// 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 "TGridJobStatus.h"
#include "TFileMerger.h"
#include "AliAnalysisManager.h"
+#include "AliAnalysisTaskCfg.h"
#include "AliVEventHandler.h"
#include "AliAnalysisDataContainer.h"
-#include "AliAnalysisAlien.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(),
fNproofWorkers(0),
fNproofWorkersPerSlave(0),
fProofReset(0),
+ fNMCevents(0),
+ fNMCjobs(0),
fRunNumbers(),
fExecutable(),
fExecutableCommand(),
fValidationScript(),
fAdditionalRootLibs(),
fAdditionalLibs(),
+ fGeneratorLibs(),
fSplitMode(),
fAPIVersion(),
fROOTVersion(),
fJDLName(),
fTerminateFiles(),
fMergeExcludes(),
+ fRegisterExcludes(),
fIncludePath(),
fCloseSE(),
fFriendChainName(),
fProofCluster(),
fProofDataSet(),
fFileForTestMode(),
- fRootVersionForProof(),
fAliRootMode(),
+ fProofProcessOpt(),
fMergeDirName(),
fInputFiles(0),
- fPackages(0)
+ fPackages(0),
+ fModules(0),
+ fProofParam(),
+ fDropToShell(true),
+ fMCLoop(false),
+ fGridJobIDs(""),
+ fGridStages(""),
+ fFriendLibs(""),
+ fTreeName()
{
// Dummy ctor.
SetDefaults();
fNproofWorkers(0),
fNproofWorkersPerSlave(0),
fProofReset(0),
+ fNMCevents(0),
+ fNMCjobs(0),
fRunNumbers(),
fExecutable(),
fExecutableCommand(),
fValidationScript(),
fAdditionalRootLibs(),
fAdditionalLibs(),
+ fGeneratorLibs(),
fSplitMode(),
fAPIVersion(),
fROOTVersion(),
fJDLName(),
fTerminateFiles(),
fMergeExcludes(),
+ fRegisterExcludes(),
fIncludePath(),
fCloseSE(),
fFriendChainName(),
fProofCluster(),
fProofDataSet(),
fFileForTestMode(),
- fRootVersionForProof(),
fAliRootMode(),
+ fProofProcessOpt(),
fMergeDirName(),
fInputFiles(0),
- fPackages(0)
+ fPackages(0),
+ fModules(0),
+ fProofParam(),
+ fDropToShell(true),
+ fMCLoop(false),
+ fGridJobIDs(""),
+ fGridStages(""),
+ fFriendLibs(""),
+ fTreeName()
{
// Default ctor.
SetDefaults();
fNproofWorkers(other.fNproofWorkers),
fNproofWorkersPerSlave(other.fNproofWorkersPerSlave),
fProofReset(other.fProofReset),
+ fNMCevents(other.fNMCevents),
+ fNMCjobs(other.fNMCjobs),
fRunNumbers(other.fRunNumbers),
fExecutable(other.fExecutable),
fExecutableCommand(other.fExecutableCommand),
fValidationScript(other.fValidationScript),
fAdditionalRootLibs(other.fAdditionalRootLibs),
fAdditionalLibs(other.fAdditionalLibs),
+ fGeneratorLibs(other.fGeneratorLibs),
fSplitMode(other.fSplitMode),
fAPIVersion(other.fAPIVersion),
fROOTVersion(other.fROOTVersion),
fJDLName(other.fJDLName),
fTerminateFiles(other.fTerminateFiles),
fMergeExcludes(other.fMergeExcludes),
+ fRegisterExcludes(other.fRegisterExcludes),
fIncludePath(other.fIncludePath),
fCloseSE(other.fCloseSE),
fFriendChainName(other.fFriendChainName),
fProofCluster(other.fProofCluster),
fProofDataSet(other.fProofDataSet),
fFileForTestMode(other.fFileForTestMode),
- fRootVersionForProof(other.fRootVersionForProof),
fAliRootMode(other.fAliRootMode),
+ fProofProcessOpt(other.fProofProcessOpt),
fMergeDirName(other.fMergeDirName),
fInputFiles(0),
- fPackages(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()");
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.
- if (fGridJDL) delete fGridJDL;
- if (fMergingJDL) delete fMergingJDL;
- if (fInputFiles) delete fInputFiles;
- if (fPackages) delete fPackages;
+ delete fGridJDL;
+ delete fMergingJDL;
+ delete fInputFiles;
+ delete fPackages;
+ delete fModules;
+ fProofParam.DeleteAll();
}
//______________________________________________________________________________
fNproofWorkers = other.fNproofWorkers;
fNproofWorkersPerSlave = other.fNproofWorkersPerSlave;
fProofReset = other.fProofReset;
+ fNMCevents = other.fNMCevents;
+ fNMCjobs = other.fNMCjobs;
fRunNumbers = other.fRunNumbers;
fExecutable = other.fExecutable;
fExecutableCommand = other.fExecutableCommand;
fValidationScript = other.fValidationScript;
fAdditionalRootLibs = other.fAdditionalRootLibs;
fAdditionalLibs = other.fAdditionalLibs;
+ fGeneratorLibs = other.fGeneratorLibs;
fSplitMode = other.fSplitMode;
fAPIVersion = other.fAPIVersion;
fROOTVersion = other.fROOTVersion;
fJDLName = other.fJDLName;
fTerminateFiles = other.fTerminateFiles;
fMergeExcludes = other.fMergeExcludes;
+ fRegisterExcludes = other.fRegisterExcludes;
fIncludePath = other.fIncludePath;
fCloseSE = other.fCloseSE;
fFriendChainName = other.fFriendChainName;
fProofCluster = other.fProofCluster;
fProofDataSet = other.fProofDataSet;
fFileForTestMode = other.fFileForTestMode;
- fRootVersionForProof = other.fRootVersionForProof;
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);
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)
{
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.
- if (fRunNumbers.Length()) fRunNumbers += " ";
- fRunNumbers += run;
+ 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;
}
//______________________________________________________________________________
{
// 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;
Error("CheckFileCopy", "Alien path %s does not seem to exist", alienpath);
return kFALSE;
}
- TFile f("plugin_test_copy", "RECREATE");
+ 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> ?",
return kFALSE;
}
f.Close();
- if (FileExists(Form("alien://%s/%s",alienpath, f.GetName()))) gGrid->Rm(Form("alien://%s/%s",alienpath, f.GetName()));
- if (!TFile::Cp(f.GetName(), Form("alien://%s/%s",alienpath, f.GetName()))) {
+ 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(f.GetName());
+ gSystem->Unlink(stest.Data());
return kFALSE;
}
- gSystem->Unlink(f.GetName());
- gGrid->Rm(Form("%s%s",alienpath,f.GetName()));
+ gSystem->Unlink(stest.Data());
+ gGrid->Rm(Form("%s/%s",alienpath,stest.Data()));
Info("CheckFileCopy", "### ...SUCCESS ###");
return kTRUE;
}
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;
}
+//______________________________________________________________________________
+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");
// 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;
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));
- if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
- command = "find ";
- command += options;
- command += path;
- command += " ";
- 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(); > %s", 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 /event %s 2>/dev/null > /dev/null",file.Data()))==0)?kFALSE:kTRUE;
- if (nullFile) {
- Error("CreateDataset","Dataset %s produced by the previous find command is empty !", file.Data());
- return kFALSE;
+ // 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)) {
TObjString *os;
TIter next(arr);
while ((os=(TObjString*)next())) {
- path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data());
+ 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.
- if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
- command = "find ";
- command += options;
- command += path;
- command += pattern;
- command += conditions;
- TGridResult *res = gGrid->Command(command);
- if (res) delete res;
- // Write standard output to file
- gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", 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 /event %s 2>/dev/null > /dev/null",file.Data()))==0)?kFALSE:kTRUE;
- if (nullFile) {
- Warning("CreateDataset","Dataset %s produced by: <%s> is empty !", file.Data(), command.Data());
- fRunNumbers.ReplaceAll(os->GetString().Data(), "");
- continue;
+ 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;
}
- nullResult = kFALSE;
- }
+ }
if (TestBit(AliAnalysisGrid::kTest)) break;
// Check if there is one run per master job.
if (fNrunsPerMaster<2) {
} else {
cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
printf(" Merging collection <%s> into masterjob input...\n", file.Data());
- cbase->Add(cadd);
+ // 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()) {
} else {
// Process a full run range.
for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
- format = Form("%%s/%s ", fRunPrefix.Data());
+ format = Form("%%s/%s", fRunPrefix.Data());
+ nstart = 0;
+ stage = 0;
path = Form(format.Data(), fGridDataDir.Data(), irun);
if (!DirectoryExists(path)) continue;
// CdWork();
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.
- if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
- command = "find ";
- command += options;
- command += path;
- command += pattern;
- command += conditions;
- TGridResult *res = gGrid->Command(command);
- if (res) delete res;
- // Write standard output to file
- gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", 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 /event %s 2>/dev/null > /dev/null",file.Data()))==0)?kFALSE:kTRUE;
- if (nullFile) {
- Warning("CreateDataset","Dataset %s produced by: <%s> is empty !", file.Data(), command.Data());
- continue;
+ 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;
}
- nullResult = kFALSE;
}
if (TestBit(AliAnalysisGrid::kTest)) break;
// Check if there is one run per master job.
cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
} else {
cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
- cbase->Add(cadd);
+ // 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());
{
// 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;
workdir += fGridWorkingDir;
if (generate) {
TObjString *os;
- if (!fInputFiles) {
+ if (!fInputFiles && !fMCLoop) {
Error("CreateJDL()", "Define some input files for your analysis.");
error = kTRUE;
}
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);
}
if (!fUser.IsNull()) {
fGridJDL->SetValue("User", Form("\"%s\"", fUser.Data()));
fMergingJDL->SetValue("User", Form("\"%s\"", fUser.Data()));
- }
- fGridJDL->SetExecutable(fExecutable, "This is the startup script");
- TString mergeExec = fExecutable;
+ }
+ 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/%s", workdir.Data(),mergeExec.Data()), "List of input files to be uploaded to workers");
+ 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);
fGridJDL->SetValue("MaxInitFailed", Form("\"%d\"",fMaxInitFailed));
fGridJDL->SetDescription("MaxInitFailed", "Maximum number of first failing jobs to abort the master job");
}
- if (fSplitMaxInputFileNumber > 0) {
+ if (fSplitMaxInputFileNumber > 0 && !fMCLoop) {
fGridJDL->SetValue("SplitMaxInputFileNumber", Form("\"%d\"", fSplitMaxInputFileNumber));
fGridJDL->SetDescription("SplitMaxInputFileNumber", "Maximum number of input files to be processed per subjob");
}
}
delete arr;
}
- fGridJDL->SetInputDataListFormat(fInputFormat, "Format of input data");
- fGridJDL->SetInputDataList("wn.xml", "Collection name to be processed on each worker node");
+ 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");
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 (IsUsingTags() && !gSystem->AccessPathName("ConfigureCuts.C"))
- fGridJDL->AddToInputSandbox(Form("LF:%s/ConfigureCuts.C", workdir.Data()));
if (fAdditionalLibs.Length()) {
arr = fAdditionalLibs.Tokenize(" ");
TIter next(arr);
while ((os=(TObjString*)next())) {
- if (os->GetString().Contains(".so")) continue;
+ 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()));
}
fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName()));
}
}
+ const char *comment = "List of output files and archives";
if (fOutputArchive.Length()) {
- arr = fOutputArchive.Tokenize(" ");
+ 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;
- const char *comment = "Files to be archived";
- const char *comment1 = comment;
while ((os=(TObjString*)next())) {
- if (!first) comment = NULL;
if (!os->GetString().Contains("@") && fCloseSE.Length())
- fGridJDL->AddToOutputArchive(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
+ fGridJDL->AddToSet("Output", Form("%s@%s",os->GetString().Data(), fCloseSE.Data()));
else
- fGridJDL->AddToOutputArchive(os->GetString(), comment);
+ fGridJDL->AddToSet("Output", os->GetString());
+ if (first) fGridJDL->AddToSetDescription("Output", comment);
first = kFALSE;
}
delete arr;
// Output archive for the merging jdl
- TString outputArchive;
if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
outputArchive = "log_archive.zip:std*@disk=1 ";
// Add normal output files, extra files + terminate files
- TString files = GetListOfFiles("outextter");
- // Do not register merge excludes
- if (!fMergeExcludes.IsNull()) {
- arr = fMergeExcludes.Tokenize(" ");
+ 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()),"");
delete arr;
}
files.ReplaceAll(".root", "*.root");
- outputArchive += Form("root_archive.zip:%s,*.stat@disk=%d",files.Data(),fNreplicas);
+
+ 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
}
arr = outputArchive.Tokenize(" ");
TIter next2(arr);
- comment = comment1;
first = kTRUE;
while ((os=(TObjString*)next2())) {
- if (!first) comment = NULL;
TString currentfile = os->GetString();
if (!currentfile.Contains("@") && fCloseSE.Length())
- fMergingJDL->AddToOutputArchive(Form("%s@%s",currentfile.Data(), fCloseSE.Data()), comment);
+ fMergingJDL->AddToSet("Output", Form("%s@%s",currentfile.Data(), fCloseSE.Data()));
else
- fMergingJDL->AddToOutputArchive(currentfile, comment);
+ fMergingJDL->AddToSet("Output", currentfile);
+ if (first) fMergingJDL->AddToSetDescription("Output", comment);
first = kFALSE;
}
delete arr;
arr = fOutputFiles.Tokenize(",");
TIter next(arr);
Bool_t first = kTRUE;
- const char *comment = "Files to be saved";
while ((os=(TObjString*)next())) {
// Ignore ouputs in jdl that are also in outputarchive
TString sout = os->GetString();
sout.ReplaceAll(".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->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
+ fGridJDL->AddToSet("Output", Form("%s@%s",os->GetString().Data(), fCloseSE.Data()));
else
- fGridJDL->AddToOutputSandbox(os->GetString(), comment);
- first = kFALSE;
+ fGridJDL->AddToSet("Output", os->GetString());
+ if (first) fGridJDL->AddToSetDescription("Output", comment);
if (fMergeExcludes.Contains(sout)) continue;
if (!os->GetString().Contains("@") && fCloseSE.Length())
- fMergingJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
+ fMergingJDL->AddToSet("Output", Form("%s@%s",os->GetString().Data(), fCloseSE.Data()));
else
- fMergingJDL->AddToOutputSandbox(os->GetString(), comment);
+ 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");
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());
- TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.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()));
+// TFile::Cp(Form("file:%s",mergeJDLName.Data()), Form("alien://%s", locjdl1.Data()));
+ if (!copyLocal2Alien("CreateJDL", mergeJDLName.Data(), locjdl1))
+ Fatal("","Terminating");
}
}
if (fAdditionalLibs.Length()) {
TObjString *os;
TIter next(arr);
while ((os=(TObjString*)next())) {
- if (os->GetString().Contains(".so")) continue;
+ 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()));
+// 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;
}
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()));
+// 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");
}
}
}
// 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) return kFALSE;
+ if (!fInputFiles && !fMCLoop) return kFALSE;
TObject *os;
TString workdir;
if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice")) workdir = gGrid->GetHomeDirectory();
while ((os=next())) {
fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetName()), "Input xml collections");
}
- fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_04i#", fGridOutputDir.Data()));
+ 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.
fGridJDL->SetOutputDirectory(Form("#alienfulldir#/../%s",fOutputSingle.Data()), "Output directory");
else {
fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
- fMergingJDL->SetOutputDirectory(fGridOutputDir);
+// fMergingJDL->SetOutputDirectory(fGridOutputDir);
}
} else {
// One jdl to be submitted with 2 input parameters: data collection name and output dir prefix
}
TString sjdl2 = fMergingJDL->Generate();
Int_t index, index1;
- sjdl.ReplaceAll("\"LF:", "\n \"LF:");
+ sjdl.ReplaceAll("\",\"", "\",\n \"");
sjdl.ReplaceAll("(member", "\n (member");
sjdl.ReplaceAll("\",\"VO_", "\",\n \"VO_");
sjdl.ReplaceAll("{", "{\n ");
sjdl.ReplaceAll("{\n \n", "{\n");
sjdl.ReplaceAll("\n\n", "\n");
sjdl.ReplaceAll("OutputDirectory", "OutputDir");
- sjdl1.ReplaceAll("\"LF:", "\n \"LF:");
+ sjdl1.ReplaceAll("\",\"", "\",\n \"");
sjdl1.ReplaceAll("(member", "\n (member");
sjdl1.ReplaceAll("\",\"VO_", "\",\n \"VO_");
sjdl1.ReplaceAll("{", "{\n ");
sjdl1.ReplaceAll("{\n \n", "{\n");
sjdl1.ReplaceAll("\n\n", "\n");
sjdl1.ReplaceAll("OutputDirectory", "OutputDir");
- sjdl2.ReplaceAll("\"LF:", "\n \"LF:");
+ sjdl2.ReplaceAll("\",\"", "\",\n \"");
sjdl2.ReplaceAll("(member", "\n (member");
sjdl2.ReplaceAll("\",\"VO_", "\",\n \"VO_");
sjdl2.ReplaceAll("{", "{\n ");
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()));
+// 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()));
+// 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::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;
- // Check if dirname is a path
- TString dirstripped = dirname;
- dirstripped = dirstripped.Strip();
- dirstripped = dirstripped.Strip(TString::kTrailing, '/');
- TString dir = gSystem->BaseName(dirstripped);
- dir += "/";
- TString path = gSystem->DirName(dirstripped);
- TGridResult *res = gGrid->Ls(path, "-F");
- if (!res) return kFALSE;
- TIter next(res);
- TMap *map;
- TObject *obj;
- while ((map=dynamic_cast<TMap*>(next()))) {
- obj = map->GetValue("name");
- if (!obj) break;
- if (dir == obj->GetName()) {
- delete res;
- return kTRUE;
- }
+ // 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 kFALSE;
-}
+ return retval;
+}
//______________________________________________________________________________
void AliAnalysisAlien::CheckDataType(const char *lfn, Bool_t &isCollection, Bool_t &isXml, Bool_t &useTags)
in.open(fFileForTestMode);
Int_t count = 0;
// Read the input list of files and add them to the chain
- TString line;
- TChain *chain = new TChain(treeName);
- while (in.good())
- {
+ 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()) continue;
+ if (line.IsNull() || line.BeginsWith("#")) continue;
if (count++ == fNtestFiles) break;
TString esdFile(line);
TFile *file = TFile::Open(esdFile);
- if (file) {
- if (!file->IsZombie()) chain->Add(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()) {
+ }
+ 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;
- }
-// chain->ls();
- return chain;
+ }
+ return chain;
}
//______________________________________________________________________________
// 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
{
printf("= Soft reset signal will be send to master______ CHANGE BEHAVIOR AFTER COMPLETION\n");
if (fProofReset>1)
printf("= Hard reset signal will be send to master______ CHANGE BEHAVIOR AFTER COMPLETION\n");
- if (!fRootVersionForProof.IsNull())
- printf("= ROOT version requested________________________ %s\n", fRootVersionForProof.Data());
+ 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());
\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");
+ 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("= 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());
- printf("= Data base directory path requested: __________ %s\n", fGridDataDir.Data());
- printf("= Data search pattern: _________________________ %s\n", fDataPattern.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());
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);
fMaxMergeFiles = 100;
fRunNumbers = "";
fExecutable = "analysis.sh";
- fExecutableCommand = "root -b -q";
+ fExecutableCommand = "root -b -q -x";
fArguments = "";
fExecutableArgs = "";
fAnalysisMacro = "myAnalysis.C";
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)
{
}
// 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));
+// 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);
- Int_t jobId = SubmitSingleJob(query);
- if (!jobId) return kFALSE;
+ jobId = SubmitSingleJob(query);
} else {
printf("### Submiting merging stage %d\n", stage);
TString query = Form("submit %s %s %d", jdl, aliendir, stage);
- Int_t jobId = SubmitSingleJob(query);
- if (!jobId) return kFALSE;
+ 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)
{
::Error("SubmitSingleJob", "Your query %s could not be submitted", query);
return 0;
}
- printf(" Job id: %s\n", jobId.Data());
- return atoi(jobId);
+ 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)
{
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;
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());
// Loop 'find' results and get next LFN
if (countZero == nmaxmerge) {
// First file in chunk - create file merger and add previous chunk if any.
- fm = new TFileMerger(kFALSE);
+ fm = new TFileMerger(isGrid);
fm->SetFastMethod(kTRUE);
if (previousChunk.Length()) fm->AddFile(previousChunk.Data());
outputChunk = outputFile;
}
// Merging stage different than 0.
// Move to the begining of the requested chunk.
- fm = new TFileMerger(kFALSE);
+ fm = new TFileMerger(isGrid);
fm->SetFastMethod(kTRUE);
while ((nextfile=next())) fm->AddFile(nextfile->GetName());
delete listoffiles;
return kFALSE;
}
// Get the output path
- if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
+ 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;
}
// 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;
gSystem->Exec(Form("rm -f %s", outputChunk.Data()));
}
}
- if (fMergeExcludes.Length() &&
- fMergeExcludes.Contains(outputFile.Data())) continue;
+ 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");
- return kFALSE;
+ delete list;
+ return kFALSE;
}
TFile *fileOpened = (TFile*)gROOT->GetListOfFiles()->FindObject(outputFile);
if (fileOpened) fileOpened->Close();
}
+ delete list;
return kTRUE;
}
}
//______________________________________________________________________________
-void AliAnalysisAlien::SetPreferedSE(const char */*se*/)
+void AliAnalysisAlien::SetProofParameter(const char *pname, const char *value)
{
-// Setting a prefered output SE is not allowed anymore.
- Warning("SetPreferedSE", "Setting a preferential SE is not allowed anymore via the plugin. Use SetNumberOfReplicas() and SetDefaultOutputs()");
+// 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*/)
{
}
// Are we in PROOF mode ?
if (mgr->IsProofMode()) {
- Info("StartAnalysis", "##### Starting PROOF analysis on cluster <%s> via the plugin #####", fProofCluster.Data());
+ 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;
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 (!fRootVersionForProof.IsNull() && !testMode) {
- gROOT->ProcessLine(Form("TProof::Mgr(\"%s\")->SetROOTVersion(\"%s\");",
- fProofCluster.Data(), fRootVersionForProof.Data()));
+ 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;
}
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;
// Check the additional libs to be loaded
TString extraLibs;
Bool_t parMode = kFALSE;
- if (!alirootMode.IsNull()) extraLibs = "ANALYSIS:ANALYSISalice";
- // Parse the extra libs for .so
+ if (!alirootMode.IsNull()) extraLibs = "ANALYSIS:OADB:ANALYSISalice";
+ // Parse the extra libs for .so or .dylib
if (fAdditionalLibs.Length()) {
- TObjArray *list = fAdditionalLibs.Tokenize(" ");
+ 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")) {
+ 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 (list) delete list;
}
- if (!extraLibs.IsNull()) optionsList.Add(new TNamed("ALIROOT_EXTRA_LIBS",extraLibs.Data()));
+ 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("${ALICE_ROOT}","");
+ includePath.ReplaceAll("$ALICE_ROOT/","");
+ includePath.ReplaceAll("${ALICE_ROOT}/","");
includePath.ReplaceAll("-I","");
- includePath.Strip(TString::kTrailing, ':');
+ includePath.Remove(TString::kTrailing, ':');
Info("StartAnalysis", "Adding extra includes: %s",includePath.Data());
optionsList.Add(new TNamed("ALIROOT_EXTRA_INCLUDES",includePath.Data()));
}
return kFALSE;
}
} else {
- if (gROOT->ProcessLine(Form("gProof->EnablePackage(\"VO_ALICE@AliRoot::%s\", (TList*)%p, kTRUE);",
- fAliROOTVersion.Data(), &optionsList))) {
- Error("StartAnalysis", "There was an error trying to enable package VO_ALICE@AliRoot::%s", fAliROOTVersion.Data());
- return kFALSE;
- }
+ 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()) {
if (list) delete list;
}
} else {
- if (fAdditionalLibs.Contains(".so") && !testMode) {
+ 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;
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->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;
TObjString *str;
while((str=(TObjString*)next())) {
gROOT->ProcessLine(Form("gProof->Load(\"%s+g\", kTRUE);", str->GetName()));
- }
+ }
if (list) delete list;
}
if (testMode) {
}
// Compose the output archive.
fOutputArchive = "log_archive.zip:std*@disk=1 ";
- fOutputArchive += Form("root_archive.zip:%s,*.stat@disk=%d",fOutputFiles.Data(),fNreplicas);
+ 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)) {
Error("StartAnalysis", "No data to process. Please fix %s in your plugin configuration.", serror.Data());
return kFALSE;
}
- WriteAnalysisFile();
+ WriteAnalysisFile();
WriteAnalysisMacro();
WriteExecutable();
WriteValidationScript();
}
// Check if submitting is managed by LPM manager
if (fProductionMode) {
- TString prodfile = fJDLName;
- prodfile.ReplaceAll(".jdl", ".prod");
- WriteProductionFile(prodfile);
+ //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;
}
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()));
\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 {
} else {
// Submit for a range of enumeration of runs.
if (!Submit()) return kFALSE;
+ jobID = fGridJobIDs;
}
- 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");
+ 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;
}
return files.Data();
}
if (mgr->GetOutputEventHandler()) {
- aodfiles = mgr->GetOutputEventHandler()->GetOutputFileName();
- TString extraaod = mgr->GetOutputEventHandler()->GetExtraOutputs();
- if (!extraaod.IsNull()) {
- aodfiles += ",";
+ 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 (!(strcmp(filename, "default"))) continue;
if (outputfiles.Contains(filename)) continue;
if (aodfiles.Contains(filename)) continue;
- if (!outputfiles.IsNull()) outputfiles += ",";
+ if (!outputfiles.IsNull() && strlen(filename)) outputfiles += ",";
outputfiles += filename;
}
if (stype.Contains("out")) {
- if (!files.IsNull()) files += ",";
+ if (!files.IsNull() && !outputfiles.IsNull()) files += ",";
files += outputfiles;
if (stype == "out") return files.Data();
}
}
delete fextra;
if (stype.Contains("ext")) {
- if (!files.IsNull()) files += ",";
+ if (!files.IsNull() && !sextra.IsNull()) files += ",";
files += sextra;
}
}
Bool_t AliAnalysisAlien::SubmitMerging()
{
// Submit all merging jobs.
- if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
+ 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());
printf("### Submitting merging job for run <%s>\n", runOutDir.Data());
runOutDir = Form("%s/%s", fGridOutputDir.Data(), runOutDir.Data());
} 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);
+ 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(",");
outputFile = str->GetString();
Int_t index = outputFile.Index("@");
if (index > 0) outputFile.Remove(index);
- if (!fMergeExcludes.Contains(outputFile)) break;
+ if (!fMergeExcludes.Contains(outputFile) &&
+ !fRegisterExcludes.Contains(outputFile)) break;
}
delete list;
Bool_t done = CheckMergedFiles(outputFile, runOutDir, fMaxMergeFiles, mergeJDLName);
- if (!done) return kFALSE;
+ if (!done && (i==ntosubmit-1)) return kFALSE;
+ if (!fRunNumbers.Length() && !fRunRange[0]) break;
}
if (!ntosubmit) return kTRUE;
- Info("StartAnalysis", "\n#### STARTING AN ALIEN SHELL FOR YOU. EXIT WHEN YOUR MERGING JOBS HAVE FINISHED. #### \
- \n You may exit at any time and terminate the job later using the option <terminate> but disabling SetMergeViaJDL\
- \n ##################################################################################");
- gSystem->Exec("aliensh");
+ 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;
}
\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 (mgr->GetMCtruthEventHandler()) TObject::SetBit(AliAnalysisGrid::kUseMC);
handler = (TObject*)mgr->GetInputEventHandler();
if (handler) {
- if (handler->InheritsFrom("AliESDInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseESD);
- if (handler->InheritsFrom("AliAODInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseAOD);
+ if (handler->InheritsFrom("AliMultiInputEventHandler")) {
+ AliMultiInputEventHandler *multiIH = (AliMultiInputEventHandler*)handler;
+ if (multiIH->GetFirstInputEventHandler()->InheritsFrom("AliESDInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseESD);
+ if (multiIH->GetFirstInputEventHandler()->InheritsFrom("AliAODInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseAOD);
+ } else {
+ if (handler->InheritsFrom("AliESDInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseESD);
+ if (handler->InheritsFrom("AliAODInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseAOD);
+ }
}
TDirectory *cdir = gDirectory;
TFile *file = TFile::Open(analysisFile, "RECREATE");
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);
- TFile::Cp(Form("file:%s",analysisFile.Data()), Form("alien://%s/%s", workdir.Data(),analysisFile.Data()));
+ if (!copyLocal2Alien("WriteAnalysisFile",analysisFile.Data(),
+ Form("%s/%s", workdir.Data(),analysisFile.Data()))) Fatal("","Terminating");
}
}
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 (TObject::TestBit(AliAnalysisGrid::kUseESD)) comment += "ESD";
- if (TObject::TestBit(AliAnalysisGrid::kUseAOD)) {
- type = "AOD";
- comment += "AOD";
+ 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");
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;
TIter next(list);
TObjString *str;
while((str=(TObjString*)next())) {
- if (str->GetString().Contains(".so"))
+ if (str->GetString().Contains(".so") || str->GetString().Contains(".dylib"))
out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
}
if (list) delete list;
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 {
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" ||
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;
pkgname == "AOD.par" ||
pkgname == "ANALYSIS" ||
pkgname == "ANALYSIS.par" ||
+ pkgname == "OADB" ||
+ pkgname == "OADB.par" ||
pkgname == "ANALYSISalice" ||
pkgname == "ANALYSISalice.par" ||
pkgname == "CORRFW" ||
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;
- TObjArray *list = fAdditionalLibs.Tokenize(" ");
+ 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"))
+ 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;
}
- if (list) delete list;
+ delete list;
}
out << endl;
out << "// analysis source to be compiled at runtime (if any)" << endl;
out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",50);" << endl;
out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
- }
- out << "// connect to AliEn and make the chain" << endl;
- out << " if (!TGrid::Connect(\"alien://\")) return;" << endl;
+ }
out << "// read the analysis manager from file" << endl;
TString analysisFile = fExecutable;
analysisFile.ReplaceAll(".sh", ".root");
- out << " TFile *file = TFile::Open(\"" << analysisFile << "\");" << endl;
- out << " if (!file) return;" << endl;
- out << " TIter nextkey(file->GetListOfKeys());" << endl;
- out << " AliAnalysisManager *mgr = 0;" << endl;
- out << " TKey *key;" << endl;
- out << " while ((key=(TKey*)nextkey())) {" << endl;
- out << " if (!strcmp(key->GetClassName(), \"AliAnalysisManager\"))" << endl;
- out << " mgr = (AliAnalysisManager*)file->Get(key->GetName());" << endl;
- out << " };" << endl;
- out << " if (!mgr) {" << endl;
- out << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file " << analysisFile <<"\");" << endl;
- out << " return;" << endl;
- out << " }" << endl << endl;
+ 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 << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
}
}
- if (IsUsingTags()) {
- out << " TChain *chain = CreateChainFromTags(\"wn.xml\", anatype);" << endl << 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 {
- out << " TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl;
+ if (fMCLoop) {
+ out << " mgr->SetCacheSize(0);" << endl;
+ out << " mgr->EventLoop(" << fNMCevents << ");" << endl;
+ } else {
+ out << " mgr->StartAnalysis(\"localfile\");" << endl;
+ }
}
- out << " mgr->StartAnalysis(\"localfile\", chain);" << endl;
out << " timer.Stop();" << endl;
out << " timer.Print();" << endl;
out << "}" << endl << endl;
- if (IsUsingTags()) {
- out << "TChain* CreateChainFromTags(const char *xmlfile, const char *type=\"ESD\")" << endl;
- out << "{" << endl;
- out << "// Create a chain using tags from the xml file." << endl;
- out << " TAlienCollection* coll = TAlienCollection::Open(xmlfile);" << endl;
- out << " if (!coll) {" << endl;
- out << " ::Error(\"CreateChainFromTags\", \"Cannot create an AliEn collection from %s\", xmlfile);" << endl;
- out << " return NULL;" << endl;
- out << " }" << endl;
- out << " TGridResult* tagResult = coll->GetGridResult(\"\",kFALSE,kFALSE);" << endl;
- out << " AliTagAnalysis *tagAna = new AliTagAnalysis(type);" << endl;
- out << " tagAna->ChainGridTags(tagResult);" << endl << endl;
- out << " AliRunTagCuts *runCuts = new AliRunTagCuts();" << endl;
- out << " AliLHCTagCuts *lhcCuts = new AliLHCTagCuts();" << endl;
- out << " AliDetectorTagCuts *detCuts = new AliDetectorTagCuts();" << endl;
- out << " AliEventTagCuts *evCuts = new AliEventTagCuts();" << endl;
- out << " // Check if the cuts configuration file was provided" << endl;
- out << " if (!gSystem->AccessPathName(\"ConfigureCuts.C\")) {" << endl;
- out << " gROOT->LoadMacro(\"ConfigureCuts.C\");" << endl;
- out << " ConfigureCuts(runCuts, lhcCuts, detCuts, evCuts);" << endl;
- out << " }" << endl;
- if (fFriendChainName=="") {
- out << " TChain *chain = tagAna->QueryTags(runCuts, lhcCuts, detCuts, evCuts);" << endl;
- } else {
- out << " TString tmpColl=\"tmpCollection.xml\";" << endl;
- out << " tagAna->CreateXMLCollection(tmpColl.Data(),runCuts, lhcCuts, detCuts, evCuts);" << endl;
- out << " TChain *chain = CreateChain(tmpColl.Data(),type);" << endl;
- }
- out << " if (!chain || !chain->GetNtrees()) return NULL;" << endl;
- out << " chain->ls();" << endl;
- out << " return chain;" << endl;
- out << "}" << endl << endl;
- if (gSystem->AccessPathName("ConfigureCuts.C")) {
- TString msg = "\n##### You may want to provide a macro ConfigureCuts.C with a method:\n";
- msg += " void ConfigureCuts(AliRunTagCuts *runCuts,\n";
- msg += " AliLHCTagCuts *lhcCuts,\n";
- msg += " AliDetectorTagCuts *detCuts,\n";
- msg += " AliEventTagCuts *evCuts)";
- Info("WriteAnalysisMacro", "%s", msg.Data());
- }
- }
- if (!IsUsingTags() || fFriendChainName!="") {
+ 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;
- out << " TString treename = type;" << endl;
- out << " treename.ToLower();" << endl;
- out << " treename += \"Tree\";" << 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 << " }" << endl;
out << " AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();" << endl;
out << " TChain *chain = new TChain(treename);" << endl;
- if(fFriendChainName!="") {
- out << " TChain *chainFriend = 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 << " }" << endl;
out << " }" << endl;
out << " chain->Add(filename);" << endl;
- if(fFriendChainName!="") {
- out << " TString fileFriend=coll->GetTURL(\"\");" << endl;
- out << " fileFriend.ReplaceAll(\"AliAOD.root\",\""<<fFriendChainName.Data()<<"\");" << endl;
- out << " fileFriend.ReplaceAll(\"AliAODs.root\",\""<<fFriendChainName.Data()<<"\");" << endl;
- out << " chainFriend->Add(fileFriend.Data());" << 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;
- if(fFriendChainName!="") {
- out << " chain->AddFriend(chainFriend);" << endl;
- }
out << " return chain;" << endl;
out << "}" << endl << endl;
}
TString workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
if (FileExists(fAnalysisMacro)) gGrid->Rm(fAnalysisMacro);
- if (IsUsingTags() && !gSystem->AccessPathName("ConfigureCuts.C")) {
- if (FileExists("ConfigureCuts.C")) gGrid->Rm("ConfigureCuts.C");
- Info("WriteAnalysisMacro", "\n##### Copying cuts configuration macro: <ConfigureCuts.C> to your alien workspace");
- TFile::Cp("file:ConfigureCuts.C", Form("alien://%s/ConfigureCuts.C", workdir.Data()));
- }
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()));
+// 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");
}
}
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 (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
+ 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);
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;
TIter next(list);
TObjString *str;
while((str=(TObjString*)next())) {
- if (str->GetString().Contains(".so"))
+ if (str->GetString().Contains(".so") || str->GetString().Contains(".dylib"))
out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
}
if (list) delete list;
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 {
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" ||
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;
pkgname == "AOD.par" ||
pkgname == "ANALYSIS" ||
pkgname == "ANALYSIS.par" ||
+ pkgname == "OADB" ||
+ pkgname == "OADB.par" ||
pkgname == "ANALYSISalice" ||
pkgname == "ANALYSISalice.par" ||
pkgname == "CORRFW" ||
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;
- TObjArray *list = fAdditionalLibs.Tokenize(" ");
+ 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"))
+ if (str->GetString().Contains(".so") || str->GetString().Contains(".dylib"))
out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
}
if (list) delete list;
out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
}
// Change temp directory to current one
- out << "// Set temporary merging directory to current one" << endl;
- out << " gSystem->Setenv(\"TMPDIR\", gSystem->pwd());" << endl << endl;
out << "// Connect to AliEn" << 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;
- out << " TString outputFiles = \"" << GetListOfFiles("out") << "\";" << endl;
- out << " TString mergeExcludes = \"" << fMergeExcludes << "\";" << 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 << " 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.\",outputFile.Data());" << 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 << " 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;
- TString analysisFile = fExecutable;
- analysisFile.ReplaceAll(".sh", ".root");
- out << " if (!outputDir.Contains(\"Stage\")) return;" << endl;
- out << " TFile *file = TFile::Open(\"" << analysisFile << "\");" << endl;
- out << " if (!file) return;" << endl;
- out << " TIter nextkey(file->GetListOfKeys());" << endl;
- out << " AliAnalysisManager *mgr = 0;" << endl;
- out << " TKey *key;" << endl;
- out << " while ((key=(TKey*)nextkey())) {" << endl;
- out << " if (!strcmp(key->GetClassName(), \"AliAnalysisManager\"))" << endl;
- out << " mgr = (AliAnalysisManager*)file->Get(key->GetName());" << endl;
- out << " };" << endl;
- out << " if (!mgr) {" << endl;
- out << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file" << analysisFile <<"\");" << endl;
- out << " return;" << endl;
- out << " }" << endl << 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 (AliAnalysisManager::GetAnalysisManager()) {
- if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) {
+ if (mgr) {
+ if (mgr->GetDebugLevel()>3) {
out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
} else {
if (TestBit(AliAnalysisGrid::kTest))
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()));
+// 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");
}
}
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);
out << "free -m" << endl;
out << "echo \"=========================================\"" << endl << endl;
out << fExecutableCommand << " ";
- out << fAnalysisMacro.Data() << " " << fExecutableArgs.Data() << endl << endl;
- out << "echo \"======== " << fAnalysisMacro.Data() << " finished with exit code: $? ========\"" << endl;
+ out << fAnalysisMacro.Data() << " " << fExecutableArgs.Data() << endl;
+ out << "RET=$?" << 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;
}
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
- TString bindir = Form("%s/bin", workdir.Data());
- if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir,"-p");
workdir += fGridWorkingDir;
- TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), fExecutable.Data());
+ 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());
- TFile::Cp(Form("file:%s",fExecutable.Data()), Form("alien://%s", executable.Data()));
+ if (!copyLocal2Alien("WriteExecutable",fExecutable.Data(),
+ executable.Data())) Fatal("","Terminating");
}
}
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: $? ========\"" << endl;
out << "echo \"############## memory after: ##############\"" << endl;
out << "free -m" << endl;
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
- TString bindir = Form("%s/bin", workdir.Data());
- if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir,"-p");
workdir += fGridWorkingDir;
- TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), mergeExec.Data());
+ TString executable = TString::Format("%s/%s", workdir.Data(), mergeExec.Data());
if (FileExists(executable)) gGrid->Rm(executable);
Info("WriteMergeExecutable", "\n##### Copying executable file <%s> to your AliEn bin directory", mergeExec.Data());
- TFile::Cp(Form("file:%s",mergeExec.Data()), Form("alien://%s", executable.Data()));
+ if (!copyLocal2Alien("WriteMergeExecutable",mergeExec.Data(),
+ executable.Data())) Fatal("","Terminating");
}
}
if (gGrid) {
Info("WriteProductionFile", "\n##### Copying production file <%s> to your work directory", filename);
if (FileExists(filename)) gGrid->Rm(filename);
- TFile::Cp(Form("file:%s",filename), Form("alien://%s/%s", workdir.Data(),filename));
+// TFile::Cp(Form("file:%s",filename), Form("alien://%s/%s", workdir.Data(),filename));
+ if (!copyLocal2Alien("WriteProductionFile", filename,
+ Form("%s/%s", workdir.Data(),filename))) Fatal("","Terminating");
}
}
out << "parArch=`grep -Ei \"Cannot Build the PAR Archive\" stderr`" << endl;
out << "segViol=`grep -Ei \"Segmentation violation\" stderr`" << endl;
out << "segFault=`grep -Ei \"Segmentation fault\" stderr`" << endl;
- out << "glibcErr=`grep -Ei \"*** glibc detected ***\" stderr`" << endl;
+ out << "glibcErr=`grep -Ei '\\*\\*\\* glibc detected \\*\\*\\*' stderr`" << endl;
out << "" << endl;
out << "if [ \"$parArch\" != \"\" ] ; then" << endl;
TString outputFiles = fOutputFiles;
if (merge && !fTerminateFiles.IsNull()) {
- outputFiles += ",";
+ if (!outputFiles.IsNull()) outputFiles += ",";
outputFiles += fTerminateFiles;
}
TObjArray *arr = outputFiles.Tokenize(",");
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()));
+// 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");
}
}
git://git.uio.no / u / mrichter / AliRoot.git / blobdiff