/************************************************************************** * Copyright(c) 1998-2007, ALICE Experiment at CERN, All rights reserved. * * * * Author: The ALICE Off-line Project. * * Contributors are mentioned in the code where appropriate. * * * * Permission to use, copy, modify and distribute this software and its * * documentation strictly for non-commercial purposes is hereby granted * * without fee, provided that the above copyright notice appears in all * * copies and that both the copyright notice and this permission notice * * appear in the supporting documentation. The authors make no claims * * about the suitability of this software for any purpose. It is * * provided "as is" without express or implied warranty. * **************************************************************************/ // Author: Mihaela Gheata, 01/09/2008 //============================================================================== // AliAnalysisAlien - AliEn utility class. Provides interface for creating // a personalized JDL, finding and creating a dataset. //============================================================================== #include "AliAnalysisAlien.h" #include "Riostream.h" #include "TEnv.h" #include "TKey.h" #include "TBits.h" #include "TError.h" #include "TROOT.h" #include "TSystem.h" #include "TInterpreter.h" #include "TFile.h" #include "TFileCollection.h" #include "TChain.h" #include "TObjString.h" #include "TObjArray.h" #include "TMacro.h" #include "TGrid.h" #include "TGridResult.h" #include "TGridCollection.h" #include "TGridJDL.h" #include "TGridJobStatusList.h" #include "TGridJobStatus.h" #include "TFileMerger.h" #include "AliAnalysisManager.h" #include "AliAnalysisTaskCfg.h" #include "AliVEventHandler.h" #include "AliAnalysisDataContainer.h" #include "AliMultiInputEventHandler.h" using std::ofstream; using std::ifstream; using std::ios; using std::endl; ClassImp(AliAnalysisAlien) #if 0 ; #endif namespace { Bool_t copyLocal2Alien(const char* where, const char* loc, const char* rem) { TString sl(Form("file:%s", loc)); TString sr(Form("alien://%s", rem)); Bool_t ret = TFile::Cp(sl, sr); if (!ret) { Warning(where, "Failed to copy %s to %s", sl.Data(), sr.Data()); } return ret; } } //______________________________________________________________________________ AliAnalysisAlien::AliAnalysisAlien() :AliAnalysisGrid(), fGridJDL(NULL), fMergingJDL(NULL), fPrice(0), fTTL(0), fSplitMaxInputFileNumber(0), fMaxInitFailed(0), fMasterResubmitThreshold(0), fNtestFiles(0), fNrunsPerMaster(0), fMaxMergeFiles(0), fMaxMergeStages(0), fNsubmitted(0), fProductionMode(0), fOutputToRunNo(0), fMergeViaJDL(0), fFastReadOption(0), fOverwriteMode(1), fNreplicas(2), fNproofWorkers(0), fNproofWorkersPerSlave(0), fProofReset(0), fNMCevents(0), fNMCjobs(0), fRunNumbers(), fExecutable(), fExecutableCommand(), fArguments(), fExecutableArgs(), fAnalysisMacro(), fAnalysisSource(), fValidationScript(), fAdditionalRootLibs(), fAdditionalLibs(), fGeneratorLibs(), fSplitMode(), fAPIVersion(), fROOTVersion(), fAliROOTVersion(), fExternalPackages(), fUser(), fGridWorkingDir(), fGridDataDir(), fDataPattern(), fGridOutputDir(), fOutputArchive(), fOutputFiles(), fInputFormat(), fDatasetName(), fJDLName(), fTerminateFiles(), fMergeExcludes(), fRegisterExcludes(), fIncludePath(), fCloseSE(), fFriendChainName(), fJobTag(), fOutputSingle(), fRunPrefix(), fProofCluster(), fProofDataSet(), fFileForTestMode(), fAliRootMode(), fProofProcessOpt(), fMergeDirName(), fInputFiles(0), fPackages(0), fModules(0), fProofParam(), fDropToShell(true), fMCLoop(false), fGridJobIDs(""), fGridStages(""), fFriendLibs(""), fTreeName() { // Dummy ctor. SetDefaults(); } //______________________________________________________________________________ AliAnalysisAlien::AliAnalysisAlien(const char *name) :AliAnalysisGrid(name), fGridJDL(NULL), fMergingJDL(NULL), fPrice(0), fTTL(0), fSplitMaxInputFileNumber(0), fMaxInitFailed(0), fMasterResubmitThreshold(0), fNtestFiles(0), fNrunsPerMaster(0), fMaxMergeFiles(0), fMaxMergeStages(0), fNsubmitted(0), fProductionMode(0), fOutputToRunNo(0), fMergeViaJDL(0), fFastReadOption(0), fOverwriteMode(1), fNreplicas(2), fNproofWorkers(0), fNproofWorkersPerSlave(0), fProofReset(0), fNMCevents(0), fNMCjobs(0), fRunNumbers(), fExecutable(), fExecutableCommand(), fArguments(), fExecutableArgs(), fAnalysisMacro(), fAnalysisSource(), fValidationScript(), fAdditionalRootLibs(), fAdditionalLibs(), fGeneratorLibs(), fSplitMode(), fAPIVersion(), fROOTVersion(), fAliROOTVersion(), fExternalPackages(), fUser(), fGridWorkingDir(), fGridDataDir(), fDataPattern(), fGridOutputDir(), fOutputArchive(), fOutputFiles(), fInputFormat(), fDatasetName(), fJDLName(), fTerminateFiles(), fMergeExcludes(), fRegisterExcludes(), fIncludePath(), fCloseSE(), fFriendChainName(), fJobTag(), fOutputSingle(), fRunPrefix(), fProofCluster(), fProofDataSet(), fFileForTestMode(), fAliRootMode(), fProofProcessOpt(), fMergeDirName(), fInputFiles(0), fPackages(0), fModules(0), fProofParam(), fDropToShell(true), fMCLoop(false), fGridJobIDs(""), fGridStages(""), fFriendLibs(""), fTreeName() { // Default ctor. SetDefaults(); } //______________________________________________________________________________ AliAnalysisAlien::AliAnalysisAlien(const AliAnalysisAlien& other) :AliAnalysisGrid(other), fGridJDL(NULL), fMergingJDL(NULL), fPrice(other.fPrice), fTTL(other.fTTL), fSplitMaxInputFileNumber(other.fSplitMaxInputFileNumber), fMaxInitFailed(other.fMaxInitFailed), fMasterResubmitThreshold(other.fMasterResubmitThreshold), fNtestFiles(other.fNtestFiles), fNrunsPerMaster(other.fNrunsPerMaster), fMaxMergeFiles(other.fMaxMergeFiles), fMaxMergeStages(other.fMaxMergeStages), fNsubmitted(other.fNsubmitted), fProductionMode(other.fProductionMode), fOutputToRunNo(other.fOutputToRunNo), fMergeViaJDL(other.fMergeViaJDL), fFastReadOption(other.fFastReadOption), fOverwriteMode(other.fOverwriteMode), fNreplicas(other.fNreplicas), fNproofWorkers(other.fNproofWorkers), fNproofWorkersPerSlave(other.fNproofWorkersPerSlave), fProofReset(other.fProofReset), fNMCevents(other.fNMCevents), fNMCjobs(other.fNMCjobs), fRunNumbers(other.fRunNumbers), fExecutable(other.fExecutable), fExecutableCommand(other.fExecutableCommand), fArguments(other.fArguments), fExecutableArgs(other.fExecutableArgs), fAnalysisMacro(other.fAnalysisMacro), fAnalysisSource(other.fAnalysisSource), fValidationScript(other.fValidationScript), fAdditionalRootLibs(other.fAdditionalRootLibs), fAdditionalLibs(other.fAdditionalLibs), fGeneratorLibs(other.fGeneratorLibs), fSplitMode(other.fSplitMode), fAPIVersion(other.fAPIVersion), fROOTVersion(other.fROOTVersion), fAliROOTVersion(other.fAliROOTVersion), fExternalPackages(other.fExternalPackages), fUser(other.fUser), fGridWorkingDir(other.fGridWorkingDir), fGridDataDir(other.fGridDataDir), fDataPattern(other.fDataPattern), fGridOutputDir(other.fGridOutputDir), fOutputArchive(other.fOutputArchive), fOutputFiles(other.fOutputFiles), fInputFormat(other.fInputFormat), fDatasetName(other.fDatasetName), fJDLName(other.fJDLName), fTerminateFiles(other.fTerminateFiles), fMergeExcludes(other.fMergeExcludes), fRegisterExcludes(other.fRegisterExcludes), fIncludePath(other.fIncludePath), fCloseSE(other.fCloseSE), fFriendChainName(other.fFriendChainName), fJobTag(other.fJobTag), fOutputSingle(other.fOutputSingle), fRunPrefix(other.fRunPrefix), fProofCluster(other.fProofCluster), fProofDataSet(other.fProofDataSet), fFileForTestMode(other.fFileForTestMode), fAliRootMode(other.fAliRootMode), fProofProcessOpt(other.fProofProcessOpt), fMergeDirName(other.fMergeDirName), fInputFiles(0), fPackages(0), fModules(0), fProofParam(), fDropToShell(other.fDropToShell), fMCLoop(other.fMCLoop), fGridJobIDs(other.fGridJobIDs), fGridStages(other.fGridStages), fFriendLibs(other.fFriendLibs), fTreeName(other.fTreeName) { // Copy ctor. fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()"); fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()"); fRunRange[0] = other.fRunRange[0]; fRunRange[1] = other.fRunRange[1]; if (other.fInputFiles) { fInputFiles = new TObjArray(); TIter next(other.fInputFiles); TObject *obj; while ((obj=next())) fInputFiles->Add(new TObjString(obj->GetName())); fInputFiles->SetOwner(); } if (other.fPackages) { fPackages = new TObjArray(); TIter next(other.fPackages); TObject *obj; while ((obj=next())) fPackages->Add(new TObjString(obj->GetName())); fPackages->SetOwner(); } if (other.fModules) { fModules = new TObjArray(); fModules->SetOwner(); TIter next(other.fModules); AliAnalysisTaskCfg *mod, *crt; while ((crt=(AliAnalysisTaskCfg*)next())) { mod = new AliAnalysisTaskCfg(*crt); fModules->Add(mod); } } } //______________________________________________________________________________ AliAnalysisAlien::~AliAnalysisAlien() { // Destructor. delete fGridJDL; delete fMergingJDL; delete fInputFiles; delete fPackages; delete fModules; fProofParam.DeleteAll(); } //______________________________________________________________________________ AliAnalysisAlien &AliAnalysisAlien::operator=(const AliAnalysisAlien& other) { // Assignment. if (this != &other) { AliAnalysisGrid::operator=(other); fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()"); fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()"); fPrice = other.fPrice; fTTL = other.fTTL; fSplitMaxInputFileNumber = other.fSplitMaxInputFileNumber; fMaxInitFailed = other.fMaxInitFailed; fMasterResubmitThreshold = other.fMasterResubmitThreshold; fNtestFiles = other.fNtestFiles; fNrunsPerMaster = other.fNrunsPerMaster; fMaxMergeFiles = other.fMaxMergeFiles; fMaxMergeStages = other.fMaxMergeStages; fNsubmitted = other.fNsubmitted; fProductionMode = other.fProductionMode; fOutputToRunNo = other.fOutputToRunNo; fMergeViaJDL = other.fMergeViaJDL; fFastReadOption = other.fFastReadOption; fOverwriteMode = other.fOverwriteMode; fNreplicas = other.fNreplicas; fNproofWorkers = other.fNproofWorkers; fNproofWorkersPerSlave = other.fNproofWorkersPerSlave; fProofReset = other.fProofReset; fNMCevents = other.fNMCevents; fNMCjobs = other.fNMCjobs; fRunNumbers = other.fRunNumbers; fExecutable = other.fExecutable; fExecutableCommand = other.fExecutableCommand; fArguments = other.fArguments; fExecutableArgs = other.fExecutableArgs; fAnalysisMacro = other.fAnalysisMacro; fAnalysisSource = other.fAnalysisSource; fValidationScript = other.fValidationScript; fAdditionalRootLibs = other.fAdditionalRootLibs; fAdditionalLibs = other.fAdditionalLibs; fGeneratorLibs = other.fGeneratorLibs; fSplitMode = other.fSplitMode; fAPIVersion = other.fAPIVersion; fROOTVersion = other.fROOTVersion; fAliROOTVersion = other.fAliROOTVersion; fExternalPackages = other.fExternalPackages; fUser = other.fUser; fGridWorkingDir = other.fGridWorkingDir; fGridDataDir = other.fGridDataDir; fDataPattern = other.fDataPattern; fGridOutputDir = other.fGridOutputDir; fOutputArchive = other.fOutputArchive; fOutputFiles = other.fOutputFiles; fInputFormat = other.fInputFormat; fDatasetName = other.fDatasetName; fJDLName = other.fJDLName; fTerminateFiles = other.fTerminateFiles; fMergeExcludes = other.fMergeExcludes; fRegisterExcludes = other.fRegisterExcludes; fIncludePath = other.fIncludePath; fCloseSE = other.fCloseSE; fFriendChainName = other.fFriendChainName; fJobTag = other.fJobTag; fOutputSingle = other.fOutputSingle; fRunPrefix = other.fRunPrefix; fProofCluster = other.fProofCluster; fProofDataSet = other.fProofDataSet; fFileForTestMode = other.fFileForTestMode; fAliRootMode = other.fAliRootMode; fProofProcessOpt = other.fProofProcessOpt; fMergeDirName = other.fMergeDirName; fDropToShell = other.fDropToShell; fMCLoop = other.fMCLoop; fGridJobIDs = other.fGridJobIDs; fGridStages = other.fGridStages; fFriendLibs = other.fFriendLibs; fTreeName = other.fTreeName; if (other.fInputFiles) { fInputFiles = new TObjArray(); TIter next(other.fInputFiles); TObject *obj; while ((obj=next())) fInputFiles->Add(new TObjString(obj->GetName())); fInputFiles->SetOwner(); } if (other.fPackages) { fPackages = new TObjArray(); TIter next(other.fPackages); TObject *obj; while ((obj=next())) fPackages->Add(new TObjString(obj->GetName())); fPackages->SetOwner(); } if (other.fModules) { fModules = new TObjArray(); fModules->SetOwner(); TIter next(other.fModules); AliAnalysisTaskCfg *mod, *crt; while ((crt=(AliAnalysisTaskCfg*)next())) { mod = new AliAnalysisTaskCfg(*crt); fModules->Add(mod); } } } return *this; } //______________________________________________________________________________ void AliAnalysisAlien::AddAdditionalLibrary(const char *name) { // Add a single additional library to be loaded. Extension must be present. TString lib(name); if (!lib.Contains(".")) { Error("AddAdditionalLibrary", "Extension not defined for %s", name); return; } if (fAdditionalLibs.Contains(name)) { Warning("AddAdditionalLibrary", "Library %s already added.", name); return; } if (!fAdditionalLibs.IsNull()) fAdditionalLibs += " "; fAdditionalLibs += lib; } //______________________________________________________________________________ void AliAnalysisAlien::AddModule(AliAnalysisTaskCfg *module) { // Adding a module. Checks if already existing. Becomes owned by this. if (!module) return; if (GetModule(module->GetName())) { Error("AddModule", "A module having the same name %s already added", module->GetName()); return; } if (!fModules) { fModules = new TObjArray(); fModules->SetOwner(); } fModules->Add(module); } //______________________________________________________________________________ void AliAnalysisAlien::AddModules(TObjArray *list) { // Adding a list of modules. Checks if already existing. Becomes owned by this. TIter next(list); AliAnalysisTaskCfg *module; while ((module = (AliAnalysisTaskCfg*)next())) AddModule(module); } //______________________________________________________________________________ Bool_t AliAnalysisAlien::CheckDependencies() { // Check if all dependencies are satisfied. Reorder modules if needed. Int_t nmodules = GetNmodules(); if (!nmodules) { Warning("CheckDependencies", "No modules added yet to check their dependencies"); return kTRUE; } AliAnalysisTaskCfg *mod = 0; AliAnalysisTaskCfg *dep = 0; TString depname; Int_t i, j, k; for (i=0; i<nmodules; i++) { mod = (AliAnalysisTaskCfg*) fModules->At(i); Int_t ndeps = mod->GetNdeps(); Int_t istart = i; for (j=0; j<ndeps; j++) { depname = mod->GetDependency(j); dep = GetModule(depname); if (!dep) { Error("CheckDependencies","Dependency %s not added for module %s", depname.Data(), mod->GetName()); return kFALSE; } if (dep->NeedsDependency(mod->GetName())) { Error("CheckDependencies","Modules %s and %s circularly depend on each other", mod->GetName(), dep->GetName()); return kFALSE; } Int_t idep = fModules->IndexOf(dep); // The dependency task must come first if (idep>i) { // Remove at idep and move all objects below up one slot // down to index i included. fModules->RemoveAt(idep); for (k=idep-1; k>=i; k--) fModules->AddAt(fModules->RemoveAt(k),k+1); fModules->AddAt(dep, i++); } //Redo from istart if dependencies were inserted if (i>istart) i=istart-1; } } return kTRUE; } //______________________________________________________________________________ AliAnalysisManager *AliAnalysisAlien::CreateAnalysisManager(const char *name, const char *filename) { // Create the analysis manager and optionally execute the macro in filename. AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager(); if (mgr) { mgr->SetMCLoop(fMCLoop); return mgr; } mgr = new AliAnalysisManager(name); mgr->SetGridHandler((AliAnalysisGrid*)this); mgr->SetMCLoop(fMCLoop); if (strlen(filename)) { TString line = gSystem->ExpandPathName(filename); line.Prepend(".x "); gROOT->ProcessLine(line.Data()); } return mgr; } //______________________________________________________________________________ Int_t AliAnalysisAlien::GetNmodules() const { // Get number of modules. if (!fModules) return 0; return fModules->GetEntries(); } //______________________________________________________________________________ AliAnalysisTaskCfg *AliAnalysisAlien::GetModule(const char *name) { // Get a module by name. if (!fModules) return 0; return (AliAnalysisTaskCfg*)fModules->FindObject(name); } //______________________________________________________________________________ Bool_t AliAnalysisAlien::LoadModule(AliAnalysisTaskCfg *mod) { // Load a given module. if (mod->IsLoaded()) return kTRUE; AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager(); if (!mgr) { Error("LoadModule", "No analysis manager created yet. Use CreateAnalysisManager first."); return kFALSE; } Int_t ndeps = mod->GetNdeps(); TString depname; for (Int_t j=0; j<ndeps; j++) { depname = mod->GetDependency(j); AliAnalysisTaskCfg *dep = GetModule(depname); if (!dep) { Error("LoadModule","Dependency %s not existing for module %s", depname.Data(), mod->GetName()); return kFALSE; } if (!LoadModule(dep)) { Error("LoadModule","Dependency %s for module %s could not be loaded", depname.Data(), mod->GetName()); return kFALSE; } } // Load libraries for the module if (!mod->CheckLoadLibraries()) { Error("LoadModule", "Cannot load all libraries for module %s", mod->GetName()); return kFALSE; } // Check if a custom file name was requested if (strlen(mod->GetOutputFileName())) mgr->SetCommonFileName(mod->GetOutputFileName()); // Check if a custom terminate file name was requested if (strlen(mod->GetTerminateFileName())) { if (!fTerminateFiles.IsNull()) fTerminateFiles += ","; fTerminateFiles += mod->GetTerminateFileName(); } // Execute the macro if (mod->ExecuteMacro()<0) { Error("LoadModule", "Executing the macro %s with arguments: %s for module %s returned a negative value", mod->GetMacroName(), mod->GetMacroArgs(), mod->GetName()); return kFALSE; } // Configure dependencies if (mod->GetConfigMacro() && mod->ExecuteConfigMacro()<0) { Error("LoadModule", "There was an error executing the deps config macro %s for module %s", mod->GetConfigMacro()->GetTitle(), mod->GetName()); return kFALSE; } // Adjust extra libraries Int_t nlibs = mod->GetNlibs(); TString lib; for (Int_t i=0; i<nlibs; i++) { lib = mod->GetLibrary(i); lib = Form("lib%s.so", lib.Data()); if (fAdditionalLibs.Contains(lib)) continue; if (!fAdditionalLibs.IsNull()) fAdditionalLibs += " "; fAdditionalLibs += lib; } return kTRUE; } //______________________________________________________________________________ Bool_t AliAnalysisAlien::GenerateTrain(const char *name) { // Generate the full train. fAdditionalLibs = ""; if (!LoadModules()) return kFALSE; AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager(); if (!mgr->InitAnalysis()) return kFALSE; mgr->RunLocalInit(); mgr->PrintStatus(); Int_t productionMode = fProductionMode; SetProductionMode(); TString macro = fAnalysisMacro; TString executable = fExecutable; TString validation = fValidationScript; TString execCommand = fExecutableCommand; SetAnalysisMacro(Form("%s.C", name)); SetExecutable(Form("%s.sh", name)); // SetExecutableCommand("aliroot -b -q "); SetValidationScript(Form("%s_validation.sh", name)); StartAnalysis(); SetProductionMode(productionMode); fAnalysisMacro = macro; fExecutable = executable; fExecutableCommand = execCommand; fValidationScript = validation; return kTRUE; } //______________________________________________________________________________ Bool_t AliAnalysisAlien::GenerateTest(const char *name, const char *modname) { // Generate test macros for a single module or for the full train. fAdditionalLibs = ""; if (strlen(modname)) { if (!CheckDependencies()) return kFALSE; AliAnalysisTaskCfg *mod = GetModule(modname); if (!mod) { Error("GenerateTest", "cannot generate test for inexistent module %s", modname); return kFALSE; } if (!LoadModule(mod)) return kFALSE; if (!LoadFriendLibs()) return kFALSE; } else if (!LoadModules()) return kFALSE; AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager(); if (!mgr->InitAnalysis()) return kFALSE; mgr->RunLocalInit(); mgr->PrintStatus(); SetLocalTest(kTRUE); Int_t productionMode = fProductionMode; SetProductionMode(); TString macro = fAnalysisMacro; TString executable = fExecutable; TString validation = fValidationScript; TString execCommand = fExecutableCommand; SetAnalysisMacro(Form("%s.C", name)); SetExecutable(Form("%s.sh", name)); fOutputFiles = GetListOfFiles("outaod"); // Add extra files registered to the analysis manager TString extra = GetListOfFiles("ext"); if (!extra.IsNull()) { extra.ReplaceAll(".root", "*.root"); if (!fOutputFiles.IsNull()) fOutputFiles += ","; fOutputFiles += extra; } // SetExecutableCommand("aliroot -b -q "); SetValidationScript(Form("%s_validation.sh", name)); WriteAnalysisFile(); WriteAnalysisMacro(); WriteExecutable(); WriteValidationScript(); WriteMergingMacro(); WriteMergeExecutable(); WriteValidationScript(kTRUE); SetLocalTest(kFALSE); SetProductionMode(productionMode); fAnalysisMacro = macro; fExecutable = executable; fExecutableCommand = execCommand; fValidationScript = validation; return kTRUE; } //______________________________________________________________________________ Bool_t AliAnalysisAlien::LoadModules() { // Load all modules by executing the AddTask macros. Checks first the dependencies. fAdditionalLibs = ""; Int_t nmodules = GetNmodules(); if (!nmodules) { Warning("LoadModules", "No module to be loaded"); return kTRUE; } AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager(); if (!mgr) { Error("LoadModules", "No analysis manager created yet. Use CreateAnalysisManager first."); return kFALSE; } if (!CheckDependencies()) return kFALSE; nmodules = GetNmodules(); AliAnalysisTaskCfg *mod; for (Int_t imod=0; imod<nmodules; imod++) { mod = (AliAnalysisTaskCfg*)fModules->At(imod); if (!LoadModule(mod)) return kFALSE; } // Load additional friend libraries return LoadFriendLibs(); } //______________________________________________________________________________ Bool_t AliAnalysisAlien::LoadFriendLibs() const { // Load libraries required for reading friends. if (fFriendLibs.Length()) { TObjArray *list = 0; TString lib; if (fFriendLibs.Contains(",")) list = fFriendLibs.Tokenize(","); else list = fFriendLibs.Tokenize(" "); for (Int_t ilib=0; ilib<list->GetEntriesFast(); ilib++) { lib = list->At(ilib)->GetName(); lib.ReplaceAll(".so",""); lib.ReplaceAll(".dylib",""); lib.ReplaceAll(" ",""); if (lib.BeginsWith("lib")) lib.Remove(0, 3); lib.Prepend("lib"); Int_t loaded = strlen(gSystem->GetLibraries(lib,"",kFALSE)); if (!loaded) loaded = gSystem->Load(lib); if (loaded < 0) { Error("LoadModules", "Cannot load library for friends %s", lib.Data()); return kFALSE; } } delete list; } return kTRUE; } //______________________________________________________________________________ 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. TString p(path); if (p.Contains("-I")) fIncludePath += Form("%s ", path); else fIncludePath += Form("-I%s ", path); } //______________________________________________________________________________ void AliAnalysisAlien::AddRunNumber(Int_t run) { // Add a run number to the list of runs to be processed. if (fRunNumbers.Length()) fRunNumbers += " "; 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. TString runs = run; TObjString *os; TObjArray *arr = runs.Tokenize(" "); TIter next(arr); TString prefix; prefix.Append(fRunPrefix, fRunPrefix.Index("%d")); while ((os=(TObjString*)next())){ if (fRunNumbers.Length()) fRunNumbers += " "; fRunNumbers += Form("%s%s", prefix.Data(), os->GetString().Data()); } delete arr; } //______________________________________________________________________________ void AliAnalysisAlien::AddDataFile(const char *lfn) { // Adds a data file to the input to be analysed. The file should be a valid LFN // or point to an existing file in the alien workdir. if (!fInputFiles) fInputFiles = new TObjArray(); fInputFiles->Add(new TObjString(lfn)); } //______________________________________________________________________________ void AliAnalysisAlien::AddExternalPackage(const char *package) { // Adds external packages w.r.t to the default ones (root,aliroot and gapi) if (fExternalPackages) fExternalPackages += " "; fExternalPackages += package; } //______________________________________________________________________________ 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://"); } if (!gGrid || !gGrid->IsConnected()) { Error("Connect", "Did not managed to connect to AliEn. Make sure you have a valid token."); return kFALSE; } fUser = gGrid->GetUser(); Info("Connect", "\n##### Connected to AliEn as user %s. Setting analysis user to <%s>", fUser.Data(), fUser.Data()); return kTRUE; } //______________________________________________________________________________ void AliAnalysisAlien::CdWork() { // Check validity of alien workspace. Create directory if possible. if (!Connect()) { Error("CdWork", "Alien connection required"); return; } TString homedir = gGrid->GetHomeDirectory(); TString workdir = homedir + fGridWorkingDir; if (DirectoryExists(workdir)) { gGrid->Cd(workdir); return; } // Work directory not existing - create it gGrid->Cd(homedir); if (gGrid->Mkdir(workdir, "-p")) { gGrid->Cd(fGridWorkingDir); Info("CdWork", "\n##### Created alien working directory %s", fGridWorkingDir.Data()); } else { Warning("CdWork", "Working directory %s cannot be created.\n Using %s instead.", workdir.Data(), homedir.Data()); fGridWorkingDir = ""; } } //______________________________________________________________________________ Bool_t AliAnalysisAlien::CheckFileCopy(const char *alienpath) { // Check if file copying is possible. if (fProductionMode) return kTRUE; TString salienpath(alienpath); if (salienpath.Contains(" ")) { Error("CheckFileCopy", "path: <%s> contains blancs - FIX IT !",alienpath); return kFALSE; } if (!Connect()) { Error("CheckFileCopy", "Not connected to AliEn. File copying cannot be tested."); return kFALSE; } Info("CheckFileCopy", "Checking possibility to copy files to your AliEn home directory... \ \n +++ NOTE: You can disable this via: plugin->SetCheckCopy(kFALSE);"); // Check if alien_CLOSE_SE is defined TString closeSE = gSystem->Getenv("alien_CLOSE_SE"); if (!closeSE.IsNull()) { Info("CheckFileCopy", "Your current close storage is pointing to: \ \n alien_CLOSE_SE = \"%s\"", closeSE.Data()); } else { Warning("CheckFileCopy", "Your current close storage is empty ! Depending on your location, file copying may fail."); } // Check if grid directory exists. if (!DirectoryExists(alienpath)) { Error("CheckFileCopy", "Alien path %s does not seem to exist", alienpath); return kFALSE; } TString stest = "plugin_test_copy"; TFile f(stest, "RECREATE"); // User may not have write permissions to current directory if (f.IsZombie()) { Error("CheckFileCopy", "Cannot create local test file. Do you have write access to current directory: <%s> ?", gSystem->WorkingDirectory()); return kFALSE; } f.Close(); if (FileExists(Form("alien://%s/%s",alienpath, stest.Data()))) gGrid->Rm(Form("alien://%s/%s",alienpath, stest.Data())); if (!TFile::Cp(stest.Data(), Form("alien://%s/%s",alienpath, stest.Data()))) { Error("CheckFileCopy", "Cannot copy files to Alien destination: <%s> This may be temporary, or: \ \n# 1. Make sure you have write permissions there. If this is the case: \ \n# 2. Check the storage availability at: http://alimonitor.cern.ch/stats?page=SE/table \ \n# Do: export alien_CLOSE_SE=\"working_disk_SE\" \ \n# To make this permanent put in in your .bashrc (in .alienshrc is not enough) \ \n# Redo token: rm /tmp/x509up_u$UID then: alien-token-init <username>", alienpath); gSystem->Unlink(stest.Data()); return kFALSE; } gSystem->Unlink(stest.Data()); gGrid->Rm(Form("%s/%s",alienpath,stest.Data())); Info("CheckFileCopy", "### ...SUCCESS ###"); return kTRUE; } //______________________________________________________________________________ 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 Bool_t isCollection = kFALSE; Bool_t isXml = kFALSE; Bool_t useTags = kFALSE; Bool_t checked = kFALSE; if (!TestBit(AliAnalysisGrid::kTest)) CdWork(); TString file; TString workdir = gGrid->GetHomeDirectory(); workdir += fGridWorkingDir; if (fInputFiles) { TObjString *objstr; TIter next(fInputFiles); while ((objstr=(TObjString*)next())) { file = workdir; file += "/"; file += objstr->GetString(); // Store full lfn path if (FileExists(file)) objstr->SetString(file); else { file = objstr->GetName(); if (!FileExists(objstr->GetName())) { Error("CheckInputData", "Data file %s not found or not in your working dir: %s", objstr->GetName(), workdir.Data()); return kFALSE; } } Bool_t iscoll, isxml, usetags; CheckDataType(file, iscoll, isxml, usetags); if (!checked) { checked = kTRUE; isCollection = iscoll; isXml = isxml; useTags = usetags; TObject::SetBit(AliAnalysisGrid::kUseTags, useTags); } else { if ((iscoll != isCollection) || (isxml != isXml) || (usetags != useTags)) { Error("CheckInputData", "Some conflict was found in the types of inputs"); return kFALSE; } } } } // Process requested run numbers if (!fRunNumbers.Length() && !fRunRange[0]) return kTRUE; // Check validity of alien data directory if (!fGridDataDir.Length()) { Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()"); return kFALSE; } if (!DirectoryExists(fGridDataDir)) { Error("CheckInputData", "Data directory %s not existing.", fGridDataDir.Data()); return kFALSE; } if (isCollection) { Error("CheckInputData", "You are using raw AliEn collections as input. Cannot process run numbers."); return kFALSE; } if (checked && !isXml) { Error("CheckInputData", "Cannot mix processing of full runs with non-xml files"); return kFALSE; } // Check validity of run number(s) TObjArray *arr; TObjString *os; TString format; Int_t nruns = 0; TString schunk, schunk2; TString path; if (!checked) { checked = kTRUE; useTags = fDataPattern.Contains("tag"); TObject::SetBit(AliAnalysisGrid::kUseTags, useTags); } if (useTags != fDataPattern.Contains("tag")) { Error("CheckInputData", "Cannot mix input files using/not using tags"); return kFALSE; } if (fRunNumbers.Length()) { Info("CheckDataType", "Using supplied run numbers (run ranges are ignored)"); arr = fRunNumbers.Tokenize(" "); TIter next(arr); while ((os=(TObjString*)next())) { path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data()); if (!DirectoryExists(path)) { Warning("CheckInputData", "Run number %s not found in path: <%s>", os->GetString().Data(), path.Data()); continue; } path = Form("%s/%s.xml", workdir.Data(),os->GetString().Data()); TString msg = "\n##### file: "; msg += path; msg += " type: xml_collection;"; if (useTags) msg += " using_tags: Yes"; else msg += " using_tags: No"; Info("CheckDataType", "%s", msg.Data()); if (fNrunsPerMaster<2) { AddDataFile(Form("%s.xml", os->GetString().Data())); } else { nruns++; if (((nruns-1)%fNrunsPerMaster) == 0) { schunk = os->GetString(); } if ((nruns%fNrunsPerMaster)!=0 && os!=arr->Last()) continue; schunk += Form("_%s.xml", os->GetString().Data()); AddDataFile(schunk); } } delete arr; } else { Info("CheckDataType", "Using run range [%d, %d]", fRunRange[0], fRunRange[1]); for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) { format = Form("%%s/%s ", fRunPrefix.Data()); path = Form(format.Data(), fGridDataDir.Data(), irun); if (!DirectoryExists(path)) { continue; } 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", "%s", msg.Data()); if (fNrunsPerMaster<2) { format = Form("%s.xml", fRunPrefix.Data()); AddDataFile(Form(format.Data(),irun)); } else { nruns++; if (((nruns-1)%fNrunsPerMaster) == 0) { schunk = Form(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); } } if (!fInputFiles) { schunk += schunk2; AddDataFile(schunk); } } return kTRUE; } //______________________________________________________________________________ Int_t AliAnalysisAlien::CopyLocalDataset(const char *griddir, const char *pattern, Int_t nfiles, const char *output, const char *archivefile, const char *outputdir) { // Copy data from the given grid directory according a pattern and make a local // dataset. // archivefile (optional) results in that the archive containing the file <pattern> is copied. archivefile can contain a list of files (semicolon-separated) which are all copied if (!Connect()) { Error("CopyLocalDataset", "Cannot copy local dataset with no grid connection"); return 0; } if (!DirectoryExists(griddir)) { Error("CopyLocalDataset", "Data directory %s not existing.", griddir); return 0; } TString command = Form("find -z -l %d %s %s", nfiles, griddir, pattern); printf("Running command: %s\n", command.Data()); TGridResult *res = gGrid->Command(command); Int_t nfound = res->GetEntries(); if (!nfound) { Error("CopyLocalDataset", "No file found in <%s> having pattern <%s>", griddir, pattern); return 0; } printf("... found %d files. Copying locally ...\n", nfound); // archives TObjArray* additionalArchives = 0; if (strlen(archivefile) > 0 && TString(archivefile).Contains(";")) { additionalArchives = TString(archivefile).Tokenize(";"); archivefile = additionalArchives->At(0)->GetName(); additionalArchives->RemoveAt(0); additionalArchives->Compress(); } // Copy files locally ofstream out; out.open(output, ios::out); TMap *map; TString turl, dirname, filename, temp; TString cdir = gSystem->WorkingDirectory(); gSystem->MakeDirectory(outputdir); gSystem->ChangeDirectory(outputdir); Int_t ncopied = 0; for (Int_t i=0; i<nfound; i++) { map = (TMap*)res->At(i); turl = map->GetValue("turl")->GetName(); filename = gSystem->BaseName(turl.Data()); dirname = gSystem->DirName(turl.Data()); dirname = gSystem->BaseName(dirname.Data()); gSystem->MakeDirectory(dirname); TString source(turl); TString targetFileName(filename); if (strlen(archivefile) > 0) { // TODO here the archive in which the file resides should be determined // however whereis returns only a guid, and guid2lfn does not work // Therefore we use the one provided as argument for now source = Form("%s/%s", gSystem->DirName(source.Data()), archivefile); targetFileName = archivefile; } if (TFile::Cp(source, Form("file:./%s/%s", dirname.Data(), targetFileName.Data()))) { Bool_t success = kTRUE; if (additionalArchives) { for (Int_t j=0; j<additionalArchives->GetEntriesFast(); j++) { TString target; target.Form("./%s/%s", dirname.Data(), additionalArchives->At(j)->GetName()); gSystem->MakeDirectory(gSystem->DirName(target)); success &= TFile::Cp(Form("%s/%s", gSystem->DirName(source.Data()), additionalArchives->At(j)->GetName()), Form("file:%s", target.Data())); } } if (success) { if (strlen(archivefile) > 0) targetFileName = Form("%s#%s", targetFileName.Data(), gSystem->BaseName(turl.Data())); out << cdir << Form("/%s/%s/%s", outputdir, dirname.Data(), targetFileName.Data()) << endl; ncopied++; } } } gSystem->ChangeDirectory(cdir); delete res; delete additionalArchives; return ncopied; } //______________________________________________________________________________ Bool_t AliAnalysisAlien::CreateDataset(const char *pattern) { // Create dataset for the grid data directory + run number. const Int_t gMaxEntries = 15000; if (fProductionMode || TestBit(AliAnalysisGrid::kOffline)) return kTRUE; if (!Connect()) { Error("CreateDataset", "Cannot create dataset with no grid connection"); return kFALSE; } // Cd workspace if (!TestBit(AliAnalysisGrid::kTest)) CdWork(); TString workdir = gGrid->GetHomeDirectory(); workdir += fGridWorkingDir; // Compose the 'find' command arguments TString format; TString command; TString delimiter = pattern; delimiter.Strip(); if (delimiter.Contains(" ")) delimiter = ""; else delimiter = " "; TString options = "-x collection "; if (TestBit(AliAnalysisGrid::kTest)) options += Form("-l %d ", fNtestFiles); else options += Form("-l %d ", gMaxEntries); // Protection for the find command TString conditions = ""; Int_t nstart = 0; Int_t ncount = 0; Int_t stage = 0; TString file; TString path; Int_t nruns = 0; TString schunk, schunk2; TGridCollection *cbase=0, *cadd=0; if (!fRunNumbers.Length() && !fRunRange[0]) { if (fInputFiles && fInputFiles->GetEntries()) return kTRUE; // Make a single data collection from data directory. path = fGridDataDir; if (!DirectoryExists(path)) { Error("CreateDataset", "Path to data directory %s not valid",fGridDataDir.Data()); return kFALSE; } // CdWork(); if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml"; else file = Form("%s.xml", gSystem->BaseName(path)); // cholm - Identical loop - should be put in common function for code simplification while (1) { ncount = 0; stage++; if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) { command = "find "; command += Form("%s -o %d ",options.Data(), nstart); command += path; command += delimiter; command += pattern; command += conditions; printf("command: %s\n", command.Data()); TGridResult *res = gGrid->Command(command); if (res) delete res; // Write standard output to file gROOT->ProcessLine(Form("gGrid->Stdout(); > __tmp%d__%s", stage, file.Data())); Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE; Bool_t nullFile = kFALSE; if (!hasGrep) { Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command"); } else { nullFile = (gSystem->Exec(Form("grep -c /event __tmp%d__%s 2>/dev/null > __tmp__",stage,file.Data()))==0)?kFALSE:kTRUE; if (nullFile) { Error("CreateDataset","Dataset %s produced by the previous find command is empty !", file.Data()); gSystem->Exec("rm -f __tmp*"); return kFALSE; } TString line; ifstream in; in.open("__tmp__"); in >> line; in.close(); gSystem->Exec("rm -f __tmp__"); ncount = line.Atoi(); } } if (ncount == gMaxEntries) { Info("CreateDataset", "Dataset %s has more than 15K entries. Trying to merge...", file.Data()); cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"__tmp%d__%s\", 1000000);",stage,file.Data())); if (!cbase) cbase = cadd; else { // cholm - Avoid using very slow TAlienCollection // cbase->Add(cadd); // cholm - Use AddFast (via interpreter) gROOT->ProcessLine(Form("((TAlienCollection*)%p)->AddFast((TGridCollection*)%p)",cbase,cadd)); delete cadd; } nstart += ncount; } else { if (cbase) { cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"__tmp%d__%s\", 1000000);",stage,file.Data())); printf("... please wait - TAlienCollection::Add() scales badly...\n"); // cholm - Avoid using very slow TAlienCollection // cbase->Add(cadd); // cholm - Use AddFast (via interpreter) gROOT->ProcessLine(Form("((TAlienCollection*)%p)->AddFast((TGridCollection*)%p)",cbase,cadd)); delete cadd; cbase->ExportXML(Form("file://%s", file.Data()),kFALSE,kFALSE, file, "Merged entries for a run"); delete cbase; cbase = 0; } else { TFile::Cp(Form("__tmp%d__%s",stage, file.Data()), file.Data()); } gSystem->Exec("rm -f __tmp*"); Info("CreateDataset", "Created dataset %s with %d files", file.Data(), nstart+ncount); break; } } Bool_t fileExists = FileExists(file); if (!TestBit(AliAnalysisGrid::kTest) && (!fileExists || fOverwriteMode)) { // Copy xml file to alien space if (fileExists) gGrid->Rm(file); TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data())); if (!FileExists(file)) { Error("CreateDataset", "Command %s did NOT succeed", command.Data()); return kFALSE; } // Update list of files to be processed. } AddDataFile(Form("%s/%s", workdir.Data(), file.Data())); return kTRUE; } // Several runs Bool_t nullResult = kTRUE; if (fRunNumbers.Length()) { TObjArray *arr = fRunNumbers.Tokenize(" "); TObjString *os; TIter next(arr); while ((os=(TObjString*)next())) { nstart = 0; stage = 0; path = Form("%s/%s", fGridDataDir.Data(), os->GetString().Data()); if (!DirectoryExists(path)) continue; // CdWork(); if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml"; else file = Form("%s.xml", os->GetString().Data()); // cholm - Identical loop - should be put in common function for code simplification // If local collection file does not exist, create it via 'find' command. while (1) { ncount = 0; stage++; if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) { command = "find "; command += Form("%s -o %d ",options.Data(), nstart); command += path; command += delimiter; command += pattern; command += conditions; TGridResult *res = gGrid->Command(command); if (res) delete res; // Write standard output to file gROOT->ProcessLine(Form("gGrid->Stdout(); > __tmp%d__%s", stage,file.Data())); Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE; Bool_t nullFile = kFALSE; if (!hasGrep) { Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command"); } else { nullFile = (gSystem->Exec(Form("grep -c /event __tmp%d__%s 2>/dev/null > __tmp__",stage,file.Data()))==0)?kFALSE:kTRUE; if (nullFile) { Warning("CreateDataset","Dataset %s produced by: <%s> is empty !", file.Data(), command.Data()); gSystem->Exec("rm -f __tmp*"); fRunNumbers.ReplaceAll(os->GetString().Data(), ""); break; } TString line; ifstream in; in.open("__tmp__"); in >> line; in.close(); gSystem->Exec("rm -f __tmp__"); ncount = line.Atoi(); } nullResult = kFALSE; } if (ncount == gMaxEntries) { Info("CreateDataset", "Dataset %s has more than 15K entries. Trying to merge...", file.Data()); if (fNrunsPerMaster > 1) { Error("CreateDataset", "File %s has more than %d entries. Please set the number of runs per master to 1 !", file.Data(),gMaxEntries); return kFALSE; } cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"__tmp%d__%s\", 1000000);",stage,file.Data())); if (!cbase) cbase = cadd; else { // cholm - Avoid using very slow TAlienCollection // cbase->Add(cadd); // cholm - Use AddFast (via interpreter) gROOT->ProcessLine(Form("((TAlienCollection*)%p)->AddFast((TGridCollection*)%p)",cbase,cadd)); delete cadd; } nstart += ncount; } else { if (cbase && fNrunsPerMaster<2) { cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"__tmp%d__%s\", 1000000);",stage,file.Data())); printf("... please wait - TAlienCollection::Add() scales badly...\n"); // cholm - Avoid using very slow TAlienCollection // cbase->Add(cadd); // cholm - Use AddFast (via interpreter) gROOT->ProcessLine(Form("((TAlienCollection*)%p)->AddFast((TGridCollection*)%p)",cbase,cadd)); delete cadd; cbase->ExportXML(Form("file://%s", file.Data()),kFALSE,kFALSE, file, "Merged entries for a run"); delete cbase; cbase = 0; } else { TFile::Cp(Form("__tmp%d__%s",stage, file.Data()), file.Data()); } gSystem->Exec("rm -f __tmp*"); Info("CreateDataset", "Created dataset %s with %d files", file.Data(), nstart+ncount); break; } } if (TestBit(AliAnalysisGrid::kTest)) break; // Check if there is one run per master job. if (fNrunsPerMaster<2) { if (FileExists(file)) { if (fOverwriteMode) gGrid->Rm(file); else { Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data()); continue; } } // Copy xml file to alien space TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data())); if (!FileExists(file)) { Error("CreateDataset", "Command %s did NOT succeed", command.Data()); delete arr; return kFALSE; } } else { nruns++; if (((nruns-1)%fNrunsPerMaster) == 0) { schunk = os->GetString(); cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data())); } else { cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data())); printf(" Merging collection <%s> into masterjob input...\n", file.Data()); // cholm - Avoid using very slow TAlienCollection // cbase->Add(cadd); // cholm - Use AddFast (via interpreter) gROOT->ProcessLine(Form("((TAlienCollection*)%p)->AddFast((TGridCollection*)%p)",cbase,cadd)); delete cadd; } if ((nruns%fNrunsPerMaster)!=0 && os!=arr->Last()) { continue; } schunk += Form("_%s.xml", os->GetString().Data()); if (FileExists(schunk)) { if (fOverwriteMode) gGrid->Rm(file); else { Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data()); continue; } } printf("Exporting merged collection <%s> and copying to AliEn\n", schunk.Data()); cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs"); TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data())); if (!FileExists(schunk)) { Error("CreateDataset", "Copy command did NOT succeed for %s", schunk.Data()); delete arr; return kFALSE; } } } delete arr; if (nullResult) { Error("CreateDataset", "No valid dataset corresponding to the query!"); return kFALSE; } } else { // Process a full run range. for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) { format = Form("%%s/%s", fRunPrefix.Data()); nstart = 0; stage = 0; 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(format.Data(), irun); if (FileExists(file) && fNrunsPerMaster<2 && !TestBit(AliAnalysisGrid::kTest)) { if (fOverwriteMode) gGrid->Rm(file); else { Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data()); continue; } } // cholm - Identical loop - should be put in common function for code simplification // If local collection file does not exist, create it via 'find' command. while (1) { ncount = 0; stage++; if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) { command = "find "; command += Form("%s -o %d ",options.Data(), nstart); command += path; command += delimiter; command += pattern; command += conditions; TGridResult *res = gGrid->Command(command); if (res) delete res; // Write standard output to file gROOT->ProcessLine(Form("gGrid->Stdout(); > __tmp%d__%s", stage,file.Data())); Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE; Bool_t nullFile = kFALSE; if (!hasGrep) { Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command"); } else { nullFile = (gSystem->Exec(Form("grep -c /event __tmp%d__%s 2>/dev/null > __tmp__",stage,file.Data()))==0)?kFALSE:kTRUE; if (nullFile) { Warning("CreateDataset","Dataset %s produced by: <%s> is empty !", file.Data(), command.Data()); gSystem->Exec("rm -f __tmp*"); break; } TString line; ifstream in; in.open("__tmp__"); in >> line; in.close(); gSystem->Exec("rm -f __tmp__"); ncount = line.Atoi(); } nullResult = kFALSE; } if (ncount == gMaxEntries) { Info("CreateDataset", "Dataset %s has more than 15K entries. Trying to merge...", file.Data()); if (fNrunsPerMaster > 1) { Error("CreateDataset", "File %s has more than %d entries. Please set the number of runs per master to 1 !", file.Data(),gMaxEntries); return kFALSE; } cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"__tmp%d__%s\", 1000000);",stage,file.Data())); if (!cbase) cbase = cadd; else { // cholm - Avoid using very slow TAlienCollection // cbase->Add(cadd); // cholm - Use AddFast (via interpreter) gROOT->ProcessLine(Form("((TAlienCollection*)%p)->AddFast((TGridCollection*)%p)",cbase,cadd)); delete cadd; } nstart += ncount; } else { if (cbase && fNrunsPerMaster<2) { cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"__tmp%d__%s\", 1000000);",stage,file.Data())); printf("... please wait - TAlienCollection::Add() scales badly...\n"); // cholm - Avoid using very slow TAlienCollection // cbase->Add(cadd); // cholm - Use AddFast (via interpreter) gROOT->ProcessLine(Form("((TAlienCollection*)%p)->AddFast((TGridCollection*)%p)",cbase,cadd)); delete cadd; cbase->ExportXML(Form("file://%s", file.Data()),kFALSE,kFALSE, file, "Merged entries for a run"); delete cbase; cbase = 0; } else { TFile::Cp(Form("__tmp%d__%s",stage, file.Data()), file.Data()); } Info("CreateDataset", "Created dataset %s with %d files", file.Data(), nstart+ncount); break; } } if (TestBit(AliAnalysisGrid::kTest)) break; // Check if there is one run per master job. if (fNrunsPerMaster<2) { if (FileExists(file)) { if (fOverwriteMode) gGrid->Rm(file); else { Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data()); continue; } } // Copy xml file to alien space TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data())); if (!FileExists(file)) { Error("CreateDataset", "Command %s did NOT succeed", command.Data()); return kFALSE; } } else { nruns++; // Check if the collection for the chunk exist locally. Int_t nchunk = (nruns-1)/fNrunsPerMaster; if (FileExists(fInputFiles->At(nchunk)->GetName())) { if (fOverwriteMode) gGrid->Rm(fInputFiles->At(nchunk)->GetName()); else continue; } printf(" Merging collection <%s> into %d runs chunk...\n",file.Data(),fNrunsPerMaster); if (((nruns-1)%fNrunsPerMaster) == 0) { 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())); // cholm - Avoid using very slow TAlienCollection // cbase->Add(cadd); // cholm - Use AddFast (via interpreter) gROOT->ProcessLine(Form("((TAlienCollection*)%p)->AddFast((TGridCollection*)%p)",cbase,cadd)); delete cadd; } 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; } schunk = schunk2; if (FileExists(schunk)) { if (fOverwriteMode) gGrid->Rm(schunk); else { Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data()); continue; } } printf("Exporting merged collection <%s> and copying to AliEn.\n", schunk.Data()); cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs"); if (FileExists(schunk)) { if (fOverwriteMode) gGrid->Rm(schunk); else { Info("CreateDataset", "\n##### Dataset %s exist. Skipping copy...", schunk.Data()); continue; } } TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data())); if (!FileExists(schunk)) { Error("CreateDataset", "Copy command did NOT succeed for %s", schunk.Data()); return kFALSE; } } } if (nullResult) { Error("CreateDataset", "No valid dataset corresponding to the query!"); return kFALSE; } } return kTRUE; } //______________________________________________________________________________ Bool_t AliAnalysisAlien::CreateJDL() { // Generate a JDL file according to current settings. The name of the file is // specified by fJDLName. AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager(); Bool_t error = kFALSE; TObjArray *arr = 0; Bool_t copy = kTRUE; 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()) { Error("CreateJDL", "Alien connection required"); return kFALSE; } // Check validity of alien workspace TString workdir; if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice")) workdir = gGrid->GetHomeDirectory(); if (!fProductionMode && !TestBit(AliAnalysisGrid::kTest)) CdWork(); workdir += fGridWorkingDir; if (generate) { TObjString *os; if (!fInputFiles && !fMCLoop) { Error("CreateJDL()", "Define some input files for your analysis."); error = kTRUE; } // Compose list of input files // Check if output files were defined if (!fOutputFiles.Length()) { Error("CreateJDL", "You must define at least one output file"); error = kTRUE; } // Check if an output directory was defined and valid if (!fGridOutputDir.Length()) { Error("CreateJDL", "You must define AliEn output directory"); error = kTRUE; } else { 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 { 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; // Set JDL fields if (!fUser.IsNull()) { fGridJDL->SetValue("User", Form("\"%s\"", fUser.Data())); fMergingJDL->SetValue("User", Form("\"%s\"", fUser.Data())); } TString executable = fExecutable; if (!executable.BeginsWith("/")) executable.Prepend(Form("%s/", workdir.Data())); fGridJDL->SetExecutable(executable, "This is the startup script"); TString mergeExec = executable; mergeExec.ReplaceAll(".sh", "_merge.sh"); fMergingJDL->SetExecutable(mergeExec, "This is the startup script"); mergeExec.ReplaceAll(".sh", ".C"); fMergingJDL->AddToInputSandbox(Form("LF:%s", mergeExec.Data()), "List of input files to be uploaded to workers"); if (!fArguments.IsNull()) fGridJDL->SetArguments(fArguments, "Arguments for the executable command"); 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)); fMergingJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60)); if (fMaxInitFailed > 0) { fGridJDL->SetValue("MaxInitFailed", Form("\"%d\"",fMaxInitFailed)); fGridJDL->SetDescription("MaxInitFailed", "Maximum number of first failing jobs to abort the master job"); } if (fSplitMaxInputFileNumber > 0 && !fMCLoop) { 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"); } if (!fROOTVersion.IsNull()) { fGridJDL->AddToPackages("ROOT", fROOTVersion); fMergingJDL->AddToPackages("ROOT", fROOTVersion); } if (!fAPIVersion.IsNull()) { fGridJDL->AddToPackages("APISCONFIG", fAPIVersion); fMergingJDL->AddToPackages("APISCONFIG", fAPIVersion); } if (!fExternalPackages.IsNull()) { arr = fExternalPackages.Tokenize(" "); TIter next(arr); while ((os=(TObjString*)next())) { TString pkgname = os->GetString(); Int_t index = pkgname.Index("::"); TString pkgversion = pkgname(index+2, pkgname.Length()); pkgname.Remove(index); fGridJDL->AddToPackages(pkgname, pkgversion); fMergingJDL->AddToPackages(pkgname, pkgversion); } delete arr; } if (!fMCLoop) { 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"); fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),analysisFile.Data())); fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),analysisFile.Data())); if (fAdditionalLibs.Length()) { arr = fAdditionalLibs.Tokenize(" "); TIter next(arr); while ((os=(TObjString*)next())) { if (os->GetString().Contains(".so") || os->GetString().Contains(".dylib")) continue; fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), os->GetString().Data())); fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), os->GetString().Data())); } delete arr; } if (fPackages) { TIter next(fPackages); TObject *obj; while ((obj=next())) { fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName())); fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName())); } } const char *comment = "List of output files and archives"; if (fOutputArchive.Length()) { TString outputArchive = fOutputArchive; if (!fRegisterExcludes.IsNull()) { arr = fRegisterExcludes.Tokenize(" "); TIter next1(arr); while ((os=(TObjString*)next1())) { outputArchive.ReplaceAll(Form("%s,",os->GetString().Data()),""); outputArchive.ReplaceAll(os->GetString(),""); } delete arr; } arr = outputArchive.Tokenize(" "); TIter next(arr); Bool_t first = kTRUE; while ((os=(TObjString*)next())) { if (!os->GetString().Contains("@") && fCloseSE.Length()) fGridJDL->AddToSet("Output", Form("%s@%s",os->GetString().Data(), fCloseSE.Data())); else fGridJDL->AddToSet("Output", os->GetString()); if (first) fGridJDL->AddToSetDescription("Output", comment); first = kFALSE; } delete arr; // Output archive for the merging jdl if (TestBit(AliAnalysisGrid::kDefaultOutputs)) { outputArchive = "log_archive.zip:std*@disk=1 "; // Add normal output files, extra files + terminate files TString files; if (IsMergeAOD()) files = GetListOfFiles("outaodextter"); else files = GetListOfFiles("outextter"); // Do not register files in fRegisterExcludes if (!fRegisterExcludes.IsNull()) { arr = fRegisterExcludes.Tokenize(" "); TIter next1(arr); while ((os=(TObjString*)next1())) { files.ReplaceAll(Form("%s,",os->GetString().Data()),""); files.ReplaceAll(os->GetString(),""); } delete arr; } files.ReplaceAll(".root", "*.root"); if (mgr->IsCollectThroughput()) outputArchive += Form("root_archive.zip:%s,*.stat@disk=%d %s@disk=%d",files.Data(),fNreplicas, mgr->GetFileInfoLog(),fNreplicas); else 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); first = kTRUE; while ((os=(TObjString*)next2())) { TString currentfile = os->GetString(); if (!currentfile.Contains("@") && fCloseSE.Length()) fMergingJDL->AddToSet("Output", Form("%s@%s",currentfile.Data(), fCloseSE.Data())); else fMergingJDL->AddToSet("Output", currentfile); if (first) fMergingJDL->AddToSetDescription("Output", comment); first = kFALSE; } delete arr; } arr = fOutputFiles.Tokenize(","); TIter next(arr); Bool_t first = kTRUE; 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; // Ignore fRegisterExcludes if (fRegisterExcludes.Contains(sout)) continue; if (!first) comment = NULL; if (!os->GetString().Contains("@") && fCloseSE.Length()) fGridJDL->AddToSet("Output", Form("%s@%s",os->GetString().Data(), fCloseSE.Data())); else fGridJDL->AddToSet("Output", os->GetString()); if (first) fGridJDL->AddToSetDescription("Output", comment); if (fMergeExcludes.Contains(sout)) continue; if (!os->GetString().Contains("@") && fCloseSE.Length()) fMergingJDL->AddToSet("Output", Form("%s@%s",os->GetString().Data(), fCloseSE.Data())); else fMergingJDL->AddToSet("Output", os->GetString()); if (first) fMergingJDL->AddToSetDescription("Output", comment); first = kFALSE; } delete arr; fGridJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job"); fMergingJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job"); TString validationScript = fValidationScript; fGridJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob"); 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)); fGridJDL->SetDescription("MasterResubmitThreshold", "Resubmit failed jobs until DONE rate reaches this percentage"); } // Write a jdl with 2 input parameters: collection name and output dir name. WriteJDL(copy); } // Copy jdl to grid workspace if (copy) { // Check if an output directory was defined and valid if (!fGridOutputDir.Length()) { Error("CreateJDL", "You must define AliEn output directory"); return kFALSE; } else { if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data()); if (!fProductionMode && !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()); return kFALSE; } } gGrid->Cd(workdir); } if (TestBit(AliAnalysisGrid::kSubmit)) { TString mergeJDLName = fExecutable; mergeJDLName.ReplaceAll(".sh", "_merge.jdl"); TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data()); TString locjdl1 = Form("%s/%s", fGridOutputDir.Data(),mergeJDLName.Data()); if (fProductionMode) { locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data()); locjdl1 = Form("%s/%s", workdir.Data(),mergeJDLName.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 (!copyLocal2Alien("CreateJDL", fJDLName, locjdl)) Fatal("","Terminating"); // 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()); // TFile::Cp(Form("file:%s",mergeJDLName.Data()), Form("alien://%s", locjdl1.Data())); if (!copyLocal2Alien("CreateJDL", mergeJDLName.Data(), locjdl1)) Fatal("","Terminating"); } } if (fAdditionalLibs.Length()) { arr = fAdditionalLibs.Tokenize(" "); TObjString *os; TIter next(arr); while ((os=(TObjString*)next())) { if (os->GetString().Contains(".so") || os->GetString().Contains(".dylib")) continue; Info("CreateJDL", "\n##### Copying dependency: <%s> to your alien workspace", os->GetString().Data()); if (FileExists(os->GetString())) gGrid->Rm(os->GetString()); // TFile::Cp(Form("file:%s",os->GetString().Data()), Form("alien://%s/%s", workdir.Data(), os->GetString().Data())); if (!copyLocal2Alien("CreateJDL", os->GetString().Data(), Form("%s/%s", workdir.Data(), os->GetString().Data()))) Fatal("","Terminating"); } delete arr; } if (fPackages) { TIter next(fPackages); TObject *obj; while ((obj=next())) { if (FileExists(obj->GetName())) gGrid->Rm(obj->GetName()); Info("CreateJDL", "\n##### Copying dependency: <%s> to your alien workspace", obj->GetName()); // TFile::Cp(Form("file:%s",obj->GetName()), Form("alien://%s/%s", workdir.Data(), obj->GetName())); if (!copyLocal2Alien("CreateJDL",obj->GetName(), Form("%s/%s", workdir.Data(), obj->GetName()))) Fatal("","Terminating"); } } } return kTRUE; } //______________________________________________________________________________ Bool_t AliAnalysisAlien::WriteJDL(Bool_t copy) { // Writes one or more JDL's corresponding to findex. If findex is negative, // all run numbers are considered in one go (jdl). For non-negative indices // they correspond to the indices in the array fInputFiles. if (!fInputFiles && !fMCLoop) return kFALSE; TObject *os; TString workdir; if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice")) workdir = gGrid->GetHomeDirectory(); workdir += fGridWorkingDir; 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 { 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"); } if (!fOutputToRunNo) fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_04i#", fGridOutputDir.Data())); else fGridJDL->SetOutputDirectory(fGridOutputDir); } 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(); // 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("\",\"", "\",\n \""); sjdl.ReplaceAll("(member", "\n (member"); sjdl.ReplaceAll("\",\"VO_", "\",\n \"VO_"); sjdl.ReplaceAll("{", "{\n "); sjdl.ReplaceAll("};", "\n};"); sjdl.ReplaceAll("{\n \n", "{\n"); sjdl.ReplaceAll("\n\n", "\n"); sjdl.ReplaceAll("OutputDirectory", "OutputDir"); sjdl1.ReplaceAll("\",\"", "\",\n \""); sjdl1.ReplaceAll("(member", "\n (member"); sjdl1.ReplaceAll("\",\"VO_", "\",\n \"VO_"); sjdl1.ReplaceAll("{", "{\n "); sjdl1.ReplaceAll("};", "\n};"); sjdl1.ReplaceAll("{\n \n", "{\n"); sjdl1.ReplaceAll("\n\n", "\n"); sjdl1.ReplaceAll("OutputDirectory", "OutputDir"); sjdl2.ReplaceAll("\",\"", "\",\n \""); 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"; 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("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 (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("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); 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 (!copyLocal2Alien("WriteJDL",fJDLName.Data(),locjdl.Data())) Fatal("","Terminating"); if (fMergeViaJDL) { 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())); if (!copyLocal2Alien("WriteJDL",mergeJDLName.Data(),locjdl1.Data())) Fatal("","Terminating"); if (!copyLocal2Alien("WriteJDL",finalJDL.Data(),locjdl2.Data())) Fatal("","Terminating"); } } return kTRUE; } //______________________________________________________________________________ Bool_t AliAnalysisAlien::FileExists(const char *lfn) { // Returns true if file exists. if (!gGrid) return kFALSE; 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) { delete res; return kFALSE; } TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("name")); if (!objs || !objs->GetString().Length()) { delete res; return kFALSE; } delete res; return kTRUE; } //______________________________________________________________________________ Bool_t AliAnalysisAlien::DirectoryExists(const char *dirname) { // Returns true if directory exists. Can be also a path. // Since there is not API in TAlien, we use the Cd trick: if (!gGrid) return kFALSE; // Backup current path TString cpath = gGrid->Pwd(); TString command = "cd "; TString sdir(dirname); sdir.ReplaceAll("alien://", ""); command += sdir; TGridResult *res = gGrid->Command(command); if (!res) { gGrid->Cd(cpath); return kFALSE; } TMap *map = (TMap*)res->At(0); if (!map) { gGrid->Cd(cpath); delete res; return kFALSE; } TString sval = map->GetValue("__result__")->GetName(); Bool_t retval = (Bool_t)sval.Atoi(); gGrid->Cd(cpath); delete res; return retval; } //______________________________________________________________________________ void AliAnalysisAlien::CheckDataType(const char *lfn, Bool_t &isCollection, Bool_t &isXml, Bool_t &useTags) { // Check input data type. isCollection = kFALSE; isXml = kFALSE; useTags = kFALSE; if (!gGrid) { Error("CheckDataType", "No connection to grid"); return; } isCollection = IsCollection(lfn); TString msg = "\n##### file: "; msg += lfn; if (isCollection) { msg += " type: raw_collection;"; // special treatment for collections isXml = kFALSE; // check for tag files in the collection TGridResult *res = gGrid->Command(Form("listFilesFromCollection -z -v %s",lfn), kFALSE); if (!res) { msg += " using_tags: No (unknown)"; Info("CheckDataType", "%s", msg.Data()); return; } const char* typeStr = res->GetKey(0, "origLFN"); if (!typeStr || !strlen(typeStr)) { msg += " using_tags: No (unknown)"; 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", "%s", msg.Data()); return; } TString slfn(lfn); slfn.ToLower(); isXml = slfn.Contains(".xml"); if (isXml) { // Open xml collection and check if there are tag files inside msg += " type: xml_collection;"; TGridCollection *coll = (TGridCollection*)gROOT->ProcessLine(Form("TAlienCollection::Open(\"alien://%s\",1);",lfn)); if (!coll) { msg += " using_tags: No (unknown)"; Info("CheckDataType", "%s", msg.Data()); return; } TMap *map = coll->Next(); if (!map) { msg += " using_tags: No (unknown)"; Info("CheckDataType", "%s", msg.Data()); return; } map = (TMap*)map->GetValue(""); TString file; if (map && map->GetValue("name")) file = map->GetValue("name")->GetName(); useTags = file.Contains(".tag"); delete coll; if (useTags) msg += " using_tags: Yes"; else msg += " using_tags: No"; Info("CheckDataType", "%s", msg.Data()); return; } useTags = slfn.Contains(".tag"); if (slfn.Contains(".root")) msg += " type: root file;"; else msg += " type: unknown file;"; if (useTags) msg += " using_tags: Yes"; else msg += " using_tags: No"; Info("CheckDataType", "%s", msg.Data()); } //______________________________________________________________________________ void AliAnalysisAlien::EnablePackage(const char *package) { // Enables a par file supposed to exist in the current directory. TString pkg(package); pkg.ReplaceAll(".par", ""); pkg += ".par"; if (gSystem->AccessPathName(pkg)) { Fatal("EnablePackage", "Package %s not found", pkg.Data()); return; } if (!TObject::TestBit(AliAnalysisGrid::kUsePars)) Info("EnablePackage", "AliEn plugin will use .par packages"); TObject::SetBit(AliAnalysisGrid::kUsePars, kTRUE); if (!fPackages) { fPackages = new TObjArray(); fPackages->SetOwner(); } fPackages->Add(new TObjString(pkg)); } //______________________________________________________________________________ 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; TString streeName(treeName); if (IsUseMCchain()) streeName = "TE"; TChain *chain = new TChain(streeName); TList *friends = new TList(); TChain *cfriend = 0; if (!fFriendChainName.IsNull()) { TObjArray *list = fFriendChainName.Tokenize(" "); TIter next(list); TObjString *str; while((str=(TObjString*)next())) { cfriend = new TChain(streeName, str->GetName()); friends->Add(cfriend); chain->AddFriend(cfriend); } delete list; } TString bpath; TIter nextfriend(friends); while (in.good()) { in >> line; if (line.IsNull() || line.BeginsWith("#")) continue; if (count++ == fNtestFiles) break; TString esdFile(line); TFile *file = TFile::Open(esdFile); if (file && !file->IsZombie()) { chain->Add(esdFile); file->Close(); if (!fFriendChainName.IsNull()) { if (esdFile.Index("#") > -1) esdFile.Remove(esdFile.Index("#")); bpath = gSystem->DirName(esdFile); bpath += "/"; TString fileFriend; nextfriend.Reset(); while ((cfriend=(TChain*)nextfriend())) { fileFriend = bpath; fileFriend += cfriend->GetTitle(); file = TFile::Open(fileFriend); if (file && !file->IsZombie()) { file->Close(); cfriend->Add(fileFriend); } else { Fatal("GetChainForTestMode", "Cannot open friend file: %s", fileFriend.Data()); return 0; } } } } 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; friends->Delete(); delete friends; return NULL; } 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. static char mstatus[20]; mstatus[0] = '\0'; nrunning = 0; nwaiting = 0; nerror = 0; ndone = 0; TGridJobStatusList *list = gGrid->Ps(""); if (!list) return mstatus; Int_t nentries = list->GetSize(); TGridJobStatus *status; Int_t pid; for (Int_t ijob=0; ijob<nentries; ijob++) { status = (TGridJobStatus *)list->At(ijob); pid = gROOT->ProcessLine(Form("atoi(((TAlienJobStatus*)%p)->GetKey(\"queueId\"));", status)); if (pid<jobidstart) continue; if (pid == lastid) { gROOT->ProcessLine(Form("sprintf((char*)%p,((TAlienJobStatus*)%p)->GetKey(\"status\"));",mstatus, status)); } switch (status->GetStatus()) { case TGridJobStatus::kWAITING: nwaiting++; break; case TGridJobStatus::kRUNNING: nrunning++; break; case TGridJobStatus::kABORTED: case TGridJobStatus::kFAIL: case TGridJobStatus::kUNKNOWN: nerror++; break; case TGridJobStatus::kDONE: ndone++; } } list->Delete(); delete list; return mstatus; } //______________________________________________________________________________ Bool_t AliAnalysisAlien::IsCollection(const char *lfn) const { // Returns true if file is a collection. Functionality duplicated from // TAlien::Type() because we don't want to directly depend on TAlien. if (!gGrid) { Error("IsCollection", "No connection to grid"); return kFALSE; } TGridResult *res = gGrid->Command(Form("type -z %s",lfn),kFALSE); if (!res) return kFALSE; const char* typeStr = res->GetKey(0, "type"); if (!typeStr || !strlen(typeStr)) return kFALSE; if (!strcmp(typeStr, "collection")) return kTRUE; delete res; return kFALSE; } //______________________________________________________________________________ Bool_t AliAnalysisAlien::IsSingleOutput() const { // Check if single-ouput option is on. return (!fOutputSingle.IsNull()); } //______________________________________________________________________________ Long64_t AliAnalysisAlien::RunMacroAndExtractLibs(const char* macro, const char *args, TString &libs) { // Tries to run the specified macro and return the libraries that it loads. TString expname; if (strlen(macro)) expname = gSystem->ExpandPathName(macro); if (expname.IsNull() || gSystem->AccessPathName(expname)) { ::Error("RunMacroAndExtractLibs","Cannot find macro %s in current directory", macro); return -1; } TString oldlibs = gSystem->GetLibraries(); TMacro m(expname); Int_t error = 0; Long64_t retval = m.Exec(args, &error); if (error != TInterpreter::kNoError) { ::Error("RunMacroAndExtractLibs", "Macro interpretation %s failed", macro); return -1; } libs = gSystem->GetLibraries(); libs.ReplaceAll(oldlibs, ""); libs.Strip(TString::kLeading); TObjArray *libTokens = libs.Tokenize(" "); libs = ""; for (Int_t i=0; i<libTokens->GetEntries(); i++) { if (!libs.IsNull()) libs += " "; libs += gSystem->BaseName(libTokens->At(i)->GetName()); } delete libTokens; return retval; } //______________________________________________________________________________ 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 (!fROOTVersion.IsNull()) printf("= ROOT version requested________________________ %s\n", fROOTVersion.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. \ \n***** To disable, use: plugin->SetOverwriteMode(kFALSE);\n"); } printf("= Copy files to grid: __________________________ %s\n", (IsUseCopy())?"YES":"NO"); printf("= Check if files can be copied to grid: ________ %s\n", (IsCheckCopy())?"YES":"NO:Print"); printf("= Production mode:______________________________ %d\n", fProductionMode); printf("= Version of API requested: ____________________ %s\n", fAPIVersion.Data()); printf("= Version of ROOT requested: ___________________ %s\n", fROOTVersion.Data()); printf("= Version of AliRoot requested: ________________ %s\n", fAliROOTVersion.Data()); if (fUser.Length()) printf("= User running the plugin: _____________________ %s\n", fUser.Data()); printf("= Grid workdir relative to user $HOME: _________ %s\n", fGridWorkingDir.Data()); printf("= Grid output directory relative to workdir: ___ %s\n", fGridOutputDir.Data()); TString basedatadir = fGridDataDir; TString pattern = fDataPattern; pattern.Strip(); Int_t ind = pattern.Index(" "); if (ind>=0) { basedatadir += "/%run%/"; basedatadir += pattern(0, ind); pattern = pattern(ind+1, pattern.Length()); } printf("= Data base directory path requested: __________ %s\n", basedatadir.Data()); printf("= Data search pattern: _________________________ %s\n", pattern.Data()); printf("= Input data format: ___________________________ %s\n", fInputFormat.Data()); if (fRunNumbers.Length()) printf("= Run numbers to be processed: _________________ %s\n", fRunNumbers.Data()); if (fRunRange[0]) printf("= Run range to be processed: ___________________ %d-%d\n", fRunRange[0], fRunRange[1]); if (!fRunRange[0] && !fRunNumbers.Length()) { TIter next(fInputFiles); TObject *obj; TString list; while ((obj=next())) list += obj->GetName(); printf("= Input files to be processed: _________________ %s\n", list.Data()); } if (TestBit(AliAnalysisGrid::kTest)) printf("= Number of input files used in test mode: _____ %d\n", fNtestFiles); 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 that should not be registered: %s\n", fRegisterExcludes.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); printf("= Max files per subjob: ________________________ %d\n", fSplitMaxInputFileNumber); if (fMaxInitFailed>0) printf("= Max number of subjob fails to kill: __________ %d\n", fMaxInitFailed); if (fMasterResubmitThreshold>0) printf("= Resubmit master job if failed subjobs >_______ %d\n", fMasterResubmitThreshold); printf("= Number of replicas for the output files_______ %d\n", fNreplicas); if (fNrunsPerMaster>0) printf("= Number of runs per master job: _______________ %d\n", fNrunsPerMaster); printf("= Number of files in one chunk to be merged: ___ %d\n", fMaxMergeFiles); printf("= Name of the generated execution script: ______ %s\n", fExecutable.Data()); printf("= Executable command: __________________________ %s\n", fExecutableCommand.Data()); if (fArguments.Length()) printf("= Arguments for the execution script: __________ %s\n",fArguments.Data()); if (fExecutableArgs.Length()) printf("= Arguments after macro name in executable______ %s\n",fExecutableArgs.Data()); printf("= Name of the generated analysis macro: ________ %s\n",fAnalysisMacro.Data()); printf("= User analysis files to be deployed: __________ %s\n",fAnalysisSource.Data()); printf("= Additional libs to be loaded or souces to be compiled runtime: <%s>\n",fAdditionalLibs.Data()); printf("= Master jobs split mode: ______________________ %s\n",fSplitMode.Data()); if (fDatasetName) printf("= Custom name for the dataset to be created: ___ %s\n", fDatasetName.Data()); printf("= Name of the generated JDL: ___________________ %s\n", fJDLName.Data()); if (fIncludePath.Data()) printf("= Include path for runtime task compilation: ___ %s\n", fIncludePath.Data()); if (fCloseSE.Length()) 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 && 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()); } } //______________________________________________________________________________ void AliAnalysisAlien::SetDefaults() { // Set default values for everything. What cannot be filled will be left empty. if (fGridJDL) delete fGridJDL; fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()"); fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()"); fPrice = 1; fTTL = 30000; fSplitMaxInputFileNumber = 100; fMaxInitFailed = 0; fMasterResubmitThreshold = 0; fNtestFiles = 10; fNreplicas = 2; fRunRange[0] = 0; fRunRange[1] = 0; fRunPrefix = "%d"; fNrunsPerMaster = 1; fMaxMergeFiles = 100; fRunNumbers = ""; fExecutable = "analysis.sh"; fExecutableCommand = "root -b -q -x"; fArguments = ""; fExecutableArgs = ""; fAnalysisMacro = "myAnalysis.C"; fAnalysisSource = ""; fAdditionalLibs = ""; fSplitMode = "se"; fAPIVersion = ""; fROOTVersion = ""; fAliROOTVersion = ""; fUser = ""; // Your alien user name fGridWorkingDir = ""; fGridDataDir = ""; // Can be like: /alice/sim/PDC_08a/LHC08c9/ fDataPattern = "*AliESDs.root"; // Can be like: *AliESDs.root, */pass1/*AliESDs.root, ... fFriendChainName = ""; fGridOutputDir = "output"; fOutputArchive = "log_archive.zip:std*@disk=1 root_archive.zip:*.root@disk=2"; fOutputFiles = ""; // Like "AliAODs.root histos.root" fInputFormat = "xml-single"; fJDLName = "analysis.jdl"; fJobTag = "Automatically generated analysis JDL"; fMergeExcludes = ""; fMergeViaJDL = 0; SetUseCopy(kTRUE); SetCheckCopy(kTRUE); SetDefaultOutputs(kTRUE); fOverwriteMode = 1; } //______________________________________________________________________________ void AliAnalysisAlien::SetFriendChainName(const char *name, const char *libnames) { // Set file name for the chain of friends and optionally additional libs to be loaded. // Libs should be separated by blancs. fFriendChainName = name; fFriendChainName.ReplaceAll(",", " "); fFriendChainName.Strip(); fFriendChainName.ReplaceAll(" ", " "); fFriendLibs = libnames; if (fFriendLibs.Length()) { if(!fFriendLibs.Contains(".so") && !fFriendLibs.Contains(".dylib")) Fatal("SetFriendChainName()", "You should provide explicit library names (with extension)"); fFriendLibs.ReplaceAll(",", " "); fFriendLibs.Strip(); fFriendLibs.ReplaceAll(" ", " "); } } //______________________________________________________________________________ void AliAnalysisAlien::SetRootVersionForProof(const char *version) { // Obsolete method. Use SetROOTVersion instead Warning("SetRootVersionForProof", "Obsolete. Use SetROOTVersion instead"); if (fROOTVersion.IsNull()) SetROOTVersion(version); else Error("SetRootVersionForProof", "ROOT version already set to %s", fROOTVersion.Data()); } //______________________________________________________________________________ Bool_t AliAnalysisAlien::CheckMergedFiles(const char *filename, const char *aliendir, Int_t nperchunk, const char *jdl) { // 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)); if (!copyLocal2Alien("CheckMergedFiles", Form("Stage_%d.xml",stage), Form("%s/Stage_%d.xml",aliendir,stage))) Fatal("","Terminating"); // Check if this is the last stage to be done. Bool_t laststage = (nfiles<nperchunk); if (fMaxMergeStages && stage>=fMaxMergeStages) laststage = kTRUE; Int_t jobId = 0; 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); jobId = SubmitSingleJob(query); } else { printf("### Submiting merging stage %d\n", stage); TString query = Form("submit %s %s %d", jdl, aliendir, stage); jobId = SubmitSingleJob(query); } if (!jobId) return kFALSE; if (!fGridJobIDs.IsNull()) fGridJobIDs.Append(" "); fGridJobIDs.Append(Form("%d", jobId)); if (!fGridStages.IsNull()) fGridStages.Append(" "); fGridStages.Append(Form("%s_merge_stage%d", laststage ? "final" : "partial", stage)); return kTRUE; } //______________________________________________________________________________ AliAnalysisManager *AliAnalysisAlien::LoadAnalysisManager(const char *fname) { // Loat the analysis manager from a file. TFile *file = TFile::Open(fname); if (!file) { ::Error("LoadAnalysisManager", "Cannot open file %s", fname); return 0; } TIter nextkey(file->GetListOfKeys()); AliAnalysisManager *mgr = 0; TKey *key; while ((key=(TKey*)nextkey())) { if (!strcmp(key->GetClassName(), "AliAnalysisManager")) mgr = (AliAnalysisManager*)file->Get(key->GetName()); } if (!mgr) ::Error("LoadAnalysisManager", "No analysis manager found in file %s", fname); return mgr; } //______________________________________________________________________________ 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; } Int_t ijobId = jobId.Atoi(); printf(" Job id: '%s' (%d)\n", jobId.Data(), ijobId); return ijobId; } //______________________________________________________________________________ Bool_t AliAnalysisAlien::MergeInfo(const char *output, const char *collection) { // Merges a collection of output files using concatenation. TString scoll(collection); if (!scoll.Contains(".xml")) return kFALSE; TGridCollection *coll = (TGridCollection*)gROOT->ProcessLine(Form("TAlienCollection::Open(\"%s\");", collection)); if (!coll) { ::Error("MergeInfo", "Input XML %s collection empty.", collection); return kFALSE; } // Iterate grid collection TString outtmp; Bool_t merged = kFALSE; Int_t ifile = 0; while (coll->Next()) { TString fname = gSystem->DirName(coll->GetTURL()); fname += "/"; fname += output; outtmp = Form("%d_%s", ifile, output); if (!TFile::Cp(fname, outtmp)) { ::Error("MergeInfo", "Could not copy %s", fname.Data()); continue; } ifile++; if (ifile<2) { gSystem->Exec(Form("cp %s lastmerged", outtmp.Data())); continue; } gSystem->Exec(Form("cat lastmerged %s > tempmerged", outtmp.Data())); gSystem->Exec("cp tempmerged lastmerged"); } if (ifile) { gSystem->Exec(Form("cp lastmerged %s", output)); gSystem->Exec(Form("rm tempmerged lastmerged *_%s", output)); merged = kTRUE; } return merged; } //______________________________________________________________________________ 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; Bool_t isGrid = kTRUE; Int_t index = outputFile.Index("@"); if (index > 0) outputFile.Remove(index); 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 if (sbasedir.Contains(".txt")) { // The file having the .txt extension is expected to contain a list of // folders where the output files will be looked. For alien folders, // the full folder LFN is expected (starting with alien://) // Assume lfn's on each line TString line; ifstream in; in.open(sbasedir); if (in.fail()) { ::Error("MergeOutput", "File %s cannot be opened. Merging stopped." ,sbasedir.Data()); return kTRUE; } Int_t nfiles = 0; while (in.good()) { in >> line; if (line.IsNull() || line.BeginsWith("#")) continue; line.Strip(); if (!line.Contains("alien:")) isGrid = kFALSE; line += "/"; line += outputFile; nfiles++; listoffiles->Add(new TNamed(line.Data(),"")); } in.close(); if (!nfiles) { ::Error("MergeOutput","Input file %s contains no files to be merged\n", sbasedir.Data()); delete listoffiles; return kFALSE; } } 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 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 // 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; } } countZero = nmaxmerge; 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(isGrid); 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 (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; } } delete listoffiles; delete fm; return merged; } // Merging stage different than 0. // Move to the begining of the requested chunk. fm = new TFileMerger(isGrid); 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()); } delete fm; return kTRUE; } //______________________________________________________________________________ Bool_t AliAnalysisAlien::MergeOutputs() { // Merge analysis outputs existing in the AliEn space. if (TestBit(AliAnalysisGrid::kTest)) return kTRUE; if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE; if (!Connect()) { Error("MergeOutputs", "Cannot merge outputs without grid connection. Terminate will NOT be executed"); return kFALSE; } if (fMergeViaJDL) { if (!TestBit(AliAnalysisGrid::kMerge)) { Info("MergeOutputs", "### Re-run with <MergeViaJDL> option in terminate mode of the plugin to submit merging jobs ###"); return kFALSE; } if (fProductionMode) { Info("MergeOutputs", "### Merging will be submitted by LPM manager... ###"); return kFALSE; } Info("MergeOutputs", "Submitting merging JDL"); if (!SubmitMerging()) return kFALSE; Info("MergeOutputs", "### Re-run with <MergeViaJDL> off to collect results after merging jobs are done ###"); Info("MergeOutputs", "### The Terminate() method is executed by the merging jobs"); return kFALSE; } // Get the output path if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data()); if (!DirectoryExists(fGridOutputDir)) { Error("MergeOutputs", "Grid output directory %s not found. Terminate() will NOT be executed", fGridOutputDir.Data()); return kFALSE; } if (!fOutputFiles.Length()) { Error("MergeOutputs", "No output file names defined. Are you running the right AliAnalysisAlien configuration ?"); return kFALSE; } // Check if fast read option was requested Info("MergeOutputs", "Started local merging of output files from: alien://%s \ \n======= overwrite mode = %d", fGridOutputDir.Data(), (Int_t)fOverwriteMode); 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",50); gEnv->SetValue("XNet.RequestTimeout",50); gEnv->SetValue("XNet.MaxRedirectCount",2); 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; TString outputFile; Bool_t merged = kTRUE; while((str=(TObjString*)next())) { outputFile = str->GetString(); Int_t index = outputFile.Index("@"); if (index > 0) outputFile.Remove(index); TString outputChunk = outputFile; outputChunk.ReplaceAll(".root", "_*.root"); // Skip already merged outputs if (!gSystem->AccessPathName(outputFile)) { if (fOverwriteMode) { Info("MergeOutputs", "Overwrite mode. Existing file %s was deleted.", outputFile.Data()); gSystem->Unlink(outputFile); if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) { Info("MergeOutput", "Overwrite mode: partial merged files %s will removed", outputChunk.Data()); gSystem->Exec(Form("rm -f %s", outputChunk.Data())); } } else { Info("MergeOutputs", "Output file <%s> found. Not merging again.", outputFile.Data()); continue; } } else { if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) { Info("MergeOutput", "Overwrite mode: partial merged files %s will removed", outputChunk.Data()); gSystem->Exec(Form("rm -f %s", outputChunk.Data())); } } if (fMergeExcludes.Contains(outputFile.Data()) || fRegisterExcludes.Contains(outputFile.Data())) continue; // Perform a 'find' command in the output directory, looking for registered outputs merged = MergeOutput(outputFile, fGridOutputDir, fMaxMergeFiles); if (!merged) { Error("MergeOutputs", "Terminate() will NOT be executed"); delete list; return kFALSE; } TFile *fileOpened = (TFile*)gROOT->GetListOfFiles()->FindObject(outputFile); if (fileOpened) fileOpened->Close(); } delete list; return kTRUE; } //______________________________________________________________________________ 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"); TObject::SetBit(AliAnalysisGrid::kDefaultOutputs, flag); } //______________________________________________________________________________ void AliAnalysisAlien::SetOutputFiles(const char *list) { // Manually set the output files list. // Removes duplicates. Not allowed if default outputs are not disabled. if (TObject::TestBit(AliAnalysisGrid::kDefaultOutputs)) { Fatal("SetOutputFiles", "You have to explicitly call SetDefaultOutputs(kFALSE) to manually set output files."); return; } Info("SetOutputFiles", "Output file list is set manually - you are on your own."); fOutputFiles = ""; TString slist = list; if (slist.Contains("@")) Warning("SetOutputFiles","The plugin does not allow explicit SE's. Please use: SetNumberOfReplicas() instead."); TObjArray *arr = slist.Tokenize(" "); TObjString *os; TIter next(arr); TString sout; while ((os=(TObjString*)next())) { sout = os->GetString(); if (sout.Index("@")>0) sout.Remove(sout.Index("@")); if (fOutputFiles.Contains(sout)) continue; if (!fOutputFiles.IsNull()) fOutputFiles += ","; fOutputFiles += sout; } delete arr; } //______________________________________________________________________________ void AliAnalysisAlien::SetOutputArchive(const char *list) { // Manually set the output archive list. Free text - you are on your own... // Not allowed if default outputs are not disabled. if (TObject::TestBit(AliAnalysisGrid::kDefaultOutputs)) { Fatal("SetOutputArchive", "You have to explicitly call SetDefaultOutputs(kFALSE) to manually set the output archives."); return; } Info("SetOutputArchive", "Output archive is set manually - you are on your own."); fOutputArchive = list; } //______________________________________________________________________________ void AliAnalysisAlien::SetProofParameter(const char *pname, const char *value) { // Set some PROOF special parameter. TPair *pair = dynamic_cast<TPair*>(fProofParam.FindObject(pname)); if (pair) { TObject *old = pair->Key(); TObject *val = pair->Value(); fProofParam.Remove(old); delete old; delete val; } fProofParam.Add(new TObjString(pname), new TObjString(value)); } //______________________________________________________________________________ const char *AliAnalysisAlien::GetProofParameter(const char *pname) const { // Returns a special PROOF parameter. TPair *pair = dynamic_cast<TPair*>(fProofParam.FindObject(pname)); if (!pair) return 0; return pair->Value()->GetName(); } //______________________________________________________________________________ Bool_t AliAnalysisAlien::StartAnalysis(Long64_t /*nentries*/, Long64_t /*firstEntry*/) { // Start remote grid analysis. 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()) { if (testMode) Info("StartAnalysis", "##### Starting PROOF analysis with Proof Lite via the plugin #####"); else 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; } if (!testMode) { // Check if there is an old active session Long_t nsessions = gROOT->ProcessLine(Form("TProof::Mgr(\"%s\")->QuerySessions(\"\")->GetEntries();", fProofCluster.Data())); if (nsessions) { Error("StartAnalysis","You have to reset your old session first\n"); return kFALSE; } } // Do we need to change the ROOT version ? The success of this cannot be checked. if (!fROOTVersion.IsNull() && !testMode) { gROOT->ProcessLine(Form("TProof::Mgr(\"%s\")->SetROOTVersion(\"VO_ALICE@ROOT::%s\");", fProofCluster.Data(), fROOTVersion.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)); // Set proof special parameters if any TIter nextpp(&fProofParam); TObject *proofparam; while ((proofparam=nextpp())) { TString svalue = GetProofParameter(proofparam->GetName()); gROOT->ProcessLine(Form("gProof->SetParameter(\"%s\",%s);", proofparam->GetName(), svalue.Data())); } // 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:OADB:ANALYSISalice"; // Parse the extra libs for .so or .dylib if (fAdditionalLibs.Length()) { TString additionalLibs = fAdditionalLibs; additionalLibs.Strip(); if (additionalLibs.Length() && fFriendLibs.Length()) additionalLibs += " "; additionalLibs += fFriendLibs; TObjArray *list = additionalLibs.Tokenize(" "); TIter next(list); TObjString *str; while((str=(TObjString*)next())) { if (str->GetString().Contains(".so") || str->GetString().Contains(".dylib") ) { 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",""); stmp.ReplaceAll(".dylib",""); 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()) { Info("StartAnalysis", "Adding extra libs: %s",extraLibs.Data()); 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("${ALICE_ROOT}/",""); includePath.ReplaceAll("-I",""); includePath.Remove(TString::kTrailing, ':'); Info("StartAnalysis", "Adding extra includes: %s",includePath.Data()); optionsList.Add(new TNamed("ALIROOT_EXTRA_INCLUDES",includePath.Data())); } // Check if connection to grid is requested if (TestSpecialBit(kProofConnectGrid)) optionsList.Add(new TNamed("ALIROOT_ENABLE_ALIEN", "1")); // Enable AliRoot par if (testMode) { // Enable proof lite package TString alirootLite = gSystem->ExpandPathName("$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 ( ! fAliROOTVersion.IsNull() ) { 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") || fAdditionalLibs.Contains(".dylib")) && !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; } } // 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; } } } // 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 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 "; if (mgr->IsCollectThroughput()) fOutputArchive += Form("root_archive.zip:%s,*.stat@disk=%d %s@disk=%d",fOutputFiles.Data(),fNreplicas, mgr->GetFileInfoLog(),fNreplicas); else 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)) { Info("StartAnalysis","\n##### OFFLINE MODE ##### Files to be used in GRID are produced but not copied \ \n there nor any job run. You can revise the JDL and analysis \ \n macro then run the same in \"submit\" mode."); } else if (TestBit(AliAnalysisGrid::kTest)) { Info("StartAnalysis","\n##### LOCAL MODE ##### Your analysis will be run locally on a subset of the requested \ \n dataset."); } else if (TestBit(AliAnalysisGrid::kSubmit)) { Info("StartAnalysis","\n##### SUBMIT MODE ##### Files required by your analysis are copied to your grid working \ \n space and job submitted."); } else if (TestBit(AliAnalysisGrid::kMerge)) { Info("StartAnalysis","\n##### MERGE MODE ##### The registered outputs of the analysis will be merged"); if (fMergeViaJDL) CheckInputData(); return kTRUE; } else { Info("StartAnalysis","\n##### FULL ANALYSIS MODE ##### Producing needed files and submitting your analysis job..."); } Print(); if (!Connect()) { Error("StartAnalysis", "Cannot start grid analysis without grid connection"); return kFALSE; } if (IsCheckCopy() && gGrid) CheckFileCopy(gGrid->GetHomeDirectory()); if (!CheckInputData()) { Error("StartAnalysis", "There was an error in preprocessing your requested input data"); return kFALSE; } if (!CreateDataset(fDataPattern)) { TString serror; if (!fRunNumbers.Length() && !fRunRange[0]) serror = Form("path to data directory: <%s>", fGridDataDir.Data()); if (fRunNumbers.Length()) serror = "run numbers"; if (fRunRange[0]) serror = Form("run range [%d, %d]", fRunRange[0], fRunRange[1]); serror += Form("\n or data pattern <%s>", fDataPattern.Data()); Error("StartAnalysis", "No data to process. Please fix %s in your plugin configuration.", serror.Data()); return kFALSE; } WriteAnalysisFile(); WriteAnalysisMacro(); WriteExecutable(); WriteValidationScript(); if (fMergeViaJDL) { WriteMergingMacro(); WriteMergeExecutable(); WriteValidationScript(kTRUE); } if (!CreateJDL()) return kFALSE; if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE; if (testMode) { // Locally testing the analysis Info("StartAnalysis", "\n_______________________________________________________________________ \ \n Running analysis script in a daughter shell as on a worker node \ \n_______________________________________________________________________"); 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 (!gSystem->AccessPathName(outputFile)) gSystem->Exec(Form("rm %s", outputFile.Data())); } delete list; gSystem->Exec(Form("bash %s 2>stderr", fExecutable.Data())); gSystem->Exec(Form("bash %s",fValidationScript.Data())); // gSystem->Exec("cat stdout"); return kFALSE; } // Check if submitting is managed by LPM manager if (fProductionMode) { //TString prodfile = fJDLName; //prodfile.ReplaceAll(".jdl", ".prod"); //WriteProductionFile(prodfile); Info("StartAnalysis", "Job submitting is managed by LPM. Rerun in terminate mode after jobs finished."); return kFALSE; } // Submit AliEn job(s) gGrid->Cd(fGridOutputDir); TGridResult *res; TString jobID = ""; fGridJobIDs = ""; fGridStages = ""; if (!fRunNumbers.Length() && !fRunRange[0]) { // Submit a given xml or a set of runs res = gGrid->Command(Form("submit %s", fJDLName.Data())); printf("*************************** %s\n",Form("submit %s", fJDLName.Data())); if (res) { const char *cjobId = res->GetKey(0,"jobId"); if (!cjobId) { gGrid->Stdout(); gGrid->Stderr(); Error("StartAnalysis", "Your JDL %s could not be submitted", fJDLName.Data()); return kFALSE; } else { Info("StartAnalysis", "\n_______________________________________________________________________ \ \n##### Your JDL %s was successfully submitted. \nTHE JOB ID IS: %s \ \n_______________________________________________________________________", fJDLName.Data(), cjobId); jobID = cjobId; if (jobID.Atoi()) { if (!fGridJobIDs.IsNull()) fGridJobIDs.Append(" "); fGridJobIDs.Append(jobID); if (!fGridStages.IsNull()) fGridStages.Append(" "); fGridStages.Append("full"); } } delete res; } else { Error("StartAnalysis", "No grid result after submission !!! Bailing out..."); return kFALSE; } } else { // Submit for a range of enumeration of runs. if (!Submit()) return kFALSE; jobID = fGridJobIDs; } if (fDropToShell) { Info("StartAnalysis", "\n#### STARTING AN ALIEN SHELL FOR YOU. EXIT WHEN YOUR JOB %s HAS FINISHED. #### \ \n You may exit at any time and terminate the job later using the option <terminate> \ \n ##################################################################################", jobID.Data()); gSystem->Exec("aliensh"); } else { Info("StartAnalysis", "\n#### SUBMITTED JOB %s TO ALIEN QUEUE #### \ \n Remember to terminate the job later using the option <terminate> \ \n ##################################################################################", jobID.Data()); } return kTRUE; } //______________________________________________________________________________ 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 = ""; if (mgr->GetOutputEventHandler()->GetFillAOD()) aodfiles = mgr->GetOutputEventHandler()->GetOutputFileName(); TString extraaod = mgr->GetOutputEventHandler()->GetExtraOutputs(kTRUE); if (!extraaod.IsNull() && mgr->GetOutputEventHandler()->GetFillExtension()) { if (!aodfiles.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() && strlen(filename)) outputfiles += ","; outputfiles += filename; } if (stype.Contains("out")) { if (!files.IsNull() && !outputfiles.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() && !sextra.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. Int_t nmasterjobs = fInputFiles->GetEntries(); Long_t tshoot = gSystem->Now(); if (!fNsubmitted && !SubmitNext()) return kFALSE; while (fNsubmitted < nmasterjobs) { Long_t now = gSystem->Now(); if ((now-tshoot)>30000) { tshoot = now; if (!SubmitNext()) return kFALSE; } } return kTRUE; } //______________________________________________________________________________ Bool_t AliAnalysisAlien::SubmitMerging() { // Submit all merging jobs. if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data()); 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(); for (Int_t i=0; i<ntosubmit; i++) { TString runOutDir = gSystem->BaseName(fInputFiles->At(i)->GetName()); runOutDir.ReplaceAll(".xml", ""); 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 { // 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) && !fRegisterExcludes.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; if (fDropToShell) { 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"); } else { Info("StartAnalysis", "\n #### STARTED MERGING JOBS FOR YOU #### \ \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 ################################################################################################################"); } return kTRUE; } //______________________________________________________________________________ Bool_t AliAnalysisAlien::SubmitNext() { // 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; static Int_t npermaster = 0; if (iscalled) return kTRUE; iscalled = kTRUE; Int_t nrunning=0, nwaiting=0, nerror=0, ndone=0; Int_t ntosubmit = 0; TGridResult *res; TString jobID = ""; 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>500) {iscalled = kFALSE; return kTRUE;} npermaster = (nrunning+nwaiting+nerror+ndone)/fNsubmitted; 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); } for (Int_t i=0; i<ntosubmit; i++) { // Submit for a range of enumeration of runs. if (fNsubmitted>=nmasterjobs) {iscalled = kFALSE; return kTRUE;} TString query; TString runOutDir = gSystem->BaseName(fInputFiles->At(fNsubmitted)->GetName()); runOutDir.ReplaceAll(".xml", ""); if (fOutputToRunNo) query = Form("submit %s %s %s", fJDLName.Data(), fInputFiles->At(fNsubmitted)->GetName(), runOutDir.Data()); else query = Form("submit %s %s %03d", fJDLName.Data(), fInputFiles->At(fNsubmitted)->GetName(), fNsubmitted); printf("********* %s\n",query.Data()); res = gGrid->Command(query); if (res) { TString cjobId1 = res->GetKey(0,"jobId"); if (!cjobId1.Length()) { iscalled = kFALSE; gGrid->Stdout(); gGrid->Stderr(); Error("StartAnalysis", "Your JDL %s could not be submitted. The message was:", fJDLName.Data()); return kFALSE; } else { Info("StartAnalysis", "\n_______________________________________________________________________ \ \n##### Your JDL %s submitted (%d to go). \nTHE JOB ID IS: %s \ \n_______________________________________________________________________", fJDLName.Data(), nmasterjobs-fNsubmitted-1, cjobId1.Data()); if (!fGridJobIDs.IsNull()) fGridJobIDs.Append(" "); fGridJobIDs.Append(cjobId1); if (!fGridStages.IsNull()) fGridStages.Append(" "); fGridStages.Append("full"); jobID += cjobId1; jobID += " "; lastmaster = cjobId1.Atoi(); if (!firstmaster) firstmaster = lastmaster; fNsubmitted++; } delete res; } else { Error("StartAnalysis", "No grid result after submission !!! Bailing out..."); return kFALSE; } } iscalled = kFALSE; return kTRUE; } //______________________________________________________________________________ void AliAnalysisAlien::WriteAnalysisFile() { // Write current analysis manager into the file <analysisFile> TString analysisFile = fExecutable; analysisFile.ReplaceAll(".sh", ".root"); if (!TestBit(AliAnalysisGrid::kSubmit)) { AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager(); if (!mgr || !mgr->IsInitialized()) { Error("WriteAnalysisFile", "You need an initialized analysis manager for this"); return; } // Check analysis type TObject *handler; if (mgr->GetMCtruthEventHandler()) TObject::SetBit(AliAnalysisGrid::kUseMC); handler = (TObject*)mgr->GetInputEventHandler(); if (handler) { 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"); if (file) { // Skip task Terminate calls for the grid job (but not in test mode, where we want to check also the terminate mode if (!TestBit(AliAnalysisGrid::kTest)) mgr->SetSkipTerminate(kTRUE); // Unless merging makes no sense if (IsSingleOutput()) mgr->SetSkipTerminate(kFALSE); mgr->Write(); delete file; // Enable termination for local jobs mgr->SetSkipTerminate(kFALSE); } if (cdir) cdir->cd(); Info("WriteAnalysisFile", "\n##### Analysis manager: %s wrote to file <%s>\n", mgr->GetName(),analysisFile.Data()); } Bool_t copy = kTRUE; if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE; if (copy) { CdWork(); TString workdir = gGrid->GetHomeDirectory(); workdir += fGridWorkingDir; Info("WriteAnalysisFile", "\n##### Copying file <%s> containing your initialized analysis manager to your alien workspace", analysisFile.Data()); if (FileExists(analysisFile)) gGrid->Rm(analysisFile); if (!copyLocal2Alien("WriteAnalysisFile",analysisFile.Data(), Form("%s/%s", workdir.Data(),analysisFile.Data()))) Fatal("","Terminating"); } } //______________________________________________________________________________ void AliAnalysisAlien::WriteAnalysisMacro() { // Write the analysis macro that will steer the analysis in grid mode. if (!TestBit(AliAnalysisGrid::kSubmit)) { ofstream out; out.open(fAnalysisMacro.Data(), ios::out); if (!out.good()) { Error("WriteAnalysisMacro", "could not open file %s for writing", fAnalysisMacro.Data()); return; } Bool_t hasSTEERBase = kFALSE; Bool_t hasESD = kFALSE; Bool_t hasAOD = kFALSE; Bool_t hasANALYSIS = kFALSE; Bool_t hasOADB = kFALSE; Bool_t hasANALYSISalice = kFALSE; Bool_t hasCORRFW = kFALSE; TString func = fAnalysisMacro; TString type = "ESD"; TString comment = "// Analysis using "; if (fMCLoop) { type = "MCGEN"; comment += "MCGEN"; } else { 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; } if (TObject::TestBit(AliAnalysisGrid::kUseMC)) comment += "/MC"; else comment += " data"; out << "const char *anatype = \"" << type.Data() << "\";" << endl << endl; func.ReplaceAll(".C", ""); out << "void " << func.Data() << "()" << endl; out << "{" << endl; out << comment.Data() << endl; out << "// Automatically generated analysis steering macro executed in grid subjobs" << endl << endl; out << " TStopwatch timer;" << endl; out << " timer.Start();" << endl << endl; // Change temp directory to current one if (!IsLocalTest()) { out << "// connect to AliEn and make the chain" << endl; out << " if (!TGrid::Connect(\"alien://\")) return;" << endl; } 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; TObjArray *list = fAdditionalRootLibs.Tokenize(" "); TIter next(list); TObjString *str; while((str=(TObjString*)next())) { if (str->GetString().Contains(".so") || str->GetString().Contains(".dylib")) out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl; } if (list) delete list; } out << "// Load analysis framework libraries" << endl; TString setupPar = "AliAnalysisAlien::SetupPar"; if (!fPackages) { 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(\"libOADB\");" << endl; out << " gSystem->Load(\"libANALYSISalice\");" << endl; out << " gSystem->Load(\"libCORRFW\");" << endl << endl; } else { TIter next(fPackages); TObject *obj; TString pkgname; while ((obj=next())) { pkgname = obj->GetName(); if (pkgname == "STEERBase" || pkgname == "STEERBase.par") hasSTEERBase = kTRUE; if (pkgname == "ESD" || pkgname == "ESD.par") hasESD = kTRUE; if (pkgname == "AOD" || pkgname == "AOD.par") hasAOD = kTRUE; if (pkgname == "ANALYSIS" || pkgname == "ANALYSIS.par") hasANALYSIS = kTRUE; if (pkgname == "OADB" || pkgname == "OADB.par") hasOADB = kTRUE; if (pkgname == "ANALYSISalice" || pkgname == "ANALYSISalice.par") hasANALYSISalice = kTRUE; if (pkgname == "CORRFW" || pkgname == "CORRFW.par") hasCORRFW = kTRUE; } if (hasANALYSISalice) setupPar = "SetupPar"; if (!hasSTEERBase) out << " gSystem->Load(\"libSTEERBase\");" << endl; else out << " if (!" << setupPar << "(\"STEERBase\")) return;" << endl; if (!hasESD) out << " gSystem->Load(\"libESD\");" << endl; else out << " if (!" << setupPar << "(\"ESD\")) return;" << endl; if (!hasAOD) out << " gSystem->Load(\"libAOD\");" << endl; else out << " if (!" << setupPar << "(\"AOD\")) return;" << endl; if (!hasANALYSIS) out << " gSystem->Load(\"libANALYSIS\");" << endl; else out << " if (!" << setupPar << "(\"ANALYSIS\")) return;" << endl; if (!hasOADB) out << " gSystem->Load(\"libOADB\");" << endl; else out << " if (!" << setupPar << "(\"OADB\")) return;" << endl; if (!hasANALYSISalice) out << " gSystem->Load(\"libANALYSISalice\");" << endl; else out << " if (!" << setupPar << "(\"ANALYSISalice\")) return;" << endl; if (!hasCORRFW) out << " gSystem->Load(\"libCORRFW\");" << endl << endl; else out << " if (!" << setupPar << "(\"CORRFW\")) return;" << endl << endl; out << "// Compile other par packages" << endl; next.Reset(); while ((obj=next())) { pkgname = obj->GetName(); if (pkgname == "STEERBase" || pkgname == "STEERBase.par" || pkgname == "ESD" || pkgname == "ESD.par" || pkgname == "AOD" || pkgname == "AOD.par" || pkgname == "ANALYSIS" || pkgname == "ANALYSIS.par" || pkgname == "OADB" || pkgname == "OADB.par" || pkgname == "ANALYSISalice" || pkgname == "ANALYSISalice.par" || pkgname == "CORRFW" || pkgname == "CORRFW.par") continue; 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 (fMCLoop && !fGeneratorLibs.IsNull()) { out << "// MC generator libraries" << endl; TObjArray *list = fGeneratorLibs.Tokenize(" "); TIter next(list); TObjString *str; while((str=(TObjString*)next())) { out << " gSystem->Load(\"" << str->GetName() << "\");" << endl; } delete list; } if (fAdditionalLibs.Length()) { out << "// Add aditional AliRoot libraries" << endl; TString additionalLibs = fAdditionalLibs; additionalLibs.Strip(); if (additionalLibs.Length() && fFriendLibs.Length()) additionalLibs += " "; additionalLibs += fFriendLibs; TObjArray *list = additionalLibs.Tokenize(" "); TIter next(list); TObjString *str; while((str=(TObjString*)next())) { if (str->GetString().Contains(".so") || str->GetString().Contains(".dylib")) out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl; if (str->GetString().Contains(".par")) out << " if (!" << setupPar << "(\"" << str->GetString() << "\")) return;" << endl; } delete list; } out << endl; out << "// analysis source to be compiled at runtime (if any)" << endl; if (fAnalysisSource.Length()) { TObjArray *list = fAnalysisSource.Tokenize(" "); TIter next(list); TObjString *str; while((str=(TObjString*)next())) { out << " gROOT->ProcessLine(\".L " << str->GetString().Data() << "+g\");" << endl; } 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\",50);" << endl; out << " gEnv->SetValue(\"XNet.RequestTimeout\",50);" << endl; out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl; out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",50);" << endl; out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl; } out << "// read the analysis manager from file" << endl; TString analysisFile = fExecutable; analysisFile.ReplaceAll(".sh", ".root"); out << " AliAnalysisManager *mgr = AliAnalysisAlien::LoadAnalysisManager(\"" << analysisFile << "\");" << endl; out << " if (!mgr) return;" << endl; if (IsLocalTest()) { out << " AliAnalysisAlien *plugin = new AliAnalysisAlien();" << endl; out << " plugin->SetRunMode(\"test\");" << endl; if (fFileForTestMode.IsNull()) out << " plugin->SetFileForTestMode(\"data.txt\");" << endl; else out << " plugin->SetFileForTestMode(\"" << fFileForTestMode << "\");" << endl; out << " plugin->SetNtestFiles(" << fNtestFiles << ");" << endl; if (!fFriendChainName.IsNull()) out << " plugin->SetFriendChainName(\"" << fFriendChainName << "\",\"" << fFriendLibs << "\");" << endl; if (IsUseMCchain()) out << " plugin->SetUseMCchain();" << endl; if (fMCLoop) out << " plugin->SetMCLoop(kTRUE);" << endl; out << " mgr->SetGridHandler(plugin);" << endl; if (AliAnalysisManager::GetAnalysisManager()) { out << " mgr->SetDebugLevel(" << AliAnalysisManager::GetAnalysisManager()->GetDebugLevel() << ");" << endl; out << " mgr->SetNSysInfo(" << AliAnalysisManager::GetAnalysisManager()->GetNsysInfo() << ");" << endl; } else { out << " mgr->SetDebugLevel(10);" << endl; out << " mgr->SetNSysInfo(100);" << endl; } } out << " mgr->PrintStatus();" << endl; if (AliAnalysisManager::GetAnalysisManager()) { if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) { out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl; } else { if (TestBit(AliAnalysisGrid::kTest)) out << " AliLog::SetGlobalLogLevel(AliLog::kWarning);" << endl; else out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl; } } if (!IsLocalTest()) { if (fMCLoop) { out << " mgr->SetCacheSize(0);" << endl; out << " mgr->EventLoop(" << fNMCevents << ");" << endl; } else { out << " TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl; out << " mgr->StartAnalysis(\"localfile\", chain);" << endl; } } else { if (fMCLoop) { out << " mgr->SetCacheSize(0);" << endl; out << " mgr->EventLoop(" << fNMCevents << ");" << endl; } else { out << " mgr->StartAnalysis(\"localfile\");" << endl; } } out << " timer.Stop();" << endl; out << " timer.Print();" << endl; out << "}" << endl << endl; if (!IsLocalTest() && !fMCLoop) { out <<"//________________________________________________________________________________" << endl; 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 filename;" << endl; out << " Int_t run = 0;" << endl; if (IsUseMCchain()) { out << " TString treename = \"TE\";" << endl; } else { if (!fTreeName.IsNull()) { out << " TString treename = \"" << fTreeName << "\";" << 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; out << " TAlienCollection *coll = TAlienCollection::Open(xmlfile);" << endl; out << " if (!coll) {" << endl; 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.IsNull()) { out << " TList *friends = new TList();" << endl; out << " TIter nextfriend(friends);" << endl; out << " TChain *cfriend = 0;" << endl; TObjArray *list = fFriendChainName.Tokenize(" "); TIter next(list); TObjString *str; while((str=(TObjString*)next())) { out << " cfriend = new TChain(treename, \"" << str->GetName() << "\");" << endl; out << " friends->Add(cfriend);" << endl; out << " chain->AddFriend(cfriend);" << endl; } delete list; // out << " TChain *chainFriend = new TChain(treename);" << endl; } out << " coll->Reset();" << endl; out << " while (coll->Next()) {" << 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.IsNull()) { out << " TString bpath=coll->GetTURL(\"\");" << endl; out << " if (bpath.Index(\"#\") > -1) bpath.Remove(bpath.Index(\"#\"));" << endl; out << " bpath = gSystem->DirName(bpath);" << endl; out << " bpath += \"/\";" << endl; out << " TString fileFriend;" << endl; out << " nextfriend.Reset();" << endl; out << " while ((cfriend=(TChain*)nextfriend())) {" << endl; out << " fileFriend = bpath;" << endl; out << " fileFriend += cfriend->GetTitle();" << endl; out << " TFile *file = TFile::Open(fileFriend);" << endl; out << " if (file) {" << endl; out << " file->Close();" << endl; out << " cfriend->Add(fileFriend.Data());" << endl; out << " } else {" << endl; out << " ::Fatal(\"CreateChain\", \"Cannot open friend file: %s\", fileFriend.Data());" << endl; out << " return 0;" << endl; out << " }" << endl; out << " }" << endl; } out << " }" << endl; out << " if (!chain->GetNtrees()) {" << endl; out << " ::Error(\"CreateChain\", \"No tree found from collection %s\", xmlfile);" << endl; out << " return NULL;" << endl; out << " }" << endl; out << " return chain;" << endl; out << "}" << endl << endl; } if (hasANALYSISalice) { out <<"//________________________________________________________________________________" << endl; out << "Bool_t SetupPar(const char *package) {" << endl; out << "// Compile the package and set it up." << endl; out << " TString pkgdir = package;" << endl; out << " pkgdir.ReplaceAll(\".par\",\"\");" << 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; out << " if (!gSystem->AccessPathName(\"PROOF-INF/BUILD.sh\")) {" << endl; out << " printf(\"*******************************\\n\");" << endl; out << " printf(\"*** Building PAR archive ***\\n\");" << endl; out << " printf(\"*******************************\\n\");" << endl; out << " if (gSystem->Exec(\"PROOF-INF/BUILD.sh\")) {" << endl; out << " ::Error(\"SetupPar\", \"Cannot build par archive %s\", pkgdir.Data());" << endl; out << " gSystem->ChangeDirectory(cdir);" << endl; out << " return kFALSE;" << endl; out << " }" << endl; out << " } else {" << endl; out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/BUILD.sh for package %s\", pkgdir.Data());" << endl; out << " gSystem->ChangeDirectory(cdir);" << endl; out << " return kFALSE;" << endl; out << " }" << endl; out << " // Check for SETUP.C and execute" << endl; out << " if (!gSystem->AccessPathName(\"PROOF-INF/SETUP.C\")) {" << endl; out << " printf(\"*******************************\\n\");" << endl; out << " printf(\"*** Setup PAR archive ***\\n\");" << endl; out << " printf(\"*******************************\\n\");" << endl; out << " gROOT->Macro(\"PROOF-INF/SETUP.C\");" << endl; out << " } else {" << endl; out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/SETUP.C for package %s\", pkgdir.Data());" << endl; out << " gSystem->ChangeDirectory(cdir);" << endl; out << " return kFALSE;" << endl; out << " }" << endl; out << " // Restore original workdir" << endl; out << " gSystem->ChangeDirectory(cdir);" << endl; out << " return kTRUE;" << endl; out << "}" << endl; } Info("WriteAnalysisMacro", "\n##### Analysis macro to run on worker nodes <%s> written",fAnalysisMacro.Data()); } Bool_t copy = kTRUE; if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE; if (copy) { CdWork(); TString workdir = gGrid->GetHomeDirectory(); workdir += fGridWorkingDir; if (FileExists(fAnalysisMacro)) gGrid->Rm(fAnalysisMacro); Info("WriteAnalysisMacro", "\n##### Copying analysis macro: <%s> to your alien workspace", fAnalysisMacro.Data()); // TFile::Cp(Form("file:%s",fAnalysisMacro.Data()), Form("alien://%s/%s", workdir.Data(), fAnalysisMacro.Data())); if (!copyLocal2Alien("WriteAnalysisMacro",fAnalysisMacro.Data(), Form("alien://%s/%s", workdir.Data(), fAnalysisMacro.Data()))) Fatal("","Terminating"); } } //______________________________________________________________________________ void AliAnalysisAlien::WriteMergingMacro() { // Write a macro to merge the outputs per master job. if (!fMergeViaJDL) return; if (!fOutputFiles.Length()) { Error("WriteMergingMacro", "No output file names defined. Are you running the right AliAnalysisAlien configuration ?"); return; } AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager(); TString mergingMacro = fExecutable; mergingMacro.ReplaceAll(".sh","_merge.C"); if (gGrid && !fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data()); if (!TestBit(AliAnalysisGrid::kSubmit)) { ofstream out; out.open(mergingMacro.Data(), ios::out); if (!out.good()) { Error("WriteMergingMacro", "could not open file %s for writing", fAnalysisMacro.Data()); return; } Bool_t hasSTEERBase = kFALSE; Bool_t hasESD = kFALSE; Bool_t hasAOD = kFALSE; Bool_t hasANALYSIS = kFALSE; Bool_t hasOADB = kFALSE; Bool_t hasANALYSISalice = kFALSE; Bool_t hasCORRFW = kFALSE; TString func = mergingMacro; TString comment; func.ReplaceAll(".C", ""); 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; // 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; TObjArray *list = fAdditionalRootLibs.Tokenize(" "); TIter next(list); TObjString *str; while((str=(TObjString*)next())) { if (str->GetString().Contains(".so") || str->GetString().Contains(".dylib")) out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl; } if (list) delete list; } out << "// Load analysis framework libraries" << endl; if (!fPackages) { 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(\"libOADB\");" << endl; out << " gSystem->Load(\"libANALYSISalice\");" << endl; out << " gSystem->Load(\"libCORRFW\");" << endl << endl; } else { TIter next(fPackages); TObject *obj; TString pkgname; TString setupPar = "AliAnalysisAlien::SetupPar"; while ((obj=next())) { pkgname = obj->GetName(); if (pkgname == "STEERBase" || pkgname == "STEERBase.par") hasSTEERBase = kTRUE; if (pkgname == "ESD" || pkgname == "ESD.par") hasESD = kTRUE; if (pkgname == "AOD" || pkgname == "AOD.par") hasAOD = kTRUE; if (pkgname == "ANALYSIS" || pkgname == "ANALYSIS.par") hasANALYSIS = kTRUE; if (pkgname == "OADB" || pkgname == "OADB.par") hasOADB = kTRUE; if (pkgname == "ANALYSISalice" || pkgname == "ANALYSISalice.par") hasANALYSISalice = kTRUE; if (pkgname == "CORRFW" || pkgname == "CORRFW.par") hasCORRFW = kTRUE; } if (hasANALYSISalice) setupPar = "SetupPar"; if (!hasSTEERBase) out << " gSystem->Load(\"libSTEERBase\");" << endl; else out << " if (!" << setupPar << "(\"STEERBase\")) return;" << endl; if (!hasESD) out << " gSystem->Load(\"libESD\");" << endl; else out << " if (!" << setupPar << "(\"ESD\")) return;" << endl; if (!hasAOD) out << " gSystem->Load(\"libAOD\");" << endl; else out << " if (!" << setupPar << "(\"AOD\")) return;" << endl; out << " gSystem->Load(\"libOADB\");" << endl; if (!hasANALYSIS) out << " gSystem->Load(\"libANALYSIS\");" << endl; else out << " if (!" << setupPar << "(\"ANALYSIS\")) return;" << endl; if (!hasOADB) out << " gSystem->Load(\"libOADB\");" << endl; else out << " if (!" << setupPar << "(\"OADB\")) return;" << endl; if (!hasANALYSISalice) out << " gSystem->Load(\"libANALYSISalice\");" << endl; else out << " if (!" << setupPar << "(\"ANALYSISalice\")) return;" << endl; if (!hasCORRFW) out << " gSystem->Load(\"libCORRFW\");" << endl << endl; else out << " if (!" << setupPar << "(\"CORRFW\")) return;" << endl << endl; out << "// Compile other par packages" << endl; next.Reset(); while ((obj=next())) { pkgname = obj->GetName(); if (pkgname == "STEERBase" || pkgname == "STEERBase.par" || pkgname == "ESD" || pkgname == "ESD.par" || pkgname == "AOD" || pkgname == "AOD.par" || pkgname == "ANALYSIS" || pkgname == "ANALYSIS.par" || pkgname == "OADB" || pkgname == "OADB.par" || pkgname == "ANALYSISalice" || pkgname == "ANALYSISalice.par" || pkgname == "CORRFW" || pkgname == "CORRFW.par") continue; 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 (fMCLoop && !fGeneratorLibs.IsNull()) { out << "// MC generator libraries" << endl; TObjArray *list = fGeneratorLibs.Tokenize(" "); TIter next(list); TObjString *str; while((str=(TObjString*)next())) { out << " gSystem->Load(\"" << str->GetName() << "\");" << endl; } delete list; } if (fAdditionalLibs.Length()) { out << "// Add aditional AliRoot libraries" << endl; TString additionalLibs = fAdditionalLibs; additionalLibs.Strip(); if (additionalLibs.Length() && fFriendLibs.Length()) additionalLibs += " "; additionalLibs += fFriendLibs; TObjArray *list = additionalLibs.Tokenize(" "); TIter next(list); TObjString *str; while((str=(TObjString*)next())) { if (str->GetString().Contains(".so") || str->GetString().Contains(".dylib")) out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl; } if (list) delete list; } out << endl; out << "// Analysis source to be compiled at runtime (if any)" << endl; if (fAnalysisSource.Length()) { TObjArray *list = fAnalysisSource.Tokenize(" "); TIter next(list); TObjString *str; while((str=(TObjString*)next())) { out << " gROOT->ProcessLine(\".L " << str->GetString().Data() << "+g\");" << endl; } if (list) delete list; } out << endl; if (fFastReadOption) { 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\",50);" << endl; out << " gEnv->SetValue(\"XNet.RequestTimeout\",50);" << endl; out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl; out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",50);" << endl; out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl; } // Change temp directory to current one out << "// Connect to AliEn" << endl; out << " if (!TGrid::Connect(\"alien://\")) return;" << endl; 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 << " TString outputDir = dir;" << endl; if (IsMergeAOD()) out << " TString outputFiles = \"" << GetListOfFiles("outaod") << "\";" << endl; else out << " TString outputFiles = \"" << GetListOfFiles("out") << "\";" << endl; out << " TString mergeExcludes = \"" << fMergeExcludes << " " << fRegisterExcludes << "\";" << endl; out << " TObjArray *list = outputFiles.Tokenize(\",\");" << endl; out << " TIter *iter = new TIter(list);" << endl; out << " TObjString *str;" << endl; out << " TString outputFile;" << endl; out << " Bool_t merged = kTRUE;" << endl; TString analysisFile = fExecutable; analysisFile.ReplaceAll(".sh", ".root"); out << " AliAnalysisManager *mgr = AliAnalysisAlien::LoadAnalysisManager(\"" << analysisFile << "\");" << endl; out << " if (!mgr) {" << endl; out << " printf(\"ERROR: Analysis manager could not be extracted from file \");" << endl; out << " return;" << endl; out << " }" << endl; if (IsLocalTest()) { out << " printf(\"===================================\\n\");" << endl; out << " printf(\"Testing merging...\\n\");" << endl; out << " printf(\"===================================\\n\");" << 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; out << " if (!gSystem->AccessPathName(outputFile)) {" << endl; out << " printf(\"Output file <%s> found. Not merging again.\\n\",outputFile.Data());" << endl; out << " continue;" << endl; out << " }" << endl; out << " if (mergeExcludes.Contains(outputFile.Data())) continue;" << 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; if (mgr && mgr->IsCollectThroughput() && !IsLocalTest()) { out << " TString infolog = \"" << mgr->GetFileInfoLog() << "\";" << endl; out << " AliAnalysisAlien::MergeInfo(infolog, outputDir);" << 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; if (IsLocalTest()) { out << " printf(\"===================================\\n\");" << endl; out << " printf(\"Testing Terminate()...\\n\");" << endl; out << " printf(\"===================================\\n\");" << endl; } else { out << " if (!outputDir.Contains(\"Stage\")) return;" << endl; } out << " mgr->SetRunFromPath(mgr->GetRunFromAlienPath(dir));" << endl; out << " mgr->SetSkipTerminate(kFALSE);" << endl; out << " mgr->PrintStatus();" << endl; if (mgr) { if (mgr->GetDebugLevel()>3) { out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl; } else { if (TestBit(AliAnalysisGrid::kTest)) out << " AliLog::SetGlobalLogLevel(AliLog::kWarning);" << endl; else out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl; } } out << " TTree *tree = NULL;" << endl; out << " mgr->StartAnalysis(\"gridterminate\", tree);" << endl; out << "}" << endl << endl; if (hasANALYSISalice) { out <<"//________________________________________________________________________________" << endl; out << "Bool_t SetupPar(const char *package) {" << endl; out << "// Compile the package and set it up." << endl; out << " TString pkgdir = package;" << endl; out << " pkgdir.ReplaceAll(\".par\",\"\");" << 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; out << " if (!gSystem->AccessPathName(\"PROOF-INF/BUILD.sh\")) {" << endl; out << " printf(\"*******************************\\n\");" << endl; out << " printf(\"*** Building PAR archive ***\\n\");" << endl; out << " printf(\"*******************************\\n\");" << endl; out << " if (gSystem->Exec(\"PROOF-INF/BUILD.sh\")) {" << endl; out << " ::Error(\"SetupPar\", \"Cannot build par archive %s\", pkgdir.Data());" << endl; out << " gSystem->ChangeDirectory(cdir);" << endl; out << " return kFALSE;" << endl; out << " }" << endl; out << " } else {" << endl; out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/BUILD.sh for package %s\", pkgdir.Data());" << endl; out << " gSystem->ChangeDirectory(cdir);" << endl; out << " return kFALSE;" << endl; out << " }" << endl; out << " // Check for SETUP.C and execute" << endl; out << " if (!gSystem->AccessPathName(\"PROOF-INF/SETUP.C\")) {" << endl; out << " printf(\"*******************************\\n\");" << endl; out << " printf(\"*** Setup PAR archive ***\\n\");" << endl; out << " printf(\"*******************************\\n\");" << endl; out << " gROOT->Macro(\"PROOF-INF/SETUP.C\");" << endl; out << " } else {" << endl; out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/SETUP.C for package %s\", pkgdir.Data());" << endl; out << " gSystem->ChangeDirectory(cdir);" << endl; out << " return kFALSE;" << endl; out << " }" << endl; out << " // Restore original workdir" << endl; out << " gSystem->ChangeDirectory(cdir);" << endl; out << " return kTRUE;" << endl; out << "}" << endl; } } Bool_t copy = kTRUE; if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE; if (copy) { CdWork(); TString workdir = gGrid->GetHomeDirectory(); workdir += fGridWorkingDir; if (FileExists(mergingMacro)) gGrid->Rm(mergingMacro); Info("WriteMergingMacro", "\n##### Copying merging macro: <%s> to your alien workspace", mergingMacro.Data()); // TFile::Cp(Form("file:%s",mergingMacro.Data()), Form("alien://%s/%s", workdir.Data(), mergingMacro.Data())); if (!copyLocal2Alien("WriteMergeMacro",mergingMacro.Data(), Form("%s/%s", workdir.Data(), mergingMacro.Data()))) Fatal("","Terminating"); } } //______________________________________________________________________________ Bool_t AliAnalysisAlien::SetupPar(const char *package) { // 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(TString::Format("tar xzf %s.par", pkgdir.Data())); TString cdir = gSystem->WorkingDirectory(); gSystem->ChangeDirectory(pkgdir); // Check for BUILD.sh and execute if (!gSystem->AccessPathName("PROOF-INF/BUILD.sh")) { printf("**************************************************\n"); printf("*** Building PAR archive %s\n", package); printf("**************************************************\n"); if (gSystem->Exec("PROOF-INF/BUILD.sh")) { ::Error("SetupPar", "Cannot build par archive %s", pkgdir.Data()); gSystem->ChangeDirectory(cdir); return kFALSE; } } else { ::Error("SetupPar","Cannot access PROOF-INF/BUILD.sh for package %s", pkgdir.Data()); gSystem->ChangeDirectory(cdir); return kFALSE; } // Check for SETUP.C and execute if (!gSystem->AccessPathName("PROOF-INF/SETUP.C")) { printf("**************************************************\n"); printf("*** Setup PAR archive %s\n", package); printf("**************************************************\n"); gROOT->Macro("PROOF-INF/SETUP.C"); printf("*** Loaded library: %s\n", gSystem->GetLibraries(pkgdir,"",kFALSE)); } else { ::Error("SetupPar","Cannot access PROOF-INF/SETUP.C for package %s", pkgdir.Data()); gSystem->ChangeDirectory(cdir); return kFALSE; } // Restore original workdir gSystem->ChangeDirectory(cdir); return kTRUE; } //______________________________________________________________________________ void AliAnalysisAlien::WriteExecutable() { // Generate the alien executable script. // Patch executable with -x to catch error code if (fExecutableCommand.Contains("root") && fExecutableCommand.Contains("-q") && !fExecutableCommand.Contains("-x")) fExecutableCommand += " -x"; if (!TestBit(AliAnalysisGrid::kSubmit)) { ofstream out; out.open(fExecutable.Data(), ios::out); if (out.bad()) { Error("WriteExecutable", "Bad file name for executable: %s", fExecutable.Data()); 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; out << "echo \"############## LD_LIBRARY_PATH : ##############\"" << endl; out << "echo $LD_LIBRARY_PATH" << endl; out << "echo \"############## ROOTSYS : ##############\"" << endl; out << "echo $ROOTSYS" << endl; out << "echo \"############## which root : ##############\"" << endl; out << "which root" << endl; out << "echo \"############## ALICE_ROOT : ##############\"" << endl; out << "echo $ALICE_ROOT" << endl; out << "echo \"############## which aliroot : ##############\"" << endl; out << "which aliroot" << endl; out << "echo \"############## system limits : ##############\"" << endl; out << "ulimit -a" << endl; out << "echo \"############## memory : ##############\"" << endl; out << "free -m" << endl; out << "echo \"=========================================\"" << endl << endl; out << fExecutableCommand << " "; out << fAnalysisMacro.Data() << " " << fExecutableArgs.Data() << endl; out << "RET=$?" << endl; out << "if [ \"$RET\" != \"0\" ];then" << endl; out << " echo \"======== ERROR : " << fAnalysisMacro.Data() << " finished with NON zero code: $RET ========\"" << endl; out << " if [ \"$RET\" -gt 128 ] && [ \"$RET\" -lt 160 ]; then"<<endl; out << " let sig=\"$RET - 128\""<<endl; out << " sigs='HUP INT QUIT ILL TRAP ABRT BUS FPE"<<endl; out << " KILL USR1 SEGV USR2 PIPE ALRM TERM STKFLT"<<endl; out << " CHLD CONT STOP TSTP TTIN TTOU URG XCPU"<<endl; out << " XFSZ VTALRM PROF WINCH IO PWR SYS'"<<endl; out << " sig=SIG`echo $sigs | awk '{ print $'\"$sig\"' }'`"<<endl; out << " echo \"======== it appears to have been killed with signal: $sig ========\""<<endl; out << " fi"<<endl; out << " exit $RET"<< endl; out << "fi" << endl << endl ; out << "echo \"======== " << fAnalysisMacro.Data() << " finished with exit code: $RET ========\"" << endl; out << "echo \"############## memory after: ##############\"" << endl; out << "free -m" << endl; } Bool_t copy = kTRUE; if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE; if (copy) { CdWork(); TString workdir = gGrid->GetHomeDirectory(); workdir += fGridWorkingDir; TString executable = TString::Format("%s/%s", workdir.Data(), fExecutable.Data()); if (FileExists(executable)) gGrid->Rm(executable); Info("WriteExecutable", "\n##### Copying executable file <%s> to your AliEn bin directory", fExecutable.Data()); if (!copyLocal2Alien("WriteExecutable",fExecutable.Data(), executable.Data())) Fatal("","Terminating"); } } //______________________________________________________________________________ void AliAnalysisAlien::WriteMergeExecutable() { // Generate the alien executable script for the merging job. if (!fMergeViaJDL) return; TString mergeExec = fExecutable; mergeExec.ReplaceAll(".sh", "_merge.sh"); if (!TestBit(AliAnalysisGrid::kSubmit)) { ofstream out; out.open(mergeExec.Data(), ios::out); if (out.bad()) { Error("WriteMergingExecutable", "Bad file name for executable: %s", mergeExec.Data()); return; } out << "#!/bin/bash" << endl; // Make sure we can properly compile par files out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl; out << "echo \"=========================================\"" << endl; out << "echo \"############## PATH : ##############\"" << endl; out << "echo $PATH" << endl; out << "echo \"############## LD_LIBRARY_PATH : ##############\"" << endl; out << "echo $LD_LIBRARY_PATH" << endl; out << "echo \"############## ROOTSYS : ##############\"" << endl; out << "echo $ROOTSYS" << endl; out << "echo \"############## which root : ##############\"" << endl; out << "which root" << endl; out << "echo \"############## ALICE_ROOT : ##############\"" << endl; out << "echo $ALICE_ROOT" << endl; out << "echo \"############## which aliroot : ##############\"" << endl; out << "which aliroot" << endl; out << "echo \"############## system limits : ##############\"" << endl; out << "ulimit -a" << endl; out << "echo \"############## memory : ##############\"" << endl; out << "free -m" << endl; out << "echo \"=========================================\"" << endl << endl; TString mergeMacro = fExecutable; mergeMacro.ReplaceAll(".sh", "_merge.C"); if (IsOneStageMerging()) out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\")\"" << endl; else out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\",$2)\"" << endl; out << fExecutableCommand << " " << "$ARG" << endl; out << "RET=$?" << endl; out << "if [ \"$RET\" != \"0\" ];then" << endl; out << " echo \"======== ERROR : " << fAnalysisMacro.Data() << " finished with NON zero code: $RET ========\"" << endl; out << " if [ \"$RET\" -gt 128 ] && [ \"$RET\" -lt 160 ]; then"<<endl; out << " let sig=\"$RET - 128\""<<endl; out << " sigs='HUP INT QUIT ILL TRAP ABRT BUS FPE"<<endl; out << " KILL USR1 SEGV USR2 PIPE ALRM TERM STKFLT"<<endl; out << " CHLD CONT STOP TSTP TTIN TTOU URG XCPU"<<endl; out << " XFSZ VTALRM PROF WINCH IO PWR SYS'"<<endl; out << " sig=SIG`echo $sigs | awk '{ print $'\"$sig\"' }'`"<<endl; out << " echo \"======== it appears to have been killed with signal: $sig ========\""<<endl; out << " fi"<<endl; out << " exit $RET"<< endl; out << "fi" << endl << endl ; out << "echo \"======== " << mergeMacro.Data() << " finished with exit code: $? ========\"" << endl; out << "echo \"############## memory after: ##############\"" << endl; out << "free -m" << endl; } Bool_t copy = kTRUE; if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE; if (copy) { CdWork(); TString workdir = gGrid->GetHomeDirectory(); workdir += fGridWorkingDir; TString executable = TString::Format("%s/%s", workdir.Data(), mergeExec.Data()); if (FileExists(executable)) gGrid->Rm(executable); Info("WriteMergeExecutable", "\n##### Copying executable file <%s> to your AliEn bin directory", mergeExec.Data()); if (!copyLocal2Alien("WriteMergeExecutable",mergeExec.Data(), executable.Data())) Fatal("","Terminating"); } } //______________________________________________________________________________ void AliAnalysisAlien::WriteProductionFile(const char *filename) const { // Write the production file to be submitted by LPM manager. The format is: // First line: full_path_to_jdl estimated_no_subjobs_per_master // Next lines: full_path_to_dataset XXX (XXX is a string) // To submit, one has to: submit jdl XXX for all lines ofstream out; out.open(filename, ios::out); if (out.bad()) { Error("WriteProductionFile", "Bad file name: %s", filename); return; } 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()); out << locjdl << " " << njobspermaster << endl; Int_t nmasterjobs = fInputFiles->GetEntries(); for (Int_t i=0; i<nmasterjobs; i++) { TString runOutDir = gSystem->BaseName(fInputFiles->At(i)->GetName()); runOutDir.ReplaceAll(".xml", ""); if (fOutputToRunNo) out << Form("%s", fInputFiles->At(i)->GetName()) << " " << runOutDir << endl; else out << Form("%s", fInputFiles->At(i)->GetName()) << " " << Form("%03d", i) << endl; } 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)); if (!copyLocal2Alien("WriteProductionFile", filename, Form("%s/%s", workdir.Data(),filename))) Fatal("","Terminating"); } } //______________________________________________________________________________ void AliAnalysisAlien::WriteValidationScript(Bool_t merge) { // Generate the alien validation script. // Generate the validation script TObjString *os; 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)) { ofstream out; out.open(validationScript, ios::out); out << "#!/bin/bash" << endl; out << "##################################################" << endl; out << "validateout=`dirname $0`" << endl; out << "validatetime=`date`" << endl; out << "validated=\"0\";" << endl; out << "error=0" << endl; out << "if [ -z $validateout ]" << endl; out << "then" << endl; out << " validateout=\".\"" << endl; out << "fi" << endl << endl; out << "cd $validateout;" << endl; out << "validateworkdir=`pwd`;" << endl << endl; out << "echo \"*******************************************************\"" << outStream << endl; out << "echo \"* Automatically generated validation script *\"" << outStream << endl; out << "" << endl; out << "echo \"* Time: $validatetime \"" << outStream << endl; out << "echo \"* Dir: $validateout\"" << outStream << endl; out << "echo \"* Workdir: $validateworkdir\"" << outStream << endl; out << "echo \"* ----------------------------------------------------*\"" << outStream << endl; out << "ls -la ./" << outStream << endl; out << "echo \"* ----------------------------------------------------*\"" << outStream << endl << endl; out << "##################################################" << endl; out << "" << endl; out << "if [ ! -f stderr ] ; then" << endl; out << " error=1" << endl; out << " echo \"* ########## Job not validated - no stderr ###\" " << outStream << endl; out << " echo \"Error = $error\" " << outStream << endl; out << "fi" << endl; out << "parArch=`grep -Ei \"Cannot Build the PAR Archive\" stderr`" << endl; out << "segViol=`grep -Ei \"Segmentation violation\" stderr`" << endl; out << "segFault=`grep -Ei \"Segmentation fault\" stderr`" << endl; out << "glibcErr=`grep -Ei '\\*\\*\\* glibc detected \\*\\*\\*' stderr`" << endl; out << "" << endl; out << "if [ \"$parArch\" != \"\" ] ; then" << endl; out << " error=1" << endl; out << " echo \"* ########## Job not validated - PAR archive not built ###\" " << outStream << endl; out << " echo \"$parArch\" " << outStream << endl; out << " echo \"Error = $error\" " << outStream << endl; out << "fi" << endl; out << "if [ \"$segViol\" != \"\" ] ; then" << endl; out << " error=1" << endl; out << " echo \"* ########## Job not validated - Segment. violation ###\" " << outStream << endl; out << " echo \"$segViol\" " << outStream << endl; out << " echo \"Error = $error\" " << outStream << endl; out << "fi" << endl; out << "if [ \"$segFault\" != \"\" ] ; then" << endl; out << " error=1" << endl; out << " echo \"* ########## Job not validated - Segment. fault ###\" " << outStream << endl; out << " echo \"$segFault\" " << outStream << endl; out << " echo \"Error = $error\" " << outStream << endl; out << "fi" << endl; out << "if [ \"$glibcErr\" != \"\" ] ; then" << endl; out << " error=1" << endl; out << " echo \"* ########## Job not validated - *** glibc detected *** ###\" " << outStream << endl; out << " echo \"$glibcErr\" " << outStream << endl; out << " echo \"Error = $error\" " << outStream << endl; out << "fi" << endl; // Part dedicated to the specific analyses running into the train TString outputFiles = fOutputFiles; if (merge && !fTerminateFiles.IsNull()) { if (!outputFiles.IsNull()) outputFiles += ","; outputFiles += fTerminateFiles; } TObjArray *arr = outputFiles.Tokenize(","); TIter next1(arr); TString outputFile; 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 (fTerminateFiles.Contains(outputFile)) continue; if (outputFile.Contains("*")) continue; out << "if ! [ -f " << outputFile.Data() << " ] ; then" << endl; out << " error=1" << 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; 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; if (!IsKeepLogs()) { out << " echo \"* === Logs std* will be deleted === \"" << endl; outStream = ""; out << " rm -f std*" << endl; } out << "fi" << endl; out << "echo \"* ----------------------------------------------------*\"" << outStream << endl; out << "echo \"*******************************************************\"" << outStream << endl; out << "cd -" << endl; out << "exit $error" << endl; } Bool_t copy = kTRUE; if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE; if (copy) { CdWork(); TString workdir = gGrid->GetHomeDirectory(); workdir += fGridWorkingDir; 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())); if (!copyLocal2Alien("WriteValidationScript", validationScript.Data(), Form("%s/%s",workdir.Data(), validationScript.Data()))) Fatal("","Terminating"); } }
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