1 /**************************************************************************
2 * Copyright(c) 1998-2007, ALICE Experiment at CERN, All rights reserved. *
4 * Author: The ALICE Off-line Project. *
5 * Contributors are mentioned in the code where appropriate. *
7 * Permission to use, copy, modify and distribute this software and its *
8 * documentation strictly for non-commercial purposes is hereby granted *
9 * without fee, provided that the above copyright notice appears in all *
10 * copies and that both the copyright notice and this permission notice *
11 * appear in the supporting documentation. The authors make no claims *
12 * about the suitability of this software for any purpose. It is *
13 * provided "as is" without express or implied warranty. *
14 **************************************************************************/
16 // Author: Mihaela Gheata, 01/09/2008
18 //==============================================================================
19 // AliAnalysisAlien - AliEn utility class. Provides interface for creating
20 // a personalized JDL, finding and creating a dataset.
21 //==============================================================================
23 #include "Riostream.h"
29 #include "TObjString.h"
30 #include "TObjArray.h"
32 #include "TGridResult.h"
33 #include "TGridCollection.h"
35 #include "TGridJobStatusList.h"
36 #include "TGridJobStatus.h"
37 #include "TFileMerger.h"
38 #include "AliAnalysisManager.h"
39 #include "AliVEventHandler.h"
40 #include "AliAnalysisDataContainer.h"
41 #include "AliAnalysisAlien.h"
43 ClassImp(AliAnalysisAlien)
45 //______________________________________________________________________________
46 AliAnalysisAlien::AliAnalysisAlien()
52 fSplitMaxInputFileNumber(0),
54 fMasterResubmitThreshold(0),
72 fAdditionalRootLibs(),
103 //______________________________________________________________________________
104 AliAnalysisAlien::AliAnalysisAlien(const char *name)
105 :AliAnalysisGrid(name),
110 fSplitMaxInputFileNumber(0),
112 fMasterResubmitThreshold(0),
125 fExecutableCommand(),
130 fAdditionalRootLibs(),
161 //______________________________________________________________________________
162 AliAnalysisAlien::AliAnalysisAlien(const AliAnalysisAlien& other)
163 :AliAnalysisGrid(other),
166 fPrice(other.fPrice),
168 fSplitMaxInputFileNumber(other.fSplitMaxInputFileNumber),
169 fMaxInitFailed(other.fMaxInitFailed),
170 fMasterResubmitThreshold(other.fMasterResubmitThreshold),
171 fNtestFiles(other.fNtestFiles),
172 fNrunsPerMaster(other.fNrunsPerMaster),
173 fMaxMergeFiles(other.fMaxMergeFiles),
174 fNsubmitted(other.fNsubmitted),
175 fProductionMode(other.fProductionMode),
176 fOutputToRunNo(other.fOutputToRunNo),
177 fMergeViaJDL(other.fMergeViaJDL),
178 fFastReadOption(other.fFastReadOption),
179 fOverwriteMode(other.fOverwriteMode),
180 fNreplicas(other.fNreplicas),
181 fRunNumbers(other.fRunNumbers),
182 fExecutable(other.fExecutable),
183 fExecutableCommand(other.fExecutableCommand),
184 fArguments(other.fArguments),
185 fExecutableArgs(other.fExecutableArgs),
186 fAnalysisMacro(other.fAnalysisMacro),
187 fAnalysisSource(other.fAnalysisSource),
188 fAdditionalRootLibs(other.fAdditionalRootLibs),
189 fAdditionalLibs(other.fAdditionalLibs),
190 fSplitMode(other.fSplitMode),
191 fAPIVersion(other.fAPIVersion),
192 fROOTVersion(other.fROOTVersion),
193 fAliROOTVersion(other.fAliROOTVersion),
194 fExternalPackages(other.fExternalPackages),
196 fGridWorkingDir(other.fGridWorkingDir),
197 fGridDataDir(other.fGridDataDir),
198 fDataPattern(other.fDataPattern),
199 fGridOutputDir(other.fGridOutputDir),
200 fOutputArchive(other.fOutputArchive),
201 fOutputFiles(other.fOutputFiles),
202 fInputFormat(other.fInputFormat),
203 fDatasetName(other.fDatasetName),
204 fJDLName(other.fJDLName),
205 fMergeExcludes(other.fMergeExcludes),
206 fIncludePath(other.fIncludePath),
207 fCloseSE(other.fCloseSE),
208 fFriendChainName(other.fFriendChainName),
209 fJobTag(other.fJobTag),
210 fOutputSingle(other.fOutputSingle),
211 fRunPrefix(other.fRunPrefix),
216 fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
217 fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
218 fRunRange[0] = other.fRunRange[0];
219 fRunRange[1] = other.fRunRange[1];
220 if (other.fInputFiles) {
221 fInputFiles = new TObjArray();
222 TIter next(other.fInputFiles);
224 while ((obj=next())) fInputFiles->Add(new TObjString(obj->GetName()));
225 fInputFiles->SetOwner();
227 if (other.fPackages) {
228 fPackages = new TObjArray();
229 TIter next(other.fPackages);
231 while ((obj=next())) fPackages->Add(new TObjString(obj->GetName()));
232 fPackages->SetOwner();
236 //______________________________________________________________________________
237 AliAnalysisAlien::~AliAnalysisAlien()
240 if (fGridJDL) delete fGridJDL;
241 if (fMergingJDL) delete fMergingJDL;
242 if (fInputFiles) delete fInputFiles;
243 if (fPackages) delete fPackages;
246 //______________________________________________________________________________
247 AliAnalysisAlien &AliAnalysisAlien::operator=(const AliAnalysisAlien& other)
250 if (this != &other) {
251 AliAnalysisGrid::operator=(other);
252 fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
253 fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
254 fPrice = other.fPrice;
256 fSplitMaxInputFileNumber = other.fSplitMaxInputFileNumber;
257 fMaxInitFailed = other.fMaxInitFailed;
258 fMasterResubmitThreshold = other.fMasterResubmitThreshold;
259 fNtestFiles = other.fNtestFiles;
260 fNrunsPerMaster = other.fNrunsPerMaster;
261 fMaxMergeFiles = other.fMaxMergeFiles;
262 fNsubmitted = other.fNsubmitted;
263 fProductionMode = other.fProductionMode;
264 fOutputToRunNo = other.fOutputToRunNo;
265 fMergeViaJDL = other.fMergeViaJDL;
266 fFastReadOption = other.fFastReadOption;
267 fOverwriteMode = other.fOverwriteMode;
268 fNreplicas = other.fNreplicas;
269 fRunNumbers = other.fRunNumbers;
270 fExecutable = other.fExecutable;
271 fExecutableCommand = other.fExecutableCommand;
272 fArguments = other.fArguments;
273 fExecutableArgs = other.fExecutableArgs;
274 fAnalysisMacro = other.fAnalysisMacro;
275 fAnalysisSource = other.fAnalysisSource;
276 fAdditionalRootLibs = other.fAdditionalRootLibs;
277 fAdditionalLibs = other.fAdditionalLibs;
278 fSplitMode = other.fSplitMode;
279 fAPIVersion = other.fAPIVersion;
280 fROOTVersion = other.fROOTVersion;
281 fAliROOTVersion = other.fAliROOTVersion;
282 fExternalPackages = other.fExternalPackages;
284 fGridWorkingDir = other.fGridWorkingDir;
285 fGridDataDir = other.fGridDataDir;
286 fDataPattern = other.fDataPattern;
287 fGridOutputDir = other.fGridOutputDir;
288 fOutputArchive = other.fOutputArchive;
289 fOutputFiles = other.fOutputFiles;
290 fInputFormat = other.fInputFormat;
291 fDatasetName = other.fDatasetName;
292 fJDLName = other.fJDLName;
293 fMergeExcludes = other.fMergeExcludes;
294 fIncludePath = other.fIncludePath;
295 fCloseSE = other.fCloseSE;
296 fFriendChainName = other.fFriendChainName;
297 fJobTag = other.fJobTag;
298 fOutputSingle = other.fOutputSingle;
299 fRunPrefix = other.fRunPrefix;
300 if (other.fInputFiles) {
301 fInputFiles = new TObjArray();
302 TIter next(other.fInputFiles);
304 while ((obj=next())) fInputFiles->Add(new TObjString(obj->GetName()));
305 fInputFiles->SetOwner();
307 if (other.fPackages) {
308 fPackages = new TObjArray();
309 TIter next(other.fPackages);
311 while ((obj=next())) fPackages->Add(new TObjString(obj->GetName()));
312 fPackages->SetOwner();
318 //______________________________________________________________________________
319 void AliAnalysisAlien::AddIncludePath(const char *path)
321 // Add include path in the remote analysis macro.
323 if (p.Contains("-I")) fIncludePath += Form("%s ", path);
324 else fIncludePath += Form("-I%s ", path);
327 //______________________________________________________________________________
328 void AliAnalysisAlien::AddRunNumber(Int_t run)
330 // Add a run number to the list of runs to be processed.
331 if (fRunNumbers.Length()) fRunNumbers += " ";
332 fRunNumbers += Form("%s%d", fRunPrefix.Data(), run);
335 //______________________________________________________________________________
336 void AliAnalysisAlien::AddRunNumber(const char* run)
338 // Add a run number to the list of runs to be processed.
339 if (fRunNumbers.Length()) fRunNumbers += " ";
343 //______________________________________________________________________________
344 void AliAnalysisAlien::AddDataFile(const char *lfn)
346 // Adds a data file to the input to be analysed. The file should be a valid LFN
347 // or point to an existing file in the alien workdir.
348 if (!fInputFiles) fInputFiles = new TObjArray();
349 fInputFiles->Add(new TObjString(lfn));
352 //______________________________________________________________________________
353 void AliAnalysisAlien::AddExternalPackage(const char *package)
355 // Adds external packages w.r.t to the default ones (root,aliroot and gapi)
356 if (fExternalPackages) fExternalPackages += " ";
357 fExternalPackages += package;
360 //______________________________________________________________________________
361 Bool_t AliAnalysisAlien::Connect()
363 // Try to connect to AliEn. User needs a valid token and /tmp/gclient_env_$UID sourced.
364 if (gGrid && gGrid->IsConnected()) return kTRUE;
366 Info("Connect", "Trying to connect to AliEn ...");
367 TGrid::Connect("alien://");
369 if (!gGrid || !gGrid->IsConnected()) {
370 Error("Connect", "Did not managed to connect to AliEn. Make sure you have a valid token.");
373 fUser = gGrid->GetUser();
374 Info("Connect", "\n##### Connected to AliEn as user %s. Setting analysis user to <%s>", fUser.Data(), fUser.Data());
378 //______________________________________________________________________________
379 void AliAnalysisAlien::CdWork()
381 // Check validity of alien workspace. Create directory if possible.
383 Error("CdWork", "Alien connection required");
386 TString homedir = gGrid->GetHomeDirectory();
387 TString workdir = homedir + fGridWorkingDir;
388 if (DirectoryExists(workdir)) {
392 // Work directory not existing - create it
394 if (gGrid->Mkdir(workdir)) {
395 gGrid->Cd(fGridWorkingDir);
396 Info("CreateJDL", "\n##### Created alien working directory %s", fGridWorkingDir.Data());
398 Warning("CreateJDL", "Working directory %s cannot be created.\n Using %s instead.",
399 workdir.Data(), homedir.Data());
400 fGridWorkingDir = "";
404 //______________________________________________________________________________
405 Bool_t AliAnalysisAlien::CheckFileCopy(const char *alienpath)
407 // Check if file copying is possible.
409 Error("CheckFileCopy", "Not connected to AliEn. File copying cannot be tested.");
412 Info("CheckFileCopy", "Checking possibility to copy files to your AliEn home directory... \
413 \n +++ NOTE: You can disable this via: plugin->SetCheckCopy(kFALSE);");
414 // Check if alien_CLOSE_SE is defined
415 TString closeSE = gSystem->Getenv("alien_CLOSE_SE");
416 if (!closeSE.IsNull()) {
417 Info("CheckFileCopy", "Your current close storage is pointing to: \
418 \n alien_CLOSE_SE = \"%s\"", closeSE.Data());
420 Warning("CheckFileCopy", "Your current close storage is empty ! Depending on your location, file copying may fail.");
422 // Check if grid directory exists.
423 if (!DirectoryExists(alienpath)) {
424 Error("CheckFileCopy", "Alien path %s does not seem to exist", alienpath);
427 TFile f("plugin_test_copy", "RECREATE");
428 // User may not have write permissions to current directory
430 Error("CheckFileCopy", "Cannot create local test file. Do you have write access to current directory: <%s> ?",
431 gSystem->WorkingDirectory());
435 if (FileExists(Form("alien://%s/%s",alienpath, f.GetName()))) gGrid->Rm(Form("alien://%s/%s",alienpath, f.GetName()));
436 if (!TFile::Cp(f.GetName(), Form("alien://%s/%s",alienpath, f.GetName()))) {
437 Error("CheckFileCopy", "Cannot copy files to Alien destination: <%s> This may be temporary, or: \
438 \n# 1. Make sure you have write permissions there. If this is the case: \
439 \n# 2. Check the storage availability at: http://alimonitor.cern.ch/stats?page=SE/table \
440 \n# Do: export alien_CLOSE_SE=\"working_disk_SE\" \
441 \n# To make this permanent put in in your .bashrc (in .alienshrc is not enough) \
442 \n# Redo token: rm /tmp/x509up_u$UID then: alien-token-init <username>", alienpath);
443 gSystem->Unlink(f.GetName());
446 gSystem->Unlink(f.GetName());
447 gGrid->Rm(Form("%s%s",alienpath,f.GetName()));
448 Info("CheckFileCopy", "### ...SUCCESS ###");
452 //______________________________________________________________________________
453 Bool_t AliAnalysisAlien::CheckInputData()
455 // Check validity of input data. If necessary, create xml files.
456 if (!fInputFiles && !fRunNumbers.Length() && !fRunRange[0]) {
457 if (!fGridDataDir.Length()) {
458 Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
461 Info("CheckInputData", "Analysis will make a single xml for base data directory %s",fGridDataDir.Data());
464 // Process declared files
465 Bool_t isCollection = kFALSE;
466 Bool_t isXml = kFALSE;
467 Bool_t useTags = kFALSE;
468 Bool_t checked = kFALSE;
471 TString workdir = gGrid->GetHomeDirectory();
472 workdir += fGridWorkingDir;
475 TIter next(fInputFiles);
476 while ((objstr=(TObjString*)next())) {
479 file += objstr->GetString();
480 // Store full lfn path
481 if (FileExists(file)) objstr->SetString(file);
483 file = objstr->GetName();
484 if (!FileExists(objstr->GetName())) {
485 Error("CheckInputData", "Data file %s not found or not in your working dir: %s",
486 objstr->GetName(), workdir.Data());
490 Bool_t iscoll, isxml, usetags;
491 CheckDataType(file, iscoll, isxml, usetags);
494 isCollection = iscoll;
497 TObject::SetBit(AliAnalysisGrid::kUseTags, useTags);
499 if ((iscoll != isCollection) || (isxml != isXml) || (usetags != useTags)) {
500 Error("CheckInputData", "Some conflict was found in the types of inputs");
506 // Process requested run numbers
507 if (!fRunNumbers.Length() && !fRunRange[0]) return kTRUE;
508 // Check validity of alien data directory
509 if (!fGridDataDir.Length()) {
510 Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
513 if (!DirectoryExists(fGridDataDir)) {
514 Error("CheckInputData", "Data directory %s not existing.", fGridDataDir.Data());
518 Error("CheckInputData", "You are using raw AliEn collections as input. Cannot process run numbers.");
522 if (checked && !isXml) {
523 Error("CheckInputData", "Cannot mix processing of full runs with non-xml files");
526 // Check validity of run number(s)
530 TString schunk, schunk2;
534 useTags = fDataPattern.Contains("tag");
535 TObject::SetBit(AliAnalysisGrid::kUseTags, useTags);
537 if (useTags != fDataPattern.Contains("tag")) {
538 Error("CheckInputData", "Cannot mix input files using/not using tags");
541 if (fRunNumbers.Length()) {
542 Info("CheckDataType", "Using supplied run numbers (run ranges are ignored)");
543 arr = fRunNumbers.Tokenize(" ");
545 while ((os=(TObjString*)next())) {
546 path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data());
547 if (!DirectoryExists(path)) {
548 Warning("CheckInputData", "Run number %s not found in path: <%s>", os->GetString().Data(), path.Data());
551 path = Form("%s/%s.xml", workdir.Data(),os->GetString().Data());
552 TString msg = "\n##### file: ";
554 msg += " type: xml_collection;";
555 if (useTags) msg += " using_tags: Yes";
556 else msg += " using_tags: No";
557 Info("CheckDataType", msg.Data());
558 if (fNrunsPerMaster<2) {
559 AddDataFile(Form("%s.xml", os->GetString().Data()));
562 if (((nruns-1)%fNrunsPerMaster) == 0) {
563 schunk = os->GetString();
565 if ((nruns%fNrunsPerMaster)!=0 && os!=arr->Last()) continue;
566 schunk += Form("_%s.xml", os->GetString().Data());
572 Info("CheckDataType", "Using run range [%d, %d]", fRunRange[0], fRunRange[1]);
573 for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
574 path = Form("%s/%s%d ", fGridDataDir.Data(), fRunPrefix.Data(), irun);
575 if (!DirectoryExists(path)) {
576 // Warning("CheckInputData", "Run number %d not found in path: <%s>", irun, path.Data());
579 path = Form("%s/%s%d.xml", workdir.Data(),fRunPrefix.Data(),irun);
580 TString msg = "\n##### file: ";
582 msg += " type: xml_collection;";
583 if (useTags) msg += " using_tags: Yes";
584 else msg += " using_tags: No";
585 Info("CheckDataType", msg.Data());
586 if (fNrunsPerMaster<2) {
587 AddDataFile(Form("%s%d.xml",fRunPrefix.Data(),irun));
590 if (((nruns-1)%fNrunsPerMaster) == 0) {
591 schunk = Form("%s%d", fRunPrefix.Data(),irun);
593 schunk2 = Form("_%s%d.xml", fRunPrefix.Data(), irun);
594 if ((nruns%fNrunsPerMaster)!=0 && irun != fRunRange[1]) continue;
607 //______________________________________________________________________________
608 Bool_t AliAnalysisAlien::CreateDataset(const char *pattern)
610 // Create dataset for the grid data directory + run number.
611 if (TestBit(AliAnalysisGrid::kOffline)) return kTRUE;
613 Error("CreateDataset", "Cannot create dataset with no grid connection");
619 TString workdir = gGrid->GetHomeDirectory();
620 workdir += fGridWorkingDir;
622 // Compose the 'find' command arguments
624 TString options = "-x collection ";
625 if (TestBit(AliAnalysisGrid::kTest)) options += Form("-l %d ", fNtestFiles);
626 TString conditions = "";
631 TString schunk, schunk2;
632 TGridCollection *cbase=0, *cadd=0;
633 if (!fRunNumbers.Length() && !fRunRange[0]) {
634 if (fInputFiles && fInputFiles->GetEntries()) return kTRUE;
635 // Make a single data collection from data directory.
637 if (!DirectoryExists(path)) {
638 Error("CreateDataset", "Path to data directory %s not valid",fGridDataDir.Data());
642 if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
643 else file = Form("%s.xml", gSystem->BaseName(path));
644 if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
650 command += conditions;
651 printf("command: %s\n", command.Data());
652 TGridResult *res = gGrid->Command(command);
654 // Write standard output to file
655 gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
656 Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE;
657 Bool_t nullFile = kFALSE;
659 Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command");
661 nullFile = (gSystem->Exec(Form("grep /event %s 2>/dev/null > /dev/null",file.Data()))==0)?kFALSE:kTRUE;
663 Error("CreateDataset","Dataset %s produced by the previous find command is empty !", file.Data());
668 Bool_t fileExists = FileExists(file);
669 if (!TestBit(AliAnalysisGrid::kTest) && (!fileExists || fOverwriteMode)) {
670 // Copy xml file to alien space
671 if (fileExists) gGrid->Rm(file);
672 TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
673 if (!FileExists(file)) {
674 Error("CreateDataset", "Command %s did NOT succeed", command.Data());
677 // Update list of files to be processed.
679 AddDataFile(Form("%s/%s", workdir.Data(), file.Data()));
683 Bool_t nullResult = kTRUE;
684 if (fRunNumbers.Length()) {
685 TObjArray *arr = fRunNumbers.Tokenize(" ");
688 while ((os=(TObjString*)next())) {
689 path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data());
690 if (!DirectoryExists(path)) continue;
692 if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
693 else file = Form("%s.xml", os->GetString().Data());
694 // If local collection file does not exist, create it via 'find' command.
695 if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
700 command += conditions;
701 TGridResult *res = gGrid->Command(command);
703 // Write standard output to file
704 gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
705 Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE;
706 Bool_t nullFile = kFALSE;
708 Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command");
710 nullFile = (gSystem->Exec(Form("grep /event %s 2>/dev/null > /dev/null",file.Data()))==0)?kFALSE:kTRUE;
712 Warning("CreateDataset","Dataset %s produced by: <%s> is empty !", file.Data(), command.Data());
713 fRunNumbers.ReplaceAll(os->GetString().Data(), "");
719 if (TestBit(AliAnalysisGrid::kTest)) break;
720 // Check if there is one run per master job.
721 if (fNrunsPerMaster<2) {
722 if (FileExists(file)) {
723 if (fOverwriteMode) gGrid->Rm(file);
725 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
729 // Copy xml file to alien space
730 TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
731 if (!FileExists(file)) {
732 Error("CreateDataset", "Command %s did NOT succeed", command.Data());
738 if (((nruns-1)%fNrunsPerMaster) == 0) {
739 schunk = os->GetString();
740 cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
742 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
743 printf(" Merging collection <%s> into masterjob input...\n", file.Data());
747 if ((nruns%fNrunsPerMaster)!=0 && os!=arr->Last()) {
750 schunk += Form("_%s.xml", os->GetString().Data());
751 if (FileExists(schunk)) {
752 if (fOverwriteMode) gGrid->Rm(file);
754 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
758 printf("Exporting merged collection <%s> and copying to AliEn\n", schunk.Data());
759 cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs");
760 TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data()));
761 if (!FileExists(schunk)) {
762 Error("CreateDataset", "Copy command did NOT succeed for %s", schunk.Data());
770 Error("CreateDataset", "No valid dataset corresponding to the query!");
774 // Process a full run range.
775 for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
776 path = Form("%s/%s%d ", fGridDataDir.Data(), fRunPrefix.Data(), irun);
777 if (!DirectoryExists(path)) continue;
779 if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
780 else file = Form("%s%d.xml", fRunPrefix.Data(), irun);
781 if (FileExists(file) && fNrunsPerMaster<2 && !TestBit(AliAnalysisGrid::kTest)) {
782 if (fOverwriteMode) gGrid->Rm(file);
784 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
788 // If local collection file does not exist, create it via 'find' command.
789 if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
794 command += conditions;
795 TGridResult *res = gGrid->Command(command);
797 // Write standard output to file
798 gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
799 Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE;
800 Bool_t nullFile = kFALSE;
802 Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command");
804 nullFile = (gSystem->Exec(Form("grep /event %s 2>/dev/null > /dev/null",file.Data()))==0)?kFALSE:kTRUE;
806 Warning("CreateDataset","Dataset %s produced by: <%s> is empty !", file.Data(), command.Data());
812 if (TestBit(AliAnalysisGrid::kTest)) break;
813 // Check if there is one run per master job.
814 if (fNrunsPerMaster<2) {
815 if (FileExists(file)) {
816 if (fOverwriteMode) gGrid->Rm(file);
818 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
822 // Copy xml file to alien space
823 TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
824 if (!FileExists(file)) {
825 Error("CreateDataset", "Command %s did NOT succeed", command.Data());
830 // Check if the collection for the chunk exist locally.
831 Int_t nchunk = (nruns-1)/fNrunsPerMaster;
832 if (FileExists(fInputFiles->At(nchunk)->GetName())) {
833 if (fOverwriteMode) gGrid->Rm(fInputFiles->At(nchunk)->GetName());
836 printf(" Merging collection <%s> into %d runs chunk...\n",file.Data(),fNrunsPerMaster);
837 if (((nruns-1)%fNrunsPerMaster) == 0) {
838 schunk = Form("%s%d", fRunPrefix.Data(), irun);
839 cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
841 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
845 schunk2 = Form("%s_%s%d.xml", schunk.Data(), fRunPrefix.Data(), irun);
846 if ((nruns%fNrunsPerMaster)!=0 && irun!=fRunRange[1] && schunk2 != fInputFiles->Last()->GetName()) {
850 if (FileExists(schunk)) {
851 if (fOverwriteMode) gGrid->Rm(schunk);
853 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
857 printf("Exporting merged collection <%s> and copying to AliEn.\n", schunk.Data());
858 cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs");
859 if (FileExists(schunk)) {
860 if (fOverwriteMode) gGrid->Rm(schunk);
862 Info("CreateDataset", "\n##### Dataset %s exist. Skipping copy...", schunk.Data());
866 TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data()));
867 if (!FileExists(schunk)) {
868 Error("CreateDataset", "Copy command did NOT succeed for %s", schunk.Data());
874 Error("CreateDataset", "No valid dataset corresponding to the query!");
881 //______________________________________________________________________________
882 Bool_t AliAnalysisAlien::CreateJDL()
884 // Generate a JDL file according to current settings. The name of the file is
885 // specified by fJDLName.
886 Bool_t error = kFALSE;
889 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
890 Bool_t generate = kTRUE;
891 if (TestBit(AliAnalysisGrid::kTest) || TestBit(AliAnalysisGrid::kSubmit)) generate = kFALSE;
893 Error("CreateJDL", "Alien connection required");
896 // Check validity of alien workspace
898 TString workdir = gGrid->GetHomeDirectory();
899 workdir += fGridWorkingDir;
903 Error("CreateJDL()", "Define some input files for your analysis.");
906 // Compose list of input files
907 // Check if output files were defined
908 if (!fOutputFiles.Length()) {
909 Error("CreateJDL", "You must define at least one output file");
912 // Check if an output directory was defined and valid
913 if (!fGridOutputDir.Length()) {
914 Error("CreateJDL", "You must define AliEn output directory");
917 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
918 if (!DirectoryExists(fGridOutputDir)) {
919 if (gGrid->Mkdir(fGridOutputDir)) {
920 Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
922 Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
928 // Exit if any error up to now
929 if (error) return kFALSE;
931 if (!fUser.IsNull()) {
932 fGridJDL->SetValue("User", Form("\"%s\"", fUser.Data()));
933 fMergingJDL->SetValue("User", Form("\"%s\"", fUser.Data()));
935 fGridJDL->SetExecutable(fExecutable, "This is the startup script");
936 TString mergeExec = fExecutable;
937 mergeExec.ReplaceAll(".sh", "_merge.sh");
938 fMergingJDL->SetExecutable(mergeExec, "This is the startup script");
939 mergeExec.ReplaceAll(".sh", ".C");
940 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),mergeExec.Data()), "List of input files to be uploaded to workers");
941 if (!fArguments.IsNull())
942 fGridJDL->SetArguments(fArguments, "Arguments for the executable command");
943 fMergingJDL->SetArguments("$1");
944 fGridJDL->SetValue("TTL", Form("\"%d\"",fTTL));
945 fGridJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60));
946 fMergingJDL->SetValue("TTL", Form("\"%d\"",fTTL));
947 fMergingJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60));
949 if (fMaxInitFailed > 0) {
950 fGridJDL->SetValue("MaxInitFailed", Form("\"%d\"",fMaxInitFailed));
951 fGridJDL->SetDescription("MaxInitFailed", "Maximum number of first failing jobs to abort the master job");
953 if (fSplitMaxInputFileNumber > 0) {
954 fGridJDL->SetValue("SplitMaxInputFileNumber", Form("\"%d\"", fSplitMaxInputFileNumber));
955 fGridJDL->SetDescription("SplitMaxInputFileNumber", "Maximum number of input files to be processed per subjob");
957 if (fSplitMode.Length()) {
958 fGridJDL->SetValue("Split", Form("\"%s\"", fSplitMode.Data()));
959 fGridJDL->SetDescription("Split", "We split per SE or file");
961 if (!fAliROOTVersion.IsNull()) {
962 fGridJDL->AddToPackages("AliRoot", fAliROOTVersion,"VO_ALICE", "List of requested packages");
963 fMergingJDL->AddToPackages("AliRoot", fAliROOTVersion, "VO_ALICE", "List of requested packages");
965 if (!fROOTVersion.IsNull()) {
966 fGridJDL->AddToPackages("ROOT", fROOTVersion);
967 fMergingJDL->AddToPackages("ROOT", fROOTVersion);
969 if (!fAPIVersion.IsNull()) {
970 fGridJDL->AddToPackages("APISCONFIG", fAPIVersion);
971 fMergingJDL->AddToPackages("APISCONFIG", fAPIVersion);
973 if (!fExternalPackages.IsNull()) {
974 arr = fExternalPackages.Tokenize(" ");
976 while ((os=(TObjString*)next())) {
977 TString pkgname = os->GetString();
978 Int_t index = pkgname.Index("::");
979 TString pkgversion = pkgname(index+2, pkgname.Length());
980 pkgname.Remove(index);
981 fGridJDL->AddToPackages(pkgname, pkgversion);
982 fMergingJDL->AddToPackages(pkgname, pkgversion);
986 fGridJDL->SetInputDataListFormat(fInputFormat, "Format of input data");
987 fGridJDL->SetInputDataList("wn.xml", "Collection name to be processed on each worker node");
988 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), fAnalysisMacro.Data()), "List of input files to be uploaded to workers");
989 TString analysisFile = fExecutable;
990 analysisFile.ReplaceAll(".sh", ".root");
991 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),analysisFile.Data()));
992 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),analysisFile.Data()));
993 if (IsUsingTags() && !gSystem->AccessPathName("ConfigureCuts.C"))
994 fGridJDL->AddToInputSandbox(Form("LF:%s/ConfigureCuts.C", workdir.Data()));
995 if (fAdditionalLibs.Length()) {
996 arr = fAdditionalLibs.Tokenize(" ");
998 while ((os=(TObjString*)next())) {
999 if (os->GetString().Contains(".so")) continue;
1000 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), os->GetString().Data()));
1001 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), os->GetString().Data()));
1006 TIter next(fPackages);
1008 while ((obj=next())) {
1009 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName()));
1010 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName()));
1013 if (fOutputArchive.Length()) {
1014 arr = fOutputArchive.Tokenize(" ");
1016 Bool_t first = kTRUE;
1017 const char *comment = "Files to be archived";
1018 const char *comment1 = comment;
1019 while ((os=(TObjString*)next())) {
1020 if (!first) comment = NULL;
1021 if (!os->GetString().Contains("@") && fCloseSE.Length())
1022 fGridJDL->AddToOutputArchive(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
1024 fGridJDL->AddToOutputArchive(os->GetString(), comment);
1028 TString outputArchive = fOutputArchive;
1029 if (!fMergeExcludes.IsNull()) {
1030 arr = fMergeExcludes.Tokenize(" ");
1032 while ((os=(TObjString*)next1())) {
1033 outputArchive.ReplaceAll(Form("%s,",os->GetString().Data()),"");
1034 outputArchive.ReplaceAll(os->GetString(),"");
1038 arr = outputArchive.Tokenize(" ");
1042 while ((os=(TObjString*)next2())) {
1043 if (!first) comment = NULL;
1044 if (!os->GetString().Contains("@") && fCloseSE.Length())
1045 fMergingJDL->AddToOutputArchive(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
1047 fMergingJDL->AddToOutputArchive(os->GetString(), comment);
1052 arr = fOutputFiles.Tokenize(",");
1054 Bool_t first = kTRUE;
1055 const char *comment = "Files to be archived";
1056 const char *comment1 = comment;
1057 while ((os=(TObjString*)next())) {
1058 // Ignore ouputs in jdl that are also in outputarchive
1059 TString sout = os->GetString();
1060 if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
1061 if (fOutputArchive.Contains(sout)) continue;
1062 if (!first) comment = NULL;
1063 if (!os->GetString().Contains("@") && fCloseSE.Length())
1064 fGridJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
1066 fGridJDL->AddToOutputSandbox(os->GetString(), comment);
1070 if (fOutputFiles.Length()) {
1071 TString outputFiles = fOutputFiles;
1072 if (!fMergeExcludes.IsNull()) {
1073 arr = fMergeExcludes.Tokenize(" ");
1075 while ((os=(TObjString*)next1())) {
1076 outputFiles.ReplaceAll(Form("%s,",os->GetString().Data()),"");
1077 outputFiles.ReplaceAll(os->GetString(),"");
1081 arr = outputFiles.Tokenize(" ");
1085 while ((os=(TObjString*)next2())) {
1086 // Ignore ouputs in jdl that are also in outputarchive
1087 TString sout = os->GetString();
1088 if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
1089 if (fOutputArchive.Contains(sout)) continue;
1090 if (!first) comment = NULL;
1091 if (!os->GetString().Contains("@") && fCloseSE.Length())
1092 fMergingJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
1094 fMergingJDL->AddToOutputSandbox(os->GetString(), comment);
1098 fGridJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
1099 fMergingJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
1100 TString validationScript = fExecutable;
1101 validationScript.ReplaceAll(".sh", "_validation.sh");
1102 fGridJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
1103 validationScript = fExecutable;
1104 validationScript.ReplaceAll(".sh", "_mergevalidation.sh");
1105 fMergingJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
1106 if (fMasterResubmitThreshold) {
1107 fGridJDL->SetValue("MasterResubmitThreshold", Form("\"%d%%\"", fMasterResubmitThreshold));
1108 fGridJDL->SetDescription("MasterResubmitThreshold", "Resubmit failed jobs until DONE rate reaches this percentage");
1110 // Write a jdl with 2 input parameters: collection name and output dir name.
1113 // Copy jdl to grid workspace
1115 // Check if an output directory was defined and valid
1116 if (!fGridOutputDir.Length()) {
1117 Error("CreateJDL", "You must define AliEn output directory");
1120 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
1121 if (!fProductionMode && !DirectoryExists(fGridOutputDir)) {
1122 if (gGrid->Mkdir(fGridOutputDir)) {
1123 Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
1125 Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
1131 if (TestBit(AliAnalysisGrid::kSubmit)) {
1132 TString mergeJDLName = fExecutable;
1133 mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
1134 TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
1135 TString locjdl1 = Form("%s/%s", fGridOutputDir.Data(),mergeJDLName.Data());
1136 if (fProductionMode) {
1137 locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
1138 locjdl1 = Form("%s/%s", workdir.Data(),mergeJDLName.Data());
1140 if (FileExists(locjdl)) gGrid->Rm(locjdl);
1141 if (FileExists(locjdl1)) gGrid->Rm(locjdl1);
1142 Info("CreateJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
1143 TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
1145 Info("CreateJDL", "\n##### Copying merging JDL file <%s> to your AliEn output directory", mergeJDLName.Data());
1146 TFile::Cp(Form("file:%s",mergeJDLName.Data()), Form("alien://%s", locjdl1.Data()));
1149 if (fAdditionalLibs.Length()) {
1150 arr = fAdditionalLibs.Tokenize(" ");
1153 while ((os=(TObjString*)next())) {
1154 if (os->GetString().Contains(".so")) continue;
1155 Info("CreateJDL", "\n##### Copying dependency: <%s> to your alien workspace", os->GetString().Data());
1156 if (FileExists(os->GetString())) gGrid->Rm(os->GetString());
1157 TFile::Cp(Form("file:%s",os->GetString().Data()), Form("alien://%s/%s", workdir.Data(), os->GetString().Data()));
1162 TIter next(fPackages);
1164 while ((obj=next())) {
1165 if (FileExists(obj->GetName())) gGrid->Rm(obj->GetName());
1166 Info("CreateJDL", "\n##### Copying dependency: <%s> to your alien workspace", obj->GetName());
1167 TFile::Cp(Form("file:%s",obj->GetName()), Form("alien://%s/%s", workdir.Data(), obj->GetName()));
1174 //______________________________________________________________________________
1175 Bool_t AliAnalysisAlien::WriteJDL(Bool_t copy)
1177 // Writes one or more JDL's corresponding to findex. If findex is negative,
1178 // all run numbers are considered in one go (jdl). For non-negative indices
1179 // they correspond to the indices in the array fInputFiles.
1180 if (!fInputFiles) return kFALSE;
1182 TString workdir = gGrid->GetHomeDirectory();
1183 workdir += fGridWorkingDir;
1185 if (!fRunNumbers.Length() && !fRunRange[0]) {
1186 // One jdl with no parameters in case input data is specified by name.
1187 TIter next(fInputFiles);
1188 while ((os=(TObjString*)next()))
1189 fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetString().Data()), "Input xml collections");
1190 if (!fOutputSingle.IsNull())
1191 fGridJDL->SetOutputDirectory(Form("#alienfulldir#/../%s",fOutputSingle.Data()), "Output directory");
1193 fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
1194 fMergingJDL->SetOutputDirectory(fGridOutputDir);
1197 // One jdl to be submitted with 2 input parameters: data collection name and output dir prefix
1198 fGridJDL->AddToInputDataCollection(Form("LF:%s/$1,nodownload", workdir.Data()), "Input xml collections");
1199 if (!fOutputSingle.IsNull()) {
1200 if (!fOutputToRunNo) fGridJDL->SetOutputDirectory(Form("#alienfulldir#/%s",fOutputSingle.Data()), "Output directory");
1201 else fGridJDL->SetOutputDirectory(Form("%s/$2",fGridOutputDir.Data()), "Output directory");
1203 fGridJDL->SetOutputDirectory(Form("%s/$2/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
1204 fMergingJDL->SetOutputDirectory(Form("%s/$1", fGridOutputDir.Data()), "Output directory");
1209 // Generate the JDL as a string
1210 TString sjdl = fGridJDL->Generate();
1211 TString sjdl1 = fMergingJDL->Generate();
1213 sjdl.ReplaceAll("\"LF:", "\n \"LF:");
1214 sjdl.ReplaceAll("(member", "\n (member");
1215 sjdl.ReplaceAll("\",\"VO_", "\",\n \"VO_");
1216 sjdl.ReplaceAll("{", "{\n ");
1217 sjdl.ReplaceAll("};", "\n};");
1218 sjdl.ReplaceAll("{\n \n", "{\n");
1219 sjdl.ReplaceAll("\n\n", "\n");
1220 sjdl.ReplaceAll("OutputDirectory", "OutputDir");
1221 sjdl1.ReplaceAll("\"LF:", "\n \"LF:");
1222 sjdl1.ReplaceAll("(member", "\n (member");
1223 sjdl1.ReplaceAll("\",\"VO_", "\",\n \"VO_");
1224 sjdl1.ReplaceAll("{", "{\n ");
1225 sjdl1.ReplaceAll("};", "\n};");
1226 sjdl1.ReplaceAll("{\n \n", "{\n");
1227 sjdl1.ReplaceAll("\n\n", "\n");
1228 sjdl1.ReplaceAll("OutputDirectory", "OutputDir");
1229 sjdl += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
1230 sjdl.Prepend(Form("Jobtag = {\n \"comment:%s\"\n};\n", fJobTag.Data()));
1231 index = sjdl.Index("JDLVariables");
1232 if (index >= 0) sjdl.Insert(index, "\n# JDL variables\n");
1233 sjdl1 += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
1234 sjdl1.Prepend(Form("Jobtag = {\n \"comment:Merging_%s\"\n};\n", fJobTag.Data()));
1235 index = sjdl1.Index("JDLVariables");
1236 if (index >= 0) sjdl1.Insert(index, "\n# JDL variables\n");
1237 // Write jdl to file
1239 out.open(fJDLName.Data(), ios::out);
1241 Error("CreateJDL", "Bad file name: %s", fJDLName.Data());
1244 out << sjdl << endl;
1245 TString mergeJDLName = fExecutable;
1246 mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
1249 out1.open(mergeJDLName.Data(), ios::out);
1251 Error("CreateJDL", "Bad file name: %s", mergeJDLName.Data());
1254 out1 << sjdl1 << endl;
1257 // Copy jdl to grid workspace
1259 Info("CreateJDL", "\n##### You may want to review jdl:%s and analysis macro:%s before running in <submit> mode", fJDLName.Data(), fAnalysisMacro.Data());
1261 TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
1262 TString locjdl1 = Form("%s/%s", fGridOutputDir.Data(),mergeJDLName.Data());
1263 if (fProductionMode) {
1264 locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
1265 locjdl1 = Form("%s/%s", workdir.Data(),mergeJDLName.Data());
1267 if (FileExists(locjdl)) gGrid->Rm(locjdl);
1268 if (FileExists(locjdl1)) gGrid->Rm(locjdl1);
1269 Info("CreateJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
1270 TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
1272 Info("CreateJDL", "\n##### Copying merging JDL file <%s> to your AliEn output directory", mergeJDLName.Data());
1273 TFile::Cp(Form("file:%s",mergeJDLName.Data()), Form("alien://%s", locjdl1.Data()));
1279 //______________________________________________________________________________
1280 Bool_t AliAnalysisAlien::FileExists(const char *lfn)
1282 // Returns true if file exists.
1283 if (!gGrid) return kFALSE;
1284 TGridResult *res = gGrid->Ls(lfn);
1285 if (!res) return kFALSE;
1286 TMap *map = dynamic_cast<TMap*>(res->At(0));
1291 TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("name"));
1292 if (!objs || !objs->GetString().Length()) {
1300 //______________________________________________________________________________
1301 Bool_t AliAnalysisAlien::DirectoryExists(const char *dirname)
1303 // Returns true if directory exists. Can be also a path.
1304 if (!gGrid) return kFALSE;
1305 // Check if dirname is a path
1306 TString dirstripped = dirname;
1307 dirstripped = dirstripped.Strip();
1308 dirstripped = dirstripped.Strip(TString::kTrailing, '/');
1309 TString dir = gSystem->BaseName(dirstripped);
1311 TString path = gSystem->DirName(dirstripped);
1312 TGridResult *res = gGrid->Ls(path, "-F");
1313 if (!res) return kFALSE;
1317 while ((map=dynamic_cast<TMap*>(next()))) {
1318 obj = map->GetValue("name");
1320 if (dir == obj->GetName()) {
1329 //______________________________________________________________________________
1330 void AliAnalysisAlien::CheckDataType(const char *lfn, Bool_t &isCollection, Bool_t &isXml, Bool_t &useTags)
1332 // Check input data type.
1333 isCollection = kFALSE;
1337 Error("CheckDataType", "No connection to grid");
1340 isCollection = IsCollection(lfn);
1341 TString msg = "\n##### file: ";
1344 msg += " type: raw_collection;";
1345 // special treatment for collections
1347 // check for tag files in the collection
1348 TGridResult *res = gGrid->Command(Form("listFilesFromCollection -z -v %s",lfn), kFALSE);
1350 msg += " using_tags: No (unknown)";
1351 Info("CheckDataType", msg.Data());
1354 const char* typeStr = res->GetKey(0, "origLFN");
1355 if (!typeStr || !strlen(typeStr)) {
1356 msg += " using_tags: No (unknown)";
1357 Info("CheckDataType", msg.Data());
1360 TString file = typeStr;
1361 useTags = file.Contains(".tag");
1362 if (useTags) msg += " using_tags: Yes";
1363 else msg += " using_tags: No";
1364 Info("CheckDataType", msg.Data());
1369 isXml = slfn.Contains(".xml");
1371 // Open xml collection and check if there are tag files inside
1372 msg += " type: xml_collection;";
1373 TGridCollection *coll = (TGridCollection*)gROOT->ProcessLine(Form("TAlienCollection::Open(\"alien://%s\",1);",lfn));
1375 msg += " using_tags: No (unknown)";
1376 Info("CheckDataType", msg.Data());
1379 TMap *map = coll->Next();
1381 msg += " using_tags: No (unknown)";
1382 Info("CheckDataType", msg.Data());
1385 map = (TMap*)map->GetValue("");
1387 if (map && map->GetValue("name")) file = map->GetValue("name")->GetName();
1388 useTags = file.Contains(".tag");
1390 if (useTags) msg += " using_tags: Yes";
1391 else msg += " using_tags: No";
1392 Info("CheckDataType", msg.Data());
1395 useTags = slfn.Contains(".tag");
1396 if (slfn.Contains(".root")) msg += " type: root file;";
1397 else msg += " type: unknown file;";
1398 if (useTags) msg += " using_tags: Yes";
1399 else msg += " using_tags: No";
1400 Info("CheckDataType", msg.Data());
1403 //______________________________________________________________________________
1404 void AliAnalysisAlien::EnablePackage(const char *package)
1406 // Enables a par file supposed to exist in the current directory.
1407 TString pkg(package);
1408 pkg.ReplaceAll(".par", "");
1410 if (gSystem->AccessPathName(pkg)) {
1411 Fatal("EnablePackage", "Package %s not found", pkg.Data());
1414 if (!TObject::TestBit(AliAnalysisGrid::kUsePars))
1415 Info("EnablePackage", "AliEn plugin will use .par packages");
1416 TObject::SetBit(AliAnalysisGrid::kUsePars, kTRUE);
1418 fPackages = new TObjArray();
1419 fPackages->SetOwner();
1421 fPackages->Add(new TObjString(pkg));
1424 //______________________________________________________________________________
1425 const char *AliAnalysisAlien::GetJobStatus(Int_t jobidstart, Int_t lastid, Int_t &nrunning, Int_t &nwaiting, Int_t &nerror, Int_t &ndone)
1427 // Get job status for all jobs with jobid>jobidstart.
1428 static char mstatus[20];
1434 TGridJobStatusList *list = gGrid->Ps("");
1435 if (!list) return mstatus;
1436 Int_t nentries = list->GetSize();
1437 TGridJobStatus *status;
1439 for (Int_t ijob=0; ijob<nentries; ijob++) {
1440 status = (TGridJobStatus *)list->At(ijob);
1441 pid = gROOT->ProcessLine(Form("atoi(((TAlienJobStatus*)0x%lx)->GetKey(\"queueId\"));", (ULong_t)status));
1442 if (pid<jobidstart) continue;
1443 if (pid == lastid) {
1444 gROOT->ProcessLine(Form("sprintf((char*)0x%lx,((TAlienJobStatus*)0x%lx)->GetKey(\"status\"));",(ULong_t)mstatus, (ULong_t)status));
1446 switch (status->GetStatus()) {
1447 case TGridJobStatus::kWAITING:
1449 case TGridJobStatus::kRUNNING:
1451 case TGridJobStatus::kABORTED:
1452 case TGridJobStatus::kFAIL:
1453 case TGridJobStatus::kUNKNOWN:
1455 case TGridJobStatus::kDONE:
1464 //______________________________________________________________________________
1465 Bool_t AliAnalysisAlien::IsCollection(const char *lfn) const
1467 // Returns true if file is a collection. Functionality duplicated from
1468 // TAlien::Type() because we don't want to directly depend on TAlien.
1470 Error("IsCollection", "No connection to grid");
1473 TGridResult *res = gGrid->Command(Form("type -z %s",lfn),kFALSE);
1474 if (!res) return kFALSE;
1475 const char* typeStr = res->GetKey(0, "type");
1476 if (!typeStr || !strlen(typeStr)) return kFALSE;
1477 if (!strcmp(typeStr, "collection")) return kTRUE;
1482 //______________________________________________________________________________
1483 Bool_t AliAnalysisAlien::IsSingleOutput() const
1485 // Check if single-ouput option is on.
1486 return (!fOutputSingle.IsNull());
1489 //______________________________________________________________________________
1490 void AliAnalysisAlien::Print(Option_t *) const
1492 // Print current plugin settings.
1493 printf("### AliEn analysis plugin current settings ###\n");
1494 printf("= OverwriteMode:________________________________ %d\n", fOverwriteMode);
1495 if (fOverwriteMode) {
1496 printf("***** NOTE: Overwrite mode will overwrite the input generated datasets and partial results from previous analysis. \
1497 \n***** To disable, use: plugin->SetOverwriteMode(kFALSE);\n");
1499 printf("= Copy files to grid: __________________________ %s\n", (IsUseCopy())?"YES":"NO");
1500 printf("= Check if files can be copied to grid: ________ %s\n", (IsCheckCopy())?"YES":"NO");
1501 printf("= Production mode:______________________________ %d\n", fProductionMode);
1502 printf("= Version of API requested: ____________________ %s\n", fAPIVersion.Data());
1503 printf("= Version of ROOT requested: ___________________ %s\n", fROOTVersion.Data());
1504 printf("= Version of AliRoot requested: ________________ %s\n", fAliROOTVersion.Data());
1506 printf("= User running the plugin: _____________________ %s\n", fUser.Data());
1507 printf("= Grid workdir relative to user $HOME: _________ %s\n", fGridWorkingDir.Data());
1508 printf("= Grid output directory relative to workdir: ___ %s\n", fGridOutputDir.Data());
1509 printf("= Data base directory path requested: __________ %s\n", fGridDataDir.Data());
1510 printf("= Data search pattern: _________________________ %s\n", fDataPattern.Data());
1511 printf("= Input data format: ___________________________ %s\n", fInputFormat.Data());
1512 if (fRunNumbers.Length())
1513 printf("= Run numbers to be processed: _________________ %s\n", fRunNumbers.Data());
1515 printf("= Run range to be processed: ___________________ %s%d-%s%d\n", fRunPrefix.Data(), fRunRange[0], fRunPrefix.Data(), fRunRange[1]);
1516 if (!fRunRange[0] && !fRunNumbers.Length()) {
1517 TIter next(fInputFiles);
1520 while ((obj=next())) list += obj->GetName();
1521 printf("= Input files to be processed: _________________ %s\n", list.Data());
1523 if (TestBit(AliAnalysisGrid::kTest))
1524 printf("= Number of input files used in test mode: _____ %d\n", fNtestFiles);
1525 printf("= List of output files to be registered: _______ %s\n", fOutputFiles.Data());
1526 printf("= List of outputs going to be archived: ________ %s\n", fOutputArchive.Data());
1527 printf("= List of outputs that should not be merged: ___ %s\n", fMergeExcludes.Data());
1528 printf("=====================================================================\n");
1529 printf("= Job price: ___________________________________ %d\n", fPrice);
1530 printf("= Time to live (TTL): __________________________ %d\n", fTTL);
1531 printf("= Max files per subjob: ________________________ %d\n", fSplitMaxInputFileNumber);
1532 if (fMaxInitFailed>0)
1533 printf("= Max number of subjob fails to kill: __________ %d\n", fMaxInitFailed);
1534 if (fMasterResubmitThreshold>0)
1535 printf("= Resubmit master job if failed subjobs >_______ %d\n", fMasterResubmitThreshold);
1536 printf("= Number of replicas for the output files_______ %d\n", fNreplicas);
1537 if (fNrunsPerMaster>0)
1538 printf("= Number of runs per master job: _______________ %d\n", fNrunsPerMaster);
1539 printf("= Number of files in one chunk to be merged: ___ %d\n", fMaxMergeFiles);
1540 printf("= Name of the generated execution script: ______ %s\n", fExecutable.Data());
1541 printf("= Executable command: __________________________ %s\n", fExecutableCommand.Data());
1542 if (fArguments.Length())
1543 printf("= Arguments for the execution script: __________ %s\n",fArguments.Data());
1544 if (fExecutableArgs.Length())
1545 printf("= Arguments after macro name in executable______ %s\n",fExecutableArgs.Data());
1546 printf("= Name of the generated analysis macro: ________ %s\n",fAnalysisMacro.Data());
1547 printf("= User analysis files to be deployed: __________ %s\n",fAnalysisSource.Data());
1548 printf("= Additional libs to be loaded or souces to be compiled runtime: <%s>\n",fAdditionalLibs.Data());
1549 printf("= Master jobs split mode: ______________________ %s\n",fSplitMode.Data());
1551 printf("= Custom name for the dataset to be created: ___ %s\n", fDatasetName.Data());
1552 printf("= Name of the generated JDL: ___________________ %s\n", fJDLName.Data());
1553 if (fIncludePath.Data())
1554 printf("= Include path for runtime task compilation: ___ %s\n", fIncludePath.Data());
1555 if (fCloseSE.Length())
1556 printf("= Force job outputs to storage element: ________ %s\n", fCloseSE.Data());
1557 if (fFriendChainName.Length())
1558 printf("= Open friend chain file on worker: ____________ %s\n", fFriendChainName.Data());
1560 TIter next(fPackages);
1563 while ((obj=next())) list += obj->GetName();
1564 printf("= Par files to be used: ________________________ %s\n", list.Data());
1568 //______________________________________________________________________________
1569 void AliAnalysisAlien::SetDefaults()
1571 // Set default values for everything. What cannot be filled will be left empty.
1572 if (fGridJDL) delete fGridJDL;
1573 fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
1574 fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
1577 fSplitMaxInputFileNumber = 100;
1579 fMasterResubmitThreshold = 0;
1584 fNrunsPerMaster = 1;
1585 fMaxMergeFiles = 100;
1587 fExecutable = "analysis.sh";
1588 fExecutableCommand = "root -b -q";
1590 fExecutableArgs = "";
1591 fAnalysisMacro = "myAnalysis.C";
1592 fAnalysisSource = "";
1593 fAdditionalLibs = "";
1597 fAliROOTVersion = "";
1598 fUser = ""; // Your alien user name
1599 fGridWorkingDir = "";
1600 fGridDataDir = ""; // Can be like: /alice/sim/PDC_08a/LHC08c9/
1601 fDataPattern = "*AliESDs.root"; // Can be like: *AliESDs.root, */pass1/*AliESDs.root, ...
1602 fFriendChainName = "";
1603 fGridOutputDir = "output";
1604 fOutputArchive = "log_archive.zip:std*@disk=1 root_archive.zip:*.root@disk=2";
1605 fOutputFiles = ""; // Like "AliAODs.root histos.root"
1606 fInputFormat = "xml-single";
1607 fJDLName = "analysis.jdl";
1608 fJobTag = "Automatically generated analysis JDL";
1609 fMergeExcludes = "";
1612 SetCheckCopy(kTRUE);
1613 SetDefaultOutputs(kTRUE);
1617 //______________________________________________________________________________
1618 Bool_t AliAnalysisAlien::MergeOutput(const char *output, const char *basedir, Int_t nmaxmerge)
1620 // Merge all registered outputs from basedir.
1621 TString outputFile = output;
1623 TString outputChunk;
1624 TString previousChunk = "";
1625 Int_t countChunk = 0;
1626 Int_t countZero = nmaxmerge;
1627 Bool_t merged = kTRUE;
1628 Int_t index = outputFile.Index("@");
1629 if (index > 0) outputFile.Remove(index);
1630 command = Form("find %s/ *%s", basedir, outputFile.Data());
1631 printf("command: %s\n", command.Data());
1632 TGridResult *res = gGrid->Command(command);
1634 printf("Error: No result for the find command\n");
1638 TFileMerger *fm = 0;
1641 // Check if there is a merge operation to resume
1642 outputChunk = outputFile;
1643 outputChunk.ReplaceAll(".root", "_*.root");
1644 // Check for existent temporary merge files
1645 // Check overwrite mode and remove previous partial results if needed
1646 if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
1648 // Skip as many input files as in a chunk
1649 for (Int_t counter=0; counter<nmaxmerge; counter++) map = (TMap*)nextmap();
1651 ::Error("MergeOutputs", "Cannot resume merging for <%s>, nentries=%d", outputFile.Data(), res->GetSize());
1655 outputChunk = outputFile;
1656 outputChunk.ReplaceAll(".root", Form("_%04d.root", countChunk));
1658 if (gSystem->AccessPathName(outputChunk)) continue;
1659 // Merged file with chunks up to <countChunk> found
1660 printf("Resume merging of <%s> from <%s>\n", outputFile.Data(), outputChunk.Data());
1661 previousChunk = outputChunk;
1665 countZero = nmaxmerge;
1667 while ((map=(TMap*)nextmap())) {
1668 // Loop 'find' results and get next LFN
1669 if (countZero == nmaxmerge) {
1670 // First file in chunk - create file merger and add previous chunk if any.
1671 fm = new TFileMerger(kFALSE);
1672 fm->SetFastMethod(kTRUE);
1673 if (previousChunk.Length()) fm->AddFile(previousChunk.Data());
1674 outputChunk = outputFile;
1675 outputChunk.ReplaceAll(".root", Form("_%04d.root", countChunk));
1677 // If last file found, put merged results in the output file
1678 if (map == res->Last()) outputChunk = outputFile;
1679 TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl"));
1680 if (!objs || !objs->GetString().Length()) {
1681 // Nothing found - skip this output
1686 // Add file to be merged and decrement chunk counter.
1687 fm->AddFile(objs->GetString());
1689 if (countZero==0 || map == res->Last()) {
1690 fm->OutputFile(outputChunk);
1691 if (!fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
1692 // Nothing found - skip this output
1693 ::Warning("MergeOutputs", "No <%s> files found.", outputFile.Data());
1698 // Merge the outputs, then go to next chunk
1700 ::Error("MergeOutputs", "Could not merge all <%s> files", outputFile.Data());
1706 ::Info("MergeOutputs", "\n##### Merged %d output files to <%s>", fm->GetMergeList()->GetSize(), outputChunk.Data());
1707 gSystem->Unlink(previousChunk);
1709 if (map == res->Last()) {
1715 countZero = nmaxmerge;
1716 previousChunk = outputChunk;
1722 //______________________________________________________________________________
1723 Bool_t AliAnalysisAlien::MergeOutputs()
1725 // Merge analysis outputs existing in the AliEn space.
1726 if (TestBit(AliAnalysisGrid::kTest)) return kTRUE;
1727 if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
1729 Error("MergeOutputs", "Cannot merge outputs without grid connection. Terminate will NOT be executed");
1733 if (!TestBit(AliAnalysisGrid::kMerge)) {
1734 Info("MergeOutputs", "### Re-run with <MergeViaJDL> option in terminate mode of the plugin to submit merging jobs ###");
1737 if (fProductionMode) {
1738 Info("MergeOutputs", "### Merging will be submitted by LPM manager... ###");
1741 Info("MergeOutputs", "Submitting merging JDL");
1742 if (!SubmitMerging()) return kFALSE;
1743 Info("MergeOutputs", "### Re-run with <MergeViaJDL> off to collect results after merging jobs are done ###");
1744 Info("MergeOutputs", "### The Terminate() method is executed by the merging jobs");
1747 // Get the output path
1748 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
1749 if (!DirectoryExists(fGridOutputDir)) {
1750 Error("MergeOutputs", "Grid output directory %s not found. Terminate() will NOT be executed", fGridOutputDir.Data());
1753 if (!fOutputFiles.Length()) {
1754 Error("MergeOutputs", "No output file names defined. Are you running the right AliAnalysisAlien configuration ?");
1757 // Check if fast read option was requested
1758 Info("MergeOutputs", "Started local merging of output files from: alien://%s \
1759 \n======= overwrite mode = %d", fGridOutputDir.Data(), (Int_t)fOverwriteMode);
1760 if (fFastReadOption) {
1761 Warning("MergeOutputs", "You requested FastRead option. Using xrootd flags to reduce timeouts. This may skip some files that could be accessed ! \
1762 \n+++ NOTE: To disable this option, use: plugin->SetFastReadOption(kFALSE)");
1763 gEnv->SetValue("XNet.ConnectTimeout",10);
1764 gEnv->SetValue("XNet.RequestTimeout",10);
1765 gEnv->SetValue("XNet.MaxRedirectCount",2);
1766 gEnv->SetValue("XNet.ReconnectTimeout",10);
1767 gEnv->SetValue("XNet.FirstConnectMaxCnt",1);
1769 TObjArray *list = fOutputFiles.Tokenize(",");
1773 Bool_t merged = kTRUE;
1774 while((str=(TObjString*)next())) {
1775 outputFile = str->GetString();
1776 Int_t index = outputFile.Index("@");
1777 if (index > 0) outputFile.Remove(index);
1778 TString outputChunk = outputFile;
1779 outputChunk.ReplaceAll(".root", "_*.root");
1780 // Skip already merged outputs
1781 if (!gSystem->AccessPathName(outputFile)) {
1782 if (fOverwriteMode) {
1783 Info("MergeOutputs", "Overwrite mode. Existing file %s was deleted.", outputFile.Data());
1784 gSystem->Unlink(outputFile);
1785 if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
1786 Info("MergeOutput", "Overwrite mode: partial merged files %s will removed",
1787 outputChunk.Data());
1788 gSystem->Exec(Form("rm -f %s", outputChunk.Data()));
1791 Info("MergeOutputs", "Output file <%s> found. Not merging again.", outputFile.Data());
1795 if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
1796 Info("MergeOutput", "Overwrite mode: partial merged files %s will removed",
1797 outputChunk.Data());
1798 gSystem->Exec(Form("rm -f %s", outputChunk.Data()));
1801 if (fMergeExcludes.Length() &&
1802 fMergeExcludes.Contains(outputFile.Data())) continue;
1803 // Perform a 'find' command in the output directory, looking for registered outputs
1804 merged = MergeOutput(outputFile, fGridOutputDir, fMaxMergeFiles);
1806 Error("MergeOutputs", "Terminate() will NOT be executed");
1809 TFile *fileOpened = (TFile*)gROOT->GetListOfFiles()->FindObject(outputFile);
1810 if (fileOpened) fileOpened->Close();
1815 //______________________________________________________________________________
1816 void AliAnalysisAlien::SetDefaultOutputs(Bool_t flag)
1818 // Use the output files connected to output containers from the analysis manager
1819 // rather than the files defined by SetOutputFiles
1820 if (flag && !TObject::TestBit(AliAnalysisGrid::kDefaultOutputs))
1821 Info("SetDefaultOutputs", "Plugin will use the output files taken from \
1823 TObject::SetBit(AliAnalysisGrid::kDefaultOutputs, flag);
1826 //______________________________________________________________________________
1827 void AliAnalysisAlien::SetOutputFiles(const char *list)
1829 // Manually set the output files list.
1830 // Removes duplicates. Not allowed if default outputs are not disabled.
1831 if (TObject::TestBit(AliAnalysisGrid::kDefaultOutputs)) {
1832 Fatal("SetOutputFiles", "You have to explicitly call SetDefaultOutputs(kFALSE) to manually set output files.");
1835 Info("SetOutputFiles", "Output file list is set manually - you are on your own.");
1837 TString slist = list;
1838 if (slist.Contains("@")) Warning("SetOutputFiles","The plugin does not allow explicit SE's. Please use: SetNumberOfReplicas() instead.");
1839 TObjArray *arr = slist.Tokenize(" ");
1843 while ((os=(TObjString*)next())) {
1844 sout = os->GetString();
1845 if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
1846 if (fOutputFiles.Contains(sout)) continue;
1847 if (!fOutputFiles.IsNull()) fOutputFiles += ",";
1848 fOutputFiles += sout;
1853 //______________________________________________________________________________
1854 void AliAnalysisAlien::SetOutputArchive(const char *list)
1856 // Manually set the output archive list. Free text - you are on your own...
1857 // Not allowed if default outputs are not disabled.
1858 if (TObject::TestBit(AliAnalysisGrid::kDefaultOutputs)) {
1859 Fatal("SetOutputArchive", "You have to explicitly call SetDefaultOutputs(kFALSE) to manually set the output archives.");
1862 Info("SetOutputArchive", "Output archive is set manually - you are on your own.");
1863 fOutputArchive = list;
1866 //______________________________________________________________________________
1867 void AliAnalysisAlien::SetPreferedSE(const char */*se*/)
1869 // Setting a prefered output SE is not allowed anymore.
1870 Warning("SetPreferedSE", "Setting a preferential SE is not allowed anymore via the plugin. Use SetNumberOfReplicas() and SetDefaultOutputs()");
1873 //______________________________________________________________________________
1874 Bool_t AliAnalysisAlien::StartAnalysis(Long64_t /*nentries*/, Long64_t /*firstEntry*/)
1876 // Start remote grid analysis.
1878 // Check if output files have to be taken from the analysis manager
1879 if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
1880 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
1881 if (!mgr || !mgr->IsInitialized()) {
1882 Error("StartAnalysis", "You need an initialized analysis manager for this");
1886 TIter next(mgr->GetOutputs());
1887 AliAnalysisDataContainer *output;
1888 while ((output=(AliAnalysisDataContainer*)next())) {
1889 const char *filename = output->GetFileName();
1890 if (!(strcmp(filename, "default"))) {
1891 if (!mgr->GetOutputEventHandler()) continue;
1892 filename = mgr->GetOutputEventHandler()->GetOutputFileName();
1894 if (fOutputFiles.Contains(filename)) continue;
1895 if (fOutputFiles.Length()) fOutputFiles += ",";
1896 fOutputFiles += filename;
1898 // Add extra files registered to the analysis manager
1899 if (mgr->GetExtraFiles().Length()) {
1900 if (fOutputFiles.Length()) fOutputFiles += ",";
1901 TString extra = mgr->GetExtraFiles();
1902 extra.ReplaceAll(" ", ",");
1903 // Protection in case extra files do not exist (will it work?)
1904 extra.ReplaceAll(".root", "*.root");
1905 fOutputFiles += extra;
1907 // Compose the output archive.
1908 fOutputArchive = "log_archive.zip:std*@disk=1 ";
1909 fOutputArchive += Form("root_archive.zip:%s@disk=%d",fOutputFiles.Data(),fNreplicas);
1911 // if (!fCloseSE.Length()) fCloseSE = gSystem->Getenv("alien_CLOSE_SE");
1912 if (TestBit(AliAnalysisGrid::kOffline)) {
1913 Info("StartAnalysis","\n##### OFFLINE MODE ##### Files to be used in GRID are produced but not copied \
1914 \n there nor any job run. You can revise the JDL and analysis \
1915 \n macro then run the same in \"submit\" mode.");
1916 } else if (TestBit(AliAnalysisGrid::kTest)) {
1917 Info("StartAnalysis","\n##### LOCAL MODE ##### Your analysis will be run locally on a subset of the requested \
1919 } else if (TestBit(AliAnalysisGrid::kSubmit)) {
1920 Info("StartAnalysis","\n##### SUBMIT MODE ##### Files required by your analysis are copied to your grid working \
1921 \n space and job submitted.");
1922 } else if (TestBit(AliAnalysisGrid::kMerge)) {
1923 Info("StartAnalysis","\n##### MERGE MODE ##### The registered outputs of the analysis will be merged");
1924 if (fMergeViaJDL) CheckInputData();
1927 Info("StartAnalysis","\n##### FULL ANALYSIS MODE ##### Producing needed files and submitting your analysis job...");
1932 Error("StartAnalysis", "Cannot start grid analysis without grid connection");
1935 if (IsCheckCopy()) CheckFileCopy(gGrid->GetHomeDirectory());
1936 if (!CheckInputData()) {
1937 Error("StartAnalysis", "There was an error in preprocessing your requested input data");
1940 if (!CreateDataset(fDataPattern)) {
1942 if (!fRunNumbers.Length() && !fRunRange[0]) serror = Form("path to data directory: <%s>", fGridDataDir.Data());
1943 if (fRunNumbers.Length()) serror = "run numbers";
1944 if (fRunRange[0]) serror = Form("run range [%d, %d]", fRunRange[0], fRunRange[1]);
1945 serror += Form("\n or data pattern <%s>", fDataPattern.Data());
1946 Error("StartAnalysis", "No data to process. Please fix %s in your plugin configuration.", serror.Data());
1949 WriteAnalysisFile();
1950 WriteAnalysisMacro();
1952 WriteValidationScript();
1954 WriteMergingMacro();
1955 WriteMergeExecutable();
1956 WriteValidationScript(kTRUE);
1958 if (!CreateJDL()) return kFALSE;
1959 if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
1960 if (TestBit(AliAnalysisGrid::kTest)) {
1961 // Locally testing the analysis
1962 Info("StartAnalysis", "\n_______________________________________________________________________ \
1963 \n Running analysis script in a daughter shell as on a worker node \
1964 \n_______________________________________________________________________");
1965 TObjArray *list = fOutputFiles.Tokenize(",");
1969 while((str=(TObjString*)next())) {
1970 outputFile = str->GetString();
1971 Int_t index = outputFile.Index("@");
1972 if (index > 0) outputFile.Remove(index);
1973 if (!gSystem->AccessPathName(outputFile)) gSystem->Exec(Form("rm %s", outputFile.Data()));
1976 gSystem->Exec(Form("bash %s 2>stderr", fExecutable.Data()));
1977 TString validationScript = fExecutable;
1978 validationScript.ReplaceAll(".sh", "_validation.sh");
1979 gSystem->Exec(Form("bash %s",validationScript.Data()));
1980 // gSystem->Exec("cat stdout");
1983 // Check if submitting is managed by LPM manager
1984 if (fProductionMode) {
1985 TString prodfile = fJDLName;
1986 prodfile.ReplaceAll(".jdl", ".prod");
1987 WriteProductionFile(prodfile);
1988 Info("StartAnalysis", "Job submitting is managed by LPM. Rerun in terminate mode after jobs finished.");
1991 // Submit AliEn job(s)
1992 gGrid->Cd(fGridOutputDir);
1995 if (!fRunNumbers.Length() && !fRunRange[0]) {
1996 // Submit a given xml or a set of runs
1997 res = gGrid->Command(Form("submit %s", fJDLName.Data()));
1998 printf("*************************** %s\n",Form("submit %s", fJDLName.Data()));
2000 const char *cjobId = res->GetKey(0,"jobId");
2004 Error("StartAnalysis", "Your JDL %s could not be submitted", fJDLName.Data());
2007 Info("StartAnalysis", "\n_______________________________________________________________________ \
2008 \n##### Your JDL %s was successfully submitted. \nTHE JOB ID IS: %s \
2009 \n_______________________________________________________________________",
2010 fJDLName.Data(), cjobId);
2015 Error("StartAnalysis", "No grid result after submission !!! Bailing out...");
2019 // Submit for a range of enumeration of runs.
2020 if (!Submit()) return kFALSE;
2023 Info("StartAnalysis", "\n#### STARTING AN ALIEN SHELL FOR YOU. EXIT WHEN YOUR JOB %s HAS FINISHED. #### \
2024 \n You may exit at any time and terminate the job later using the option <terminate> \
2025 \n ##################################################################################", jobID.Data());
2026 gSystem->Exec("aliensh");
2030 //______________________________________________________________________________
2031 Bool_t AliAnalysisAlien::Submit()
2033 // Submit all master jobs.
2034 Int_t nmasterjobs = fInputFiles->GetEntries();
2035 Long_t tshoot = gSystem->Now();
2036 if (!fNsubmitted && !SubmitNext()) return kFALSE;
2037 while (fNsubmitted < nmasterjobs) {
2038 Long_t now = gSystem->Now();
2039 if ((now-tshoot)>30000) {
2041 if (!SubmitNext()) return kFALSE;
2047 //______________________________________________________________________________
2048 Bool_t AliAnalysisAlien::SubmitMerging()
2050 // Submit all merging jobs.
2051 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
2052 gGrid->Cd(fGridOutputDir);
2053 TString mergeJDLName = fExecutable;
2054 mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
2055 Int_t ntosubmit = fInputFiles->GetEntries();
2056 printf("### Submitting %d merging jobs...\n", ntosubmit);
2057 for (Int_t i=0; i<ntosubmit; i++) {
2059 TString runOutDir = gSystem->BaseName(fInputFiles->At(i)->GetName());
2060 runOutDir.ReplaceAll(".xml", "");
2062 query = Form("submit %s %s", mergeJDLName.Data(), runOutDir.Data());
2064 query = Form("submit %s %03d", mergeJDLName.Data(), i);
2065 printf("********* %s\n",query.Data());
2066 TGridResult *res = gGrid->Command(query);
2068 const char *cjobId = res->GetKey(0,"jobId");
2072 Error("StartAnalysis", "Your JDL %s could not be submitted", mergeJDLName.Data());
2075 Info("StartAnalysis", "\n_______________________________________________________________________ \
2076 \n##### Your JDL %s was successfully submitted. \nTHE JOB ID IS: %s \
2077 \n_______________________________________________________________________",
2078 mergeJDLName.Data(), cjobId);
2082 Error("SubmitMerging", "No grid result after submission !!! Bailing out...");
2086 if (!ntosubmit) return kTRUE;
2087 Info("StartAnalysis", "\n#### STARTING AN ALIEN SHELL FOR YOU. EXIT WHEN YOUR MERGING JOBS HAVE FINISHED. #### \
2088 \n You may exit at any time and terminate the job later using the option <terminate> but disabling SetMergeViaJDL\
2089 \n ##################################################################################");
2090 gSystem->Exec("aliensh");
2094 //______________________________________________________________________________
2095 Bool_t AliAnalysisAlien::SubmitNext()
2097 // Submit next bunch of master jobs if the queue is free.
2098 static Bool_t iscalled = kFALSE;
2099 static Int_t firstmaster = 0;
2100 static Int_t lastmaster = 0;
2101 static Int_t npermaster = 0;
2102 if (iscalled) return kTRUE;
2104 Int_t nrunning=0, nwaiting=0, nerror=0, ndone=0;
2105 Int_t ntosubmit = 0;
2108 if (!fNsubmitted) ntosubmit = 1;
2110 TString status = GetJobStatus(firstmaster, lastmaster, nrunning, nwaiting, nerror, ndone);
2111 printf("=== master %d: %s\n", lastmaster, status.Data());
2112 // If last master not split, just return
2113 if (status != "SPLIT") {iscalled = kFALSE; return kTRUE;}
2114 // No more than 100 waiting jobs
2115 if (nwaiting>100) {iscalled = kFALSE; return kTRUE;}
2116 npermaster = (nrunning+nwaiting+nerror+ndone)/fNsubmitted;
2117 if (npermaster) ntosubmit = (100-nwaiting)/npermaster;
2118 if (!ntosubmit) ntosubmit = 1;
2119 printf("=== WAITING(%d) RUNNING(%d) DONE(%d) OTHER(%d) NperMaster=%d => to submit %d jobs\n",
2120 nwaiting, nrunning, ndone, nerror, npermaster, ntosubmit);
2122 Int_t nmasterjobs = fInputFiles->GetEntries();
2123 for (Int_t i=0; i<ntosubmit; i++) {
2124 // Submit for a range of enumeration of runs.
2125 if (fNsubmitted>=nmasterjobs) {iscalled = kFALSE; return kTRUE;}
2127 TString runOutDir = gSystem->BaseName(fInputFiles->At(fNsubmitted)->GetName());
2128 runOutDir.ReplaceAll(".xml", "");
2130 query = Form("submit %s %s %s", fJDLName.Data(), fInputFiles->At(fNsubmitted)->GetName(), runOutDir.Data());
2132 query = Form("submit %s %s %03d", fJDLName.Data(), fInputFiles->At(fNsubmitted)->GetName(), fNsubmitted);
2133 printf("********* %s\n",query.Data());
2134 res = gGrid->Command(query);
2136 TString cjobId1 = res->GetKey(0,"jobId");
2137 if (!cjobId1.Length()) {
2141 Error("StartAnalysis", "Your JDL %s could not be submitted. The message was:", fJDLName.Data());
2144 Info("StartAnalysis", "\n_______________________________________________________________________ \
2145 \n##### Your JDL %s submitted (%d to go). \nTHE JOB ID IS: %s \
2146 \n_______________________________________________________________________",
2147 fJDLName.Data(), nmasterjobs-fNsubmitted-1, cjobId1.Data());
2150 lastmaster = cjobId1.Atoi();
2151 if (!firstmaster) firstmaster = lastmaster;
2156 Error("StartAnalysis", "No grid result after submission !!! Bailing out...");
2164 //______________________________________________________________________________
2165 void AliAnalysisAlien::WriteAnalysisFile()
2167 // Write current analysis manager into the file <analysisFile>
2168 TString analysisFile = fExecutable;
2169 analysisFile.ReplaceAll(".sh", ".root");
2170 if (!TestBit(AliAnalysisGrid::kSubmit)) {
2171 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
2172 if (!mgr || !mgr->IsInitialized()) {
2173 Error("WriteAnalysisFile", "You need an initialized analysis manager for this");
2176 // Check analysis type
2178 if (mgr->GetMCtruthEventHandler()) TObject::SetBit(AliAnalysisGrid::kUseMC);
2179 handler = (TObject*)mgr->GetInputEventHandler();
2181 if (handler->InheritsFrom("AliESDInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseESD);
2182 if (handler->InheritsFrom("AliAODInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseAOD);
2184 TDirectory *cdir = gDirectory;
2185 TFile *file = TFile::Open(analysisFile, "RECREATE");
2187 // Skip task Terminate calls for the grid job (but not in test mode, where we want to check also the terminate mode
2188 if (!TestBit(AliAnalysisGrid::kTest)) mgr->SetSkipTerminate(kTRUE);
2189 // Unless merging makes no sense
2190 if (IsSingleOutput()) mgr->SetSkipTerminate(kFALSE);
2193 // Enable termination for local jobs
2194 mgr->SetSkipTerminate(kFALSE);
2196 if (cdir) cdir->cd();
2197 Info("WriteAnalysisFile", "\n##### Analysis manager: %s wrote to file <%s>\n", mgr->GetName(),analysisFile.Data());
2199 Bool_t copy = kTRUE;
2200 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
2203 TString workdir = gGrid->GetHomeDirectory();
2204 workdir += fGridWorkingDir;
2205 Info("CreateJDL", "\n##### Copying file <%s> containing your initialized analysis manager to your alien workspace", analysisFile.Data());
2206 if (FileExists(analysisFile)) gGrid->Rm(analysisFile);
2207 TFile::Cp(Form("file:%s",analysisFile.Data()), Form("alien://%s/%s", workdir.Data(),analysisFile.Data()));
2211 //______________________________________________________________________________
2212 void AliAnalysisAlien::WriteAnalysisMacro()
2214 // Write the analysis macro that will steer the analysis in grid mode.
2215 if (!TestBit(AliAnalysisGrid::kSubmit)) {
2217 out.open(fAnalysisMacro.Data(), ios::out);
2219 Error("WriteAnalysisMacro", "could not open file %s for writing", fAnalysisMacro.Data());
2222 Bool_t hasSTEERBase = kFALSE;
2223 Bool_t hasESD = kFALSE;
2224 Bool_t hasAOD = kFALSE;
2225 Bool_t hasANALYSIS = kFALSE;
2226 Bool_t hasANALYSISalice = kFALSE;
2227 Bool_t hasCORRFW = kFALSE;
2228 TString func = fAnalysisMacro;
2229 TString type = "ESD";
2230 TString comment = "// Analysis using ";
2231 if (TObject::TestBit(AliAnalysisGrid::kUseESD)) comment += "ESD";
2232 if (TObject::TestBit(AliAnalysisGrid::kUseAOD)) {
2236 if (type!="AOD" && fFriendChainName!="") {
2237 Error("WriteAnalysisMacro", "Friend chain can be attached only to AOD");
2240 if (TObject::TestBit(AliAnalysisGrid::kUseMC)) comment += "/MC";
2241 else comment += " data";
2242 out << "const char *anatype = \"" << type.Data() << "\";" << endl << endl;
2243 func.ReplaceAll(".C", "");
2244 out << "void " << func.Data() << "()" << endl;
2246 out << comment.Data() << endl;
2247 out << "// Automatically generated analysis steering macro executed in grid subjobs" << endl << endl;
2248 out << " TStopwatch timer;" << endl;
2249 out << " timer.Start();" << endl << endl;
2250 out << "// load base root libraries" << endl;
2251 out << " gSystem->Load(\"libTree\");" << endl;
2252 out << " gSystem->Load(\"libGeom\");" << endl;
2253 out << " gSystem->Load(\"libVMC\");" << endl;
2254 out << " gSystem->Load(\"libPhysics\");" << endl << endl;
2255 out << " gSystem->Load(\"libMinuit\");" << endl << endl;
2256 if (fAdditionalRootLibs.Length()) {
2257 // in principle libtree /lib geom libvmc etc. can go into this list, too
2258 out << "// Add aditional libraries" << endl;
2259 TObjArray *list = fAdditionalRootLibs.Tokenize(" ");
2262 while((str=(TObjString*)next())) {
2263 if (str->GetString().Contains(".so"))
2264 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
2266 if (list) delete list;
2268 out << "// include path" << endl;
2269 if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
2270 out << " gSystem->AddIncludePath(\"-I$ALICE_ROOT/include\");" << endl << endl;
2271 out << "// Load analysis framework libraries" << endl;
2273 out << " gSystem->Load(\"libSTEERBase\");" << endl;
2274 out << " gSystem->Load(\"libESD\");" << endl;
2275 out << " gSystem->Load(\"libAOD\");" << endl;
2276 out << " gSystem->Load(\"libANALYSIS\");" << endl;
2277 out << " gSystem->Load(\"libANALYSISalice\");" << endl;
2278 out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
2280 TIter next(fPackages);
2283 TString setupPar = "AliAnalysisAlien::SetupPar";
2284 while ((obj=next())) {
2285 pkgname = obj->GetName();
2286 if (pkgname == "STEERBase" ||
2287 pkgname == "STEERBase.par") hasSTEERBase = kTRUE;
2288 if (pkgname == "ESD" ||
2289 pkgname == "ESD.par") hasESD = kTRUE;
2290 if (pkgname == "AOD" ||
2291 pkgname == "AOD.par") hasAOD = kTRUE;
2292 if (pkgname == "ANALYSIS" ||
2293 pkgname == "ANALYSIS.par") hasANALYSIS = kTRUE;
2294 if (pkgname == "ANALYSISalice" ||
2295 pkgname == "ANALYSISalice.par") hasANALYSISalice = kTRUE;
2296 if (pkgname == "CORRFW" ||
2297 pkgname == "CORRFW.par") hasCORRFW = kTRUE;
2299 if (hasANALYSISalice) setupPar = "SetupPar";
2300 if (!hasSTEERBase) out << " gSystem->Load(\"libSTEERBase\");" << endl;
2301 else out << " if (!" << setupPar << "(\"STEERBase\")) return;" << endl;
2302 if (!hasESD) out << " gSystem->Load(\"libESD\");" << endl;
2303 else out << " if (!" << setupPar << "(\"ESD\")) return;" << endl;
2304 if (!hasAOD) out << " gSystem->Load(\"libAOD\");" << endl;
2305 else out << " if (!" << setupPar << "(\"AOD\")) return;" << endl;
2306 if (!hasANALYSIS) out << " gSystem->Load(\"libANALYSIS\");" << endl;
2307 else out << " if (!" << setupPar << "(\"ANALYSIS\")) return;" << endl;
2308 if (!hasANALYSISalice) out << " gSystem->Load(\"libANALYSISalice\");" << endl;
2309 else out << " if (!" << setupPar << "(\"ANALYSISalice\")) return;" << endl;
2310 if (!hasCORRFW) out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
2311 else out << " if (!" << setupPar << "(\"CORRFW\")) return;" << endl << endl;
2312 out << "// Compile other par packages" << endl;
2314 while ((obj=next())) {
2315 pkgname = obj->GetName();
2316 if (pkgname == "STEERBase" ||
2317 pkgname == "STEERBase.par" ||
2319 pkgname == "ESD.par" ||
2321 pkgname == "AOD.par" ||
2322 pkgname == "ANALYSIS" ||
2323 pkgname == "ANALYSIS.par" ||
2324 pkgname == "ANALYSISalice" ||
2325 pkgname == "ANALYSISalice.par" ||
2326 pkgname == "CORRFW" ||
2327 pkgname == "CORRFW.par") continue;
2328 out << " if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
2331 if (fAdditionalLibs.Length()) {
2332 out << "// Add aditional AliRoot libraries" << endl;
2333 TObjArray *list = fAdditionalLibs.Tokenize(" ");
2336 while((str=(TObjString*)next())) {
2337 if (str->GetString().Contains(".so"))
2338 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
2340 if (list) delete list;
2343 out << "// analysis source to be compiled at runtime (if any)" << endl;
2344 if (fAnalysisSource.Length()) {
2345 TObjArray *list = fAnalysisSource.Tokenize(" ");
2348 while((str=(TObjString*)next())) {
2349 out << " gROOT->ProcessLine(\".L " << str->GetString().Data() << "+g\");" << endl;
2351 if (list) delete list;
2354 if (fFastReadOption) {
2355 Warning("WriteAnalysisMacro", "!!! You requested FastRead option. Using xrootd flags to reduce timeouts in the grid jobs. This may skip some files that could be accessed !!! \
2356 \n+++ NOTE: To disable this option, use: plugin->SetFastReadOption(kFALSE)");
2357 out << "// fast xrootd reading enabled" << endl;
2358 out << " printf(\"!!! You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !!!\");" << endl;
2359 out << " gEnv->SetValue(\"XNet.ConnectTimeout\",10);" << endl;
2360 out << " gEnv->SetValue(\"XNet.RequestTimeout\",10);" << endl;
2361 out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
2362 out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",10);" << endl;
2363 out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
2365 out << "// connect to AliEn and make the chain" << endl;
2366 out << " if (!TGrid::Connect(\"alien://\")) return;" << endl;
2367 if (IsUsingTags()) {
2368 out << " TChain *chain = CreateChainFromTags(\"wn.xml\", anatype);" << endl << endl;
2370 if(fFriendChainName!="AliAOD.VertexingHF.root") {
2371 out << " TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl;
2373 out << " // Check if the macro to create the chain was provided" << endl;
2374 out << " if (gSystem->AccessPathName(\"MakeAODInputChain.C\")) {" << endl;
2375 out << " ::Error(\"" << func.Data() << "\", \"File MakeAODInputChain.C not provided. Aborting.\");" << endl;
2376 out << " return;" << endl;
2377 out << " }" << endl;
2378 out << " gROOT->LoadMacro(\"MakeAODInputChain.C\");" << endl;
2379 out << " TChain *chain = MakeAODInputChain(\"wn.xml\",\"none\");" << endl << endl;
2382 out << "// read the analysis manager from file" << endl;
2383 TString analysisFile = fExecutable;
2384 analysisFile.ReplaceAll(".sh", ".root");
2385 out << " TFile *file = TFile::Open(\"" << analysisFile << "\");" << endl;
2386 out << " if (!file) return;" << endl;
2387 out << " TIter nextkey(file->GetListOfKeys());" << endl;
2388 out << " AliAnalysisManager *mgr = 0;" << endl;
2389 out << " TKey *key;" << endl;
2390 out << " while ((key=(TKey*)nextkey())) {" << endl;
2391 out << " if (!strcmp(key->GetClassName(), \"AliAnalysisManager\"))" << endl;
2392 out << " mgr = (AliAnalysisManager*)file->Get(key->GetName());" << endl;
2393 out << " };" << endl;
2394 out << " if (!mgr) {" << endl;
2395 out << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file" << analysisFile <<"\");" << endl;
2396 out << " return;" << endl;
2397 out << " }" << endl << endl;
2398 out << " mgr->PrintStatus();" << endl;
2399 if (AliAnalysisManager::GetAnalysisManager()) {
2400 if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) {
2401 out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
2403 out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
2406 out << " mgr->StartAnalysis(\"localfile\", chain);" << endl;
2407 out << " timer.Stop();" << endl;
2408 out << " timer.Print();" << endl;
2409 out << "}" << endl << endl;
2410 if (IsUsingTags()) {
2411 out << "TChain* CreateChainFromTags(const char *xmlfile, const char *type=\"ESD\")" << endl;
2413 out << "// Create a chain using tags from the xml file." << endl;
2414 out << " TAlienCollection* coll = TAlienCollection::Open(xmlfile);" << endl;
2415 out << " if (!coll) {" << endl;
2416 out << " ::Error(\"CreateChainFromTags\", \"Cannot create an AliEn collection from %s\", xmlfile);" << endl;
2417 out << " return NULL;" << endl;
2418 out << " }" << endl;
2419 out << " TGridResult* tagResult = coll->GetGridResult(\"\",kFALSE,kFALSE);" << endl;
2420 out << " AliTagAnalysis *tagAna = new AliTagAnalysis(type);" << endl;
2421 out << " tagAna->ChainGridTags(tagResult);" << endl << endl;
2422 out << " AliRunTagCuts *runCuts = new AliRunTagCuts();" << endl;
2423 out << " AliLHCTagCuts *lhcCuts = new AliLHCTagCuts();" << endl;
2424 out << " AliDetectorTagCuts *detCuts = new AliDetectorTagCuts();" << endl;
2425 out << " AliEventTagCuts *evCuts = new AliEventTagCuts();" << endl;
2426 out << " // Check if the cuts configuration file was provided" << endl;
2427 out << " if (!gSystem->AccessPathName(\"ConfigureCuts.C\")) {" << endl;
2428 out << " gROOT->LoadMacro(\"ConfigureCuts.C\");" << endl;
2429 out << " ConfigureCuts(runCuts, lhcCuts, detCuts, evCuts);" << endl;
2430 out << " }" << endl;
2431 if (fFriendChainName=="") {
2432 out << " TChain *chain = tagAna->QueryTags(runCuts, lhcCuts, detCuts, evCuts);" << endl;
2434 out << " TString tmpColl=\"tmpCollection.xml\";" << endl;
2435 out << " tagAna->CreateXMLCollection(tmpColl.Data(),runCuts, lhcCuts, detCuts, evCuts);" << endl;
2436 out << " TChain *chain = CreateChain(tmpColl.Data(),type);" << endl;
2438 out << " if (!chain || !chain->GetNtrees()) return NULL;" << endl;
2439 out << " chain->ls();" << endl;
2440 out << " return chain;" << endl;
2441 out << "}" << endl << endl;
2442 if (gSystem->AccessPathName("ConfigureCuts.C")) {
2443 TString msg = "\n##### You may want to provide a macro ConfigureCuts.C with a method:\n";
2444 msg += " void ConfigureCuts(AliRunTagCuts *runCuts,\n";
2445 msg += " AliLHCTagCuts *lhcCuts,\n";
2446 msg += " AliDetectorTagCuts *detCuts,\n";
2447 msg += " AliEventTagCuts *evCuts)";
2448 Info("WriteAnalysisMacro", msg.Data());
2451 if (!IsUsingTags() || fFriendChainName!="") {
2452 out <<"//________________________________________________________________________________" << endl;
2453 out << "TChain* CreateChain(const char *xmlfile, const char *type=\"ESD\")" << endl;
2455 out << "// Create a chain using url's from xml file" << endl;
2456 out << " TString treename = type;" << endl;
2457 out << " treename.ToLower();" << endl;
2458 out << " treename += \"Tree\";" << endl;
2459 out << " printf(\"***************************************\\n\");" << endl;
2460 out << " printf(\" Getting chain of trees %s\\n\", treename.Data());" << endl;
2461 out << " printf(\"***************************************\\n\");" << endl;
2462 out << " TAlienCollection *coll = TAlienCollection::Open(xmlfile);" << endl;
2463 out << " if (!coll) {" << endl;
2464 out << " ::Error(\"CreateChain\", \"Cannot create an AliEn collection from %s\", xmlfile);" << endl;
2465 out << " return NULL;" << endl;
2466 out << " }" << endl;
2467 out << " TChain *chain = new TChain(treename);" << endl;
2468 if(fFriendChainName!="") {
2469 out << " TChain *chainFriend = new TChain(treename);" << endl;
2471 out << " coll->Reset();" << endl;
2472 out << " while (coll->Next()) {" << endl;
2473 out << " chain->Add(coll->GetTURL(\"\"));" << endl;
2474 if(fFriendChainName!="") {
2475 out << " TString fileFriend=coll->GetTURL(\"\");" << endl;
2476 out << " fileFriend.ReplaceAll(\"AliAOD.root\",\""<<fFriendChainName.Data()<<"\");" << endl;
2477 out << " fileFriend.ReplaceAll(\"AliAODs.root\",\""<<fFriendChainName.Data()<<"\");" << endl;
2478 out << " chainFriend->Add(fileFriend.Data());" << endl;
2480 out << " }" << endl;
2481 out << " if (!chain->GetNtrees()) {" << endl;
2482 out << " ::Error(\"CreateChain\", \"No tree found from collection %s\", xmlfile);" << endl;
2483 out << " return NULL;" << endl;
2484 out << " }" << endl;
2485 if(fFriendChainName!="") {
2486 out << " chain->AddFriend(chainFriend);" << endl;
2488 out << " return chain;" << endl;
2489 out << "}" << endl << endl;
2491 if (hasANALYSISalice) {
2492 out <<"//________________________________________________________________________________" << endl;
2493 out << "Bool_t SetupPar(const char *package) {" << endl;
2494 out << "// Compile the package and set it up." << endl;
2495 out << " TString pkgdir = package;" << endl;
2496 out << " pkgdir.ReplaceAll(\".par\",\"\");" << endl;
2497 out << " gSystem->Exec(Form(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
2498 out << " TString cdir = gSystem->WorkingDirectory();" << endl;
2499 out << " gSystem->ChangeDirectory(pkgdir);" << endl;
2500 out << " // Check for BUILD.sh and execute" << endl;
2501 out << " if (!gSystem->AccessPathName(\"PROOF-INF/BUILD.sh\")) {" << endl;
2502 out << " printf(\"*******************************\\n\");" << endl;
2503 out << " printf(\"*** Building PAR archive ***\\n\");" << endl;
2504 out << " printf(\"*******************************\\n\");" << endl;
2505 out << " if (gSystem->Exec(\"PROOF-INF/BUILD.sh\")) {" << endl;
2506 out << " ::Error(\"SetupPar\", \"Cannot build par archive %s\", pkgdir.Data());" << endl;
2507 out << " gSystem->ChangeDirectory(cdir);" << endl;
2508 out << " return kFALSE;" << endl;
2509 out << " }" << endl;
2510 out << " } else {" << endl;
2511 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/BUILD.sh for package %s\", pkgdir.Data());" << endl;
2512 out << " gSystem->ChangeDirectory(cdir);" << endl;
2513 out << " return kFALSE;" << endl;
2514 out << " }" << endl;
2515 out << " // Check for SETUP.C and execute" << endl;
2516 out << " if (!gSystem->AccessPathName(\"PROOF-INF/SETUP.C\")) {" << endl;
2517 out << " printf(\"*******************************\\n\");" << endl;
2518 out << " printf(\"*** Setup PAR archive ***\\n\");" << endl;
2519 out << " printf(\"*******************************\\n\");" << endl;
2520 out << " gROOT->Macro(\"PROOF-INF/SETUP.C\");" << endl;
2521 out << " } else {" << endl;
2522 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/SETUP.C for package %s\", pkgdir.Data());" << endl;
2523 out << " gSystem->ChangeDirectory(cdir);" << endl;
2524 out << " return kFALSE;" << endl;
2525 out << " }" << endl;
2526 out << " // Restore original workdir" << endl;
2527 out << " gSystem->ChangeDirectory(cdir);" << endl;
2528 out << " return kTRUE;" << endl;
2531 Info("WriteAnalysisMacro", "\n##### Analysis macro to run on worker nodes <%s> written",fAnalysisMacro.Data());
2533 Bool_t copy = kTRUE;
2534 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
2537 TString workdir = gGrid->GetHomeDirectory();
2538 workdir += fGridWorkingDir;
2539 if (FileExists(fAnalysisMacro)) gGrid->Rm(fAnalysisMacro);
2540 if (IsUsingTags() && !gSystem->AccessPathName("ConfigureCuts.C")) {
2541 if (FileExists("ConfigureCuts.C")) gGrid->Rm("ConfigureCuts.C");
2542 Info("WriteAnalysisMacro", "\n##### Copying cuts configuration macro: <ConfigureCuts.C> to your alien workspace");
2543 TFile::Cp("file:ConfigureCuts.C", Form("alien://%s/ConfigureCuts.C", workdir.Data()));
2545 Info("WriteAnalysisMacro", "\n##### Copying analysis macro: <%s> to your alien workspace", fAnalysisMacro.Data());
2546 TFile::Cp(Form("file:%s",fAnalysisMacro.Data()), Form("alien://%s/%s", workdir.Data(), fAnalysisMacro.Data()));
2550 //______________________________________________________________________________
2551 void AliAnalysisAlien::WriteMergingMacro()
2553 // Write a macro to merge the outputs per master job.
2554 if (!fMergeViaJDL) return;
2555 if (!fOutputFiles.Length()) {
2556 Error("WriteMergingMacro", "No output file names defined. Are you running the right AliAnalysisAlien configuration ?");
2559 TString mergingMacro = fExecutable;
2560 mergingMacro.ReplaceAll(".sh","_merge.C");
2561 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
2562 if (!TestBit(AliAnalysisGrid::kSubmit)) {
2564 out.open(mergingMacro.Data(), ios::out);
2566 Error("WriteMergingMacro", "could not open file %s for writing", fAnalysisMacro.Data());
2569 Bool_t hasSTEERBase = kFALSE;
2570 Bool_t hasESD = kFALSE;
2571 Bool_t hasAOD = kFALSE;
2572 Bool_t hasANALYSIS = kFALSE;
2573 Bool_t hasANALYSISalice = kFALSE;
2574 Bool_t hasCORRFW = kFALSE;
2575 TString func = mergingMacro;
2577 func.ReplaceAll(".C", "");
2578 out << "void " << func.Data() << "(const char *dir)" << endl;
2580 out << "// Automatically generated merging macro executed in grid subjobs" << endl << endl;
2581 out << " TStopwatch timer;" << endl;
2582 out << " timer.Start();" << endl << endl;
2583 out << "// load base root libraries" << endl;
2584 out << " gSystem->Load(\"libTree\");" << endl;
2585 out << " gSystem->Load(\"libGeom\");" << endl;
2586 out << " gSystem->Load(\"libVMC\");" << endl;
2587 out << " gSystem->Load(\"libPhysics\");" << endl << endl;
2588 out << " gSystem->Load(\"libMinuit\");" << endl << endl;
2589 if (fAdditionalRootLibs.Length()) {
2590 // in principle libtree /lib geom libvmc etc. can go into this list, too
2591 out << "// Add aditional libraries" << endl;
2592 TObjArray *list = fAdditionalRootLibs.Tokenize(" ");
2595 while((str=(TObjString*)next())) {
2596 if (str->GetString().Contains(".so"))
2597 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
2599 if (list) delete list;
2601 out << "// include path" << endl;
2602 if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
2603 out << " gSystem->AddIncludePath(\"-I$ALICE_ROOT/include\");" << endl << endl;
2604 out << "// Load analysis framework libraries" << endl;
2606 out << " gSystem->Load(\"libSTEERBase\");" << endl;
2607 out << " gSystem->Load(\"libESD\");" << endl;
2608 out << " gSystem->Load(\"libAOD\");" << endl;
2609 out << " gSystem->Load(\"libANALYSIS\");" << endl;
2610 out << " gSystem->Load(\"libANALYSISalice\");" << endl;
2611 out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
2613 TIter next(fPackages);
2616 TString setupPar = "AliAnalysisAlien::SetupPar";
2617 while ((obj=next())) {
2618 pkgname = obj->GetName();
2619 if (pkgname == "STEERBase" ||
2620 pkgname == "STEERBase.par") hasSTEERBase = kTRUE;
2621 if (pkgname == "ESD" ||
2622 pkgname == "ESD.par") hasESD = kTRUE;
2623 if (pkgname == "AOD" ||
2624 pkgname == "AOD.par") hasAOD = kTRUE;
2625 if (pkgname == "ANALYSIS" ||
2626 pkgname == "ANALYSIS.par") hasANALYSIS = kTRUE;
2627 if (pkgname == "ANALYSISalice" ||
2628 pkgname == "ANALYSISalice.par") hasANALYSISalice = kTRUE;
2629 if (pkgname == "CORRFW" ||
2630 pkgname == "CORRFW.par") hasCORRFW = kTRUE;
2632 if (hasANALYSISalice) setupPar = "SetupPar";
2633 if (!hasSTEERBase) out << " gSystem->Load(\"libSTEERBase\");" << endl;
2634 else out << " if (!" << setupPar << "(\"STEERBase\")) return;" << endl;
2635 if (!hasESD) out << " gSystem->Load(\"libESD\");" << endl;
2636 else out << " if (!" << setupPar << "(\"ESD\")) return;" << endl;
2637 if (!hasAOD) out << " gSystem->Load(\"libAOD\");" << endl;
2638 else out << " if (!" << setupPar << "(\"AOD\")) return;" << endl;
2639 if (!hasANALYSIS) out << " gSystem->Load(\"libANALYSIS\");" << endl;
2640 else out << " if (!" << setupPar << "(\"ANALYSIS\")) return;" << endl;
2641 if (!hasANALYSISalice) out << " gSystem->Load(\"libANALYSISalice\");" << endl;
2642 else out << " if (!" << setupPar << "(\"ANALYSISalice\")) return;" << endl;
2643 if (!hasCORRFW) out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
2644 else out << " if (!" << setupPar << "(\"CORRFW\")) return;" << endl << endl;
2645 out << "// Compile other par packages" << endl;
2647 while ((obj=next())) {
2648 pkgname = obj->GetName();
2649 if (pkgname == "STEERBase" ||
2650 pkgname == "STEERBase.par" ||
2652 pkgname == "ESD.par" ||
2654 pkgname == "AOD.par" ||
2655 pkgname == "ANALYSIS" ||
2656 pkgname == "ANALYSIS.par" ||
2657 pkgname == "ANALYSISalice" ||
2658 pkgname == "ANALYSISalice.par" ||
2659 pkgname == "CORRFW" ||
2660 pkgname == "CORRFW.par") continue;
2661 out << " if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
2664 if (fAdditionalLibs.Length()) {
2665 out << "// Add aditional AliRoot libraries" << endl;
2666 TObjArray *list = fAdditionalLibs.Tokenize(" ");
2669 while((str=(TObjString*)next())) {
2670 if (str->GetString().Contains(".so"))
2671 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
2673 if (list) delete list;
2676 out << "// Analysis source to be compiled at runtime (if any)" << endl;
2677 if (fAnalysisSource.Length()) {
2678 TObjArray *list = fAnalysisSource.Tokenize(" ");
2681 while((str=(TObjString*)next())) {
2682 out << " gROOT->ProcessLine(\".L " << str->GetString().Data() << "+g\");" << endl;
2684 if (list) delete list;
2688 if (fFastReadOption) {
2689 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 !!!");
2690 out << "// fast xrootd reading enabled" << endl;
2691 out << " printf(\"!!! You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !!!\");" << endl;
2692 out << " gEnv->SetValue(\"XNet.ConnectTimeout\",10);" << endl;
2693 out << " gEnv->SetValue(\"XNet.RequestTimeout\",10);" << endl;
2694 out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
2695 out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",10);" << endl;
2696 out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
2698 out << "// Connect to AliEn" << endl;
2699 out << " if (!TGrid::Connect(\"alien://\")) return;" << endl;
2700 out << " TString outputDir = \"" << fGridOutputDir << "/\";" << endl;
2701 out << " outputDir += dir;" << endl;
2702 out << " TString outputFiles = \"" << fOutputFiles << "\";" << endl;
2703 out << " TString mergeExcludes = \"" << fMergeExcludes << "\";" << endl;
2704 out << " mergeExcludes += \"" << AliAnalysisManager::GetAnalysisManager()->GetExtraFiles() << "\";" << endl;
2705 out << " TObjArray *list = outputFiles.Tokenize(\" \");" << endl;
2706 out << " TIter *iter = new TIter(list);" << endl;
2707 out << " TObjString *str;" << endl;
2708 out << " TString outputFile;" << endl;
2709 out << " Bool_t merged = kTRUE;" << endl;
2710 out << " while((str=(TObjString*)iter->Next())) {" << endl;
2711 out << " outputFile = str->GetString();" << endl;
2712 out << " Int_t index = outputFile.Index(\"@\");" << endl;
2713 out << " if (index > 0) outputFile.Remove(index);" << endl;
2714 out << " // Skip already merged outputs" << endl;
2715 out << " if (!gSystem->AccessPathName(outputFile)) {" << endl;
2716 out << " printf(\"Output file <%s> found. Not merging again.\",outputFile.Data());" << endl;
2717 out << " continue;" << endl;
2718 out << " }" << endl;
2719 out << " if (mergeExcludes.Contains(outputFile.Data())) continue;" << endl;
2720 out << " merged = AliAnalysisAlien::MergeOutput(outputFile, outputDir, " << fMaxMergeFiles << ");" << endl;
2721 out << " if (!merged) {" << endl;
2722 out << " printf(\"ERROR: Cannot merge %s\\n\", outputFile.Data());" << endl;
2723 out << " }" << endl;
2724 out << " }" << endl;
2725 out << "// read the analysis manager from file" << endl;
2726 TString analysisFile = fExecutable;
2727 analysisFile.ReplaceAll(".sh", ".root");
2728 out << " TFile *file = TFile::Open(\"" << analysisFile << "\");" << endl;
2729 out << " if (!file) return;" << endl;
2730 out << " TIter nextkey(file->GetListOfKeys());" << endl;
2731 out << " AliAnalysisManager *mgr = 0;" << endl;
2732 out << " TKey *key;" << endl;
2733 out << " while ((key=(TKey*)nextkey())) {" << endl;
2734 out << " if (!strcmp(key->GetClassName(), \"AliAnalysisManager\"))" << endl;
2735 out << " mgr = (AliAnalysisManager*)file->Get(key->GetName());" << endl;
2736 out << " };" << endl;
2737 out << " if (!mgr) {" << endl;
2738 out << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file" << analysisFile <<"\");" << endl;
2739 out << " return;" << endl;
2740 out << " }" << endl << endl;
2741 out << " mgr->SetSkipTerminate(kFALSE);" << endl;
2742 out << " mgr->PrintStatus();" << endl;
2743 if (AliAnalysisManager::GetAnalysisManager()) {
2744 if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) {
2745 out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
2747 out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
2750 out << " mgr->StartAnalysis(\"gridterminate\");" << endl;
2751 out << "}" << endl << endl;
2752 if (hasANALYSISalice) {
2753 out <<"//________________________________________________________________________________" << endl;
2754 out << "Bool_t SetupPar(const char *package) {" << endl;
2755 out << "// Compile the package and set it up." << endl;
2756 out << " TString pkgdir = package;" << endl;
2757 out << " pkgdir.ReplaceAll(\".par\",\"\");" << endl;
2758 out << " gSystem->Exec(Form(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
2759 out << " TString cdir = gSystem->WorkingDirectory();" << endl;
2760 out << " gSystem->ChangeDirectory(pkgdir);" << endl;
2761 out << " // Check for BUILD.sh and execute" << endl;
2762 out << " if (!gSystem->AccessPathName(\"PROOF-INF/BUILD.sh\")) {" << endl;
2763 out << " printf(\"*******************************\\n\");" << endl;
2764 out << " printf(\"*** Building PAR archive ***\\n\");" << endl;
2765 out << " printf(\"*******************************\\n\");" << endl;
2766 out << " if (gSystem->Exec(\"PROOF-INF/BUILD.sh\")) {" << endl;
2767 out << " ::Error(\"SetupPar\", \"Cannot build par archive %s\", pkgdir.Data());" << endl;
2768 out << " gSystem->ChangeDirectory(cdir);" << endl;
2769 out << " return kFALSE;" << endl;
2770 out << " }" << endl;
2771 out << " } else {" << endl;
2772 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/BUILD.sh for package %s\", pkgdir.Data());" << endl;
2773 out << " gSystem->ChangeDirectory(cdir);" << endl;
2774 out << " return kFALSE;" << endl;
2775 out << " }" << endl;
2776 out << " // Check for SETUP.C and execute" << endl;
2777 out << " if (!gSystem->AccessPathName(\"PROOF-INF/SETUP.C\")) {" << endl;
2778 out << " printf(\"*******************************\\n\");" << endl;
2779 out << " printf(\"*** Setup PAR archive ***\\n\");" << endl;
2780 out << " printf(\"*******************************\\n\");" << endl;
2781 out << " gROOT->Macro(\"PROOF-INF/SETUP.C\");" << endl;
2782 out << " } else {" << endl;
2783 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/SETUP.C for package %s\", pkgdir.Data());" << endl;
2784 out << " gSystem->ChangeDirectory(cdir);" << endl;
2785 out << " return kFALSE;" << endl;
2786 out << " }" << endl;
2787 out << " // Restore original workdir" << endl;
2788 out << " gSystem->ChangeDirectory(cdir);" << endl;
2789 out << " return kTRUE;" << endl;
2793 Bool_t copy = kTRUE;
2794 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
2797 TString workdir = gGrid->GetHomeDirectory();
2798 workdir += fGridWorkingDir;
2799 if (FileExists(mergingMacro)) gGrid->Rm(mergingMacro);
2800 Info("WriteMergingMacro", "\n##### Copying merging macro: <%s> to your alien workspace", mergingMacro.Data());
2801 TFile::Cp(Form("file:%s",mergingMacro.Data()), Form("alien://%s/%s", workdir.Data(), mergingMacro.Data()));
2805 //______________________________________________________________________________
2806 Bool_t AliAnalysisAlien::SetupPar(const char *package)
2808 // Compile the par file archive pointed by <package>. This must be present in the current durectory.
2809 // Note that for loading the compiled library. The current directory should have precedence in
2811 TString pkgdir = package;
2812 pkgdir.ReplaceAll(".par","");
2813 gSystem->Exec(Form("tar xvzf %s.par", pkgdir.Data()));
2814 TString cdir = gSystem->WorkingDirectory();
2815 gSystem->ChangeDirectory(pkgdir);
2816 // Check for BUILD.sh and execute
2817 if (!gSystem->AccessPathName("PROOF-INF/BUILD.sh")) {
2818 printf("**************************************************\n");
2819 printf("*** Building PAR archive %s\n", package);
2820 printf("**************************************************\n");
2821 if (gSystem->Exec("PROOF-INF/BUILD.sh")) {
2822 ::Error("SetupPar", "Cannot build par archive %s", pkgdir.Data());
2823 gSystem->ChangeDirectory(cdir);
2827 ::Error("SetupPar","Cannot access PROOF-INF/BUILD.sh for package %s", pkgdir.Data());
2828 gSystem->ChangeDirectory(cdir);
2831 // Check for SETUP.C and execute
2832 if (!gSystem->AccessPathName("PROOF-INF/SETUP.C")) {
2833 printf("**************************************************\n");
2834 printf("*** Setup PAR archive %s\n", package);
2835 printf("**************************************************\n");
2836 gROOT->Macro("PROOF-INF/SETUP.C");
2837 printf("*** Loaded library: %s\n", gSystem->GetLibraries(pkgdir,"",kFALSE));
2839 ::Error("SetupPar","Cannot access PROOF-INF/SETUP.C for package %s", pkgdir.Data());
2840 gSystem->ChangeDirectory(cdir);
2843 // Restore original workdir
2844 gSystem->ChangeDirectory(cdir);
2848 //______________________________________________________________________________
2849 void AliAnalysisAlien::WriteExecutable()
2851 // Generate the alien executable script.
2852 if (!TestBit(AliAnalysisGrid::kSubmit)) {
2854 out.open(fExecutable.Data(), ios::out);
2856 Error("WriteExecutable", "Bad file name for executable: %s", fExecutable.Data());
2859 out << "#!/bin/bash" << endl;
2860 out << "echo \"=========================================\"" << endl;
2861 out << "echo \"############## PATH : ##############\"" << endl;
2862 out << "echo $PATH" << endl;
2863 out << "echo \"############## LD_LIBRARY_PATH : ##############\"" << endl;
2864 out << "echo $LD_LIBRARY_PATH" << endl;
2865 out << "echo \"############## ROOTSYS : ##############\"" << endl;
2866 out << "echo $ROOTSYS" << endl;
2867 out << "echo \"############## which root : ##############\"" << endl;
2868 out << "which root" << endl;
2869 out << "echo \"############## ALICE_ROOT : ##############\"" << endl;
2870 out << "echo $ALICE_ROOT" << endl;
2871 out << "echo \"############## which aliroot : ##############\"" << endl;
2872 out << "which aliroot" << endl;
2873 out << "echo \"############## system limits : ##############\"" << endl;
2874 out << "ulimit -a" << endl;
2875 out << "echo \"############## memory : ##############\"" << endl;
2876 out << "free -m" << endl;
2877 out << "echo \"=========================================\"" << endl << endl;
2878 // Make sure we can properly compile par files
2879 if (TObject::TestBit(AliAnalysisGrid::kUsePars)) out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
2880 out << fExecutableCommand << " ";
2881 out << fAnalysisMacro.Data() << " " << fExecutableArgs.Data() << endl << endl;
2882 out << "echo \"======== " << fAnalysisMacro.Data() << " finished with exit code: $? ========\"" << endl;
2883 out << "echo \"############## memory after: ##############\"" << endl;
2884 out << "free -m" << endl;
2886 Bool_t copy = kTRUE;
2887 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
2890 TString workdir = gGrid->GetHomeDirectory();
2891 TString bindir = Form("%s/bin", workdir.Data());
2892 if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir);
2893 workdir += fGridWorkingDir;
2894 TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), fExecutable.Data());
2895 if (FileExists(executable)) gGrid->Rm(executable);
2896 Info("CreateJDL", "\n##### Copying executable file <%s> to your AliEn bin directory", fExecutable.Data());
2897 TFile::Cp(Form("file:%s",fExecutable.Data()), Form("alien://%s", executable.Data()));
2901 //______________________________________________________________________________
2902 void AliAnalysisAlien::WriteMergeExecutable()
2904 // Generate the alien executable script for the merging job.
2905 if (!fMergeViaJDL) return;
2906 TString mergeExec = fExecutable;
2907 mergeExec.ReplaceAll(".sh", "_merge.sh");
2908 if (!TestBit(AliAnalysisGrid::kSubmit)) {
2910 out.open(mergeExec.Data(), ios::out);
2912 Error("WriteMergingExecutable", "Bad file name for executable: %s", mergeExec.Data());
2915 out << "#!/bin/bash" << endl;
2916 out << "echo \"=========================================\"" << endl;
2917 out << "echo \"############## PATH : ##############\"" << endl;
2918 out << "echo $PATH" << endl;
2919 out << "echo \"############## LD_LIBRARY_PATH : ##############\"" << endl;
2920 out << "echo $LD_LIBRARY_PATH" << endl;
2921 out << "echo \"############## ROOTSYS : ##############\"" << endl;
2922 out << "echo $ROOTSYS" << endl;
2923 out << "echo \"############## which root : ##############\"" << endl;
2924 out << "which root" << endl;
2925 out << "echo \"############## ALICE_ROOT : ##############\"" << endl;
2926 out << "echo $ALICE_ROOT" << endl;
2927 out << "echo \"############## which aliroot : ##############\"" << endl;
2928 out << "which aliroot" << endl;
2929 out << "echo \"############## system limits : ##############\"" << endl;
2930 out << "ulimit -a" << endl;
2931 out << "echo \"############## memory : ##############\"" << endl;
2932 out << "free -m" << endl;
2933 out << "echo \"=========================================\"" << endl << endl;
2934 // Make sure we can properly compile par files
2935 if (TObject::TestBit(AliAnalysisGrid::kUsePars)) out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
2936 TString mergeMacro = fExecutable;
2937 mergeMacro.ReplaceAll(".sh", "_merge.C");
2938 out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\")\"" << endl;
2939 out << fExecutableCommand << " " << "$ARG" << endl;
2940 out << "echo \"======== " << mergeMacro.Data() << " finished with exit code: $? ========\"" << endl;
2941 out << "echo \"############## memory after: ##############\"" << endl;
2942 out << "free -m" << endl;
2944 Bool_t copy = kTRUE;
2945 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
2948 TString workdir = gGrid->GetHomeDirectory();
2949 TString bindir = Form("%s/bin", workdir.Data());
2950 if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir);
2951 workdir += fGridWorkingDir;
2952 TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), mergeExec.Data());
2953 if (FileExists(executable)) gGrid->Rm(executable);
2954 Info("CreateJDL", "\n##### Copying executable file <%s> to your AliEn bin directory", mergeExec.Data());
2955 TFile::Cp(Form("file:%s",mergeExec.Data()), Form("alien://%s", executable.Data()));
2959 //______________________________________________________________________________
2960 void AliAnalysisAlien::WriteProductionFile(const char *filename) const
2962 // Write the production file to be submitted by LPM manager. The format is:
2963 // First line: full_path_to_jdl estimated_no_subjobs_per_master
2964 // Next lines: full_path_to_dataset XXX (XXX is a string)
2965 // To submit, one has to: submit jdl XXX for all lines
2967 out.open(filename, ios::out);
2969 Error("WriteProductionFile", "Bad file name: %s", filename);
2972 TString workdir = gGrid->GetHomeDirectory();
2973 workdir += fGridWorkingDir;
2974 Int_t njobspermaster = 1000*fNrunsPerMaster/fSplitMaxInputFileNumber;
2975 TString locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
2976 out << locjdl << " " << njobspermaster << endl;
2977 Int_t nmasterjobs = fInputFiles->GetEntries();
2978 for (Int_t i=0; i<nmasterjobs; i++) {
2979 TString runOutDir = gSystem->BaseName(fInputFiles->At(i)->GetName());
2980 runOutDir.ReplaceAll(".xml", "");
2982 out << Form("%s", fInputFiles->At(i)->GetName()) << " " << runOutDir << endl;
2984 out << Form("%s", fInputFiles->At(i)->GetName()) << " " << Form("%03d", i) << endl;
2986 Info("WriteProductionFile", "\n##### Copying production file <%s> to your work directory", filename);
2987 if (FileExists(filename)) gGrid->Rm(filename);
2988 TFile::Cp(Form("file:%s",filename), Form("alien://%s/%s", workdir.Data(),filename));
2991 //______________________________________________________________________________
2992 void AliAnalysisAlien::WriteValidationScript(Bool_t merge)
2994 // Generate the alien validation script.
2995 // Generate the validation script
2997 TString validationScript = fExecutable;
2998 if (merge) validationScript.ReplaceAll(".sh", "_mergevalidation.sh");
2999 else validationScript.ReplaceAll(".sh", "_validation.sh");
3001 Error("WriteValidationScript", "Alien connection required");
3004 TString outStream = "";
3005 if (!TestBit(AliAnalysisGrid::kTest)) outStream = " >> stdout";
3006 if (!TestBit(AliAnalysisGrid::kSubmit)) {
3008 out.open(validationScript, ios::out);
3009 out << "#!/bin/bash" << endl;
3010 out << "##################################################" << endl;
3011 out << "validateout=`dirname $0`" << endl;
3012 out << "validatetime=`date`" << endl;
3013 out << "validated=\"0\";" << endl;
3014 out << "error=0" << endl;
3015 out << "if [ -z $validateout ]" << endl;
3016 out << "then" << endl;
3017 out << " validateout=\".\"" << endl;
3018 out << "fi" << endl << endl;
3019 out << "cd $validateout;" << endl;
3020 out << "validateworkdir=`pwd`;" << endl << endl;
3021 out << "echo \"*******************************************************\"" << outStream << endl;
3022 out << "echo \"* Automatically generated validation script *\"" << outStream << endl;
3024 out << "echo \"* Time: $validatetime \"" << outStream << endl;
3025 out << "echo \"* Dir: $validateout\"" << outStream << endl;
3026 out << "echo \"* Workdir: $validateworkdir\"" << outStream << endl;
3027 out << "echo \"* ----------------------------------------------------*\"" << outStream << endl;
3028 out << "ls -la ./" << outStream << endl;
3029 out << "echo \"* ----------------------------------------------------*\"" << outStream << endl << endl;
3030 out << "##################################################" << endl;
3033 out << "if [ ! -f stderr ] ; then" << endl;
3034 out << " error=1" << endl;
3035 out << " echo \"* ########## Job not validated - no stderr ###\" " << outStream << endl;
3036 out << " echo \"Error = $error\" " << outStream << endl;
3037 out << "fi" << endl;
3039 out << "parArch=`grep -Ei \"Cannot Build the PAR Archive\" stderr`" << endl;
3040 out << "segViol=`grep -Ei \"Segmentation violation\" stderr`" << endl;
3041 out << "segFault=`grep -Ei \"Segmentation fault\" stderr`" << endl;
3042 out << "glibcErr=`grep -Ei \"*** glibc detected ***\" stderr`" << endl;
3045 out << "if [ \"$parArch\" != \"\" ] ; then" << endl;
3046 out << " error=1" << endl;
3047 out << " echo \"* ########## Job not validated - PAR archive not built ###\" " << outStream << endl;
3048 out << " echo \"$parArch\" " << outStream << endl;
3049 out << " echo \"Error = $error\" " << outStream << endl;
3050 out << "fi" << endl;
3052 out << "if [ \"$segViol\" != \"\" ] ; then" << endl;
3053 out << " error=1" << endl;
3054 out << " echo \"* ########## Job not validated - Segment. violation ###\" " << outStream << endl;
3055 out << " echo \"$segViol\" " << outStream << endl;
3056 out << " echo \"Error = $error\" " << outStream << endl;
3057 out << "fi" << endl;
3059 out << "if [ \"$segFault\" != \"\" ] ; then" << endl;
3060 out << " error=1" << endl;
3061 out << " echo \"* ########## Job not validated - Segment. fault ###\" " << outStream << endl;
3062 out << " echo \"$segFault\" " << outStream << endl;
3063 out << " echo \"Error = $error\" " << outStream << endl;
3064 out << "fi" << endl;
3066 out << "if [ \"$glibcErr\" != \"\" ] ; then" << endl;
3067 out << " error=1" << endl;
3068 out << " echo \"* ########## Job not validated - *** glibc detected *** ###\" " << outStream << endl;
3069 out << " echo \"$glibcErr\" " << outStream << endl;
3070 out << " echo \"Error = $error\" " << outStream << endl;
3071 out << "fi" << endl;
3073 // Part dedicated to the specific analyses running into the train
3075 TObjArray *arr = fOutputFiles.Tokenize(",");
3078 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
3079 TString extra = mgr->GetExtraFiles();
3080 while ((os=(TObjString*)next1())) {
3081 outputFile = os->GetString();
3082 Int_t index = outputFile.Index("@");
3083 if (index > 0) outputFile.Remove(index);
3084 if (merge && fMergeExcludes.Contains(outputFile)) continue;
3085 if (extra.Contains(outputFile)) continue;
3086 if (outputFile.Contains("*")) continue;
3087 out << "if ! [ -f " << outputFile.Data() << " ] ; then" << endl;
3088 out << " error=1" << endl;
3089 out << " echo \"Output file(s) not found. Job FAILED !\"" << outStream << endl;
3090 out << " echo \"Output file(s) not found. Job FAILED !\" >> stderr" << endl;
3091 out << "fi" << endl;
3095 out << "if ! [ -f outputs_valid ] ; then" << endl;
3096 out << " error=1" << endl;
3097 out << " echo \"Output files were not validated by the analysis manager\" >> stdout" << endl;
3098 out << " echo \"Output files were not validated by the analysis manager\" >> stderr" << endl;
3099 out << "fi" << endl;
3102 out << "if [ $error = 0 ] ; then" << endl;
3103 out << " echo \"* ---------------- Job Validated ------------------*\"" << outStream << endl;
3104 if (!IsKeepLogs()) {
3105 out << " echo \"* === Logs std* will be deleted === \"" << endl;
3107 out << " rm -f std*" << endl;
3109 out << "fi" << endl;
3111 out << "echo \"* ----------------------------------------------------*\"" << outStream << endl;
3112 out << "echo \"*******************************************************\"" << outStream << endl;
3113 out << "cd -" << endl;
3114 out << "exit $error" << endl;
3116 Bool_t copy = kTRUE;
3117 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
3120 TString workdir = gGrid->GetHomeDirectory();
3121 workdir += fGridWorkingDir;
3122 Info("CreateJDL", "\n##### Copying validation script <%s> to your AliEn working space", validationScript.Data());
3123 if (FileExists(validationScript)) gGrid->Rm(validationScript);
3124 TFile::Cp(Form("file:%s",validationScript.Data()), Form("alien://%s/%s", workdir.Data(),validationScript.Data()));