//==============================================================================
#include "Riostream.h"
+#include "TEnv.h"
+#include "TError.h"
#include "TROOT.h"
#include "TSystem.h"
#include "TFile.h"
AliAnalysisAlien::AliAnalysisAlien()
:AliAnalysisGrid(),
fGridJDL(NULL),
+ fMergingJDL(NULL),
fPrice(0),
fTTL(0),
fSplitMaxInputFileNumber(0),
fMaxMergeFiles(0),
fNsubmitted(0),
fProductionMode(0),
+ fOutputToRunNo(0),
+ fMergeViaJDL(0),
+ fFastReadOption(0),
+ fOverwriteMode(0),
fRunNumbers(),
fExecutable(),
+ fExecutableCommand(),
fArguments(),
+ fExecutableArgs(),
fAnalysisMacro(),
fAnalysisSource(),
+ fAdditionalRootLibs(),
fAdditionalLibs(),
fSplitMode(),
fAPIVersion(),
fROOTVersion(),
fAliROOTVersion(),
+ fExternalPackages(),
fUser(),
fGridWorkingDir(),
fGridDataDir(),
fIncludePath(),
fCloseSE(),
fFriendChainName(),
+ fJobTag(),
+ fOutputSingle(),
+ fRunPrefix(),
fInputFiles(0),
fPackages(0)
{
AliAnalysisAlien::AliAnalysisAlien(const char *name)
:AliAnalysisGrid(name),
fGridJDL(NULL),
+ fMergingJDL(NULL),
fPrice(0),
fTTL(0),
fSplitMaxInputFileNumber(0),
fMaxMergeFiles(0),
fNsubmitted(0),
fProductionMode(0),
+ fOutputToRunNo(0),
+ fMergeViaJDL(0),
+ fFastReadOption(0),
+ fOverwriteMode(0),
fRunNumbers(),
fExecutable(),
+ fExecutableCommand(),
fArguments(),
+ fExecutableArgs(),
fAnalysisMacro(),
fAnalysisSource(),
+ fAdditionalRootLibs(),
fAdditionalLibs(),
fSplitMode(),
fAPIVersion(),
fROOTVersion(),
fAliROOTVersion(),
+ fExternalPackages(),
fUser(),
fGridWorkingDir(),
fGridDataDir(),
fIncludePath(),
fCloseSE(),
fFriendChainName(),
+ fJobTag(),
+ fOutputSingle(),
+ fRunPrefix(),
fInputFiles(0),
fPackages(0)
{
AliAnalysisAlien::AliAnalysisAlien(const AliAnalysisAlien& other)
:AliAnalysisGrid(other),
fGridJDL(NULL),
+ fMergingJDL(NULL),
fPrice(other.fPrice),
fTTL(other.fTTL),
fSplitMaxInputFileNumber(other.fSplitMaxInputFileNumber),
fMaxMergeFiles(other.fMaxMergeFiles),
fNsubmitted(other.fNsubmitted),
fProductionMode(other.fProductionMode),
+ fOutputToRunNo(other.fOutputToRunNo),
+ fMergeViaJDL(other.fMergeViaJDL),
+ fFastReadOption(other.fFastReadOption),
+ fOverwriteMode(other.fOverwriteMode),
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),
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()");
+ fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
fRunRange[0] = other.fRunRange[0];
fRunRange[1] = other.fRunRange[1];
if (other.fInputFiles) {
{
// Destructor.
if (fGridJDL) delete fGridJDL;
+ if (fMergingJDL) delete fMergingJDL;
if (fInputFiles) delete fInputFiles;
if (fPackages) delete fPackages;
}
if (this != &other) {
AliAnalysisGrid::operator=(other);
fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
+ fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
fPrice = other.fPrice;
fTTL = other.fTTL;
fSplitMaxInputFileNumber = other.fSplitMaxInputFileNumber;
fMaxMergeFiles = other.fMaxMergeFiles;
fNsubmitted = other.fNsubmitted;
fProductionMode = other.fProductionMode;
+ fOutputToRunNo = other.fOutputToRunNo;
+ fMergeViaJDL = other.fMergeViaJDL;
+ fFastReadOption = other.fFastReadOption;
+ fOverwriteMode = other.fOverwriteMode;
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;
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 = "";
+ }
}
//______________________________________________________________________________
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;
}
TObjArray *arr;
TObjString *os;
Int_t nruns = 0;
- TString schunk;
+ TString schunk, schunk2;
TString path;
if (!checked) {
checked = kTRUE;
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());
} 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/%d ", fGridDataDir.Data(), irun);
- if (!gGrid->Cd(path)) {
- Warning("CheckInputData", "Run number %d not found in path: %s", irun, path.Data());
+ 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/%d.xml", workdir.Data(),irun);
+ path = Form("%s/%s%d.xml", workdir.Data(),fRunPrefix.Data(),irun);
TString msg = "\n##### file: ";
msg += path;
msg += " type: xml_collection;";
else msg += " using_tags: No";
Info("CheckDataType", msg.Data());
if (fNrunsPerMaster<2) {
- AddDataFile(Form("%d.xml",irun));
+ AddDataFile(Form("%s%d.xml",fRunPrefix.Data(),irun));
} else {
nruns++;
if (((nruns-1)%fNrunsPerMaster) == 0) {
- schunk = Form("%d", irun);
+ schunk = Form("%s%d", fRunPrefix.Data(),irun);
}
+ schunk2 = Form("_%s%d.xml", fRunPrefix.Data(), irun);
if ((nruns%fNrunsPerMaster)!=0 && irun != fRunRange[1]) continue;
- schunk += Form("_%d.xml", irun);
+ schunk += schunk2;
AddDataFile(schunk);
}
}
+ if (!fInputFiles) {
+ schunk += schunk2;
+ AddDataFile(schunk);
+ }
}
return kTRUE;
}
TString file;
TString path;
Int_t nruns = 0;
- TString schunk;
+ 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 (!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) || fOverwriteMode) {
command = "find ";
command += options;
command += path;
if (res) delete res;
// Write standard output to file
gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
- }
- if (!TestBit(AliAnalysisGrid::kTest) && !FileExists(file)) {
+ }
+ Bool_t fileExists = FileExists(file);
+ if (!TestBit(AliAnalysisGrid::kTest) && (!fileExists || fOverwriteMode)) {
// Copy xml file to alien space
+ if (fileExists) gGrid->Rm(file);
TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
if (!FileExists(file)) {
Error("CreateDataset", "Command %s did NOT succeed", command.Data());
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.
// 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;
+ if (fOverwriteMode) gGrid->Rm(file);
+ else {
+ Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
+ continue;
+ }
}
// Copy xml file to alien space
TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
continue;
}
schunk += Form("_%s.xml", os->GetString().Data());
- if (FileExists(schunk)) {
- Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
- continue;
+ if (FileExists(schunk)) {
+ if (fOverwriteMode) gGrid->Rm(file);
+ else {
+ Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
+ continue;
+ }
}
- printf("Exporting merged collection <%s> and copying to AliEn.\n", schunk.Data());
+ 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;
} else {
// 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();
+ 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("%d.xml", irun);
- if (FileExists(file) && fNrunsPerMaster<2 && !TestBit(AliAnalysisGrid::kTest)) {
- Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
-// gGrid->Rm(file);
- continue;
+ else file = Form("%s%d.xml", fRunPrefix.Data(), irun);
+ if (FileExists(file) && fNrunsPerMaster<2 && !TestBit(AliAnalysisGrid::kTest)) {
+ if (fOverwriteMode) gGrid->Rm(file);
+ else {
+ Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
+ continue;
+ }
}
// If local collection file does not exist, create it via 'find' command.
- if (gSystem->AccessPathName(file)) {
+ if (gSystem->AccessPathName(file) || fOverwriteMode) {
command = "find ";
command += options;
command += path;
// 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;
+ if (fOverwriteMode) gGrid->Rm(file);
+ else {
+ Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
+ continue;
+ }
}
// Copy xml file to alien space
TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
nruns++;
// Check if the collection for the chunk exist locally.
Int_t nchunk = (nruns-1)/fNrunsPerMaster;
- if (FileExists(fInputFiles->At(nchunk)->GetName())) continue;
+ if (FileExists(fInputFiles->At(nchunk)->GetName())) {
+ if (fOverwriteMode) gGrid->Rm(fInputFiles->At(nchunk)->GetName());
+ else continue;
+ }
printf(" Merging collection <%s> into %d runs chunk...\n",file.Data(),fNrunsPerMaster);
if (((nruns-1)%fNrunsPerMaster) == 0) {
- schunk = Form("%d", irun);
+ 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;
}
- if ((nruns%fNrunsPerMaster)!=0 && irun!=fRunRange[1]) {
+ schunk2 = Form("%s_%s%d.xml", schunk.Data(), fRunPrefix.Data(), irun);
+ if ((nruns%fNrunsPerMaster)!=0 && irun!=fRunRange[1] && schunk2 != fInputFiles->Last()->GetName()) {
continue;
}
- schunk += Form("_%d.xml", irun);
+ schunk = schunk2;
if (FileExists(schunk)) {
- Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
- continue;
+ if (fOverwriteMode) gGrid->Rm(schunk);
+ else {
+ Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
+ continue;
+ }
}
printf("Exporting merged collection <%s> and copying to AliEn.\n", schunk.Data());
cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs");
if (FileExists(schunk)) {
- Info("CreateDataset", "\n##### Dataset %s exist. Skipping copy...", schunk.Data());
- continue;
+ if (fOverwriteMode) gGrid->Rm(schunk);
+ else {
+ Info("CreateDataset", "\n##### Dataset %s exist. Skipping copy...", schunk.Data());
+ continue;
+ }
}
TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data()));
if (!FileExists(schunk)) {
error = 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 {
// Exit if any error up to now
if (error) return kFALSE;
// Set JDL fields
- fGridJDL->SetValue("User", Form("\"%s\"", fUser.Data()));
- fGridJDL->SetExecutable(fExecutable);
-// fGridJDL->SetTTL((UInt_t)fTTL);
- fGridJDL->SetValue("TTL", Form("\"%d\"", fTTL));
- if (fMaxInitFailed > 0)
+ 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;
+ 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");
+ if (!fArguments.IsNull())
+ fGridJDL->SetArguments(fArguments, "Arguments for the executable command");
+ fMergingJDL->SetArguments("$1");
+ fGridJDL->SetValue("TTL", Form("\"%d\"",fTTL));
+ fGridJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60));
+ fMergingJDL->SetValue("TTL", Form("\"%d\"",fTTL));
+ fMergingJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60));
+
+ if (fMaxInitFailed > 0) {
fGridJDL->SetValue("MaxInitFailed", Form("\"%d\"",fMaxInitFailed));
- if (fSplitMaxInputFileNumber > 0)
+ fGridJDL->SetDescription("MaxInitFailed", "Maximum number of first failing jobs to abort the master job");
+ }
+ if (fSplitMaxInputFileNumber > 0) {
fGridJDL->SetValue("SplitMaxInputFileNumber", Form("\"%d\"", fSplitMaxInputFileNumber));
- if (fSplitMode.Length())
+ fGridJDL->SetDescription("SplitMaxInputFileNumber", "Maximum number of input files to be processed per subjob");
+ }
+ if (fSplitMode.Length()) {
fGridJDL->SetValue("Split", Form("\"%s\"", fSplitMode.Data()));
-// fGridJDL->SetSplitMode(fSplitMode, (UInt_t)fSplitMaxInputFileNumber);
- if (fAliROOTVersion.Length())
- fGridJDL->AddToPackages("AliRoot", fAliROOTVersion);
- if (fROOTVersion.Length())
+ fGridJDL->SetDescription("Split", "We split per SE or file");
+ }
+ if (!fAliROOTVersion.IsNull()) {
+ fGridJDL->AddToPackages("AliRoot", fAliROOTVersion,"VO_ALICE", "List of requested packages");
+ fMergingJDL->AddToPackages("AliRoot", fAliROOTVersion, "VO_ALICE", "List of requested packages");
+ }
+ if (!fROOTVersion.IsNull()) {
fGridJDL->AddToPackages("ROOT", fROOTVersion);
- if (fAPIVersion.Length())
+ fMergingJDL->AddToPackages("ROOT", fROOTVersion);
+ }
+ if (!fAPIVersion.IsNull()) {
fGridJDL->AddToPackages("APISCONFIG", fAPIVersion);
- 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()));
+ fMergingJDL->AddToPackages("APISCONFIG", fAPIVersion);
+ }
+ if (!fExternalPackages.IsNull()) {
+ arr = fExternalPackages.Tokenize(" ");
+ TIter next(arr);
+ while ((os=(TObjString*)next())) {
+ TString pkgname = os->GetString();
+ Int_t index = pkgname.Index("::");
+ TString pkgversion = pkgname(index+2, pkgname.Length());
+ pkgname.Remove(index);
+ fGridJDL->AddToPackages(pkgname, pkgversion);
+ fMergingJDL->AddToPackages(pkgname, pkgversion);
+ }
+ delete arr;
+ }
+ fGridJDL->SetInputDataListFormat(fInputFormat, "Format of input data");
+ fGridJDL->SetInputDataList("wn.xml", "Collection name to be processed on each worker node");
+ fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), fAnalysisMacro.Data()), "List of input files to be uploaded to workers");
+ TString analysisFile = fExecutable;
+ analysisFile.ReplaceAll(".sh", ".root");
+ fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),analysisFile.Data()));
+ fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),analysisFile.Data()));
if (IsUsingTags() && !gSystem->AccessPathName("ConfigureCuts.C"))
fGridJDL->AddToInputSandbox(Form("LF:%s/ConfigureCuts.C", workdir.Data()));
if (fAdditionalLibs.Length()) {
while ((os=(TObjString*)next())) {
if (os->GetString().Contains(".so")) continue;
fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), os->GetString().Data()));
+ fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), os->GetString().Data()));
}
delete arr;
}
if (fPackages) {
TIter next(fPackages);
TObject *obj;
- while ((obj=next()))
+ while ((obj=next())) {
fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName()));
+ fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName()));
+ }
}
if (fOutputArchive.Length()) {
arr = fOutputArchive.Tokenize(" ");
TIter next(arr);
- while ((os=(TObjString*)next()))
- if (!os->GetString().Contains("@") && fCloseSE.Length())
- fGridJDL->AddToOutputArchive(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()));
- else
- fGridJDL->AddToOutputArchive(os->GetString());
+ 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);
+ else
+ fGridJDL->AddToOutputArchive(os->GetString(), comment);
+ first = kFALSE;
+ }
delete arr;
+ TString outputArchive = fOutputArchive;
+ if (!fMergeExcludes.IsNull()) {
+ arr = fMergeExcludes.Tokenize(" ");
+ TIter next1(arr);
+ while ((os=(TObjString*)next1())) {
+ outputArchive.ReplaceAll(Form("%s,",os->GetString().Data()),"");
+ outputArchive.ReplaceAll(os->GetString(),"");
+ }
+ delete arr;
+ }
+ arr = outputArchive.Tokenize(" ");
+ TIter next2(arr);
+ comment = comment1;
+ first = kTRUE;
+ while ((os=(TObjString*)next2())) {
+ if (!first) comment = NULL;
+ if (!os->GetString().Contains("@") && fCloseSE.Length())
+ fMergingJDL->AddToOutputArchive(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
+ else
+ fMergingJDL->AddToOutputArchive(os->GetString(), comment);
+ first = kFALSE;
+ }
+ delete arr;
}
arr = fOutputFiles.Tokenize(" ");
TIter next(arr);
+ Bool_t first = kTRUE;
+ const char *comment = "Files to be archived";
+ const char *comment1 = comment;
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 (!first) comment = NULL;
if (!os->GetString().Contains("@") && fCloseSE.Length())
- fGridJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()));
+ fGridJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
else
- fGridJDL->AddToOutputSandbox(os->GetString());
+ fGridJDL->AddToOutputSandbox(os->GetString(), comment);
+ first = kFALSE;
}
delete arr;
-// fGridJDL->SetPrice((UInt_t)fPrice);
- fGridJDL->SetValue("Price", Form("\"%d\"", fPrice));
- fGridJDL->SetValidationCommand(Form("%s/validate.sh", workdir.Data()));
- if (fMasterResubmitThreshold) fGridJDL->SetValue("MasterResubmitThreshold", Form("\"%d%%\"", fMasterResubmitThreshold));
+ if (fOutputFiles.Length()) {
+ TString outputFiles = fOutputFiles;
+ if (!fMergeExcludes.IsNull()) {
+ arr = fMergeExcludes.Tokenize(" ");
+ TIter next1(arr);
+ while ((os=(TObjString*)next1())) {
+ outputFiles.ReplaceAll(Form("%s,",os->GetString().Data()),"");
+ outputFiles.ReplaceAll(os->GetString(),"");
+ }
+ delete arr;
+ }
+ arr = outputFiles.Tokenize(" ");
+ TIter next2(arr);
+ comment = comment1;
+ first = kTRUE;
+ while ((os=(TObjString*)next2())) {
+ // Ignore ouputs in jdl that are also in outputarchive
+ TString sout = os->GetString();
+ if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
+ if (fOutputArchive.Contains(sout)) continue;
+ if (!first) comment = NULL;
+ if (!os->GetString().Contains("@") && fCloseSE.Length())
+ fMergingJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
+ else
+ fMergingJDL->AddToOutputSandbox(os->GetString(), comment);
+ }
+ delete arr;
+ }
+ fGridJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
+ fMergingJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
+ TString validationScript = fExecutable;
+ validationScript.ReplaceAll(".sh", "_validation.sh");
+ fGridJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
+ validationScript = fExecutable;
+ validationScript.ReplaceAll(".sh", "_mergevalidation.sh");
+ fMergingJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
+ if (fMasterResubmitThreshold) {
+ fGridJDL->SetValue("MasterResubmitThreshold", Form("\"%d%%\"", fMasterResubmitThreshold));
+ fGridJDL->SetDescription("MasterResubmitThreshold", "Resubmit failed jobs until DONE rate reaches this percentage");
+ }
// Write a jdl with 2 input parameters: collection name and output dir name.
WriteJDL(copy);
}
// Copy jdl to grid workspace
if (copy) {
+ // Check if an output directory was defined and valid
+ if (!fGridOutputDir.Length()) {
+ Error("CreateJDL", "You must define AliEn output directory");
+ return kFALSE;
+ } else {
+ if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
+ if (!fProductionMode && !DirectoryExists(fGridOutputDir)) {
+ if (gGrid->Mkdir(fGridOutputDir)) {
+ Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
+ } else {
+ Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
+ return kFALSE;
+ }
+ }
+ gGrid->Cd(workdir);
+ }
+ if (TestBit(AliAnalysisGrid::kSubmit)) {
+ TString mergeJDLName = fExecutable;
+ mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
+ TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
+ TString locjdl1 = Form("%s/%s", fGridOutputDir.Data(),mergeJDLName.Data());
+ if (fProductionMode) {
+ locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
+ locjdl1 = Form("%s/%s", workdir.Data(),mergeJDLName.Data());
+ }
+ if (FileExists(locjdl)) gGrid->Rm(locjdl);
+ if (FileExists(locjdl1)) gGrid->Rm(locjdl1);
+ Info("CreateJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
+ TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
+ if (fMergeViaJDL) {
+ Info("CreateJDL", "\n##### Copying merging JDL file <%s> to your AliEn output directory", mergeJDLName.Data());
+ TFile::Cp(Form("file:%s",mergeJDLName.Data()), Form("alien://%s", locjdl1.Data()));
+ }
+ }
if (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()));
}
// 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()));
- fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_03i#", fGridOutputDir.Data()));
+ fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetString().Data()), "Input xml collections");
+ if (!fOutputSingle.IsNull())
+ fGridJDL->SetOutputDirectory(Form("#alienfulldir#/../%s",fOutputSingle.Data()), "Output directory");
+ else {
+ fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
+ fMergingJDL->SetOutputDirectory(fGridOutputDir);
+ }
} 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->AddToInputDataCollection(Form("LF:%s/$1,nodownload", workdir.Data()), "Input xml collections");
+ if (!fOutputSingle.IsNull()) {
+ if (!fOutputToRunNo) fGridJDL->SetOutputDirectory(Form("#alienfulldir#/%s",fOutputSingle.Data()), "Output directory");
+ else fGridJDL->SetOutputDirectory(Form("%s/$2",fGridOutputDir.Data()), "Output directory");
+ } else {
+ fGridJDL->SetOutputDirectory(Form("%s/$2/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
+ fMergingJDL->SetOutputDirectory(Form("%s/$1", fGridOutputDir.Data()), "Output directory");
+ }
}
// Generate the JDL as a string
TString sjdl = fGridJDL->Generate();
+ TString sjdl1 = fMergingJDL->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 \n", "{\n");
sjdl.ReplaceAll("\n\n", "\n");
sjdl.ReplaceAll("OutputDirectory", "OutputDir");
+ sjdl1.ReplaceAll("\"LF:", "\n \"LF:");
+ sjdl1.ReplaceAll("(member", "\n (member");
+ sjdl1.ReplaceAll("\",\"VO_", "\",\n \"VO_");
+ sjdl1.ReplaceAll("{", "{\n ");
+ sjdl1.ReplaceAll("};", "\n};");
+ sjdl1.ReplaceAll("{\n \n", "{\n");
+ sjdl1.ReplaceAll("\n\n", "\n");
+ sjdl1.ReplaceAll("OutputDirectory", "OutputDir");
sjdl += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
- sjdl.Prepend("JobTag = \"Automatically generated analysis JDL\";\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");
+ sjdl1 += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
+ sjdl1.Prepend(Form("Jobtag = {\n \"comment:Merging_%s\"\n};\n", fJobTag.Data()));
+ index = sjdl1.Index("JDLVariables");
+ if (index >= 0) sjdl1.Insert(index, "\n# JDL variables\n");
// Write jdl to file
ofstream out;
out.open(fJDLName.Data(), ios::out);
return kFALSE;
}
out << sjdl << endl;
+ TString mergeJDLName = fExecutable;
+ mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
+ if (fMergeViaJDL) {
+ ofstream out1;
+ out1.open(mergeJDLName.Data(), ios::out);
+ if (out.bad()) {
+ Error("CreateJDL", "Bad file name: %s", mergeJDLName.Data());
+ return kFALSE;
+ }
+ out1 << sjdl1 << 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)
+ TString locjdl1 = Form("%s/%s", fGridOutputDir.Data(),mergeJDLName.Data());
+ if (fProductionMode) {
locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
+ locjdl1 = Form("%s/%s", workdir.Data(),mergeJDLName.Data());
+ }
if (FileExists(locjdl)) gGrid->Rm(locjdl);
+ if (FileExists(locjdl1)) gGrid->Rm(locjdl1);
+ Info("CreateJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
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()));
+ }
}
return kTRUE;
}
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)
{
}
use_tags = slfn.Contains(".tag");
if (slfn.Contains(".root")) msg += " type: root file;";
- else msg += " type: unhnown file;";
+ else msg += " type: unknown file;";
if (use_tags) msg += " using_tags: Yes";
else msg += " using_tags: No";
Info("CheckDataType", msg.Data());
pkg.ReplaceAll(".par", "");
pkg += ".par";
if (gSystem->AccessPathName(pkg)) {
- Error("EnablePackage", "Package %s not found", pkg.Data());
+ Fatal("EnablePackage", "Package %s not found", pkg.Data());
return;
}
if (!TObject::TestBit(AliAnalysisGrid::kUsePars))
return kFALSE;
}
+//______________________________________________________________________________
+Bool_t AliAnalysisAlien::IsSingleOutput() const
+{
+// Check if single-ouput option is on.
+ return (!fOutputSingle.IsNull());
+}
+
//______________________________________________________________________________
void AliAnalysisAlien::Print(Option_t *) const
{
if (fRunNumbers.Length())
printf("= Run numbers to be processed: _________________ %s\n", fRunNumbers.Data());
if (fRunRange[0])
- printf("= Run range to be processed: ___________________ %d-%d\n", fRunRange[0], fRunRange[1]);
+ 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;
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("= 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());
// Set default values for everything. What cannot be filled will be left empty.
if (fGridJDL) delete fGridJDL;
fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
+ fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
fPrice = 1;
fTTL = 30000;
fSplitMaxInputFileNumber = 100;
fMaxMergeFiles = 100;
fRunNumbers = "";
fExecutable = "analysis.sh";
+ fExecutableCommand = "root -b -q";
fArguments = "";
+ fExecutableArgs = "";
fAnalysisMacro = "myAnalysis.C";
fAnalysisSource = "";
fAdditionalLibs = "";
fOutputFiles = ""; // Like "AliAODs.root histos.root"
fInputFormat = "xml-single";
fJDLName = "analysis.jdl";
+ fJobTag = "Automatically generated analysis JDL";
fMergeExcludes = "";
+ fMergeViaJDL = 0;
}
+//______________________________________________________________________________
+Bool_t AliAnalysisAlien::MergeOutput(const char *output, const char *basedir, Int_t nmaxmerge)
+{
+// Merge all registered outputs from basedir.
+ TString output_file = output;
+ TString command;
+ TString output_chunk;
+ TString previous_chunk = "";
+ Int_t count_chunk = 0;
+ Int_t count_zero = nmaxmerge;
+ Bool_t merged = kTRUE;
+ Int_t index = output_file.Index("@");
+ if (index > 0) output_file.Remove(index);
+ command = Form("find %s/ *%s", basedir, output_file.Data());
+ printf("command: %s\n", command.Data());
+ TGridResult *res = gGrid->Command(command);
+ if (!res) {
+ printf("Error: No result for the find command\n");
+ return kFALSE;
+ }
+
+ TFileMerger *fm = 0;
+ TIter nextmap(res);
+ TMap *map = 0;
+ // Check if there is a merge operation to resume
+ output_chunk = output_file;
+ output_chunk.ReplaceAll(".root", "_*.root");
+ // Check for existent temporary merge files
+ if (!gSystem->Exec(Form("ls %s", output_chunk.Data()))) {
+ while (1) {
+ // Skip as many input files as in a chunk
+ for (Int_t counter=0; counter<nmaxmerge; counter++) map = (TMap*)nextmap();
+ if (!map) {
+ ::Error("MergeOutputs", "Cannot resume merging for <%s>, nentries=%d", output_file.Data(), res->GetSize());
+ delete res;
+ return kFALSE;
+ }
+ output_chunk = output_file;
+ output_chunk.ReplaceAll(".root", Form("_%04d.root", count_chunk));
+ 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 = nmaxmerge;
+
+ while ((map=(TMap*)nextmap())) {
+ // Loop 'find' results and get next LFN
+ if (count_zero == nmaxmerge) {
+ // 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;
+ delete fm;
+ return kFALSE;
+ }
+ // 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;
+ return kFALSE;
+ }
+ // 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;
+ return kFALSE;
+ } 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 = nmaxmerge;
+ previous_chunk = output_chunk;
+ }
+ }
+ return merged;
+}
+
//______________________________________________________________________________
Bool_t AliAnalysisAlien::MergeOutputs()
{
if (!Connect()) {
Error("MergeOutputs", "Cannot merge outputs without grid connection. Terminate will NOT be executed");
return kFALSE;
+ }
+ if (fMergeViaJDL) {
+ if (!TestBit(AliAnalysisGrid::kMerge)) {
+ Info("MergeOutputs", "### Re-run with <MergeViaJDL> option in terminate mode of the plugin to submit merging jobs ###");
+ return kFALSE;
+ }
+ if (fProductionMode) {
+ Info("MergeOutputs", "### Merging will be submitted by LPM manager... ###");
+ return kFALSE;
+ }
+ Info("MergeOutputs", "Submitting merging JDL");
+ SubmitMerging();
+ Info("MergeOutputs", "### Re-run with <MergeViaJDL> off to collect results after merging jobs are done ###");
+ Info("MergeOutputs", "### The Terminate() method is executed by the merging jobs");
+ return kFALSE;
}
// Get the output path
if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
- if (!gGrid->Cd(fGridOutputDir)) {
+ if (!DirectoryExists(fGridOutputDir)) {
Error("MergeOutputs", "Grid output directory %s not found. Terminate() will NOT be executed", fGridOutputDir.Data());
return kFALSE;
}
if (!fOutputFiles.Length()) {
Error("MergeOutputs", "No output file names defined. Are you running the right AliAnalysisAlien configuration ?");
return kFALSE;
+ }
+ // Check if fast read option was requested
+ if (fFastReadOption) {
+ Warning("MergeOutputs", "You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !");
+ gEnv->SetValue("XNet.ConnectTimeout",5);
+ gEnv->SetValue("XNet.RequestTimeout",5);
+ gEnv->SetValue("XNet.MaxRedirectCount",2);
+ gEnv->SetValue("XNet.ReconnectTimeout",5);
+ gEnv->SetValue("XNet.FirstConnectMaxCnt",1);
}
TObjArray *list = fOutputFiles.Tokenize(" ");
TIter next(list);
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();
if (fMergeExcludes.Length() &&
fMergeExcludes.Contains(output_file.Data())) continue;
// 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 = 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;
- 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;
- }
- }
+ merged = MergeOutput(output_file, fGridOutputDir, fMaxMergeFiles);
+ if (!merged) {
+ Error("MergeOutputs", "Terminate() will NOT be executed");
+ return kFALSE;
+ }
}
- if (!merged) {
- Error("MergeOutputs", "Terminate() will NOT be executed");
- }
- return merged;
+ return kTRUE;
}
//______________________________________________________________________________
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)) {
\n space and job submitted.");
} else if (TestBit(AliAnalysisGrid::kMerge)) {
Info("StartAnalysis","\n##### MERGE MODE ##### The registered outputs of the analysis will be merged");
+ if (fMergeViaJDL) CheckInputData();
return kTRUE;
} else {
Info("StartAnalysis","\n##### FULL ANALYSIS MODE ##### Producing needed files and submitting your analysis job...");
WriteAnalysisMacro();
WriteExecutable();
WriteValidationScript();
+ if (fMergeViaJDL) {
+ WriteMergingMacro();
+ WriteMergeExecutable();
+ WriteValidationScript(kTRUE);
+ }
if (!CreateJDL()) return kFALSE;
if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
if (TestBit(AliAnalysisGrid::kTest)) {
}
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::SubmitMerging()
+{
+// Submit all merging jobs.
+ if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
+ gGrid->Cd(fGridOutputDir);
+ TString mergeJDLName = fExecutable;
+ mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
+ Int_t ntosubmit = fInputFiles->GetEntries();
+ printf("### Submitting %d merging jobs...\n", ntosubmit);
+ for (Int_t i=0; i<ntosubmit; i++) {
+ TString query;
+ TString runOutDir = gSystem->BaseName(fInputFiles->At(i)->GetName());
+ runOutDir.ReplaceAll(".xml", "");
+ if (fOutputToRunNo)
+ query = Form("submit %s %s", mergeJDLName.Data(), runOutDir.Data());
+ else
+ query = Form("submit %s %03d", mergeJDLName.Data(), i);
+ printf("********* %s\n",query.Data());
+ TGridResult *res = gGrid->Command(query);
+ if (res) {
+ const char *cjobId = res->GetKey(0,"jobId");
+ if (!cjobId) {
+ Error("StartAnalysis", "Your JDL %s could not be submitted", mergeJDLName.Data());
+ return;
+ } else {
+ Info("StartAnalysis", "\n_______________________________________________________________________ \
+ \n##### Your JDL %s was successfully submitted. \nTHE JOB ID IS: %s \
+ \n_______________________________________________________________________",
+ mergeJDLName.Data(), cjobId);
+ }
+ delete res;
+ }
+ }
+ if (!ntosubmit) return;
+ 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");
+}
+
//______________________________________________________________________________
void AliAnalysisAlien::SubmitNext()
{
// Submit for a range of enumeration of runs.
if (fNsubmitted>=nmasterjobs) {iscalled = kFALSE; return;}
TString query;
- query = Form("submit %s %s %03d", fJDLName.Data(), fInputFiles->At(fNsubmitted)->GetName(), fNsubmitted);
+ 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) {
//______________________________________________________________________________
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()));
}
}
Error("WriteAnalysisMacro", "could not open file %s for writing", fAnalysisMacro.Data());
return;
}
+ Bool_t hasSTEERBase = kFALSE;
+ Bool_t hasESD = kFALSE;
+ Bool_t hasAOD = kFALSE;
+ Bool_t hasANALYSIS = kFALSE;
+ Bool_t hasANALYSISalice = kFALSE;
+ Bool_t hasCORRFW = kFALSE;
TString func = fAnalysisMacro;
TString type = "ESD";
TString comment = "// Analysis using ";
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 << "// include path" << endl;
+ if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
+ out << " gSystem->AddIncludePath(\"-I$ALICE_ROOT/include\");" << endl << endl;
out << "// Load analysis framework libraries" << endl;
if (!fPackages) {
out << " gSystem->Load(\"libSTEERBase\");" << endl;
TIter next(fPackages);
TObject *obj;
TString pkgname;
- Bool_t hasSTEERBase = kFALSE;
- Bool_t hasESD = kFALSE;
- Bool_t hasAOD = kFALSE;
- Bool_t hasANALYSIS = kFALSE;
- Bool_t hasANALYSISalice = kFALSE;
- Bool_t hasCORRFW = kFALSE;
+ TString setupPar = "AliAnalysisAlien::SetupPar";
while ((obj=next())) {
pkgname = obj->GetName();
if (pkgname == "STEERBase" ||
pkgname == "ANALYSISalice.par") hasANALYSISalice = kTRUE;
if (pkgname == "CORRFW" ||
pkgname == "CORRFW.par") hasCORRFW = kTRUE;
- }
+ }
+ if (hasANALYSISalice) setupPar = "SetupPar";
if (!hasSTEERBase) out << " gSystem->Load(\"libSTEERBase\");" << endl;
- else out << " if (!SetupPar(\"STEERBase\")) return;" << endl;
+ else out << " if (!" << setupPar << "(\"STEERBase\")) return;" << endl;
if (!hasESD) out << " gSystem->Load(\"libESD\");" << endl;
- else out << " if (!SetupPar(\"ESD\")) return;" << endl;
+ else out << " if (!" << setupPar << "(\"ESD\")) return;" << endl;
if (!hasAOD) out << " gSystem->Load(\"libAOD\");" << endl;
- else out << " if (!SetupPar(\"AOD\")) return;" << endl;
+ else out << " if (!" << setupPar << "(\"AOD\")) return;" << endl;
if (!hasANALYSIS) out << " gSystem->Load(\"libANALYSIS\");" << endl;
- else out << " if (!SetupPar(\"ANALYSIS\")) return;" << endl;
+ else out << " if (!" << setupPar << "(\"ANALYSIS\")) return;" << endl;
if (!hasANALYSISalice) out << " gSystem->Load(\"libANALYSISalice\");" << endl;
- else out << " if (!SetupPar(\"ANALYSISalice\")) return;" << endl;
+ else out << " if (!" << setupPar << "(\"ANALYSISalice\")) return;" << endl;
if (!hasCORRFW) out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
- else out << " if (!SetupPar(\"CORRFW\")) return;" << endl << endl;
+ else out << " if (!" << setupPar << "(\"CORRFW\")) return;" << endl << endl;
out << "// Compile other par packages" << endl;
next.Reset();
while ((obj=next())) {
pkgname == "ANALYSISalice.par" ||
pkgname == "CORRFW" ||
pkgname == "CORRFW.par") continue;
- out << " if (!SetupPar(\"" << obj->GetName() << "\")) return;" << endl;
+ out << " if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
}
}
- out << "// include path" << endl;
- if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
- out << " gSystem->AddIncludePath(\"-I$ALICE_ROOT/include\");" << endl << endl;
if (fAdditionalLibs.Length()) {
out << "// Add aditional AliRoot libraries" << endl;
TObjArray *list = fAdditionalLibs.Tokenize(" ");
if (list) delete list;
}
out << endl;
+ if (fFastReadOption) {
+ Warning("WriteAnalysisMacro", "!!! You requested FastRead option. Using xrootd flags to reduce timeouts in the grid jobs. Note that this may skip some files that could be accessed !!!");
+ out << "// fast xrootd reading enabled" << endl;
+ out << " printf(\"!!! You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !!!\");" << endl;
+ out << " gEnv->SetValue(\"XNet.ConnectTimeout\",5);" << endl;
+ out << " gEnv->SetValue(\"XNet.RequestTimeout\",5);" << endl;
+ out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
+ out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",5);" << 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;
if (IsUsingTags()) {
}
}
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;
+ if (AliAnalysisManager::GetAnalysisManager()) {
+ if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) {
+ out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
+ } else {
+ out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
+ }
+ }
out << " mgr->StartAnalysis(\"localfile\", chain);" << endl;
out << " timer.Stop();" << endl;
out << " timer.Print();" << endl;
out << " return chain;" << endl;
out << "}" << endl << endl;
}
- if (fPackages) {
+ if (hasANALYSISalice) {
out <<"//________________________________________________________________________________" << endl;
out << "Bool_t SetupPar(const char *package) {" << endl;
out << "// Compile the package and set it up." << endl;
}
}
+//______________________________________________________________________________
+void AliAnalysisAlien::WriteMergingMacro()
+{
+// Write a macro to merge the outputs per master job.
+ if (!fMergeViaJDL) return;
+ if (!fOutputFiles.Length()) {
+ Error("WriteMergingMacro", "No output file names defined. Are you running the right AliAnalysisAlien configuration ?");
+ return;
+ }
+ TString mergingMacro = fExecutable;
+ mergingMacro.ReplaceAll(".sh","_merge.C");
+ if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
+ if (!TestBit(AliAnalysisGrid::kSubmit)) {
+ ofstream out;
+ out.open(mergingMacro.Data(), ios::out);
+ if (!out.good()) {
+ Error("WriteMergingMacro", "could not open file %s for writing", fAnalysisMacro.Data());
+ return;
+ }
+ Bool_t hasSTEERBase = kFALSE;
+ Bool_t hasESD = kFALSE;
+ Bool_t hasAOD = kFALSE;
+ Bool_t hasANALYSIS = kFALSE;
+ Bool_t hasANALYSISalice = kFALSE;
+ Bool_t hasCORRFW = kFALSE;
+ TString func = mergingMacro;
+ TString comment;
+ func.ReplaceAll(".C", "");
+ out << "void " << func.Data() << "(const char *dir)" << endl;
+ out << "{" << endl;
+ out << "// Automatically generated merging macro executed in grid subjobs" << endl << endl;
+ out << " TStopwatch timer;" << endl;
+ out << " timer.Start();" << endl << endl;
+ out << "// load base root libraries" << endl;
+ out << " gSystem->Load(\"libTree\");" << endl;
+ out << " gSystem->Load(\"libGeom\");" << endl;
+ out << " gSystem->Load(\"libVMC\");" << endl;
+ out << " gSystem->Load(\"libPhysics\");" << endl << endl;
+ out << " gSystem->Load(\"libMinuit\");" << endl << endl;
+ 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 << "// include path" << endl;
+ if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
+ out << " gSystem->AddIncludePath(\"-I$ALICE_ROOT/include\");" << endl << endl;
+ out << "// Load analysis framework libraries" << endl;
+ if (!fPackages) {
+ out << " gSystem->Load(\"libSTEERBase\");" << endl;
+ out << " gSystem->Load(\"libESD\");" << endl;
+ out << " gSystem->Load(\"libAOD\");" << endl;
+ out << " gSystem->Load(\"libANALYSIS\");" << endl;
+ out << " gSystem->Load(\"libANALYSISalice\");" << endl;
+ out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
+ } else {
+ TIter next(fPackages);
+ TObject *obj;
+ TString pkgname;
+ TString setupPar = "AliAnalysisAlien::SetupPar";
+ while ((obj=next())) {
+ pkgname = obj->GetName();
+ if (pkgname == "STEERBase" ||
+ pkgname == "STEERBase.par") hasSTEERBase = kTRUE;
+ if (pkgname == "ESD" ||
+ pkgname == "ESD.par") hasESD = kTRUE;
+ if (pkgname == "AOD" ||
+ pkgname == "AOD.par") hasAOD = kTRUE;
+ if (pkgname == "ANALYSIS" ||
+ pkgname == "ANALYSIS.par") hasANALYSIS = kTRUE;
+ if (pkgname == "ANALYSISalice" ||
+ pkgname == "ANALYSISalice.par") hasANALYSISalice = kTRUE;
+ if (pkgname == "CORRFW" ||
+ pkgname == "CORRFW.par") hasCORRFW = kTRUE;
+ }
+ if (hasANALYSISalice) setupPar = "SetupPar";
+ if (!hasSTEERBase) out << " gSystem->Load(\"libSTEERBase\");" << endl;
+ else out << " if (!" << setupPar << "(\"STEERBase\")) return;" << endl;
+ if (!hasESD) out << " gSystem->Load(\"libESD\");" << endl;
+ else out << " if (!" << setupPar << "(\"ESD\")) return;" << endl;
+ if (!hasAOD) out << " gSystem->Load(\"libAOD\");" << endl;
+ else out << " if (!" << setupPar << "(\"AOD\")) return;" << endl;
+ if (!hasANALYSIS) out << " gSystem->Load(\"libANALYSIS\");" << endl;
+ else out << " if (!" << setupPar << "(\"ANALYSIS\")) return;" << endl;
+ if (!hasANALYSISalice) out << " gSystem->Load(\"libANALYSISalice\");" << endl;
+ else out << " if (!" << setupPar << "(\"ANALYSISalice\")) return;" << endl;
+ if (!hasCORRFW) out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
+ else out << " if (!" << setupPar << "(\"CORRFW\")) return;" << endl << endl;
+ out << "// Compile other par packages" << endl;
+ next.Reset();
+ while ((obj=next())) {
+ pkgname = obj->GetName();
+ if (pkgname == "STEERBase" ||
+ pkgname == "STEERBase.par" ||
+ pkgname == "ESD" ||
+ pkgname == "ESD.par" ||
+ pkgname == "AOD" ||
+ pkgname == "AOD.par" ||
+ pkgname == "ANALYSIS" ||
+ pkgname == "ANALYSIS.par" ||
+ pkgname == "ANALYSISalice" ||
+ pkgname == "ANALYSISalice.par" ||
+ pkgname == "CORRFW" ||
+ pkgname == "CORRFW.par") continue;
+ out << " if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
+ }
+ }
+ if (fAdditionalLibs.Length()) {
+ out << "// Add aditional AliRoot libraries" << endl;
+ TObjArray *list = fAdditionalLibs.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 << endl;
+ out << "// Analysis source to be compiled at runtime (if any)" << endl;
+ if (fAnalysisSource.Length()) {
+ TObjArray *list = fAnalysisSource.Tokenize(" ");
+ TIter next(list);
+ TObjString *str;
+ while((str=(TObjString*)next())) {
+ out << " gROOT->ProcessLine(\".L " << str->GetString().Data() << "+g\");" << endl;
+ }
+ if (list) delete list;
+ }
+ out << endl;
+ if (fFastReadOption) {
+ Warning("WriteMergingMacro", "!!! You requested FastRead option. Using xrootd flags to reduce timeouts in the grid merging jobs. Note that this may skip some files that could be accessed !!!");
+ out << "// fast xrootd reading enabled" << endl;
+ out << " printf(\"!!! You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !!!\");" << endl;
+ out << " gEnv->SetValue(\"XNet.ConnectTimeout\",5);" << endl;
+ out << " gEnv->SetValue(\"XNet.RequestTimeout\",5);" << endl;
+ out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
+ out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",5);" << endl;
+ out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
+ }
+ out << "// Connect to AliEn" << endl;
+ out << " if (!TGrid::Connect(\"alien://\")) return;" << endl;
+ out << " TString outputDir = \"" << fGridOutputDir << "/\";" << endl;
+ out << " outputDir += dir;" << endl;
+ out << " TString outputFiles = \"" << fOutputFiles << "\";" << endl;
+ out << " TString mergeExcludes = \"" << fMergeExcludes << "\";" << endl;
+ out << " mergeExcludes += \"" << AliAnalysisManager::GetAnalysisManager()->GetExtraFiles() << "\";" << endl;
+ out << " TObjArray *list = outputFiles.Tokenize(\" \");" << endl;
+ out << " TIter *iter = new TIter(list);" << endl;
+ out << " TObjString *str;" << endl;
+ out << " TString output_file;" << endl;
+ out << " Bool_t merged = kTRUE;" << endl;
+ out << " while((str=(TObjString*)iter->Next())) {" << endl;
+ out << " output_file = str->GetString();" << endl;
+ out << " Int_t index = output_file.Index(\"@\");" << endl;
+ out << " if (index > 0) output_file.Remove(index);" << endl;
+ out << " // Skip already merged outputs" << endl;
+ out << " if (!gSystem->AccessPathName(output_file)) {" << endl;
+ out << " printf(\"Output file <%s> found. Not merging again.\",output_file.Data());" << endl;
+ out << " continue;" << endl;
+ out << " }" << endl;
+ out << " if (mergeExcludes.Contains(output_file.Data())) continue;" << endl;
+ out << " merged = AliAnalysisAlien::MergeOutput(output_file, outputDir, " << fMaxMergeFiles << ");" << endl;
+ out << " if (!merged) {" << endl;
+ out << " printf(\"ERROR: Cannot merge %s\\n\", output_file.Data());" << endl;
+ out << " }" << endl;
+ out << " }" << 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 << " mgr->SetSkipTerminate(kFALSE);" << endl;
+ out << " mgr->PrintStatus();" << endl;
+ if (AliAnalysisManager::GetAnalysisManager()) {
+ if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) {
+ out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
+ } else {
+ out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
+ }
+ }
+ out << " mgr->StartAnalysis(\"gridterminate\");" << endl;
+ out << "}" << endl << endl;
+ if (hasANALYSISalice) {
+ out <<"//________________________________________________________________________________" << endl;
+ out << "Bool_t SetupPar(const char *package) {" << endl;
+ out << "// Compile the package and set it up." << endl;
+ out << " TString pkgdir = package;" << endl;
+ out << " pkgdir.ReplaceAll(\".par\",\"\");" << endl;
+ out << " gSystem->Exec(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 << " if (!gSystem->AccessPathName(\"PROOF-INF/BUILD.sh\")) {" << endl;
+ out << " printf(\"*******************************\\n\");" << endl;
+ out << " printf(\"*** Building PAR archive ***\\n\");" << endl;
+ out << " printf(\"*******************************\\n\");" << endl;
+ out << " if (gSystem->Exec(\"PROOF-INF/BUILD.sh\")) {" << endl;
+ out << " ::Error(\"SetupPar\", \"Cannot build par archive %s\", pkgdir.Data());" << endl;
+ out << " gSystem->ChangeDirectory(cdir);" << endl;
+ out << " return kFALSE;" << endl;
+ out << " }" << endl;
+ out << " } else {" << endl;
+ out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/BUILD.sh for package %s\", pkgdir.Data());" << endl;
+ out << " gSystem->ChangeDirectory(cdir);" << endl;
+ out << " return kFALSE;" << endl;
+ out << " }" << endl;
+ out << " // Check for SETUP.C and execute" << endl;
+ out << " if (!gSystem->AccessPathName(\"PROOF-INF/SETUP.C\")) {" << endl;
+ out << " printf(\"*******************************\\n\");" << endl;
+ out << " printf(\"*** Setup PAR archive ***\\n\");" << endl;
+ out << " printf(\"*******************************\\n\");" << endl;
+ out << " gROOT->Macro(\"PROOF-INF/SETUP.C\");" << endl;
+ out << " } else {" << endl;
+ out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/SETUP.C for package %s\", pkgdir.Data());" << endl;
+ out << " gSystem->ChangeDirectory(cdir);" << endl;
+ out << " return kFALSE;" << endl;
+ out << " }" << endl;
+ out << " // Restore original workdir" << endl;
+ out << " gSystem->ChangeDirectory(cdir);" << endl;
+ out << " return kTRUE;" << endl;
+ out << "}" << endl;
+ }
+ }
+ Bool_t copy = kTRUE;
+ if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+ if (copy) {
+ CdWork();
+ TString workdir = gGrid->GetHomeDirectory();
+ workdir += fGridWorkingDir;
+ if (FileExists(mergingMacro)) gGrid->Rm(mergingMacro);
+ Info("WriteMergingMacro", "\n##### Copying merging macro: <%s> to your alien workspace", mergingMacro.Data());
+ TFile::Cp(Form("file:%s",mergingMacro.Data()), Form("alien://%s/%s", workdir.Data(), mergingMacro.Data()));
+ }
+}
+
+//______________________________________________________________________________
+Bool_t AliAnalysisAlien::SetupPar(const char *package)
+{
+// Compile the par file archive pointed by <package>. This must be present in the current durectory.
+// Note that for loading the compiled library. The current directory should have precedence in
+// LD_LIBRARY_PATH
+ TString pkgdir = package;
+ pkgdir.ReplaceAll(".par","");
+ gSystem->Exec(Form("tar xvzf %s.par", pkgdir.Data()));
+ TString cdir = gSystem->WorkingDirectory();
+ gSystem->ChangeDirectory(pkgdir);
+ // Check for BUILD.sh and execute
+ if (!gSystem->AccessPathName("PROOF-INF/BUILD.sh")) {
+ printf("**************************************************\n");
+ printf("*** Building PAR archive %s\n", package);
+ printf("**************************************************\n");
+ if (gSystem->Exec("PROOF-INF/BUILD.sh")) {
+ ::Error("SetupPar", "Cannot build par archive %s", pkgdir.Data());
+ gSystem->ChangeDirectory(cdir);
+ return kFALSE;
+ }
+ } else {
+ ::Error("SetupPar","Cannot access PROOF-INF/BUILD.sh for package %s", pkgdir.Data());
+ gSystem->ChangeDirectory(cdir);
+ return kFALSE;
+ }
+ // Check for SETUP.C and execute
+ if (!gSystem->AccessPathName("PROOF-INF/SETUP.C")) {
+ printf("**************************************************\n");
+ printf("*** Setup PAR archive %s\n", package);
+ printf("**************************************************\n");
+ gROOT->Macro("PROOF-INF/SETUP.C");
+ printf("*** Loaded library: %s\n", gSystem->GetLibraries(pkgdir,"",kFALSE));
+ } else {
+ ::Error("SetupPar","Cannot access PROOF-INF/SETUP.C for package %s", pkgdir.Data());
+ gSystem->ChangeDirectory(cdir);
+ return kFALSE;
+ }
+ // Restore original workdir
+ gSystem->ChangeDirectory(cdir);
+ return kTRUE;
+}
+
//______________________________________________________________________________
void AliAnalysisAlien::WriteExecutable()
{
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::WriteMergeExecutable()
+{
+// Generate the alien executable script for the merging job.
+ if (!fMergeViaJDL) return;
+ TString mergeExec = fExecutable;
+ mergeExec.ReplaceAll(".sh", "_merge.sh");
+ if (!TestBit(AliAnalysisGrid::kSubmit)) {
+ ofstream out;
+ out.open(mergeExec.Data(), ios::out);
+ if (out.bad()) {
+ Error("WriteMergingExecutable", "Bad file name for executable: %s", mergeExec.Data());
+ return;
+ }
+ out << "#!/bin/bash" << endl;
+ out << "echo \"=========================================\"" << endl;
+ out << "echo \"############## PATH : ##############\"" << endl;
+ out << "echo $PATH" << endl;
+ out << "echo \"############## LD_LIBRARY_PATH : ##############\"" << endl;
+ out << "echo $LD_LIBRARY_PATH" << endl;
+ out << "echo \"############## ROOTSYS : ##############\"" << endl;
+ out << "echo $ROOTSYS" << endl;
+ out << "echo \"############## which root : ##############\"" << endl;
+ out << "which root" << endl;
+ out << "echo \"############## ALICE_ROOT : ##############\"" << endl;
+ out << "echo $ALICE_ROOT" << endl;
+ out << "echo \"############## which aliroot : ##############\"" << endl;
+ out << "which aliroot" << endl;
+ out << "echo \"############## system limits : ##############\"" << endl;
+ out << "ulimit -a" << endl;
+ out << "echo \"############## memory : ##############\"" << endl;
+ out << "free -m" << endl;
+ out << "echo \"=========================================\"" << endl << endl;
+ // Make sure we can properly compile par files
+ if (TObject::TestBit(AliAnalysisGrid::kUsePars)) out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
+ TString mergeMacro = fExecutable;
+ mergeMacro.ReplaceAll(".sh", "_merge.C");
+ out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\")\"" << endl;
+ out << fExecutableCommand << " " << "$ARG" << endl;
+ out << "echo \"======== " << mergeMacro.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(), mergeExec.Data());
+ if (FileExists(executable)) gGrid->Rm(executable);
+ Info("CreateJDL", "\n##### Copying executable file <%s> to your AliEn bin directory", mergeExec.Data());
+ TFile::Cp(Form("file:%s",mergeExec.Data()), Form("alien://%s", executable.Data()));
+ }
+}
+
//______________________________________________________________________________
void AliAnalysisAlien::WriteProductionFile(const char *filename) const
{
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;
+ TString runOutDir = gSystem->BaseName(fInputFiles->At(i)->GetName());
+ runOutDir.ReplaceAll(".xml", "");
+ if (fOutputToRunNo)
+ out << Form("%s", fInputFiles->At(i)->GetName()) << " " << runOutDir << endl;
+ else
+ out << Form("%s", fInputFiles->At(i)->GetName()) << " " << Form("%03d", i) << endl;
}
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()
+void AliAnalysisAlien::WriteValidationScript(Bool_t merge)
{
// Generate the alien validation script.
// Generate the validation script
TObjString *os;
+ TString validationScript = fExecutable;
+ if (merge) validationScript.ReplaceAll(".sh", "_mergevalidation.sh");
+ else validationScript.ReplaceAll(".sh", "_validation.sh");
if (!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;
TObjArray *arr = fOutputFiles.Tokenize(" ");
TIter next1(arr);
TString output_file;
+ AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
+ TString extra = mgr->GetExtraFiles();
while ((os=(TObjString*)next1())) {
output_file = os->GetString();
Int_t index = output_file.Index("@");
if (index > 0) output_file.Remove(index);
+ if (merge && fMergeExcludes.Contains(output_file)) continue;
+ if (extra.Contains(output_file)) continue;
out << "if ! [ -f " << output_file.Data() << " ] ; then" << endl;
out << " error=1" << endl;
out << " echo \"Output file(s) not found. Job FAILED !\"" << out_stream << endl;
out << "fi" << endl;
}
delete arr;
+ if (!merge) {
+ out << "if ! [ -f outputs_valid ] ; then" << endl;
+ out << " error=1" << endl;
+ out << " echo \"Output files were not validated by the analysis manager\" >> stdout" << endl;
+ out << " echo \"Output files were not validated by the analysis manager\" >> stderr" << endl;
+ out << "fi" << endl;
+ }
+
out << "if [ $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