Renamed
[u/mrichter/AliRoot.git] / ANALYSIS / AliAnalysisAlien.cxx
index a5bbc78..3e78fb7 100644 (file)
 // a personalized JDL, finding and creating a dataset.
 //==============================================================================
 
+#include "AliAnalysisAlien.h"
+
 #include "Riostream.h"
 #include "TEnv.h"
+#include "TBits.h"
 #include "TError.h"
 #include "TROOT.h"
 #include "TSystem.h"
 #include "TFile.h"
+#include "TFileCollection.h"
+#include "TChain.h"
 #include "TObjString.h"
 #include "TObjArray.h"
 #include "TGrid.h"
@@ -38,7 +43,7 @@
 #include "AliAnalysisManager.h"
 #include "AliVEventHandler.h"
 #include "AliAnalysisDataContainer.h"
-#include "AliAnalysisAlien.h"
+#include "AliMultiInputEventHandler.h"
 
 ClassImp(AliAnalysisAlien)
 
@@ -55,6 +60,7 @@ AliAnalysisAlien::AliAnalysisAlien()
                   fNtestFiles(0),
                   fNrunsPerMaster(0),
                   fMaxMergeFiles(0),
+                  fMaxMergeStages(0),
                   fNsubmitted(0),
                   fProductionMode(0),
                   fOutputToRunNo(0),
@@ -62,6 +68,9 @@ AliAnalysisAlien::AliAnalysisAlien()
                   fFastReadOption(0),
                   fOverwriteMode(1),
                   fNreplicas(2),
+                  fNproofWorkers(0),
+                  fNproofWorkersPerSlave(0),
+                  fProofReset(0),
                   fRunNumbers(),
                   fExecutable(),
                   fExecutableCommand(),
@@ -69,6 +78,7 @@ AliAnalysisAlien::AliAnalysisAlien()
                   fExecutableArgs(),
                   fAnalysisMacro(),
                   fAnalysisSource(),
+                  fValidationScript(),
                   fAdditionalRootLibs(),
                   fAdditionalLibs(),
                   fSplitMode(),
@@ -86,6 +96,7 @@ AliAnalysisAlien::AliAnalysisAlien()
                   fInputFormat(),
                   fDatasetName(),
                   fJDLName(),
+                  fTerminateFiles(),
                            fMergeExcludes(),
                   fIncludePath(),
                   fCloseSE(),
@@ -93,6 +104,12 @@ AliAnalysisAlien::AliAnalysisAlien()
                   fJobTag(),
                   fOutputSingle(),
                   fRunPrefix(),
+                  fProofCluster(),
+                  fProofDataSet(),
+                  fFileForTestMode(),
+                  fRootVersionForProof(),
+                  fAliRootMode(),
+                  fMergeDirName(),
                   fInputFiles(0),
                   fPackages(0)
 {
@@ -113,6 +130,7 @@ AliAnalysisAlien::AliAnalysisAlien(const char *name)
                   fNtestFiles(0),
                   fNrunsPerMaster(0),
                   fMaxMergeFiles(0),
+                  fMaxMergeStages(0),
                   fNsubmitted(0),
                   fProductionMode(0),
                   fOutputToRunNo(0),
@@ -120,6 +138,9 @@ AliAnalysisAlien::AliAnalysisAlien(const char *name)
                   fFastReadOption(0),
                   fOverwriteMode(1),
                   fNreplicas(2),
+                  fNproofWorkers(0),
+                  fNproofWorkersPerSlave(0),
+                  fProofReset(0),
                   fRunNumbers(),
                   fExecutable(),
                   fExecutableCommand(),
@@ -127,6 +148,7 @@ AliAnalysisAlien::AliAnalysisAlien(const char *name)
                   fExecutableArgs(),
                   fAnalysisMacro(),
                   fAnalysisSource(),
+                  fValidationScript(),
                   fAdditionalRootLibs(),
                   fAdditionalLibs(),
                   fSplitMode(),
@@ -144,6 +166,7 @@ AliAnalysisAlien::AliAnalysisAlien(const char *name)
                   fInputFormat(),
                   fDatasetName(),
                   fJDLName(),
+                  fTerminateFiles(),
                   fMergeExcludes(),
                   fIncludePath(),
                   fCloseSE(),
@@ -151,6 +174,12 @@ AliAnalysisAlien::AliAnalysisAlien(const char *name)
                   fJobTag(),
                   fOutputSingle(),
                   fRunPrefix(),
+                  fProofCluster(),
+                  fProofDataSet(),
+                  fFileForTestMode(),
+                  fRootVersionForProof(),
+                  fAliRootMode(),
+                  fMergeDirName(),
                   fInputFiles(0),
                   fPackages(0)
 {
@@ -171,6 +200,7 @@ AliAnalysisAlien::AliAnalysisAlien(const AliAnalysisAlien& other)
                   fNtestFiles(other.fNtestFiles),
                   fNrunsPerMaster(other.fNrunsPerMaster),
                   fMaxMergeFiles(other.fMaxMergeFiles),
+                  fMaxMergeStages(other.fMaxMergeStages),
                   fNsubmitted(other.fNsubmitted),
                   fProductionMode(other.fProductionMode),
                   fOutputToRunNo(other.fOutputToRunNo),
@@ -178,6 +208,9 @@ AliAnalysisAlien::AliAnalysisAlien(const AliAnalysisAlien& other)
                   fFastReadOption(other.fFastReadOption),
                   fOverwriteMode(other.fOverwriteMode),
                   fNreplicas(other.fNreplicas),
+                  fNproofWorkers(other.fNproofWorkers),
+                  fNproofWorkersPerSlave(other.fNproofWorkersPerSlave),
+                  fProofReset(other.fProofReset),
                   fRunNumbers(other.fRunNumbers),
                   fExecutable(other.fExecutable),
                   fExecutableCommand(other.fExecutableCommand),
@@ -185,6 +218,7 @@ AliAnalysisAlien::AliAnalysisAlien(const AliAnalysisAlien& other)
                   fExecutableArgs(other.fExecutableArgs),
                   fAnalysisMacro(other.fAnalysisMacro),
                   fAnalysisSource(other.fAnalysisSource),
+                  fValidationScript(other.fValidationScript),
                   fAdditionalRootLibs(other.fAdditionalRootLibs),
                   fAdditionalLibs(other.fAdditionalLibs),
                   fSplitMode(other.fSplitMode),
@@ -202,6 +236,7 @@ AliAnalysisAlien::AliAnalysisAlien(const AliAnalysisAlien& other)
                   fInputFormat(other.fInputFormat),
                   fDatasetName(other.fDatasetName),
                   fJDLName(other.fJDLName),
+                  fTerminateFiles(other.fTerminateFiles),
                   fMergeExcludes(other.fMergeExcludes),
                   fIncludePath(other.fIncludePath),
                   fCloseSE(other.fCloseSE),
@@ -209,6 +244,12 @@ AliAnalysisAlien::AliAnalysisAlien(const AliAnalysisAlien& other)
                   fJobTag(other.fJobTag),
                   fOutputSingle(other.fOutputSingle),
                   fRunPrefix(other.fRunPrefix),
+                  fProofCluster(other.fProofCluster),
+                  fProofDataSet(other.fProofDataSet),
+                  fFileForTestMode(other.fFileForTestMode),
+                  fRootVersionForProof(other.fRootVersionForProof),
+                  fAliRootMode(other.fAliRootMode),
+                  fMergeDirName(other.fMergeDirName),
                   fInputFiles(0),
                   fPackages(0)
 {
@@ -259,6 +300,7 @@ AliAnalysisAlien &AliAnalysisAlien::operator=(const AliAnalysisAlien& other)
       fNtestFiles              = other.fNtestFiles;
       fNrunsPerMaster          = other.fNrunsPerMaster;
       fMaxMergeFiles           = other.fMaxMergeFiles;
+      fMaxMergeStages          = other.fMaxMergeStages;
       fNsubmitted              = other.fNsubmitted;
       fProductionMode          = other.fProductionMode;
       fOutputToRunNo           = other.fOutputToRunNo;
@@ -266,6 +308,9 @@ AliAnalysisAlien &AliAnalysisAlien::operator=(const AliAnalysisAlien& other)
       fFastReadOption          = other.fFastReadOption;
       fOverwriteMode           = other.fOverwriteMode;
       fNreplicas               = other.fNreplicas;
+      fNproofWorkers           = other.fNproofWorkers;
+      fNproofWorkersPerSlave   = other.fNproofWorkersPerSlave;
+      fProofReset              = other.fProofReset;
       fRunNumbers              = other.fRunNumbers;
       fExecutable              = other.fExecutable;
       fExecutableCommand       = other.fExecutableCommand;
@@ -273,6 +318,7 @@ AliAnalysisAlien &AliAnalysisAlien::operator=(const AliAnalysisAlien& other)
       fExecutableArgs          = other.fExecutableArgs;
       fAnalysisMacro           = other.fAnalysisMacro;
       fAnalysisSource          = other.fAnalysisSource;
+      fValidationScript        = other.fValidationScript;
       fAdditionalRootLibs      = other.fAdditionalRootLibs;
       fAdditionalLibs          = other.fAdditionalLibs;
       fSplitMode               = other.fSplitMode;
@@ -290,6 +336,7 @@ AliAnalysisAlien &AliAnalysisAlien::operator=(const AliAnalysisAlien& other)
       fInputFormat             = other.fInputFormat;
       fDatasetName             = other.fDatasetName;
       fJDLName                 = other.fJDLName;
+      fTerminateFiles          = other.fTerminateFiles;
       fMergeExcludes           = other.fMergeExcludes;
       fIncludePath             = other.fIncludePath;
       fCloseSE                 = other.fCloseSE;
@@ -297,6 +344,12 @@ AliAnalysisAlien &AliAnalysisAlien::operator=(const AliAnalysisAlien& other)
       fJobTag                  = other.fJobTag;
       fOutputSingle            = other.fOutputSingle;
       fRunPrefix               = other.fRunPrefix;
+      fProofCluster            = other.fProofCluster;
+      fProofDataSet            = other.fProofDataSet;
+      fFileForTestMode         = other.fFileForTestMode;
+      fRootVersionForProof     = other.fRootVersionForProof;
+      fAliRootMode             = other.fAliRootMode;
+      fMergeDirName            = other.fMergeDirName;
       if (other.fInputFiles) {
          fInputFiles = new TObjArray();
          TIter next(other.fInputFiles);
@@ -316,6 +369,14 @@ AliAnalysisAlien &AliAnalysisAlien::operator=(const AliAnalysisAlien& other)
 }
 
 //______________________________________________________________________________
+void AliAnalysisAlien::SetRunPrefix(const char *prefix)
+{
+// Set the run number format. Can be a prefix or a format like "%09d"
+   fRunPrefix = prefix;
+   if (!fRunPrefix.Contains("%")) fRunPrefix += "%d";
+}   
+
+//______________________________________________________________________________
 void AliAnalysisAlien::AddIncludePath(const char *path)
 {
 // Add include path in the remote analysis macro.
@@ -329,10 +390,24 @@ void AliAnalysisAlien::AddRunNumber(Int_t run)
 {
 // Add a run number to the list of runs to be processed.
    if (fRunNumbers.Length()) fRunNumbers += " ";
-   fRunNumbers += Form("%s%d", fRunPrefix.Data(), run);
+   fRunNumbers += Form(fRunPrefix.Data(), run);
 }   
 
 //______________________________________________________________________________
+void AliAnalysisAlien::AddRunList(const char* runList)
+{
+// Add several runs into the list of runs; they are expected to be separated by a blank character.  
+  TString    sList = runList;
+  TObjArray *list  = sList.Tokenize(" ");
+  Int_t n = list->GetEntries();
+  for (Int_t i = 0; i < n; i++) {
+    TObjString *os = (TObjString*)list->At(i);
+    AddRunNumber(os->GetString().Atoi());
+  }
+  delete list;
+}
+
+//______________________________________________________________________________
 void AliAnalysisAlien::AddRunNumber(const char* run)
 {
 // Add a run number to the list of runs to be processed.
@@ -362,6 +437,7 @@ Bool_t AliAnalysisAlien::Connect()
 {
 // Try to connect to AliEn. User needs a valid token and /tmp/gclient_env_$UID sourced.
    if (gGrid && gGrid->IsConnected()) return kTRUE;
+   if (fProductionMode) return kTRUE;
    if (!gGrid) {
       Info("Connect", "Trying to connect to AliEn ...");
       TGrid::Connect("alien://");
@@ -391,11 +467,11 @@ void AliAnalysisAlien::CdWork()
    }   
    // Work directory not existing - create it
    gGrid->Cd(homedir);
-   if (gGrid->Mkdir(workdir)) {
+   if (gGrid->Mkdir(workdir, "-p")) {
       gGrid->Cd(fGridWorkingDir);
-      Info("CreateJDL", "\n#####   Created alien working directory %s", fGridWorkingDir.Data());
+      Info("CdWork", "\n#####   Created alien working directory %s", fGridWorkingDir.Data());
    } else {
-      Warning("CreateJDL", "Working directory %s cannot be created.\n Using %s instead.",
+      Warning("CdWork", "Working directory %s cannot be created.\n Using %s instead.",
               workdir.Data(), homedir.Data());
       fGridWorkingDir = "";
    }          
@@ -405,6 +481,7 @@ void AliAnalysisAlien::CdWork()
 Bool_t AliAnalysisAlien::CheckFileCopy(const char *alienpath)
 {
 // Check if file copying is possible.
+   if (fProductionMode) return kTRUE;
    if (!Connect()) {
       Error("CheckFileCopy", "Not connected to AliEn. File copying cannot be tested.");
       return kFALSE;
@@ -453,12 +530,19 @@ Bool_t AliAnalysisAlien::CheckFileCopy(const char *alienpath)
 Bool_t AliAnalysisAlien::CheckInputData()
 {
 // Check validity of input data. If necessary, create xml files.
+   if (fProductionMode) return kTRUE;
    if (!fInputFiles && !fRunNumbers.Length() && !fRunRange[0]) {
       if (!fGridDataDir.Length()) {
          Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
          return kFALSE;
       }
+      if (fMergeViaJDL) {
+         Error("CheckInputData", "Merging via jdl works only with run numbers, run range or provided xml");
+         return kFALSE;
+      }   
       Info("CheckInputData", "Analysis will make a single xml for base data directory %s",fGridDataDir.Data());
+      if (fDataPattern.Contains("tag") && TestBit(AliAnalysisGrid::kTest))
+         TObject::SetBit(AliAnalysisGrid::kUseTags, kTRUE); // ADDED (fix problem in determining the tag usage in test mode) 
       return kTRUE;
    }
    // Process declared files
@@ -466,7 +550,7 @@ Bool_t AliAnalysisAlien::CheckInputData()
    Bool_t isXml = kFALSE;
    Bool_t useTags = kFALSE;
    Bool_t checked = kFALSE;
-   CdWork();
+   if (!TestBit(AliAnalysisGrid::kTest)) CdWork();
    TString file;
    TString workdir = gGrid->GetHomeDirectory();
    workdir += fGridWorkingDir;
@@ -526,6 +610,7 @@ Bool_t AliAnalysisAlien::CheckInputData()
    // Check validity of run number(s)
    TObjArray *arr;
    TObjString *os;
+   TString format;
    Int_t nruns = 0;
    TString schunk, schunk2;
    TString path;
@@ -554,7 +639,7 @@ Bool_t AliAnalysisAlien::CheckInputData()
          msg += " type: xml_collection;";
          if (useTags) msg += " using_tags: Yes";
          else          msg += " using_tags: No";
-         Info("CheckDataType", msg.Data());
+         Info("CheckDataType", "%s", msg.Data());
          if (fNrunsPerMaster<2) {
             AddDataFile(Form("%s.xml", os->GetString().Data()));
          } else {
@@ -571,26 +656,29 @@ Bool_t AliAnalysisAlien::CheckInputData()
    } else {
       Info("CheckDataType", "Using run range [%d, %d]", fRunRange[0], fRunRange[1]);
       for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
-         path = Form("%s/%s%d ", fGridDataDir.Data(), fRunPrefix.Data(), irun);
+         format = Form("%%s/%s ", fRunPrefix.Data());
+         path = Form(format.Data(), fGridDataDir.Data(), irun);
          if (!DirectoryExists(path)) {
-//            Warning("CheckInputData", "Run number %d not found in path: <%s>", irun, path.Data());
             continue;
          }
-         path = Form("%s/%s%d.xml", workdir.Data(),fRunPrefix.Data(),irun);
+         format = Form("%%s/%s.xml", fRunPrefix.Data());
+         path = Form(format.Data(), workdir.Data(),irun);
          TString msg = "\n#####   file: ";
          msg += path;
          msg += " type: xml_collection;";
          if (useTags) msg += " using_tags: Yes";
          else          msg += " using_tags: No";
-         Info("CheckDataType", msg.Data());
+         Info("CheckDataType", "%s", msg.Data());
          if (fNrunsPerMaster<2) {
-            AddDataFile(Form("%s%d.xml",fRunPrefix.Data(),irun));
+            format = Form("%s.xml", fRunPrefix.Data());
+            AddDataFile(Form(format.Data(),irun));
          } else {
             nruns++;
             if (((nruns-1)%fNrunsPerMaster) == 0) {
-               schunk = Form("%s%d", fRunPrefix.Data(),irun);
+               schunk = Form(fRunPrefix.Data(),irun);
             }
-            schunk2 = Form("_%s%d.xml", fRunPrefix.Data(), irun);
+            format = Form("_%s.xml", fRunPrefix.Data());
+            schunk2 = Form(format.Data(), irun);
             if ((nruns%fNrunsPerMaster)!=0 && irun != fRunRange[1]) continue;
             schunk += schunk2;
             AddDataFile(schunk);
@@ -608,18 +696,19 @@ Bool_t AliAnalysisAlien::CheckInputData()
 Bool_t AliAnalysisAlien::CreateDataset(const char *pattern)
 {
 // Create dataset for the grid data directory + run number.
-   if (TestBit(AliAnalysisGrid::kOffline)) return kTRUE;
+   if (fProductionMode || TestBit(AliAnalysisGrid::kOffline)) return kTRUE;
    if (!Connect()) {
       Error("CreateDataset", "Cannot create dataset with no grid connection");
       return kFALSE;
    }   
 
    // Cd workspace
-   CdWork();
+   if (!TestBit(AliAnalysisGrid::kTest)) CdWork();
    TString workdir = gGrid->GetHomeDirectory();
    workdir += fGridWorkingDir;
 
    // Compose the 'find' command arguments
+   TString format;
    TString command;
    TString options = "-x collection ";
    if (TestBit(AliAnalysisGrid::kTest)) options += Form("-l %d ", fNtestFiles);
@@ -773,11 +862,13 @@ Bool_t AliAnalysisAlien::CreateDataset(const char *pattern)
    } else {
       // Process a full run range.
       for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
-         path = Form("%s/%s%d ", fGridDataDir.Data(), fRunPrefix.Data(), irun);
+         format = Form("%%s/%s ", fRunPrefix.Data());
+         path = Form(format.Data(), fGridDataDir.Data(), irun);
          if (!DirectoryExists(path)) continue;
 //         CdWork();
+         format = Form("%s.xml", fRunPrefix.Data());
          if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
-         else file = Form("%s%d.xml", fRunPrefix.Data(), irun);
+         else file = Form(format.Data(), irun);
          if (FileExists(file) && fNrunsPerMaster<2 && !TestBit(AliAnalysisGrid::kTest)) {         
             if (fOverwriteMode) gGrid->Rm(file);
             else {
@@ -835,14 +926,15 @@ Bool_t AliAnalysisAlien::CreateDataset(const char *pattern)
             }   
             printf("   Merging collection <%s> into %d runs chunk...\n",file.Data(),fNrunsPerMaster);
             if (((nruns-1)%fNrunsPerMaster) == 0) {
-               schunk = Form("%s%d", fRunPrefix.Data(), irun);
+               schunk = Form(fRunPrefix.Data(), irun);
                cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
             } else {
                cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
                cbase->Add(cadd);
                delete cadd;
             }
-            schunk2 = Form("%s_%s%d.xml", schunk.Data(), fRunPrefix.Data(), irun);
+            format = Form("%%s_%s.xml", fRunPrefix.Data());
+            schunk2 = Form(format.Data(), schunk.Data(), irun);
             if ((nruns%fNrunsPerMaster)!=0 && irun!=fRunRange[1] && schunk2 != fInputFiles->Last()->GetName()) {
                continue;
             }   
@@ -886,7 +978,7 @@ Bool_t AliAnalysisAlien::CreateJDL()
    Bool_t error = kFALSE;
    TObjArray *arr = 0;
    Bool_t copy = kTRUE;
-   if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+   if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
    Bool_t generate = kTRUE;
    if (TestBit(AliAnalysisGrid::kTest) || TestBit(AliAnalysisGrid::kSubmit)) generate = kFALSE;
    if (!Connect()) {
@@ -894,8 +986,9 @@ Bool_t AliAnalysisAlien::CreateJDL()
       return kFALSE;
    }   
    // Check validity of alien workspace
-   CdWork();
-   TString workdir = gGrid->GetHomeDirectory();
+   TString workdir;
+   if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice")) workdir = gGrid->GetHomeDirectory();
+   if (!fProductionMode &&  !TestBit(AliAnalysisGrid::kTest)) CdWork();
    workdir += fGridWorkingDir;
    if (generate) {
       TObjString *os;
@@ -914,16 +1007,20 @@ Bool_t AliAnalysisAlien::CreateJDL()
          Error("CreateJDL", "You must define AliEn output directory");
          error = kTRUE;
       } else {
-         if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
-         if (!DirectoryExists(fGridOutputDir)) {
-            if (gGrid->Mkdir(fGridOutputDir)) {
-               Info("CreateJDL", "\n#####   Created alien output directory %s", fGridOutputDir.Data());
+         if (!fProductionMode) {
+            if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
+            if (!DirectoryExists(fGridOutputDir)) {
+               if (gGrid->Mkdir(fGridOutputDir,"-p")) {
+                  Info("CreateJDL", "\n#####   Created alien output directory %s", fGridOutputDir.Data());
+               } else {
+                  Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
+                  // error = kTRUE;
+               }
             } else {
-               Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
-               // error = kTRUE;
-            }
-         }
-         gGrid->Cd(workdir);
+               Warning("CreateJDL", "#### Output directory %s exists! If this contains old data, jobs will fail with ERROR_SV !!! ###", fGridOutputDir.Data());
+            }   
+            gGrid->Cd(workdir);
+         }   
       }   
       // Exit if any error up to now
       if (error) return kFALSE;   
@@ -940,7 +1037,12 @@ Bool_t AliAnalysisAlien::CreateJDL()
       fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),mergeExec.Data()), "List of input files to be uploaded to workers");
       if (!fArguments.IsNull())
          fGridJDL->SetArguments(fArguments, "Arguments for the executable command");
-      fMergingJDL->SetArguments("$1"); 
+      if (IsOneStageMerging()) fMergingJDL->SetArguments(fGridOutputDir);
+      else {
+         if (fProductionMode)  fMergingJDL->SetArguments("wn.xml $4");    // xml, stage
+         else                  fMergingJDL->SetArguments("wn.xml $2");    // xml, stage
+     }               
+
       fGridJDL->SetValue("TTL", Form("\"%d\"",fTTL));
       fGridJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60));
       fMergingJDL->SetValue("TTL", Form("\"%d\"",fTTL));
@@ -953,11 +1055,17 @@ Bool_t AliAnalysisAlien::CreateJDL()
       if (fSplitMaxInputFileNumber > 0) {
          fGridJDL->SetValue("SplitMaxInputFileNumber", Form("\"%d\"", fSplitMaxInputFileNumber));
          fGridJDL->SetDescription("SplitMaxInputFileNumber", "Maximum number of input files to be processed per subjob");
+      }
+      if (!IsOneStageMerging()) {
+         fMergingJDL->SetValue("SplitMaxInputFileNumber", Form("\"%d\"",fMaxMergeFiles));
+         fMergingJDL->SetDescription("SplitMaxInputFileNumber", "Maximum number of input files to be merged in one go");
       }   
       if (fSplitMode.Length()) {
          fGridJDL->SetValue("Split", Form("\"%s\"", fSplitMode.Data()));
          fGridJDL->SetDescription("Split", "We split per SE or file");
-      }   
+      }
+      fMergingJDL->SetValue("Split", "\"se\""); 
+      fMergingJDL->SetDescription("Split", "We split per SE for merging in stages");
       if (!fAliROOTVersion.IsNull()) {
          fGridJDL->AddToPackages("AliRoot", fAliROOTVersion,"VO_ALICE", "List of requested packages");
          fMergingJDL->AddToPackages("AliRoot", fAliROOTVersion, "VO_ALICE", "List of requested packages");
@@ -985,6 +1093,8 @@ Bool_t AliAnalysisAlien::CreateJDL()
       }   
       fGridJDL->SetInputDataListFormat(fInputFormat, "Format of input data");
       fGridJDL->SetInputDataList("wn.xml", "Collection name to be processed on each worker node");
+      fMergingJDL->SetInputDataListFormat(fInputFormat, "Format of input data");
+      fMergingJDL->SetInputDataList("wn.xml", "Collection name to be processed on each worker node");
       fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), fAnalysisMacro.Data()), "List of input files to be uploaded to workers");
       TString analysisFile = fExecutable;
       analysisFile.ReplaceAll(".sh", ".root");
@@ -1025,26 +1135,40 @@ Bool_t AliAnalysisAlien::CreateJDL()
             first = kFALSE;   
          }      
          delete arr;
-         TString outputArchive = fOutputArchive;
-         if (!fMergeExcludes.IsNull()) {
-            arr = fMergeExcludes.Tokenize(" ");
-            TIter next1(arr);
-            while ((os=(TObjString*)next1())) {
-               outputArchive.ReplaceAll(Form("%s,",os->GetString().Data()),"");
-               outputArchive.ReplaceAll(os->GetString(),"");
+         // Output archive for the merging jdl
+         TString outputArchive;
+         if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
+            outputArchive = "log_archive.zip:std*@disk=1 ";
+            // Add normal output files, extra files + terminate files
+            TString files = GetListOfFiles("outextter");
+            // Do not register merge excludes
+            if (!fMergeExcludes.IsNull()) {
+               arr = fMergeExcludes.Tokenize(" ");
+               TIter next1(arr);
+               while ((os=(TObjString*)next1())) {
+                  files.ReplaceAll(Form("%s,",os->GetString().Data()),"");
+                  files.ReplaceAll(os->GetString(),"");
+               }   
+               delete arr;
             }
-            delete arr;
-         }
+            files.ReplaceAll(".root", "*.root");
+            outputArchive += Form("root_archive.zip:%s,*.stat@disk=%d",files.Data(),fNreplicas);
+         } else {
+            TString files = fOutputArchive;
+            files.ReplaceAll(".root", "*.root"); // nreplicas etc should be already atttached by use
+            outputArchive = files;
+         }   
          arr = outputArchive.Tokenize(" ");
          TIter next2(arr);
          comment = comment1;
          first = kTRUE;
          while ((os=(TObjString*)next2())) {
             if (!first) comment = NULL;
-            if (!os->GetString().Contains("@") && fCloseSE.Length())
-               fMergingJDL->AddToOutputArchive(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment); 
+            TString currentfile = os->GetString();
+            if (!currentfile.Contains("@") && fCloseSE.Length())
+               fMergingJDL->AddToOutputArchive(Form("%s@%s",currentfile.Data(), fCloseSE.Data()), comment);
             else
-               fMergingJDL->AddToOutputArchive(os->GetString(), comment);
+               fMergingJDL->AddToOutputArchive(currentfile, comment);
             first = kFALSE;   
          }      
          delete arr;         
@@ -1052,11 +1176,12 @@ Bool_t AliAnalysisAlien::CreateJDL()
       arr = fOutputFiles.Tokenize(",");
       TIter next(arr);
       Bool_t first = kTRUE;
-      const char *comment = "Files to be archived";
-      const char *comment1 = comment;
+      const char *comment = "Files to be saved";
       while ((os=(TObjString*)next())) {
          // Ignore ouputs in jdl that are also in outputarchive
          TString sout = os->GetString();
+         sout.ReplaceAll("*", "");
+         sout.ReplaceAll(".root", "");
          if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
          if (fOutputArchive.Contains(sout)) continue;
          if (!first) comment = NULL;
@@ -1064,44 +1189,19 @@ Bool_t AliAnalysisAlien::CreateJDL()
             fGridJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment); 
          else
             fGridJDL->AddToOutputSandbox(os->GetString(), comment);
-         first = kFALSE;   
+         first = kFALSE;
+         if (fMergeExcludes.Contains(sout)) continue;   
+         if (!os->GetString().Contains("@") && fCloseSE.Length())
+            fMergingJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment); 
+         else
+            fMergingJDL->AddToOutputSandbox(os->GetString(), comment);
       }   
       delete arr;
-      if (fOutputFiles.Length()) {
-         TString outputFiles = fOutputFiles;
-         if (!fMergeExcludes.IsNull()) {
-            arr = fMergeExcludes.Tokenize(" ");
-            TIter next1(arr);
-            while ((os=(TObjString*)next1())) {
-               outputFiles.ReplaceAll(Form("%s,",os->GetString().Data()),"");
-               outputFiles.ReplaceAll(os->GetString(),"");
-            }
-            delete arr;
-         }
-         arr = outputFiles.Tokenize(" ");
-         TIter next2(arr);
-         comment = comment1;
-         first = kTRUE;
-         while ((os=(TObjString*)next2())) {
-            // Ignore ouputs in jdl that are also in outputarchive
-            TString sout = os->GetString();
-            if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
-            if (fOutputArchive.Contains(sout)) continue;
-            if (!first) comment = NULL;
-            if (!os->GetString().Contains("@") && fCloseSE.Length())
-               fMergingJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment); 
-            else
-               fMergingJDL->AddToOutputSandbox(os->GetString(), comment);
-         }   
-         delete arr;
-      }
       fGridJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
       fMergingJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
-      TString validationScript = fExecutable;
-      validationScript.ReplaceAll(".sh", "_validation.sh");
+      TString validationScript = fValidationScript;
       fGridJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
-      validationScript = fExecutable;
-      validationScript.ReplaceAll(".sh", "_mergevalidation.sh");
+      validationScript.ReplaceAll(".sh", "_merge.sh");
       fMergingJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
       if (fMasterResubmitThreshold) {
          fGridJDL->SetValue("MasterResubmitThreshold", Form("\"%d%%\"", fMasterResubmitThreshold));
@@ -1119,7 +1219,7 @@ Bool_t AliAnalysisAlien::CreateJDL()
       } else {
          if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
          if (!fProductionMode && !DirectoryExists(fGridOutputDir)) {
-            if (gGrid->Mkdir(fGridOutputDir)) {
+            if (gGrid->Mkdir(fGridOutputDir,"-p")) {
                Info("CreateJDL", "\n#####   Created alien output directory %s", fGridOutputDir.Data());
             } else {
                Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
@@ -1178,38 +1278,62 @@ Bool_t AliAnalysisAlien::WriteJDL(Bool_t copy)
 // all run numbers are considered in one go (jdl). For non-negative indices
 // they correspond to the indices in the array fInputFiles.
    if (!fInputFiles) return kFALSE;
-   TObjString *os;
-   TString workdir = gGrid->GetHomeDirectory();
+   TObject *os;
+   TString workdir;
+   if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice")) workdir = gGrid->GetHomeDirectory();
    workdir += fGridWorkingDir;
-   
-   if (!fRunNumbers.Length() && !fRunRange[0]) {
-      // One jdl with no parameters in case input data is specified by name.
-      TIter next(fInputFiles);
-      while ((os=(TObjString*)next()))
-         fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetString().Data()), "Input xml collections");
-      if (!fOutputSingle.IsNull())
-         fGridJDL->SetOutputDirectory(Form("#alienfulldir#/../%s",fOutputSingle.Data()), "Output directory");
-      else {
-         fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
-         fMergingJDL->SetOutputDirectory(fGridOutputDir);         
-      }   
+   TString stageName = "$2";
+   if (fProductionMode) stageName = "$4";
+   if (!fMergeDirName.IsNull()) {
+     fMergingJDL->AddToInputDataCollection(Form("LF:$1/%s/Stage_%s.xml,nodownload",fMergeDirName.Data(),stageName.Data()), "Collection of files to be merged for current stage");
+     fMergingJDL->SetOutputDirectory(Form("$1/%s/Stage_%s/#alien_counter_03i#",fMergeDirName.Data(),stageName.Data()), "Output directory");
    } else {
-      // One jdl to be submitted with 2 input parameters: data collection name and output dir prefix
-      fGridJDL->AddToInputDataCollection(Form("LF:%s/$1,nodownload", workdir.Data()), "Input xml collections");
-      if (!fOutputSingle.IsNull()) {
-         if (!fOutputToRunNo) fGridJDL->SetOutputDirectory(Form("#alienfulldir#/%s",fOutputSingle.Data()), "Output directory");
-         else fGridJDL->SetOutputDirectory(Form("%s/$2",fGridOutputDir.Data()), "Output directory");
-      } else {   
-         fGridJDL->SetOutputDirectory(Form("%s/$2/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
-         fMergingJDL->SetOutputDirectory(Form("%s/$1", fGridOutputDir.Data()), "Output directory");
-      }   
+     fMergingJDL->AddToInputDataCollection(Form("LF:$1/Stage_%s.xml,nodownload",stageName.Data()), "Collection of files to be merged for current stage");
+     fMergingJDL->SetOutputDirectory(Form("$1/Stage_%s/#alien_counter_03i#",stageName.Data()), "Output directory");
+   }
+   if (fProductionMode) {
+      TIter next(fInputFiles);
+      while ((os=next())) {
+         fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetName()), "Input xml collections");
+      }
+      fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_04i#", fGridOutputDir.Data()));
+   } else {            
+      if (!fRunNumbers.Length() && !fRunRange[0]) {
+         // One jdl with no parameters in case input data is specified by name.
+         TIter next(fInputFiles);
+         while ((os=next()))
+            fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetName()), "Input xml collections");
+         if (!fOutputSingle.IsNull())
+            fGridJDL->SetOutputDirectory(Form("#alienfulldir#/../%s",fOutputSingle.Data()), "Output directory");
+         else {
+            fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
+            fMergingJDL->SetOutputDirectory(fGridOutputDir);         
+         }   
+      } else {
+         // One jdl to be submitted with 2 input parameters: data collection name and output dir prefix
+         fGridJDL->AddToInputDataCollection(Form("LF:%s/$1,nodownload", workdir.Data()), "Input xml collections");
+         if (!fOutputSingle.IsNull()) {
+            if (!fOutputToRunNo) fGridJDL->SetOutputDirectory(Form("#alienfulldir#/%s",fOutputSingle.Data()), "Output directory");
+            else fGridJDL->SetOutputDirectory(Form("%s/$2",fGridOutputDir.Data()), "Output directory");
+         } else {   
+            fGridJDL->SetOutputDirectory(Form("%s/$2/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
+         }   
+      }
    }
       
-
    // Generate the JDL as a string
    TString sjdl = fGridJDL->Generate();
    TString sjdl1 = fMergingJDL->Generate();
-   Int_t index;
+   // Final merge jdl
+   if (!fMergeDirName.IsNull()) {
+     fMergingJDL->SetOutputDirectory(Form("$1/%s",fMergeDirName.Data()), "Output directory");
+     fMergingJDL->AddToInputSandbox(Form("LF:$1/%s/Stage_%s.xml",fMergeDirName.Data(),stageName.Data()));
+   } else {  
+     fMergingJDL->SetOutputDirectory("$1", "Output directory");
+     fMergingJDL->AddToInputSandbox(Form("LF:$1/Stage_%s.xml",stageName.Data()));
+   }  
+   TString sjdl2 = fMergingJDL->Generate();
+   Int_t index, index1;
    sjdl.ReplaceAll("\"LF:", "\n   \"LF:");
    sjdl.ReplaceAll("(member", "\n   (member");
    sjdl.ReplaceAll("\",\"VO_", "\",\n   \"VO_");
@@ -1226,51 +1350,138 @@ Bool_t AliAnalysisAlien::WriteJDL(Bool_t copy)
    sjdl1.ReplaceAll("{\n   \n", "{\n");
    sjdl1.ReplaceAll("\n\n", "\n");
    sjdl1.ReplaceAll("OutputDirectory", "OutputDir");
+   sjdl2.ReplaceAll("\"LF:", "\n   \"LF:");
+   sjdl2.ReplaceAll("(member", "\n   (member");
+   sjdl2.ReplaceAll("\",\"VO_", "\",\n   \"VO_");
+   sjdl2.ReplaceAll("{", "{\n   ");
+   sjdl2.ReplaceAll("};", "\n};");
+   sjdl2.ReplaceAll("{\n   \n", "{\n");
+   sjdl2.ReplaceAll("\n\n", "\n");
+   sjdl2.ReplaceAll("OutputDirectory", "OutputDir");
    sjdl += "JDLVariables = \n{\n   \"Packages\",\n   \"OutputDir\"\n};\n";
    sjdl.Prepend(Form("Jobtag = {\n   \"comment:%s\"\n};\n", fJobTag.Data()));
    index = sjdl.Index("JDLVariables");
    if (index >= 0) sjdl.Insert(index, "\n# JDL variables\n");
+   sjdl += "Workdirectorysize = {\"5000MB\"};";
+   sjdl1 += "Workdirectorysize = {\"5000MB\"};";
    sjdl1 += "JDLVariables = \n{\n   \"Packages\",\n   \"OutputDir\"\n};\n";
-   sjdl1.Prepend(Form("Jobtag = {\n   \"comment:Merging_%s\"\n};\n", fJobTag.Data()));
+   index = fJobTag.Index(":");
+   if (index < 0) index = fJobTag.Length();
+   TString jobTag = fJobTag;
+   if (fProductionMode) jobTag.Insert(index,"_Stage$4");
+   sjdl1.Prepend(Form("Jobtag = {\n   \"comment:%s_Merging\"\n};\n", jobTag.Data()));
+   if (fProductionMode) {   
+     sjdl1.Prepend("# Generated merging jdl (production mode) \
+                    \n# $1 = full alien path to output directory to be merged \
+                    \n# $2 = train number \
+                    \n# $3 = production (like LHC10b) \
+                    \n# $4 = merging stage \
+                    \n# Stage_<n>.xml made via: find <OutputDir> *Stage<n-1>/*root_archive.zip\n");
+     sjdl2.Prepend(Form("Jobtag = {\n   \"comment:%s_FinalMerging\"\n};\n", jobTag.Data()));
+     sjdl2.Prepend("# Generated merging jdl \
+                    \n# $1 = full alien path to output directory to be merged \
+                    \n# $2 = train number \
+                    \n# $3 = production (like LHC10b) \
+                    \n# $4 = merging stage \
+                    \n# Stage_<n>.xml made via: find <OutputDir> *Stage<n-1>/*root_archive.zip\n");
+   } else {
+     sjdl1.Prepend("# Generated merging jdl \
+                    \n# $1 = full alien path to output directory to be merged \
+                    \n# $2 = merging stage \
+                    \n# xml made via: find <OutputDir> *Stage<n-1>/*root_archive.zip\n");
+     sjdl2.Prepend(Form("Jobtag = {\n   \"comment:%s_FinalMerging\"\n};\n", jobTag.Data()));
+     sjdl2.Prepend("# Generated merging jdl \
+                    \n# $1 = full alien path to output directory to be merged \
+                    \n# $2 = merging stage \
+                    \n# xml made via: find <OutputDir> *Stage<n-1>/*root_archive.zip\n");
+   }
    index = sjdl1.Index("JDLVariables");
    if (index >= 0) sjdl1.Insert(index, "\n# JDL variables\n");
+   index = sjdl2.Index("JDLVariables");
+   if (index >= 0) sjdl2.Insert(index, "\n# JDL variables\n");
+   sjdl1 += "Workdirectorysize = {\"5000MB\"};";
+   sjdl2 += "Workdirectorysize = {\"5000MB\"};";
+   index = sjdl2.Index("Split =");
+   if (index>=0) {
+      index1 = sjdl2.Index("\n", index);
+      sjdl2.Remove(index, index1-index+1);
+   }
+   index = sjdl2.Index("SplitMaxInputFileNumber");
+   if (index>=0) {
+      index1 = sjdl2.Index("\n", index);
+      sjdl2.Remove(index, index1-index+1);
+   }
+   index = sjdl2.Index("InputDataCollection");
+   if (index>=0) {
+      index1 = sjdl2.Index(";", index);
+      sjdl2.Remove(index, index1-index+1);
+   }
+   index = sjdl2.Index("InputDataListFormat");
+   if (index>=0) {
+      index1 = sjdl2.Index("\n", index);
+      sjdl2.Remove(index, index1-index+1);
+   }
+   index = sjdl2.Index("InputDataList");
+   if (index>=0) {
+      index1 = sjdl2.Index("\n", index);
+      sjdl2.Remove(index, index1-index+1);
+   }
+   sjdl2.ReplaceAll("wn.xml", Form("Stage_%s.xml",stageName.Data()));
    // Write jdl to file
    ofstream out;
    out.open(fJDLName.Data(), ios::out);
    if (out.bad()) {
-      Error("CreateJDL", "Bad file name: %s", fJDLName.Data());
+      Error("WriteJDL", "Bad file name: %s", fJDLName.Data());
       return kFALSE;
    }
    out << sjdl << endl;
+   out.close();
    TString mergeJDLName = fExecutable;
    mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
    if (fMergeViaJDL) {
       ofstream out1;
       out1.open(mergeJDLName.Data(), ios::out);
-      if (out.bad()) {
-         Error("CreateJDL", "Bad file name: %s", mergeJDLName.Data());
+      if (out1.bad()) {
+         Error("WriteJDL", "Bad file name: %s", mergeJDLName.Data());
          return kFALSE;
       }
       out1 << sjdl1 << endl;
+      out1.close();
+      ofstream out2;
+      TString finalJDL = mergeJDLName;
+      finalJDL.ReplaceAll(".jdl", "_final.jdl");
+      out2.open(finalJDL.Data(), ios::out);
+      if (out2.bad()) {
+         Error("WriteJDL", "Bad file name: %s", finalJDL.Data());
+         return kFALSE;
+      }
+      out2 << sjdl2 << endl;
+      out2.close();
    }   
 
    // Copy jdl to grid workspace   
    if (!copy) {
-      Info("CreateJDL", "\n#####   You may want to review jdl:%s and analysis macro:%s before running in <submit> mode", fJDLName.Data(), fAnalysisMacro.Data());
+      Info("WriteJDL", "\n#####   You may want to review jdl:%s and analysis macro:%s before running in <submit> mode", fJDLName.Data(), fAnalysisMacro.Data());
    } else {
       TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
       TString locjdl1 = Form("%s/%s", fGridOutputDir.Data(),mergeJDLName.Data());
+      TString finalJDL = mergeJDLName;
+      finalJDL.ReplaceAll(".jdl", "_final.jdl");
+      TString locjdl2 = Form("%s/%s", fGridOutputDir.Data(),finalJDL.Data());
       if (fProductionMode) {
          locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
          locjdl1 = Form("%s/%s", workdir.Data(),mergeJDLName.Data());
+         locjdl2 = Form("%s/%s", workdir.Data(),finalJDL.Data());
       }   
       if (FileExists(locjdl)) gGrid->Rm(locjdl);
       if (FileExists(locjdl1)) gGrid->Rm(locjdl1);
-      Info("CreateJDL", "\n#####   Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
+      if (FileExists(locjdl2)) gGrid->Rm(locjdl2);
+      Info("WriteJDL", "\n#####   Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
       TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
       if (fMergeViaJDL) {
-         Info("CreateJDL", "\n#####   Copying merging JDL file <%s> to your AliEn output directory", mergeJDLName.Data());
+         Info("WriteJDL", "\n#####   Copying merging JDL files <%s> to your AliEn output directory", mergeJDLName.Data());
          TFile::Cp(Form("file:%s",mergeJDLName.Data()), Form("alien://%s", locjdl1.Data()));
+         TFile::Cp(Form("file:%s",finalJDL.Data()), Form("alien://%s", locjdl2.Data()));
       }   
    } 
    return kTRUE;
@@ -1281,7 +1492,9 @@ Bool_t AliAnalysisAlien::FileExists(const char *lfn)
 {
 // Returns true if file exists.
    if (!gGrid) return kFALSE;
-   TGridResult *res = gGrid->Ls(lfn);
+   TString slfn = lfn;
+   slfn.ReplaceAll("alien://","");
+   TGridResult *res = gGrid->Ls(slfn);
    if (!res) return kFALSE;
    TMap *map = dynamic_cast<TMap*>(res->At(0));
    if (!map) {
@@ -1348,20 +1561,20 @@ void AliAnalysisAlien::CheckDataType(const char *lfn, Bool_t &isCollection, Bool
       TGridResult *res = gGrid->Command(Form("listFilesFromCollection -z -v %s",lfn), kFALSE);
       if (!res) {
          msg += " using_tags: No (unknown)";
-         Info("CheckDataType", msg.Data());
+         Info("CheckDataType", "%s", msg.Data());
          return;
       }   
       const char* typeStr = res->GetKey(0, "origLFN");
       if (!typeStr || !strlen(typeStr)) {
          msg += " using_tags: No (unknown)";
-         Info("CheckDataType", msg.Data());
+         Info("CheckDataType", "%s", msg.Data());
          return;
       }   
       TString file = typeStr;
       useTags = file.Contains(".tag");
       if (useTags) msg += " using_tags: Yes";
       else          msg += " using_tags: No";
-      Info("CheckDataType", msg.Data());
+      Info("CheckDataType", "%s", msg.Data());
       return;
    }
    TString slfn(lfn);
@@ -1373,13 +1586,13 @@ void AliAnalysisAlien::CheckDataType(const char *lfn, Bool_t &isCollection, Bool
       TGridCollection *coll = (TGridCollection*)gROOT->ProcessLine(Form("TAlienCollection::Open(\"alien://%s\",1);",lfn));
       if (!coll) {
          msg += " using_tags: No (unknown)";
-         Info("CheckDataType", msg.Data());
+         Info("CheckDataType", "%s", msg.Data());
          return;
       }   
       TMap *map = coll->Next();
       if (!map) {
          msg += " using_tags: No (unknown)";
-         Info("CheckDataType", msg.Data());
+         Info("CheckDataType", "%s", msg.Data());
          return;
       }   
       map = (TMap*)map->GetValue("");
@@ -1389,7 +1602,7 @@ void AliAnalysisAlien::CheckDataType(const char *lfn, Bool_t &isCollection, Bool
       delete coll;
       if (useTags) msg += " using_tags: Yes";
       else          msg += " using_tags: No";
-      Info("CheckDataType", msg.Data());
+      Info("CheckDataType", "%s", msg.Data());
       return;
    }
    useTags = slfn.Contains(".tag");
@@ -1397,7 +1610,7 @@ void AliAnalysisAlien::CheckDataType(const char *lfn, Bool_t &isCollection, Bool
    else                        msg += " type: unknown file;";
    if (useTags) msg += " using_tags: Yes";
    else          msg += " using_tags: No";
-   Info("CheckDataType", msg.Data());
+   Info("CheckDataType", "%s", msg.Data());
 }
 
 //______________________________________________________________________________
@@ -1422,6 +1635,50 @@ void AliAnalysisAlien::EnablePackage(const char *package)
 }      
 
 //______________________________________________________________________________
+TChain *AliAnalysisAlien::GetChainForTestMode(const char *treeName) const
+{
+// Make a tree from files having the location specified in fFileForTestMode. 
+// Inspired from JF's CreateESDChain.
+   if (fFileForTestMode.IsNull()) {
+      Error("GetChainForTestMode", "For proof test mode please use SetFileForTestMode() pointing to a file that contains data file locations.");
+      return NULL;
+   }
+   if (gSystem->AccessPathName(fFileForTestMode)) {
+      Error("GetChainForTestMode", "File not found: %s", fFileForTestMode.Data());
+      return NULL;
+   }   
+   // Open the file
+   ifstream in;
+   in.open(fFileForTestMode);
+   Int_t count = 0;
+    // Read the input list of files and add them to the chain
+    TString line;
+    TChain *chain = new TChain(treeName);
+    while (in.good())
+    {
+      in >> line;
+      if (line.IsNull()) continue;
+      if (count++ == fNtestFiles) break;
+      TString esdFile(line);
+      TFile *file = TFile::Open(esdFile);
+      if (file) {
+         if (!file->IsZombie()) chain->Add(esdFile);
+         file->Close();
+      } else {
+         Error("GetChainforTestMode", "Skipping un-openable file: %s", esdFile.Data());
+      }   
+    }
+    in.close();
+    if (!chain->GetListOfFiles()->GetEntries()) {
+       Error("GetChainForTestMode", "No file from %s could be opened", fFileForTestMode.Data());
+       delete chain;
+       return NULL;
+    }
+//    chain->ls();
+    return chain;
+}    
+
+//______________________________________________________________________________
 const char *AliAnalysisAlien::GetJobStatus(Int_t jobidstart, Int_t lastid, Int_t &nrunning, Int_t &nwaiting, Int_t &nerror, Int_t &ndone)
 {
 // Get job status for all jobs with jobid>jobidstart.
@@ -1438,10 +1695,10 @@ const char *AliAnalysisAlien::GetJobStatus(Int_t jobidstart, Int_t lastid, Int_t
    Int_t pid;
    for (Int_t ijob=0; ijob<nentries; ijob++) {
       status = (TGridJobStatus *)list->At(ijob);
-      pid = gROOT->ProcessLine(Form("atoi(((TAlienJobStatus*)0x%lx)->GetKey(\"queueId\"));", (ULong_t)status));
+      pid = gROOT->ProcessLine(Form("atoi(((TAlienJobStatus*)%p)->GetKey(\"queueId\"));", status));
       if (pid<jobidstart) continue;
       if (pid == lastid) {
-         gROOT->ProcessLine(Form("sprintf((char*)0x%lx,((TAlienJobStatus*)0x%lx)->GetKey(\"status\"));",(ULong_t)mstatus, (ULong_t)status));
+         gROOT->ProcessLine(Form("sprintf((char*)%p,((TAlienJobStatus*)%p)->GetKey(\"status\"));",mstatus, status));
       }   
       switch (status->GetStatus()) {
          case TGridJobStatus::kWAITING:
@@ -1491,6 +1748,45 @@ void AliAnalysisAlien::Print(Option_t *) const
 {
 // Print current plugin settings.
    printf("### AliEn analysis plugin current settings ###\n");
+   AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
+   if (mgr && mgr->IsProofMode()) {
+      TString proofType = "=   PLUGIN IN PROOF MODE ON CLUSTER:_________________";
+      if (TestBit(AliAnalysisGrid::kTest))
+         proofType = "=   PLUGIN IN PROOF LITE MODE ON CLUSTER:____________";
+      printf("%s %s\n", proofType.Data(), fProofCluster.Data());
+      if (!fProofDataSet.IsNull())
+      printf("=   Requested data set:___________________________ %s\n", fProofDataSet.Data());
+      if (fProofReset==1)
+      printf("=   Soft reset signal will be send to master______ CHANGE BEHAVIOR AFTER COMPLETION\n");      
+      if (fProofReset>1)   
+      printf("=   Hard reset signal will be send to master______ CHANGE BEHAVIOR AFTER COMPLETION\n");      
+      if (!fRootVersionForProof.IsNull())
+      printf("=   ROOT version requested________________________ %s\n", fRootVersionForProof.Data());
+      else
+      printf("=   ROOT version requested________________________ default\n");
+      printf("=   AliRoot version requested_____________________ %s\n", fAliROOTVersion.Data());
+      if (!fAliRootMode.IsNull())
+      printf("=   Requested AliRoot mode________________________ %s\n", fAliRootMode.Data());  
+      if (fNproofWorkers)
+      printf("=   Number of PROOF workers limited to____________ %d\n", fNproofWorkers);
+      if  (fNproofWorkersPerSlave)
+      printf("=   Maximum number of workers per slave___________ %d\n", fNproofWorkersPerSlave);
+      if (TestSpecialBit(kClearPackages))
+      printf("=   ClearPackages requested...\n");
+      if (fIncludePath.Data())
+      printf("=   Include path for runtime task compilation: ___ %s\n", fIncludePath.Data());
+      printf("=   Additional libs to be loaded or souces to be compiled runtime: <%s>\n",fAdditionalLibs.Data());
+      if (fPackages && fPackages->GetEntries()) {
+         TIter next(fPackages);
+         TObject *obj;
+         TString list;
+         while ((obj=next())) list += obj->GetName();
+         printf("=   Par files to be used: ________________________ %s\n", list.Data());
+      } 
+      if (TestSpecialBit(kProofConnectGrid))
+      printf("=   Requested PROOF connection to grid\n");
+      return;
+   }
    printf("=   OverwriteMode:________________________________ %d\n", fOverwriteMode);
    if (fOverwriteMode) {
       printf("***** NOTE: Overwrite mode will overwrite the input generated datasets and partial results from previous analysis. \
@@ -1512,7 +1808,7 @@ void AliAnalysisAlien::Print(Option_t *) const
    if (fRunNumbers.Length()) 
    printf("=   Run numbers to be processed: _________________ %s\n", fRunNumbers.Data());
    if (fRunRange[0])
-   printf("=   Run range to be processed: ___________________ %s%d-%s%d\n", fRunPrefix.Data(), fRunRange[0], fRunPrefix.Data(), fRunRange[1]);
+   printf("=   Run range to be processed: ___________________ %d-%d\n", fRunRange[0], fRunRange[1]);
    if (!fRunRange[0] && !fRunNumbers.Length()) {
       TIter next(fInputFiles);
       TObject *obj;
@@ -1525,6 +1821,7 @@ void AliAnalysisAlien::Print(Option_t *) const
    printf("=   List of output files to be registered: _______ %s\n", fOutputFiles.Data());
    printf("=   List of outputs going to be archived: ________ %s\n", fOutputArchive.Data());
    printf("=   List of outputs that should not be merged: ___ %s\n", fMergeExcludes.Data());
+   printf("=   List of outputs produced during Terminate: ___ %s\n", fTerminateFiles.Data());
    printf("=====================================================================\n");
    printf("=   Job price: ___________________________________ %d\n", fPrice);
    printf("=   Time to live (TTL): __________________________ %d\n", fTTL);
@@ -1556,7 +1853,7 @@ void AliAnalysisAlien::Print(Option_t *) const
    printf("=   Force job outputs to storage element: ________ %s\n", fCloseSE.Data());
    if (fFriendChainName.Length())
    printf("=   Open friend chain file on worker: ____________ %s\n", fFriendChainName.Data());
-   if (fPackages) {
+   if (fPackages && fPackages->GetEntries()) {
       TIter next(fPackages);
       TObject *obj;
       TString list;
@@ -1581,6 +1878,7 @@ void AliAnalysisAlien::SetDefaults()
    fNreplicas                  = 2;
    fRunRange[0]                = 0;
    fRunRange[1]                = 0;
+   fRunPrefix                  = "%d";
    fNrunsPerMaster             = 1;
    fMaxMergeFiles              = 100;
    fRunNumbers                 = "";
@@ -1615,108 +1913,282 @@ void AliAnalysisAlien::SetDefaults()
 }   
 
 //______________________________________________________________________________
-Bool_t AliAnalysisAlien::MergeOutput(const char *output, const char *basedir, Int_t nmaxmerge)
+Bool_t AliAnalysisAlien::CheckMergedFiles(const char *filename, const char *aliendir, Int_t nperchunk, const char *jdl)
 {
-// Merge all registered outputs from basedir.
+// Checks current merge stage, makes xml for the next stage, counts number of files, submits next stage.
+   // First check if the result is already in the output directory.
+   if (FileExists(Form("%s/%s",aliendir,filename))) {
+      printf("Final merged results found. Not merging again.\n");
+      return kFALSE;
+   }
+   // Now check the last stage done.
+   Int_t stage = 0;
+   while (1) {
+      if (!FileExists(Form("%s/Stage_%d.xml",aliendir, stage+1))) break;
+      stage++;
+   }
+   // Next stage of merging
+   stage++;
+   TString pattern = "*root_archive.zip";
+   if (stage>1) pattern = Form("Stage_%d/*root_archive.zip", stage-1);
+   TGridResult *res = gGrid->Command(Form("find -x Stage_%d %s %s", stage, aliendir, pattern.Data()));
+   if (res) delete res;
+   // Write standard output to file
+   gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", Form("Stage_%d.xml",stage)));
+   // Count the number of files inside
+   ifstream ifile;
+   ifile.open(Form("Stage_%d.xml",stage));
+   if (!ifile.good()) {
+      ::Error("CheckMergedFiles", "Could not redirect result of the find command to file %s", Form("Stage_%d.xml",stage));
+      return kFALSE;
+   }   
+   TString line;
+   Int_t nfiles = 0;
+   while (!ifile.eof()) {
+      ifile >> line;
+      if (line.Contains("/event")) nfiles++;
+   }
+   ifile.close();
+   if (!nfiles) {
+      ::Error("CheckMergedFiles", "Cannot start Stage_%d merging since Stage_%d did not produced yet output", stage, stage-1);
+      return kFALSE;
+   } else {
+      printf("=== Stage_%d produced %d files\n", stage-1, nfiles);
+   }   
+   // Copy the file in the output directory
+   printf("===> Copying collection %s in the output directory %s\n", Form("Stage_%d.xml",stage), aliendir);
+   TFile::Cp(Form("Stage_%d.xml",stage), Form("alien://%s/Stage_%d.xml",aliendir,stage));
+   // Check if this is the last stage to be done.
+   Bool_t laststage = (nfiles<nperchunk);
+   if (fMaxMergeStages && stage>=fMaxMergeStages) laststage = kTRUE;
+   if (laststage) {
+      printf("### Submiting final merging stage %d\n", stage);
+      TString finalJDL = jdl;
+      finalJDL.ReplaceAll(".jdl", "_final.jdl");
+      TString query = Form("submit %s %s %d", finalJDL.Data(), aliendir, stage);
+      Int_t jobId = SubmitSingleJob(query);
+      if (!jobId) return kFALSE;      
+   } else {
+      printf("### Submiting merging stage %d\n", stage);
+      TString query = Form("submit %s %s %d", jdl, aliendir, stage);
+      Int_t jobId = SubmitSingleJob(query);
+      if (!jobId) return kFALSE;           
+   }
+   return kTRUE;   
+}        
+
+//______________________________________________________________________________
+Int_t AliAnalysisAlien::SubmitSingleJob(const char *query)
+{
+// Submits a single job corresponding to the query and returns job id. If 0 submission failed.
+   if (!gGrid) return 0;
+   printf("=> %s ------> ",query);
+   TGridResult *res = gGrid->Command(query);
+   if (!res) return 0;
+   TString jobId = res->GetKey(0,"jobId");
+   delete res;
+   if (jobId.IsNull()) {
+      printf("submission failed. Reason:\n");
+      gGrid->Stdout();
+      gGrid->Stderr();
+      ::Error("SubmitSingleJob", "Your query %s could not be submitted", query);
+      return 0;
+   }
+   printf(" Job id: %s\n", jobId.Data());
+   return atoi(jobId);
+}  
+
+//______________________________________________________________________________
+Bool_t AliAnalysisAlien::MergeOutput(const char *output, const char *basedir, Int_t nmaxmerge, Int_t stage)
+{
+// Merge given output files from basedir. Basedir can be an alien output directory
+// but also an xml file with root_archive.zip locations. The file merger will merge nmaxmerge
+// files in a group (ignored for xml input). Merging can be done in stages:
+// stage=0 : will merge all existing files in a single stage, supporting resume if run locally
+// stage=1 : works with an xml of all root_archive.zip in the output directory
+// stage>1 : works with an xml of all root_archive.zip in the Stage_<n-1> directory
    TString outputFile = output;
    TString command;
    TString outputChunk;
    TString previousChunk = "";
+   TObjArray *listoffiles = new TObjArray();
+//   listoffiles->SetOwner();
    Int_t countChunk = 0;
    Int_t countZero = nmaxmerge;
    Bool_t merged = kTRUE;
    Int_t index = outputFile.Index("@");
    if (index > 0) outputFile.Remove(index);
-   command = Form("find %s/ *%s", basedir, outputFile.Data());
-   printf("command: %s\n", command.Data());
-   TGridResult *res = gGrid->Command(command);
-   if (!res) {
-      printf("Error: No result for the find command\n");
+   TString inputFile = outputFile;
+   TString sbasedir = basedir;
+   if (sbasedir.Contains(".xml")) {
+      // Merge files pointed by the xml - ignore nmaxmerge and set ichunk to 0
+      nmaxmerge = 9999999;
+      TGridCollection *coll = (TGridCollection*)gROOT->ProcessLine(Form("TAlienCollection::Open(\"%s\");", basedir));
+      if (!coll) {
+         ::Error("MergeOutput", "Input XML collection empty.");
+         return kFALSE;
+      }
+      // Iterate grid collection
+      while (coll->Next()) {
+         TString fname = gSystem->DirName(coll->GetTURL());
+         fname += "/";
+         fname += inputFile;      
+         listoffiles->Add(new TNamed(fname.Data(),""));
+      }   
+   } else {   
+      command = Form("find %s/ *%s", basedir, inputFile.Data());
+      printf("command: %s\n", command.Data());
+      TGridResult *res = gGrid->Command(command);
+      if (!res) {
+         ::Error("MergeOutput","No result for the find command\n");
+         delete listoffiles;
+         return kFALSE;
+      }     
+      TIter nextmap(res);
+      TMap *map = 0;
+      while ((map=(TMap*)nextmap())) {
+         TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl"));
+         if (!objs || !objs->GetString().Length()) {
+            // Nothing found - skip this output
+            delete res;
+            delete listoffiles;
+            return kFALSE;
+         }
+         listoffiles->Add(new TNamed(objs->GetName(),""));
+      }
+      delete res;
+   }
+   if (!listoffiles->GetEntries()) {
+      ::Error("MergeOutput","No result for the find command\n");
+      delete listoffiles;
       return kFALSE;
    }     
 
    TFileMerger *fm = 0;
-   TIter nextmap(res);
-   TMap *map = 0;
-   // Check if there is a merge operation to resume
+   TIter next0(listoffiles);
+   TObjArray *listoffilestmp = new TObjArray();
+   listoffilestmp->SetOwner();
+   TObject *nextfile;
+   TString snextfile;
+   // Keep only the files at upper level
+   Int_t countChar = 0;
+   while ((nextfile=next0())) {
+      snextfile = nextfile->GetName();
+      Int_t crtCount = snextfile.CountChar('/');
+      if (nextfile == listoffiles->First()) countChar = crtCount;
+      if (crtCount < countChar) countChar = crtCount;
+   }
+   next0.Reset();
+   while ((nextfile=next0())) {
+      snextfile = nextfile->GetName();
+      Int_t crtCount = snextfile.CountChar('/');
+      if (crtCount > countChar) {
+         delete nextfile;
+         continue;
+      }   
+      listoffilestmp->Add(nextfile);
+   }
+   delete listoffiles;
+   listoffiles = listoffilestmp;  // Now contains 'good' files
+   listoffiles->Print();
+   TIter next(listoffiles);   
+   // Check if there is a merge operation to resume. Works only for stage 0 or 1.
    outputChunk = outputFile;
    outputChunk.ReplaceAll(".root", "_*.root");
    // Check for existent temporary merge files
    // Check overwrite mode and remove previous partial results if needed
-   if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
-      while (1) {
-         // Skip as many input files as in a chunk
-         for (Int_t counter=0; counter<nmaxmerge; counter++) map = (TMap*)nextmap();
-         if (!map) {
-            ::Error("MergeOutputs", "Cannot resume merging for <%s>, nentries=%d", outputFile.Data(), res->GetSize());
-            delete res;
-            return kFALSE;
+   // Preserve old merging functionality for stage 0.
+   if (stage==0) {
+      if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
+         while (1) {
+            // Skip as many input files as in a chunk
+            for (Int_t counter=0; counter<nmaxmerge; counter++) {
+               nextfile = next();
+               if (!nextfile) {
+                  ::Error("MergeOutput", "Mismatch found. Please remove partial merged files from local dir.");
+                  delete listoffiles;
+                  return kFALSE;
+               }   
+               snextfile = nextfile->GetName();
+            }
+            outputChunk = outputFile;
+            outputChunk.ReplaceAll(".root", Form("_%04d.root", countChunk));
+            countChunk++;
+            if (gSystem->AccessPathName(outputChunk)) continue;
+            // Merged file with chunks up to <countChunk> found
+            ::Info("MergeOutput", "Resume merging of <%s> from <%s>\n", outputFile.Data(), outputChunk.Data());
+            previousChunk = outputChunk;
+            break;
          }
-         outputChunk = outputFile;
-         outputChunk.ReplaceAll(".root", Form("_%04d.root", countChunk));
-         countChunk++;
-         if (gSystem->AccessPathName(outputChunk)) continue;
-         // Merged file with chunks up to <countChunk> found
-         printf("Resume merging of <%s> from <%s>\n", outputFile.Data(), outputChunk.Data());
-         previousChunk = outputChunk;
-         break;
-      }
-   }   
-   countZero = nmaxmerge;
+      }   
+      countZero = nmaxmerge;
    
-   while ((map=(TMap*)nextmap())) {
-   // Loop 'find' results and get next LFN
-      if (countZero == nmaxmerge) {
-         // First file in chunk - create file merger and add previous chunk if any.
-         fm = new TFileMerger(kFALSE);
-         fm->SetFastMethod(kTRUE);
-         if (previousChunk.Length()) fm->AddFile(previousChunk.Data());
-         outputChunk = outputFile;
-         outputChunk.ReplaceAll(".root", Form("_%04d.root", countChunk));
-      }
-      // If last file found, put merged results in the output file
-      if (map == res->Last()) outputChunk = outputFile;
-      TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl"));
-      if (!objs || !objs->GetString().Length()) {
-         // Nothing found - skip this output
-         delete res;
-         delete fm;
-         return kFALSE;
-      } 
-      // Add file to be merged and decrement chunk counter.
-      fm->AddFile(objs->GetString());
-      countZero--;
-      if (countZero==0 || map == res->Last()) {            
-         fm->OutputFile(outputChunk);
-         if (!fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
-         // Nothing found - skip this output
-            ::Warning("MergeOutputs", "No <%s> files found.", outputFile.Data());
-            delete res;
-            delete fm;
-            return kFALSE;
+      while ((nextfile=next())) {
+         snextfile = nextfile->GetName();
+         // Loop 'find' results and get next LFN
+         if (countZero == nmaxmerge) {
+            // First file in chunk - create file merger and add previous chunk if any.
+            fm = new TFileMerger(kFALSE);
+            fm->SetFastMethod(kTRUE);
+            if (previousChunk.Length()) fm->AddFile(previousChunk.Data());
+            outputChunk = outputFile;
+            outputChunk.ReplaceAll(".root", Form("_%04d.root", countChunk));
          }
-         // Merge the outputs, then go to next chunk      
-         if (!fm->Merge()) {
-            ::Error("MergeOutputs", "Could not merge all <%s> files", outputFile.Data());
-            delete res;
-            delete fm;
-            merged = kFALSE;
-            return kFALSE;
-         } else {
-            ::Info("MergeOutputs", "\n#####   Merged %d output files to <%s>", fm->GetMergeList()->GetSize(), outputChunk.Data());
-            gSystem->Unlink(previousChunk);
+         // If last file found, put merged results in the output file
+         if (nextfile == listoffiles->Last()) outputChunk = outputFile;
+         // Add file to be merged and decrement chunk counter.
+         fm->AddFile(snextfile);
+         countZero--;
+         if (countZero==0 || nextfile == listoffiles->Last()) {            
+            if (!fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
+            // Nothing found - skip this output
+               ::Warning("MergeOutput", "No <%s> files found.", inputFile.Data());
+               merged = kFALSE;
+               break;
+            }
+            fm->OutputFile(outputChunk);
+            // Merge the outputs, then go to next chunk      
+            if (!fm->Merge()) {
+               ::Error("MergeOutput", "Could not merge all <%s> files", outputFile.Data());
+               merged = kFALSE;
+               break;
+            } else {
+               ::Info("MergeOutputs", "\n#####   Merged %d output files to <%s>", fm->GetMergeList()->GetSize(), outputChunk.Data());
+               gSystem->Unlink(previousChunk);
+            }
+            if (nextfile == listoffiles->Last()) break;
+            countChunk++;
+            countZero = nmaxmerge;
+            previousChunk = outputChunk;
          }
-         if (map == res->Last()) {
-            delete res;
-            delete fm;
-            break;
-         }      
-         countChunk++;
-         countZero = nmaxmerge;
-         previousChunk = outputChunk;
       }
+      delete listoffiles;
+      delete fm;
+      return merged;
+   }
+   // Merging stage different than 0.
+   // Move to the begining of the requested chunk.
+   fm = new TFileMerger(kFALSE);
+   fm->SetFastMethod(kTRUE);
+   while ((nextfile=next())) fm->AddFile(nextfile->GetName());
+   delete listoffiles;
+   if (!fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
+      // Nothing found - skip this output
+      ::Warning("MergeOutput", "No <%s> files found.", inputFile.Data());
+      delete fm;
+      return kFALSE;
+   }
+   fm->OutputFile(outputFile);
+   // Merge the outputs
+   if (!fm->Merge()) {
+      ::Error("MergeOutput", "Could not merge all <%s> files", outputFile.Data());
+      delete fm;
+      return kFALSE;
+   } else {
+      ::Info("MergeOutput", "\n#####   Merged %d output files to <%s>", fm->GetMergeList()->GetSize(), outputFile.Data());
    }
-   return merged;
+   delete fm;
+   return kTRUE;
 } 
 
 //______________________________________________________________________________
@@ -1760,14 +2232,16 @@ Bool_t AliAnalysisAlien::MergeOutputs()
    if (fFastReadOption) {
       Warning("MergeOutputs", "You requested FastRead option. Using xrootd flags to reduce timeouts. This may skip some files that could be accessed ! \
              \n+++ NOTE: To disable this option, use: plugin->SetFastReadOption(kFALSE)");
-      gEnv->SetValue("XNet.ConnectTimeout",10);
-      gEnv->SetValue("XNet.RequestTimeout",10);
+      gEnv->SetValue("XNet.ConnectTimeout",50);
+      gEnv->SetValue("XNet.RequestTimeout",50);
       gEnv->SetValue("XNet.MaxRedirectCount",2);
-      gEnv->SetValue("XNet.ReconnectTimeout",10);
+      gEnv->SetValue("XNet.ReconnectTimeout",50);
       gEnv->SetValue("XNet.FirstConnectMaxCnt",1);
    }   
    // Make sure we change the temporary directory
    gSystem->Setenv("TMPDIR", gSystem->pwd());
+   // Set temporary compilation directory to current one
+   gSystem->SetBuildDir(gSystem->pwd(), kTRUE);   
    TObjArray *list = fOutputFiles.Tokenize(",");
    TIter next(list);
    TObjString *str;
@@ -1820,8 +2294,7 @@ void AliAnalysisAlien::SetDefaultOutputs(Bool_t flag)
 // Use the output files connected to output containers from the analysis manager
 // rather than the files defined by SetOutputFiles
    if (flag && !TObject::TestBit(AliAnalysisGrid::kDefaultOutputs))
-      Info("SetDefaultOutputs", "Plugin will use the output files taken from \
-      analysis manager");
+      Info("SetDefaultOutputs", "Plugin will use the output files taken from analysis manager");
    TObject::SetBit(AliAnalysisGrid::kDefaultOutputs, flag);
 }
       
@@ -1850,7 +2323,7 @@ void AliAnalysisAlien::SetOutputFiles(const char *list)
       fOutputFiles += sout;
    }
    delete arr;   
-}      
+}
 
 //______________________________________________________________________________
 void AliAnalysisAlien::SetOutputArchive(const char *list)
@@ -1876,39 +2349,252 @@ void AliAnalysisAlien::SetPreferedSE(const char */*se*/)
 Bool_t AliAnalysisAlien::StartAnalysis(Long64_t /*nentries*/, Long64_t /*firstEntry*/)
 {
 // Start remote grid analysis.
-   
-   // Check if output files have to be taken from the analysis manager
-   if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
-      AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
-      if (!mgr || !mgr->IsInitialized()) {
-         Error("StartAnalysis", "You need an initialized analysis manager for this");
+   AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
+   Bool_t testMode = TestBit(AliAnalysisGrid::kTest);
+   if (!mgr || !mgr->IsInitialized()) {
+      Error("StartAnalysis", "You need an initialized analysis manager for this");
+      return kFALSE;
+   }
+   // Are we in PROOF mode ?
+   if (mgr->IsProofMode()) {
+      Info("StartAnalysis", "##### Starting PROOF analysis on cluster <%s> via the plugin #####", fProofCluster.Data());
+      if (fProofCluster.IsNull()) {
+         Error("StartAnalysis", "You need to specify the proof cluster name via SetProofCluster");
          return kFALSE;
+      }   
+      if (fProofDataSet.IsNull() && !testMode) {
+         Error("StartAnalysis", "You need to specify a dataset using SetProofDataSet()");
+         return kFALSE;
+      }   
+      // Set the needed environment
+      gEnv->SetValue("XSec.GSI.DelegProxy","2");
+      // Do we need to reset PROOF ? The success of the Reset operation cannot be checked
+      if (fProofReset && !testMode) {
+         if (fProofReset==1) {
+            Info("StartAnalysis", "Sending soft reset signal to proof cluster %s", fProofCluster.Data());
+            gROOT->ProcessLine(Form("TProof::Reset(\"%s\", kFALSE);", fProofCluster.Data()));
+         } else {         
+            Info("StartAnalysis", "Sending hard reset signal to proof cluster %s", fProofCluster.Data());
+            gROOT->ProcessLine(Form("TProof::Reset(\"%s\", kTRUE);", fProofCluster.Data()));
+         }
+         Info("StartAnalysis", "Stopping the analysis. Please use SetProofReset(0) to resume.");
+         return kFALSE;
+      }
+      // Do we need to change the ROOT version ? The success of this cannot be checked.
+      if (!fRootVersionForProof.IsNull() && !testMode) {
+         gROOT->ProcessLine(Form("TProof::Mgr(\"%s\")->SetROOTVersion(\"%s\");", 
+                            fProofCluster.Data(), fRootVersionForProof.Data()));
+      }
+      // Connect to PROOF and check the status
+      Long_t proof = 0;
+      TString sworkers;
+      if (fNproofWorkersPerSlave) sworkers = Form("workers=%dx", fNproofWorkersPerSlave);
+      else if (fNproofWorkers) sworkers = Form("workers=%d", fNproofWorkers);
+      if (!testMode) {
+         if (!sworkers.IsNull()) 
+            proof = gROOT->ProcessLine(Form("TProof::Open(\"%s\", \"%s\");", fProofCluster.Data(), sworkers.Data()));
+         else   
+            proof = gROOT->ProcessLine(Form("TProof::Open(\"%s\");", fProofCluster.Data()));
+      } else {
+         proof = gROOT->ProcessLine("TProof::Open(\"\");");
+         if (!proof) {
+            Error("StartAnalysis", "Could not start PROOF in test mode");
+            return kFALSE;
+         }   
+      }
+      if (!proof) {
+         Error("StartAnalysis", "Could not connect to PROOF cluster <%s>", fProofCluster.Data());
+         return kFALSE;
+      }   
+      if (fNproofWorkersPerSlave*fNproofWorkers > 0)
+         gROOT->ProcessLine(Form("gProof->SetParallel(%d);", fNproofWorkers));
+      // Is dataset existing ?
+      if (!testMode) {
+         TString dataset = fProofDataSet;
+         Int_t index = dataset.Index("#");
+         if (index>=0) dataset.Remove(index);
+//         if (!gROOT->ProcessLine(Form("gProof->ExistsDataSet(\"%s\");",fProofDataSet.Data()))) {
+//            Error("StartAnalysis", "Dataset %s not existing", fProofDataSet.Data());
+//            return kFALSE;
+//         }
+//         Info("StartAnalysis", "Dataset %s found", dataset.Data());
+      }
+      // Is ClearPackages() needed ?
+      if (TestSpecialBit(kClearPackages)) {
+         Info("StartAnalysis", "ClearPackages signal sent to PROOF. Use SetClearPackages(kFALSE) to reset this.");
+         gROOT->ProcessLine("gProof->ClearPackages();");
+      }
+      // Is a given aliroot mode requested ?
+      TList optionsList;
+      TString parLibs;
+      if (!fAliRootMode.IsNull()) {
+         TString alirootMode = fAliRootMode;
+         if (alirootMode == "default") alirootMode = "";
+         Info("StartAnalysis", "You are requesting AliRoot mode: %s", fAliRootMode.Data());
+         optionsList.SetOwner();
+         optionsList.Add(new TNamed("ALIROOT_MODE", alirootMode.Data()));
+         // Check the additional libs to be loaded
+         TString extraLibs;
+         Bool_t parMode = kFALSE;
+         if (!alirootMode.IsNull()) extraLibs = "ANALYSIS:ANALYSISalice";
+         // Parse the extra libs for .so
+         if (fAdditionalLibs.Length()) {
+            TObjArray *list = fAdditionalLibs.Tokenize(" ");
+            TIter next(list);
+            TObjString *str;
+            while((str=(TObjString*)next())) {
+               if (str->GetString().Contains(".so")) {
+                  if (parMode) {
+                     Warning("StartAnalysis", "Plugin does not support loading libs after par files in PROOF mode. Library %s and following will not load on workers", str->GetName());
+                     break;
+                  }   
+                  TString stmp = str->GetName();
+                  if (stmp.BeginsWith("lib")) stmp.Remove(0,3);
+                  stmp.ReplaceAll(".so","");
+                  if (!extraLibs.IsNull()) extraLibs += ":";
+                  extraLibs += stmp;
+                  continue;
+               }
+               if (str->GetString().Contains(".par")) {
+                  // The first par file found in the list will not allow any further .so
+                  parMode = kTRUE;
+                  if (!parLibs.IsNull()) parLibs += ":";
+                  parLibs += str->GetName();
+                  continue;
+               }   
+            }
+            if (list) delete list;            
+         }
+         if (!extraLibs.IsNull()) optionsList.Add(new TNamed("ALIROOT_EXTRA_LIBS",extraLibs.Data()));
+         // Check extra includes
+         if (!fIncludePath.IsNull()) {
+            TString includePath = fIncludePath;
+            includePath.ReplaceAll(" ",":");
+            includePath.ReplaceAll("$ALICE_ROOT","");
+            includePath.ReplaceAll("${ALICE_ROOT}","");
+            includePath.ReplaceAll("-I","");
+            includePath.Strip(TString::kTrailing, ':');
+            Info("StartAnalysis", "Adding extra includes: %s",includePath.Data()); 
+            optionsList.Add(new TNamed("ALIROOT_EXTRA_INCLUDES",includePath.Data()));
+         }
+         // Check if connection to grid is requested
+         if (TestSpecialBit(kProofConnectGrid)) 
+            optionsList.Add(new TNamed("ALIROOT_ENABLE_ALIEN", "1"));
+         // Enable AliRoot par
+         if (testMode) {
+         // Enable proof lite package
+            TString alirootLite = gSystem->ExpandPathName("$ALICE_ROOT/ANALYSIS/macros/AliRootProofLite.par");
+            for (Int_t i=0; i<optionsList.GetSize(); i++) {
+               TNamed *obj = (TNamed*)optionsList.At(i);
+               printf("%s  %s\n", obj->GetName(), obj->GetTitle());
+            }   
+            if (!gROOT->ProcessLine(Form("gProof->UploadPackage(\"%s\");",alirootLite.Data()))
+              && !gROOT->ProcessLine(Form("gProof->EnablePackage(\"%s\", (TList*)%p);",alirootLite.Data(),&optionsList))) {
+                  Info("StartAnalysis", "AliRootProofLite enabled");
+            } else {                      
+               Error("StartAnalysis", "There was an error trying to enable package AliRootProofLite.par");
+               return kFALSE;
+            }   
+         } else {
+            if (gROOT->ProcessLine(Form("gProof->EnablePackage(\"VO_ALICE@AliRoot::%s\", (TList*)%p, kTRUE);", 
+                                   fAliROOTVersion.Data(), &optionsList))) {
+               Error("StartAnalysis", "There was an error trying to enable package VO_ALICE@AliRoot::%s", fAliROOTVersion.Data());
+               return kFALSE;
+            }         
+         }
+         // Enable first par files from fAdditionalLibs
+         if (!parLibs.IsNull()) {
+            TObjArray *list = parLibs.Tokenize(":");
+            TIter next(list);
+            TObjString *package;
+            while((package=(TObjString*)next())) {
+               TString spkg = package->GetName();
+               spkg.ReplaceAll(".par", "");
+               gSystem->Exec(TString::Format("rm -rf %s", spkg.Data()));
+               if (!gROOT->ProcessLine(Form("gProof->UploadPackage(\"%s\");", package->GetName()))) {
+                  TString enablePackage = (testMode)?Form("gProof->EnablePackage(\"%s\",kFALSE);", package->GetName()):Form("gProof->EnablePackage(\"%s\",kTRUE);", package->GetName());
+                  if (gROOT->ProcessLine(enablePackage)) {
+                     Error("StartAnalysis", "There was an error trying to enable package %s", package->GetName());
+                     return kFALSE;
+                  }
+               } else {
+                  Error("StartAnalysis", "There was an error trying to upload package %s", package->GetName());
+                  return kFALSE;
+               }
+            }
+            if (list) delete list; 
+         }
+      } else {
+         if (fAdditionalLibs.Contains(".so") && !testMode) {
+            Error("StartAnalysis", "You request additional libs to be loaded but did not enabled any AliRoot mode. Please refer to: \
+                   \n http://aaf.cern.ch/node/83 and use a parameter for SetAliRootMode()");
+            return kFALSE;       
+         }
       }
-      fOutputFiles = "";
-      TIter next(mgr->GetOutputs());
-      AliAnalysisDataContainer *output;
-      while ((output=(AliAnalysisDataContainer*)next())) {
-         const char *filename = output->GetFileName();
-         if (!(strcmp(filename, "default"))) {
-            if (!mgr->GetOutputEventHandler()) continue;
-            filename = mgr->GetOutputEventHandler()->GetOutputFileName();
+      // Enable par files if requested
+      if (fPackages && fPackages->GetEntries()) {
+         TIter next(fPackages);
+         TObject *package;
+         while ((package=next())) {
+            // Skip packages already enabled
+            if (parLibs.Contains(package->GetName())) continue;
+            TString spkg = package->GetName();
+            spkg.ReplaceAll(".par", "");
+            gSystem->Exec(TString::Format("rm -rf %s", spkg.Data()));
+            if (gROOT->ProcessLine(Form("gProof->UploadPackage(\"%s\");", package->GetName()))) {
+               if (gROOT->ProcessLine(Form("gProof->EnablePackage(\"%s\",kTRUE);", package->GetName()))) {
+                  Error("StartAnalysis", "There was an error trying to enable package %s", package->GetName());
+                  return kFALSE;
+               }
+            } else {
+               Error("StartAnalysis", "There was an error trying to upload package %s", package->GetName());
+               return kFALSE;
+            }
          }
-         if (fOutputFiles.Contains(filename)) continue;
-         if (fOutputFiles.Length()) fOutputFiles += ",";
-         fOutputFiles += filename;
       }
+      // Do we need to load analysis source files ?
+      // NOTE: don't load on client since this is anyway done by the user to attach his task.
+      if (fAnalysisSource.Length()) {
+         TObjArray *list = fAnalysisSource.Tokenize(" ");
+         TIter next(list);
+         TObjString *str;
+         while((str=(TObjString*)next())) {
+            gROOT->ProcessLine(Form("gProof->Load(\"%s+g\", kTRUE);", str->GetName()));
+         }   
+         if (list) delete list;
+      }
+      if (testMode) {
+      // Register dataset to proof lite.
+         if (fFileForTestMode.IsNull()) {
+            Error("GetChainForTestMode", "For proof test mode please use SetFileForTestMode() pointing to a file that contains data file locations.");
+            return kFALSE;
+         }
+         if (gSystem->AccessPathName(fFileForTestMode)) {
+            Error("GetChainForTestMode", "File not found: %s", fFileForTestMode.Data());
+            return kFALSE;
+         }   
+         TFileCollection *coll = new TFileCollection();
+         coll->AddFromFile(fFileForTestMode);
+         gROOT->ProcessLine(Form("gProof->RegisterDataSet(\"test_collection\", (TFileCollection*)%p, \"OV\");", coll));
+         gROOT->ProcessLine("gProof->ShowDataSets()");
+      }
+      return kTRUE;
+   }
+   
+   // Check if output files have to be taken from the analysis manager
+   if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
+      // Add output files and AOD files
+      fOutputFiles = GetListOfFiles("outaod");
       // Add extra files registered to the analysis manager
-      if (mgr->GetExtraFiles().Length()) {
-         if (fOutputFiles.Length()) fOutputFiles += ",";
-         TString extra = mgr->GetExtraFiles();
-         extra.ReplaceAll(" ", ",");
-         // Protection in case extra files do not exist (will it work?)
+      TString extra = GetListOfFiles("ext");
+      if (!extra.IsNull()) {
          extra.ReplaceAll(".root", "*.root");
+         if (!fOutputFiles.IsNull()) fOutputFiles += ",";
          fOutputFiles += extra;
       }
       // Compose the output archive.
       fOutputArchive = "log_archive.zip:std*@disk=1 ";
-      fOutputArchive += Form("root_archive.zip:%s@disk=%d",fOutputFiles.Data(),fNreplicas);
+      fOutputArchive += Form("root_archive.zip:%s,*.stat@disk=%d",fOutputFiles.Data(),fNreplicas);
    }
 //   if (!fCloseSE.Length()) fCloseSE = gSystem->Getenv("alien_CLOSE_SE");
    if (TestBit(AliAnalysisGrid::kOffline)) {
@@ -1934,7 +2620,7 @@ Bool_t AliAnalysisAlien::StartAnalysis(Long64_t /*nentries*/, Long64_t /*firstEn
       Error("StartAnalysis", "Cannot start grid analysis without grid connection");
       return kFALSE;
    }
-   if (IsCheckCopy()) CheckFileCopy(gGrid->GetHomeDirectory());
+   if (IsCheckCopy() && gGrid) CheckFileCopy(gGrid->GetHomeDirectory());
    if (!CheckInputData()) {
       Error("StartAnalysis", "There was an error in preprocessing your requested input data");
       return kFALSE;
@@ -1959,7 +2645,7 @@ Bool_t AliAnalysisAlien::StartAnalysis(Long64_t /*nentries*/, Long64_t /*firstEn
    }   
    if (!CreateJDL()) return kFALSE;
    if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
-   if (TestBit(AliAnalysisGrid::kTest)) {
+   if (testMode) {
       // Locally testing the analysis
       Info("StartAnalysis", "\n_______________________________________________________________________ \
       \n   Running analysis script in a daughter shell as on a worker node \
@@ -1976,9 +2662,7 @@ Bool_t AliAnalysisAlien::StartAnalysis(Long64_t /*nentries*/, Long64_t /*firstEn
       }
       delete list;
       gSystem->Exec(Form("bash %s 2>stderr", fExecutable.Data()));
-      TString validationScript = fExecutable;
-      validationScript.ReplaceAll(".sh", "_validation.sh");
-      gSystem->Exec(Form("bash %s",validationScript.Data()));
+      gSystem->Exec(Form("bash %s",fValidationScript.Data()));
 //      gSystem->Exec("cat stdout");
       return kFALSE;
    }
@@ -2030,6 +2714,104 @@ Bool_t AliAnalysisAlien::StartAnalysis(Long64_t /*nentries*/, Long64_t /*firstEn
 }
 
 //______________________________________________________________________________
+const char *AliAnalysisAlien::GetListOfFiles(const char *type)
+{
+// Get a comma-separated list of output files of the requested type.
+// Type can be (case unsensitive):
+//    aod - list of aod files (std, extensions and filters)
+//    out - list of output files connected to containers (but not aod's or extras)
+//    ext - list of extra files registered to the manager
+//    ter - list of files produced in terminate
+   static TString files;
+   files = "";
+   TString stype = type;
+   stype.ToLower();
+   TString aodfiles, extra;
+   AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
+   if (!mgr) {
+      ::Error("GetListOfFiles", "Cannot call this without analysis manager");
+      return files.Data();
+   }
+   if (mgr->GetOutputEventHandler()) {
+      aodfiles = mgr->GetOutputEventHandler()->GetOutputFileName();
+      TString extraaod = mgr->GetOutputEventHandler()->GetExtraOutputs();
+      if (!extraaod.IsNull()) {
+         aodfiles += ",";
+         aodfiles += extraaod;
+      }
+   }
+   if (stype.Contains("aod")) {
+      files = aodfiles;
+      if (stype == "aod") return files.Data();
+   }  
+   // Add output files that are not in the list of AOD files 
+   TString outputfiles = "";
+   TIter next(mgr->GetOutputs());
+   AliAnalysisDataContainer *output;
+   const char *filename = 0;
+   while ((output=(AliAnalysisDataContainer*)next())) {
+      filename = output->GetFileName();
+      if (!(strcmp(filename, "default"))) continue;
+      if (outputfiles.Contains(filename)) continue;
+      if (aodfiles.Contains(filename))    continue;
+      if (!outputfiles.IsNull()) outputfiles += ",";
+      outputfiles += filename;
+   }
+   if (stype.Contains("out")) {
+      if (!files.IsNull()) files += ",";
+      files += outputfiles;
+      if (stype == "out") return files.Data();
+   }   
+   // Add extra files registered to the analysis manager
+   TString sextra;
+   extra = mgr->GetExtraFiles();
+   if (!extra.IsNull()) {
+      extra.Strip();
+      extra.ReplaceAll(" ", ",");
+      TObjArray *fextra = extra.Tokenize(",");
+      TIter nextx(fextra);
+      TObject *obj;
+      while ((obj=nextx())) {
+         if (aodfiles.Contains(obj->GetName())) continue;
+         if (outputfiles.Contains(obj->GetName())) continue;
+         if (sextra.Contains(obj->GetName())) continue;
+         if (!sextra.IsNull()) sextra += ",";
+         sextra += obj->GetName();
+      }
+      delete fextra;
+      if (stype.Contains("ext")) {
+         if (!files.IsNull()) files += ",";
+         files += sextra;
+      }
+   }   
+   if (stype == "ext") return files.Data();
+   TString termfiles;
+   if (!fTerminateFiles.IsNull()) {
+      fTerminateFiles.Strip();
+      fTerminateFiles.ReplaceAll(" ",",");
+      TObjArray *fextra = fTerminateFiles.Tokenize(",");
+      TIter nextx(fextra);
+      TObject *obj;
+      while ((obj=nextx())) {
+         if (aodfiles.Contains(obj->GetName())) continue;
+         if (outputfiles.Contains(obj->GetName())) continue;
+         if (termfiles.Contains(obj->GetName())) continue;
+         if (sextra.Contains(obj->GetName())) continue;
+         if (!termfiles.IsNull()) termfiles += ",";
+         termfiles += obj->GetName();
+      }
+      delete fextra;
+   }   
+   if (stype.Contains("ter")) {
+      if (!files.IsNull() && !termfiles.IsNull()) {
+         files += ",";
+         files += termfiles;
+      }   
+   }   
+   return files.Data();
+}   
+
+//______________________________________________________________________________
 Bool_t AliAnalysisAlien::Submit()
 {
 // Submit all master jobs.
@@ -2054,41 +2836,51 @@ Bool_t AliAnalysisAlien::SubmitMerging()
    gGrid->Cd(fGridOutputDir);
    TString mergeJDLName = fExecutable;
    mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
+   if (!fInputFiles) {
+      Error("SubmitMerging", "You have to use explicit run numbers or run range to merge via JDL!");
+      return kFALSE;
+   }   
    Int_t ntosubmit = fInputFiles->GetEntries();
-   printf("### Submitting %d merging jobs...\n", ntosubmit);
    for (Int_t i=0; i<ntosubmit; i++) {
-      TString query;
       TString runOutDir = gSystem->BaseName(fInputFiles->At(i)->GetName());
       runOutDir.ReplaceAll(".xml", "");
-      if (fOutputToRunNo)
-         query = Form("submit %s %s", mergeJDLName.Data(), runOutDir.Data());
-      else
-         query = Form("submit %s %03d", mergeJDLName.Data(), i);
-      printf("********* %s\n",query.Data());
-      TGridResult *res = gGrid->Command(query);
-      if (res) {
-         const char *cjobId = res->GetKey(0,"jobId");
-         if (!cjobId) {
-            gGrid->Stdout();
-            gGrid->Stderr();
-            Error("StartAnalysis", "Your JDL %s could not be submitted", mergeJDLName.Data());
-            return kFALSE;
+      if (fOutputToRunNo) {
+         // The output directory is the run number
+         printf("### Submitting merging job for run <%s>\n", runOutDir.Data());
+         runOutDir = Form("%s/%s", fGridOutputDir.Data(), runOutDir.Data());
+      } else {
+         if (!fRunNumbers.Length() && !fRunRange[0]) {
+            // The output directory is the grid outdir
+            printf("### Submitting merging job for the full output directory %s.\n", fGridOutputDir.Data());
+            runOutDir = fGridOutputDir;
          } else {
-            Info("StartAnalysis", "\n_______________________________________________________________________ \
-            \n#####   Your JDL %s was successfully submitted. \nTHE JOB ID IS: %s \
-            \n_______________________________________________________________________",
-                   mergeJDLName.Data(), cjobId);
-         }
-         delete res;
-      } else {     
-         Error("SubmitMerging", "No grid result after submission !!! Bailing out...");
-         return kFALSE;
-      }             
+            // The output directory is the master number in 3 digits format
+            printf("### Submitting merging job for master <%03d>\n", i);
+            runOutDir = Form("%s/%03d",fGridOutputDir.Data(), i);
+         }   
+      }
+      // Check now the number of merging stages.
+      TObjArray *list = fOutputFiles.Tokenize(",");
+      TIter next(list);
+      TObjString *str;
+      TString outputFile;
+      while((str=(TObjString*)next())) {
+         outputFile = str->GetString();
+         Int_t index = outputFile.Index("@");
+         if (index > 0) outputFile.Remove(index);
+         if (!fMergeExcludes.Contains(outputFile)) break;
+      }
+      delete list;
+      Bool_t done = CheckMergedFiles(outputFile, runOutDir, fMaxMergeFiles, mergeJDLName);
+      if (!done && (i==ntosubmit-1)) return kFALSE;
+      if (!fRunNumbers.Length() && !fRunRange[0]) break;
    }
    if (!ntosubmit) return kTRUE;
-   Info("StartAnalysis", "\n#### STARTING AN ALIEN SHELL FOR YOU. EXIT WHEN YOUR MERGING JOBS HAVE FINISHED. #### \
-   \n You may exit at any time and terminate the job later using the option <terminate> but disabling SetMergeViaJDL\
-   \n ##################################################################################");
+   Info("StartAnalysis", "\n #### STARTING AN ALIEN SHELL FOR YOU. You can exit any time or inspect your jobs in a different shell.##########\
+                          \n Make sure your jobs are in a final state (you can resubmit failed ones via 'masterjob <id> resubmit ERROR_ALL')\
+                          \n Rerun in 'terminate' mode to submit all merging stages, each AFTER the previous one completed. The final merged \
+                          \n output will be written to your alien output directory, while separate stages in <Stage_n>. \
+                          \n ################################################################################################################");
    gSystem->Exec("aliensh");
    return kTRUE;
 }
@@ -2096,7 +2888,10 @@ Bool_t AliAnalysisAlien::SubmitMerging()
 //______________________________________________________________________________
 Bool_t AliAnalysisAlien::SubmitNext()
 {
-// Submit next bunch of master jobs if the queue is free.
+// Submit next bunch of master jobs if the queue is free. The first master job is
+// submitted right away, while the next will not be unless the previous was split.
+// The plugin will not submit new master jobs if there are more that 500 jobs in
+// waiting phase.
    static Bool_t iscalled = kFALSE;
    static Int_t firstmaster = 0;
    static Int_t lastmaster = 0;
@@ -2107,21 +2902,28 @@ Bool_t AliAnalysisAlien::SubmitNext()
    Int_t ntosubmit = 0;
    TGridResult *res;
    TString jobID = "";
-   if (!fNsubmitted) ntosubmit = 1;
-   else {
+   Int_t nmasterjobs = fInputFiles->GetEntries();
+   if (!fNsubmitted) {
+      ntosubmit = 1;
+      if (!IsUseSubmitPolicy()) {
+         if (nmasterjobs>5)
+            Info("SubmitNext","### Warning submit policy not used ! Submitting too many jobs at a time may be prohibitted. \
+                \n### You can use SetUseSubmitPolicy() to enable if you have problems.");
+         ntosubmit = nmasterjobs;
+      }   
+   } else {
       TString status = GetJobStatus(firstmaster, lastmaster, nrunning, nwaiting, nerror, ndone);
       printf("=== master %d: %s\n", lastmaster, status.Data());
       // If last master not split, just return
       if (status != "SPLIT") {iscalled = kFALSE; return kTRUE;}
       // No more than 100 waiting jobs
-      if (nwaiting>100) {iscalled = kFALSE; return kTRUE;}
+      if (nwaiting>500) {iscalled = kFALSE; return kTRUE;}
       npermaster = (nrunning+nwaiting+nerror+ndone)/fNsubmitted;      
-      if (npermaster) ntosubmit = (100-nwaiting)/npermaster;
+      if (npermaster) ntosubmit = (500-nwaiting)/npermaster;
       if (!ntosubmit) ntosubmit = 1;
       printf("=== WAITING(%d) RUNNING(%d) DONE(%d) OTHER(%d) NperMaster=%d => to submit %d jobs\n", 
              nwaiting, nrunning, ndone, nerror, npermaster, ntosubmit);
    }
-   Int_t nmasterjobs = fInputFiles->GetEntries();
    for (Int_t i=0; i<ntosubmit; i++) {
       // Submit for a range of enumeration of runs.
       if (fNsubmitted>=nmasterjobs) {iscalled = kFALSE; return kTRUE;}
@@ -2180,8 +2982,14 @@ void AliAnalysisAlien::WriteAnalysisFile()
       if (mgr->GetMCtruthEventHandler()) TObject::SetBit(AliAnalysisGrid::kUseMC);
       handler = (TObject*)mgr->GetInputEventHandler();
       if (handler) {
-         if (handler->InheritsFrom("AliESDInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseESD);
-         if (handler->InheritsFrom("AliAODInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseAOD);
+         if (handler->InheritsFrom("AliMultiInputEventHandler")) {
+            AliMultiInputEventHandler *multiIH = (AliMultiInputEventHandler*)handler;
+            if (multiIH->GetFirstInputEventHandler()->InheritsFrom("AliESDInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseESD);
+            if (multiIH->GetFirstInputEventHandler()->InheritsFrom("AliAODInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseAOD);
+         } else {
+            if (handler->InheritsFrom("AliESDInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseESD);
+            if (handler->InheritsFrom("AliAODInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseAOD);
+         }
       }
       TDirectory *cdir = gDirectory;
       TFile *file = TFile::Open(analysisFile, "RECREATE");
@@ -2199,12 +3007,12 @@ void AliAnalysisAlien::WriteAnalysisFile()
       Info("WriteAnalysisFile", "\n#####   Analysis manager: %s wrote to file <%s>\n", mgr->GetName(),analysisFile.Data());
    }   
    Bool_t copy = kTRUE;
-   if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+   if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
    if (copy) {
       CdWork();
       TString workdir = gGrid->GetHomeDirectory();
       workdir += fGridWorkingDir;
-      Info("CreateJDL", "\n#####   Copying file <%s> containing your initialized analysis manager to your alien workspace", analysisFile.Data());
+      Info("WriteAnalysisFile", "\n#####   Copying file <%s> containing your initialized analysis manager to your alien workspace", analysisFile.Data());
       if (FileExists(analysisFile)) gGrid->Rm(analysisFile);
       TFile::Cp(Form("file:%s",analysisFile.Data()), Form("alien://%s/%s", workdir.Data(),analysisFile.Data()));
    }   
@@ -2230,11 +3038,16 @@ void AliAnalysisAlien::WriteAnalysisMacro()
       TString func = fAnalysisMacro;
       TString type = "ESD";
       TString comment = "// Analysis using ";
-      if (TObject::TestBit(AliAnalysisGrid::kUseESD)) comment += "ESD";
-      if (TObject::TestBit(AliAnalysisGrid::kUseAOD)) {
-         type = "AOD";
-         comment += "AOD";
-      }   
+      if (IsUseMCchain()) {
+         type = "MC";
+         comment += "MC";
+      } else {   
+         if (TObject::TestBit(AliAnalysisGrid::kUseESD)) comment += "ESD";
+         if (TObject::TestBit(AliAnalysisGrid::kUseAOD)) {
+            type = "AOD";
+            comment += "AOD";
+         }   
+      }
       if (type!="AOD" && fFriendChainName!="") {
          Error("WriteAnalysisMacro", "Friend chain can be attached only to AOD");
          return;
@@ -2249,12 +3062,22 @@ void AliAnalysisAlien::WriteAnalysisMacro()
       out << "// Automatically generated analysis steering macro executed in grid subjobs" << endl << endl;
       out << "   TStopwatch timer;" << endl;
       out << "   timer.Start();" << endl << endl;
-      out << "// load base root libraries" << endl;
-      out << "   gSystem->Load(\"libTree\");" << endl;
-      out << "   gSystem->Load(\"libGeom\");" << endl;
-      out << "   gSystem->Load(\"libVMC\");" << endl;
-      out << "   gSystem->Load(\"libPhysics\");" << endl << endl;
-      out << "   gSystem->Load(\"libMinuit\");" << endl << endl;
+      // Change temp directory to current one
+      out << "// Set temporary merging directory to current one" << endl;
+      out << "   gSystem->Setenv(\"TMPDIR\", gSystem->pwd());" << endl << endl;   
+      out << "// Set temporary compilation directory to current one" << endl;
+      out << "   gSystem->SetBuildDir(gSystem->pwd(), kTRUE);" << endl << endl;   
+      // Reset existing include path
+      out << "// Reset existing include path and add current directory first in the search" << endl;
+      out << "   gSystem->SetIncludePath(\"-I.\");" << endl;
+      if (!fExecutableCommand.Contains("aliroot")) {
+         out << "// load base root libraries" << endl;
+         out << "   gSystem->Load(\"libTree\");" << endl;
+         out << "   gSystem->Load(\"libGeom\");" << endl;
+         out << "   gSystem->Load(\"libVMC\");" << endl;
+         out << "   gSystem->Load(\"libPhysics\");" << endl << endl;
+         out << "   gSystem->Load(\"libMinuit\");" << endl << endl;
+      }   
       if (fAdditionalRootLibs.Length()) {
          // in principle libtree /lib geom libvmc etc. can go into this list, too
          out << "// Add aditional libraries" << endl;
@@ -2267,14 +3090,14 @@ void AliAnalysisAlien::WriteAnalysisMacro()
          }
          if (list) delete list;
       }
-      out << "// include path" << endl;
-      if (fIncludePath.Length()) out << "   gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
-      out << "   gSystem->AddIncludePath(\"-I$ALICE_ROOT/include\");" << endl << endl;
       out << "// Load analysis framework libraries" << endl;
+      TString setupPar = "AliAnalysisAlien::SetupPar";
       if (!fPackages) {
-         out << "   gSystem->Load(\"libSTEERBase\");" << endl;
-         out << "   gSystem->Load(\"libESD\");" << endl;
-         out << "   gSystem->Load(\"libAOD\");" << endl;
+         if (!fExecutableCommand.Contains("aliroot")) {         
+            out << "   gSystem->Load(\"libSTEERBase\");" << endl;
+            out << "   gSystem->Load(\"libESD\");" << endl;
+            out << "   gSystem->Load(\"libAOD\");" << endl;
+         }   
          out << "   gSystem->Load(\"libANALYSIS\");" << endl;
          out << "   gSystem->Load(\"libANALYSISalice\");" << endl;
          out << "   gSystem->Load(\"libCORRFW\");" << endl << endl;
@@ -2282,7 +3105,6 @@ void AliAnalysisAlien::WriteAnalysisMacro()
          TIter next(fPackages);
          TObject *obj;
          TString pkgname;
-         TString setupPar = "AliAnalysisAlien::SetupPar";
          while ((obj=next())) {
             pkgname = obj->GetName();
             if (pkgname == "STEERBase" ||
@@ -2330,6 +3152,21 @@ void AliAnalysisAlien::WriteAnalysisMacro()
             out << "   if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
          }   
       }   
+      out << "// include path" << endl;
+      // Get the include path from the interpreter and remove entries pointing to AliRoot
+      out << "   TString intPath = gInterpreter->GetIncludePath();" << endl;
+      out << "   TObjArray *listpaths = intPath.Tokenize(\" \");" << endl;
+      out << "   TIter nextpath(listpaths);" << endl;
+      out << "   TObjString *pname;" << endl;
+      out << "   while ((pname=(TObjString*)nextpath())) {" << endl;
+      out << "      TString current = pname->GetName();" << endl;
+      out << "      if (current.Contains(\"AliRoot\") || current.Contains(\"ALICE_ROOT\")) continue;" << endl;
+      out << "      gSystem->AddIncludePath(current);" << endl;
+      out << "   }" << endl;
+      out << "   if (listpaths) delete listpaths;" << endl;
+      if (fIncludePath.Length()) out << "   gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
+      out << "   gROOT->ProcessLine(\".include $ALICE_ROOT/include\");" << endl;
+      out << "   printf(\"Include path: %s\\n\", gSystem->GetIncludePath());" << endl << endl;
       if (fAdditionalLibs.Length()) {
          out << "// Add aditional AliRoot libraries" << endl;
          TObjArray *list = fAdditionalLibs.Tokenize(" ");
@@ -2338,6 +3175,8 @@ void AliAnalysisAlien::WriteAnalysisMacro()
          while((str=(TObjString*)next())) {
             if (str->GetString().Contains(".so"))
                out << "   gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
+            if (str->GetString().Contains(".par"))
+               out << "   if (!" << setupPar << "(\"" << str->GetString() << "\")) return;" << endl;
          }
          if (list) delete list;
       }
@@ -2353,37 +3192,21 @@ void AliAnalysisAlien::WriteAnalysisMacro()
          if (list) delete list;
       }
       out << endl;
+//      out << "   printf(\"Currently load libraries:\\n\");" << endl;
+//      out << "   printf(\"%s\\n\", gSystem->GetLibraries());" << endl;
       if (fFastReadOption) {
          Warning("WriteAnalysisMacro", "!!! You requested FastRead option. Using xrootd flags to reduce timeouts in the grid jobs. This may skip some files that could be accessed !!! \
                 \n+++ NOTE: To disable this option, use: plugin->SetFastReadOption(kFALSE)");
          out << "// fast xrootd reading enabled" << endl;
          out << "   printf(\"!!! You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !!!\");" << endl;
-         out << "   gEnv->SetValue(\"XNet.ConnectTimeout\",10);" << endl;
-         out << "   gEnv->SetValue(\"XNet.RequestTimeout\",10);" << endl;
+         out << "   gEnv->SetValue(\"XNet.ConnectTimeout\",50);" << endl;
+         out << "   gEnv->SetValue(\"XNet.RequestTimeout\",50);" << endl;
          out << "   gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
-         out << "   gEnv->SetValue(\"XNet.ReconnectTimeout\",10);" << endl;
+         out << "   gEnv->SetValue(\"XNet.ReconnectTimeout\",50);" << endl;
          out << "   gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
       }   
-      // Change temp directory to current one
-      out << "// Set temporary merging directory to current one" << endl;
-      out << "   gSystem->Setenv(\"TMPDIR\", gSystem->pwd());" << endl << endl;   
       out << "// connect to AliEn and make the chain" << endl;
       out << "   if (!TGrid::Connect(\"alien://\")) return;" << endl;
-      if (IsUsingTags()) {
-         out << "   TChain *chain = CreateChainFromTags(\"wn.xml\", anatype);" << endl << endl;
-      } else {
-         if(fFriendChainName!="AliAOD.VertexingHF.root") {
-            out << "   TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl;    
-         } else {
-            out << "   // Check if the macro to create the chain was provided" << endl;
-            out << "   if (gSystem->AccessPathName(\"MakeAODInputChain.C\")) {" << endl;
-            out << "      ::Error(\"" << func.Data() << "\", \"File MakeAODInputChain.C not provided. Aborting.\");" << endl;
-            out << "      return;" << endl;
-            out << "   }" << endl;
-            out << "   gROOT->LoadMacro(\"MakeAODInputChain.C\");" << endl;
-            out << "   TChain *chain = MakeAODInputChain(\"wn.xml\",\"none\");" << endl << endl;
-         }  
-      }   
       out << "// read the analysis manager from file" << endl;
       TString analysisFile = fExecutable;
       analysisFile.ReplaceAll(".sh", ".root");
@@ -2397,7 +3220,7 @@ void AliAnalysisAlien::WriteAnalysisMacro()
       out << "         mgr = (AliAnalysisManager*)file->Get(key->GetName());" << endl;
       out << "   };" << endl;
       out << "   if (!mgr) {" << endl;
-      out << "      ::Error(\"" << func.Data() << "\", \"No analysis manager found in file" << analysisFile <<"\");" << endl;
+      out << "      ::Error(\"" << func.Data() << "\", \"No analysis manager found in file " << analysisFile <<"\");" << endl;
       out << "      return;" << endl;
       out << "   }" << endl << endl;
       out << "   mgr->PrintStatus();" << endl;
@@ -2405,9 +3228,17 @@ void AliAnalysisAlien::WriteAnalysisMacro()
          if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) {
             out << "   gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
          } else {
-            out << "   AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
+            if (TestBit(AliAnalysisGrid::kTest))            
+               out << "   AliLog::SetGlobalLogLevel(AliLog::kWarning);" << endl;
+            else
+               out << "   AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
          }
       }   
+      if (IsUsingTags()) {
+         out << "   TChain *chain = CreateChainFromTags(\"wn.xml\", anatype);" << endl << endl;
+      } else {
+         out << "   TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl;   
+      }   
       out << "   mgr->StartAnalysis(\"localfile\", chain);" << endl;
       out << "   timer.Stop();" << endl;
       out << "   timer.Print();" << endl;
@@ -2450,7 +3281,7 @@ void AliAnalysisAlien::WriteAnalysisMacro()
             msg += "                      AliLHCTagCuts *lhcCuts,\n";
             msg += "                      AliDetectorTagCuts *detCuts,\n";
             msg += "                      AliEventTagCuts *evCuts)";
-            Info("WriteAnalysisMacro", msg.Data());
+            Info("WriteAnalysisMacro", "%s", msg.Data());
          }
       } 
       if (!IsUsingTags() || fFriendChainName!="") {
@@ -2458,9 +3289,15 @@ void AliAnalysisAlien::WriteAnalysisMacro()
          out << "TChain* CreateChain(const char *xmlfile, const char *type=\"ESD\")" << endl;
          out << "{" << endl;
          out << "// Create a chain using url's from xml file" << endl;
-         out << "   TString treename = type;" << endl;
-         out << "   treename.ToLower();" << endl;
-         out << "   treename += \"Tree\";" << endl;
+         out << "   TString filename;" << endl;
+         out << "   Int_t run = 0;" << endl;
+         if (IsUseMCchain()) {
+            out << "   TString treename = \"TE\";" << endl;
+         } else {   
+            out << "   TString treename = type;" << endl;
+            out << "   treename.ToLower();" << endl;
+            out << "   treename += \"Tree\";" << endl;
+         }   
          out << "   printf(\"***************************************\\n\");" << endl;
          out << "   printf(\"    Getting chain of trees %s\\n\", treename.Data());" << endl;
          out << "   printf(\"***************************************\\n\");" << endl;
@@ -2469,13 +3306,23 @@ void AliAnalysisAlien::WriteAnalysisMacro()
          out << "      ::Error(\"CreateChain\", \"Cannot create an AliEn collection from %s\", xmlfile);" << endl;
          out << "      return NULL;" << endl;
          out << "   }" << endl;
+         out << "   AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();" << endl;
          out << "   TChain *chain = new TChain(treename);" << endl;
          if(fFriendChainName!="") {
             out << "   TChain *chainFriend = new TChain(treename);" << endl;
          }
          out << "   coll->Reset();" << endl;
          out << "   while (coll->Next()) {" << endl;
-         out << "      chain->Add(coll->GetTURL(\"\"));" << endl;
+         out << "      filename = coll->GetTURL("");" << endl;
+         out << "      if (mgr) {" << endl;
+         out << "         Int_t nrun = AliAnalysisManager::GetRunFromAlienPath(filename);" << endl;
+         out << "         if (nrun && nrun != run) {" << endl;
+         out << "            printf(\"### Run number detected from chain: %d\\n\", nrun);" << endl;
+         out << "            mgr->SetRunFromPath(nrun);" << endl;
+         out << "            run = nrun;" << endl;
+         out << "         }" << endl;
+         out << "      }" << endl;
+         out << "      chain->Add(filename);" << endl;
          if(fFriendChainName!="") {
             out << "      TString fileFriend=coll->GetTURL(\"\");" << endl;
             out << "      fileFriend.ReplaceAll(\"AliAOD.root\",\""<<fFriendChainName.Data()<<"\");" << endl;
@@ -2499,7 +3346,7 @@ void AliAnalysisAlien::WriteAnalysisMacro()
          out << "// Compile the package and set it up." << endl;
          out << "   TString pkgdir = package;" << endl;
          out << "   pkgdir.ReplaceAll(\".par\",\"\");" << endl;
-         out << "   gSystem->Exec(Form(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
+         out << "   gSystem->Exec(TString::Format(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
          out << "   TString cdir = gSystem->WorkingDirectory();" << endl;
          out << "   gSystem->ChangeDirectory(pkgdir);" << endl;
          out << "   // Check for BUILD.sh and execute" << endl;
@@ -2536,7 +3383,7 @@ void AliAnalysisAlien::WriteAnalysisMacro()
       Info("WriteAnalysisMacro", "\n#####   Analysis macro to run on worker nodes <%s> written",fAnalysisMacro.Data());
    }   
    Bool_t copy = kTRUE;
-   if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+   if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
    if (copy) {
       CdWork();
       TString workdir = gGrid->GetHomeDirectory();
@@ -2580,17 +3427,22 @@ void AliAnalysisAlien::WriteMergingMacro()
       TString func = mergingMacro;
       TString comment;
       func.ReplaceAll(".C", "");
-      out << "void " << func.Data() << "(const char *dir)" << endl;
+      out << "void " << func.Data() << "(const char *dir, Int_t stage=0)" << endl;
       out << "{" << endl;
       out << "// Automatically generated merging macro executed in grid subjobs" << endl << endl;
       out << "   TStopwatch timer;" << endl;
       out << "   timer.Start();" << endl << endl;
-      out << "// load base root libraries" << endl;
-      out << "   gSystem->Load(\"libTree\");" << endl;
-      out << "   gSystem->Load(\"libGeom\");" << endl;
-      out << "   gSystem->Load(\"libVMC\");" << endl;
-      out << "   gSystem->Load(\"libPhysics\");" << endl << endl;
-      out << "   gSystem->Load(\"libMinuit\");" << endl << endl;
+      // Reset existing include path
+      out << "// Reset existing include path and add current directory first in the search" << endl;
+      out << "   gSystem->SetIncludePath(\"-I.\");" << endl;
+      if (!fExecutableCommand.Contains("aliroot")) {
+         out << "// load base root libraries" << endl;
+         out << "   gSystem->Load(\"libTree\");" << endl;
+         out << "   gSystem->Load(\"libGeom\");" << endl;
+         out << "   gSystem->Load(\"libVMC\");" << endl;
+         out << "   gSystem->Load(\"libPhysics\");" << endl << endl;
+         out << "   gSystem->Load(\"libMinuit\");" << endl << endl;
+      }   
       if (fAdditionalRootLibs.Length()) {
          // in principle libtree /lib geom libvmc etc. can go into this list, too
          out << "// Add aditional libraries" << endl;
@@ -2603,14 +3455,13 @@ void AliAnalysisAlien::WriteMergingMacro()
          }
          if (list) delete list;
       }
-      out << "// include path" << endl;
-      if (fIncludePath.Length()) out << "   gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
-      out << "   gSystem->AddIncludePath(\"-I$ALICE_ROOT/include\");" << endl << endl;
       out << "// Load analysis framework libraries" << endl;
       if (!fPackages) {
-         out << "   gSystem->Load(\"libSTEERBase\");" << endl;
-         out << "   gSystem->Load(\"libESD\");" << endl;
-         out << "   gSystem->Load(\"libAOD\");" << endl;
+         if (!fExecutableCommand.Contains("aliroot")) {
+            out << "   gSystem->Load(\"libSTEERBase\");" << endl;
+            out << "   gSystem->Load(\"libESD\");" << endl;
+            out << "   gSystem->Load(\"libAOD\");" << endl;
+         }
          out << "   gSystem->Load(\"libANALYSIS\");" << endl;
          out << "   gSystem->Load(\"libANALYSISalice\");" << endl;
          out << "   gSystem->Load(\"libCORRFW\");" << endl << endl;
@@ -2666,6 +3517,21 @@ void AliAnalysisAlien::WriteMergingMacro()
             out << "   if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
          }   
       }   
+      out << "// include path" << endl;
+      // Get the include path from the interpreter and remove entries pointing to AliRoot
+      out << "   TString intPath = gInterpreter->GetIncludePath();" << endl;
+      out << "   TObjArray *listpaths = intPath.Tokenize(\" \");" << endl;
+      out << "   TIter nextpath(listpaths);" << endl;
+      out << "   TObjString *pname;" << endl;
+      out << "   while ((pname=(TObjString*)nextpath())) {" << endl;
+      out << "      TString current = pname->GetName();" << endl;
+      out << "      if (current.Contains(\"AliRoot\") || current.Contains(\"ALICE_ROOT\")) continue;" << endl;
+      out << "      gSystem->AddIncludePath(current);" << endl;
+      out << "   }" << endl;
+      out << "   if (listpaths) delete listpaths;" << endl;
+      if (fIncludePath.Length()) out << "   gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
+      out << "   gROOT->ProcessLine(\".include $ALICE_ROOT/include\");" << endl;
+      out << "   printf(\"Include path: %s\\n\", gSystem->GetIncludePath());" << endl << endl;
       if (fAdditionalLibs.Length()) {
          out << "// Add aditional AliRoot libraries" << endl;
          TObjArray *list = fAdditionalLibs.Tokenize(" ");
@@ -2694,22 +3560,22 @@ void AliAnalysisAlien::WriteMergingMacro()
          Warning("WriteMergingMacro", "!!! You requested FastRead option. Using xrootd flags to reduce timeouts in the grid merging jobs. Note that this may skip some files that could be accessed !!!");
          out << "// fast xrootd reading enabled" << endl;
          out << "   printf(\"!!! You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !!!\");" << endl;
-         out << "   gEnv->SetValue(\"XNet.ConnectTimeout\",10);" << endl;
-         out << "   gEnv->SetValue(\"XNet.RequestTimeout\",10);" << endl;
+         out << "   gEnv->SetValue(\"XNet.ConnectTimeout\",50);" << endl;
+         out << "   gEnv->SetValue(\"XNet.RequestTimeout\",50);" << endl;
          out << "   gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
-         out << "   gEnv->SetValue(\"XNet.ReconnectTimeout\",10);" << endl;
+         out << "   gEnv->SetValue(\"XNet.ReconnectTimeout\",50);" << endl;
          out << "   gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
       }
       // Change temp directory to current one
       out << "// Set temporary merging directory to current one" << endl;
       out << "   gSystem->Setenv(\"TMPDIR\", gSystem->pwd());" << endl << endl;   
+      out << "// Set temporary compilation directory to current one" << endl;
+      out << "   gSystem->SetBuildDir(gSystem->pwd(), kTRUE);" << endl << endl;   
       out << "// Connect to AliEn" << endl;
       out << "   if (!TGrid::Connect(\"alien://\")) return;" << endl;
-      out << "   TString outputDir = \"" << fGridOutputDir << "/\";" << endl;  
-      out << "   outputDir += dir;" << endl;    
-      out << "   TString outputFiles = \"" << fOutputFiles << "\";" << endl;
+      out << "   TString outputDir = dir;" << endl;  
+      out << "   TString outputFiles = \"" << GetListOfFiles("out") << "\";" << endl;
       out << "   TString mergeExcludes = \"" << fMergeExcludes << "\";" << endl;
-      out << "   mergeExcludes += \"" << AliAnalysisManager::GetAnalysisManager()->GetExtraFiles() << "\";" << endl;
       out << "   TObjArray *list = outputFiles.Tokenize(\",\");" << endl;
       out << "   TIter *iter = new TIter(list);" << endl;
       out << "   TObjString *str;" << endl;
@@ -2717,6 +3583,7 @@ void AliAnalysisAlien::WriteMergingMacro()
       out << "   Bool_t merged = kTRUE;" << endl;
       out << "   while((str=(TObjString*)iter->Next())) {" << endl;
       out << "      outputFile = str->GetString();" << endl;
+      out << "      if (outputFile.Contains(\"*\")) continue;" << endl;
       out << "      Int_t index = outputFile.Index(\"@\");" << endl;
       out << "      if (index > 0) outputFile.Remove(index);" << endl;
       out << "      // Skip already merged outputs" << endl;
@@ -2725,16 +3592,22 @@ void AliAnalysisAlien::WriteMergingMacro()
       out << "         continue;" << endl;
       out << "      }" << endl;
       out << "      if (mergeExcludes.Contains(outputFile.Data())) continue;" << endl;
-      out << "      merged = AliAnalysisAlien::MergeOutput(outputFile, outputDir, " << fMaxMergeFiles << ");" << endl;
+      out << "      merged = AliAnalysisAlien::MergeOutput(outputFile, outputDir, " << fMaxMergeFiles << ", stage);" << endl;
       out << "      if (!merged) {" << endl;
       out << "         printf(\"ERROR: Cannot merge %s\\n\", outputFile.Data());" << endl;
+      out << "         return;" << endl;
       out << "      }" << endl;
       out << "   }" << endl;
-      out << "// read the analysis manager from file" << endl;
+      out << "   // all outputs merged, validate" << endl;
+      out << "   ofstream out;" << endl;
+      out << "   out.open(\"outputs_valid\", ios::out);" << endl;
+      out << "   out.close();" << endl;
+      out << "   // read the analysis manager from file" << endl;
       TString analysisFile = fExecutable;
       analysisFile.ReplaceAll(".sh", ".root");
+      out << "   if (!outputDir.Contains(\"Stage\")) return;" << endl;
       out << "   TFile *file = TFile::Open(\"" << analysisFile << "\");" << endl;
-      out << "   if (!file) return;" << endl; 
+      out << "   if (!file) return;" << endl;
       out << "   TIter nextkey(file->GetListOfKeys());" << endl;
       out << "   AliAnalysisManager *mgr = 0;" << endl;
       out << "   TKey *key;" << endl;
@@ -2746,16 +3619,21 @@ void AliAnalysisAlien::WriteMergingMacro()
       out << "      ::Error(\"" << func.Data() << "\", \"No analysis manager found in file" << analysisFile <<"\");" << endl;
       out << "      return;" << endl;
       out << "   }" << endl << endl;
+      out << "   mgr->SetRunFromPath(mgr->GetRunFromAlienPath(dir));" << endl;
       out << "   mgr->SetSkipTerminate(kFALSE);" << endl;
       out << "   mgr->PrintStatus();" << endl;
       if (AliAnalysisManager::GetAnalysisManager()) {
          if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) {
             out << "   gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
          } else {
-            out << "   AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
+            if (TestBit(AliAnalysisGrid::kTest))            
+               out << "   AliLog::SetGlobalLogLevel(AliLog::kWarning);" << endl;
+            else
+               out << "   AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
          }
       }   
-      out << "   mgr->StartAnalysis(\"gridterminate\");" << endl;
+      out << "   TTree *tree = NULL;" << endl;
+      out << "   mgr->StartAnalysis(\"gridterminate\", tree);" << endl;
       out << "}" << endl << endl;
       if (hasANALYSISalice) {
          out <<"//________________________________________________________________________________" << endl;
@@ -2763,7 +3641,7 @@ void AliAnalysisAlien::WriteMergingMacro()
          out << "// Compile the package and set it up." << endl;
          out << "   TString pkgdir = package;" << endl;
          out << "   pkgdir.ReplaceAll(\".par\",\"\");" << endl;
-         out << "   gSystem->Exec(Form(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
+         out << "   gSystem->Exec(TString::Format(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
          out << "   TString cdir = gSystem->WorkingDirectory();" << endl;
          out << "   gSystem->ChangeDirectory(pkgdir);" << endl;
          out << "   // Check for BUILD.sh and execute" << endl;
@@ -2799,7 +3677,7 @@ void AliAnalysisAlien::WriteMergingMacro()
       }
    }   
    Bool_t copy = kTRUE;
-   if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+   if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
    if (copy) {
       CdWork();
       TString workdir = gGrid->GetHomeDirectory();
@@ -2813,12 +3691,12 @@ void AliAnalysisAlien::WriteMergingMacro()
 //______________________________________________________________________________
 Bool_t AliAnalysisAlien::SetupPar(const char *package)
 {
-// Compile the par file archive pointed by <package>. This must be present in the current durectory.
+// Compile the par file archive pointed by <package>. This must be present in the current directory.
 // Note that for loading the compiled library. The current directory should have precedence in
 // LD_LIBRARY_PATH
    TString pkgdir = package;
    pkgdir.ReplaceAll(".par","");
-   gSystem->Exec(Form("tar xvzf %s.par", pkgdir.Data()));
+   gSystem->Exec(TString::Format("tar xzf %s.par", pkgdir.Data()));
    TString cdir = gSystem->WorkingDirectory();
    gSystem->ChangeDirectory(pkgdir);
    // Check for BUILD.sh and execute
@@ -2865,6 +3743,8 @@ void AliAnalysisAlien::WriteExecutable()
          return;
       }
       out << "#!/bin/bash" << endl;
+      // Make sure we can properly compile par files
+      out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
       out << "echo \"=========================================\"" << endl; 
       out << "echo \"############## PATH : ##############\"" << endl;
       out << "echo $PATH" << endl;
@@ -2883,8 +3763,6 @@ void AliAnalysisAlien::WriteExecutable()
       out << "echo \"############## memory : ##############\"" << endl;
       out << "free -m" << endl;
       out << "echo \"=========================================\"" << endl << endl;
-      // Make sure we can properly compile par files
-      if (TObject::TestBit(AliAnalysisGrid::kUsePars)) out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
       out << fExecutableCommand << " "; 
       out << fAnalysisMacro.Data() << " " << fExecutableArgs.Data() << endl << endl;
       out << "echo \"======== " << fAnalysisMacro.Data() << " finished with exit code: $? ========\"" << endl;
@@ -2892,16 +3770,16 @@ void AliAnalysisAlien::WriteExecutable()
       out << "free -m" << endl;
    }   
    Bool_t copy = kTRUE;
-   if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+   if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
    if (copy) {
       CdWork();
       TString workdir = gGrid->GetHomeDirectory();
       TString bindir = Form("%s/bin", workdir.Data());
-      if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir);
+      if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir,"-p");
       workdir += fGridWorkingDir;
       TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), fExecutable.Data());
       if (FileExists(executable)) gGrid->Rm(executable);
-      Info("CreateJDL", "\n#####   Copying executable file <%s> to your AliEn bin directory", fExecutable.Data());
+      Info("WriteExecutable", "\n#####   Copying executable file <%s> to your AliEn bin directory", fExecutable.Data());
       TFile::Cp(Form("file:%s",fExecutable.Data()), Form("alien://%s", executable.Data()));
    } 
 }
@@ -2921,6 +3799,8 @@ void AliAnalysisAlien::WriteMergeExecutable()
          return;
       }
       out << "#!/bin/bash" << endl;
+      // Make sure we can properly compile par files
+      out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
       out << "echo \"=========================================\"" << endl; 
       out << "echo \"############## PATH : ##############\"" << endl;
       out << "echo $PATH" << endl;
@@ -2939,27 +3819,28 @@ void AliAnalysisAlien::WriteMergeExecutable()
       out << "echo \"############## memory : ##############\"" << endl;
       out << "free -m" << endl;
       out << "echo \"=========================================\"" << endl << endl;
-      // Make sure we can properly compile par files
-      if (TObject::TestBit(AliAnalysisGrid::kUsePars)) out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
       TString mergeMacro = fExecutable;
       mergeMacro.ReplaceAll(".sh", "_merge.C");
-      out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\")\"" << endl;
+      if (IsOneStageMerging())
+         out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\")\"" << endl;
+      else
+         out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\",$2)\"" << endl;
       out << fExecutableCommand << " " << "$ARG" << endl; 
       out << "echo \"======== " << mergeMacro.Data() << " finished with exit code: $? ========\"" << endl;
       out << "echo \"############## memory after: ##############\"" << endl;
       out << "free -m" << endl;
    }   
    Bool_t copy = kTRUE;
-   if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+   if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
    if (copy) {
       CdWork();
       TString workdir = gGrid->GetHomeDirectory();
       TString bindir = Form("%s/bin", workdir.Data());
-      if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir);
+      if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir,"-p");
       workdir += fGridWorkingDir;
       TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), mergeExec.Data());
       if (FileExists(executable)) gGrid->Rm(executable);
-      Info("CreateJDL", "\n#####   Copying executable file <%s> to your AliEn bin directory", mergeExec.Data());
+      Info("WriteMergeExecutable", "\n#####   Copying executable file <%s> to your AliEn bin directory", mergeExec.Data());
       TFile::Cp(Form("file:%s",mergeExec.Data()), Form("alien://%s", executable.Data()));
    } 
 }
@@ -2977,7 +3858,9 @@ void AliAnalysisAlien::WriteProductionFile(const char *filename) const
       Error("WriteProductionFile", "Bad file name: %s", filename);
       return;
    }
-   TString workdir = gGrid->GetHomeDirectory();
+   TString workdir;
+   if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice"))
+      workdir = gGrid->GetHomeDirectory();
    workdir += fGridWorkingDir;
    Int_t njobspermaster = 1000*fNrunsPerMaster/fSplitMaxInputFileNumber;
    TString locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
@@ -2991,9 +3874,11 @@ void AliAnalysisAlien::WriteProductionFile(const char *filename) const
       else
          out << Form("%s", fInputFiles->At(i)->GetName()) << " " << Form("%03d", i) << endl;
    }
-   Info("WriteProductionFile", "\n#####   Copying production file <%s> to your work directory", filename);
-   if (FileExists(filename)) gGrid->Rm(filename);
-   TFile::Cp(Form("file:%s",filename), Form("alien://%s/%s", workdir.Data(),filename));   
+   if (gGrid) {
+      Info("WriteProductionFile", "\n#####   Copying production file <%s> to your work directory", filename);
+      if (FileExists(filename)) gGrid->Rm(filename);
+      TFile::Cp(Form("file:%s",filename), Form("alien://%s/%s", workdir.Data(),filename));
+   }   
 }
 
 //______________________________________________________________________________
@@ -3002,13 +3887,20 @@ void AliAnalysisAlien::WriteValidationScript(Bool_t merge)
 // Generate the alien validation script.
    // Generate the validation script
    TObjString *os;
-   TString validationScript = fExecutable;
-   if (merge) validationScript.ReplaceAll(".sh", "_mergevalidation.sh");
-   else       validationScript.ReplaceAll(".sh", "_validation.sh");
+   if (fValidationScript.IsNull()) {
+      fValidationScript = fExecutable;
+      fValidationScript.ReplaceAll(".sh", "_validation.sh");
+   }   
+   TString validationScript = fValidationScript;
+   if (merge) validationScript.ReplaceAll(".sh", "_merge.sh");
    if (!Connect()) {
       Error("WriteValidationScript", "Alien connection required");
       return;
    }
+   if (!fTerminateFiles.IsNull()) {
+      fTerminateFiles.Strip();
+      fTerminateFiles.ReplaceAll(" ",",");
+   }   
    TString outStream = "";
    if (!TestBit(AliAnalysisGrid::kTest)) outStream = " >> stdout";
    if (!TestBit(AliAnalysisGrid::kSubmit)) {  
@@ -3080,32 +3972,33 @@ void AliAnalysisAlien::WriteValidationScript(Bool_t merge)
 
       // Part dedicated to the specific analyses running into the train
 
-      TObjArray *arr = fOutputFiles.Tokenize(",");
+      TString outputFiles = fOutputFiles;
+      if (merge && !fTerminateFiles.IsNull()) {
+         outputFiles += ",";
+         outputFiles += fTerminateFiles;
+      }
+      TObjArray *arr = outputFiles.Tokenize(",");
       TIter next1(arr);
       TString outputFile;
-      AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
-      TString extra = mgr->GetExtraFiles();
-      while ((os=(TObjString*)next1())) { 
+      while (!merge && (os=(TObjString*)next1())) { 
+         // No need to validate outputs produced by merging since the merging macro does this
          outputFile = os->GetString();
          Int_t index = outputFile.Index("@");
          if (index > 0) outputFile.Remove(index);
-         if (merge && fMergeExcludes.Contains(outputFile)) continue;
-         if (extra.Contains(outputFile)) continue;
+         if (fTerminateFiles.Contains(outputFile)) continue;
          if (outputFile.Contains("*")) continue;
          out << "if ! [ -f " << outputFile.Data() << " ] ; then" << endl;
          out << "   error=1" << endl;
-         out << "   echo \"Output file(s) not found. Job FAILED !\""  << outStream << endl;
-         out << "   echo \"Output file(s) not found. Job FAILED !\" >> stderr" << endl;
+         out << "   echo \"Output file " << outputFile << " not found. Job FAILED !\""  << outStream << endl;
+         out << "   echo \"Output file " << outputFile << " not found. Job FAILED !\" >> stderr" << endl;
          out << "fi" << endl;
       }   
       delete arr;
-      if (!merge) {
-        out << "if ! [ -f outputs_valid ] ; then" << endl;
-        out << "   error=1" << endl;
-        out << "   echo \"Output files were not validated by the analysis manager\" >> stdout" << endl;
-        out << "   echo \"Output files were not validated by the analysis manager\" >> stderr" << endl;
-        out << "fi" << endl;
-      }  
+      out << "if ! [ -f outputs_valid ] ; then" << endl;
+      out << "   error=1" << endl;
+      out << "   echo \"Output files were not validated by the analysis manager\" >> stdout" << endl;
+      out << "   echo \"Output files were not validated by the analysis manager\" >> stderr" << endl;
+      out << "fi" << endl;
       
       out << "if [ $error = 0 ] ; then" << endl;
       out << "   echo \"* ----------------   Job Validated  ------------------*\""  << outStream << endl;
@@ -3122,12 +4015,12 @@ void AliAnalysisAlien::WriteValidationScript(Bool_t merge)
       out << "exit $error" << endl;
    }    
    Bool_t copy = kTRUE;
-   if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+   if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
    if (copy) {
       CdWork();
       TString workdir = gGrid->GetHomeDirectory();
       workdir += fGridWorkingDir;
-      Info("CreateJDL", "\n#####   Copying validation script <%s> to your AliEn working space", validationScript.Data());
+      Info("WriteValidationScript", "\n#####   Copying validation script <%s> to your AliEn working space", validationScript.Data());
       if (FileExists(validationScript)) gGrid->Rm(validationScript);
       TFile::Cp(Form("file:%s",validationScript.Data()), Form("alien://%s/%s", workdir.Data(),validationScript.Data()));
    }