fMaxMergeFiles(0),
fNsubmitted(0),
fProductionMode(0),
+ fOutputToRunNo(0),
fRunNumbers(),
fExecutable(),
fExecutableCommand(),
fArguments(),
+ fExecutableArgs(),
fAnalysisMacro(),
fAnalysisSource(),
+ fAdditionalRootLibs(),
fAdditionalLibs(),
fSplitMode(),
fAPIVersion(),
fFriendChainName(),
fJobTag(),
fOutputSingle(),
+ fRunPrefix(),
fInputFiles(0),
fPackages(0)
{
fMaxMergeFiles(0),
fNsubmitted(0),
fProductionMode(0),
+ fOutputToRunNo(0),
fRunNumbers(),
fExecutable(),
fExecutableCommand(),
fArguments(),
+ fExecutableArgs(),
fAnalysisMacro(),
fAnalysisSource(),
+ fAdditionalRootLibs(),
fAdditionalLibs(),
fSplitMode(),
fAPIVersion(),
fFriendChainName(),
fJobTag(),
fOutputSingle(),
+ fRunPrefix(),
fInputFiles(0),
fPackages(0)
{
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),
fFriendChainName(other.fFriendChainName),
fJobTag(other.fJobTag),
fOutputSingle(other.fOutputSingle),
+ fRunPrefix(other.fRunPrefix),
fInputFiles(0),
fPackages(0)
{
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;
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);
}
//______________________________________________________________________________
TObjArray *arr;
TObjString *os;
Int_t nruns = 0;
- TString schunk;
+ TString schunk, schunk2;
TString path;
if (!checked) {
checked = kTRUE;
} 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);
+ 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;
} else {
// Process a full run range.
for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
- path = Form("%s/%d ", fGridDataDir.Data(), 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("%d.xml", irun);
+ 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);
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("%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;
// 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)
}
// 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 (!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());
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()));
}
while ((os=(TObjString*)next()))
fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetString().Data()));
if (!fOutputSingle.IsNull())
- fGridJDL->SetOutputDirectory(Form("#alienfulldir#/%s",fOutputSingle.Data()));
+ 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())
- fGridJDL->SetOutputDirectory(Form("#alienfulldir#/%s",fOutputSingle.Data()));
- fGridJDL->SetOutputDirectory(Form("%s/$2/#alien_counter_03i#", fGridOutputDir.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()));
+ }
}
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());
fExecutable = "analysis.sh";
fExecutableCommand = "root -b -q";
fArguments = "";
+ fExecutableArgs = "";
fAnalysisMacro = "myAnalysis.C";
fAnalysisSource = "";
fAdditionalLibs = "";
// 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) {
TDirectory *cdir = gDirectory;
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 <%s>\n", mgr->GetName(),analysisFile.Data());
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;
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;
out << fExecutableCommand << " ";
- out << fAnalysisMacro.Data() << endl << endl;
- out << "echo \"======== " << fAnalysisMacro.Data() << " finished ========\"" << endl;
+ 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;
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));
}
git://git.uio.no / u / mrichter / AliRoot.git / blobdiff