Updated to Jet embedding to add real jets (J. Klein)
[u/mrichter/AliRoot.git] / PWG4 / macros / AnalysisTrainPWG4Jets.C
1 //===================== ANALYSIS TRAIN =========================================
2 // To use: copy this macro to your work directory, modify the global part to match
3 // your needs, then run root.
4 //    root[0] .L AnalysisTrain.C
5 // Grid full mode as below (other modes: test, offline, submit, terminate)
6 //    root[1] AnalysisTrainPWG-244Jets("grid", "full")
7 // CAF mode (requires root v5-23-02 + aliroot v4-16-Rev08)
8 //    root[2] AnalysisTrainPWG4Jets("proof")
9 // Local mode requires AliESds.root or AliAOD.root in ./data directory
10 //    root[3] AnalysisTrainPWG4Jets("local")
11 // In proof and grid modes, a token is needed and sourcing the produced environment file.
12 //
13 // If 'saveTrain' flag is set, the train will generate a directory name and run
14 // in this directory. A configuration file 'ConfigTrain.C' will be generated. 
15 // One can replay at any time the train via:
16 //    root[1] AnalysisTrainPWG4Jets(ana_mode, plugin_mode, "train_default_<date>/ConfigTrain.C")
17
18 // For Usage with fastjet run in "offline" first and then "submit"
19 // jdl and analysismacro are automatically patched after "offline" mode
20
21 // =============================================================================
22 // ### General Steering variables
23 // =============================================================================
24 //== general setup variables
25 TString     kTrainName         = "testAnalysis"; // *CHANGE ME* (no blancs or special characters)
26 TString     kJobTag            = "PWG4 Jet Tasks analysis train configured"; // *CHANGE ME*
27
28 // Usage of par files ONLY in grid mode and ONLY if the code is not available
29 // in the deployed AliRoot versions. Par file search path: local dir, if not there $ALICE_ROOT.
30 // To refresh par files, remove the ones in the workdir, then do "make <target.par>" in 
31 // AliRoot.
32 Bool_t      kUsePAR             = kFALSE;  // use par files for extra libs
33 Bool_t      kUseCPAR            = kFALSE;  // use par files for common libs
34 Bool_t      kFillAOD = kFALSE;  // switch of AOD filling for on the fly analysis
35 Bool_t      kFilterAOD = kTRUE;
36 Int_t       kSaveAOD = 8;        // Bit switch 1 = Full AOD 2 = Jet AOD , 4 = PartCorr, 8 = JCORRAN 
37 //== general input and output variables
38
39 Int_t       iAODanalysis       = 1;      // Analysis on input AOD's
40 Int_t       iAODhandler        = 1;      // Analysis produces an AOD or dAOD's
41 Int_t       iCentralitySelection  = 0;      // Use the centrality
42 Int_t       iESDfilter         = 0;      // ESD to AOD filter (barrel + muon tracks)
43 Int_t       iPhysicsSelection  = 1;      // ESD to AOD filter (barrel + muon tracks)
44 UInt_t      iPhysicsSelectionFlag = 1; // set by pyshics selection and passed to the task, kMB, kUserDefined etc
45 Bool_t      useTender           = kFALSE; // use tender wagon 
46 Bool_t      kUseKinefilter     = kFALSE; // use Kinematics filter
47 Bool_t      kUseMuonfilter     = kFALSE; // use Kinematics filter
48 TString     kCommonOutputFileName = "PWG4_JetTasksOutput.root";
49 TString     kCaloQAOutputFileName = "PWG4_CaloQAOutput.root";
50
51
52 //== general process variables
53
54 // ### Other flags to steer the analysis
55 //==============================================================================
56 Bool_t      kSkipTerminate      = kTRUE; // Do not call Teminate
57 Bool_t      kUseDate            = kFALSE; // use date in train name
58 Bool_t      kUseDebug           = kTRUE; // activate debugging
59 Int_t         kErrorIgnoreLevel = -1; // takes the errror print level from .rootrc 
60 // From TError.h:
61 // const Int_t kUnset    =  -1;
62 // const Int_t kPrint    =   0;
63 // const Int_t kInfo     =   1000;
64 // const Int_t kWarning  =   2000;
65 // const Int_t kError    =   3000;
66 // const Int_t kBreak    =   4000;
67 // const Int_t kSysError =   5000;
68 // const Int_t kFatal    =   6000; 
69 Int_t         kUseSysInfo         = 0; // activate debugging
70 Long64_t    kNumberOfEvents     = 1234567890; // number of events to process from the chain
71 Bool_t      kUseMC              = kTRUE;  // use MC info
72 Bool_t      kIsMC               = kTRUE;  // is MC info, if false it overwrites Use(AOD)MC
73 Bool_t      kUseAODMC           = kTRUE;  // use MC infA
74 Bool_t      kUseESDTags         = kFALSE; // use ESD tags for selection
75 Bool_t      kUseTR              = kFALSE;  // use track references
76 Bool_t      kUseAODTags         = kFALSE;  // use AOD tags
77 Bool_t      kSaveTrain          = kFALSE;  // save train configuration as: 
78 Bool_t      kIsPbPb             = kFALSE;  // Pb+Pb
79
80
81 // ### Analysis modules to be included. Some may not be yet fully implemented.
82 //==============================================================================
83 Int_t       iJETAN             = 1;      // Jet analysis (PWG4) // 1 write standard 2 write non-standard jets, 3 wrtie both
84 Int_t       iJETSUBTRACT        = 1;      // Jet background subtration
85 TString     kDefaultJetBranch     = "";      // is currently set when filled (iJETAN or clusters) or from config macro 
86 TString     kDefaultJetBackgroundBranch     = "";      // is currently set when filled (jet clsuters  
87 TString     kDefaultJetBackgroundBranch_extra     = "";      // is currently set when filled (jet clsuters  
88 TString     kJetSubtractBranches     = "";      // is currently set when filled (jet clsuters  
89 TString     kJetSubtractBranches_extra     = "";      // is currently set when filled (jet clsuters  
90
91 TString     kDefaultJetBranchMC     = "";      // is currently set when filled (iJETAN or clusters) or from config macro 
92 TString     kDefaultJetBackgroundBranchMC     = "";      // is currently set when filled (jet clsuters  
93 TString     kDefaultJetBranchMC2     = "";      // is currently set when filled (iJETAN or clusters) or from config macro 
94 TString     kDefaultJetBackgroundBranchMC2     = "";      // is currently set when filled (jet clsuters  
95 TString     kJetSubtractMask1 = "B0";
96 TString     kJetSubtractMask2 = "B%d";
97 Int_t       iDIJETAN           = 1;
98 Int_t       iJETANLib          = 1;
99 Int_t       iPWG1QASym         = 0;      // Eva's QA task compiled on the fly...
100 Int_t       iPWG4FastEmbedding = 0;      // Generate non-standard AOD for embedding
101 Int_t       iPWG4JetTasks      = 0;      // all jet tasks flag for lib laoding
102 Int_t       iPWG4JetServices   = 0;      // jet spectrum analysis
103 Int_t       iPWG4JetSpectrum   = 0;      // jet spectrum analysis
104 Int_t       iPWG4JetResponse   = 0;      // jet response matrix
105 Int_t       iPWG4JCORRAN       = 0;      // JCORRAN module
106 Int_t       iPWG4UE            = 0;      // Underlying Event analysis
107 Int_t       iPWG4LeadingUE     = 0;      // Underlying Event analysis
108 Int_t       iPWG4CorrectionsUE = 0;      // Underlying Event analysis
109 Int_t       iPWG4TmpSourceSara = 0;      // Underlying Event analysis not in svn
110 Int_t       iPWG4Fragmentation = 0;      // Official Fragmentation
111 Int_t       iPWG4JetChem       = 0;      // Jet chemistry 
112 Int_t       iPWG4PtQAMC        = 0;      // Marta's QA tasks 
113 Int_t       iPWG4PtSpectra     = 0;      // Marta's QA tasks 
114 Int_t       iPWG4PtQATPC       = 0;      // Marta's QA tasks 
115 Int_t       iPWG4Cosmics     = 0;      // Marta's Cosmics Taks 
116 Int_t       iPWG4ThreeJets     = 0;      // Sona's thrust task
117 Int_t       iPWG4QGSep     = 0;          // Sona's QG Separation task
118 Int_t       iPWG4Minijet       = 0;      // Eva's Mini Jet Task cluster task 
119 Int_t       iPWG4KMeans        = 0;      // Andreas' KMeans task 
120 Int_t       iPWG4Cluster       = 0;      // CKB cluster task 
121 Int_t       iEMCUtilLibs       = 0;      // Flag to satisfy dependence on EMC utils
122 Int_t       iPWG4PartCorrLibs  = 0;      // Gustavo's part corr analysis
123 Int_t       iPWG4PartCorr      = 0;      // Gustavo's part corr analysis
124 Int_t       iPWG4CaloQA        = 0;      // Gustavo's part corr analysis
125 Int_t       iPWG4JetCorr       = 0;     // Paul's jet corr analysis
126 Int_t       iPWG4Tagged        = 0;      // Gustavo's part corr analysis
127 Int_t       iPWG4omega3pi      = 0;      // Omega to 3 pi analysis (PWG4) 
128 Int_t       iPWG4GammaConvLib     = 0;      // Gamma Conversio
129 Int_t       iPWG4GammaConv     = 0;      // Gamma Conversio
130 Int_t       iPWG4CaloConv     = 0;      // Gamma Conversio
131 Int_t       kHighPtFilterMask  = 32;     // change depending on the used AOD Filter
132 TString     kDeltaAODJetName   = "AliAOD.Jets.root";     
133 TString     kDeltaAODJCORRANName   = "AliAOD.JCORRAN.root";     
134 TString     kDeltaAODPartCorrName   = "AliAOD.PartCorr.root";     
135 TString     kFastEmbeddingAOD  = "emb/AliAOD.root";
136 TString     kFastEmbAODList    = "";
137
138 //==============================================================================
139 // ### PROOF Steering varibales
140 //==============================================================================
141 //== proof setup variables
142 TString     kProofCluster      = "alicecaf.cern.ch";
143 Bool_t      kProofUseAFPAR     = kFALSE;  // use AF special par file
144 TString     kProofAFversion          = "AF-v4-17";
145 //== proof input and output variables
146 TString     kProofDataSet      = "/COMMON/COMMON/LHC09a4_run8100X#/esdTree";
147 Bool_t      kProofSaveToAlien   = kFALSE; // save proof outputs in AliEn train_[trainName]_ddMonthyyyy_time.C
148 TString     kProofOutdir       = "";
149 Bool_t      kProofClearPackages = kFALSE;
150 Int_t       kProofEvents = 10000;
151 Int_t       kProofOffset = 0;
152 //== proof process variables
153
154
155 //==============================================================================
156 // ### Grid plugin Steering varibiables
157 //==============================================================================
158 //== grid plugin setup variables
159 Bool_t      kPluginUse         = kTRUE;   // do not change
160 Bool_t      kPluginUseProductionMode  = kFALSE;   // use the plugin in production mode
161 TString     kPluginRootVersion       = "v5-27-06b";  // *CHANGE ME IF MORE RECENT IN GRID*
162 TString     kPluginAliRootVersion    = "v4-19-15-AN";  // *CHANGE ME IF MORE RECENT IN GRID*                                          
163 Bool_t      kPluginMergeViaJDL       = kTRUE;  // merge via JDL
164 Bool_t      kPluginFastReadOption   = kFALSE;  // use xrootd tweaks
165 Bool_t      kPluginOverwriteMode    = kTRUE;  // overwrite existing collections
166 Int_t       kPluginOutputToRunNumber = 1;     // write the output to subdirs named after run number
167 // TString kPluginExecutableCommand = "root -b -q";
168 TString     kPluginExecutableCommand = "source /Users/kleinb/setup_32bit_aliroot_trunk_clean_root_trunk.sh; alienroot -b -q ";
169
170 // == grid plugin input and output variables
171 TString     kGridDatadir      = "/alice/sim/PDC_08b/LHC09a1/AOD/";
172 Int_t         kGridMaxRunsFromList = 999999999;
173 Int_t         kGridOffsetRunFromList = 0; // skip the first n runs from the list
174 TString     kGridLocalRunList = "";
175 TString     kGridOutdir       = ""; // AliEn output directory. If blank will become output_<kTrainName>
176 TString     kGridDataSet      = ""; // sub working directory not to confuse different run xmls 
177 Int_t         kGridRunRange[2]       =  {0, -1}; // Set the run range
178 TString     kGridRunPattern        = "%03d"; // important for leading zeroes!!
179 TString     kGridPassPattern       = "";
180 TString     kGridExtraFiles        = ""; // files that will be added to the input list in the JDL...
181 Int_t         kGridMaxMergeFiles      = 25; // Number of files merged in a chunk grid run range
182 TString     kGridMergeExclude       = "AliAOD.root"; // Files that should not be merged
183 TString     kGridOutputStorages      = "disk=2"; // Make replicas on the storages
184 // == grid process variables
185 Int_t       kGridRunsPerMaster     = 100; // Number of runs per master job
186 Int_t       kGridFilesPerJob       = 100; // Maximum number of files per job (gives size of AOD)
187
188 //==============================================================================
189 // ### Local Steering variables
190 //==============================================================================
191 //== local setup variables
192 //== local input and output variables
193 TString     kLocalXMLDataset   = ""; // Change local xml dataset for local interactive analysis
194 TString     kLocalDataList   = "local_deltaaod.txt"; // Change local xml dataset for local interactive analysis
195 // == local process variables
196
197 TString kPluginMode = "";
198 TString kAnalysisMode = "";
199
200
201 // Temporaries.
202 TString anaPars = "";
203 TString anaLibs = "";
204 TString anaLibsExtra = "";
205 TString anaSources = "";
206 // Function signatures
207 class AliAnalysisAlien;
208
209 //______________________________________________________________________________
210 void AnalysisTrainPWG4Jets(const char *analysis_mode="local", 
211                            const char *plugin_mode="",
212                            const char *config_file="",Int_t iOffset = 0,Int_t iTotal = 0)
213 {
214 // Main analysis train macro. If a configuration file is provided, all parameters
215 // are taken from there but may be altered by CheckModuleFlags.
216
217   // these flag may be needed by the config file
218   kPluginMode   = plugin_mode;
219   kAnalysisMode = analysis_mode;
220   
221   if (strlen(config_file) && !LoadConfig(config_file)) return;
222   if(iTotal>0)kGridMaxRunsFromList = iTotal; // overwrites the settings from config file
223   if(iOffset)kGridOffsetRunFromList = iOffset;
224   if(iOffset)kProofOffset = iOffset;
225
226
227    TString smode(analysis_mode);
228    smode.ToUpper();
229    if (kSaveTrain)WriteConfig();
230    // Check compatibility of selected modules 
231    CheckModuleFlags(smode);
232    //     gROOT->ProcessLine(".trace");
233
234    printf("==================================================================\n");
235    printf("===========    RUNNING ANALYSIS TRAIN %s IN %s MODE   ==========\n", kTrainName.Data(),smode.Data());
236    printf("==================================================================\n");
237                               printf("=  Configuring analysis train for:                               =\n");
238    if (iAODanalysis) printf("=  AOD analysis                                                  =\n");
239    else                     printf("=  ESD analysis                                                  =\n");
240    if (iPhysicsSelection)   printf("=  Physics selection                                                =\n");
241    if(iCentralitySelection)printf("=  Centrality selection                                                =\n");
242    if (useTender)   printf("=  Using tender                                                =\n");
243    if (iESDfilter)   printf("=  ESD filter                                                    =\n");
244    if (iJETAN)       printf("=  Jet analysis                                                  =\n");
245    printf("==================================================================\n");
246
247    char *printMask = ":: %20s  %10d\n";
248    printf(printMask,"Fill AOD",(UInt_t)kFillAOD);
249    printf(printMask,"Save AOD", (UInt_t)kSaveAOD);
250    printf(printMask,"MC truth", (UInt_t)kUseMC);
251    printf(printMask,"KINE filter", (UInt_t)kUseKinefilter);
252    printf(printMask,"track refs", (UInt_t)kUseTR);
253    printf(printMask,"tags", (UInt_t)kUseESDTags);
254    printf(printMask,"AOD tags", (UInt_t)kUseAODTags);
255    printf(printMask,"debugging", (UInt_t)kUseDebug);
256    printf(printMask,"PAR files", (UInt_t)kUsePAR);
257    printf(printMask,"AliEn plugin", (UInt_t)kPluginUse);
258    printf(printMask,"JETAN subtract", (UInt_t)iJETSUBTRACT);
259    printf(printMask,"PWG1 QA sym", iPWG1QASym);
260    printf(printMask,"PWG4 Source Sara",iPWG4TmpSourceSara);
261    printf(printMask,"PWG4 Fragmentation",iPWG4Fragmentation);
262    printf(printMask,"PWG4 Jet Chem",iPWG4JetChem);
263    printf(printMask,"PWG4 Jet tasks",iPWG4JetTasks);
264    printf(printMask,"PWG4 Jet Services",iPWG4JetServices);     
265    printf(printMask,"PWG4 Jet Spectrum",iPWG4JetSpectrum);
266    printf(printMask,"PWG4 JCORRAN",iPWG4JCORRAN);
267    printf(printMask,"PWG4 UE",iPWG4UE); 
268    printf(printMask,"PWG4 Leading UE",iPWG4LeadingUE); 
269    printf(printMask,"PWG4 Corrections UE",iPWG4CorrectionsUE); 
270    printf(printMask,"PWG4 Pt QA MC",iPWG4PtQAMC);
271    printf(printMask,"PWG4 Pt Spectra",iPWG4PtSpectra);
272    printf(printMask,"PWG4 Pt QA TPC",iPWG4PtQATPC);     
273    printf(printMask,"PWG4 Cosmics",iPWG4Cosmics);     
274    printf(printMask,"PWG4 Three Jets",iPWG4ThreeJets);
275    printf(printMask,"PWG4 QGSep",iPWG4QGSep);
276    printf(printMask,"PWG4 Minijet",iPWG4Minijet);
277    printf(printMask,"PWG4 KMeans",iPWG4KMeans);
278    printf(printMask,"PWG4 Cluster",iPWG4Cluster);
279    printf(printMask,"PWG4 Part Corr",iPWG4PartCorr);
280    printf(printMask,"PWG4 Calo QA",iPWG4CaloQA);
281    printf(printMask,"PWG4 Jet Corr",iPWG4JetCorr);
282    printf(printMask,"PWG4 JCORRAN",iPWG4JCORRAN);
283    printf(printMask,"PWG4 Tagged",iPWG4Tagged);
284    printf(printMask,"PWG4 omega to 3 pi ",iPWG4omega3pi);
285    printf(printMask,"PWG4 Gamma Conv",iPWG4GammaConv);
286    printf(printMask,"PWG4 Calo Conv",iPWG4CaloConv);
287    printf(printMask,"HighPt FilterMask",kHighPtFilterMask);    
288    
289    //==========================================================================
290    // Connect to back-end system
291    if (!Connect(smode)) {
292       ::Error("AnalysisTrain", "Could not connect to %s back-end", analysis_mode);
293       return;
294    }   
295
296    // Load common libraries and set include path
297    if (!LoadCommonLibraries(smode)) {
298       ::Error("AnalysisTrain", "Could not load common libraries");
299       return;
300    }
301
302
303     
304    // Make the analysis manager and connect event handlers
305    AliAnalysisManager *mgr  = new AliAnalysisManager("PWG4Train", "pwg4 mini train");
306    if (kCommonOutputFileName.Length()>0)mgr->SetCommonFileName(kCommonOutputFileName.Data());
307    if (kProofSaveToAlien) mgr->SetSpecialOutputLocation(kProofOutdir);
308    mgr->SetNSysInfo(0);
309    if (!strcmp(plugin_mode, "test")) mgr->SetNSysInfo(1);
310    if (kUseSysInfo)mgr->SetNSysInfo(kUseSysInfo);
311    mgr->SetSkipTerminate(kSkipTerminate);
312
313    // Load analysis specific libraries
314    if (!LoadAnalysisLibraries(smode)) {
315       ::Error("AnalysisTrain", "Could not load analysis libraries");
316      return;
317    }   
318
319    // Create input handler (input container created automatically)
320    if (iAODanalysis) {
321    // AOD input handler
322       AliAODInputHandler *aodH = new AliAODInputHandler();
323       mgr->SetInputEventHandler(aodH);
324       //      if (iPWG4JetTasks) aodH->AddFriend(Form("deltas/%s",kDeltaAODJetName.Data()));
325       //      if (iPWG4PartCorr) aodH->AddFriend(Form("deltas/%s"kDeltaAODJetName.Data()));
326    } else {   
327    // ESD input handler
328       AliESDInputHandler *esdHandler = new AliESDInputHandler();
329       if (kUseESDTags) esdHandler->SetReadTags();
330       esdHandler->SetReadFriends(kFALSE);
331       mgr->SetInputEventHandler(esdHandler);       
332       //      if(iPWG4PtQATPC&& !kTrainName.Contains("pass5"))esdHandler->SetActiveBranches("ESDfriend");
333
334    }
335
336    // Monte Carlo handler
337    if (kUseMC && !iAODanalysis) {
338       AliMCEventHandler* mcHandler = new AliMCEventHandler();
339       mgr->SetMCtruthEventHandler(mcHandler);
340       mcHandler->SetReadTR(kUseTR); 
341    }   
342    // AOD output container, created automatically when setting an AOD handler
343    if (iAODhandler) {
344       // AOD output handler
345       AliAODHandler* aodHandler   = new AliAODHandler();
346       aodHandler->SetOutputFileName("AliAOD.root");
347       aodHandler->SetFillAODforRun(kFillAOD);
348       //
349       mgr->SetOutputEventHandler(aodHandler);
350       AliAnalysisDataContainer * cout_aod = mgr->GetCommonOutputContainer();
351       cout_aod->SetSpecialOutput();
352    }
353    // Debugging if needed
354
355    if (kUseDebug){
356      mgr->SetDebugLevel(3);
357    }
358    if(kUseSysInfo>0){
359      mgr->RegisterExtraFile("syswatch.root");
360      if(kGridMergeExclude.Length())kGridMergeExclude += " ";
361      kGridMergeExclude += "syswatch.root";
362    }
363    else{
364      AliLog::SetGlobalLogLevel(AliLog::kError);
365    }
366
367
368    //==========================================================================
369    // Create the chain. In this example it is created only from ALIEN files but
370    // can be done to work in batch or grid mode as well.
371    TChain *chain = CreateChain(smode, plugin_mode);
372         
373    //==========================================================================
374    // Load the tasks configuration macros for all wagons. These files are supposed now to be
375    // in the current workdir, but in AliEn they will be in the file catalog, 
376    // mapped from AliRoot and pecified in the jdl input list.
377     
378    // For now connection to top input container and common AOD output container
379    // is done in this macro, but in future these containers will be connected
380    // from each task configuration macro.
381    
382    //                                                                                                                              
383    // Tender and supplies. Needs to be called for every event.                                                                     
384    //                                                                                                                              
385
386    if (useTender) {
387       gROOT->LoadMacro("$ALICE_ROOT_SRC/ANALYSIS/TenderSupplies/AddTaskTender.C");
388       AliAnalysisTaskSE *tender = AddTaskTender(kTRUE);
389       //      tender->SelectCollisionCandidates();                                                                                      
390       tender->SetDebugLevel(2);
391    }
392
393
394
395    if(iPhysicsSelection && !iAODanalysis){
396      gROOT->LoadMacro("$ALICE_ROOT_SRC/ANALYSIS/macros/AddTaskPhysicsSelection.C");
397      Int_t iTriggerHIC = 0;
398      Bool_t rejectBkg = true;
399      if(kIsPbPb){
400        iTriggerHIC = 2;
401        rejectBkg = false; // for the moment...
402      }
403      AliPhysicsSelectionTask* physSelTask = AddTaskPhysicsSelection(kIsMC,rejectBkg);  
404      iPhysicsSelectionFlag = AliVEvent::kMB;
405      mgr->RegisterExtraFile("EventStat_temp.root");
406      mgr->AddStatisticsTask();
407    }
408
409    if(iCentralitySelection){
410
411      // has to run before AOD filter
412      gROOT->LoadMacro("$ALICE_ROOT_SRC/ANALYSIS/macros/AddTaskCentrality.C");
413      //     const char* file1="$ALICE_ROOT/ANALYSIS/macros/AliCentralityBy1D_137161.root";
414      //     const char* file2="$ALICE_ROOT/ANALYSIS/macros/AliCentralityByFunction_137161.root";
415      AliCentralitySelectionTask *taskC = AddTaskCentrality();
416       if (!taskC) ::Warning("AnalysisTrainPWG4Jets", "AliCentralitySelectionTask cannot run for this train conditions - EXCLUDED");
417    }
418
419    if (iESDfilter && !iAODanalysis) {
420       //  ESD filter task configuration.
421       gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskESDFilterPWG4Train.C");
422       AliAnalysisTaskESDfilter *taskesdfilter = AddTaskESDFilter(kUseKinefilter,kUseMuonfilter);
423       taskesdfilter->SetEnableFillAOD(!kFilterAOD);
424
425       if(kIsMC){
426         mgr->RegisterExtraFile("pyxsec_hists.root");
427         if(kGridMergeExclude.Length())kGridMergeExclude += " ";
428         kGridMergeExclude += "pyxsec_hists.root";
429
430       }
431    }   
432
433    // AOD tags
434    if (kUseAODTags) {
435       AliAnalysisTaskTagCreator* tagTask = new AliAnalysisTaskTagCreator("AOD Tag Creator");
436       mgr->AddTask(tagTask);
437       AliAnalysisDataContainer *coutTags = mgr->CreateContainer("cTag",  TTree::Class(), 
438                                            AliAnalysisManager::kOutputContainer, "AOD.tag.root");
439       mgr->ConnectInput (tagTask, 0, mgr->GetCommonInputContainer());
440       mgr->ConnectOutput(tagTask, 1, coutTags);
441    }   
442
443    if (iPWG4FastEmbedding) {
444      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskFastEmbedding.C");
445      AliAnalysisTaskFastEmbedding *taskEmbedding = 0;
446      if(kFastEmbAODList.Length()) taskEmbedding = AddTaskFastEmbedding(kFastEmbAODList, 1);
447      else                         taskEmbedding = AddTaskFastEmbedding(kFastEmbeddingAOD, 0);
448      taskEmbedding->SetJetBranch("jetsAOD_UA104_B0_Filter00256_Cut01000");
449      // taskEmbedding->SetEvtSelecMode(AliAnalysisTaskFastEmbedding::kEventsAll);
450      // taskEmbedding->SetDebugLevel(10);
451    }
452
453     // Jet analysis
454    if (iJETAN) {
455       gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskJets.C");
456       AliAnalysisTaskJets *taskjets = 0;
457       if(iJETAN&1){
458         /*
459         taskjets = AddTaskJets(kHighPtFilterMask); 
460         taskjets->SetName("StandardJets");
461         taskjets->SetNonStdBranch("");
462         */
463       }
464       if(iJETAN&2){
465         // Set only few jet finders  backgroudn subtraction w an wo 
466         
467         taskjets = AddTaskJets("AOD","UA1",0.4,kHighPtFilterMask,1.,0); // no background subtraction
468         if(kDeltaAODJetName.Length()>0)taskjets->SetNonStdOutputFile(kDeltaAODJetName.Data());
469
470         // STANDARD UA jet finders pT cut 1 GeV background mode 2 R = 0.4
471         if(kIsPbPb){
472           taskjets = AddTaskJets("AOD","UA1",0.4,kHighPtFilterMask,1.,2); // background subtraction
473           if(kDeltaAODJetName.Length()>0)taskjets->SetNonStdOutputFile(kDeltaAODJetName.Data());
474         }
475
476         TString cTmp("");
477
478         // SICONE 
479         taskjets = AddTaskJets("AOD","SISCONE",0.4,kHighPtFilterMask,0.15,0); //no background subtraction to be done later....
480         if(kDeltaAODJetName.Length()>0)taskjets->SetNonStdOutputFile(kDeltaAODJetName.Data());
481         cTmp = taskjets->GetNonStdBranch();
482         if(cTmp.Length()>0)kJetSubtractBranches += Form("%s ",cTmp.Data());
483
484         if(kUseAODMC){
485           // STANDARD UA jet finders pT cut 1 GeV background mode 2 R = 0.4
486           if(kIsPbPb){
487             taskjets = AddTaskJets("AODMC","UA1",0.4,kHighPtFilterMask,1.,2); // background subtraction
488             taskjets = AddTaskJets("AODMC2","UA1",0.4,kHighPtFilterMask,1.,2); // background subtraction
489           }
490           else{
491             taskjets = AddTaskJets("AODMC","UA1",0.4,kHighPtFilterMask,1.,0); // no background subtraction
492             taskjets = AddTaskJets("AODMC2","UA1",0.4,kHighPtFilterMask,1.,0); // no background subtraction
493           }
494         }
495         if(kDeltaAODJetName.Length()>0)mgr->RegisterExtraFile(kDeltaAODJetName.Data()); 
496       }
497       if (!taskjets) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJets cannot run for this train conditions - EXCLUDED");
498    }
499
500
501    if (iPWG4FastEmbedding && iJETAN) {
502      AliAnalysisTaskJets *taskEmbJets = AddTaskJets("AODextra", "FASTJET", 0.4, kHighPtFilterMask);
503      taskEmbJets->ReadAODFromOutput();
504      kJetSubtractBranches_extra += Form("%s ", taskEmbJets->GetNonStdBranch());
505
506      taskEmbJets = AddTaskJets("AODextraonly", "FASTJET", 0.4, kHighPtFilterMask);
507      taskEmbJets->ReadAODFromOutput();
508     
509      taskEmbJets = AddTaskJets("AODextra", "UA1", 0.4, kHighPtFilterMask,1.,0);
510      taskEmbJets->ReadAODFromOutput();
511      taskEmbJets = AddTaskJets("AODextraonly", "UA1", 0.4, kHighPtFilterMask,1.,0);
512      taskEmbJets->ReadAODFromOutput();
513      taskEmbJets = AddTaskJets("AODextra", "UA1", 0.4, kHighPtFilterMask,1.,2);
514      taskEmbJets->ReadAODFromOutput();
515    }
516
517    if(iPWG4Cluster){
518      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskJetCluster.C");
519      AliAnalysisTaskJetCluster *taskCl = 0;
520      Float_t fCenUp = 0;
521      Float_t fCenLo = 0;
522      if(kIsPbPb&&!kIsMC){
523        fCenLo = 0;
524        fCenUp = 80;
525      }
526      if(iPWG4Cluster&1){
527
528        if(kIsPbPb){
529          taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.4,0,1, kDeltaAODJetName.Data(),0.15); // this one is for the background and random jets
530          taskCl->SetBackgroundCalc(kTRUE);
531          taskCl->SetCentralityCut(fCenLo,fCenUp);
532          taskCl->SetGhostEtamax(0.9);
533          kDefaultJetBackgroundBranch = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskCl->GetJetOutputBranch());
534          
535          if (iPWG4FastEmbedding) {
536            AliAnalysisTaskJetCluster *taskClEmb = 0;
537            taskClEmb = AddTaskJetCluster("AODextra","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.4,0,1, kDeltaAODJetName.Data(),0.15); // this one is for the background and random jets
538            taskClEmb->SetBackgroundCalc(kTRUE);
539            taskClEmb->SetCentralityCut(fCenLo,fCenUp);
540            taskClEmb->SetGhostEtamax(0.9);
541            kDefaultJetBackgroundBranch_extra = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskClEmb->GetJetOutputBranch());
542
543            taskClEmb = AddTaskJetCluster("AODextraonly","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.4,0,1, kDeltaAODJetName.Data(),0.15); // this one is for the background and random jets
544            taskClEmb->SetBackgroundCalc(kFALSE);
545            taskClEmb->SetCentralityCut(fCenLo,fCenUp);
546            taskClEmb->SetGhostEtamax(0.9);
547
548            taskClEmb = AddTaskJetCluster("AODextra","",kHighPtFilterMask,iPhysicsSelectionFlag,"ANTIKT",0.4,0,1,kDeltaAODJetName.Data(),0.15);
549            taskClEmb->SetCentralityCut(fCenLo,fCenUp);
550            taskClEmb->SetBackgroundBranch(kDefaultJetBackgroundBranch_extra.Data());
551            kJetSubtractBranches_extra += Form("%s ",taskClEmb->GetJetOutputBranch());
552
553            taskClEmb = AddTaskJetCluster("AODextraonly","",kHighPtFilterMask,iPhysicsSelectionFlag,"ANTIKT",0.4,0,1,kDeltaAODJetName.Data(),0.15);
554            taskClEmb->SetCentralityCut(fCenLo,fCenUp);
555          }
556
557          taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.2,0,1, kDeltaAODJetName.Data(),0.15); // this one is for the background and random jets
558          taskCl->SetBackgroundCalc(kTRUE);
559          taskCl->SetCentralityCut(fCenLo,fCenUp);
560          taskCl->SetGhostEtamax(0.9);
561        }
562        else{
563          taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.6,0,1,kDeltaAODJetName.Data(),0.15); // this one is for the background jets
564          taskCl->SetBackgroundCalc(kTRUE);
565          kDefaultJetBackgroundBranch = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskCl->GetJetOutputBranch());
566          taskCl->SetGhostEtamax(0.9);
567
568          taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.4,0,1,kDeltaAODJetName.Data(),0.15); 
569          taskCl->SetBackgroundCalc(kTRUE);
570          taskCl->SetGhostEtamax(0.9);
571        } 
572
573        taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"ANTIKT",0.4,0,1,kDeltaAODJetName.Data(),0.15);
574        taskCl->SetCentralityCut(fCenLo,fCenUp);
575        if(kIsPbPb)taskCl->SetBackgroundBranch(kDefaultJetBackgroundBranch.Data());
576        taskCl->SetNRandomCones(10);
577        taskCl->SetNSkipLeadingRan(2);
578        kDefaultJetBranch = taskCl->GetJetOutputBranch();
579        if(kDeltaAODJetName.Length()==0&&kFilterAOD){
580          if(kIsPbPb)taskCl->SetJetTriggerPtCut(40.);
581          else taskCl->SetJetTriggerPtCut(20.);
582        }
583
584        kJetSubtractBranches += Form("%s ",taskCl->GetJetOutputBranch());
585   
586        taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"ANTIKT",0.2,0,1,kDeltaAODJetName.Data(),0.15);
587        taskCl->SetCentralityCut(fCenLo,fCenUp);
588        if(kIsPbPb)taskCl->SetBackgroundBranch(kDefaultJetBackgroundBranch.Data());
589        kJetSubtractBranches += Form("%s ",taskCl->GetJetOutputBranch());
590
591        if(kUseAODMC){
592          if(kIsPbPb){
593            taskCl = AddTaskJetCluster("AODMC","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.4,0,1, kDeltaAODJetName.Data(),0.15); // this one is for the background and random jets
594            taskCl->SetBackgroundCalc(kTRUE);
595            taskCl->SetGhostEtamax(0.9);
596            kDefaultJetBackgroundBranchMC = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskCl->GetJetOutputBranch());
597            
598            taskCl = AddTaskJetCluster("AODMC2","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.4,0,1, kDeltaAODJetName.Data(),0.15); // this one is for the background and random jets
599            taskCl->SetBackgroundCalc(kTRUE);
600            taskCl->SetGhostEtamax(0.9);
601            kDefaultJetBackgroundBranchMC2 = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskCl->GetJetOutputBranch()); 
602          }
603          else{
604            taskCl = AddTaskJetCluster("AODMC","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.6,0,1, kDeltaAODJetName.Data(),0.15); // this one is for the background and random jets
605            taskCl->SetBackgroundCalc(kTRUE);
606            taskCl->SetGhostEtamax(0.9);
607            kDefaultJetBackgroundBranchMC = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskCl->GetJetOutputBranch());
608            
609            taskCl = AddTaskJetCluster("AODMC2","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.6,0,1, kDeltaAODJetName.Data(),0.15); // this one is for the background and random jets
610            taskCl->SetBackgroundCalc(kTRUE);
611            taskCl->SetGhostEtamax(0.9);
612            kDefaultJetBackgroundBranchMC2 = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskCl->GetJetOutputBranch()); 
613            // pp background calcs...
614          }
615          
616          taskCl = AddTaskJetCluster("AODMC","",kHighPtFilterMask,iPhysicsSelectionFlag,"ANTIKT",0.4,0,1, kDeltaAODJetName.Data(),0.15); // this one is for the background and random jets
617          taskCl->SetGhostEtamax(0.9);
618          if(kIsPbPb)taskCl->SetBackgroundBranch(kDefaultJetBackgroundBranchMC.Data());   
619          kDefaultJetBranchMC = taskCl->GetJetOutputBranch();
620
621          taskCl = AddTaskJetCluster("AODMC2","",kHighPtFilterMask,iPhysicsSelectionFlag,"ANTIKT",0.4,0,1, kDeltaAODJetName.Data(),0.15); // this one is for the background and random jets
622          if(kIsPbPb)taskCl->SetBackgroundBranch(kDefaultJetBackgroundBranchMC2.Data());  
623          kDefaultJetBranchMC2 = taskCl->GetJetOutputBranch();
624
625        }
626        
627        
628        if (!taskCl) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskCluster cannot run for this train conditions - EXCLUDED");
629      }
630    }
631
632    if(iJETSUBTRACT){
633       gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskJetBackgroundSubtract.C");
634       AliAnalysisTaskJetBackgroundSubtract *taskSubtract = 0;
635       if(kJetSubtractBranches.Length()){
636
637         taskSubtract = AddTaskJetBackgroundSubtract(kJetSubtractBranches,3,kJetSubtractMask1.Data(),kJetSubtractMask2.Data());
638         taskSubtract->SetBackgroundBranch(kDefaultJetBackgroundBranch.Data()); 
639         if(kDeltaAODJetName.Length()>0)taskSubtract->SetNonStdOutputFile(kDeltaAODJetName.Data());
640
641         taskSubtract = AddTaskJetBackgroundSubtract(kJetSubtractBranches,2,kJetSubtractMask1.Data(),kJetSubtractMask2.Data());
642         taskSubtract->SetBackgroundBranch(kDefaultJetBackgroundBranch.Data());          taskSubtract->SelectCollisionCandidates(iPhysicsSelectionFlag);
643         if(kDeltaAODJetName.Length()>0)taskSubtract->SetNonStdOutputFile(kDeltaAODJetName.Data());
644
645         //      taskSubtract->SetDebugLevel(3);
646
647         taskSubtract = AddTaskJetBackgroundSubtract(kJetSubtractBranches,1,kJetSubtractMask1.Data(),kJetSubtractMask2.Data());
648         taskSubtract->SetBackgroundBranch(kDefaultJetBackgroundBranch.Data());          taskSubtract->SelectCollisionCandidates(iPhysicsSelectionFlag);
649         if(kDeltaAODJetName.Length()>0)taskSubtract->SetNonStdOutputFile(kDeltaAODJetName.Data());
650
651         if(kJetSubtractBranches.Contains(kDefaultJetBranch.Data())&&kIsPbPb){
652           kDefaultJetBranch.ReplaceAll(taskSubtract->GetToReplace(),Form(taskSubtract->GetReplacementMask(),taskSubtract->GetSubtractionMethod()));
653         }
654       }
655       if(kJetSubtractBranches_extra.Length()){
656         taskSubtract = AddTaskJetBackgroundSubtract(kJetSubtractBranches_extra,1,kJetSubtractMask1.Data(),kJetSubtractMask2.Data(),"extra");
657         taskSubtract->SetBackgroundBranch(kDefaultJetBackgroundBranch_extra.Data());
658         taskSubtract->SelectCollisionCandidates(iPhysicsSelectionFlag);
659         //taskSubtract->SetDebugLevel(3);
660         if(kDeltaAODJetName.Length()>0)taskSubtract->SetNonStdOutputFile(kDeltaAODJetName.Data());
661         if(kJetSubtractBranches_extra.Contains(kDefaultJetBranch.Data())){
662           kDefaultJetBranch.ReplaceAll(taskSubtract->GetToReplace(),Form(taskSubtract->GetReplacementMask(),taskSubtract->GetSubtractionMethod()));
663         }
664       }
665       if (!taskSubtract) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJetBackgroundSubtrac cannot run for this train conditions - EXCLUDED");     
666    }
667
668    if (iDIJETAN) {
669       gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskDiJets.C");
670       AliAnalysisTaskDiJets *taskdijets = 0;
671       if(iDIJETAN&1)taskdijets = AddTaskDiJets(); 
672       if (!taskdijets) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJets cannot run for this train conditions - EXCLUDED");
673       if(iDIJETAN&2){
674         taskdijets = AddTaskDiJets("jetsAOD_CDF07"); 
675         taskdijets = AddTaskDiJets("jetsAOD_DA07"); 
676         taskdijets = AddTaskDiJets("jetsAOD_FASTJET07"); 
677         taskdijets = AddTaskDiJets("jetsAOD_FASTKT07"); 
678         taskdijets = AddTaskDiJets("jetsAOD_SISCONE07"); 
679         taskdijets = AddTaskDiJets("jetsAOD_UA107");
680       }
681    }
682
683    if(iPWG1QASym){
684      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG1/PilotTrain/AddTaskQAsym.C");
685      AliAnalysisTaskQASym *taskQASym = AddTaskQAsym(-1);
686      if (!taskQASym) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskQASym cannot run for this train conditions - EXCLUDED");
687    }
688
689
690
691    if(iPWG4TmpSourceSara){
692      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskEta.C");
693      AliAnalysisTaskEta *taskEta = AddTaskEta();
694      if (!taskEta) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskEta cannot run for this train conditions - EXCLUDED");
695    }
696
697
698    if(iPWG4JetServices){
699      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskJetServices.C");
700      AliAnalysisTaskJetServices *taskjetServ = 0;
701      taskjetServ = AddTaskJetServices();
702      if (!taskjetServ) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJetServices cannot run for this train conditions - EXCLUDED");
703      if(kGridRunRange[0]>0)taskjetServ->SetRunRange(kGridRunRange[0],kGridRunRange[1]);
704      else taskjetServ->SetRunRange(110000,160000);
705      taskjetServ->SetMCData(kIsMC);
706      taskjetServ->SetUsePhysicsSelection((Bool_t)iPhysicsSelection);
707      taskjetServ->SetPhysicsSelectionFlag(iPhysicsSelectionFlag); // 
708      taskjetServ->SetNonStdFile(kDeltaAODJetName.Data());
709      if(kIsPbPb){
710        if(kDeltaAODJetName.Length()>0&&kFilterAOD)taskjetServ->SetFilterAODCollisions(kTRUE);
711        //       else if(iAODanalysis)taskjetServ->SetFilterAODCollisions(kTRUE);
712
713        taskjetServ->SetZVertexCut(8.);
714      }
715      if(iAODanalysis){
716        //       taskjetServ->SetDebugLevel(3);
717        taskjetServ->SetAODInput(kTRUE);
718      }
719    }
720
721    if(iPWG4JetSpectrum){
722      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskJetSpectrum2.C");
723      AliAnalysisTaskJetSpectrum2 *taskjetSpectrum = 0;
724      if(iPWG4JetSpectrum&1){
725        if(kIsPbPb){
726          for(int i = 0;i<5;i++){
727            TString tmp(kDefaultJetBranch.Data());
728            //      tmp.ReplaceAll(Form(kJetSubtractMask2.Data(),1),kJetSubtractMask1.Data());
729            //      tmp.ReplaceAll(Form(kJetSubtractMask2.Data(),1),kJetSubtractMask1.Data());
730            tmp.ReplaceAll(Form(kJetSubtractMask2.Data(),1),Form(kJetSubtractMask1.Data(),0));
731            taskjetSpectrum = AddTaskJetSpectrum2(kDefaultJetBranch.Data(),tmp.Data(),"",kHighPtFilterMask,AliVEvent::kMB,0,kFALSE,0,i);
732            //      taskjetSpectrum->SetDebugLevel(3);
733            //      taskjetSpectrum->SetMinJetPt(10);
734            taskjetSpectrum->SetTrackEtaWindow(0.8);
735            taskjetSpectrum->SetJetEtaWindow(0.4);
736            if(iAODanalysis)SetAODInput(taskjetSpectrum);
737
738            
739            // check the old subtracted vs. the new subtracted
740            TString tmp2(kDefaultJetBranch.Data());
741            tmp2.ReplaceAll(Form(kJetSubtractMask2.Data(),1),Form(kJetSubtractMask2.Data(),2));
742            taskjetSpectrum = AddTaskJetSpectrum2(tmp2.Data(),kDefaultJetBranch.Data(),"",kHighPtFilterMask,AliVEvent::kMB,0,kFALSE,0,i);
743            //      taskjetSpectrum->SetDebugLevel(3);
744            //      taskjetSpectrum->SetMinJetPt(10);
745            taskjetSpectrum->SetTrackEtaWindow(0.8);
746            taskjetSpectrum->SetJetEtaWindow(0.4);
747            if(iAODanalysis)SetAODInput(taskjetSpectrum);
748
749            // check the old subtracted vs. the new subtracted
750            TString tmp3(kDefaultJetBranch.Data());
751            tmp3.ReplaceAll(Form(kJetSubtractMask2.Data(),1),Form(kJetSubtractMask2.Data(),3));
752
753            taskjetSpectrum = AddTaskJetSpectrum2(tmp3.Data(),kDefaultJetBranch.Data(),"",kHighPtFilterMask,AliVEvent::kMB,0,kFALSE,0,i);
754            //      taskjetSpectrum->SetDebugLevel(3);
755            //      taskjetSpectrum->SetMinJetPt(10);
756            taskjetSpectrum->SetTrackEtaWindow(0.8);
757            taskjetSpectrum->SetJetEtaWindow(0.4);
758            if(iAODanalysis)SetAODInput(taskjetSpectrum);
759
760
761            taskjetSpectrum = AddTaskJetSpectrum2(Form("jetsAOD_UA104_B2_Filter%05d_Cut01000",kHighPtFilterMask),kDefaultJetBranch.Data(),"",kHighPtFilterMask,AliVEvent::kMB,0,kFALSE,0,i);
762            //      taskjetSpectrum->SetDebugLevel(3);
763            //      taskjetSpectrum->SetMinJetPt(10);
764            taskjetSpectrum->SetTrackEtaWindow(0.8);
765            taskjetSpectrum->SetJetEtaWindow(0.4);
766            if(iAODanalysis)SetAODInput(taskjetSpectrum);
767
768          }
769        }
770        else{ // ! PbPb
771          Int_t i = 0;
772          TString tmp(kDefaultJetBranch.Data());
773          //        tmp.ReplaceAll(Form(kJetSubtractMask2.Data(),1),kJetSubtractMask1.Data());
774          //        tmp.ReplaceAll(Form(kJetSubtractMask2.Data(),1),kJetSubtractMask1.Data());
775          tmp.ReplaceAll(Form(kJetSubtractMask2.Data(),0),Form(kJetSubtractMask1.Data(),1));
776          taskjetSpectrum = AddTaskJetSpectrum2(kDefaultJetBranch.Data(),tmp.Data(),"",kHighPtFilterMask,AliVEvent::kMB,0,kFALSE,0,i);
777          taskjetSpectrum->SetDebugLevel(3);
778          //        taskjetSpectrum->SetMinJetPt(10);
779          taskjetSpectrum->SetTrackEtaWindow(0.8);
780          taskjetSpectrum->SetJetEtaWindow(0.4);
781          if(iAODanalysis)SetAODInput(taskjetSpectrum);
782          
783
784          TString tmp2(kDefaultJetBranch.Data());
785          tmp2.ReplaceAll(Form(kJetSubtractMask2.Data(),0),Form(kJetSubtractMask2.Data(),2));
786          taskjetSpectrum = AddTaskJetSpectrum2(tmp2.Data(),kDefaultJetBranch.Data(),"",kHighPtFilterMask,AliVEvent::kMB,0,kFALSE,0,i);
787          //      taskjetSpectrum->SetDebugLevel(3);
788          //        taskjetSpectrum->SetMinJetPt(10);
789          taskjetSpectrum->SetTrackEtaWindow(0.8);
790          taskjetSpectrum->SetJetEtaWindow(0.4);
791
792          // check the old subtracted vs. the new subtracted
793          TString tmp3(kDefaultJetBranch.Data());
794          tmp3.ReplaceAll(Form(kJetSubtractMask2.Data(),0),Form(kJetSubtractMask2.Data(),3));
795          taskjetSpectrum = AddTaskJetSpectrum2(tmp3.Data(),kDefaultJetBranch.Data(),"",kHighPtFilterMask,AliVEvent::kMB,0,kFALSE,0,i);
796          //      taskjetSpectrum->SetDebugLevel(3);
797          //        taskjetSpectrum->SetMinJetPt(10);
798          taskjetSpectrum->SetTrackEtaWindow(0.8);
799          taskjetSpectrum->SetJetEtaWindow(0.4);
800          if(iAODanalysis)SetAODInput(taskjetSpectrum);
801        }
802        if (!taskjetSpectrum) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJetSpectrum2 cannot run for this train conditions - EXCLUDED");
803      }
804    }
805
806    if(iPWG4Fragmentation){
807      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskFragmentationFunction.C");
808        AliAnalysisTaskFragmentationFunction *taskFrag = 0;
809      if(kUseAODMC){
810
811      }
812      else{
813        taskFrag = AddTaskFragmentationFunction(kDefaultJetBranch.Data(),"","","",kHighPtFilterMask);
814      }
815      if (!taskFrag) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskFragmentationFunction cannot run for this train conditions - EXCLUDED");
816    }
817
818    if(iPWG4JetChem){
819      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskJetChem.C");
820      AliAnalysisTask *taskChem = AddTaskJetChem(kHighPtFilterMask);
821      if (!taskChem) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJetChem cannot run for this train conditions - EXCLUDED");
822    }
823
824    if (iPWG4JetResponse) {
825      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskJetResponse.C");
826      AliAnalysisTask *taskJetResponse = 0;
827
828      if(iJETAN){
829         taskJetResponse = AddTaskJetResponse("jets", "FASTJET", 0.4, kHighPtFilterMask, 0.15, 0);
830         taskJetResponse = AddTaskJetResponse("jets", "FASTJET", 0.4, kHighPtFilterMask, 0.15, 1);
831
832         taskJetResponse = AddTaskJetResponse("jets", "UA1", 0.4, kHighPtFilterMask, 1., 0);
833         taskJetResponse = AddTaskJetResponse("jets", "UA1", 0.4, kHighPtFilterMask, 1., 2);
834      }
835      if(iPWG4Cluster){
836         taskJetResponse = AddTaskJetResponse("clusters", "ANTIKT", 0.4, kHighPtFilterMask, 0.15, 0);
837         taskJetResponse = AddTaskJetResponse("clusters", "ANTIKT", 0.4, kHighPtFilterMask, 0.15, 1);
838      }
839      if (!taskJetResponse) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJetResponse cannot run for this train conditions - EXCLUDED");
840
841    }
842
843    if(iPWG4JCORRAN){
844      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskJCORRANTask.C");
845      AliJCORRANTask* corran = AddTaskJCORRAN(kDeltaAODJCORRANName.Data(),0);
846      if(!corran)::Warning("AnalysisTrainPWG4Jets", "AliJCORRANTask cannot run for this train conditions - EXCLUDED");
847      else{
848        if(kDeltaAODJCORRANName.Length()>0)mgr->RegisterExtraFile(kDeltaAODJCORRANName.Data()); 
849      }
850    }
851
852    if(iPWG4UE){
853      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskUE.C");
854      AliAnalysisTaskUE *taskUE = 0;
855      if(iPWG4UE&1)taskUE = AddTaskUE(); 
856      if(iPWG4UE&2){
857        taskUE  =AddTaskUE("jetsAOD_CDF04","CDF", "LJ", "TRANSV","MSP"); //finder not yet in train
858        //       taskUE  =AddTaskUE("jetsAOD_CDF07","CDF", "LJ", "TRANSV","MSP");
859        taskUE  =AddTaskUE("jetsAOD_SISCONE04","CDF", "LJ", "TRANSV","MSP");
860        //       taskUE  =AddTaskUE("jetsAOD_SISCONE07","CDF", "LJ", "TRANSV","MSP"); //finder not yet in train
861        taskUE  =AddTaskUE("jetsAOD_ICDF","CDF","LJ","TRANSV","MSP");
862        taskUE  =AddTaskUE("jetsAOD_FASTKT04","CDF", "LJ", "TRANSV","MSP");
863        //       taskUE  =AddTaskUE("jetsAOD_FASTKT07","CDF", "LJ", "TRANSV","MSP"); //finder not yet in train
864        taskUE  =AddTaskUE("jetsAOD_NONE","CDF", "MP_eta05", "TRANSV","MSP");
865        taskUE  =AddTaskUE("jetsAOD_NONE","CDF", "MP_eta09", "TRANSV","MSP");
866      }
867
868      if (!taskUE) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskUE cannot run for this train conditions - EXCLUDED");
869    }
870
871    if(iPWG4LeadingUE){
872      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskLeadingTrackUE.C");
873      AliAnalysisTaskLeadingTrackUE *taskLeadingUE = AddTaskLeadingTrackUE(kUseMC);
874      if (!taskLeadingUE) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTasLeadingTrackkUE cannot run for this train conditions - EXCLUDED");
875      //     taskLeadingUE->SetFilterBit(64);
876    }
877
878
879    if(iPWG4CorrectionsUE){
880      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskCorrectionsUE.C");
881      AliAnalysisTaskCorrectionsUE *taskCorrectionsUE = 0;
882      if(iPWG4CorrectionsUE&1)taskCorrectionsUE = AddTaskCorrectionsUE("jetsAOD_NONE","CDF","MP_eta05","TRANSV","MSP",kFALSE);
883      if (!taskCorrectionsUE) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskCorrectionsUE cannot run for this train conditions - EXCLUDED");
884    }
885
886    if(iPWG4ThreeJets){
887      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskThreeJets.C");
888      AliAnalysisTaskThreeJets *taskThree = AddTaskThreeJets();
889      if(!taskThree)::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskThreets cannot run for this train conditions - EXCLUDED");
890    }
891    if(iPWG4QGSep){
892      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskQGSep.C");
893      AliAnalysisTaskQGSep *taskQGSep = AddTaskQGSep(kUseMC,iAODanalysis);
894      if(!taskQGSep)::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskQGSep cannot run for this train conditions - EXCLUDED");
895    }
896   
897
898    if(iPWG4Minijet){
899      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskMinijet.C");
900      AliAnalysisTaskMinijet *taskMini = AddTaskMinijet(-1,"esd",kUseMC,kGridDataSet);
901      // if we ha highmult trigger add another task
902      if(!taskMini)::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskMinjet cannot run for this train conditions - EXCLUDED");
903    }
904
905
906    if(iPWG4PtQAMC){
907      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskPWG4HighPtQAMC.C");
908      AliPWG4HighPtQAMC *taskQAMC = 0;
909      if(kUseMC){
910        if(iPWG4PtQAMC&1){
911          taskQAMC = AddTaskPWG4HighPtQAMC(kGridDataSet.Data(),0);
912          taskQAMC = AddTaskPWG4HighPtQAMC(kGridDataSet.Data(),1);
913          taskQAMC = AddTaskPWG4HighPtQAMC(kGridDataSet.Data(),2);
914        }
915      }
916      if (!taskQAMC) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskQAMC cannot run for this train conditions - EXCLUDED");
917    }
918
919    if(iPWG4PtQATPC){
920      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskPWG4HighPtQATPConly.C");
921      AliPWG4HighPtQATPConly *taskQATPC = 0;
922      if(iPWG4PtQATPC&1)taskQATPC = AddTaskPWG4HighPtQATPConly(kGridDataSet.Data(),1);
923      if(iPWG4PtQATPC&2)taskQATPC = AddTaskPWG4HighPtQATPConly(kGridDataSet.Data(),2);
924
925  if (!taskQATPC) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskQATPC cannot run for this train conditions - EXCLUDED");
926    }
927
928    if(iPWG4Cosmics){
929      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskPWG4CosmicCandidates.C");
930
931      AliPWG4CosmicCandidates *taskPWG4CosmicCandidates = AddTaskPWG4CosmicCandidates(0);
932      taskPWG4CosmicCandidates = AddTaskPWG4CosmicCandidates(1);
933
934      if (!taskPWG4CosmicCandidates) ::Warning("AnalysisTrainPWG4Jets", "AddTaskPWG4CosmicCandidates cannot run for this train conditions - EXCLUDED");
935    }
936
937
938    if(iPWG4PtSpectra){
939      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskPWG4HighPtSpectra.C");
940      AliPWG4HighPtSpectra *taskPtSpectra = AddTaskPWG4HighPtSpectra(kGridDataSet.Data());
941      if (!taskPtSpectra) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskPtSpectra cannot run for this train conditions - EXCLUDED");
942    }
943    if(iPWG4KMeans){
944      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskKMeans.C");
945      AliAnalysisTaskKMeans *taskKMeans = AddTaskKMeans();
946      if (!taskKMeans) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskKMenans cannot run for this train conditions - EXCLUDED");
947    }
948
949    if(iPWG4PartCorr){
950      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskPartCorr.C");
951      AliAnalysisTaskParticleCorrelation *taskpartcorrPHOS = AddTaskPartCorr("AOD", "PHOS",kFALSE,kIsMC);
952      if (!taskpartcorrPHOS) ::Warning("AnalysisTrainNew", "AliAnalysisTaskParticleCorrelation PHOS cannot run for this train conditions - EXCLUDED");
953      AliAnalysisTaskParticleCorrelation *taskpartcorrEMCAL = AddTaskPartCorr("AOD", "EMCAL",kFALSE,kIsMC);
954      if (!taskpartcorrEMCAL) ::Warning("AnalysisTrainNew", "AliAnalysisTaskParticleCorrelation EMCAL cannot run for this train conditions - EXCLUDED");
955      if(kDeltaAODPartCorrName.Length()>0)mgr->RegisterExtraFile(kDeltaAODPartCorrName.Data());
956    } 
957
958    if(iPWG4CaloQA){
959      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/QA/AddTaskCalorimeterQA.C");
960      AliAnalysisTaskParticleCorrelation *taskcaloQA =  AddTaskCalorimeterQA("ESD",kFALSE,kIsMC,kCaloQAOutputFileName.Data());
961      if(!taskcaloQA)::Warning("AnalysisTrainNew", "AliAnalysisTaskParticleCorrelation QA cannot run - EXCLUDED");
962      //  if(kCaloQAOutputFileName.Length()>0)mgr->RegisterExtraFile(kCaloQAOutputFileName.Data());
963    } 
964
965    if(iPWG4JetCorr){
966      //     using namespace JetCorrelHD;
967      TString cdir = gSystem->WorkingDirectory();
968      gSystem->ChangeDirectory(gSystem->ExpandPathName("$ALICE_ROOT_SRC/PWG4/macros/"));
969      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskJetCorrel.C");
970      AliAnalysisTaskJetCorrel *taskjetcorr = AddTaskJetCorrel();
971      gSystem->ChangeDirectory(cdir);
972      if (!taskjetcorr) ::Warning("AnalysisTrainNew", "AliAnalysisTaskJetCorrel  cannot run for this train conditions - EXCLUDED");
973    } 
974
975    if(iPWG4Tagged){
976      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskTaggedPhotons.C");
977      AliAnalysisTaskTaggedPhotons * taskTagged = AddTaskTaggedPhotons(kFALSE); // EMCAL
978      taskTagged = AddTaskTaggedPhotons(kTRUE); // PHOS 
979      if (!taskTagged) ::Warning("AnalysisTrainNew", "AliAnalysisTaskTaggedPhotons  cannot run for this train conditions - EXCLUDED");     
980    }
981    if (iPWG4omega3pi) {
982      gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskomega3pi.C");
983      AliAnalysisTaskOmegaPi0PiPi *taskomega3pi = AddTaskomega3pi();
984      if (!taskomega3pi) ::Warning("AnalysisTrainNew", "AliAnalysisTaskomega3pi cannot run\
985  for these train conditions - EXCLUDED");
986    }
987
988    // PWG4 gamma conversion analysis
989    if (iPWG4GammaConv) {
990       gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskGammaConversion.C");
991       TString cdir = gSystem->WorkingDirectory();
992       gSystem->ChangeDirectory(gSystem->ExpandPathName("$ALICE_ROOT_SRC/PWG4/macros/"));
993       //      TString gcArguments = "-run-on-train -run-jet -run-chic -run-neutralmeson -run-cf";
994       //      TString gcArguments = "-run-on-train -run-jet -run-neutralmeson -run-cf -use-own-xyz";
995       //      TString gcArguments = "-run-on-train -run-jet -run-neutralmeson -run-cf -use-own-xyz";
996       TString gcArguments = "-run-on-train -run-jet -run-omega-meson -use-own-xyz -run-neutralmeson -no-aod";
997       //      TString kGCAnalysisCutSelectionId="9003562000100310";
998       //      TString kGCAnalysisCutSelectionId="9003562000100312";
999       //      gcArguments.Append(Form(" -set-cut-selection %s ",kGCAnalysisCutSelectionId.Data()));
1000       if(!kIsMC)gcArguments += " -mc-off";
1001       AliAnalysisTaskGammaConversion * taskGammaConversion = AddTaskGammaConversion(gcArguments,mgr->GetCommonInputContainer());
1002       gSystem->ChangeDirectory(cdir);
1003       taskGammaConversion->SelectCollisionCandidates();
1004       if (!taskGammaConversion) ::Warning("AnalysisTrainNew", "AliAnalysisTaskGammaConversion cannot run for these train conditions - EXCLUDED");
1005    }   
1006
1007    if (iPWG4CaloConv) {
1008       gROOT->LoadMacro("$ALICE_ROOT_SRC/PWG4/macros/AddTaskCaloConv.C");
1009       AliAnalysisTaskCaloConv * taskCaloConv = AddTaskCaloConv();
1010       if (!taskCaloConv) ::Warning("AnalysisTrainNew", "AliAnalysisTaskCaloConv cannot run for these train conditions - EXCLUDED");
1011    }   
1012
1013
1014
1015    //==========================================================================
1016    // FOR THE REST OF THE TASKS THE MACRO AddTaskXXX() is not yet implemented/
1017    // Run the analysis
1018    //    
1019    if (kPluginUse) {
1020       AliAnalysisGrid *alienHandler = CreateAlienHandler(plugin_mode);
1021       AliAnalysisManager::GetAnalysisManager()->SetGridHandler(alienHandler);
1022    }
1023    
1024    if (mgr->InitAnalysis()) {
1025      mgr->PrintStatus();
1026      // if (kSaveTrain || strlen(config_file)) gSystem->ChangeDirectory(kTrainName);
1027      if (!strcmp(plugin_mode,"submit")&&smode=="GRID"){
1028        TString alien_workdir = gGrid->GetHomeDirectory();
1029        if (iAODanalysis) alien_workdir += "analysisAOD";
1030        else              alien_workdir += "analysisESD";
1031        if(kGridDataSet.Length()>0)alien_workdir += Form("/%s",kGridDataSet.Data());
1032        AliAnalysisAlien *gridhandler = (AliAnalysisAlien*)mgr->GetGridHandler();
1033        printf("=== AnalysisTrainPWG4Jets:: Registering jdl in the work directory alien://%s/%s, should be done by the manager! ===\n",
1034               alien_workdir.Data(),gridhandler->GetGridOutputDir());
1035
1036        TString dest;
1037        dest = Form("%s/%s/%s.jdl",alien_workdir.Data(),gridhandler->GetGridOutputDir(),kTrainName.Data());
1038        if(AliAnalysisAlien::FileExists(dest.Data())){
1039          Printf("%s exist on grid removing...",dest.Data());
1040          gGrid->Rm(dest.Data());
1041        }
1042        Printf("%s copy ...",dest.Data());
1043        TFile::Cp(Form("file:%s.jdl",kTrainName.Data()),Form("alien://%s",dest.Data()));
1044
1045
1046        TString dest;
1047        dest = Form("%s/%s/%s_merge.jdl",alien_workdir.Data(),gridhandler->GetGridOutputDir(),kTrainName.Data());
1048        if(AliAnalysisAlien::FileExists(dest.Data())){
1049          Printf("%s exist on grid removing...",dest.Data());
1050          gGrid->Rm(dest.Data());
1051        }
1052        Printf("%s copy ...",dest.Data());
1053        TFile::Cp(Form("file:%s_merge.jdl",kTrainName.Data()),Form("alien://%s",dest.Data()));
1054        
1055        dest = Form("%s/%s/%s_merge_final.jdl",alien_workdir.Data(),gridhandler->GetGridOutputDir(),kTrainName.Data());
1056        if(AliAnalysisAlien::FileExists(dest.Data())){
1057          Printf("%s exist on grid removing...",dest.Data());
1058          gGrid->Rm(dest.Data());
1059        }
1060        Printf("%s copy ...",dest.Data());
1061        TFile::Cp(Form("file:%s_merge.jdl",kTrainName.Data()),Form("alien://%s",dest.Data()));
1062
1063
1064        /*
1065        dest = Form("%s/rootfiles/STEER/LQ1dRef_v1.root",gGrid->GetHomeDirectory());
1066        if(AliAnalysisAlien::FileExists(dest.Data())){
1067          Printf("%s exist on grid removing...",dest.Data());
1068          gGrid->Rm(dest.Data());
1069        }
1070        TFile::Cp(Form("file:%s/STEER/LQ1dRef_v1.root",
1071                       gSystem->ExpandPathName("$ALICE_ROOT")),Form("alien://%s",dest.Data()));
1072        */
1073      }
1074      AliLog::SetGlobalLogLevel(AliLog::kError);
1075      if((kUseSysInfo>0&&smode=="LOCAL")||!strcmp(plugin_mode, "test")){
1076        TFile * fM = TFile::Open("manager_local.root","RECREATE");
1077        mgr->Write();
1078        fM->Close();
1079      }
1080      
1081      // grmpf, aliroot error handler overwrites root
1082      gErrorIgnoreLevel = kErrorIgnoreLevel;
1083      if(gErrorIgnoreLevel>3000) AliLog::SetGlobalLogLevel(AliLog::kFatal);
1084      StartAnalysis(smode, chain);
1085      if((kUseSysInfo>0&&smode=="LOCAL")||!strcmp(plugin_mode, "test")){
1086        for(int i = 0;i < mgr->GetTopTasks()->GetEntries();i++){
1087          mgr->ProfileTask(i);
1088        }
1089      }
1090      if (!strcmp(plugin_mode, "offline")&&smode=="GRID"){
1091        // Offline mode path files
1092        //       PatchJDL();
1093        //       PatchAnalysisMacro();
1094      }
1095
1096      if (kSaveTrain && smode=="GRID") {
1097        AliAnalysisAlien *gridhandler = (AliAnalysisAlien*)mgr->GetGridHandler();
1098        TString alien_workdir = gGrid->GetHomeDirectory();
1099        if (iAODanalysis) alien_workdir += "analysisAOD";
1100        else              alien_workdir += "analysisESD";
1101        if(kGridDataSet.Length()>0)alien_workdir += Form("/%s",kGridDataSet.Data());
1102        //     kGridOutdir = gridhandler->GetGridOutputDir();
1103        printf("=== Registering ConfigTrain.C in the work directory <%s> ===\n",
1104                 alien_workdir.Data());
1105        if (AliAnalysisAlien::FileExists(Form("%s/%sConfig.C", alien_workdir.Data(), kTrainName.Data())))
1106          gGrid->Rm(Form("%s/%sConfig.C", alien_workdir.Data(), kTrainName.Data()));
1107        if (strcmp(plugin_mode, "test"))
1108          TFile::Cp(Form("file:%sConfig.C",kTrainName.Data()), Form("alien://%s/%sConfig.C", alien_workdir.Data(), kTrainName.Data()));
1109      }
1110    }
1111 }
1112
1113 //______________________________________________________________________________
1114 void StartAnalysis(const char *mode, TChain *chain) {
1115 // Start analysis.
1116    Int_t imode = -1;
1117    AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
1118    if (!strcmp(mode, "LOCAL")) imode = 0;
1119    if (!strcmp(mode, "PROOF")) imode = 1;
1120    if (!strcmp(mode, "GRID"))  imode = 2;
1121    switch (imode) {
1122       case 0:
1123          if (!chain) {
1124             ::Error("AnalysisTrainPWG4Jets.C::StartAnalysis", "Cannot create the chain");
1125             return;
1126          }   
1127          mgr->StartAnalysis(mode, chain,kNumberOfEvents);
1128          return;
1129       case 1:
1130          if (!kProofDataSet.Length()) {
1131             ::Error("AnalysisTrainPWG4Jets.C::StartAnalysis", "kProofDataSet is empty");
1132             return;
1133          }   
1134          mgr->StartAnalysis(mode, kProofDataSet, kProofEvents,kProofOffset);
1135          return;
1136       case 2:
1137          if (kPluginUse) {
1138             if (!mgr->GetGridHandler()) {
1139                ::Error("AnalysisTrainPWG4Jets.C::StartAnalysis", "Grid plugin not initialized");
1140                return;
1141             }   
1142             mgr->StartAnalysis("grid",chain,kNumberOfEvents);
1143          } else {
1144             if (!chain) {
1145                ::Error("AnalysisTrainPWG4Jets.C::StartAnalysis", "Cannot create the chain");
1146                return;
1147             }   
1148             mgr->StartAnalysis(mode, chain);
1149             mgr->StartAnalysis(mode, chain,kNumberOfEvents);
1150          }   
1151          return;
1152    }      
1153 }          
1154     
1155 //______________________________________________________________________________
1156 void CheckModuleFlags(const char *mode) {
1157 // Checks selected modules and insure compatibility
1158    Int_t imode = -1;
1159    if (!strcmp(mode, "LOCAL")) imode = 0;
1160    if (!strcmp(mode, "PROOF")) imode = 1;
1161    if (!strcmp(mode, "GRID"))  imode = 2;
1162
1163
1164    if (kUseCPAR) {
1165      kPluginAliRootVersion    = ""; // NO aliroot if we use CPAR
1166    }
1167
1168    if (imode==1) {
1169       if (!kUsePAR) {
1170          ::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PAR files enabled due to PROOF analysis");
1171          kUsePAR = kTRUE;
1172       }   
1173    }  
1174    if (imode != 2) {
1175       ::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "AliEn plugin disabled since not in GRID mode");
1176       kPluginUse = kFALSE; 
1177    }   
1178
1179
1180    if(!kIsMC){
1181      // switch off anthin related to MC
1182      kUseMC = 0;
1183      kUseAODMC = 0;
1184      kUseTR = kFALSE;
1185    }
1186
1187    // Decide if we have PbPb
1188    if(kGridDataSet.CompareTo("LHC10h")==0||kGridDataSet.Contains("LHC10h")) {
1189      Printf("Using settings for Pb+Pb");
1190      kIsPbPb = true;
1191    }
1192
1193    
1194
1195    if (iAODanalysis) {
1196    // AOD analysis
1197       if (kUseMC)
1198          ::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "MC usage disabled in analysis on AOD's");
1199       if (kUseAODTags)
1200          ::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "AOD tags usage disabled in analysis on AOD's");
1201       kUseMC = kFALSE;
1202       kUseTR = kFALSE;
1203       kUseAODTags = kFALSE;
1204       if (iESDfilter)
1205          ::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "ESD filter disabled in analysis on AOD's");
1206       iESDfilter   = 0;
1207       if (iPhysicsSelection)
1208          ::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "Physics Selection disabled in analysis on AOD's");
1209       iPhysicsSelection   = 0;
1210       if (!iAODhandler) {
1211          if (iJETAN) 
1212             ::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "JETAN disabled in analysis on AOD's without AOD handler");
1213          iJETAN = 0;
1214          iDIJETAN = 0;
1215       }
1216       // Disable tasks that do not work yet on AOD data
1217       if(iPWG4JCORRAN)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4 JCORRAN disabled in analysis on AOD's");
1218       iPWG4JCORRAN = 0;
1219       if( iPWG4PtQAMC)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4 PtQAMC disabled in analysis on AOD's");
1220       iPWG4PtQAMC        = 0;
1221       if( iPWG4PtQATPC)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4 PtTPC disabled in analysis on AOD's");
1222       iPWG4PtQATPC        = 0;
1223       if( iPWG4Cosmics)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4 Comics disabled in analysis on AOD's");
1224       iPWG4Cosmics        = 0;
1225
1226       if( iPWG4PtSpectra)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4 PtQAMC disabled in analysis on AOD's");
1227       iPWG4PtSpectra     = 0;
1228       if(iPWG4KMeans)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4KMeans disabled on AOD's");
1229       iPWG4KMeans       = 0;
1230       if (iPWG4JetCorr)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4Jetcorr disabled on AOD's");
1231       iPWG4JetCorr = 0;
1232       if (iPWG4PartCorr)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4partcorr disabled on AOD's");
1233       iPWG4PartCorr = 0;
1234       if (iPWG4CaloQA)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4CaloQA disabled on AOD's");
1235       iPWG4CaloQA = 0;
1236       if (iPWG4Tagged)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4tagged disabled on AOD's");
1237       iPWG4Tagged = 0;
1238       if (iPWG4omega3pi)
1239         ::Info("AnalysisTrainNew.C::CheckModuleFlags", "PWG4omega3pi disabled on AOD's");
1240       iPWG4omega3pi = 0;
1241       if(iPWG1QASym)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG1 QA Sym disabled in analysis on AOD's");
1242       if (iPWG4GammaConv)::Info("AnalysisPWG4Jets.C::CheckModuleFlags", "PWG4gammaconv disabled on AOD's");
1243       iPWG4GammaConv = 0;   
1244       iPWG1QASym     = 0;
1245       iCentralitySelection = 0;
1246    } else {   
1247    // ESD analysis
1248
1249      if(kIsPbPb){
1250        iCentralitySelection = 1;
1251      }
1252
1253      if (!kUseMC){
1254        kUseTR = kFALSE;
1255        
1256        if(kUseKinefilter)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4 Kine Filter disabled in analysis without MC");
1257        kUseKinefilter = kFALSE;
1258        if( iPWG4PtQAMC)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4 PtQAMC disabled in analysis without MC");
1259        iPWG4PtQAMC        = 0;
1260        if( iPWG4CorrectionsUE)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4 CorrectionsUE disabled in analysis without MC");
1261        iPWG4CorrectionsUE = 0;
1262      }
1263      if (!kUseTR) {
1264        if(iPWG4PtQAMC)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "iPWG4QATPCMC disabled if not reading track references");
1265        iPWG4PtQAMC        = 0;
1266      }   
1267      if (iJETAN){
1268        iESDfilter=1;
1269      }
1270       if (!iESDfilter){
1271         kUseKinefilter = kFALSE;
1272         kUseMuonfilter = kFALSE;
1273       }
1274       if(!iJETAN){
1275         iPWG4JetSpectrum = iPWG4UE =  iPWG4CorrectionsUE = iPWG4ThreeJets = iPWG4QGSep = iDIJETAN = 0;
1276       }
1277    }
1278    iPWG4JetTasks = iPWG4JetServices||iPWG4JetSpectrum||iPWG4UE||iPWG4LeadingUE||iPWG4PtQAMC||iPWG4PtSpectra||iPWG4PtQATPC||iPWG4Cosmics||iPWG4ThreeJets||iPWG4QGSep||iPWG4JetChem||iPWG4Minijet||iPWG4Fragmentation;
1279    iPWG4PartCorrLibs = iPWG4PartCorr||iPWG4Tagged||iPWG4CaloQA;
1280    iPWG4GammaConvLib = iPWG4GammaConv||iPWG4CaloConv;
1281
1282
1283    iEMCUtilLibs = iPWG4PartCorrLibs||iPWG4JCORRAN||iPWG4GammaConvLib;
1284    iJETANLib = iPWG4JetTasks||iJETAN||iDIJETAN;
1285
1286    if (iESDfilter) {iAODhandler=1;}
1287    if (kUseKinefilter && !kUseMC) kUseKinefilter = kFALSE;
1288    if (kUseAODTags && !iAODhandler) kUseAODTags = kFALSE;
1289
1290
1291    
1292 }
1293
1294 //______________________________________________________________________________
1295 Bool_t Connect(const char *mode) {
1296 // Connect <username> to the back-end system.
1297    Int_t imode = -1;
1298    if (!strcmp(mode, "LOCAL")) imode = 0;
1299    if (!strcmp(mode, "PROOF")) imode = 1;
1300    if (!strcmp(mode, "GRID"))  imode = 2;
1301    TString username = gSystem->Getenv("alien_API_USER");
1302    switch (imode) {
1303       case 0:
1304          break;
1305       case 1:
1306          if  (!username.Length()) {
1307             ::Error(Form("AnalysisTrainPWG4Jets.C::Connect <%s>", mode), "Make sure you:\n \
1308                            1. Have called: alien-token-init <username>\n \
1309                            2. Have called: >source /tmp/gclient_env_$UID");
1310             return kFALSE;
1311          }
1312          ::Info("AnalysisTrainPWG4Jets.C::Connect", "Connecting user <%s> to PROOF cluster <%s>", 
1313                 username.Data(), kProofCluster.Data());
1314          gEnv->SetValue("XSec.GSI.DelegProxy", "2");
1315 //         TProof::Open(Form("%s@%s:31093", username.Data(), kProofCluster.Data()));       
1316          TProof::Open(Form("%s@%s", username.Data(), kProofCluster.Data()));       
1317          if (!gProof) {
1318             if (strcmp(gSystem->Getenv("XrdSecGSISRVNAMES"), "lxfsrd0506.cern.ch"))
1319                ::Error(Form("AnalysisTrainPWG4Jets.C::Connect <%s>", mode), "Environment XrdSecGSISRVNAMES different from lxfsrd0506.cern.ch");
1320             return kFALSE;
1321          }
1322          if(kProofClearPackages)gProof->ClearPackages();
1323
1324          if(kProofSaveToAlien){
1325            TGrid::Connect("alien://");
1326            if (gGrid) {
1327              TString homedir = gGrid->GetHomeDirectory();
1328              TString workdir = homedir + kTrainName;
1329              if (!gGrid->Cd(workdir)) {
1330                gGrid->Cd(homedir);
1331                if (gGrid->Mkdir(workdir)) {
1332                  gGrid->Cd(kTrainName);
1333                  ::Info("AnalysisTrainPWG4Jets::Connect()", "Directory %s created", gGrid->Pwd());
1334                }
1335              }
1336              gGrid->Mkdir("proof_output");
1337              gGrid->Cd("proof_output");
1338              kProofOutdir = Form("alien://%s", gGrid->Pwd());
1339            }   
1340          }
1341          break;
1342       case 2:      
1343          if  (!username.Length()) {
1344             ::Error(Form("AnalysisTrainPWG4Jets.C::Connect <%s>", mode), "Make sure you:\n \
1345                            1. Have called: alien-token-init <username>\n \
1346                            2. Have called: >source /tmp/gclient_env_$UID");
1347             return kFALSE;
1348          }
1349          if (kPluginUse && !gSystem->Getenv("alien_CLOSE_SE")) {
1350             ::Error(Form("AnalysisTrainPWG4Jets.C::Connect <%s>", mode), 
1351                            "When using the AliEn plugin it is preferable to define the \
1352                            variable alien_CLOSE_SE in your environment.");
1353             return kFALSE;
1354          }
1355          ::Info("AnalysisTrainPWG4Jets.C::Connect", "Connecting user <%s> to AliEn ...", 
1356                 username.Data());
1357          TGrid::Connect("alien://");
1358          if (!gGrid || !gGrid->IsConnected()) return kFALSE;
1359          break;
1360       default:
1361          ::Error("AnalysisTrainPWG4Jets.C::Connect", "Unknown run mode: %s", mode);
1362          return kFALSE;
1363    }
1364    ::Info("AnalysisTrainPWG4Jets.C::Connect","Connected in %s mode", mode);
1365    return kTRUE;
1366 }
1367
1368 //______________________________________________________________________________
1369 Bool_t LoadCommonLibraries(const char *mode)
1370 {
1371    if (!gSystem->Getenv("ALICE_ROOT_SRC")) {
1372       ::Error("AnalysisTrainPWG4Jets.C", "Analysis train requires that ALICE_ROOT_SRC is set to pick up Configurations"); 
1373       return kFALSE;
1374    }   
1375    
1376    // Load common analysis libraries.
1377    Int_t imode = -1;
1378    if (!strcmp(mode, "LOCAL")) imode = 0;
1379    if (!strcmp(mode, "PROOF")) imode = 1;
1380    if (!strcmp(mode, "GRID"))  imode = 2;
1381    Bool_t success = kTRUE;
1382    // ROOT libraries
1383    gSystem->Load("libTree.so");
1384    gSystem->Load("libGeom.so");
1385    gSystem->Load("libVMC.so");
1386    gSystem->Load("libPhysics.so");
1387    
1388    // Load framework classes. Par option ignored here.
1389    switch (imode) {
1390       case 0:
1391       case 2:
1392          if (kUseCPAR) {
1393             success &= LoadLibrary("STEERBase", mode, kTRUE);
1394             success &= LoadLibrary("ESD", mode, kTRUE);
1395             success &= LoadLibrary("AOD", mode, kTRUE);
1396             success &= LoadLibrary("ANALYSIS", mode, kTRUE);
1397             success &= LoadLibrary("ANALYSISalice", mode, kTRUE);
1398             success &= LoadLibrary("ROOTFILES", mode, kTRUE);
1399             // success &= LoadLibrary("EventMixing", mode,kTRUE);
1400             success &= LoadLibrary("CORRFW", mode, kTRUE);
1401          } else {   
1402             success &= LoadLibrary("libSTEERBase.so", mode);
1403             success &= LoadLibrary("libESD.so", mode);
1404             success &= LoadLibrary("libAOD.so", mode);
1405             success &= LoadLibrary("libANALYSIS.so", mode);
1406             success &= LoadLibrary("libANALYSISalice.so", mode);
1407             // success &= LoadLibrary("libEventMixing.so", mode);
1408             success &= LoadLibrary("libCORRFW.so", mode);
1409             gROOT->ProcessLine(".include $ALICE_ROOT/include");
1410          }   
1411          break;
1412       case 1:
1413          Int_t ires = -1;
1414          if (kProofUseAFPAR && !gSystem->AccessPathName(kProofAFversion)) ires = gProof->UploadPackage(kProofAFversion);
1415          if (ires < 0) {
1416             success &= LoadLibrary("STEERBase", mode);
1417             success &= LoadLibrary("ESD", mode);
1418             success &= LoadLibrary("AOD", mode);
1419             success &= LoadLibrary("ANALYSIS", mode);
1420             success &= LoadLibrary("ANALYSISalice", mode);
1421             success &= LoadLibrary("EventMixing", mode);
1422             success &= LoadLibrary("CORRFW", mode);
1423          } else { 
1424             ires = gProof->EnablePackage(kProofAFversion);
1425             if (ires<0) success = kFALSE;
1426             success &= LoadLibrary("CORRFW", mode);
1427          }
1428          break;         
1429       default:
1430          ::Error("AnalysisTrainPWG4Jets.C::LoadCommonLibraries", "Unknown run mode: %s", mode);
1431          return kFALSE;
1432    }
1433    if (success) {
1434       ::Info("AnalysisTrainPWG4Jets.C::LoadCommodLibraries", "Load common libraries:    SUCCESS");
1435       ::Info("AnalysisTrainPWG4Jets.C::LoadCommodLibraries", "Include path for Aclic compilation:\n%s",
1436               gSystem->GetIncludePath());
1437    } else {           
1438       ::Info("AnalysisTrainPWG4Jets.C::LoadCommodLibraries", "Load common libraries:    FAILED");
1439    }   
1440       
1441    return success;
1442 }
1443
1444 //______________________________________________________________________________
1445 Bool_t LoadAnalysisLibraries(const char *mode)
1446 {
1447 // Load common analysis libraries.
1448   Bool_t success = kTRUE;
1449   if (useTender) {
1450       if (!LoadLibrary("TENDER", mode, kTRUE) ||
1451           !LoadLibrary("TENDERSupplies", mode, kTRUE)) return kFALSE;
1452    }
1453    if (iESDfilter) {
1454      /*
1455       if (!LoadLibrary("PWG3base", mode, kTRUE) ||
1456           !LoadLibrary("PWG3muon", mode, kTRUE)) return kFALSE;
1457      */
1458    }   
1459    // JETAN
1460    if (iJETANLib) {
1461      // this part needs some rework in case we do not need the fastjed finders for processing
1462      if (!LoadLibrary("JETAN", mode, kTRUE)) return kFALSE;
1463      if (!strcmp(mode, "PROOF")){
1464        gProof->Exec("gSystem->Load\(\"/afs/cern.ch/user/d/dperrino/public/libCGAL.so\"\)", kTRUE); 
1465        gProof->Exec("gSystem->Load\(\"/afs/cern.ch/user/d/dperrino/public/libfastjet.so\"\)", kTRUE); 
1466        // problem when loading siscone copiled with different gcc version??
1467        // gProof->Exec("gSystem->Load\(\"/afs/cern.ch/user/d/dperrino/public/libsiscone.so\"\)", kTRUE); 
1468        gProof->Exec("gSystem->Load\(\"/afs/cern.ch/user/d/dperrino/public/libSISConePlugin.so\"\)", kTRUE);      
1469      }
1470      if(!kUsePAR){ 
1471        if (!LoadLibrary("CGAL", mode, kTRUE)) return kFALSE;
1472        if (!LoadLibrary("fastjet", mode, kTRUE)) return kFALSE;
1473        if (!LoadLibrary("siscone", mode, kTRUE)) return kFALSE;
1474        if (!LoadLibrary("SISConePlugin", mode, kTRUE)) return kFALSE;
1475      }
1476      else{
1477        // par files plus FASTJET needs some extra work... need to change
1478        // the loading sequence in the auto generated .C file
1479        if (!LoadLibrary("libCGAL.so", mode, kTRUE)) return kFALSE;
1480        if (!LoadLibrary("libfastjet.so", mode, kTRUE)) return kFALSE;
1481        if (!LoadLibrary("libsiscone.so", mode, kTRUE)) return kFALSE;
1482        if (!LoadLibrary("libSISConePlugin.so", mode, kTRUE)) return kFALSE;
1483      }
1484      if (!LoadLibrary("FASTJETAN", mode, kTRUE)) return kFALSE;
1485    }
1486    if(iPWG4JetTasks){
1487      if (!LoadLibrary("PWG4JetTasks", mode, kTRUE)) return kFALSE;
1488    }
1489
1490    if(iPWG1QASym){
1491      if (!LoadSource(Form("%s/PWG1/AliAnalysisTaskQASym.cxx",gSystem->ExpandPathName("$ALICE_ROOT_SRC")), mode, kTRUE))return kFALSE;
1492    }
1493    if(iPWG4TmpSourceSara){
1494      if(!kUsePAR)gSystem->AddIncludePath("-I$ALICE_ROOT/include/JetTasks"); // ugly hack!!
1495      if(!LoadSource(Form("%s/PWG4/JetTasks/AliAnalysisTaskEta.cxx",gSystem->ExpandPathName("$ALICE_ROOT_SRC")), mode, kTRUE))return kFALSE;
1496    }
1497
1498    /*
1499    if(iPWG4JetChem){
1500      if(!kUsePAR)gSystem->AddIncludePath("-I$ALICE_ROOT/include/JetTasks"); // ugly hack!!
1501      if(!LoadSource(Form("%s/PWG4/JetTasks/AliAnalysisTaskJetChem.cxx",gSystem->ExpandPathName("$ALICE_ROOT")), mode, kTRUE))return kFALSE;
1502    }
1503    */
1504
1505    if(iEMCUtilLibs){
1506      if (!LoadLibrary("EMCALUtils", mode, kTRUE) ||
1507          !LoadLibrary("PHOSUtils", mode, kTRUE)) return kFALSE;
1508    }
1509
1510    if (iPWG4PartCorrLibs) {   
1511       if (!LoadLibrary("PWG4PartCorrBase", mode, kTRUE) ||
1512           !LoadLibrary("PWG4PartCorrDep", mode, kTRUE)) return kFALSE;
1513    }
1514    if(iPWG4JCORRAN){
1515      // PWG4 particle correlations
1516      if(!LoadLibrary("PWG4JCORRAN",mode,kTRUE))return kFALSE;
1517    }
1518    if (iPWG4JetCorr) { 
1519      if (!LoadLibrary("PWG4JetCorrel", mode, kTRUE)) return kFALSE;
1520    }  
1521    if (iPWG4omega3pi) {
1522      if (!LoadLibrary("PWG4omega3pi", mode, kTRUE)) return kFALSE;
1523    }
1524    if (iPWG4GammaConvLib) {
1525       if (!LoadLibrary("PWG4GammaConv", mode, kTRUE)) return kFALSE;
1526    }      
1527
1528    ::Info("AnalysisTrainPWG4Jets.C::LoadAnalysisLibraries", "Load other libraries:   SUCCESS");
1529    return kTRUE;
1530 }
1531
1532 //______________________________________________________________________________
1533 Bool_t LoadLibrary(const char *module, const char *mode, Bool_t rec=kFALSE)
1534 {
1535 // Load a module library in a given mode. Reports success.
1536    Int_t imode = -1;
1537    Int_t result;
1538    TString smodule(module);
1539    if (!strcmp(mode, "LOCAL")) imode = 0;
1540    if (!strcmp(mode, "PROOF")) imode = 1;
1541    if (!strcmp(mode, "GRID"))  imode = 2;
1542    TString mod(module);
1543    if (!mod.Length()) {
1544       ::Error("AnalysisTrainPWG4Jets.C::LoadLibrary", "Empty module name");
1545       return kFALSE;
1546    }   
1547    // If a library is specified, just load it
1548    if (smodule.EndsWith(".so")) {
1549       mod.Remove(mod.Index(".so"));
1550       result = gSystem->Load(mod);
1551       if (result < 0) {
1552          ::Error("AnalysisTrainPWG4Jets.C::LoadLibrary", "Could not load library %s", module);
1553          return kFALSE;
1554       }
1555       if (rec) anaLibs += Form("%s.so ",mod.Data()); 
1556       if (rec) anaLibsExtra += Form("%s.so ",mod.Data()); 
1557       return kTRUE;
1558    } 
1559    // Check if the library is already loaded
1560    if (strlen(gSystem->GetLibraries(Form("%s.so", module), "", kFALSE)) > 0)
1561       return kTRUE;    
1562    switch (imode) {
1563       case 0:
1564       case 2:
1565          if (kUsePAR) {
1566             result = SetupPar(module);
1567             if (rec) anaPars += Form("%s.par ", module);
1568          } else {
1569             result = gSystem->Load(Form("lib%s.so", module));
1570             if (rec) anaLibs += Form("lib%s.so ", module);
1571          }   
1572          break;
1573       case 1:
1574         if(!gSystem->AccessPathName(module)){
1575           ::Info("AnalysisTrainPWG4Jets.C::LoadLibrary", "Removing directory %s",module);
1576           gSystem->Exec(Form("rm -rf %s",module));
1577         }
1578          result = gProof->UploadPackage(module);
1579          if (result<0) {
1580             result = gProof->UploadPackage(gSystem->ExpandPathName(Form("$ALICE_ROOT/%s.par", module)));
1581             if (result<0) {
1582                ::Error("AnalysisTrainPWG4Jets.C::LoadLibrary", "Could not find module %s.par in current directory nor in $ALICE_ROOT", module);
1583                return kFALSE;
1584             }
1585          }   
1586          result = gProof->EnablePackage(module);
1587          break;
1588       default:
1589          return kFALSE;
1590    }         
1591    if (result < 0) {
1592       ::Error("AnalysisTrainPWG4Jets.C::LoadLibrary", "Could not load module %s", module);
1593       return kFALSE;
1594    }
1595    return kTRUE;
1596 }           
1597
1598
1599
1600 //______________________________________________________________________________
1601 Bool_t LoadSource(const char *source, const char *mode, Bool_t rec=kFALSE)
1602 {
1603 // Load a module library in a given mode. Reports success.
1604    Int_t imode = -1;
1605    Int_t result = -1;
1606    if (!strcmp(mode, "LOCAL")) imode = 0;
1607    if (!strcmp(mode, "PROOF")) imode = 1;
1608    if (!strcmp(mode, "GRID"))  imode = 2;
1609    TString ssource(source);
1610    TString basename = gSystem->BaseName(ssource.Data());
1611    if (!ssource.Length()) {
1612       ::Error("AnalysisTrainPWG4Jets.C::LoadSource", "Empty task name");
1613       return kFALSE;
1614    }   
1615    // we have a source code so compile it
1616    if (ssource.EndsWith(".cxx")) {
1617      // need to copy it here other wise the path is also used on grid...
1618      ssource.Remove(ssource.Index(".cxx"));
1619      basename.Remove(basename.Index(".cxx"));
1620      Printf("LoadSources:: Copying...  path %s{cxx,h}",ssource.Data());
1621      gSystem->Exec(Form("cp %s.cxx . ",ssource.Data()));
1622      gSystem->Exec(Form("cp %s.h . ",ssource.Data()));
1623      // Path to code
1624      // only needed for local compilation, in grid and proof mode 
1625      // the task headers are uploaded 
1626      //     path.Remove(path.Index(gSystem->BaseName(path.Data())));
1627      // Printf("LoadSources:: Including path %s",path.Data());
1628      //  if(path.Length()>0)gROOT->ProcessLine(Form(".include %s",path.Data()));
1629      Printf("LoadSources:: Loading...  path %s",basename.Data());
1630      switch (imode) {
1631      case 0:
1632        result = gROOT->LoadMacro(Form("%s.cxx++g",basename.Data()));
1633        break;
1634      case 1:
1635        result = gProof->LoadMacro(Form("%s.cxx++g",basename.Data()));
1636        break;
1637      case 2:
1638        result = gROOT->LoadMacro(Form("%s.cxx++g",basename.Data()));
1639        if (rec){
1640          // what we want to compile
1641          anaSources += Form("%s.cxx ",basename.Data()); 
1642          // what we need as input...
1643          anaLibs += Form("%s.cxx %s.h ",basename.Data(),basename.Data()); 
1644        }
1645        break;
1646      default:
1647        return kFALSE;
1648      }
1649    } 
1650    if (result < 0) {
1651       ::Error("AnalysisTrainPWG4Jets.C::LoadSources", "Could not load source %s", source);
1652       return kFALSE;
1653    }
1654    return kTRUE;
1655 }           
1656
1657
1658 //______________________________________________________________________________
1659 TChain *CreateChain(const char *mode, const char *plugin_mode)
1660 {
1661 // Create the input chain
1662    Int_t imode = -1;
1663    if (!strcmp(mode, "LOCAL")) imode = 0;
1664    if (!strcmp(mode, "PROOF")) imode = 1;
1665    if (!strcmp(mode, "GRID"))  imode = 2;
1666    TChain *chain = NULL;
1667    // Local chain
1668    switch (imode) {
1669       case 0:
1670          if (iAODanalysis) {
1671             if (!kLocalXMLDataset.Length()) {
1672                // Local AOD
1673                chain = new TChain("aodTree");
1674                TString line;
1675                ifstream in;
1676                in.open(kLocalDataList.Data());
1677                while (in.good()) {
1678                  in >> line;
1679                  if (line.Length() == 0) continue;
1680                  // cout << " line = " << line << endl;
1681                  chain->Add(line.Data());
1682                }       
1683             } else {
1684                // Interactive AOD
1685                chain = CreateChainSingle(kLocalXMLDataset, "aodTree");
1686             }
1687          } else {      
1688            if (!kLocalXMLDataset.Length()) {
1689              // Local ESD
1690              chain = new TChain("esdTree");
1691              TString line;
1692              ifstream in;
1693              in.open(kLocalDataList.Data());
1694              while (in.good()) {
1695                in >> line;
1696                if (line.Length() == 0) continue;
1697                cout << " line = " << line << endl;
1698                chain->Add(line.Data());
1699              }       
1700            } else {
1701              // Interactive ESD
1702                chain = CreateChainSingle(kLocalXMLDataset, "esdTree");
1703            }   
1704          }
1705          break;
1706       case 1:
1707          break;
1708       case 2:
1709          if (kPluginUse) {
1710 //            AliAnalysisGrid *alienHandler = CreateAlienHandler(plugin_mode);
1711 //            AliAnalysisManager::GetAnalysisManager()->SetGridHandler(alienHandler);
1712          } else {
1713             TString           treeName = "esdTree";
1714             if (iAODanalysis) treeName = "aodTree";
1715             chain = CreateChainSingle("wn.xml", treeName);
1716          }
1717          break;      
1718       default:   
1719    }
1720    if (chain && chain->GetNtrees()) return chain;
1721    return NULL;
1722 }   
1723
1724 //______________________________________________________________________________
1725 TChain* CreateChainSingle(const char* xmlfile, const char *treeName)
1726 {
1727    printf("*******************************\n");
1728    printf("*** Getting the ESD Chain   ***\n");
1729    printf("*******************************\n");
1730    TAlienCollection * myCollection  = TAlienCollection::Open(xmlfile);
1731
1732    if (!myCollection) {
1733       ::Error("AnalysisTrainPWG4Jets.C::CreateChainSingle", "Cannot create an AliEn collection from %s", xmlfile) ;
1734       return NULL ;
1735    }
1736
1737    TChain* chain = new TChain(treeName);
1738    myCollection->Reset() ;
1739    while ( myCollection->Next() ) chain->Add(myCollection->GetTURL("")) ;
1740    chain->ls();
1741    return chain;
1742 }
1743
1744 //______________________________________________________________________________
1745 Int_t SetupPar(char* pararchivename)
1746 {
1747    if (!pararchivename || !strlen(pararchivename)) return -1;
1748    char processline[1024];
1749    if (gSystem->AccessPathName(Form("%s.par", pararchivename))) {
1750       if (!gSystem->AccessPathName(Form("%s/%s.par", gSystem->Getenv("ALICE_ROOT"),pararchivename))) {
1751          ::Info("AnalysisTrainPWG4Jets.C::SetupPar", "Getting %s.par from $ALICE_ROOT", pararchivename);
1752         TFile::Cp(gSystem->ExpandPathName(Form("$ALICE_ROOT/%s.par", pararchivename)), 
1753                   Form("%s.par",pararchivename));
1754       } else {
1755          ::Error("AnalysisTrainPWG4Jets.C::SetupPar", "Cannot find %s.par", pararchivename);
1756          return -1;
1757       }   
1758    }
1759    if (kPluginUse && kSaveTrain) gSystem->Exec(Form("ln -s ../%s.par %s",pararchivename, kTrainName.Data()));
1760    gSystem->Exec(Form("tar xvzf %s.par", pararchivename));
1761
1762    TString ocwd = gSystem->WorkingDirectory();
1763    if (!gSystem->ChangeDirectory(pararchivename)) return -1;
1764         
1765    // check for BUILD.sh and execute
1766    if (!gSystem->AccessPathName("PROOF-INF/BUILD.sh")) {
1767       printf("*******************************\n");
1768       printf("*** Building PAR archive    ***\n");
1769       printf("*******************************\n");          
1770       if (gSystem->Exec("PROOF-INF/BUILD.sh")) {
1771          Error("runProcess","Cannot Build the PAR Archive! - Abort!");
1772          return -1;
1773       }
1774    }
1775
1776         // check for SETUP.C and execute
1777         if (!gSystem->AccessPathName("PROOF-INF/SETUP.C")) {
1778             printf("*******************************\n");
1779             printf("*** Setup PAR archive       ***\n");
1780             printf("*******************************\n");
1781             gROOT->Macro("PROOF-INF/SETUP.C");
1782         }       
1783         if (!gSystem->ChangeDirectory(ocwd.Data())){
1784           Error("Change back directory",Form("Cannot change to %s",ocwd.Data()));
1785           return -1;
1786         }
1787    return 0;
1788 }
1789
1790 //______________________________________________________________________________
1791 AliAnalysisAlien* CreateAlienHandler(const char *plugin_mode)
1792 {
1793 // Check if user has a valid token, otherwise make one. This has limitations.
1794 // One can always follow the standard procedure of calling alien-token-init then
1795 //   source /tmp/gclient_env_$UID in the current shell.
1796 //   if (!AliAnalysisGrid::CreateToken()) return NULL;
1797    AliAnalysisAlien *plugin = new AliAnalysisAlien();
1798 // Set the run mode (can be "full", "test", "offline", "submit" or "terminate")
1799    plugin->SetRunMode(plugin_mode);
1800    if (kPluginUseProductionMode) plugin->SetProductionMode();
1801    plugin->SetJobTag(kJobTag);
1802    plugin->SetNtestFiles(1);
1803 //   plugin->SetPreferedSE("ALICE::NIHAM::File");
1804 // Set versions of used packages
1805    plugin->SetAPIVersion("V1.1x");
1806    //   plugin->SetAPIVersion("V1.0x");
1807 //   plugin->SetAPIVersion("V2.4");
1808    plugin->SetROOTVersion(kPluginRootVersion);
1809    plugin->SetAliROOTVersion(kPluginAliRootVersion);
1810 // Declare input data to be processed.
1811 // Method 1: Create automatically XML collections using alien 'find' command.
1812 // Define production directory LFN
1813    plugin->SetGridDataDir(kGridDatadir.Data());
1814 // Set data search pattern
1815    if (iAODanalysis) plugin->SetDataPattern(" *AliAOD.Jets.root");
1816    //   else              plugin->SetDataPattern(Form(" %s/*/*ESD.tag.root",kGridPassPattern.Data()));
1817    else              plugin->SetDataPattern(Form(" %s/*/*AliESDs.root",kGridPassPattern.Data()));
1818 // ...then add run numbers to be considered
1819 //   plugin->SetRunRange(kGridRunRange[0], kGridRunRange[1]);
1820    for (Int_t i=kGridRunRange[0]; i<=kGridRunRange[1]; i++) {
1821      Printf("AnalysisTrainPWG4Jets Adding run number %s", Form(kGridRunPattern.Data(),i));
1822      plugin->AddRunNumber(Form(kGridRunPattern.Data(),i));
1823    }   
1824
1825    if(kGridLocalRunList.Length()>0){
1826      ifstream in1;
1827      in1.open(kGridLocalRunList.Data());
1828      int iRun;
1829      int icount = 0;
1830      /*
1831      char c;
1832      char cLine[250];
1833      while(!in1.eof()){
1834        c = in1.get();
1835        if ( (c >= '0') && (c <= '9') )
1836          {
1837            in1.putback (c)s;
1838            in1>>iRun;
1839            Printf("AnalysisTrainPWG4Jets Adding run number from File %s", Form(kGridRunPattern.Data(),iRun));
1840            plugin->AddRunNumber(Form(kGridRunPattern.Data(),iRun));
1841        }
1842      else
1843        {
1844          in1.putback (c);
1845          in1.getline(cLine,250);
1846
1847        }
1848      }
1849      */
1850      
1851      Int_t nRun = 0;
1852
1853      // just use run numbers, negatives will be excluded
1854      while(in1>>iRun){
1855        if(iRun>=0){
1856          if(iRun>=0&&nRun>=kGridOffsetRunFromList&&(nRun<kGridMaxRunsFromList)){
1857            Printf("AnalysisTrainPWG4Jets Adding run number from File %d: %s",nRun,Form(kGridRunPattern.Data(),iRun));
1858            plugin->AddRunNumber(Form(kGridRunPattern.Data(),iRun));
1859
1860          }
1861          else{
1862            Printf("AnalysisTrainPWG4Jets Skipping run number from File %d: %d",nRun, iRun);
1863          }
1864          nRun++;
1865        }
1866        else{
1867          Printf("AnalysisTrainPWG4Jets Skipping run number from File %d: %d",nRun, iRun);
1868        }
1869      }
1870    }
1871
1872 // Method 2: Declare existing data files (raw collections, xml collections, root file)
1873 // If no path mentioned data is supposed to be in the work directory (see SetGridWorkingDir())
1874 // XML collections added via this method can be combined with the first method if
1875 // the content is compatible (using or not tags)
1876 //   plugin->AddDataFile("tag.xml");
1877 //   plugin->AddDataFile("/alice/data/2008/LHC08c/000057657/raw/Run57657.Merged.RAW.tag.root");
1878 // Define alien work directory where all files will be copied. Relative to alien $HOME.
1879    TString alien_workdir = "";
1880    
1881    if (iAODanalysis)  alien_workdir += "analysisAOD";
1882    else               alien_workdir += "analysisESD";    
1883    if(kGridDataSet.Length()>0)alien_workdir += Form("/%s",kGridDataSet.Data());
1884    plugin->SetGridWorkingDir(alien_workdir.Data());
1885
1886    // Declare alien output directory. Relative to working directory.
1887    if (!kGridOutdir.Length()) kGridOutdir = Form("output_%s",kTrainName.Data());
1888    plugin->SetGridOutputDir(kGridOutdir);
1889
1890    // Add external packages
1891    if (iJETAN||iDIJETAN) {
1892       plugin->AddExternalPackage("boost::v1_43_0");
1893       plugin->AddExternalPackage("cgal::v3.6");
1894       plugin->AddExternalPackage("fastjet::v2.4.2");
1895    }   
1896
1897
1898    // set extra libs before par file compilation
1899    anaLibs += kGridExtraFiles;
1900    anaLibs     = anaLibs.Strip();   
1901    Printf("anaLibs %s",anaLibs.Data());
1902    Printf("anaLibsExtra %s",anaLibsExtra.Data());
1903
1904    if (anaLibs.Length())          plugin->SetAdditionalLibs(anaLibs.Data());
1905    if (anaLibsExtra.Length())     plugin->SetAdditionalRootLibs(anaLibsExtra.Data());
1906
1907    TString ana_sources = "";
1908    TString ana_add = "";
1909    if (kUsePAR && anaPars.Length()) {
1910       printf("%s\n", anaPars.Data());
1911       TObjArray *arr;
1912       TObjString *objstr;
1913       arr = anaPars.Tokenize(" ");
1914       TIter next(arr);
1915       while ((objstr=(TObjString*)next())) plugin->EnablePackage(objstr->GetString());
1916       delete arr;
1917    } 
1918    
1919 // Declare the analysis source files names separated by blancs. To be compiled runtime
1920 // using ACLiC on the worker nodes.
1921    ana_sources = anaSources.Strip();
1922 // Declare all libraries (other than the default ones for the framework. These will be
1923 // loaded by the generated analysis macro. Add all extra files (task .cxx/.h) here.
1924
1925    if (ana_sources.Length()) plugin->SetAnalysisSource(ana_sources);
1926    plugin->SetExecutableCommand(kPluginExecutableCommand.Data());  
1927    // Declare the output file names separated by blancs.
1928    // (can be like: file.root or file.root@ALICE::Niham::File)
1929    plugin->SetMergeExcludes(kGridMergeExclude);
1930    plugin->SetMaxMergeFiles(kGridMaxMergeFiles);
1931    plugin->SetNrunsPerMaster(kGridRunsPerMaster);
1932    plugin->SetMergeViaJDL(kPluginMergeViaJDL);
1933    // Use fastread option
1934    plugin->SetFastReadOption(kPluginFastReadOption);
1935    // UseOverwrite mode
1936    plugin->SetOverwriteMode(kPluginOverwriteMode); 
1937    // Optionally define the files to be archived.
1938    //   plugin->SetOutputArchive("log_archive.zip:stdout,stderr@ALICE::NIHAM::File root_archive.zip:AliAOD.root,AOD.tag.root@ALICE::NIHAM::File");
1939    plugin->SetOutputToRunNo(kPluginOutputToRunNumber);     // write the output to subdirs named after run number
1940    
1941    // Put default output files to archive
1942    TString listhists = "";
1943    TString listaods  = "";
1944    AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
1945    TIter next(mgr->GetOutputs());
1946    AliAnalysisDataContainer *output;
1947    while ((output=(AliAnalysisDataContainer*)next())) {
1948       const char *filename = output->GetFileName();
1949       if (!(strcmp(filename, "default"))) {
1950         if (!mgr->GetOutputEventHandler()) continue;
1951          filename = mgr->GetOutputEventHandler()->GetOutputFileName();
1952          if (listaods.Length()) listaods += " ";
1953          listaods += filename;
1954       } else {
1955         if(!listhists.Contains(filename)){
1956           if (listhists.Length()) listhists += " ";
1957           listhists += filename;
1958         }
1959       }
1960    }
1961
1962    if (mgr->GetExtraFiles().Length()) {
1963      if (listaods.Length()) listaods += " ";
1964      listaods += mgr->GetExtraFiles();
1965    }
1966
1967    // if we do not fill the aod we do not need to store it
1968    //   kGridMergeExclude = listaods;
1969    
1970    if(kSaveAOD>=0){
1971      TString outputFiles =  "";
1972      outputFiles += mgr->GetExtraFiles();
1973      if (listhists.Length()) outputFiles += " ";
1974      outputFiles += listhists;
1975      plugin->SetDefaultOutputs(kFALSE);
1976      Printf("%s:%d Starting with the files %s",(char*)__FILE__,__LINE__,outputFiles.Data());
1977      // remove
1978      // no harm done when we try to remove something that is not there :)
1979      if(!(kSaveAOD&(1<<0))){
1980        outputFiles.ReplaceAll("AliAOD.root ","");
1981        listaods.ReplaceAll("AliAOD.root ","");
1982      }
1983      if(!(kSaveAOD&(1<<1))){
1984        if(kDeltaAODJetName.Length())outputFiles.ReplaceAll(kDeltaAODJetName.Data(),"");
1985        if(kDeltaAODJetName.Length())listaods.ReplaceAll(kDeltaAODJetName.Data(),"");
1986        
1987      }
1988      if(!(kSaveAOD&(1<<2))){
1989        if(kDeltaAODPartCorrName.Length())outputFiles.ReplaceAll(kDeltaAODPartCorrName.Data(),"");
1990        if(kDeltaAODPartCorrName.Length())listaods.ReplaceAll(kDeltaAODPartCorrName.Data(),"");
1991      }
1992      if(!(kSaveAOD&(1<<3))){
1993        if(kDeltaAODJCORRANName.Length())outputFiles.ReplaceAll(kDeltaAODJCORRANName.Data(),"");
1994        if(kDeltaAODJCORRANName.Length())listaods.ReplaceAll(kDeltaAODJCORRANName.Data(),"");
1995      }
1996      
1997      // 
1998      plugin->SetDefaultOutputs(kFALSE);
1999      Printf("%s:%d Saving the files %s",(char*)__FILE__,__LINE__,outputFiles.Data());
2000      plugin->SetOutputFiles(outputFiles.Data());
2001    }
2002
2003    TString outputArchive;
2004    outputArchive = Form("log_archive.zip:std*@%s","disk=1");
2005    listaods.ReplaceAll(" ", ",");
2006    listhists.ReplaceAll(" ", ",");
2007    if (listhists.Length()){
2008      outputArchive += " ";
2009      outputArchive += "root_archive.zip:";
2010      outputArchive += listhists;
2011      if (listaods.Length()){
2012        outputArchive += ",";
2013        outputArchive += listaods;
2014      }
2015      outputArchive += Form("@%s", kGridOutputStorages.Data());
2016    }
2017    else{
2018      
2019      if (listaods.Length()){
2020        // we have only aod'ish output
2021        outputArchive += " ";
2022        outputArchive += "root_archive.zip:";
2023        outputArchive += listaods;
2024        outputArchive += Form("@%s", kGridOutputStorages.Data());
2025      }
2026      else{
2027        // no other outputs than std..
2028       ::Fatal("AnalysisTrainPWG4Jets", "No task output !");
2029      }
2030    }
2031
2032    plugin->SetDefaultOutputs(kFALSE);
2033    plugin->SetOutputArchive(outputArchive);
2034
2035
2036    // Optionally set a name for the generated analysis macro (default MyAnalysis.C)
2037    plugin->SetAnalysisMacro(Form("%s.C", kTrainName.Data()));
2038    // Optionally set maximum number of input files/subjob (default 100, put 0 to ignore)
2039    plugin->SetSplitMaxInputFileNumber(kGridFilesPerJob);
2040    // Optionally set number of failed jobs that will trigger killing waiting sub-jobs.
2041    //   plugin->SetMaxInitFailed(5);
2042    // Optionally resubmit threshold.
2043    // plugin->SetMasterResubmitThreshold(90);
2044    // Optionally set time to live (default 30000 sec)
2045    plugin->SetTTL(54000); // 15h...
2046    // Optionally set input format (default xml-single)
2047    plugin->SetInputFormat("xml-single");
2048    // Optionally modify the name of the generated JDL (default analysis.jdl)
2049    plugin->SetJDLName(Form("%s.jdl", kTrainName.Data()));
2050    // Optionally modify the executable name (default analysis.sh)
2051    plugin->SetExecutable(Form("%s.sh", kTrainName.Data()));
2052    // Optionally modify job price (default 1)
2053    plugin->SetPrice(1);      
2054    // Optionally modify split mode (default 'se')    
2055    plugin->SetSplitMode("se");
2056    return plugin;
2057 }
2058
2059 //______________________________________________________________________________
2060 void WriteConfig()
2061 {
2062 // Write train configuration in a file. The file name has the format:
2063 // train_[trainName]_ddMonthyyyy_time.C
2064    if (kUseDate) {
2065       gSystem->Exec("date +%d%b%Y_%Hh%M > date.tmp");
2066       ifstream fdate("date.tmp");
2067       if (!fdate.is_open()) {
2068          ::Error("AnalysisTrainPWG4Jets.C::Export","Could not generate file name");
2069          return;
2070       }
2071       const char date[64];
2072       fdate.getline(date,64);
2073       fdate.close();
2074       gSystem->Exec("rm date.tmp");
2075       kTrainName = Form("train_%s_%s", kTrainName.Data(), date);
2076    } else {
2077       kTrainName = Form("train_%s", kTrainName.Data());
2078    }   
2079    TString cdir = gSystem->WorkingDirectory();
2080    gSystem->MakeDirectory(kTrainName);
2081    gSystem->ChangeDirectory(kTrainName);
2082    ofstream out;
2083    out.open(Form("%sConfig.C",kTrainName.Data()), ios::out); 
2084    if (out.bad()) {
2085       ::Error("AnalysisTrainPWG4Jets.C::Export", "Cannot open ConfigTrain.C for writing");
2086       return;
2087    }
2088    out << "{" << endl;
2089    out << "   kTrainName      = " << "\"" << kTrainName.Data() << "\";" << endl;
2090    out << "   kProofCluster   = " << "\"" << kProofCluster.Data() << "\";" << endl;
2091    out << "   kProofUseAFPAR        = " << kProofUseAFPAR << ";" << endl;
2092    if (kProofUseAFPAR) 
2093       out << "   kProofAFversion       = " << kProofAFversion.Data() << ";" << endl;
2094    out << "   kProofDataSet   = " << "\"" << kProofDataSet.Data() << "\";" << endl;
2095    out << "   kPluginUse       = " << kPluginUse << ";" << endl;
2096    out << "   kUsePAR          = " << kUsePAR << ";" << endl;
2097    out << "   kUseCPAR         = " << kUseCPAR << ";" << endl;
2098    out << "   kPluginRootVersion    = " << "\"" << kPluginRootVersion.Data() << "\";" << endl;
2099    out << "   kPluginAliRootVersion = " << "\"" << kPluginAliRootVersion.Data() << "\";" << endl;
2100    out << "   kGridDatadir   = " << "\"" << kGridDatadir.Data() << "\";" << endl;
2101    if (!kGridOutdir.Length()) kGridOutdir = Form("output_%s",kTrainName.Data());
2102    out << "   kGridOutdir    = " << "\"" << kGridOutdir.Data() << "\";" << endl;
2103    out << "   kGridMaxMergeFiles   = " << kGridMaxMergeFiles << ";" << endl;
2104    out << "   kGridMergeExclude    = " << "\"" << kGridMergeExclude.Data() << "\";" << endl;
2105    out << "   kGridRunsPerMaster  = " << kGridRunsPerMaster << ";" << endl;
2106    out << "   kGridFilesPerJob    = " << kGridFilesPerJob << ";" << endl;
2107    out << "   kGridRunRange[0]    = " << kGridRunRange[0] << ";" << endl;
2108    out << "   kGridRunRange[1]    = " << kGridRunRange[1] << ";" << endl;
2109    out << "   kUseDebug          = " << kUseDebug << ";" << endl;
2110    out << "   kUseMC           = " << kUseMC << ";" << endl;
2111    out << "   kUseESDTags         = " << kUseESDTags << ";" << endl;
2112    out << "   kUseKinefilter      = " << kUseKinefilter << ";" << endl;
2113    out << "   kUseTR           = " << kUseTR << ";" << endl;
2114    out << "   kUseAODTags      = " << kUseAODTags << ";" << endl;
2115    out << "   kSaveTrain       = " << "kFALSE;" << endl << endl;
2116    out << "   // Analysis modules" << endl;
2117    out << "   iAODanalysis    = " << iAODanalysis << ";" << endl;
2118    out << "   iAODhandler     = " << iAODhandler << ";" << endl;
2119    out << "   iESDfilter      = " << iESDfilter << ";" << endl;
2120    out << "   iJETAN          = " << iJETAN << ";" << endl;
2121    out << "// Configuration fot the wagons" << endl;
2122    out << "}" << endl;
2123    ::Info("AnalysisTrainPWG4Jets.C::WriteConfig", "Train configuration wrote to file %s", Form("config_%s.C", kTrainName.Data()));
2124    gSystem->ChangeDirectory(cdir);
2125 }   
2126
2127 //______________________________________________________________________________
2128 Bool_t LoadConfig(const char *filename)
2129 {
2130 // Read train configuration from file
2131    if (gSystem->AccessPathName(filename)) {
2132       ::Error("AnalysisTrainPWG4Jets.C::LoadConfig", "Config file name not found");
2133       return kFALSE;
2134    }   
2135    gROOT->ProcessLine(Form(".x %s", filename));
2136    ::Info("AnalysisTrainPWG4Jets.C::LoadConfig", "Train configuration loaded from file %s", filename);
2137    return kTRUE;
2138 }
2139
2140 Bool_t PatchJDL(){
2141   Printf(">>> Patching JDL");
2142   AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
2143   AliAnalysisAlien*    gridHandler = (AliAnalysisAlien*)mgr->GetGridHandler();
2144   TGridJDL *jdl = gridHandler->GetGridJDL();
2145   if(iJETAN)jdl->AddToPackages("fastjet","v2.4.0");
2146   gridHandler->WriteJDL(kFALSE);
2147   Printf("<<<  Patching JDL");
2148   return kTRUE;
2149 }
2150
2151 Bool_t PatchAnalysisMacro(){
2152   Printf(">>> Patching AnalysisMacro");
2153   gSystem->Exec(Form("mv %s.C %s.C_tmp",kTrainName.Data(),kTrainName.Data()));
2154
2155   ifstream in1; 
2156   in1.open(Form("%s.C_tmp", kTrainName.Data()));
2157   char cLine[250];
2158   TString st;
2159   while(in1.getline(cLine,250)){
2160     st += cLine;
2161     st += "\n";
2162   }
2163   Int_t index= -1;
2164   index = st.Index("gSystem->Load(\"libPhysics\");");
2165   index += strlen("gSystem->Load(\"libPhysics\");");
2166   /*
2167     TObjArray *arr;
2168     TObjString *objstr;
2169     arr = anaLibs.Tokenize(" ");
2170     TIter next(arr);
2171
2172     add += "\n\n // added by CKB \n";
2173     while ((objstr=(TObjString*)next())){
2174       if(objstr->GetString().Contains("PWG3"))continue;
2175       if(objstr->GetString().EndsWith(".so"))add += Form("gSystem->Load(\"%s\");\n",objstr->GetString().Data());
2176     }
2177     delete arr; 
2178     */
2179     //    add += Form("AliLog::SetGlobalLogLevel(%d);\n",AliLog::GetGlobalLogLevel());
2180   TString add = "";
2181
2182   if(index<0)Printf("%s:%d index out of bounds",(char*)__FILE__,__LINE__);
2183   add += "\n\n // added by CKB \n";
2184   if(kErrorIgnoreLevel>0)add += Form("gErrorIgnoreLevel = %d;\n",kErrorIgnoreLevel);
2185   add += "\n gSystem->AddIncludePath(\"./\"); \n";
2186   add += "\n gSystem->SetFPEMask(); \n";
2187
2188
2189   if(gGrid&&kPluginAliRootVersion.Length()==0){
2190     /*
2191     add += "\n // Dirty hack for TRD reference data \n";
2192     add += "\n gSystem->Setenv(\"ALICE_ROOT\",\"";
2193     add += Form("alien://%s/rootfiles/",gGrid->GetHomeDirectory());
2194     add += "\"); \n";
2195     */
2196   }
2197
2198   add += "// BKC \n\n";
2199   st.Insert(index,add.Data());
2200
2201   if(kUseDebug){
2202     //    st.Insert(index,"\n gROOT->ProcessLine(\".trace\"); // CKB \n");
2203   }
2204
2205   if(kUseCPAR&&kPluginAliRootVersion.Length()==0){
2206     index = st.Index("gSystem->AddIncludePath(\"-I$"); // uncommen $ALICE_ROOT include for par files
2207     if(index<0)Printf("%s:%d index out of bounds",(char*)__FILE__,__LINE__);
2208     st.Insert(index,"// CKB comment out whehn no aliroot is provided \n //");
2209   }
2210
2211   if(AliLog::GetGlobalLogLevel()==AliLog::kFatal){
2212     index = st.Index("AliLog::SetGlobal"); // ncomment setting of log level, do my own
2213     if(index<0)Printf("%s:%d index out of bounds",(char*)__FILE__,__LINE__);
2214     st.Insert(index,"AliLog::SetGlobalLogLevel(AliLog::kFatal);// CKB \n  // CKB comment out for own setting \n  //");
2215   }
2216
2217   ofstream out;
2218   out.open(Form("%s.C", kTrainName.Data()));
2219   if (out.bad()) {
2220     return kFALSE;
2221   }
2222   out << st << endl;
2223   Printf("<<< Patching AnalysisMacro");
2224
2225
2226
2227
2228
2229   Printf(">>> Patching Merge Macro");
2230   gSystem->Exec(Form("mv %s_merge.C %s_merge.C_tmp",kTrainName.Data(),kTrainName.Data()));
2231
2232   ifstream in2; 
2233   in2.open(Form("%s_merge.C_tmp", kTrainName.Data()));
2234   TString st2;
2235   while(in2.getline(cLine,250)){
2236     st2 += cLine;
2237     st2 += "\n";
2238   }
2239   index = st2.Index("gSystem->Load(\"libPhysics\");");
2240   index += strlen("gSystem->Load(\"libPhysics\");");
2241   TString add2 = "";
2242   add2 += "\n gSystem->AddIncludePath(\"./\"); \n";
2243   if(gGrid&&kPluginAliRootVersion.Length()==0){
2244     /*
2245     add2 += "\n // Dirty hack for TRD reference data \n";
2246     add2 += "\n gSystem->Setenv(\"ALICE_ROOT\",\"";
2247     add2 += Form("alien://%s/rootfiles/",gGrid->GetHomeDirectory());
2248     add2 += "\"); \n";
2249     */
2250   }
2251   add2 += "// BKC \n\n";
2252   if(index<0)Printf("%s:%d index out of bounds",(char*)__FILE__,__LINE__);
2253   st2.Insert(index,add.Data());
2254
2255
2256   if(kUseDebug){
2257     //    st2.Insert(index,"\n gROOT->ProcessLine(\".trace\"); // CKB \n");
2258   }
2259
2260   if(kUseCPAR&&kPluginAliRootVersion.Length()==0){
2261     index = st2.Index("gSystem->AddIncludePath(\"-I$"); // uncomment $ALICE_ROOT include for par files
2262     if(index<0)Printf("%s:%d index out of bounds",(char*)__FILE__,__LINE__);
2263     st2.Insert(index,"// CKB comment out whehn no aliroot is provided \n //");
2264   }
2265
2266   // do not exclude the extra files from merign, this is done explicitly in this train script
2267   //  index = st2.Index("mergeExcludes +="); // uncommen $ALICE_ROOT include for par files
2268   //  if(index<0)Printf("%s:%d index out of bounds",(char*)__FILE__,__LINE__);
2269   // st2.Insert(index,"// CKB comment out, handled explicitly by the train macro \n //");
2270
2271
2272   ofstream out2;
2273   out2.open(Form("%s_merge.C", kTrainName.Data()));
2274   if (out2.bad()) {
2275     return kFALSE;
2276   }
2277   out2 << st2 << endl;
2278   Printf("<<< Patching Merging Macro");
2279
2280
2281
2282   return kTRUE;
2283
2284 }