fProductionMode(0),
fRunNumbers(),
fExecutable(),
+ fExecutableCommand(),
fArguments(),
fAnalysisMacro(),
fAnalysisSource(),
fProductionMode(0),
fRunNumbers(),
fExecutable(),
+ fExecutableCommand(),
fArguments(),
fAnalysisMacro(),
fAnalysisSource(),
fProductionMode(other.fProductionMode),
fRunNumbers(other.fRunNumbers),
fExecutable(other.fExecutable),
+ fExecutableCommand(other.fExecutableCommand),
fArguments(other.fArguments),
fAnalysisMacro(other.fAnalysisMacro),
fAnalysisSource(other.fAnalysisSource),
fProductionMode = other.fProductionMode;
fRunNumbers = other.fRunNumbers;
fExecutable = other.fExecutable;
+ fExecutableCommand = other.fExecutableCommand;
fArguments = other.fArguments;
fAnalysisMacro = other.fAnalysisMacro;
fAnalysisSource = other.fAnalysisSource;
fRunNumbers += Form("%d", run);
}
+//______________________________________________________________________________
+void AliAnalysisAlien::AddRunNumber(const char* run)
+{
+// Add a run number to the list of runs to be processed.
+ if (fRunNumbers.Length()) fRunNumbers += " ";
+ fRunNumbers += run;
+}
+
//______________________________________________________________________________
void AliAnalysisAlien::AddDataFile(const char *lfn)
{
}
TString homedir = gGrid->GetHomeDirectory();
TString workdir = homedir + fGridWorkingDir;
- if (!gGrid->Cd(workdir)) {
- gGrid->Cd(homedir);
- if (gGrid->Mkdir(workdir)) {
- gGrid->Cd(fGridWorkingDir);
- Info("CreateJDL", "\n##### Created alien working directory %s", fGridWorkingDir.Data());
- } else {
- Warning("CreateJDL", "Working directory %s cannot be created.\n Using %s instead.",
- workdir.Data(), homedir.Data());
- fGridWorkingDir = "";
- }
- }
+ if (DirectoryExists(workdir)) {
+ gGrid->Cd(workdir);
+ return;
+ }
+ // Work directory not existing - create it
+ gGrid->Cd(homedir);
+ if (gGrid->Mkdir(workdir)) {
+ gGrid->Cd(fGridWorkingDir);
+ Info("CreateJDL", "\n##### Created alien working directory %s", fGridWorkingDir.Data());
+ } else {
+ Warning("CreateJDL", "Working directory %s cannot be created.\n Using %s instead.",
+ workdir.Data(), homedir.Data());
+ fGridWorkingDir = "";
+ }
}
//______________________________________________________________________________
Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
return kFALSE;
}
- if (!gGrid->Cd(fGridDataDir)) {
+ if (!DirectoryExists(fGridDataDir)) {
Error("CheckInputData", "Data directory %s not existing.", fGridDataDir.Data());
return kFALSE;
}
TIter next(arr);
while ((os=(TObjString*)next())) {
path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data());
- if (!gGrid->Cd(path)) {
- Warning("CheckInputData", "Run number %s not found in path: %s", os->GetString().Data(), path.Data());
+ if (!DirectoryExists(path)) {
+ Warning("CheckInputData", "Run number %s not found in path: <%s>", os->GetString().Data(), path.Data());
continue;
}
path = Form("%s/%s.xml", workdir.Data(),os->GetString().Data());
Info("CheckDataType", "Using run range [%d, %d]", fRunRange[0], fRunRange[1]);
for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
path = Form("%s/%d ", fGridDataDir.Data(), irun);
- if (!gGrid->Cd(path)) {
- Warning("CheckInputData", "Run number %d not found in path: %s", irun, path.Data());
+ if (!DirectoryExists(path)) {
+// Warning("CheckInputData", "Run number %d not found in path: <%s>", irun, path.Data());
continue;
}
path = Form("%s/%d.xml", workdir.Data(),irun);
if (fInputFiles && fInputFiles->GetEntries()) return kTRUE;
// Make a single data collection from data directory.
path = fGridDataDir;
- if (!gGrid->Cd(path)) {
+ if (!DirectoryExists(path)) {
Error("CreateDataset", "Path to data directory %s not valid",fGridDataDir.Data());
return kFALSE;
}
- CdWork();
+// CdWork();
if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
else file = Form("%s.xml", gSystem->BaseName(path));
- if (gSystem->AccessPathName(file)) {
+ if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest)) {
command = "find ";
command += options;
command += path;
TIter next(arr);
while ((os=(TObjString*)next())) {
path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data());
- if (!gGrid->Cd(path)) continue;
- CdWork();
+ if (!DirectoryExists(path)) continue;
+// CdWork();
if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
else file = Form("%s.xml", os->GetString().Data());
// If local collection file does not exist, create it via 'find' command.
Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
continue;
}
- printf("Exporting merged collection <%s> and copying to AliEn.\n", schunk.Data());
+ printf("Exporting merged collection <%s> and copying to AliEn\n", schunk.Data());
cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs");
- TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
+ TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data()));
if (!FileExists(schunk)) {
Error("CreateDataset", "Copy command did NOT succeed for %s", schunk.Data());
delete arr;
// Process a full run range.
for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
path = Form("%s/%d ", fGridDataDir.Data(), irun);
- if (!gGrid->Cd(path)) continue;
- CdWork();
+ if (!DirectoryExists(path)) continue;
+// CdWork();
if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
else file = Form("%d.xml", irun);
if (FileExists(file) && fNrunsPerMaster<2 && !TestBit(AliAnalysisGrid::kTest)) {
error = kTRUE;
} else {
if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
- if (!gGrid->Cd(fGridOutputDir)) {
+ if (!DirectoryExists(fGridOutputDir)) {
if (gGrid->Mkdir(fGridOutputDir)) {
Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
} else {
fGridJDL->SetInputDataListFormat(fInputFormat);
fGridJDL->SetInputDataList("wn.xml");
fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), fAnalysisMacro.Data()));
- fGridJDL->AddToInputSandbox(Form("LF:%s/analysis.root", workdir.Data()));
+ TString analysisFile = fExecutable;
+ analysisFile.ReplaceAll(".sh", ".root");
+ fGridJDL->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 = fOutputFiles.Tokenize(" ");
TIter next(arr);
while ((os=(TObjString*)next())) {
+ // Ignore ouputs in jdl that are also in outputarchive
+ TString sout = os->GetString();
+ if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
+ if (fOutputArchive.Contains(sout)) continue;
if (!os->GetString().Contains("@") && fCloseSE.Length())
fGridJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()));
else
delete arr;
// fGridJDL->SetPrice((UInt_t)fPrice);
fGridJDL->SetValue("Price", Form("\"%d\"", fPrice));
- fGridJDL->SetValidationCommand(Form("%s/validate.sh", workdir.Data()));
+ TString validationScript = fExecutable;
+ validationScript.ReplaceAll(".sh", "_validation.sh");
+ fGridJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()));
if (fMasterResubmitThreshold) fGridJDL->SetValue("MasterResubmitThreshold", Form("\"%d%%\"", fMasterResubmitThreshold));
// Write a jdl with 2 input parameters: collection name and output dir name.
WriteJDL(copy);
} else {
// One jdl to be submitted with 2 input parameters: data collection name and output dir prefix
fGridJDL->AddToInputDataCollection(Form("LF:%s/$1,nodownload", workdir.Data()));
- fGridJDL->SetOutputDirectory(Form("%s/$2#alien_counter_03i#", fGridOutputDir.Data()));
+ fGridJDL->SetOutputDirectory(Form("%s/$2/#alien_counter_03i#", fGridOutputDir.Data()));
}
return kTRUE;
}
+//______________________________________________________________________________
+Bool_t AliAnalysisAlien::DirectoryExists(const char *dirname)
+{
+// Returns true if directory exists. Can be also a path.
+ 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;
+ }
+ }
+ delete res;
+ return kFALSE;
+}
+
//______________________________________________________________________________
void AliAnalysisAlien::CheckDataType(const char *lfn, Bool_t &is_collection, Bool_t &is_xml, Bool_t &use_tags)
{
fMaxMergeFiles = 100;
fRunNumbers = "";
fExecutable = "analysis.sh";
+ fExecutableCommand = "root -b -q";
fArguments = "";
fAnalysisMacro = "myAnalysis.C";
fAnalysisSource = "";
}
// Get the output path
if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
- if (!gGrid->Cd(fGridOutputDir)) {
+ if (!DirectoryExists(fGridOutputDir)) {
Error("MergeOutputs", "Grid output directory %s not found. Terminate() will NOT be executed", fGridOutputDir.Data());
return kFALSE;
}
if (!mgr->GetOutputEventHandler()) continue;
filename = mgr->GetOutputEventHandler()->GetOutputFileName();
}
+ if (fOutputFiles.Contains(filename)) continue;
if (fOutputFiles.Length()) fOutputFiles += " ";
fOutputFiles += filename;
}
if (mgr->GetExtraFiles().Length()) {
if (fOutputFiles.Length()) fOutputFiles += " ";
fOutputFiles += mgr->GetExtraFiles();
- }
+ }
}
// if (!fCloseSE.Length()) fCloseSE = gSystem->Getenv("alien_CLOSE_SE");
if (TestBit(AliAnalysisGrid::kOffline)) {
}
delete list;
gSystem->Exec(Form("bash %s 2>stderr", fExecutable.Data()));
- gSystem->Exec("bash validate.sh");
+ TString validationScript = fExecutable;
+ validationScript.ReplaceAll(".sh", "_validation.sh");
+ gSystem->Exec(Form("bash %s",validationScript.Data()));
// gSystem->Exec("cat stdout");
return kFALSE;
}
//______________________________________________________________________________
void AliAnalysisAlien::WriteAnalysisFile()
{
-// Write current analysis manager into the file analysis.root
+// Write current analysis manager into the file <analysisFile>
+ TString analysisFile = fExecutable;
+ analysisFile.ReplaceAll(".sh", ".root");
if (!TestBit(AliAnalysisGrid::kSubmit)) {
AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
if (!mgr || !mgr->IsInitialized()) {
if (handler->InheritsFrom("AliAODInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseAOD);
}
TDirectory *cdir = gDirectory;
- TFile *file = TFile::Open("analysis.root", "RECREATE");
+ TFile *file = TFile::Open(analysisFile, "RECREATE");
if (file) {
mgr->Write();
delete file;
}
if (cdir) cdir->cd();
- Info("WriteAnalysisFile", "\n##### Analysis manager: %s wrote to file <analysis.root>\n", mgr->GetName());
+ Info("WriteAnalysisFile", "\n##### Analysis manager: %s wrote to file <%s>\n", mgr->GetName(),analysisFile.Data());
}
Bool_t copy = kTRUE;
if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
CdWork();
TString workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
- Info("CreateJDL", "\n##### Copying file <analysis.root> containing your initialized analysis manager to your alien workspace");
- if (FileExists("analysis.root")) gGrid->Rm("analysis.root");
- TFile::Cp("file:analysis.root", Form("alien://%s/analysis.root", workdir.Data()));
+ Info("CreateJDL", "\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()));
}
}
}
}
out << "// read the analysis manager from file" << endl;
- out << " TFile *file = TFile::Open(\"analysis.root\");" << 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 << " mgr = (AliAnalysisManager*)file->Get(key->GetName());" << endl;
out << " };" << endl;
out << " if (!mgr) {" << endl;
- out << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file analysis.root\");" << endl;
+ out << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file" << analysisFile <<"\");" << endl;
out << " return;" << endl;
out << " }" << endl << endl;
out << " mgr->PrintStatus();" << endl;
return;
}
out << "#!/bin/bash" << endl;
- out << "export GCLIENT_SERVER_LIST=\"pcapiserv04.cern.ch:10000|pcapiserv05.cern.ch:10000|pcapiserv06.cern.ch:10000|pcapiserv07.cern.ch:10000\"" << endl;
out << "echo \"=========================================\"" << endl;
out << "echo \"############## PATH : ##############\"" << endl;
out << "echo $PATH" << endl;
out << "which aliroot" << endl;
out << "echo \"=========================================\"" << endl << endl;
// if (TestBit(AliAnalysisGrid::kTest)) out << "root ";
- out << "root -b -q ";
+ out << fExecutableCommand << " ";
out << fAnalysisMacro.Data() << endl << endl;
out << "echo \"======== " << fAnalysisMacro.Data() << " finished ========\"" << endl;
}
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
+ TString bindir = Form("%s/bin", workdir.Data());
+ if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir);
workdir += fGridWorkingDir;
TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), fExecutable.Data());
if (FileExists(executable)) gGrid->Rm(executable);
// Generate the alien validation script.
// Generate the validation script
TObjString *os;
+ TString validationScript = fExecutable;
+ validationScript.ReplaceAll(".sh", "_validation.sh");
if (!Connect()) {
Error("WriteValidationScript", "Alien connection required");
return;
if (!TestBit(AliAnalysisGrid::kTest)) out_stream = " >> stdout";
if (!TestBit(AliAnalysisGrid::kSubmit)) {
ofstream out;
- out.open("validate.sh", ios::out);
+ out.open(validationScript, ios::out);
out << "#!/bin/bash" << endl;
out << "##################################################" << endl;
out << "validateout=`dirname $0`" << endl;
out << "fi" << endl;
}
delete arr;
+ out << "if ! [ -f outputs_valid ] ; then" << endl;
+ out << " error=1" << endl;
+ out << " echo \"Output files were not validated by the analysis manager\" >> stdout" << endl;
+ out << " echo \"Output files were not validated by the analysis manager\" >> stderr" << endl;
+ out << "fi" << endl;
+
out << "if [ $error = 0 ] ; then" << endl;
out << " echo \"* ---------------- Job Validated ------------------*\"" << out_stream << endl;
out << "fi" << endl;
CdWork();
TString workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
- Info("CreateJDL", "\n##### Copying validation script <validate.sh> to your AliEn working space");
- if (FileExists("validate.sh")) gGrid->Rm("validate.sh");
- TFile::Cp("file:validate.sh", Form("alien://%s/validate.sh", workdir.Data()));
+ Info("CreateJDL", "\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()));
}
}
git://git.uio.no / u / mrichter / AliRoot.git / blobdiff