fExecutableArgs(),
fAnalysisMacro(),
fAnalysisSource(),
+ fValidationScript(),
fAdditionalRootLibs(),
fAdditionalLibs(),
fSplitMode(),
fInputFormat(),
fDatasetName(),
fJDLName(),
+ fTerminateFiles(),
fMergeExcludes(),
fIncludePath(),
fCloseSE(),
fExecutableArgs(),
fAnalysisMacro(),
fAnalysisSource(),
+ fValidationScript(),
fAdditionalRootLibs(),
fAdditionalLibs(),
fSplitMode(),
fInputFormat(),
fDatasetName(),
fJDLName(),
+ fTerminateFiles(),
fMergeExcludes(),
fIncludePath(),
fCloseSE(),
fExecutableArgs(other.fExecutableArgs),
fAnalysisMacro(other.fAnalysisMacro),
fAnalysisSource(other.fAnalysisSource),
+ fValidationScript(other.fValidationScript),
fAdditionalRootLibs(other.fAdditionalRootLibs),
fAdditionalLibs(other.fAdditionalLibs),
fSplitMode(other.fSplitMode),
fInputFormat(other.fInputFormat),
fDatasetName(other.fDatasetName),
fJDLName(other.fJDLName),
+ fTerminateFiles(other.fTerminateFiles),
fMergeExcludes(other.fMergeExcludes),
fIncludePath(other.fIncludePath),
fCloseSE(other.fCloseSE),
fExecutableArgs = other.fExecutableArgs;
fAnalysisMacro = other.fAnalysisMacro;
fAnalysisSource = other.fAnalysisSource;
+ fValidationScript = other.fValidationScript;
fAdditionalRootLibs = other.fAdditionalRootLibs;
fAdditionalLibs = other.fAdditionalLibs;
fSplitMode = other.fSplitMode;
fInputFormat = other.fInputFormat;
fDatasetName = other.fDatasetName;
fJDLName = other.fJDLName;
+ fTerminateFiles = other.fTerminateFiles;
fMergeExcludes = other.fMergeExcludes;
fIncludePath = other.fIncludePath;
fCloseSE = other.fCloseSE;
{
// Try to connect to AliEn. User needs a valid token and /tmp/gclient_env_$UID sourced.
if (gGrid && gGrid->IsConnected()) return kTRUE;
+ if (fProductionMode) return kTRUE;
if (!gGrid) {
Info("Connect", "Trying to connect to AliEn ...");
TGrid::Connect("alien://");
gGrid->Cd(homedir);
if (gGrid->Mkdir(workdir, "-p")) {
gGrid->Cd(fGridWorkingDir);
- Info("CreateJDL", "\n##### Created alien working directory %s", fGridWorkingDir.Data());
+ Info("CdWork", "\n##### Created alien working directory %s", fGridWorkingDir.Data());
} else {
- Warning("CreateJDL", "Working directory %s cannot be created.\n Using %s instead.",
+ Warning("CdWork", "Working directory %s cannot be created.\n Using %s instead.",
workdir.Data(), homedir.Data());
fGridWorkingDir = "";
}
Bool_t AliAnalysisAlien::CheckFileCopy(const char *alienpath)
{
// Check if file copying is possible.
+ if (fProductionMode) return kTRUE;
if (!Connect()) {
Error("CheckFileCopy", "Not connected to AliEn. File copying cannot be tested.");
return kFALSE;
Bool_t AliAnalysisAlien::CheckInputData()
{
// Check validity of input data. If necessary, create xml files.
+ if (fProductionMode) return kTRUE;
if (!fInputFiles && !fRunNumbers.Length() && !fRunRange[0]) {
if (!fGridDataDir.Length()) {
Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
Bool_t isXml = kFALSE;
Bool_t useTags = kFALSE;
Bool_t checked = kFALSE;
- CdWork();
+ if (!TestBit(AliAnalysisGrid::kTest)) CdWork();
TString file;
TString workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
Bool_t AliAnalysisAlien::CreateDataset(const char *pattern)
{
// Create dataset for the grid data directory + run number.
- if (TestBit(AliAnalysisGrid::kOffline)) return kTRUE;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline)) return kTRUE;
if (!Connect()) {
Error("CreateDataset", "Cannot create dataset with no grid connection");
return kFALSE;
}
// Cd workspace
- CdWork();
+ if (!TestBit(AliAnalysisGrid::kTest)) CdWork();
TString workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
Bool_t error = kFALSE;
TObjArray *arr = 0;
Bool_t copy = kTRUE;
- if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
Bool_t generate = kTRUE;
if (TestBit(AliAnalysisGrid::kTest) || TestBit(AliAnalysisGrid::kSubmit)) generate = kFALSE;
if (!Connect()) {
return kFALSE;
}
// Check validity of alien workspace
- CdWork();
- TString workdir = gGrid->GetHomeDirectory();
+ TString workdir;
+ if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice")) workdir = gGrid->GetHomeDirectory();
+ if (!fProductionMode && !TestBit(AliAnalysisGrid::kTest)) CdWork();
workdir += fGridWorkingDir;
if (generate) {
TObjString *os;
Error("CreateJDL", "You must define AliEn output directory");
error = kTRUE;
} else {
- if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
- if (!DirectoryExists(fGridOutputDir)) {
- if (gGrid->Mkdir(fGridOutputDir,"-p")) {
- Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
- } else {
- Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
- // error = kTRUE;
- }
- }
- gGrid->Cd(workdir);
+ if (!fProductionMode) {
+ if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
+ if (!DirectoryExists(fGridOutputDir)) {
+ if (gGrid->Mkdir(fGridOutputDir,"-p")) {
+ Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
+ } else {
+ Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
+ // error = kTRUE;
+ }
+ }
+ gGrid->Cd(workdir);
+ }
}
// Exit if any error up to now
if (error) return kFALSE;
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 $2 $3");
+ if (IsOneStageMerging()) fMergingJDL->SetArguments(fGridOutputDir);
+ else fMergingJDL->SetArguments("$1 $2 $3");
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));
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(),"");
+ // Output archive for the merging jdl
+ TString outputArchive;
+ if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
+ outputArchive = "log_archive.zip:std*,*.stat@disk=1 ";
+ // Add normal output files, extra files + terminate files
+ TString files = GetListOfFiles("outextter");
+ // Do not register merge excludes
+ if (!fMergeExcludes.IsNull()) {
+ arr = fMergeExcludes.Tokenize(" ");
+ TIter next1(arr);
+ while ((os=(TObjString*)next1())) {
+ files.ReplaceAll(Form("%s,",os->GetString().Data()),"");
+ files.ReplaceAll(os->GetString(),"");
+ }
+ delete arr;
}
- delete arr;
- }
+ files.ReplaceAll(".root", "*.root");
+ outputArchive += Form("root_archive.zip:%s@disk=%d",files.Data(),fNreplicas);
+ } else {
+ TString files = fOutputArchive;
+ files.ReplaceAll(".root", "*.root"); // nreplicas etc should be already atttached by use
+ outputArchive = files;
+ }
arr = outputArchive.Tokenize(" ");
TIter next2(arr);
comment = comment1;
while ((os=(TObjString*)next2())) {
if (!first) comment = NULL;
TString currentfile = os->GetString();
- currentfile.ReplaceAll(".root", "*.root");
- currentfile.ReplaceAll(".zip", "-Stage$2_$3.zip");
+ if (!IsOneStageMerging()) currentfile.ReplaceAll(".zip", "-Stage$2_$3.zip");
if (!currentfile.Contains("@") && fCloseSE.Length())
- fMergingJDL->AddToOutputArchive(Form("%s@%s",currentfile.Data(), fCloseSE.Data()), comment);
+ fMergingJDL->AddToOutputArchive(Form("%s@%s",currentfile.Data(), fCloseSE.Data()), comment);
else
fMergingJDL->AddToOutputArchive(currentfile, comment);
first = kFALSE;
arr = fOutputFiles.Tokenize(",");
TIter next(arr);
Bool_t first = kTRUE;
- const char *comment = "Files to be archived";
- const char *comment1 = comment;
+ const char *comment = "Files to be saved";
while ((os=(TObjString*)next())) {
// Ignore ouputs in jdl that are also in outputarchive
TString sout = os->GetString();
+ sout.ReplaceAll("*", "");
+ sout.ReplaceAll(".root", "");
if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
if (fOutputArchive.Contains(sout)) continue;
if (!first) comment = NULL;
else
fGridJDL->AddToOutputSandbox(os->GetString(), comment);
first = kFALSE;
+ if (fMergeExcludes.Contains(sout)) continue;
+ 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;
- 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);
- first = kFALSE;
- }
- 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");
+ TString validationScript = fValidationScript;
fGridJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
- validationScript = fExecutable;
- validationScript.ReplaceAll(".sh", "_mergevalidation.sh");
+ validationScript.ReplaceAll(".sh", "_merge.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));
// all run numbers are considered in one go (jdl). For non-negative indices
// they correspond to the indices in the array fInputFiles.
if (!fInputFiles) return kFALSE;
- TObjString *os;
- TString workdir = gGrid->GetHomeDirectory();
+ TObject *os;
+ TString workdir;
+ if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice")) workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
- if (!fRunNumbers.Length() && !fRunRange[0]) {
- // One jdl with no parameters in case input data is specified by name.
+ if (fProductionMode) {
TIter next(fInputFiles);
- while ((os=(TObjString*)next()))
- 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()), "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("$1", "Output directory");
- }
+ while ((os=next()))
+ fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetName()), "Input xml collections");
+ fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_04i#", fGridOutputDir.Data()));
+ fMergingJDL->SetOutputDirectory(fGridOutputDir);
+ } else {
+ if (!fRunNumbers.Length() && !fRunRange[0]) {
+ // One jdl with no parameters in case input data is specified by name.
+ TIter next(fInputFiles);
+ while ((os=next()))
+ fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetName()), "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()), "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("$1", "Output directory");
+ }
+ }
}
-
// Generate the JDL as a string
TString sjdl = fGridJDL->Generate();
TString sjdl1 = fMergingJDL->Generate();
if (index >= 0) sjdl.Insert(index, "\n# JDL variables\n");
sjdl += "Workdirectorysize = {\"5000MB\"};";
sjdl1 += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
- sjdl1.Prepend(Form("Jobtag = {\n \"comment:%s_Merging\"\n};\n", fJobTag.Data()));
+ index = fJobTag.Index(":");
+ if (index < 0) index = fJobTag.Length();
+ TString jobTag = fJobTag;
+ jobTag.Insert(index, "_Merging");
+ sjdl1.Prepend(Form("Jobtag = {\n \"comment:%s_Merging\"\n};\n", jobTag.Data()));
sjdl1.Prepend("# Generated merging jdl\n# $1 = full alien path to output directory to be merged\n# $2 = merging stage\n# $3 = merged chunk\n");
index = sjdl1.Index("JDLVariables");
if (index >= 0) sjdl1.Insert(index, "\n# JDL variables\n");
ofstream out;
out.open(fJDLName.Data(), ios::out);
if (out.bad()) {
- Error("CreateJDL", "Bad file name: %s", fJDLName.Data());
+ Error("WriteJDL", "Bad file name: %s", fJDLName.Data());
return kFALSE;
}
out << sjdl << endl;
ofstream out1;
out1.open(mergeJDLName.Data(), ios::out);
if (out.bad()) {
- Error("CreateJDL", "Bad file name: %s", mergeJDLName.Data());
+ Error("WriteJDL", "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());
+ Info("WriteJDL", "\n##### You may want to review jdl:%s and analysis macro:%s before running in <submit> mode", fJDLName.Data(), fAnalysisMacro.Data());
} else {
TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
TString locjdl1 = Form("%s/%s", fGridOutputDir.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());
+ Info("WriteJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
if (fMergeViaJDL) {
- Info("CreateJDL", "\n##### Copying merging JDL file <%s> to your AliEn output directory", mergeJDLName.Data());
+ Info("WriteJDL", "\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()));
}
}
{
// Returns true if file exists.
if (!gGrid) return kFALSE;
- TGridResult *res = gGrid->Ls(lfn);
+ TString slfn = lfn;
+ slfn.ReplaceAll("alien://","");
+ TGridResult *res = gGrid->Ls(slfn);
if (!res) return kFALSE;
TMap *map = dynamic_cast<TMap*>(res->At(0));
if (!map) {
{
// Print current plugin settings.
printf("### AliEn analysis plugin current settings ###\n");
+ AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
+ if (mgr && mgr->IsProofMode()) {
+ TString proofType = "= PLUGIN IN PROOF MODE ON CLUSTER:_________________";
+ if (TestBit(AliAnalysisGrid::kTest))
+ proofType = "= PLUGIN IN PROOF LITE MODE ON CLUSTER:____________";
+ printf("%s %s\n", proofType.Data(), fProofCluster.Data());
+ if (!fProofDataSet.IsNull())
+ printf("= Requested data set:___________________________ %s\n", fProofDataSet.Data());
+ if (fProofReset==1)
+ printf("= Soft reset signal will be send to master______ CHANGE BEHAVIOR AFTER COMPLETION\n");
+ if (fProofReset>1)
+ printf("= Hard reset signal will be send to master______ CHANGE BEHAVIOR AFTER COMPLETION\n");
+ if (!fRootVersionForProof.IsNull())
+ printf("= ROOT version requested________________________ %s\n", fRootVersionForProof.Data());
+ else
+ printf("= ROOT version requested________________________ default\n");
+ printf("= AliRoot version requested_____________________ %s\n", fAliROOTVersion.Data());
+ if (!fAliRootMode.IsNull())
+ printf("= Requested AliRoot mode________________________ %s\n", fAliRootMode.Data());
+ if (fNproofWorkers)
+ printf("= Number of PROOF workers limited to____________ %d\n", fNproofWorkers);
+ if (fNproofWorkersPerSlave)
+ printf("= Maximum number of workers per slave___________ %d\n", fNproofWorkersPerSlave);
+ if (TestSpecialBit(kClearPackages))
+ printf("= ClearPackages requested...\n");
+ if (fIncludePath.Data())
+ printf("= Include path for runtime task compilation: ___ %s\n", fIncludePath.Data());
+ printf("= Additional libs to be loaded or souces to be compiled runtime: <%s>\n",fAdditionalLibs.Data());
+ if (fPackages && fPackages->GetEntries()) {
+ TIter next(fPackages);
+ TObject *obj;
+ TString list;
+ while ((obj=next())) list += obj->GetName();
+ printf("= Par files to be used: ________________________ %s\n", list.Data());
+ }
+ if (TestSpecialBit(kProofConnectGrid))
+ printf("= Requested PROOF connection to grid\n");
+ return;
+ }
printf("= OverwriteMode:________________________________ %d\n", fOverwriteMode);
if (fOverwriteMode) {
printf("***** NOTE: Overwrite mode will overwrite the input generated datasets and partial results from previous analysis. \
printf("= List of output files to be registered: _______ %s\n", fOutputFiles.Data());
printf("= List of outputs going to be archived: ________ %s\n", fOutputArchive.Data());
printf("= List of outputs that should not be merged: ___ %s\n", fMergeExcludes.Data());
+ printf("= List of outputs produced during Terminate: ___ %s\n", fTerminateFiles.Data());
printf("=====================================================================\n");
printf("= Job price: ___________________________________ %d\n", fPrice);
printf("= Time to live (TTL): __________________________ %d\n", fTTL);
printf("= Force job outputs to storage element: ________ %s\n", fCloseSE.Data());
if (fFriendChainName.Length())
printf("= Open friend chain file on worker: ____________ %s\n", fFriendChainName.Data());
- if (fPackages) {
+ if (fPackages && fPackages->GetEntries()) {
TIter next(fPackages);
TObject *obj;
TString list;
fDataPattern = "*AliESDs.root"; // Can be like: *AliESDs.root, */pass1/*AliESDs.root, ...
fFriendChainName = "";
fGridOutputDir = "output";
- fOutputArchive = "log_archive.zip:std*@disk=1 root_archive.zip:*.root@disk=2";
+ fOutputArchive = "log_archive.zip:std*,*.stat@disk=1 root_archive.zip:*.root@disk=2";
fOutputFiles = ""; // Like "AliAODs.root histos.root"
fInputFormat = "xml-single";
fJDLName = "analysis.jdl";
// Sumbit merging jobs for all missing chunks for the current stage.
TString query = Form("submit %s %s", jdl, aliendir);
Int_t ichunk = -1;
+ chunksDone.SetBitNumber(ntotstage); // expand the array to the maximum number of chunks
if (nmissing) {
for (i=0; i<nmissing; i++) {
ichunk = chunksDone.FirstNullBit(ichunk+1);
// Check overwrite mode and remove previous partial results if needed
// Preserve old merging functionality for stage 0.
if (stage==0) {
+ Int_t countChar = 0;
if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
while (1) {
// Skip as many input files as in a chunk
- for (Int_t counter=0; counter<nmaxmerge; counter++) map = (TMap*)nextmap();
+ for (Int_t counter=0; counter<nmaxmerge; counter++) {
+ map = (TMap*)nextmap();
+ if (!map) {
+ ::Error("MergeOutput", "Mismatch found. Please remove partial merged files from local dir.");
+ delete res;
+ return kFALSE;
+ }
+ TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl"));
+ // Count the '/' characters in the path to the current file.
+ Int_t crtCount = objs->GetString().CountChar('/');
+ if (!countChar) {
+ countChar = crtCount;
+ // Make sure we check if the same file in the parent dir exists
+ if (FileExists(Form("%s/../%s", basedir, output))) countChar--;
+ }
+ if (crtCount > countChar) counter--;
+ }
if (!map) {
::Error("MergeOutput", "Cannot resume merging for <%s>, nentries=%d", outputFile.Data(), res->GetSize());
delete res;
countZero = nmaxmerge;
while ((map=(TMap*)nextmap())) {
- // Loop 'find' results and get next LFN
+ TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl"));
+ if (!objs || !objs->GetString().Length()) {
+ // Nothing found - skip this output
+ delete res;
+ delete fm;
+ return kFALSE;
+ }
+ // Make sure this is a good file and not one from a subjob directory in case we merge runs
+ // Count the '/' characters in the path to the current file.
+ Int_t crtCount = objs->GetString().CountChar('/');
+ if (!countChar) {
+ countChar = crtCount;
+ // Make sure we check if the same file in the parent dir exists
+ if (FileExists(Form("%s/../%s", basedir, output))) countChar--;
+ }
+ if (crtCount > countChar) continue;
+ // Loop 'find' results and get next LFN
if (countZero == nmaxmerge) {
// First file in chunk - create file merger and add previous chunk if any.
fm = new TFileMerger(kFALSE);
}
// If last file found, put merged results in the output file
if (map == res->Last()) outputChunk = outputFile;
- 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());
countZero--;
delete res;
return kFALSE;
}
- for (Int_t counter=0; counter<ichunk*nmaxmerge; counter++) map = (TMap*)nextmap();
+ for (Int_t counter=0; counter<ichunk*nmaxmerge; counter++) nextmap();
outputChunk.ReplaceAll(".root", Form("-Stage%02d_%04d.root", stage, ichunk));
}
countZero = nmaxmerge;
fOutputFiles += sout;
}
delete arr;
-}
+}
//______________________________________________________________________________
void AliAnalysisAlien::SetOutputArchive(const char *list)
}
// Are we in PROOF mode ?
if (mgr->IsProofMode()) {
- Info("StartAnalysis", "##### Starting PROOF analysis on via the plugin #####");
+ Info("StartAnalysis", "##### Starting PROOF analysis on cluster <%s> via the plugin #####", fProofCluster.Data());
if (fProofCluster.IsNull()) {
Error("StartAnalysis", "You need to specify the proof cluster name via SetProofCluster");
return kFALSE;
}
// Is a given aliroot mode requested ?
TList optionsList;
+ TString parLibs;
if (!fAliRootMode.IsNull()) {
TString alirootMode = fAliRootMode;
if (alirootMode == "default") alirootMode = "";
optionsList.Add(new TNamed("ALIROOT_MODE", alirootMode.Data()));
// Check the additional libs to be loaded
TString extraLibs;
+ Bool_t parMode = kFALSE;
if (!alirootMode.IsNull()) extraLibs = "ANALYSIS:ANALYSISalice";
// Parse the extra libs for .so
if (fAdditionalLibs.Length()) {
TObjArray *list = fAdditionalLibs.Tokenize(" ");
TIter next(list);
TObjString *str;
- while((str=(TObjString*)next()) && str->GetString().Contains(".so")) {
- TString stmp = str->GetName();
- if (stmp.BeginsWith("lib")) stmp.Remove(0,3);
- stmp.ReplaceAll(".so","");
- if (!extraLibs.IsNull()) extraLibs += ":";
- extraLibs += stmp;
+ while((str=(TObjString*)next())) {
+ if (str->GetString().Contains(".so")) {
+ if (parMode) {
+ Warning("StartAnalysis", "Plugin does not support loading libs after par files in PROOF mode. Library %s and following will not load on workers", str->GetName());
+ break;
+ }
+ TString stmp = str->GetName();
+ if (stmp.BeginsWith("lib")) stmp.Remove(0,3);
+ stmp.ReplaceAll(".so","");
+ if (!extraLibs.IsNull()) extraLibs += ":";
+ extraLibs += stmp;
+ continue;
+ }
+ if (str->GetString().Contains(".par")) {
+ // The first par file found in the list will not allow any further .so
+ parMode = kTRUE;
+ if (!parLibs.IsNull()) parLibs += ":";
+ parLibs += str->GetName();
+ continue;
+ }
}
if (list) delete list;
}
return kFALSE;
}
}
+ // Enable first par files from fAdditionalLibs
+ if (!parLibs.IsNull()) {
+ TObjArray *list = parLibs.Tokenize(":");
+ TIter next(list);
+ TObjString *package;
+ while((package=(TObjString*)next())) {
+ TString spkg = package->GetName();
+ spkg.ReplaceAll(".par", "");
+ gSystem->Exec(TString::Format("rm -rf %s", spkg.Data()));
+ if (!gROOT->ProcessLine(Form("gProof->UploadPackage(\"%s\");", package->GetName()))) {
+ TString enablePackage = (testMode)?Form("gProof->EnablePackage(\"%s\",kFALSE);", package->GetName()):Form("gProof->EnablePackage(\"%s\",kTRUE);", package->GetName());
+ if (gROOT->ProcessLine(enablePackage)) {
+ Error("StartAnalysis", "There was an error trying to enable package %s", package->GetName());
+ return kFALSE;
+ }
+ } else {
+ Error("StartAnalysis", "There was an error trying to upload package %s", package->GetName());
+ return kFALSE;
+ }
+ }
+ if (list) delete list;
+ }
} else {
if (fAdditionalLibs.Contains(".so") && !testMode) {
Error("StartAnalysis", "You request additional libs to be loaded but did not enabled any AliRoot mode. Please refer to: \
TIter next(fPackages);
TObject *package;
while ((package=next())) {
+ // Skip packages already enabled
+ if (parLibs.Contains(package->GetName())) continue;
+ TString spkg = package->GetName();
+ spkg.ReplaceAll(".par", "");
+ gSystem->Exec(TString::Format("rm -rf %s", spkg.Data()));
if (gROOT->ProcessLine(Form("gProof->UploadPackage(\"%s\");", package->GetName()))) {
if (gROOT->ProcessLine(Form("gProof->EnablePackage(\"%s\",kTRUE);", package->GetName()))) {
Error("StartAnalysis", "There was an error trying to enable package %s", package->GetName());
// Check if output files have to be taken from the analysis manager
if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
- fOutputFiles = "";
- TIter next(mgr->GetOutputs());
- AliAnalysisDataContainer *output;
- while ((output=(AliAnalysisDataContainer*)next())) {
- const char *filename = output->GetFileName();
- if (!(strcmp(filename, "default"))) {
- if (!mgr->GetOutputEventHandler()) continue;
- filename = mgr->GetOutputEventHandler()->GetOutputFileName();
- }
- if (fOutputFiles.Contains(filename)) continue;
- if (fOutputFiles.Length()) fOutputFiles += ",";
- fOutputFiles += filename;
- }
+ // Add output files and AOD files
+ fOutputFiles = GetListOfFiles("outaod");
// Add extra files registered to the analysis manager
- if (mgr->GetExtraFiles().Length()) {
- if (fOutputFiles.Length()) fOutputFiles += ",";
- TString extra = mgr->GetExtraFiles();
- extra.ReplaceAll(" ", ",");
- // Protection in case extra files do not exist (will it work?)
+ TString extra = GetListOfFiles("ext");
+ if (!extra.IsNull()) {
extra.ReplaceAll(".root", "*.root");
+ if (!fOutputFiles.IsNull()) fOutputFiles += ",";
fOutputFiles += extra;
}
// Compose the output archive.
- fOutputArchive = "log_archive.zip:std*@disk=1 ";
+ fOutputArchive = "log_archive.zip:std*,*.stat@disk=1 ";
fOutputArchive += Form("root_archive.zip:%s@disk=%d",fOutputFiles.Data(),fNreplicas);
}
// if (!fCloseSE.Length()) fCloseSE = gSystem->Getenv("alien_CLOSE_SE");
Error("StartAnalysis", "Cannot start grid analysis without grid connection");
return kFALSE;
}
- if (IsCheckCopy()) CheckFileCopy(gGrid->GetHomeDirectory());
+ if (IsCheckCopy() && gGrid) CheckFileCopy(gGrid->GetHomeDirectory());
if (!CheckInputData()) {
Error("StartAnalysis", "There was an error in preprocessing your requested input data");
return kFALSE;
}
delete list;
gSystem->Exec(Form("bash %s 2>stderr", fExecutable.Data()));
- TString validationScript = fExecutable;
- validationScript.ReplaceAll(".sh", "_validation.sh");
- gSystem->Exec(Form("bash %s",validationScript.Data()));
+ gSystem->Exec(Form("bash %s",fValidationScript.Data()));
// gSystem->Exec("cat stdout");
return kFALSE;
}
return kTRUE;
}
+//______________________________________________________________________________
+const char *AliAnalysisAlien::GetListOfFiles(const char *type)
+{
+// Get a comma-separated list of output files of the requested type.
+// Type can be (case unsensitive):
+// aod - list of aod files (std, extensions and filters)
+// out - list of output files connected to containers (but not aod's or extras)
+// ext - list of extra files registered to the manager
+// ter - list of files produced in terminate
+ static TString files;
+ files = "";
+ TString stype = type;
+ stype.ToLower();
+ TString aodfiles, extra;
+ AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
+ if (!mgr) {
+ ::Error("GetListOfFiles", "Cannot call this without analysis manager");
+ return files.Data();
+ }
+ if (mgr->GetOutputEventHandler()) {
+ aodfiles = mgr->GetOutputEventHandler()->GetOutputFileName();
+ TString extraaod = mgr->GetOutputEventHandler()->GetExtraOutputs();
+ if (!extraaod.IsNull()) {
+ aodfiles += ",";
+ aodfiles += extraaod;
+ }
+ }
+ if (stype.Contains("aod")) {
+ files = aodfiles;
+ if (stype == "aod") return files.Data();
+ }
+ // Add output files that are not in the list of AOD files
+ TString outputfiles = "";
+ TIter next(mgr->GetOutputs());
+ AliAnalysisDataContainer *output;
+ const char *filename = 0;
+ while ((output=(AliAnalysisDataContainer*)next())) {
+ filename = output->GetFileName();
+ if (!(strcmp(filename, "default"))) continue;
+ if (outputfiles.Contains(filename)) continue;
+ if (aodfiles.Contains(filename)) continue;
+ if (!outputfiles.IsNull()) outputfiles += ",";
+ outputfiles += filename;
+ }
+ if (stype.Contains("out")) {
+ if (!files.IsNull()) files += ",";
+ files += outputfiles;
+ if (stype == "out") return files.Data();
+ }
+ // Add extra files registered to the analysis manager
+ TString sextra;
+ extra = mgr->GetExtraFiles();
+ if (!extra.IsNull()) {
+ extra.Strip();
+ extra.ReplaceAll(" ", ",");
+ TObjArray *fextra = extra.Tokenize(",");
+ TIter nextx(fextra);
+ TObject *obj;
+ while ((obj=nextx())) {
+ if (aodfiles.Contains(obj->GetName())) continue;
+ if (outputfiles.Contains(obj->GetName())) continue;
+ if (sextra.Contains(obj->GetName())) continue;
+ if (!sextra.IsNull()) sextra += ",";
+ sextra += obj->GetName();
+ }
+ delete fextra;
+ if (stype.Contains("ext")) {
+ if (!files.IsNull()) files += ",";
+ files += sextra;
+ }
+ }
+ if (stype == "ext") return files.Data();
+ TString termfiles;
+ if (!fTerminateFiles.IsNull()) {
+ fTerminateFiles.Strip();
+ fTerminateFiles.ReplaceAll(" ",",");
+ TObjArray *fextra = fTerminateFiles.Tokenize(",");
+ TIter nextx(fextra);
+ TObject *obj;
+ while ((obj=nextx())) {
+ if (aodfiles.Contains(obj->GetName())) continue;
+ if (outputfiles.Contains(obj->GetName())) continue;
+ if (termfiles.Contains(obj->GetName())) continue;
+ if (sextra.Contains(obj->GetName())) continue;
+ if (!termfiles.IsNull()) termfiles += ",";
+ termfiles += obj->GetName();
+ }
+ delete fextra;
+ }
+ if (stype.Contains("ter")) {
+ if (!files.IsNull() && !termfiles.IsNull()) {
+ files += ",";
+ files += termfiles;
+ }
+ }
+ return files.Data();
+}
+
//______________________________________________________________________________
Bool_t AliAnalysisAlien::Submit()
{
if (!fNsubmitted) {
ntosubmit = 1;
if (!IsUseSubmitPolicy()) {
- if (ntosubmit>5)
+ if (nmasterjobs>5)
Info("SubmitNext","### Warning submit policy not used ! Submitting too many jobs at a time may be prohibitted. \
\n### You can use SetUseSubmitPolicy() to enable if you have problems.");
ntosubmit = nmasterjobs;
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;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
- Info("CreateJDL", "\n##### Copying file <%s> containing your initialized analysis manager to your alien workspace", analysisFile.Data());
+ Info("WriteAnalysisFile", "\n##### Copying file <%s> containing your initialized analysis manager to your alien workspace", analysisFile.Data());
if (FileExists(analysisFile)) gGrid->Rm(analysisFile);
TFile::Cp(Form("file:%s",analysisFile.Data()), Form("alien://%s/%s", workdir.Data(),analysisFile.Data()));
}
// Change temp directory to current one
out << "// Set temporary merging directory to current one" << endl;
out << " gSystem->Setenv(\"TMPDIR\", gSystem->pwd());" << 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 (!fExecutableCommand.Contains("aliroot")) {
+ 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;
out << "// Load analysis framework libraries" << endl;
TString setupPar = "AliAnalysisAlien::SetupPar";
if (!fPackages) {
- out << " gSystem->Load(\"libSTEERBase\");" << endl;
- out << " gSystem->Load(\"libESD\");" << endl;
- out << " gSystem->Load(\"libAOD\");" << endl;
+ if (!fExecutableCommand.Contains("aliroot")) {
+ 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;
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\",10);" << endl;
- out << " gEnv->SetValue(\"XNet.RequestTimeout\",20);" << endl;
+ out << " gEnv->SetValue(\"XNet.RequestTimeout\",10);" << endl;
out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
- out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",50);" << endl;
+ out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",10);" << 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 << " TChain *chain = CreateChainFromTags(\"wn.xml\", anatype);" << endl << endl;
- } else {
- out << " TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl;
- }
out << "// read the analysis manager from file" << endl;
TString analysisFile = fExecutable;
analysisFile.ReplaceAll(".sh", ".root");
out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
}
}
+ if (IsUsingTags()) {
+ out << " TChain *chain = CreateChainFromTags(\"wn.xml\", anatype);" << endl << endl;
+ } else {
+ out << " TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl;
+ }
out << " mgr->StartAnalysis(\"localfile\", chain);" << endl;
out << " timer.Stop();" << endl;
out << " timer.Print();" << endl;
out << "TChain* CreateChain(const char *xmlfile, const char *type=\"ESD\")" << endl;
out << "{" << endl;
out << "// Create a chain using url's from xml file" << endl;
+ out << " TString filename;" << endl;
+ out << " Int_t run = 0;" << endl;
out << " TString treename = type;" << endl;
out << " treename.ToLower();" << endl;
out << " treename += \"Tree\";" << endl;
out << " ::Error(\"CreateChain\", \"Cannot create an AliEn collection from %s\", xmlfile);" << endl;
out << " return NULL;" << endl;
out << " }" << endl;
+ out << " AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();" << endl;
out << " TChain *chain = new TChain(treename);" << endl;
if(fFriendChainName!="") {
out << " TChain *chainFriend = new TChain(treename);" << endl;
}
out << " coll->Reset();" << endl;
out << " while (coll->Next()) {" << endl;
- out << " chain->Add(coll->GetTURL(\"\"));" << endl;
+ out << " filename = coll->GetTURL("");" << endl;
+ out << " if (mgr) {" << endl;
+ out << " Int_t nrun = AliAnalysisManager::GetRunFromAlienPath(filename);" << endl;
+ out << " if (nrun && nrun != run) {" << endl;
+ out << " printf(\"### Run number detected from chain: %d\\n\", nrun);" << endl;
+ out << " mgr->SetRunFromPath(nrun);" << endl;
+ out << " run = nrun;" << endl;
+ out << " }" << endl;
+ out << " }" << endl;
+ out << " chain->Add(filename);" << endl;
if(fFriendChainName!="") {
out << " TString fileFriend=coll->GetTURL(\"\");" << endl;
out << " fileFriend.ReplaceAll(\"AliAOD.root\",\""<<fFriendChainName.Data()<<"\");" << endl;
out << "// 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 << " gSystem->Exec(TString::Format(\"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;
Info("WriteAnalysisMacro", "\n##### Analysis macro to run on worker nodes <%s> written",fAnalysisMacro.Data());
}
Bool_t copy = kTRUE;
- if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
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\",10);" << endl;
- out << " gEnv->SetValue(\"XNet.RequestTimeout\",20);" << endl;
+ out << " gEnv->SetValue(\"XNet.RequestTimeout\",10);" << endl;
out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
- out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",50);" << endl;
+ out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",10);" << endl;
out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
}
// Change temp directory to current one
out << " if (!TGrid::Connect(\"alien://\")) return;" << endl;
out << " Bool_t laststage = kFALSE;" << endl;
out << " TString outputDir = dir;" << endl;
- out << " TString outputFiles = \"" << fOutputFiles << "\";" << endl;
+ out << " TString outputFiles = \"" << GetListOfFiles("out") << "\";" << 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 << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file" << analysisFile <<"\");" << endl;
out << " return;" << endl;
out << " }" << endl << endl;
+ out << " mgr->SetRunFromPath(mgr->GetRunFromAlienPath(dir));" << endl;
out << " mgr->SetSkipTerminate(kFALSE);" << endl;
out << " mgr->PrintStatus();" << endl;
if (AliAnalysisManager::GetAnalysisManager()) {
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 << " gSystem->Exec(TString::Format(\"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;
}
}
Bool_t copy = kTRUE;
- if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
// LD_LIBRARY_PATH
TString pkgdir = package;
pkgdir.ReplaceAll(".par","");
- gSystem->Exec(Form("tar xvzf %s.par", pkgdir.Data()));
+ gSystem->Exec(TString::Format("tar xzf %s.par", pkgdir.Data()));
TString cdir = gSystem->WorkingDirectory();
gSystem->ChangeDirectory(pkgdir);
// Check for BUILD.sh and execute
return;
}
out << "#!/bin/bash" << endl;
+ // Make sure we can properly compile par files
+ out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
out << "echo \"=========================================\"" << endl;
out << "echo \"############## PATH : ##############\"" << endl;
out << "echo $PATH" << endl;
out << "echo \"############## memory : ##############\"" << endl;
out << "free -m" << endl;
out << "echo \"=========================================\"" << endl << endl;
- // Make sure we can properly compile par files
- if (TObject::TestBit(AliAnalysisGrid::kUsePars)) out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
out << fExecutableCommand << " ";
out << fAnalysisMacro.Data() << " " << fExecutableArgs.Data() << endl << endl;
out << "echo \"======== " << fAnalysisMacro.Data() << " finished with exit code: $? ========\"" << endl;
out << "free -m" << endl;
}
Bool_t copy = kTRUE;
- if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), fExecutable.Data());
if (FileExists(executable)) gGrid->Rm(executable);
- Info("CreateJDL", "\n##### Copying executable file <%s> to your AliEn bin directory", fExecutable.Data());
+ Info("WriteExecutable", "\n##### Copying executable file <%s> to your AliEn bin directory", fExecutable.Data());
TFile::Cp(Form("file:%s",fExecutable.Data()), Form("alien://%s", executable.Data()));
}
}
return;
}
out << "#!/bin/bash" << endl;
+ // Make sure we can properly compile par files
+ out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
out << "echo \"=========================================\"" << endl;
out << "echo \"############## PATH : ##############\"" << endl;
out << "echo $PATH" << endl;
out << "echo \"############## memory : ##############\"" << endl;
out << "free -m" << endl;
out << "echo \"=========================================\"" << endl << endl;
- // Make sure we can properly compile par files
- if (TObject::TestBit(AliAnalysisGrid::kUsePars)) out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
TString mergeMacro = fExecutable;
mergeMacro.ReplaceAll(".sh", "_merge.C");
- out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\",$2,$3)\"" << endl;
+ if (IsOneStageMerging())
+ out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\")\"" << endl;
+ else
+ out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\",$2,$3)\"" << endl;
out << fExecutableCommand << " " << "$ARG" << endl;
out << "echo \"======== " << mergeMacro.Data() << " finished with exit code: $? ========\"" << endl;
out << "echo \"############## memory after: ##############\"" << endl;
out << "free -m" << endl;
}
Bool_t copy = kTRUE;
- if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
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());
+ Info("WriteMergeExecutable", "\n##### Copying executable file <%s> to your AliEn bin directory", mergeExec.Data());
TFile::Cp(Form("file:%s",mergeExec.Data()), Form("alien://%s", executable.Data()));
}
}
Error("WriteProductionFile", "Bad file name: %s", filename);
return;
}
- TString workdir = gGrid->GetHomeDirectory();
+ TString workdir;
+ if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice"))
+ workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
Int_t njobspermaster = 1000*fNrunsPerMaster/fSplitMaxInputFileNumber;
TString locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
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));
+ if (gGrid) {
+ Info("WriteProductionFile", "\n##### Copying production file <%s> to your work directory", filename);
+ if (FileExists(filename)) gGrid->Rm(filename);
+ TFile::Cp(Form("file:%s",filename), Form("alien://%s/%s", workdir.Data(),filename));
+ }
}
//______________________________________________________________________________
// 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 (fValidationScript.IsNull()) {
+ fValidationScript = fExecutable;
+ fValidationScript.ReplaceAll(".sh", "_validation.sh");
+ }
+ TString validationScript = fValidationScript;
+ if (merge) validationScript.ReplaceAll(".sh", "_merge.sh");
if (!Connect()) {
Error("WriteValidationScript", "Alien connection required");
return;
}
+ if (!fTerminateFiles.IsNull()) {
+ fTerminateFiles.Strip();
+ fTerminateFiles.ReplaceAll(" ",",");
+ }
TString outStream = "";
if (!TestBit(AliAnalysisGrid::kTest)) outStream = " >> stdout";
if (!TestBit(AliAnalysisGrid::kSubmit)) {
// Part dedicated to the specific analyses running into the train
- TObjArray *arr = fOutputFiles.Tokenize(",");
+ TString outputFiles = fOutputFiles;
+ if (merge && !fTerminateFiles.IsNull()) {
+ outputFiles += ",";
+ outputFiles += fTerminateFiles;
+ }
+ TObjArray *arr = outputFiles.Tokenize(",");
TIter next1(arr);
TString outputFile;
- AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
- TString extra = mgr->GetExtraFiles();
- while ((os=(TObjString*)next1())) {
- if (merge) break;
+ while (!merge && (os=(TObjString*)next1())) {
+ // No need to validate outputs produced by merging since the merging macro does this
outputFile = os->GetString();
Int_t index = outputFile.Index("@");
if (index > 0) outputFile.Remove(index);
- if (merge && fMergeExcludes.Contains(outputFile)) continue;
- if (extra.Contains(outputFile)) continue;
+ if (fTerminateFiles.Contains(outputFile)) continue;
if (outputFile.Contains("*")) continue;
out << "if ! [ -f " << outputFile.Data() << " ] ; then" << endl;
out << " error=1" << endl;
out << "exit $error" << endl;
}
Bool_t copy = kTRUE;
- if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
- Info("CreateJDL", "\n##### Copying validation script <%s> to your AliEn working space", validationScript.Data());
+ Info("WriteValidationScript", "\n##### Copying validation script <%s> to your AliEn working space", validationScript.Data());
if (FileExists(validationScript)) gGrid->Rm(validationScript);
TFile::Cp(Form("file:%s",validationScript.Data()), Form("alien://%s/%s", workdir.Data(),validationScript.Data()));
}
git://git.uio.no / u / mrichter / AliRoot.git / blobdiff