#include "TGridResult.h"
#include "TGridCollection.h"
#include "TGridJDL.h"
+#include "TGridJobStatusList.h"
+#include "TGridJobStatus.h"
#include "TFileMerger.h"
#include "AliAnalysisManager.h"
#include "AliVEventHandler.h"
fMaxInitFailed(0),
fMasterResubmitThreshold(0),
fNtestFiles(0),
+ fNrunsPerMaster(0),
+ fMaxMergeFiles(0),
+ fNsubmitted(0),
+ fProductionMode(0),
+ fOutputToRunNo(0),
fRunNumbers(),
fExecutable(),
+ fExecutableCommand(),
fArguments(),
+ fExecutableArgs(),
fAnalysisMacro(),
fAnalysisSource(),
+ fAdditionalRootLibs(),
fAdditionalLibs(),
fSplitMode(),
fAPIVersion(),
fROOTVersion(),
fAliROOTVersion(),
+ fExternalPackages(),
fUser(),
fGridWorkingDir(),
fGridDataDir(),
fMergeExcludes(),
fIncludePath(),
fCloseSE(),
+ fFriendChainName(),
+ fJobTag(),
+ fOutputSingle(),
+ fRunPrefix(),
fInputFiles(0),
fPackages(0)
{
fMaxInitFailed(0),
fMasterResubmitThreshold(0),
fNtestFiles(0),
+ fNrunsPerMaster(0),
+ fMaxMergeFiles(0),
+ fNsubmitted(0),
+ fProductionMode(0),
+ fOutputToRunNo(0),
fRunNumbers(),
fExecutable(),
+ fExecutableCommand(),
fArguments(),
+ fExecutableArgs(),
fAnalysisMacro(),
fAnalysisSource(),
+ fAdditionalRootLibs(),
fAdditionalLibs(),
fSplitMode(),
fAPIVersion(),
fROOTVersion(),
fAliROOTVersion(),
+ fExternalPackages(),
fUser(),
fGridWorkingDir(),
fGridDataDir(),
fMergeExcludes(),
fIncludePath(),
fCloseSE(),
+ fFriendChainName(),
+ fJobTag(),
+ fOutputSingle(),
+ fRunPrefix(),
fInputFiles(0),
fPackages(0)
{
fMaxInitFailed(other.fMaxInitFailed),
fMasterResubmitThreshold(other.fMasterResubmitThreshold),
fNtestFiles(other.fNtestFiles),
+ fNrunsPerMaster(other.fNrunsPerMaster),
+ fMaxMergeFiles(other.fMaxMergeFiles),
+ fNsubmitted(other.fNsubmitted),
+ fProductionMode(other.fProductionMode),
+ fOutputToRunNo(other.fOutputToRunNo),
fRunNumbers(other.fRunNumbers),
fExecutable(other.fExecutable),
+ fExecutableCommand(other.fExecutableCommand),
fArguments(other.fArguments),
+ fExecutableArgs(other.fExecutableArgs),
fAnalysisMacro(other.fAnalysisMacro),
fAnalysisSource(other.fAnalysisSource),
+ fAdditionalRootLibs(other.fAdditionalRootLibs),
fAdditionalLibs(other.fAdditionalLibs),
fSplitMode(other.fSplitMode),
fAPIVersion(other.fAPIVersion),
fROOTVersion(other.fROOTVersion),
fAliROOTVersion(other.fAliROOTVersion),
+ fExternalPackages(other.fExternalPackages),
fUser(other.fUser),
fGridWorkingDir(other.fGridWorkingDir),
fGridDataDir(other.fGridDataDir),
fMergeExcludes(other.fMergeExcludes),
fIncludePath(other.fIncludePath),
fCloseSE(other.fCloseSE),
+ fFriendChainName(other.fFriendChainName),
+ fJobTag(other.fJobTag),
+ fOutputSingle(other.fOutputSingle),
+ fRunPrefix(other.fRunPrefix),
fInputFiles(0),
fPackages(0)
{
// Copy ctor.
fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
+ fRunRange[0] = other.fRunRange[0];
+ fRunRange[1] = other.fRunRange[1];
if (other.fInputFiles) {
fInputFiles = new TObjArray();
TIter next(other.fInputFiles);
fMaxInitFailed = other.fMaxInitFailed;
fMasterResubmitThreshold = other.fMasterResubmitThreshold;
fNtestFiles = other.fNtestFiles;
+ fNrunsPerMaster = other.fNrunsPerMaster;
+ fMaxMergeFiles = other.fMaxMergeFiles;
+ fNsubmitted = other.fNsubmitted;
+ fProductionMode = other.fProductionMode;
+ fOutputToRunNo = other.fOutputToRunNo;
fRunNumbers = other.fRunNumbers;
fExecutable = other.fExecutable;
+ fExecutableCommand = other.fExecutableCommand;
fArguments = other.fArguments;
+ fExecutableArgs = other.fExecutableArgs;
fAnalysisMacro = other.fAnalysisMacro;
fAnalysisSource = other.fAnalysisSource;
+ fAdditionalRootLibs = other.fAdditionalRootLibs;
fAdditionalLibs = other.fAdditionalLibs;
fSplitMode = other.fSplitMode;
fAPIVersion = other.fAPIVersion;
fROOTVersion = other.fROOTVersion;
fAliROOTVersion = other.fAliROOTVersion;
+ fExternalPackages = other.fExternalPackages;
fUser = other.fUser;
fGridWorkingDir = other.fGridWorkingDir;
fGridDataDir = other.fGridDataDir;
fMergeExcludes = other.fMergeExcludes;
fIncludePath = other.fIncludePath;
fCloseSE = other.fCloseSE;
+ fFriendChainName = other.fFriendChainName;
+ fJobTag = other.fJobTag;
+ fOutputSingle = other.fOutputSingle;
+ fRunPrefix = other.fRunPrefix;
if (other.fInputFiles) {
fInputFiles = new TObjArray();
TIter next(other.fInputFiles);
{
// Add a run number to the list of runs to be processed.
if (fRunNumbers.Length()) fRunNumbers += " ";
- fRunNumbers += Form("%d", run);
+ fRunNumbers += Form("%s%d", fRunPrefix.Data(), 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;
}
//______________________________________________________________________________
if (!fInputFiles) fInputFiles = new TObjArray();
fInputFiles->Add(new TObjString(lfn));
}
-
+
+//______________________________________________________________________________
+void AliAnalysisAlien::AddExternalPackage(const char *package)
+{
+// Adds external packages w.r.t to the default ones (root,aliroot and gapi)
+ if (fExternalPackages) fExternalPackages += " ";
+ fExternalPackages += package;
+}
+
//______________________________________________________________________________
Bool_t AliAnalysisAlien::Connect()
{
}
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 = "";
+ }
}
//______________________________________________________________________________
Bool_t AliAnalysisAlien::CheckInputData()
{
// Check validity of input data. If necessary, create xml files.
- if (!fInputFiles && !fRunNumbers.Length()) {
- Error("CheckInputData", "You have to specify either a set of run numbers or some existing grid files. Use AddRunNumber()/AddDataFile().");
- return kFALSE;
+ if (!fInputFiles && !fRunNumbers.Length() && !fRunRange[0]) {
+ if (!fGridDataDir.Length()) {
+ Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
+ return kFALSE;
+ }
+ Info("CheckInputData", "Analysis will make a single xml for base data directory %s",fGridDataDir.Data());
+ return kTRUE;
}
// Process declared files
Bool_t is_collection = kFALSE;
}
}
// Process requested run numbers
- if (!fRunNumbers.Length()) return kTRUE;
+ if (!fRunNumbers.Length() && !fRunRange[0]) return kTRUE;
// Check validity of alien data directory
if (!fGridDataDir.Length()) {
Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
return kFALSE;
}
- if (!gGrid->Cd(fGridDataDir)) {
+ if (!DirectoryExists(fGridDataDir)) {
Error("CheckInputData", "Data directory %s not existing.", fGridDataDir.Data());
return kFALSE;
}
// Check validity of run number(s)
TObjArray *arr;
TObjString *os;
+ Int_t nruns = 0;
+ TString schunk, schunk2;
TString path;
if (!checked) {
checked = kTRUE;
return kFALSE;
}
if (fRunNumbers.Length()) {
+ Info("CheckDataType", "Using supplied run numbers (run ranges are ignored)");
arr = fRunNumbers.Tokenize(" ");
TIter next(arr);
while ((os=(TObjString*)next())) {
path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data());
- if (!gGrid->Cd(path)) {
- Error("CheckInputData", "Run number %s not found in path: %s", os->GetString().Data(), path.Data());
- return kFALSE;
+ if (!DirectoryExists(path)) {
+ Warning("CheckInputData", "Run number %s not found in path: <%s>", os->GetString().Data(), path.Data());
+ continue;
}
path = Form("%s/%s.xml", workdir.Data(),os->GetString().Data());
TString msg = "\n##### file: ";
if (use_tags) msg += " using_tags: Yes";
else msg += " using_tags: No";
Info("CheckDataType", msg.Data());
- AddDataFile(path);
+ if (fNrunsPerMaster<2) {
+ AddDataFile(Form("%s.xml", os->GetString().Data()));
+ } else {
+ nruns++;
+ if (((nruns-1)%fNrunsPerMaster) == 0) {
+ schunk = os->GetString();
+ }
+ if ((nruns%fNrunsPerMaster)!=0 && os!=arr->Last()) continue;
+ schunk += Form("_%s.xml", os->GetString().Data());
+ AddDataFile(schunk);
+ }
}
delete arr;
+ } else {
+ Info("CheckDataType", "Using run range [%d, %d]", fRunRange[0], fRunRange[1]);
+ for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
+ path = Form("%s/%s%d ", fGridDataDir.Data(), fRunPrefix.Data(), irun);
+ if (!DirectoryExists(path)) {
+// Warning("CheckInputData", "Run number %d not found in path: <%s>", irun, path.Data());
+ continue;
+ }
+ path = Form("%s/%s%d.xml", workdir.Data(),fRunPrefix.Data(),irun);
+ TString msg = "\n##### file: ";
+ msg += path;
+ msg += " type: xml_collection;";
+ if (use_tags) msg += " using_tags: Yes";
+ else msg += " using_tags: No";
+ Info("CheckDataType", msg.Data());
+ if (fNrunsPerMaster<2) {
+ AddDataFile(Form("%s%d.xml",fRunPrefix.Data(),irun));
+ } else {
+ nruns++;
+ if (((nruns-1)%fNrunsPerMaster) == 0) {
+ schunk = Form("%s%d", fRunPrefix.Data(),irun);
+ }
+ schunk2 = Form("_%s%d.xml", fRunPrefix.Data(), irun);
+ if ((nruns%fNrunsPerMaster)!=0 && irun != fRunRange[1]) continue;
+ schunk += schunk2;
+ AddDataFile(schunk);
+ }
+ }
+ if (!fInputFiles) {
+ schunk += schunk2;
+ AddDataFile(schunk);
+ }
}
return kTRUE;
}
TString file;
TString path;
- if (!fRunNumbers.Length()) return kTRUE;
- // Several runs
- TObjArray *arr = fRunNumbers.Tokenize(" ");
- TObjString *os;
- TIter next(arr);
- while ((os=(TObjString*)next())) {
- path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data());
- if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
- else file = Form("%s.xml", os->GetString().Data());
- if (FileExists(file) && !TestBit(AliAnalysisGrid::kTest)) {
- Info("CreateDataset", "\n##### Removing previous dataset %s", file.Data());
- gGrid->Rm(file);
- }
- command = "find ";
- command += options;
- command += path;
- command += pattern;
-// conditions = Form(" > %s", file.Data());
- command += conditions;
- TGridResult *res = gGrid->Command(command);
- if (res) delete res;
- // Write standard output to file
- gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
- if (TestBit(AliAnalysisGrid::kTest)) break;
- // Copy xml file to alien space
- TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
- if (!FileExists(file)) {
- Error("CreateDataset", "Command %s did NOT succeed", command.Data());
- delete arr;
+ Int_t nruns = 0;
+ TString schunk, schunk2;
+ TGridCollection *cbase=0, *cadd=0;
+ if (!fRunNumbers.Length() && !fRunRange[0]) {
+ if (fInputFiles && fInputFiles->GetEntries()) return kTRUE;
+ // Make a single data collection from data directory.
+ path = fGridDataDir;
+ if (!DirectoryExists(path)) {
+ Error("CreateDataset", "Path to data directory %s not valid",fGridDataDir.Data());
return kFALSE;
+ }
+// CdWork();
+ if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
+ else file = Form("%s.xml", gSystem->BaseName(path));
+ if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest)) {
+ 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()));
+ }
+ if (!TestBit(AliAnalysisGrid::kTest) && !FileExists(file)) {
+ // Copy xml file to alien space
+ TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
+ if (!FileExists(file)) {
+ Error("CreateDataset", "Command %s did NOT succeed", command.Data());
+ return kFALSE;
+ }
+ // Update list of files to be processed.
}
+ AddDataFile(Form("%s/%s", workdir.Data(), file.Data()));
+ return kTRUE;
}
- delete arr;
+ // Several runs
+ if (fRunNumbers.Length()) {
+ TObjArray *arr = fRunNumbers.Tokenize(" ");
+ TObjString *os;
+ TIter next(arr);
+ while ((os=(TObjString*)next())) {
+ 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());
+ // If local collection file does not exist, create it via 'find' command.
+ if (gSystem->AccessPathName(file)) {
+ 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()));
+ }
+ if (TestBit(AliAnalysisGrid::kTest)) break;
+ // Check if there is one run per master job.
+ if (fNrunsPerMaster<2) {
+ if (FileExists(file)) {
+ Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
+ continue;
+ }
+ // Copy xml file to alien space
+ TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
+ if (!FileExists(file)) {
+ Error("CreateDataset", "Command %s did NOT succeed", command.Data());
+ delete arr;
+ return kFALSE;
+ }
+ } else {
+ nruns++;
+ if (((nruns-1)%fNrunsPerMaster) == 0) {
+ schunk = os->GetString();
+ cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
+ } else {
+ cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
+ printf(" Merging collection <%s> into masterjob input...\n", file.Data());
+ cbase->Add(cadd);
+ delete cadd;
+ }
+ if ((nruns%fNrunsPerMaster)!=0 && os!=arr->Last()) {
+ continue;
+ }
+ schunk += Form("_%s.xml", os->GetString().Data());
+ if (FileExists(schunk)) {
+ Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
+ continue;
+ }
+ printf("Exporting merged collection <%s> and copying to AliEn\n", schunk.Data());
+ cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs");
+ TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data()));
+ if (!FileExists(schunk)) {
+ Error("CreateDataset", "Copy command did NOT succeed for %s", schunk.Data());
+ delete arr;
+ return kFALSE;
+ }
+ }
+ }
+ delete arr;
+ } else {
+ // Process a full run range.
+ for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
+ path = Form("%s/%s%d ", fGridDataDir.Data(), fRunPrefix.Data(), irun);
+ if (!DirectoryExists(path)) continue;
+// CdWork();
+ if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
+ else file = Form("%s%d.xml", fRunPrefix.Data(), irun);
+ if (FileExists(file) && fNrunsPerMaster<2 && !TestBit(AliAnalysisGrid::kTest)) {
+ Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
+// gGrid->Rm(file);
+ continue;
+ }
+ // If local collection file does not exist, create it via 'find' command.
+ if (gSystem->AccessPathName(file)) {
+ 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()));
+ }
+ if (TestBit(AliAnalysisGrid::kTest)) break;
+ // Check if there is one run per master job.
+ if (fNrunsPerMaster<2) {
+ if (FileExists(file)) {
+ Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
+ continue;
+ }
+ // Copy xml file to alien space
+ TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
+ if (!FileExists(file)) {
+ Error("CreateDataset", "Command %s did NOT succeed", command.Data());
+ return kFALSE;
+ }
+ } else {
+ nruns++;
+ // Check if the collection for the chunk exist locally.
+ Int_t nchunk = (nruns-1)/fNrunsPerMaster;
+ if (FileExists(fInputFiles->At(nchunk)->GetName())) continue;
+ printf(" Merging collection <%s> into %d runs chunk...\n",file.Data(),fNrunsPerMaster);
+ if (((nruns-1)%fNrunsPerMaster) == 0) {
+ schunk = Form("%s%d", fRunPrefix.Data(), irun);
+ cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
+ } else {
+ cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
+ cbase->Add(cadd);
+ delete cadd;
+ }
+ schunk2 = Form("%s_%s%d.xml", schunk.Data(), fRunPrefix.Data(), irun);
+ if ((nruns%fNrunsPerMaster)!=0 && irun!=fRunRange[1] && schunk2 != fInputFiles->Last()->GetName()) {
+ continue;
+ }
+ schunk = schunk2;
+ if (FileExists(schunk)) {
+ Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
+ continue;
+ }
+ printf("Exporting merged collection <%s> and copying to AliEn.\n", schunk.Data());
+ cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs");
+ if (FileExists(schunk)) {
+ Info("CreateDataset", "\n##### Dataset %s exist. Skipping copy...", schunk.Data());
+ continue;
+ }
+ TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data()));
+ if (!FileExists(schunk)) {
+ Error("CreateDataset", "Copy command did NOT succeed for %s", schunk.Data());
+ return kFALSE;
+ }
+ }
+ }
+ }
return kTRUE;
}
Error("CreateJDL", "You must define AliEn output directory");
error = kTRUE;
} else {
- if (!gGrid->Cd(fGridOutputDir)) {
+ if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
+ if (!DirectoryExists(fGridOutputDir)) {
if (gGrid->Mkdir(fGridOutputDir)) {
Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
} else {
Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
- error = kTRUE;
+ // error = kTRUE;
}
}
gGrid->Cd(workdir);
// Set JDL fields
fGridJDL->SetValue("User", Form("\"%s\"", fUser.Data()));
fGridJDL->SetExecutable(fExecutable);
+ if (!fArguments.IsNull())
+ fGridJDL->SetArguments(fArguments, "Arguments for the executable command");
// fGridJDL->SetTTL((UInt_t)fTTL);
fGridJDL->SetValue("TTL", Form("\"%d\"", fTTL));
if (fMaxInitFailed > 0)
fGridJDL->AddToPackages("ROOT", fROOTVersion);
if (fAPIVersion.Length())
fGridJDL->AddToPackages("APISCONFIG", fAPIVersion);
+ if (!fExternalPackages.IsNull()) {
+ arr = fExternalPackages.Tokenize(" ");
+ TIter next(arr);
+ while ((os=(TObjString*)next())) {
+ TString pkgname = os->GetString();
+ Int_t index = pkgname.Index("::");
+ TString pkgversion = pkgname(index+2, pkgname.Length());
+ pkgname.Remove(index);
+ fGridJDL->AddToPackages(pkgname, pkgversion);
+ }
+ delete arr;
+ }
fGridJDL->SetInputDataListFormat(fInputFormat);
fGridJDL->SetInputDataList("wn.xml");
- if (fInputFiles) {
- TIter next(fInputFiles);
- while ((os=(TObjString*)next()))
- fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetString().Data()));
- }
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()) {
fGridJDL->AddToOutputArchive(os->GetString());
delete arr;
}
- fGridJDL->SetOutputDirectory(Form("%s/%s/#alien_counter_03i#", workdir.Data(), fGridOutputDir.Data()));
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));
- // Generate the JDL as a string
- TString sjdl = fGridJDL->Generate();
- Int_t index;
- index = sjdl.Index("Executable");
- if (index >= 0) sjdl.Insert(index, "\n# This is the startup script\n");
- index = sjdl.Index("Split ");
- if (index >= 0) sjdl.Insert(index, "\n# We split per storage element\n");
- index = sjdl.Index("SplitMaxInputFileNumber");
- if (index >= 0) sjdl.Insert(index, "\n# We want each subjob to get maximum this number of input files\n");
- index = sjdl.Index("InputDataCollection");
- if (index >= 0) sjdl.Insert(index, "# Input xml collections\n");
- index = sjdl.Index("InputFile");
- if (index >= 0) sjdl.Insert(index, "\n# List of input files to be uploaded to wn's\n");
- index = sjdl.Index("InputDataList ");
- if (index >= 0) sjdl.Insert(index, "\n# Collection to be processed on wn\n");
- index = sjdl.Index("InputDataListFormat");
- if (index >= 0) sjdl.Insert(index, "\n# Format of input data\n");
- index = sjdl.Index("Price");
- if (index >= 0) sjdl.Insert(index, "\n# AliEn price for this job\n");
- index = sjdl.Index("Requirements");
- if (index >= 0) sjdl.Insert(index, "\n# Additional requirements for the computing element\n");
- index = sjdl.Index("Packages");
- if (index >= 0) sjdl.Insert(index, "\n# Packages to be used\n");
- index = sjdl.Index("User");
- if (index >= 0) sjdl.Insert(index, "\n# AliEn user\n");
- index = sjdl.Index("TTL");
- if (index >= 0) sjdl.Insert(index, "\n# Time to live for the job\n");
- index = sjdl.Index("OutputFile");
- if (index >= 0) sjdl.Insert(index, "\n# List of output files to be registered\n");
- index = sjdl.Index("OutputDir");
- if (index >= 0) sjdl.Insert(index, "\n# Output directory\n");
- index = sjdl.Index("OutputArchive");
- if (index >= 0) sjdl.Insert(index, "\n# Files to be archived\n");
- index = sjdl.Index("MaxInitFailed");
- if (index >= 0) sjdl.Insert(index, "\n# Maximum number of first failing jobs to abort the master job\n");
- index = sjdl.Index("MasterResubmitThreshold");
- if (index >= 0) sjdl.Insert(index, "\n# Resubmit failed jobs until DONE rate reaches this percentage\n");
- sjdl.ReplaceAll("ValidationCommand", "Validationcommand");
- index = sjdl.Index("Validationcommand");
- if (index >= 0) sjdl.Insert(index, "\n# Validation script to be run for each subjob\n");
- sjdl.ReplaceAll("\"LF:", "\n \"LF:");
- sjdl.ReplaceAll("(member", "\n (member");
- sjdl.ReplaceAll("\",\"VO_", "\",\n \"VO_");
- sjdl.ReplaceAll("{", "{\n ");
- sjdl.ReplaceAll("};", "\n};");
- sjdl.ReplaceAll("{\n \n", "{\n");
- sjdl.ReplaceAll("\n\n", "\n");
- sjdl.ReplaceAll("OutputDirectory", "OutputDir");
- sjdl += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
- sjdl.Prepend("JobTag = \"Automatically generated analysis JDL\";\n");
- index = sjdl.Index("JDLVariables");
- if (index >= 0) sjdl.Insert(index, "\n# JDL variables\n");
- // Write jdl to file
- ofstream out;
- out.open(fJDLName.Data(), ios::out);
- if (out.bad()) {
- Error("CreateJDL", "Bad file name: %s", fJDLName.Data());
- return kFALSE;
- }
- out << sjdl << endl;
+ // Write a jdl with 2 input parameters: collection name and output dir name.
+ WriteJDL(copy);
}
// Copy jdl to grid workspace
- if (!copy) {
- Info("CreateJDL", "\n##### You may want to review jdl:%s and analysis macro:%s before running in <submit> mode", fJDLName.Data(), fAnalysisMacro.Data());
- } else {
- Info("CreateJDL", "\n##### Copying JDL file <%s> to your AliEn working space", fJDLName.Data());
- if (FileExists(fJDLName)) gGrid->Rm(fJDLName);
- TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s/%s", workdir.Data(), fJDLName.Data()));
+ if (copy) {
+ // Check if an output directory was defined and valid
+ if (!fGridOutputDir.Length()) {
+ Error("CreateJDL", "You must define AliEn output directory");
+ return kFALSE;
+ } else {
+ if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
+ if (!DirectoryExists(fGridOutputDir)) {
+ if (gGrid->Mkdir(fGridOutputDir)) {
+ Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
+ } else {
+ Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
+ return kFALSE;
+ }
+ }
+ gGrid->Cd(workdir);
+ }
+ if (TestBit(AliAnalysisGrid::kSubmit)) {
+ Info("CreateJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
+ TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
+ if (fProductionMode)
+ locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
+ if (FileExists(locjdl)) gGrid->Rm(locjdl);
+ TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
+ }
if (fAdditionalLibs.Length()) {
arr = fAdditionalLibs.Tokenize(" ");
TObjString *os;
TIter next(fPackages);
TObject *obj;
while ((obj=next())) {
+ if (FileExists(obj->GetName())) gGrid->Rm(obj->GetName());
Info("CreateJDL", "\n##### Copying dependency: <%s> to your alien workspace", obj->GetName());
TFile::Cp(Form("file:%s",obj->GetName()), Form("alien://%s/%s", workdir.Data(), obj->GetName()));
}
}
//______________________________________________________________________________
-Bool_t AliAnalysisAlien::FileExists(const char *lfn) const
+Bool_t AliAnalysisAlien::WriteJDL(Bool_t copy)
{
-// Returns true if file exists.
- if (!gGrid) {
- Error("FileExists", "No connection to grid");
+// 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;
+ TObjString *os;
+ TString workdir = gGrid->GetHomeDirectory();
+ workdir += fGridWorkingDir;
+
+ if (!fRunNumbers.Length() && !fRunRange[0]) {
+ // One jdl with no parameters in case input data is specified by name.
+ TIter next(fInputFiles);
+ while ((os=(TObjString*)next()))
+ fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetString().Data()));
+ if (!fOutputSingle.IsNull())
+ fGridJDL->SetOutputDirectory(Form("#alienfulldir#/../%s",fOutputSingle.Data()));
+ else
+ fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_03i#", fGridOutputDir.Data()));
+ } 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()));
+ if (!fOutputSingle.IsNull()) {
+ if (!fOutputToRunNo) fGridJDL->SetOutputDirectory(Form("#alienfulldir#/%s",fOutputSingle.Data()));
+ else fGridJDL->SetOutputDirectory(Form("%s/$2",fGridOutputDir.Data()));
+ } else {
+ fGridJDL->SetOutputDirectory(Form("%s/$2/#alien_counter_03i#", fGridOutputDir.Data()));
+ }
+ }
+
+
+ // Generate the JDL as a string
+ TString sjdl = fGridJDL->Generate();
+ Int_t index;
+ index = sjdl.Index("Executable");
+ if (index >= 0) sjdl.Insert(index, "\n# This is the startup script\n");
+ index = sjdl.Index("Split ");
+ if (index >= 0) sjdl.Insert(index, "\n# We split per SE or file\n");
+ index = sjdl.Index("SplitMaxInputFileNumber");
+ if (index >= 0) sjdl.Insert(index, "\n# We want each subjob to get maximum this number of input files\n");
+ index = sjdl.Index("InputDataCollection");
+ if (index >= 0) sjdl.Insert(index, "# Input xml collections\n");
+ index = sjdl.Index("InputFile");
+ if (index >= 0) sjdl.Insert(index, "\n# List of input files to be uploaded to wn's\n");
+ index = sjdl.Index("InputDataList ");
+ if (index >= 0) sjdl.Insert(index, "\n# Collection to be processed on wn\n");
+ index = sjdl.Index("InputDataListFormat");
+ if (index >= 0) sjdl.Insert(index, "\n# Format of input data\n");
+ index = sjdl.Index("Price");
+ if (index >= 0) sjdl.Insert(index, "\n# AliEn price for this job\n");
+ index = sjdl.Index("Requirements");
+ if (index >= 0) sjdl.Insert(index, "\n# Additional requirements for the computing element\n");
+ index = sjdl.Index("Packages");
+ if (index >= 0) sjdl.Insert(index, "\n# Packages to be used\n");
+ index = sjdl.Index("User =");
+ if (index >= 0) sjdl.Insert(index, "\n# AliEn user\n");
+ index = sjdl.Index("TTL");
+ if (index >= 0) sjdl.Insert(index, "\n# Time to live for the job\n");
+ index = sjdl.Index("OutputFile");
+ if (index >= 0) sjdl.Insert(index, "\n# List of output files to be registered\n");
+ index = sjdl.Index("OutputDir");
+ if (index >= 0) sjdl.Insert(index, "\n# Output directory\n");
+ index = sjdl.Index("OutputArchive");
+ if (index >= 0) sjdl.Insert(index, "\n# Files to be archived\n");
+ index = sjdl.Index("MaxInitFailed");
+ if (index >= 0) sjdl.Insert(index, "\n# Maximum number of first failing jobs to abort the master job\n");
+ index = sjdl.Index("MasterResubmitThreshold");
+ if (index >= 0) sjdl.Insert(index, "\n# Resubmit failed jobs until DONE rate reaches this percentage\n");
+ sjdl.ReplaceAll("ValidationCommand", "Validationcommand");
+ index = sjdl.Index("Validationcommand");
+ if (index >= 0) sjdl.Insert(index, "\n# Validation script to be run for each subjob\n");
+ sjdl.ReplaceAll("\"LF:", "\n \"LF:");
+ sjdl.ReplaceAll("(member", "\n (member");
+ sjdl.ReplaceAll("\",\"VO_", "\",\n \"VO_");
+ sjdl.ReplaceAll("{", "{\n ");
+ sjdl.ReplaceAll("};", "\n};");
+ sjdl.ReplaceAll("{\n \n", "{\n");
+ sjdl.ReplaceAll("\n\n", "\n");
+ sjdl.ReplaceAll("OutputDirectory", "OutputDir");
+ sjdl += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
+ sjdl.Prepend(Form("Jobtag = {\n \"comment:%s\"\n};\n", fJobTag.Data()));
+ index = sjdl.Index("JDLVariables");
+ if (index >= 0) sjdl.Insert(index, "\n# JDL variables\n");
+ // Write jdl to file
+ ofstream out;
+ out.open(fJDLName.Data(), ios::out);
+ if (out.bad()) {
+ Error("CreateJDL", "Bad file name: %s", fJDLName.Data());
return kFALSE;
}
+ out << sjdl << endl;
+
+ // Copy jdl to grid workspace
+ if (!copy) {
+ Info("CreateJDL", "\n##### You may want to review jdl:%s and analysis macro:%s before running in <submit> mode", fJDLName.Data(), fAnalysisMacro.Data());
+ } else {
+ Info("CreateJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
+ TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
+ if (fProductionMode)
+ locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
+ if (FileExists(locjdl)) gGrid->Rm(locjdl);
+ TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
+ }
+ return kTRUE;
+}
+
+//______________________________________________________________________________
+Bool_t AliAnalysisAlien::FileExists(const char *lfn)
+{
+// Returns true if file exists.
+ if (!gGrid) return kFALSE;
TGridResult *res = gGrid->Ls(lfn);
if (!res) return kFALSE;
TMap *map = dynamic_cast<TMap*>(res->At(0));
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)
{
fPackages->Add(new TObjString(pkg));
}
+//______________________________________________________________________________
+const char *AliAnalysisAlien::GetJobStatus(Int_t jobidstart, Int_t lastid, Int_t &nrunning, Int_t &nwaiting, Int_t &nerror, Int_t &ndone)
+{
+// Get job status for all jobs with jobid>jobidstart.
+ static char mstatus[20];
+ mstatus[0] = '\0';
+ nrunning = 0;
+ nwaiting = 0;
+ nerror = 0;
+ ndone = 0;
+ TGridJobStatusList *list = gGrid->Ps("");
+ if (!list) return mstatus;
+ Int_t nentries = list->GetSize();
+ TGridJobStatus *status;
+ Int_t pid;
+ for (Int_t ijob=0; ijob<nentries; ijob++) {
+ status = (TGridJobStatus *)list->At(ijob);
+ pid = gROOT->ProcessLine(Form("atoi(((TAlienJobStatus*)0x%lx)->GetKey(\"queueId\"));", (ULong_t)status));
+ if (pid<jobidstart) continue;
+ if (pid == lastid) {
+ gROOT->ProcessLine(Form("sprintf((char*)0x%lx,((TAlienJobStatus*)0x%lx)->GetKey(\"status\"));",(ULong_t)mstatus, (ULong_t)status));
+ }
+ switch (status->GetStatus()) {
+ case TGridJobStatus::kWAITING:
+ nwaiting++; break;
+ case TGridJobStatus::kRUNNING:
+ nrunning++; break;
+ case TGridJobStatus::kABORTED:
+ case TGridJobStatus::kFAIL:
+ case TGridJobStatus::kUNKNOWN:
+ nerror++; break;
+ case TGridJobStatus::kDONE:
+ ndone++;
+ }
+ }
+ list->Delete();
+ delete list;
+ return mstatus;
+}
+
//______________________________________________________________________________
Bool_t AliAnalysisAlien::IsCollection(const char *lfn) const
{
return kFALSE;
}
+//______________________________________________________________________________
+Bool_t AliAnalysisAlien::IsSingleOutput() const
+{
+// Check if single-ouput option is on.
+ return (!fOutputSingle.IsNull());
+}
+
+//______________________________________________________________________________
+void AliAnalysisAlien::Print(Option_t *) const
+{
+// Print current plugin settings.
+ printf("### AliEn analysis plugin current settings ###\n");
+ printf("= Production mode:______________________________ %d\n", fProductionMode);
+ printf("= Version of API requested: ____________________ %s\n", fAPIVersion.Data());
+ printf("= Version of ROOT requested: ___________________ %s\n", fROOTVersion.Data());
+ printf("= Version of AliRoot requested: ________________ %s\n", fAliROOTVersion.Data());
+ if (fUser.Length())
+ printf("= User running the plugin: _____________________ %s\n", fUser.Data());
+ printf("= Grid workdir relative to user $HOME: _________ %s\n", fGridWorkingDir.Data());
+ printf("= Grid output directory relative to workdir: ___ %s\n", fGridOutputDir.Data());
+ printf("= Data base directory path requested: __________ %s\n", fGridDataDir.Data());
+ printf("= Data search pattern: _________________________ %s\n", fDataPattern.Data());
+ printf("= Input data format: ___________________________ %s\n", fInputFormat.Data());
+ if (fRunNumbers.Length())
+ printf("= Run numbers to be processed: _________________ %s\n", fRunNumbers.Data());
+ if (fRunRange[0])
+ printf("= Run range to be processed: ___________________ %s%d-%s%d\n", fRunPrefix.Data(), fRunRange[0], fRunPrefix.Data(), fRunRange[1]);
+ if (!fRunRange[0] && !fRunNumbers.Length()) {
+ TIter next(fInputFiles);
+ TObject *obj;
+ TString list;
+ while ((obj=next())) list += obj->GetName();
+ printf("= Input files to be processed: _________________ %s\n", list.Data());
+ }
+ if (TestBit(AliAnalysisGrid::kTest))
+ printf("= Number of input files used in test mode: _____ %d\n", fNtestFiles);
+ printf("= List of output files to be registered: _______ %s\n", fOutputFiles.Data());
+ printf("= List of outputs going to be archived: ________ %s\n", fOutputArchive.Data());
+ printf("= List of outputs that should not be merged: ___ %s\n", fMergeExcludes.Data());
+ printf("=====================================================================\n");
+ printf("= Job price: ___________________________________ %d\n", fPrice);
+ printf("= Time to live (TTL): __________________________ %d\n", fTTL);
+ printf("= Max files per subjob: ________________________ %d\n", fSplitMaxInputFileNumber);
+ if (fMaxInitFailed>0)
+ printf("= Max number of subjob fails to kill: __________ %d\n", fMaxInitFailed);
+ if (fMasterResubmitThreshold>0)
+ printf("= Resubmit master job if failed subjobs >_______ %d\n", fMasterResubmitThreshold);
+ if (fNrunsPerMaster>0)
+ printf("= Number of runs per master job: _______________ %d\n", fNrunsPerMaster);
+ printf("= Number of files in one chunk to be merged: ___ %d\n", fMaxMergeFiles);
+ printf("= Name of the generated execution script: ______ %s\n", fExecutable.Data());
+ printf("= Executable command: __________________________ %s\n", fExecutableCommand.Data());
+ if (fArguments.Length())
+ printf("= Arguments for the execution script: __________ %s\n",fArguments.Data());
+ if (fExecutableArgs.Length())
+ printf("= Arguments after macro name in executable______ %s\n",fExecutableArgs.Data());
+ printf("= Name of the generated analysis macro: ________ %s\n",fAnalysisMacro.Data());
+ printf("= User analysis files to be deployed: __________ %s\n",fAnalysisSource.Data());
+ printf("= Additional libs to be loaded or souces to be compiled runtime: <%s>\n",fAdditionalLibs.Data());
+ printf("= Master jobs split mode: ______________________ %s\n",fSplitMode.Data());
+ if (fDatasetName)
+ printf("= Custom name for the dataset to be created: ___ %s\n", fDatasetName.Data());
+ printf("= Name of the generated JDL: ___________________ %s\n", fJDLName.Data());
+ if (fIncludePath.Data())
+ printf("= Include path for runtime task compilation: ___ %s\n", fIncludePath.Data());
+ if (fCloseSE.Length())
+ printf("= Force job outputs to storage element: ________ %s\n", fCloseSE.Data());
+ if (fFriendChainName.Length())
+ printf("= Open friend chain file on worker: ____________ %s\n", fFriendChainName.Data());
+ if (fPackages) {
+ TIter next(fPackages);
+ TObject *obj;
+ TString list;
+ while ((obj=next())) list += obj->GetName();
+ printf("= Par files to be used: ________________________ %s\n", list.Data());
+ }
+}
+
//______________________________________________________________________________
void AliAnalysisAlien::SetDefaults()
{
fMaxInitFailed = 0;
fMasterResubmitThreshold = 0;
fNtestFiles = 10;
+ fRunRange[0] = 0;
+ fRunRange[1] = 0;
+ fNrunsPerMaster = 1;
+ fMaxMergeFiles = 100;
fRunNumbers = "";
fExecutable = "analysis.sh";
+ fExecutableCommand = "root -b -q";
fArguments = "";
+ fExecutableArgs = "";
fAnalysisMacro = "myAnalysis.C";
fAnalysisSource = "";
fAdditionalLibs = "";
fGridWorkingDir = "";
fGridDataDir = ""; // Can be like: /alice/sim/PDC_08a/LHC08c9/
fDataPattern = "*AliESDs.root"; // Can be like: *AliESDs.root, */pass1/*AliESDs.root, ...
+ fFriendChainName = "";
fGridOutputDir = "output";
fOutputArchive = "log_archive.zip:stdout,stderr root_archive.zip:*.root";
fOutputFiles = ""; // Like "AliAODs.root histos.root"
fInputFormat = "xml-single";
fJDLName = "analysis.jdl";
+ fJobTag = "Automatically generated analysis JDL";
fMergeExcludes = "";
}
return kFALSE;
}
// Get the output path
- TString output = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
- if (!gGrid->Cd(output)) output = Form("/%s/%s", gGrid->GetHomeDirectory(), fGridOutputDir.Data());
- if (!gGrid->Cd(output)) {
+ 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;
}
TObjString *str;
TString command;
TString output_file;
+ TString output_chunk;
+ TString previous_chunk;
+ Int_t count_chunk = 0;
+ Int_t count_zero = fMaxMergeFiles;
Bool_t merged = kTRUE;
while((str=(TObjString*)next())) {
output_file = str->GetString();
Int_t index = output_file.Index("@");
if (index > 0) output_file.Remove(index);
+ // Skip already merged outputs
+ if (!gSystem->AccessPathName(output_file)) {
+ Info("MergeOutputs", "Output file <%s> found. Not merging again.", output_file.Data());
+ continue;
+ }
if (fMergeExcludes.Length() &&
fMergeExcludes.Contains(output_file.Data())) continue;
- command = Form("find %s/ *%s", output.Data(), output_file.Data());
+ // Perform a 'find' command in the output directory, looking for registered outputs
+ command = Form("find %s/ *%s", fGridOutputDir.Data(), output_file.Data());
printf("command: %s\n", command.Data());
TGridResult *res = gGrid->Command(command);
if (!res) continue;
TFileMerger *fm = 0;
TIter nextmap(res);
- TMap *map;
+ TMap *map = 0;
+ previous_chunk = "";
+ count_chunk = 0;
+ // Check if there is a merge operation to resume
+ output_chunk = output_file;
+ output_chunk.ReplaceAll(".root", "_*.root");
+ if (!gSystem->Exec(Form("ls %s", output_chunk.Data()))) {
+ while (1) {
+ for (Int_t counter=0; counter<fMaxMergeFiles; counter++) map = (TMap*)nextmap();
+ if (!map) {
+ Error("MergeOutputs", "Cannot resume merging for <%s>, nentries=%d", output_file.Data(), res->GetSize());
+ delete res;
+ return kFALSE;
+ }
+ output_chunk = output_file;
+ output_chunk.ReplaceAll(".root", Form("_%04d.root", count_chunk));
+ printf("%s\n", output_chunk.Data());
+ count_chunk++;
+ if (gSystem->AccessPathName(output_chunk)) continue;
+ // Merged file with chunks up to <count_chunk> found
+ printf("Resume merging of <%s> from <%s>\n", output_file.Data(), output_chunk.Data());
+ previous_chunk = output_chunk;
+ break;
+ }
+ }
+ count_zero = fMaxMergeFiles;
while ((map=(TMap*)nextmap())) {
+ // Loop 'find' results and get next LFN
+ if (count_zero == fMaxMergeFiles) {
+ // First file in chunk - create file merger and add previous chunk if any.
+ fm = new TFileMerger(kFALSE);
+ fm->SetFastMethod(kTRUE);
+ if (previous_chunk.Length()) fm->AddFile(previous_chunk.Data());
+ output_chunk = output_file;
+ output_chunk.ReplaceAll(".root", Form("_%04d.root", count_chunk));
+ }
+ // If last file found, put merged results in the output file
+ if (map == res->Last()) output_chunk = output_file;
TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl"));
if (!objs || !objs->GetString().Length()) {
+ // Nothing found - skip this output
delete res;
- continue;
- }
- if (!fm) {
- fm = new TFileMerger(kFALSE);
- fm->SetFastMethod(kTRUE);
- fm->OutputFile(output_file);
+ delete fm;
+ break;
+ }
+ // Add file to be merged and decrement chunk counter.
+ fm->AddFile(objs->GetString());
+ count_zero--;
+ if (count_zero==0 || map == res->Last()) {
+ fm->OutputFile(output_chunk);
+ if (!fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
+ // Nothing found - skip this output
+ Warning("MergeOutputs", "No <%s> files found.", output_file.Data());
+ delete res;
+ delete fm;
+ break;
+ }
+ // Merge the outputs, then go to next chunk
+ if (!fm->Merge()) {
+ Error("MergeOutputs", "Could not merge all <%s> files", output_file.Data());
+ delete res;
+ delete fm;
+ merged = kFALSE;
+ break;
+ } else {
+ Info("MergeOutputs", "\n##### Merged %d output files to <%s>", fm->GetMergeList()->GetSize(), output_chunk.Data());
+ gSystem->Unlink(previous_chunk);
+ }
+ if (map == res->Last()) {
+ delete res;
+ delete fm;
+ break;
+ }
+ count_chunk++;
+ count_zero = fMaxMergeFiles;
+ previous_chunk = output_chunk;
}
- fm->AddFile(objs->GetString());
- }
- if (!fm || !fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
- Warning("MergeOutputs", "No <%s> files found.", output_file.Data());
- merged = kFALSE;
- delete res;
- continue;
}
- if (!fm->Merge()) {
- Error("MergeOutputs", "Could not merge all <%s> files", output_file.Data());
- merged = kFALSE;
- } else {
- Info("MergeOutputs", "\n##### Merged %d output files <%s>", fm->GetMergeList()->GetSize(), output_file.Data());
- }
- delete fm;
- delete res;
}
if (!merged) {
Error("MergeOutputs", "Terminate() will NOT be executed");
}
//______________________________________________________________________________
-void AliAnalysisAlien::StartAnalysis(Long64_t /*nentries*/, Long64_t /*firstEntry*/)
+Bool_t AliAnalysisAlien::StartAnalysis(Long64_t /*nentries*/, Long64_t /*firstEntry*/)
{
// Start remote grid analysis.
AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
if (!mgr || !mgr->IsInitialized()) {
Error("StartAnalysis", "You need an initialized analysis manager for this");
- return;
+ return kFALSE;
}
fOutputFiles = "";
TIter next(mgr->GetOutputs());
if (!mgr->GetOutputEventHandler()) continue;
filename = mgr->GetOutputEventHandler()->GetOutputFileName();
}
+ if (fOutputFiles.Contains(filename)) continue;
if (fOutputFiles.Length()) fOutputFiles += " ";
fOutputFiles += filename;
}
+ // Add extra files registered to the analysis manager
+ if (mgr->GetExtraFiles().Length()) {
+ if (fOutputFiles.Length()) fOutputFiles += " ";
+ fOutputFiles += mgr->GetExtraFiles();
+ }
}
- if (!fCloseSE.Length()) fCloseSE = gSystem->Getenv("alien_CLOSE_SE");
+// if (!fCloseSE.Length()) fCloseSE = gSystem->Getenv("alien_CLOSE_SE");
if (TestBit(AliAnalysisGrid::kOffline)) {
Info("StartAnalysis","\n##### OFFLINE MODE ##### Files to be used in GRID are produced but not copied \
\n there nor any job run. You can revise the JDL and analysis \
\n space and job submitted.");
} else if (TestBit(AliAnalysisGrid::kMerge)) {
Info("StartAnalysis","\n##### MERGE MODE ##### The registered outputs of the analysis will be merged");
- return;
+ return kTRUE;
} else {
Info("StartAnalysis","\n##### FULL ANALYSIS MODE ##### Producing needed files and submitting your analysis job...");
}
if (!Connect()) {
Error("StartAnalysis", "Cannot start grid analysis without grid connection");
- return;
- }
+ return kFALSE;
+ }
+ Print();
if (!CheckInputData()) {
Error("StartAnalysis", "There was an error in preprocessing your requested input data");
- return;
+ return kFALSE;
}
CreateDataset(fDataPattern);
WriteAnalysisFile();
WriteAnalysisMacro();
WriteExecutable();
WriteValidationScript();
- if (!CreateJDL()) return;
- if (TestBit(AliAnalysisGrid::kOffline)) return;
+ if (!CreateJDL()) return kFALSE;
+ if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
if (TestBit(AliAnalysisGrid::kTest)) {
// Locally testing the analysis
Info("StartAnalysis", "\n_______________________________________________________________________ \
}
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;
+ return kFALSE;
}
- // Submit AliEn job
- CdWork();
- TGridResult *res = gGrid->Command(Form("submit %s", fJDLName.Data()));
+ // Check if submitting is managed by LPM manager
+ if (fProductionMode) {
+ TString prodfile = fJDLName;
+ prodfile.ReplaceAll(".jdl", ".prod");
+ WriteProductionFile(prodfile);
+ Info("StartAnalysis", "Job submitting is managed by LPM. Rerun in terminate mode after jobs finished.");
+ return kFALSE;
+ }
+ // Submit AliEn job(s)
+ gGrid->Cd(fGridOutputDir);
+ TGridResult *res;
TString jobID = "";
- if (res) {
- const char *cjobId = res->GetKey(0,"jobId");
- if (!cjobId) {
- Error("StartAnalysis", "Your JDL %s could not be submitted", fJDLName.Data());
- return;
- } else {
- Info("StartAnalysis", "\n_______________________________________________________________________ \
- \n##### Your JDL %s was successfully submitted. \nTHE JOB ID IS: %s \
- \n_______________________________________________________________________",
- fJDLName.Data(), cjobId);
- jobID = cjobId;
- }
- delete res;
+ if (!fRunNumbers.Length() && !fRunRange[0]) {
+ // Submit a given xml or a set of runs
+ res = gGrid->Command(Form("submit %s", fJDLName.Data()));
+ printf("*************************** %s\n",Form("submit %s", fJDLName.Data()));
+ if (res) {
+ const char *cjobId = res->GetKey(0,"jobId");
+ if (!cjobId) {
+ Error("StartAnalysis", "Your JDL %s could not be submitted", fJDLName.Data());
+ return kFALSE;
+ } else {
+ Info("StartAnalysis", "\n_______________________________________________________________________ \
+ \n##### Your JDL %s was successfully submitted. \nTHE JOB ID IS: %s \
+ \n_______________________________________________________________________",
+ fJDLName.Data(), cjobId);
+ jobID = cjobId;
+ }
+ delete res;
+ }
+ } else {
+ // Submit for a range of enumeration of runs.
+ Submit();
}
+
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());
- //gGrid->Shell();
gSystem->Exec("aliensh");
+ return kTRUE;
+}
+
+//______________________________________________________________________________
+void AliAnalysisAlien::Submit()
+{
+// Submit all master jobs.
+ Int_t nmasterjobs = fInputFiles->GetEntries();
+ Long_t tshoot = gSystem->Now();
+ if (!fNsubmitted) SubmitNext();
+ while (fNsubmitted < nmasterjobs) {
+ Long_t now = gSystem->Now();
+ if ((now-tshoot)>30000) {
+ tshoot = now;
+ SubmitNext();
+ }
+ }
+}
+
+//______________________________________________________________________________
+void AliAnalysisAlien::SubmitNext()
+{
+// Submit next bunch of master jobs if the queue is free.
+ static Bool_t iscalled = kFALSE;
+ static Int_t firstmaster = 0;
+ static Int_t lastmaster = 0;
+ static Int_t npermaster = 0;
+ if (iscalled) return;
+ iscalled = kTRUE;
+ Int_t nrunning=0, nwaiting=0, nerror=0, ndone=0;
+ Int_t ntosubmit = 0;
+ TGridResult *res;
+ TString jobID = "";
+ if (!fNsubmitted) ntosubmit = 1;
+ else {
+ TString status = GetJobStatus(firstmaster, lastmaster, nrunning, nwaiting, nerror, ndone);
+ printf("=== master %d: %s\n", lastmaster, status.Data());
+ // If last master not split, just return
+ if (status != "SPLIT") {iscalled = kFALSE; return;}
+ // No more than 100 waiting jobs
+ if (nwaiting>100) {iscalled = kFALSE; return;}
+ npermaster = (nrunning+nwaiting+nerror+ndone)/fNsubmitted;
+ if (npermaster) ntosubmit = (100-nwaiting)/npermaster;
+ printf("=== WAITING(%d) RUNNING(%d) DONE(%d) OTHER(%d) NperMaster=%d => to submit %d jobs\n",
+ nwaiting, nrunning, ndone, nerror, npermaster, ntosubmit);
+ }
+ Int_t nmasterjobs = fInputFiles->GetEntries();
+ for (Int_t i=0; i<ntosubmit; i++) {
+ // Submit for a range of enumeration of runs.
+ if (fNsubmitted>=nmasterjobs) {iscalled = kFALSE; return;}
+ TString query;
+ TString runOutDir = gSystem->BaseName(fInputFiles->At(fNsubmitted)->GetName());
+ runOutDir.ReplaceAll(".xml", "");
+ if (fOutputToRunNo)
+ query = Form("submit %s %s %s", fJDLName.Data(), fInputFiles->At(fNsubmitted)->GetName(), runOutDir.Data());
+ else
+ query = Form("submit %s %s %03d", fJDLName.Data(), fInputFiles->At(fNsubmitted)->GetName(), fNsubmitted);
+ printf("********* %s\n",query.Data());
+ res = gGrid->Command(query);
+ if (res) {
+ TString cjobId1 = res->GetKey(0,"jobId");
+ if (!cjobId1.Length()) {
+ Error("StartAnalysis", "Your JDL %s could not be submitted", fJDLName.Data());
+ iscalled = kFALSE;
+ return;
+ } else {
+ Info("StartAnalysis", "\n_______________________________________________________________________ \
+ \n##### Your JDL %s submitted (%d to go). \nTHE JOB ID IS: %s \
+ \n_______________________________________________________________________",
+ fJDLName.Data(), nmasterjobs-fNsubmitted-1, cjobId1.Data());
+ jobID += cjobId1;
+ jobID += " ";
+ lastmaster = cjobId1.Atoi();
+ if (!firstmaster) firstmaster = lastmaster;
+ fNsubmitted++;
+ }
+ delete res;
+ }
+ }
+ iscalled = 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) {
+ // Skip task Terminate calls for the grid job
+ mgr->SetSkipTerminate(kTRUE);
+ // Unless merging makes no sense
+ if (IsSingleOutput()) mgr->SetSkipTerminate(kFALSE);
mgr->Write();
delete file;
+ // Enable termination for local jobs
+ mgr->SetSkipTerminate(kFALSE);
}
if (cdir) cdir->cd();
- Info("WriteAnalysisFile", "\n##### Analysis manager: %s wrote to file <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()));
}
}
type = "AOD";
comment += "AOD";
}
+ if (type!="AOD" && fFriendChainName!="") {
+ Error("WriteAnalysisMacro", "Friend chain can be attached only to AOD");
+ return;
+ }
if (TObject::TestBit(AliAnalysisGrid::kUseMC)) comment += "/MC";
else comment += " data";
out << "const char *anatype = \"" << type.Data() << "\";" << endl << endl;
out << "{" << endl;
out << comment.Data() << endl;
out << "// Automatically generated analysis steering macro executed in grid subjobs" << endl << endl;
+ out << " TStopwatch timer;" << endl;
+ out << " timer.Start();" << endl << endl;
out << "// load base root libraries" << endl;
out << " gSystem->Load(\"libTree\");" << endl;
out << " gSystem->Load(\"libGeom\");" << endl;
out << " gSystem->Load(\"libVMC\");" << endl;
out << " gSystem->Load(\"libPhysics\");" << endl << endl;
+ out << " gSystem->Load(\"libMinuit\");" << endl << endl;
+ if (fAdditionalRootLibs.Length()) {
+ // in principle libtree /lib geom libvmc etc. can go into this list, too
+ out << "// Add aditional libraries" << endl;
+ TObjArray *list = fAdditionalRootLibs.Tokenize(" ");
+ TIter next(list);
+ TObjString *str;
+ while((str=(TObjString*)next())) {
+ if (str->GetString().Contains(".so"))
+ out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
+ }
+ if (list) delete list;
+ }
out << "// Load analysis framework libraries" << endl;
+
+
if (!fPackages) {
out << " gSystem->Load(\"libSTEERBase\");" << endl;
out << " gSystem->Load(\"libESD\");" << endl;
Bool_t hasCORRFW = kFALSE;
while ((obj=next())) {
pkgname = obj->GetName();
- if (pkgname.Contains("STEERBase")) hasSTEERBase = kTRUE;
- if (pkgname.Contains("ESD")) hasESD = kTRUE;
- if (pkgname.Contains("AOD")) hasAOD = kTRUE;
- if (pkgname.Contains("ANALYSIS") && !pkgname.Contains("ANALYSISalice")) hasANALYSIS = kTRUE;
- if (pkgname.Contains("ANALYSISalice")) hasANALYSISalice = kTRUE;
- if (pkgname.Contains("CORRFW")) hasCORRFW = kTRUE;
+ if (pkgname == "STEERBase" ||
+ pkgname == "STEERBase.par") hasSTEERBase = kTRUE;
+ if (pkgname == "ESD" ||
+ pkgname == "ESD.par") hasESD = kTRUE;
+ if (pkgname == "AOD" ||
+ pkgname == "AOD.par") hasAOD = kTRUE;
+ if (pkgname == "ANALYSIS" ||
+ pkgname == "ANALYSIS.par") hasANALYSIS = kTRUE;
+ if (pkgname == "ANALYSISalice" ||
+ pkgname == "ANALYSISalice.par") hasANALYSISalice = kTRUE;
+ if (pkgname == "CORRFW" ||
+ pkgname == "CORRFW.par") hasCORRFW = kTRUE;
}
if (!hasSTEERBase) out << " gSystem->Load(\"libSTEERBase\");" << endl;
else out << " if (!SetupPar(\"STEERBase\")) return;" << endl;
else out << " if (!SetupPar(\"CORRFW\")) return;" << endl << endl;
out << "// Compile other par packages" << endl;
next.Reset();
- while ((obj=next()))
+ while ((obj=next())) {
+ pkgname = obj->GetName();
+ if (pkgname == "STEERBase" ||
+ pkgname == "STEERBase.par" ||
+ pkgname == "ESD" ||
+ pkgname == "ESD.par" ||
+ pkgname == "AOD" ||
+ pkgname == "AOD.par" ||
+ pkgname == "ANALYSIS" ||
+ pkgname == "ANALYSIS.par" ||
+ pkgname == "ANALYSISalice" ||
+ pkgname == "ANALYSISalice.par" ||
+ pkgname == "CORRFW" ||
+ pkgname == "CORRFW.par") continue;
out << " if (!SetupPar(\"" << obj->GetName() << "\")) return;" << endl;
+ }
}
out << "// include path" << endl;
if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
if (IsUsingTags()) {
out << " TChain *chain = CreateChainFromTags(\"wn.xml\", anatype);" << endl << endl;
} else {
- out << " TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl;
+ if(fFriendChainName!="AliAOD.VertexingHF.root") {
+ out << " TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl;
+ } else {
+ out << " // Check if the macro to create the chain was provided" << endl;
+ out << " if (gSystem->AccessPathName(\"MakeAODInputChain.C\")) {" << endl;
+ out << " ::Error(\"" << func.Data() << "\", \"File MakeAODInputChain.C not provided. Aborting.\");" << endl;
+ out << " return;" << endl;
+ out << " }" << endl;
+ out << " gROOT->LoadMacro(\"MakeAODInputChain.C\");" << endl;
+ out << " TChain *chain = MakeAODInputChain(\"wn.xml\",\"none\");" << endl << endl;
+ }
}
out << "// read the analysis manager from file" << endl;
- 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;
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 << " gROOT->LoadMacro(\"ConfigureCuts.C\");" << endl;
out << " ConfigureCuts(runCuts, lhcCuts, detCuts, evCuts);" << endl;
out << " }" << endl;
- out << " TChain *chain = tagAna->QueryTags(runCuts, lhcCuts, detCuts, evCuts);" << 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;
+ 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 += " AliEventTagCuts *evCuts)";
Info("WriteAnalysisMacro", msg.Data());
}
- } else {
+ }
+ if (!IsUsingTags() || fFriendChainName!="") {
+ 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 << " return NULL;" << endl;
out << " }" << endl;
out << " TChain *chain = new TChain(treename);" << endl;
+ if(fFriendChainName!="") {
+ out << " TChain *chainFriend = new TChain(treename);" << endl;
+ }
out << " coll->Reset();" << endl;
- out << " while (coll->Next()) chain->Add(coll->GetTURL(\"\"));" << endl;
+ out << " while (coll->Next()) {" << endl;
+ out << " chain->Add(coll->GetTURL(\"\"));" << 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;
+ }
+ 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;
+ out << "}" << endl << endl;
}
if (fPackages) {
+ out <<"//________________________________________________________________________________" << endl;
out << "Bool_t SetupPar(const char *package) {" << endl;
out << "// Compile the package and set it up." << endl;
out << " TString pkgdir = package;" << endl;
out << " pkgdir.ReplaceAll(\".par\",\"\");" << endl;
- out << " gSystem->Exec(Form(\"tar xvzf %s\", package));" << endl;
+ out << " gSystem->Exec(Form(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
out << " TString cdir = gSystem->WorkingDirectory();" << endl;
out << " gSystem->ChangeDirectory(pkgdir);" << endl;
out << " // Check for BUILD.sh and execute" << endl;
out << " printf(\"*** Building PAR archive ***\\n\");" << endl;
out << " printf(\"*******************************\\n\");" << endl;
out << " if (gSystem->Exec(\"PROOF-INF/BUILD.sh\")) {" << endl;
- out << " ::Error(\"SetupPar\", \"Cannot build par archive %s\", package);" << endl;
+ out << " ::Error(\"SetupPar\", \"Cannot build par archive %s\", pkgdir.Data());" << endl;
out << " gSystem->ChangeDirectory(cdir);" << endl;
out << " return kFALSE;" << endl;
out << " }" << endl;
out << " } else {" << endl;
- out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/BUILD.sh for package %s\", package);" << endl;
+ out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/BUILD.sh for package %s\", pkgdir.Data());" << endl;
out << " gSystem->ChangeDirectory(cdir);" << endl;
out << " return kFALSE;" << endl;
out << " }" << endl;
out << " printf(\"*******************************\\n\");" << endl;
out << " gROOT->Macro(\"PROOF-INF/SETUP.C\");" << endl;
out << " } else {" << endl;
- out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/SETUP.C for package %s\", package);" << endl;
+ out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/SETUP.C for package %s\", pkgdir.Data());" << endl;
out << " gSystem->ChangeDirectory(cdir);" << endl;
out << " return kFALSE;" << endl;
out << " }" << endl;
ofstream out;
out.open(fExecutable.Data(), ios::out);
if (out.bad()) {
- Error("CreateJDL", "Bad file name for executable: %s", fExecutable.Data());
+ Error("WriteExecutable", "Bad file name for executable: %s", fExecutable.Data());
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 << "echo $ALICE_ROOT" << endl;
out << "echo \"############## which aliroot : ##############\"" << endl;
out << "which aliroot" << endl;
+ out << "echo \"############## system limits : ##############\"" << endl;
+ out << "ulimit -a" << endl;
+ out << "echo \"############## memory : ##############\"" << endl;
+ out << "free -m" << endl;
out << "echo \"=========================================\"" << endl << endl;
-// if (TestBit(AliAnalysisGrid::kTest)) out << "root ";
- out << "root -b -q ";
- out << fAnalysisMacro.Data() << endl << endl;
- out << "echo \"======== " << fAnalysisMacro.Data() << " finished ========\"" << endl;
+ // Make sure we can properly compile par files
+ if (TObject::TestBit(AliAnalysisGrid::kUsePars)) out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
+ out << fExecutableCommand << " ";
+ out << fAnalysisMacro.Data() << " " << fExecutableArgs.Data() << endl << endl;
+ out << "echo \"======== " << fAnalysisMacro.Data() << " finished with exit code: $? ========\"" << endl;
+ out << "echo \"############## memory after: ##############\"" << endl;
+ out << "free -m" << endl;
+ out << "echo \"############## Last 10 lines from dmesg : ##############\"" << endl;
+ out << "dmesg | tail -n 10" << endl;
}
Bool_t copy = kTRUE;
if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
+ TString bindir = Form("%s/bin", workdir.Data());
+ if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir);
workdir += fGridWorkingDir;
TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), fExecutable.Data());
if (FileExists(executable)) gGrid->Rm(executable);
}
}
+//______________________________________________________________________________
+void AliAnalysisAlien::WriteProductionFile(const char *filename) const
+{
+// Write the production file to be submitted by LPM manager. The format is:
+// First line: full_path_to_jdl estimated_no_subjobs_per_master
+// Next lines: full_path_to_dataset XXX (XXX is a string)
+// To submit, one has to: submit jdl XXX for all lines
+ ofstream out;
+ out.open(filename, ios::out);
+ if (out.bad()) {
+ Error("WriteProductionFile", "Bad file name: %s", filename);
+ return;
+ }
+ TString workdir = gGrid->GetHomeDirectory();
+ workdir += fGridWorkingDir;
+ Int_t njobspermaster = 1000*fNrunsPerMaster/fSplitMaxInputFileNumber;
+ TString locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
+ out << locjdl << " " << njobspermaster << endl;
+ Int_t nmasterjobs = fInputFiles->GetEntries();
+ for (Int_t i=0; i<nmasterjobs; i++) {
+ out << Form("%s", fInputFiles->At(i)->GetName()) << " " << Form("%03d", i) << endl;
+ }
+ Info("WriteProductionFile", "\n##### Copying production file <%s> to your work directory", filename);
+ if (FileExists(filename)) gGrid->Rm(filename);
+ TFile::Cp(Form("file:%s",filename), Form("alien://%s/%s", workdir.Data(),filename));
+}
+
//______________________________________________________________________________
void AliAnalysisAlien::WriteValidationScript()
{
// 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 << "ls -la ./" << out_stream << endl;
out << "echo \"* ----------------------------------------------------*\"" << out_stream << endl << endl;
out << "##################################################" << endl;
+
+ out << "" << endl;
+ out << "parArch=`grep -Ei \"Cannot Build the PAR Archive\" stderr`" << endl;
+ out << "segViol=`grep -Ei \"Segmentation violation\" stderr`" << endl;
+ out << "segFault=`grep -Ei \"Segmentation fault\" stderr`" << endl;
+ out << "" << endl;
+
+ out << "if [ ! -f stderr ] ; then" << endl;
+ out << " error=1" << endl;
+ out << " echo \"* ########## Job not validated - no stderr ###\" " << out_stream << endl;
+ out << " echo \"Error = $error\" " << out_stream << endl;
+ out << "fi" << endl;
+
+ out << "if [ \"$parArch\" != \"\" ] ; then" << endl;
+ out << " error=1" << endl;
+ out << " echo \"* ########## Job not validated - PAR archive not built ###\" " << out_stream << endl;
+ out << " echo \"$parArch\" " << out_stream << endl;
+ out << " echo \"Error = $error\" " << out_stream << endl;
+ out << "fi" << endl;
+
+ out << "if [ \"$segViol\" != \"\" ] ; then" << endl;
+ out << " error=1" << endl;
+ out << " echo \"* ########## Job not validated - Segment. violation ###\" " << out_stream << endl;
+ out << " echo \"$segViol\" " << out_stream << endl;
+ out << " echo \"Error = $error\" " << out_stream << endl;
+ out << "fi" << endl;
+
+ out << "if [ \"$segFault\" != \"\" ] ; then" << endl;
+ out << " error=1" << endl;
+ out << " echo \"* ########## Job not validated - Segment. fault ###\" " << out_stream << endl;
+ out << " echo \"$segFault\" " << out_stream << endl;
+ out << " echo \"Error = $error\" " << out_stream << endl;
+ out << "fi" << endl;
+
+ // Part dedicated to the specific analyses running into the train
+
TObjArray *arr = fOutputFiles.Tokenize(" ");
TIter next1(arr);
TString output_file;
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