc/out/tra/${taskId}/${taskId}",
+       "rate": "1.e3",
       "treeAccessMode": "regular",
-       "parameterSource": true},
+       "parameterSource": false},
      {"id": -1,
       "path": "test_emb",
       "embedToId": 0,
@@ -103,15 +130,39 @@
      {"id": -1,
       "path": "test_beam",
       "rate": "1.e9",
-       "treeAccessMode": "regular"}
+       "treeAccessMode": "random"}
    ],
    "output": {
-      "path": "data/test_json",
+      "path": "/lustre/cbm/users/${USER}/mc/out/raw/${taskId}/${taskId}",
      "overwrite": false
    },
    "geometry": {
      "deactivate": ["", ""],
      "#deactivateAllBut": ""
    }
-  } 
+  },
+ 
+  "reconstruction": {
+    "rawFile": "/lustre/cbm/users/${USER}/mc/out/raw/${taskId}/${taskId}", 
+    "nTimeSlices": -1,
+    "firstTimeSlice": 0, 
+    "output": { 
+      "path": "/lustre/cbm/users/${USER}/mc/out/reco/${taskId}/${taskId}",
+      "overwrite": false
+    },
+    "sEvBuildRaw": "Ideal", 
+    "traFile": "/lustre/cbm/users/${USER}/mc/out/tra/${taskId}/${taskId}",
+    "isL1Matching": true,
+    "isL1EffQA": false 
+  },
+
+  "AT": {
+    "traFile": "/lustre/cbm/users/${USER}/mc/out/tra/${taskId}/${taskId}", 
+    "rawFile": "/lustre/cbm/users/${USER}/mc/out/raw/${taskId}/${taskId}", 
+    "recFile": "/lustre/cbm/users/${USER}/mc/out/reco/${taskId}/${taskId}", 
+    "unigenFile": "/lustre/cbm/users/ogolosov/mc/generators/dcmqgsm_smm/auau/pbeam12agev/mbias/root/dcmqgsm_${taskId}.root",
+    "output": {
+      "path": "/lustre/cbm/users/${USER}/mc/out/AT/${taskId}/${taskId}",
+      "overwrite": false}
+  }
 }
--- a/macro/run/config_ci.json
+++ b/macro/run/config_ci.json
 {
+  "accessory": {
+    "batch": false,
+    "nEvents": "@production_macro_events@",
+    "jobName": "cbmsim",
+    "jobRange": "1",
+    "account": "cbm",
+    "ram": "4G",
+    "partition": "debug",
+    "time": "0:20:00",
+    "excludeNodes": "",
+    "logDir": "@CMAKE_BINARY_DIR@/macro/PWG/common/production/data/log",
+    "cbmRoot": "@CMAKE_BINARY_DIR@/config.sh",
+    "jobScript": "@VMCWORKDIR@/macro/PWG/common/production/run_sim_reco_json.sh",
+    "transport": {
+      "run": true,
+      "plutoShift": 0,
+      "macro": "@VMCWORKDIR@/macro/PWG/common/production/run_transport_json_config.C"},
+    "digitization": {
+      "run": true,
+      "macro": "@VMCWORKDIR@/macro/PWG/common/production/run_digi_json_config.C"},
+    "reconstruction": {
+      "run": true,
+      "macro": "@VMCWORKDIR@/macro/PWG/common/production/run_reco_json_config.C"},
+    "AT": { 
+      "run": true,
+      "macro": "@VMCWORKDIR@/macro/PWG/common/production/run_analysis_tree_maker_json_config.C"}
+  },
  "logScreenLevel": "INFO",
  "logVerbosityLevel": "LOW",
  "transport": {
    "input": [
      {"generator": "unigen",
-       "file": "${VMCWORKDIR}/input/urqmd.auau.10gev.centr.root"},
+       "file": "@VMCWORKDIR@/input/urqmd.auau.10gev.centr.root"},
      {"generator": "pluto",
-       "file": "${VMCWORKDIR}/input/pluto.auau.8gev.omega.mpmm.0001.root",
+       "file": "@VMCWORKDIR@/input/pluto.auau.8gev.omega.mpmm.0001.root",
       "plutoPdg": 0},
-      {"generator": "beam",
+      {"#generator": "beam",
       "beamA": 197,
       "beamZ": 79,
       "beamQ": 79,
       "beamP": 12.0,
-       "beamStartZ": -1.0}
+       "beamStartZ": -45.0}
    ],
-    "output": {
-      "path": "data/test",
+    "output": { 
+      "path": "@CMAKE_BINARY_DIR@/macro/PWG/common/production/data/tra/${taskId}/${taskId}",
      "overwrite": true
    },
    "target": {
@@ -26,7 +53,7 @@
      "position": {
        "x": 0.0,
        "y": 0.0,
-        "z": 0.0
+        "z": -44.0
      },
      "rotation.y": 0.0
    },
@@ -34,7 +61,7 @@
      "position": {
        "x": 0.0,
        "y": 0.0,
-        "zFocus": 0.0,
+        "zFocus": -44.0,
        "sigmaX": 0.1,
        "sigmaY": 0.1
      },
@@ -55,25 +82,25 @@
    },
    "geometry": {
      "baseSetup": "sis100_electron",
-      "magneticField": {
+      "#magneticField": {
        "tag": "v18a",
        "scale": 1.0,
        "position": {
          "x": 0.0,
          "y": 0.0,
-          "z": 0.0
+          "z": 40.0
        }
      },
      "subsystems": {
        "magnet":   "v21a",
-        "pipe":     "v16e_1e",
-        "mvd":      "v20c_tr",
-        "sts":      "v20a",
+        "pipe":     "v21d",
+	"mvd":      "v20d_tr",
+        "sts":      "v21e",
        "rich":     "v21a",
-        "trd":      "v20c_1e",
-        "tof":      "v20c_1e",
-        "psd":      "v20c",
-        "platform": "v13a"
+        "trd":      "v20b_1e",
+        "tof":      "v21a_1e",
+        "psd":      "v22a",
+        "platform": "v22b"
      }
    },
    "stackFilter": {
@@ -86,16 +113,16 @@
  "digitization": {
    "generateRunInfo": false,
    "eventMode": false,
-    "timeSliceLength": -1.0,
+    "timeSliceLength": 1e5,
    "storeAllTimeSlices": false,
    "startTime": 1000,
-    "produceNoise": true,
+    "produceNoise": false,
    "input": [
      {"id": 0,
-       "path": "data/test",
+       "path": "@CMAKE_BINARY_DIR@/macro/PWG/common/production/data/tra/${taskId}/${taskId}",
       "rate": "1.e7",
       "treeAccessMode": "regular",
-       "parameterSource": true},
+       "parameterSource": false},
      {"id": -1,
       "path": "test_emb",
       "embedToId": 0,
@@ -103,15 +130,39 @@
      {"id": -1,
       "path": "test_beam",
       "rate": "1.e9",
-       "treeAccessMode": "regular"}
+       "treeAccessMode": "random"}
    ],
    "output": {
-      "path": "data/test_json",
+      "path": "@CMAKE_BINARY_DIR@/macro/PWG/common/production/data/raw/${taskId}/${taskId}",
      "overwrite": true
    },
    "geometry": {
      "deactivate": ["", ""],
      "#deactivateAllBut": ""
    }
-  } 
+  },
+ 
+  "reconstruction": {
+    "rawFile": "@CMAKE_BINARY_DIR@/macro/PWG/common/production/data/raw/${taskId}/${taskId}", 
+    "nTimeSlices": -1,
+    "firstTimeSlice": 0, 
+    "output": { 
+      "path": "@CMAKE_BINARY_DIR@/macro/PWG/common/production/data/reco/${taskId}/${taskId}",
+      "overwrite": true
+    },
+    "sEvBuildRaw": "Ideal", 
+    "traFile": "@CMAKE_BINARY_DIR@/macro/PWG/common/production/data/tra/${taskId}/${taskId}",
+    "isL1Matching": true,
+    "isL1EffQA": true 
+  },
+
+  "AT": {
+    "traFile": "@CMAKE_BINARY_DIR@/macro/PWG/common/production/data/tra/${taskId}/${taskId}", 
+    "rawFile": "@CMAKE_BINARY_DIR@/macro/PWG/common/production/data/raw/${taskId}/${taskId}", 
+    "recFile": "@CMAKE_BINARY_DIR@/macro/PWG/common/production/data/reco/${taskId}/${taskId}", 
+    "unigenFile": "@VMCWORKDIR@/input/urqmd.auau.10gev.centr.root",
+    "output": {
+      "path": "@CMAKE_BINARY_DIR@/macro/PWG/common/production/data/AT/${taskId}/${taskId}",
+      "overwrite": true}
+  }
 }
--- a/macro/PWG/common/production/run_analysis_tree_maker_json_config.C
+++ b/macro/PWG/common/production/run_analysis_tree_maker_json_config.C
+/* Copyright (C) 2023 GSI Helmholtzzentrum fuer Schwerionenforschung, Darmstadt
+   SPDX-License-Identifier: GPL-3.0-only
+   Authors: Viktor Klochkov, Frederic Linz [committer] */
+
+// -----   Check output file name   -------------------------------------------
+bool CheckOutFileName(TString fileName, Bool_t overwrite)
+{
+  string fName = "run_reco_json_config";
+  // --- Protect against overwriting an existing file
+  if ((!gSystem->AccessPathName(fileName.Data())) && (!overwrite)) {
+    cout << fName << ": output file " << fileName << " already exists!";
+    return false;
+  }
+
+  // --- If the directory does not yet exist, create it
+  const char* directory = gSystem->DirName(fileName.Data());
+  if (gSystem->AccessPathName(directory)) {
+    Int_t success = gSystem->mkdir(directory, kTRUE);
+    if (success == -1) {
+      cout << fName << ": output directory " << directory << " does not exist and cannot be created!";
+      return false;
+    }
+    else
+      cout << fName << ": created directory " << directory;
+  }
+  return true;
+}
+
+void run_analysis_tree_maker_json_config(TString traPath = "test", TString rawPath = "", TString recPath = "",
+                                         TString unigenFile = "", TString outPath = "", bool overwrite = true,
+                                         std::string config = "", int nEvents = 0)
+{
+  const std::string system = "Au+Au";  // TODO can we read it automatically?
+  const float beam_mom     = 12.;
+  const bool is_event_base = false;
+
+  // --- Logger settings ----------------------------------------------------
+  const TString logLevel     = "INFO";
+  const TString logVerbosity = "LOW";
+  // ------------------------------------------------------------------------
+
+  // -----   Environment   --------------------------------------------------
+  const TString myName = "run_analysis_tree_maker";
+  const TString srcDir = gSystem->Getenv("VMCWORKDIR");  // top source directory
+  // ------------------------------------------------------------------------
+
+  // -----   In- and output file names   ------------------------------------
+  if (rawPath == "") rawPath = traPath;
+  if (recPath == "") recPath = traPath;
+  if (outPath == "") outPath = traPath;
+  TString traFile = traPath + ".tra.root";
+  TString geoFile = traPath + ".geo.root";
+  TString rawFile = rawPath + ".raw.root";
+  TString recFile = recPath + ".reco.root";
+  TString parFile = rawPath + ".par.root";
+  TString outFile = outPath + ".analysistree.root";
+  // ------------------------------------------------------------------------
+
+  // -----   Remove old CTest runtime dependency file  ----------------------
+  const TString dataDir  = gSystem->DirName(outPath);
+  const TString dataName = gSystem->BaseName(outPath);
+  const TString testName = ("run_treemaker");
+  // ------------------------------------------------------------------------
+
+  // -----   Load the geometry setup   -------------------------------------
+  CbmSetup* setup = CbmSetup::Instance();
+  if (config == "") config = Form("%s/macro/run/config.json", gSystem->Getenv("VMCWORKDIR"));
+  boost::property_tree::ptree pt;
+  CbmTransportConfig::LoadFromFile(config, pt);
+  CbmTransportConfig::SetGeometry(setup, pt.get_child(CbmTransportConfig::GetModuleTag()));
+  // ------------------------------------------------------------------------
+
+  // -----   Timer   --------------------------------------------------------
+  TStopwatch timer;
+  timer.Start();
+  // ------------------------------------------------------------------------
+
+  TString geoTag;
+  auto* parFileList = new TList();
+
+  if (!CheckOutFileName(outFile, overwrite)) return;
+  std::cout << "-I- " << myName << ": Using raw file " << rawFile << std::endl;
+  std::cout << "-I- " << myName << ": Using parameter file " << parFile << std::endl;
+  std::cout << "-I- " << myName << ": Using reco file " << recFile << std::endl;
+  if (unigenFile.Length() > 0) std::cout << "-I- " << myName << ": Using unigen file " << unigenFile << std::endl;
+
+  // -----   Reconstruction run   -------------------------------------------
+  auto* run         = new FairRunAna();
+  auto* inputSource = new FairFileSource(recFile);
+  inputSource->AddFriend(traFile);
+  inputSource->AddFriend(rawFile);
+  run->SetSource(inputSource);
+  run->SetOutputFile(outFile);
+  run->SetGenerateRunInfo(kTRUE);
+  // ------------------------------------------------------------------------
+
+  // ----- Mc Data Manager   ------------------------------------------------
+  auto* mcManager = new CbmMCDataManager("MCManager", is_event_base);
+  mcManager->AddFile(traFile);
+  run->AddTask(mcManager);
+  // ------------------------------------------------------------------------
+
+  // ---   STS track matching   ----------------------------------------------
+  //  auto* matchTask = new CbmMatchRecoToMC();
+  //  run->AddTask(matchTask);
+  // ------------------------------------------------------------------------
+
+  run->AddTask(new CbmTrackingDetectorInterfaceInit());
+
+  auto* KF = new CbmKF();
+  run->AddTask(KF);
+  // needed for tracks extrapolation
+  auto* l1 = new CbmL1("CbmL1", 1, 3);
+  if (setup->IsActive(ECbmModuleId::kMvd)) {
+    setup->GetGeoTag(ECbmModuleId::kMvd, geoTag);
+    const TString mvdMatBudgetFileName = srcDir + "/parameters/mvd/mvd_matbudget_" + geoTag + ".root";
+    l1->SetMvdMaterialBudgetFileName(mvdMatBudgetFileName.Data());
+  }
+  if (setup->IsActive(ECbmModuleId::kSts)) {
+    setup->GetGeoTag(ECbmModuleId::kSts, geoTag);
+    const TString stsMatBudgetFileName = srcDir + "/parameters/sts/sts_matbudget_" + geoTag + ".root";
+    l1->SetStsMaterialBudgetFileName(stsMatBudgetFileName.Data());
+  }
+  run->AddTask(l1);
+
+  // --- TRD pid tasks
+  if (setup->IsActive(ECbmModuleId::kTrd)) {
+    CbmTrdSetTracksPidLike* trdLI = new CbmTrdSetTracksPidLike("TRDLikelihood", "TRDLikelihood");
+    trdLI->SetUseMCInfo(kTRUE);
+    trdLI->SetUseMomDependence(kTRUE);
+    run->AddTask(trdLI);
+    std::cout << "-I- : Added task " << trdLI->GetName() << std::endl;
+    //     ------------------------------------------------------------------------
+  }
+
+  // AnalysisTree converter
+  auto* man = new CbmConverterManager();
+  man->SetSystem(system);
+  man->SetBeamMomentum(beam_mom);
+
+  man->SetOutputName(outFile.Data(), "rTree");
+
+  if (!is_event_base) { man->AddTask(new CbmMatchEvents()); }
+
+  man->AddTask(new CbmSimEventHeaderConverter("SimEventHeader"));
+  man->AddTask(new CbmRecEventHeaderConverter("RecEventHeader"));
+  man->AddTask(new CbmSimTracksConverter("SimParticles"));
+
+  CbmStsTracksConverter* taskCbmStsTracksConverter = new CbmStsTracksConverter("VtxTracks", "SimParticles");
+  taskCbmStsTracksConverter->SetIsWriteKFInfo();
+  taskCbmStsTracksConverter->SetIsReproduceCbmKFPF();
+  man->AddTask(taskCbmStsTracksConverter);
+
+  man->AddTask(new CbmRichRingsConverter("RichRings", "VtxTracks"));
+  man->AddTask(new CbmTofHitsConverter("TofHits", "VtxTracks"));
+  man->AddTask(new CbmTrdTracksConverter("TrdTracks", "VtxTracks"));
+  man->AddTask(new CbmPsdModulesConverter("PsdModules"));
+
+  run->AddTask(man);
+
+  // -----  Parameter database   --------------------------------------------
+  FairRuntimeDb* rtdb = run->GetRuntimeDb();
+  auto* parIo1        = new FairParRootFileIo();
+  auto* parIo2        = new FairParAsciiFileIo();
+  parIo1->open(parFile.Data());
+  parIo2->open(parFileList, "in");
+  rtdb->setFirstInput(parIo1);
+  rtdb->setSecondInput(parIo2);
+  rtdb->setOutput(parIo1);
+  rtdb->saveOutput();
+  // ------------------------------------------------------------------------
+
+  // -----   Intialise and run   --------------------------------------------
+  run->Init();
+
+  std::cout << "Starting run" << std::endl;
+  run->Run(nEvents);
+  // ------------------------------------------------------------------------
+
+  timer.Stop();
+  const Double_t rtime = timer.RealTime();
+  const Double_t ctime = timer.CpuTime();
+  std::cout << "Macro finished succesfully." << std::endl;
+  std::cout << "Output file is " << outFile << std::endl;
+  std::cout << "Parameter file is " << parFile << std::endl;
+
+  printf("RealTime=%f seconds, CpuTime=%f seconds\n", rtime, ctime);
+
+  // -----   CTest resource monitoring   ------------------------------------
+  FairSystemInfo sysInfo;
+  const Float_t maxMemory = sysInfo.GetMaxMemory();
+  std::cout << R"(<DartMeasurement name="MaxMemory" type="numeric/double">)";
+  std::cout << maxMemory;
+  std::cout << "</DartMeasurement>" << std::endl;
+  std::cout << R"(<DartMeasurement name="WallTime" type="numeric/double">)";
+  std::cout << rtime;
+  std::cout << "</DartMeasurement>" << std::endl;
+  const Float_t cpuUsage = ctime / rtime;
+  std::cout << R"(<DartMeasurement name="CpuLoad" type="numeric/double">)";
+  std::cout << cpuUsage;
+  std::cout << "</DartMeasurement>" << std::endl;
+  // ------------------------------------------------------------------------
+
+  // -----   Finish   -------------------------------------------------------
+  std::cout << " Test passed" << std::endl;
+  std::cout << " All ok " << std::endl;
+  //   Generate_CTest_Dependency_File(depFile);
+  // ------------------------------------------------------------------------
+
+  // -----   This is to prevent a malloc error when exiting ROOT   ----------
+  // The source of the error is unknown. Related to TGeoManager.
+  RemoveGeoManager();
+  // ------------------------------------------------------------------------
+}
--- a/macro/run/run_digi_json_config.C
+++ b/macro/run/run_digi_json_config.C
--- a/macro/PWG/common/production/run_json.sh
+++ b/macro/PWG/common/production/run_json.sh
+#!/bin/bash
+
+function getJsonVal () {
+  val=$(${_python} -c "import json;print(json.dumps(json.load(open('${config}'))$1))";)
+  eval echo ${val}
+} # e.x. 'outPath=$(getJsonVal "['transport']['output']['path']")'
+
+#function checkJsonKey () {
+#  python -c "import json,sys;print ('$1' in json.load(open('${config}')))";
+#} # returns True if key exists, False if not, e.x. 'run_transport=$(checkJsonKey "transport")'
+
+function readStepInfo () {
+  run=$(getJsonVal "['accessory']['${step}']['run']")
+  if [ ${run} == true ]; then
+    overwrite=$(getJsonVal "['${step}']['output']['overwrite']")
+    outDir=$(getJsonVal "['${step}']['output']['path']")
+    [[ ${outDir} != */ ]] && outDir=$(dirname ${outFile})
+    srcDir=${outDir}/macro
+    macro=$(getJsonVal "['accessory']['${step}']['macro']")
+    macroName=$(basename ${macro})
+  fi
+}
+
+# find the proper python executable and exit if not found
+if [[ ! -z $PYHON_EXEC ]]; then
+  _python=$PYHON_EXEC
+else
+  _python=$(which python)
+  if [[ -z $_python ]]; then
+    _python=$(which python2)
+    if [[ -z $_python ]]; then
+      _python=$(which python3)
+      if [[ -z $_python ]]; then
+        echo "No python interpreter found"
+        exit 1
+      fi
+    fi
+  fi
+fi
+export _python=${_python}
+
+submitScript=${0}
+echo "Submit script : ${submitScript}"
+config=${1}
+batch=$(getJsonVal "['accessory']['batch']")
+jobScript=$(getJsonVal "['accessory']['jobScript']")
+export cbmRoot=$(getJsonVal "['accessory']['cbmRoot']")
+cbmRoot="${cbmRoot} -a"
+echo "CbmRoot : ${cbmRoot}"
+source ${cbmRoot}
+
+steps="transport digitization reconstruction AT"
+for step in ${steps}; do
+  readStepInfo
+  if [ ${run} == true ]; then
+    mkdir -pv ${srcDir}
+    cp -v ${macro} ${srcDir}
+    cp -v ${config} ${srcDir}
+    cp -v ${submitScript} ${srcDir}
+    cp -v ${jobScript} ${srcDir}
+  fi
+done
+
+export -f getJsonVal
+export -f readStepInfo
+
+export configName=$(basename ${config})
+export config=${srcDir}/${configName}
+export nEvents=$(getJsonVal "['accessory']['nEvents']")
+jobRange=$(getJsonVal "['accessory']['jobRange']")
+logDir=$(getJsonVal "['accessory']['logDir']")
+mkdir -pv ${logDir}
+
+if [ ${batch} == true ];then
+  account=$(getJsonVal "['accessory']['account']")
+  ram=$(getJsonVal "['accessory']['ram']")
+  partition=$(getJsonVal "['accessory']['partition']")
+  time=$(getJsonVal "['accessory']['time']")
+  jobName=$(getJsonVal "['accessory']['jobName']")
+  excludeNodes=$(getJsonVal "['accessory']['excludeNodes']")
+  sbatch -A ${account} --mem=${ram} -p ${partition} -t ${time} -J ${jobName}\
+    -a ${jobRange} -o ${logDir}/%a_%A.log --export=ALL \
+    --exclude=${excludeNodes} -- ${jobScript}
+else
+  echo "Jobscript: ${jobScript}"
+  export SLURM_ARRAY_TASK_ID=${jobRange}
+  ${jobScript} &> ${logDir}/${jobRange}.log
+fi
--- a/macro/PWG/common/production/run_reco_json_config.C
+++ b/macro/PWG/common/production/run_reco_json_config.C
--- a/macro/PWG/common/production/run_sim_reco_json.sh
+++ b/macro/PWG/common/production/run_sim_reco_json.sh
+#!/bin/bash
+
+steps="transport digitization reconstruction AT"
+source ${cbmRoot}
+for step in ${steps}; do
+  readStepInfo
+  if [ ${run} == true ]; then
+    export taskId=${SLURM_ARRAY_TASK_ID}
+    plutoShift=$(getJsonVal "['accessory']['transport']['plutoShift']")
+    export plutoFileId=$(printf %05d $((${taskId}-${plutoShift})))
+    config=${srcDir}/${configName}
+    macro=${srcDir}/${macroName}
+    outFile=$(getJsonVal "['${step}']['output']['path']")
+    outDir=$(dirname ${outFile})
+    log=${outDir}/${step}.log
+
+    mkdir -pv ${outDir}
+    cd ${outDir}
+    ln -sfv ${VMCWORKDIR}/macro/run/.rootrc ${outDir} 
+    if [ ${step} == reconstruction ]; then
+      rawFile=$(getJsonVal "['reconstruction']['rawFile']")
+      nTimeSlices=$(getJsonVal "['reconstruction']['nTimeSlices']")
+      firstTimeSlice=$(getJsonVal "['reconstruction']['firstTimeSlice']")
+      sEvBuildRaw=$(getJsonVal "['reconstruction']['sEvBuildRaw']")
+      traFile=$(getJsonVal "['reconstruction']['traFile']")
+      isL1Matching=$(getJsonVal "['reconstruction']['isL1Matching']")
+      isL1EffQA=$(getJsonVal "['reconstruction']['isL1EffQA']")
+      echo "  "
+      echo "Run reconstruction: ${macro}(\"${rawFile}\",${nTimeSlices},${firstTimeSlice},\"${outFile}\",\
+	${overwrite},\"${sEvBuildRaw}\",\"${config}\",\"${traFile}\",${isL1Matching},${isL1EffQA})"
+      root -b -l -q "${macro}(\"${rawFile}\",${nTimeSlices},${firstTimeSlice},\"${outFile}\",\
+        ${overwrite},\"${sEvBuildRaw}\",\"${config}\",\"${traFile}\",${isL1Matching},${isL1EffQA})" &> ${log}
+    elif [ ${step} == AT ]; then
+      traFile=$(getJsonVal "['AT']['traFile']")
+      rawFile=$(getJsonVal "['AT']['rawFile']")
+      recFile=$(getJsonVal "['AT']['recFile']")
+      unigenFile=$(getJsonVal "['AT']['unigenFile']")
+      echo "  "
+      echo "Run AT converter: ${macro}(\"${traFile}\",\"${rawFile}\",\"${recFile}\",\
+	\"${unigenFile}\",\"${outFile}\",${overwrite},\"${config}\")" 
+      root -b -l -q "${macro}(\"${traFile}\",\"${rawFile}\",\"${recFile}\",\
+	\"${unigenFile}\",\"${outFile}\",${overwrite},\"${config}\")" &> ${log}
+    else 
+      if [ ${step} == digitization ]; then
+        input=$(getJsonVal "['transport']['output']['path']")
+        if [ ! -e ${outFile}.par.root ] || [ ${overwrite} == true ]; then
+          cp -v ${input}.par.root ${outDir}
+        fi
+      echo "  "
+      echo "Run digitization: ${macro}(\"${config}\",${nEvents})"
+      fi
+      
+      if [ ${step} == transport ]; then
+	echo "  "
+	echo "Run transport: ${macro}(\"${config}\",${nEvents})"
+      fi
+       
+      root -b -l -q "${macro}(\"${config}\",${nEvents})" &> ${log}  
+    fi
+    gzip -f ${log}
+
+    rm -v .rootrc
+    if [ ${step} == reconstruction ]; then
+	if [ "${isL1EffQA}" == true ]; then
+    	  rm -v *{moni,CA}* all_*.par 
+	else
+	  rm -v *{core,moni,CA,L1,Edep}* all_*.par
+    	fi
+    fi
+    if [ ${step} == digitization ]; then
+	rm -v *{moni,Fair}* all_*.par
+    fi
+    if [ ${step} == AT ]; then
+	rm -v *{core,CA,L1}*
+    fi
+
+    cd -
+    export taskId=
+  fi
+done
--- a/macro/run/run_transport_json_config.C
+++ b/macro/run/run_transport_json_config.C
--- a/macro/run/CMakeLists.txt
+++ b/macro/run/CMakeLists.txt
 # =====   Generate the needed shell scripts   ================================
 GENERATE_ROOT_TEST_SCRIPT(${CBMROOT_SOURCE_DIR}/macro/run/run_tra_file.C)
-GENERATE_ROOT_TEST_SCRIPT(${CBMROOT_SOURCE_DIR}/macro/run/run_transport_json_config.C)
-GENERATE_ROOT_TEST_SCRIPT(${CBMROOT_SOURCE_DIR}/macro/run/run_digi_json_config.C)
 GENERATE_ROOT_TEST_SCRIPT(${CBMROOT_SOURCE_DIR}/macro/run/run_tra_beam.C)
 GENERATE_ROOT_TEST_SCRIPT(${CBMROOT_SOURCE_DIR}/macro/run/run_digi.C)
 GENERATE_ROOT_TEST_SCRIPT(${CBMROOT_SOURCE_DIR}/macro/run/run_reco.C)
@@ -79,33 +77,6 @@ foreach(setup IN LISTS cbm_setup)
  	set(sname test)
  endif()

-  # --- Test run_transport_json_config
-  # --- Transport run using run_transport_json_config.C
-  set(json_config_file ${CBMROOT_SOURCE_DIR}/macro/run/config_ci.json)
-  set(testname run_transport_json_config)
-  add_test(${testname} ${MACRO_DIR}/run_transport_json_config.sh \"${json_config_file}\" 2 ${randomSeed})
-  set_tests_properties(${testname} PROPERTIES
-  	TIMEOUT ${timeOutTime}
-	FAIL_REGULAR_EXPRESSION "segmentation violation"
-  	PASS_REGULAR_EXPRESSION "Macro finished successfully"
-  	FIXTURES_REQUIRED run_cleanup
-  	FIXTURES_SETUP fixt_tra_json_config
-  	RESOURCE_LOCK json_config_ParDb
-  )
-
-  # --- Test run_digi_json_config
-  # --- Digitization run with using run_digi_json_config.C
-  set(testname run_digi_json_config)
-  add_test(${testname} ${MACRO_DIR}/run_digi_json_config.sh \"${json_config_file}\")
-  set_tests_properties(${testname} PROPERTIES
-  	TIMEOUT ${timeOutTime}
-	FAIL_REGULAR_EXPRESSION "segmentation violation"
-  	PASS_REGULAR_EXPRESSION "Macro finished successfully"
-  	FIXTURES_REQUIRED fixt_tra_json_config
-  	FIXTURES_SETUP fixt_digi_json_config
-  	RESOURCE_LOCK json_config_ParDb
-  )
-
  # --- Test run_tra_coll
  # --- Transport run with collision events, using run_tra_file.C
  set(testname run_${sname}_tra_coll)
@@ -505,8 +476,7 @@ EndIf() # If(DEFINED ENV{RAW_DATA_PATH} )
 #####################
 # ============================================================================

-Install(FILES .rootrc run_tra_file.C run_tra_beam.C run_transport_json_config.C run_digi_json_config.C config.json
-              run_digi.C run_reco.C run_unpack_online.C run_unpack_tsa.C config_ci.json
+Install(FILES .rootrc run_tra_file.C run_tra_beam.C run_digi.C run_reco.C run_unpack_online.C run_unpack_tsa.C
        DESTINATION share/cbmroot/macro/run
       )
 Install(PROGRAMS run_tests.sh

--- a/macro/run/run_tests.sh
+++ b/macro/run/run_tests.sh
@@ -45,22 +45,6 @@ main () {
                $log_file_name \
                $check_string

-  log_file_name=data/run_tra_json.log
-  check_string="Macro finished successfully"
-
-  execute_macro "run_transport_json_config.C(\"config_ci.json\")" \
-                $log_file_name \
-                $check_string
- 
-  # Testing the digitization macros
-  log_file_name=data/run_digi_json.log
-  check_string="Macro finished successfully"
-
-  execute_macro "run_digi_json_config.C(\"config_ci.json\")" \
-                $log_file_name \
-                $check_string
-
-
  log_file_name=data/run_digi_eb.log
  check_string="Macro finished successfully"
  execute_macro "run_digi.C(\"data/${sname}_coll\", -1, \"data/${sname}_ev\", -1.)" \