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1/**************************************************************************
2 * Copyright(c) 1998-2007, ALICE Experiment at CERN, All rights reserved. *
3 * *
4 * Author: The ALICE Off-line Project. *
5 * Contributors are mentioned in the code where appropriate. *
6 * *
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 **************************************************************************/
15
16// Author: Mihaela Gheata, 01/09/2008
17
18//==============================================================================
19// AliAnalysisAlien - AliEn utility class. Provides interface for creating
20// a personalized JDL, finding and creating a dataset.
21//==============================================================================
22
23#include "AliAnalysisAlien.h"
24
25#include "Riostream.h"
26#include "TEnv.h"
27#include "TKey.h"
28#include "TBits.h"
29#include "TError.h"
30#include "TROOT.h"
31#include "TSystem.h"
32#include "TInterpreter.h"
33#include "TFile.h"
34#include "TFileCollection.h"
35#include "TChain.h"
36#include "TObjString.h"
37#include "TObjArray.h"
38#include "TMacro.h"
39#include "TGrid.h"
40#include "TGridResult.h"
41#include "TGridCollection.h"
42#include "TGridJDL.h"
43#include "TGridJobStatusList.h"
44#include "TGridJobStatus.h"
45#include "TFileMerger.h"
46#include "AliAnalysisManager.h"
47#include "AliAnalysisTaskCfg.h"
48#include "AliVEventHandler.h"
49#include "AliAnalysisDataContainer.h"
50#include "AliMultiInputEventHandler.h"
51
52using std::ofstream;
53using std::ifstream;
54using std::ios;
55using std::endl;
56ClassImp(AliAnalysisAlien)
57#if 0
58;
59#endif
60
61namespace {
62 Bool_t copyLocal2Alien(const char* where, const char* loc, const char* rem)
63 {
64 TString sl(Form("file:%s", loc));
65 TString sr(Form("alien://%s", rem));
66 Bool_t ret = TFile::Cp(sl, sr);
67 if (!ret) {
68 Warning(where, "Failed to copy %s to %s", sl.Data(), sr.Data());
69 }
70 return ret;
71 }
72}
73
74//______________________________________________________________________________
75AliAnalysisAlien::AliAnalysisAlien()
76 :AliAnalysisGrid(),
77 fGridJDL(NULL),
78 fMergingJDL(NULL),
79 fPrice(0),
80 fTTL(0),
81 fSplitMaxInputFileNumber(0),
82 fMaxInitFailed(0),
83 fMasterResubmitThreshold(0),
84 fNtestFiles(0),
85 fNrunsPerMaster(0),
86 fMaxMergeFiles(0),
87 fMaxMergeStages(0),
88 fNsubmitted(0),
89 fProductionMode(0),
90 fOutputToRunNo(0),
91 fMergeViaJDL(0),
92 fFastReadOption(0),
93 fOverwriteMode(1),
94 fNreplicas(2),
95 fNproofWorkers(0),
96 fNproofWorkersPerSlave(0),
97 fProofReset(0),
98 fNMCevents(0),
99 fNMCjobs(0),
100 fRunNumbers(),
101 fExecutable(),
102 fExecutableCommand(),
103 fArguments(),
104 fExecutableArgs(),
105 fAnalysisMacro(),
106 fAnalysisSource(),
107 fValidationScript(),
108 fAdditionalRootLibs(),
109 fAdditionalLibs(),
110 fGeneratorLibs(),
111 fSplitMode(),
112 fAPIVersion(),
113 fROOTVersion(),
114 fAliROOTVersion(),
115 fExternalPackages(),
116 fUser(),
117 fGridWorkingDir(),
118 fGridDataDir(),
119 fDataPattern(),
120 fGridOutputDir(),
121 fOutputArchive(),
122 fOutputFiles(),
123 fInputFormat(),
124 fDatasetName(),
125 fJDLName(),
126 fTerminateFiles(),
127 fMergeExcludes(),
128 fRegisterExcludes(),
129 fIncludePath(),
130 fCloseSE(),
131 fFriendChainName(),
132 fJobTag(),
133 fOutputSingle(),
134 fRunPrefix(),
135 fProofCluster(),
136 fProofDataSet(),
137 fFileForTestMode(),
138 fAliRootMode(),
139 fProofProcessOpt(),
140 fMergeDirName(),
141 fInputFiles(0),
142 fPackages(0),
143 fModules(0),
144 fProofParam(),
145 fDropToShell(true),
146 fMCLoop(false),
147 fGridJobIDs(""),
148 fGridStages(""),
149 fFriendLibs(""),
150 fTreeName()
151{
152// Dummy ctor.
153 SetDefaults();
154}
155
156//______________________________________________________________________________
157AliAnalysisAlien::AliAnalysisAlien(const char *name)
158 :AliAnalysisGrid(name),
159 fGridJDL(NULL),
160 fMergingJDL(NULL),
161 fPrice(0),
162 fTTL(0),
163 fSplitMaxInputFileNumber(0),
164 fMaxInitFailed(0),
165 fMasterResubmitThreshold(0),
166 fNtestFiles(0),
167 fNrunsPerMaster(0),
168 fMaxMergeFiles(0),
169 fMaxMergeStages(0),
170 fNsubmitted(0),
171 fProductionMode(0),
172 fOutputToRunNo(0),
173 fMergeViaJDL(0),
174 fFastReadOption(0),
175 fOverwriteMode(1),
176 fNreplicas(2),
177 fNproofWorkers(0),
178 fNproofWorkersPerSlave(0),
179 fProofReset(0),
180 fNMCevents(0),
181 fNMCjobs(0),
182 fRunNumbers(),
183 fExecutable(),
184 fExecutableCommand(),
185 fArguments(),
186 fExecutableArgs(),
187 fAnalysisMacro(),
188 fAnalysisSource(),
189 fValidationScript(),
190 fAdditionalRootLibs(),
191 fAdditionalLibs(),
192 fGeneratorLibs(),
193 fSplitMode(),
194 fAPIVersion(),
195 fROOTVersion(),
196 fAliROOTVersion(),
197 fExternalPackages(),
198 fUser(),
199 fGridWorkingDir(),
200 fGridDataDir(),
201 fDataPattern(),
202 fGridOutputDir(),
203 fOutputArchive(),
204 fOutputFiles(),
205 fInputFormat(),
206 fDatasetName(),
207 fJDLName(),
208 fTerminateFiles(),
209 fMergeExcludes(),
210 fRegisterExcludes(),
211 fIncludePath(),
212 fCloseSE(),
213 fFriendChainName(),
214 fJobTag(),
215 fOutputSingle(),
216 fRunPrefix(),
217 fProofCluster(),
218 fProofDataSet(),
219 fFileForTestMode(),
220 fAliRootMode(),
221 fProofProcessOpt(),
222 fMergeDirName(),
223 fInputFiles(0),
224 fPackages(0),
225 fModules(0),
226 fProofParam(),
227 fDropToShell(true),
228 fMCLoop(false),
229 fGridJobIDs(""),
230 fGridStages(""),
231 fFriendLibs(""),
232 fTreeName()
233{
234// Default ctor.
235 SetDefaults();
236}
237
238//______________________________________________________________________________
239AliAnalysisAlien::AliAnalysisAlien(const AliAnalysisAlien& other)
240 :AliAnalysisGrid(other),
241 fGridJDL(NULL),
242 fMergingJDL(NULL),
243 fPrice(other.fPrice),
244 fTTL(other.fTTL),
245 fSplitMaxInputFileNumber(other.fSplitMaxInputFileNumber),
246 fMaxInitFailed(other.fMaxInitFailed),
247 fMasterResubmitThreshold(other.fMasterResubmitThreshold),
248 fNtestFiles(other.fNtestFiles),
249 fNrunsPerMaster(other.fNrunsPerMaster),
250 fMaxMergeFiles(other.fMaxMergeFiles),
251 fMaxMergeStages(other.fMaxMergeStages),
252 fNsubmitted(other.fNsubmitted),
253 fProductionMode(other.fProductionMode),
254 fOutputToRunNo(other.fOutputToRunNo),
255 fMergeViaJDL(other.fMergeViaJDL),
256 fFastReadOption(other.fFastReadOption),
257 fOverwriteMode(other.fOverwriteMode),
258 fNreplicas(other.fNreplicas),
259 fNproofWorkers(other.fNproofWorkers),
260 fNproofWorkersPerSlave(other.fNproofWorkersPerSlave),
261 fProofReset(other.fProofReset),
262 fNMCevents(other.fNMCevents),
263 fNMCjobs(other.fNMCjobs),
264 fRunNumbers(other.fRunNumbers),
265 fExecutable(other.fExecutable),
266 fExecutableCommand(other.fExecutableCommand),
267 fArguments(other.fArguments),
268 fExecutableArgs(other.fExecutableArgs),
269 fAnalysisMacro(other.fAnalysisMacro),
270 fAnalysisSource(other.fAnalysisSource),
271 fValidationScript(other.fValidationScript),
272 fAdditionalRootLibs(other.fAdditionalRootLibs),
273 fAdditionalLibs(other.fAdditionalLibs),
274 fGeneratorLibs(other.fGeneratorLibs),
275 fSplitMode(other.fSplitMode),
276 fAPIVersion(other.fAPIVersion),
277 fROOTVersion(other.fROOTVersion),
278 fAliROOTVersion(other.fAliROOTVersion),
279 fExternalPackages(other.fExternalPackages),
280 fUser(other.fUser),
281 fGridWorkingDir(other.fGridWorkingDir),
282 fGridDataDir(other.fGridDataDir),
283 fDataPattern(other.fDataPattern),
284 fGridOutputDir(other.fGridOutputDir),
285 fOutputArchive(other.fOutputArchive),
286 fOutputFiles(other.fOutputFiles),
287 fInputFormat(other.fInputFormat),
288 fDatasetName(other.fDatasetName),
289 fJDLName(other.fJDLName),
290 fTerminateFiles(other.fTerminateFiles),
291 fMergeExcludes(other.fMergeExcludes),
292 fRegisterExcludes(other.fRegisterExcludes),
293 fIncludePath(other.fIncludePath),
294 fCloseSE(other.fCloseSE),
295 fFriendChainName(other.fFriendChainName),
296 fJobTag(other.fJobTag),
297 fOutputSingle(other.fOutputSingle),
298 fRunPrefix(other.fRunPrefix),
299 fProofCluster(other.fProofCluster),
300 fProofDataSet(other.fProofDataSet),
301 fFileForTestMode(other.fFileForTestMode),
302 fAliRootMode(other.fAliRootMode),
303 fProofProcessOpt(other.fProofProcessOpt),
304 fMergeDirName(other.fMergeDirName),
305 fInputFiles(0),
306 fPackages(0),
307 fModules(0),
308 fProofParam(),
309 fDropToShell(other.fDropToShell),
310 fMCLoop(other.fMCLoop),
311 fGridJobIDs(other.fGridJobIDs),
312 fGridStages(other.fGridStages),
313 fFriendLibs(other.fFriendLibs),
314 fTreeName(other.fTreeName)
315{
316// Copy ctor.
317 fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
318 fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
319 fRunRange[0] = other.fRunRange[0];
320 fRunRange[1] = other.fRunRange[1];
321 if (other.fInputFiles) {
322 fInputFiles = new TObjArray();
323 TIter next(other.fInputFiles);
324 TObject *obj;
325 while ((obj=next())) fInputFiles->Add(new TObjString(obj->GetName()));
326 fInputFiles->SetOwner();
327 }
328 if (other.fPackages) {
329 fPackages = new TObjArray();
330 TIter next(other.fPackages);
331 TObject *obj;
332 while ((obj=next())) fPackages->Add(new TObjString(obj->GetName()));
333 fPackages->SetOwner();
334 }
335 if (other.fModules) {
336 fModules = new TObjArray();
337 fModules->SetOwner();
338 TIter next(other.fModules);
339 AliAnalysisTaskCfg *mod, *crt;
340 while ((crt=(AliAnalysisTaskCfg*)next())) {
341 mod = new AliAnalysisTaskCfg(*crt);
342 fModules->Add(mod);
343 }
344 }
345}
346
347//______________________________________________________________________________
348AliAnalysisAlien::~AliAnalysisAlien()
349{
350// Destructor.
351 delete fGridJDL;
352 delete fMergingJDL;
353 delete fInputFiles;
354 delete fPackages;
355 delete fModules;
356 fProofParam.DeleteAll();
357}
358
359//______________________________________________________________________________
360AliAnalysisAlien &AliAnalysisAlien::operator=(const AliAnalysisAlien& other)
361{
362// Assignment.
363 if (this != &other) {
364 AliAnalysisGrid::operator=(other);
365 fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
366 fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
367 fPrice = other.fPrice;
368 fTTL = other.fTTL;
369 fSplitMaxInputFileNumber = other.fSplitMaxInputFileNumber;
370 fMaxInitFailed = other.fMaxInitFailed;
371 fMasterResubmitThreshold = other.fMasterResubmitThreshold;
372 fNtestFiles = other.fNtestFiles;
373 fNrunsPerMaster = other.fNrunsPerMaster;
374 fMaxMergeFiles = other.fMaxMergeFiles;
375 fMaxMergeStages = other.fMaxMergeStages;
376 fNsubmitted = other.fNsubmitted;
377 fProductionMode = other.fProductionMode;
378 fOutputToRunNo = other.fOutputToRunNo;
379 fMergeViaJDL = other.fMergeViaJDL;
380 fFastReadOption = other.fFastReadOption;
381 fOverwriteMode = other.fOverwriteMode;
382 fNreplicas = other.fNreplicas;
383 fNproofWorkers = other.fNproofWorkers;
384 fNproofWorkersPerSlave = other.fNproofWorkersPerSlave;
385 fProofReset = other.fProofReset;
386 fNMCevents = other.fNMCevents;
387 fNMCjobs = other.fNMCjobs;
388 fRunNumbers = other.fRunNumbers;
389 fExecutable = other.fExecutable;
390 fExecutableCommand = other.fExecutableCommand;
391 fArguments = other.fArguments;
392 fExecutableArgs = other.fExecutableArgs;
393 fAnalysisMacro = other.fAnalysisMacro;
394 fAnalysisSource = other.fAnalysisSource;
395 fValidationScript = other.fValidationScript;
396 fAdditionalRootLibs = other.fAdditionalRootLibs;
397 fAdditionalLibs = other.fAdditionalLibs;
398 fGeneratorLibs = other.fGeneratorLibs;
399 fSplitMode = other.fSplitMode;
400 fAPIVersion = other.fAPIVersion;
401 fROOTVersion = other.fROOTVersion;
402 fAliROOTVersion = other.fAliROOTVersion;
403 fExternalPackages = other.fExternalPackages;
404 fUser = other.fUser;
405 fGridWorkingDir = other.fGridWorkingDir;
406 fGridDataDir = other.fGridDataDir;
407 fDataPattern = other.fDataPattern;
408 fGridOutputDir = other.fGridOutputDir;
409 fOutputArchive = other.fOutputArchive;
410 fOutputFiles = other.fOutputFiles;
411 fInputFormat = other.fInputFormat;
412 fDatasetName = other.fDatasetName;
413 fJDLName = other.fJDLName;
414 fTerminateFiles = other.fTerminateFiles;
415 fMergeExcludes = other.fMergeExcludes;
416 fRegisterExcludes = other.fRegisterExcludes;
417 fIncludePath = other.fIncludePath;
418 fCloseSE = other.fCloseSE;
419 fFriendChainName = other.fFriendChainName;
420 fJobTag = other.fJobTag;
421 fOutputSingle = other.fOutputSingle;
422 fRunPrefix = other.fRunPrefix;
423 fProofCluster = other.fProofCluster;
424 fProofDataSet = other.fProofDataSet;
425 fFileForTestMode = other.fFileForTestMode;
426 fAliRootMode = other.fAliRootMode;
427 fProofProcessOpt = other.fProofProcessOpt;
428 fMergeDirName = other.fMergeDirName;
429 fDropToShell = other.fDropToShell;
430 fMCLoop = other.fMCLoop;
431 fGridJobIDs = other.fGridJobIDs;
432 fGridStages = other.fGridStages;
433 fFriendLibs = other.fFriendLibs;
434 fTreeName = other.fTreeName;
435 if (other.fInputFiles) {
436 fInputFiles = new TObjArray();
437 TIter next(other.fInputFiles);
438 TObject *obj;
439 while ((obj=next())) fInputFiles->Add(new TObjString(obj->GetName()));
440 fInputFiles->SetOwner();
441 }
442 if (other.fPackages) {
443 fPackages = new TObjArray();
444 TIter next(other.fPackages);
445 TObject *obj;
446 while ((obj=next())) fPackages->Add(new TObjString(obj->GetName()));
447 fPackages->SetOwner();
448 }
449 if (other.fModules) {
450 fModules = new TObjArray();
451 fModules->SetOwner();
452 TIter next(other.fModules);
453 AliAnalysisTaskCfg *mod, *crt;
454 while ((crt=(AliAnalysisTaskCfg*)next())) {
455 mod = new AliAnalysisTaskCfg(*crt);
456 fModules->Add(mod);
457 }
458 }
459 }
460 return *this;
461}
462
463//______________________________________________________________________________
464void AliAnalysisAlien::AddAdditionalLibrary(const char *name)
465{
466// Add a single additional library to be loaded. Extension must be present.
467 TString lib(name);
468 if (!lib.Contains(".")) {
469 Error("AddAdditionalLibrary", "Extension not defined for %s", name);
470 return;
471 }
472 if (fAdditionalLibs.Contains(name)) {
473 Warning("AddAdditionalLibrary", "Library %s already added.", name);
474 return;
475 }
476 if (!fAdditionalLibs.IsNull()) fAdditionalLibs += " ";
477 fAdditionalLibs += lib;
478}
479
480//______________________________________________________________________________
481void AliAnalysisAlien::AddModule(AliAnalysisTaskCfg *module)
482{
483// Adding a module. Checks if already existing. Becomes owned by this.
484 if (!module) return;
485 if (GetModule(module->GetName())) {
486 Error("AddModule", "A module having the same name %s already added", module->GetName());
487 return;
488 }
489 if (!fModules) {
490 fModules = new TObjArray();
491 fModules->SetOwner();
492 }
493 fModules->Add(module);
494}
495
496//______________________________________________________________________________
497void AliAnalysisAlien::AddModules(TObjArray *list)
498{
499// Adding a list of modules. Checks if already existing. Becomes owned by this.
500 TIter next(list);
501 AliAnalysisTaskCfg *module;
502 while ((module = (AliAnalysisTaskCfg*)next())) AddModule(module);
503}
504
505//______________________________________________________________________________
506Bool_t AliAnalysisAlien::CheckDependencies()
507{
508// Check if all dependencies are satisfied. Reorder modules if needed.
509 Int_t nmodules = GetNmodules();
510 if (!nmodules) {
511 Warning("CheckDependencies", "No modules added yet to check their dependencies");
512 return kTRUE;
513 }
514 AliAnalysisTaskCfg *mod = 0;
515 AliAnalysisTaskCfg *dep = 0;
516 TString depname;
517 Int_t i, j, k;
518 for (i=0; i<nmodules; i++) {
519 mod = (AliAnalysisTaskCfg*) fModules->At(i);
520 Int_t ndeps = mod->GetNdeps();
521 Int_t istart = i;
522 for (j=0; j<ndeps; j++) {
523 depname = mod->GetDependency(j);
524 dep = GetModule(depname);
525 if (!dep) {
526 Error("CheckDependencies","Dependency %s not added for module %s",
527 depname.Data(), mod->GetName());
528 return kFALSE;
529 }
530 if (dep->NeedsDependency(mod->GetName())) {
531 Error("CheckDependencies","Modules %s and %s circularly depend on each other",
532 mod->GetName(), dep->GetName());
533 return kFALSE;
534 }
535 Int_t idep = fModules->IndexOf(dep);
536 // The dependency task must come first
537 if (idep>i) {
538 // Remove at idep and move all objects below up one slot
539 // down to index i included.
540 fModules->RemoveAt(idep);
541 for (k=idep-1; k>=i; k--) fModules->AddAt(fModules->RemoveAt(k),k+1);
542 fModules->AddAt(dep, i++);
543 }
544 //Redo from istart if dependencies were inserted
545 if (i>istart) i=istart-1;
546 }
547 }
548 return kTRUE;
549}
550
551//______________________________________________________________________________
552AliAnalysisManager *AliAnalysisAlien::CreateAnalysisManager(const char *name, const char *filename)
553{
554// Create the analysis manager and optionally execute the macro in filename.
555 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
556 if (mgr) {
557 mgr->SetMCLoop(fMCLoop);
558 return mgr;
559 }
560 mgr = new AliAnalysisManager(name);
561 mgr->SetGridHandler((AliAnalysisGrid*)this);
562 mgr->SetMCLoop(fMCLoop);
563 if (strlen(filename)) {
564 TString line = gSystem->ExpandPathName(filename);
565 line.Prepend(".x ");
566 gROOT->ProcessLine(line.Data());
567 }
568 return mgr;
569}
570
571//______________________________________________________________________________
572Int_t AliAnalysisAlien::GetNmodules() const
573{
574// Get number of modules.
575 if (!fModules) return 0;
576 return fModules->GetEntries();
577}
578
579//______________________________________________________________________________
580AliAnalysisTaskCfg *AliAnalysisAlien::GetModule(const char *name)
581{
582// Get a module by name.
583 if (!fModules) return 0;
584 return (AliAnalysisTaskCfg*)fModules->FindObject(name);
585}
586
587//______________________________________________________________________________
588Bool_t AliAnalysisAlien::LoadModule(AliAnalysisTaskCfg *mod)
589{
590// Load a given module.
591 if (mod->IsLoaded()) return kTRUE;
592 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
593 if (!mgr) {
594 Error("LoadModule", "No analysis manager created yet. Use CreateAnalysisManager first.");
595 return kFALSE;
596 }
597 Int_t ndeps = mod->GetNdeps();
598 TString depname;
599 for (Int_t j=0; j<ndeps; j++) {
600 depname = mod->GetDependency(j);
601 AliAnalysisTaskCfg *dep = GetModule(depname);
602 if (!dep) {
603 Error("LoadModule","Dependency %s not existing for module %s",
604 depname.Data(), mod->GetName());
605 return kFALSE;
606 }
607 if (!LoadModule(dep)) {
608 Error("LoadModule","Dependency %s for module %s could not be loaded",
609 depname.Data(), mod->GetName());
610 return kFALSE;
611 }
612 }
613 // Load libraries for the module
614 if (!mod->CheckLoadLibraries()) {
615 Error("LoadModule", "Cannot load all libraries for module %s", mod->GetName());
616 return kFALSE;
617 }
618 // Check if a custom file name was requested
619 if (strlen(mod->GetOutputFileName())) mgr->SetCommonFileName(mod->GetOutputFileName());
620
621 // Check if a custom terminate file name was requested
622 if (strlen(mod->GetTerminateFileName())) {
623 if (!fTerminateFiles.IsNull()) fTerminateFiles += ",";
624 fTerminateFiles += mod->GetTerminateFileName();
625 }
626
627 // Execute the macro
628 if (mod->ExecuteMacro()<0) {
629 Error("LoadModule", "Executing the macro %s with arguments: %s for module %s returned a negative value",
630 mod->GetMacroName(), mod->GetMacroArgs(), mod->GetName());
631 return kFALSE;
632 }
633 // Configure dependencies
634 if (mod->GetConfigMacro() && mod->ExecuteConfigMacro()<0) {
635 Error("LoadModule", "There was an error executing the deps config macro %s for module %s",
636 mod->GetConfigMacro()->GetTitle(), mod->GetName());
637 return kFALSE;
638 }
639 // Adjust extra libraries
640 Int_t nlibs = mod->GetNlibs();
641 TString lib;
642 for (Int_t i=0; i<nlibs; i++) {
643 lib = mod->GetLibrary(i);
644 lib = Form("lib%s.so", lib.Data());
645 if (fAdditionalLibs.Contains(lib)) continue;
646 if (!fAdditionalLibs.IsNull()) fAdditionalLibs += " ";
647 fAdditionalLibs += lib;
648 }
649 return kTRUE;
650}
651
652//______________________________________________________________________________
653Bool_t AliAnalysisAlien::GenerateTrain(const char *name)
654{
655// Generate the full train.
656 fAdditionalLibs = "";
657 if (!LoadModules()) return kFALSE;
658 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
659 if (!mgr->InitAnalysis()) return kFALSE;
660 mgr->RunLocalInit();
661 mgr->PrintStatus();
662 Int_t productionMode = fProductionMode;
663 SetProductionMode();
664 TString macro = fAnalysisMacro;
665 TString executable = fExecutable;
666 TString validation = fValidationScript;
667 TString execCommand = fExecutableCommand;
668 SetAnalysisMacro(Form("%s.C", name));
669 SetExecutable(Form("%s.sh", name));
670// SetExecutableCommand("aliroot -b -q ");
671 SetValidationScript(Form("%s_validation.sh", name));
672 StartAnalysis();
673 SetProductionMode(productionMode);
674 fAnalysisMacro = macro;
675 fExecutable = executable;
676 fExecutableCommand = execCommand;
677 fValidationScript = validation;
678 return kTRUE;
679}
680
681//______________________________________________________________________________
682Bool_t AliAnalysisAlien::GenerateTest(const char *name, const char *modname)
683{
684// Generate test macros for a single module or for the full train.
685 fAdditionalLibs = "";
686 if (strlen(modname)) {
687 if (!CheckDependencies()) return kFALSE;
688 AliAnalysisTaskCfg *mod = GetModule(modname);
689 if (!mod) {
690 Error("GenerateTest", "cannot generate test for inexistent module %s", modname);
691 return kFALSE;
692 }
693 if (!LoadModule(mod)) return kFALSE;
694 if (!LoadFriendLibs()) return kFALSE;
695 } else if (!LoadModules()) return kFALSE;
696 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
697 if (!mgr->InitAnalysis()) return kFALSE;
698 mgr->RunLocalInit();
699 mgr->PrintStatus();
700 SetLocalTest(kTRUE);
701 Int_t productionMode = fProductionMode;
702 SetProductionMode();
703 TString macro = fAnalysisMacro;
704 TString executable = fExecutable;
705 TString validation = fValidationScript;
706 TString execCommand = fExecutableCommand;
707 SetAnalysisMacro(Form("%s.C", name));
708 SetExecutable(Form("%s.sh", name));
709 fOutputFiles = GetListOfFiles("outaod");
710 // Add extra files registered to the analysis manager
711 TString extra = GetListOfFiles("ext");
712 if (!extra.IsNull()) {
713 extra.ReplaceAll(".root", "*.root");
714 if (!fOutputFiles.IsNull()) fOutputFiles += ",";
715 fOutputFiles += extra;
716 }
717// SetExecutableCommand("aliroot -b -q ");
718 SetValidationScript(Form("%s_validation.sh", name));
719 WriteAnalysisFile();
720 WriteAnalysisMacro();
721 WriteExecutable();
722 WriteValidationScript();
723 WriteMergingMacro();
724 WriteMergeExecutable();
725 WriteValidationScript(kTRUE);
726 SetLocalTest(kFALSE);
727 SetProductionMode(productionMode);
728 fAnalysisMacro = macro;
729 fExecutable = executable;
730 fExecutableCommand = execCommand;
731 fValidationScript = validation;
732 return kTRUE;
733}
734
735//______________________________________________________________________________
736Bool_t AliAnalysisAlien::LoadModules()
737{
738// Load all modules by executing the AddTask macros. Checks first the dependencies.
739 fAdditionalLibs = "";
740 Int_t nmodules = GetNmodules();
741 if (!nmodules) {
742 Warning("LoadModules", "No module to be loaded");
743 return kTRUE;
744 }
745 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
746 if (!mgr) {
747 Error("LoadModules", "No analysis manager created yet. Use CreateAnalysisManager first.");
748 return kFALSE;
749 }
750 if (!CheckDependencies()) return kFALSE;
751 nmodules = GetNmodules();
752 AliAnalysisTaskCfg *mod;
753 for (Int_t imod=0; imod<nmodules; imod++) {
754 mod = (AliAnalysisTaskCfg*)fModules->At(imod);
755 if (!LoadModule(mod)) return kFALSE;
756 }
757 // Load additional friend libraries
758 return LoadFriendLibs();
759}
760
761//______________________________________________________________________________
762Bool_t AliAnalysisAlien::LoadFriendLibs() const
763{
764// Load libraries required for reading friends.
765 if (fFriendLibs.Length()) {
766 TObjArray *list = 0;
767 TString lib;
768 if (fFriendLibs.Contains(",")) list = fFriendLibs.Tokenize(",");
769 else list = fFriendLibs.Tokenize(" ");
770 for (Int_t ilib=0; ilib<list->GetEntriesFast(); ilib++) {
771 lib = list->At(ilib)->GetName();
772 lib.ReplaceAll(".so","");
773 lib.ReplaceAll(" ","");
774 if (lib.BeginsWith("lib")) lib.Remove(0, 3);
775 lib.Prepend("lib");
776 Int_t loaded = strlen(gSystem->GetLibraries(lib,"",kFALSE));
777 if (!loaded) loaded = gSystem->Load(lib);
778 if (loaded < 0) {
779 Error("LoadModules", "Cannot load library for friends %s", lib.Data());
780 return kFALSE;
781 }
782 }
783 delete list;
784 }
785 return kTRUE;
786}
787
788//______________________________________________________________________________
789void AliAnalysisAlien::SetRunPrefix(const char *prefix)
790{
791// Set the run number format. Can be a prefix or a format like "%09d"
792 fRunPrefix = prefix;
793 if (!fRunPrefix.Contains("%")) fRunPrefix += "%d";
794}
795
796//______________________________________________________________________________
797void AliAnalysisAlien::AddIncludePath(const char *path)
798{
799// Add include path in the remote analysis macro.
800 TString p(path);
801 if (p.Contains("-I")) fIncludePath += Form("%s ", path);
802 else fIncludePath += Form("-I%s ", path);
803}
804
805//______________________________________________________________________________
806void AliAnalysisAlien::AddRunNumber(Int_t run)
807{
808// Add a run number to the list of runs to be processed.
809 if (fRunNumbers.Length()) fRunNumbers += " ";
810 fRunNumbers += Form(fRunPrefix.Data(), run);
811}
812
813//______________________________________________________________________________
814void AliAnalysisAlien::AddRunList(const char* runList)
815{
816// Add several runs into the list of runs; they are expected to be separated by a blank character.
817 TString sList = runList;
818 TObjArray *list = sList.Tokenize(" ");
819 Int_t n = list->GetEntries();
820 for (Int_t i = 0; i < n; i++) {
821 TObjString *os = (TObjString*)list->At(i);
822 AddRunNumber(os->GetString().Atoi());
823 }
824 delete list;
825}
826
827//______________________________________________________________________________
828void AliAnalysisAlien::AddRunNumber(const char* run)
829{
830// Add a run number to the list of runs to be processed.
831 TString runs = run;
832 TObjString *os;
833 TObjArray *arr = runs.Tokenize(" ");
834 TIter next(arr);
835 TString prefix;
836 prefix.Append(fRunPrefix, fRunPrefix.Index("%d"));
837 while ((os=(TObjString*)next())){
838 if (fRunNumbers.Length()) fRunNumbers += " ";
839 fRunNumbers += Form("%s%s", prefix.Data(), os->GetString().Data());
840 }
841 delete arr;
842}
843
844//______________________________________________________________________________
845void AliAnalysisAlien::AddDataFile(const char *lfn)
846{
847// Adds a data file to the input to be analysed. The file should be a valid LFN
848// or point to an existing file in the alien workdir.
849 if (!fInputFiles) fInputFiles = new TObjArray();
850 fInputFiles->Add(new TObjString(lfn));
851}
852
853//______________________________________________________________________________
854void AliAnalysisAlien::AddExternalPackage(const char *package)
855{
856// Adds external packages w.r.t to the default ones (root,aliroot and gapi)
857 if (fExternalPackages) fExternalPackages += " ";
858 fExternalPackages += package;
859}
860
861//______________________________________________________________________________
862Bool_t AliAnalysisAlien::Connect()
863{
864// Try to connect to AliEn. User needs a valid token and /tmp/gclient_env_$UID sourced.
865 if (gGrid && gGrid->IsConnected()) return kTRUE;
866 if (fProductionMode) return kTRUE;
867 if (!gGrid) {
868 Info("Connect", "Trying to connect to AliEn ...");
869 TGrid::Connect("alien://");
870 }
871 if (!gGrid || !gGrid->IsConnected()) {
872 Error("Connect", "Did not managed to connect to AliEn. Make sure you have a valid token.");
873 return kFALSE;
874 }
875 fUser = gGrid->GetUser();
876 Info("Connect", "\n##### Connected to AliEn as user %s. Setting analysis user to <%s>", fUser.Data(), fUser.Data());
877 return kTRUE;
878}
879
880//______________________________________________________________________________
881void AliAnalysisAlien::CdWork()
882{
883// Check validity of alien workspace. Create directory if possible.
884 if (!Connect()) {
885 Error("CdWork", "Alien connection required");
886 return;
887 }
888 TString homedir = gGrid->GetHomeDirectory();
889 TString workdir = homedir + fGridWorkingDir;
890 if (DirectoryExists(workdir)) {
891 gGrid->Cd(workdir);
892 return;
893 }
894 // Work directory not existing - create it
895 gGrid->Cd(homedir);
896 if (gGrid->Mkdir(workdir, "-p")) {
897 gGrid->Cd(fGridWorkingDir);
898 Info("CdWork", "\n##### Created alien working directory %s", fGridWorkingDir.Data());
899 } else {
900 Warning("CdWork", "Working directory %s cannot be created.\n Using %s instead.",
901 workdir.Data(), homedir.Data());
902 fGridWorkingDir = "";
903 }
904}
905
906//______________________________________________________________________________
907Bool_t AliAnalysisAlien::CheckFileCopy(const char *alienpath)
908{
909// Check if file copying is possible.
910 if (fProductionMode) return kTRUE;
911 TString salienpath(alienpath);
912 if (salienpath.Contains(" ")) {
913 Error("CheckFileCopy", "path: <%s> contains blancs - FIX IT !",alienpath);
914 return kFALSE;
915 }
916 if (!Connect()) {
917 Error("CheckFileCopy", "Not connected to AliEn. File copying cannot be tested.");
918 return kFALSE;
919 }
920 Info("CheckFileCopy", "Checking possibility to copy files to your AliEn home directory... \
921 \n +++ NOTE: You can disable this via: plugin->SetCheckCopy(kFALSE);");
922 // Check if alien_CLOSE_SE is defined
923 TString closeSE = gSystem->Getenv("alien_CLOSE_SE");
924 if (!closeSE.IsNull()) {
925 Info("CheckFileCopy", "Your current close storage is pointing to: \
926 \n alien_CLOSE_SE = \"%s\"", closeSE.Data());
927 } else {
928 Warning("CheckFileCopy", "Your current close storage is empty ! Depending on your location, file copying may fail.");
929 }
930 // Check if grid directory exists.
931 if (!DirectoryExists(alienpath)) {
932 Error("CheckFileCopy", "Alien path %s does not seem to exist", alienpath);
933 return kFALSE;
934 }
935 TString stest = "plugin_test_copy";
936 TFile f(stest, "RECREATE");
937 // User may not have write permissions to current directory
938 if (f.IsZombie()) {
939 Error("CheckFileCopy", "Cannot create local test file. Do you have write access to current directory: <%s> ?",
940 gSystem->WorkingDirectory());
941 return kFALSE;
942 }
943 f.Close();
944 if (FileExists(Form("alien://%s/%s",alienpath, stest.Data()))) gGrid->Rm(Form("alien://%s/%s",alienpath, stest.Data()));
945 if (!TFile::Cp(stest.Data(), Form("alien://%s/%s",alienpath, stest.Data()))) {
946 Error("CheckFileCopy", "Cannot copy files to Alien destination: <%s> This may be temporary, or: \
947 \n# 1. Make sure you have write permissions there. If this is the case: \
948 \n# 2. Check the storage availability at: http://alimonitor.cern.ch/stats?page=SE/table \
949 \n# Do: export alien_CLOSE_SE=\"working_disk_SE\" \
950 \n# To make this permanent put in in your .bashrc (in .alienshrc is not enough) \
951 \n# Redo token: rm /tmp/x509up_u$UID then: alien-token-init <username>", alienpath);
952 gSystem->Unlink(stest.Data());
953 return kFALSE;
954 }
955 gSystem->Unlink(stest.Data());
956 gGrid->Rm(Form("%s/%s",alienpath,stest.Data()));
957 Info("CheckFileCopy", "### ...SUCCESS ###");
958 return kTRUE;
959}
960
961//______________________________________________________________________________
962Bool_t AliAnalysisAlien::CheckInputData()
963{
964// Check validity of input data. If necessary, create xml files.
965 if (fProductionMode) return kTRUE;
966 if (!fInputFiles && !fRunNumbers.Length() && !fRunRange[0]) {
967 if (!fGridDataDir.Length()) {
968 Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
969 return kFALSE;
970 }
971 if (fMergeViaJDL) {
972 Error("CheckInputData", "Merging via jdl works only with run numbers, run range or provided xml");
973 return kFALSE;
974 }
975 Info("CheckInputData", "Analysis will make a single xml for base data directory %s",fGridDataDir.Data());
976 if (fDataPattern.Contains("tag") && TestBit(AliAnalysisGrid::kTest))
977 TObject::SetBit(AliAnalysisGrid::kUseTags, kTRUE); // ADDED (fix problem in determining the tag usage in test mode)
978 return kTRUE;
979 }
980 // Process declared files
981 Bool_t isCollection = kFALSE;
982 Bool_t isXml = kFALSE;
983 Bool_t useTags = kFALSE;
984 Bool_t checked = kFALSE;
985 if (!TestBit(AliAnalysisGrid::kTest)) CdWork();
986 TString file;
987 TString workdir = gGrid->GetHomeDirectory();
988 workdir += fGridWorkingDir;
989 if (fInputFiles) {
990 TObjString *objstr;
991 TIter next(fInputFiles);
992 while ((objstr=(TObjString*)next())) {
993 file = workdir;
994 file += "/";
995 file += objstr->GetString();
996 // Store full lfn path
997 if (FileExists(file)) objstr->SetString(file);
998 else {
999 file = objstr->GetName();
1000 if (!FileExists(objstr->GetName())) {
1001 Error("CheckInputData", "Data file %s not found or not in your working dir: %s",
1002 objstr->GetName(), workdir.Data());
1003 return kFALSE;
1004 }
1005 }
1006 Bool_t iscoll, isxml, usetags;
1007 CheckDataType(file, iscoll, isxml, usetags);
1008 if (!checked) {
1009 checked = kTRUE;
1010 isCollection = iscoll;
1011 isXml = isxml;
1012 useTags = usetags;
1013 TObject::SetBit(AliAnalysisGrid::kUseTags, useTags);
1014 } else {
1015 if ((iscoll != isCollection) || (isxml != isXml) || (usetags != useTags)) {
1016 Error("CheckInputData", "Some conflict was found in the types of inputs");
1017 return kFALSE;
1018 }
1019 }
1020 }
1021 }
1022 // Process requested run numbers
1023 if (!fRunNumbers.Length() && !fRunRange[0]) return kTRUE;
1024 // Check validity of alien data directory
1025 if (!fGridDataDir.Length()) {
1026 Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
1027 return kFALSE;
1028 }
1029 if (!DirectoryExists(fGridDataDir)) {
1030 Error("CheckInputData", "Data directory %s not existing.", fGridDataDir.Data());
1031 return kFALSE;
1032 }
1033 if (isCollection) {
1034 Error("CheckInputData", "You are using raw AliEn collections as input. Cannot process run numbers.");
1035 return kFALSE;
1036 }
1037
1038 if (checked && !isXml) {
1039 Error("CheckInputData", "Cannot mix processing of full runs with non-xml files");
1040 return kFALSE;
1041 }
1042 // Check validity of run number(s)
1043 TObjArray *arr;
1044 TObjString *os;
1045 TString format;
1046 Int_t nruns = 0;
1047 TString schunk, schunk2;
1048 TString path;
1049 if (!checked) {
1050 checked = kTRUE;
1051 useTags = fDataPattern.Contains("tag");
1052 TObject::SetBit(AliAnalysisGrid::kUseTags, useTags);
1053 }
1054 if (useTags != fDataPattern.Contains("tag")) {
1055 Error("CheckInputData", "Cannot mix input files using/not using tags");
1056 return kFALSE;
1057 }
1058 if (fRunNumbers.Length()) {
1059 Info("CheckDataType", "Using supplied run numbers (run ranges are ignored)");
1060 arr = fRunNumbers.Tokenize(" ");
1061 TIter next(arr);
1062 while ((os=(TObjString*)next())) {
1063 path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data());
1064 if (!DirectoryExists(path)) {
1065 Warning("CheckInputData", "Run number %s not found in path: <%s>", os->GetString().Data(), path.Data());
1066 continue;
1067 }
1068 path = Form("%s/%s.xml", workdir.Data(),os->GetString().Data());
1069 TString msg = "\n##### file: ";
1070 msg += path;
1071 msg += " type: xml_collection;";
1072 if (useTags) msg += " using_tags: Yes";
1073 else msg += " using_tags: No";
1074 Info("CheckDataType", "%s", msg.Data());
1075 if (fNrunsPerMaster<2) {
1076 AddDataFile(Form("%s.xml", os->GetString().Data()));
1077 } else {
1078 nruns++;
1079 if (((nruns-1)%fNrunsPerMaster) == 0) {
1080 schunk = os->GetString();
1081 }
1082 if ((nruns%fNrunsPerMaster)!=0 && os!=arr->Last()) continue;
1083 schunk += Form("_%s.xml", os->GetString().Data());
1084 AddDataFile(schunk);
1085 }
1086 }
1087 delete arr;
1088 } else {
1089 Info("CheckDataType", "Using run range [%d, %d]", fRunRange[0], fRunRange[1]);
1090 for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
1091 format = Form("%%s/%s ", fRunPrefix.Data());
1092 path = Form(format.Data(), fGridDataDir.Data(), irun);
1093 if (!DirectoryExists(path)) {
1094 continue;
1095 }
1096 format = Form("%%s/%s.xml", fRunPrefix.Data());
1097 path = Form(format.Data(), workdir.Data(),irun);
1098 TString msg = "\n##### file: ";
1099 msg += path;
1100 msg += " type: xml_collection;";
1101 if (useTags) msg += " using_tags: Yes";
1102 else msg += " using_tags: No";
1103 Info("CheckDataType", "%s", msg.Data());
1104 if (fNrunsPerMaster<2) {
1105 format = Form("%s.xml", fRunPrefix.Data());
1106 AddDataFile(Form(format.Data(),irun));
1107 } else {
1108 nruns++;
1109 if (((nruns-1)%fNrunsPerMaster) == 0) {
1110 schunk = Form(fRunPrefix.Data(),irun);
1111 }
1112 format = Form("_%s.xml", fRunPrefix.Data());
1113 schunk2 = Form(format.Data(), irun);
1114 if ((nruns%fNrunsPerMaster)!=0 && irun != fRunRange[1]) continue;
1115 schunk += schunk2;
1116 AddDataFile(schunk);
1117 }
1118 }
1119 if (!fInputFiles) {
1120 schunk += schunk2;
1121 AddDataFile(schunk);
1122 }
1123 }
1124 return kTRUE;
1125}
1126
1127//______________________________________________________________________________
1128Int_t AliAnalysisAlien::CopyLocalDataset(const char *griddir, const char *pattern, Int_t nfiles, const char *output, const char *archivefile, const char *outputdir)
1129{
1130// Copy data from the given grid directory according a pattern and make a local
1131// dataset.
1132// archivefile (optional) results in that the archive containing the file <pattern> is copied. archivefile can contain a list of files (semicolon-separated) which are all copied
1133 if (!Connect()) {
1134 Error("CopyLocalDataset", "Cannot copy local dataset with no grid connection");
1135 return 0;
1136 }
1137 if (!DirectoryExists(griddir)) {
1138 Error("CopyLocalDataset", "Data directory %s not existing.", griddir);
1139 return 0;
1140 }
1141 TString command = Form("find -z -l %d %s %s", nfiles, griddir, pattern);
1142 printf("Running command: %s\n", command.Data());
1143 TGridResult *res = gGrid->Command(command);
1144 Int_t nfound = res->GetEntries();
1145 if (!nfound) {
1146 Error("CopyLocalDataset", "No file found in <%s> having pattern <%s>", griddir, pattern);
1147 return 0;
1148 }
1149 printf("... found %d files. Copying locally ...\n", nfound);
1150
1151 // archives
1152 TObjArray* additionalArchives = 0;
1153 if (strlen(archivefile) > 0 && TString(archivefile).Contains(";")) {
1154 additionalArchives = TString(archivefile).Tokenize(";");
1155 archivefile = additionalArchives->At(0)->GetName();
1156 additionalArchives->RemoveAt(0);
1157 additionalArchives->Compress();
1158 }
1159
1160 // Copy files locally
1161 ofstream out;
1162 out.open(output, ios::out);
1163 TMap *map;
1164 TString turl, dirname, filename, temp;
1165 TString cdir = gSystem->WorkingDirectory();
1166 gSystem->MakeDirectory(outputdir);
1167 gSystem->ChangeDirectory(outputdir);
1168 Int_t ncopied = 0;
1169 for (Int_t i=0; i<nfound; i++) {
1170 map = (TMap*)res->At(i);
1171 turl = map->GetValue("turl")->GetName();
1172 filename = gSystem->BaseName(turl.Data());
1173 dirname = gSystem->DirName(turl.Data());
1174 dirname = gSystem->BaseName(dirname.Data());
1175 gSystem->MakeDirectory(dirname);
1176
1177 TString source(turl);
1178 TString targetFileName(filename);
1179
1180 if (strlen(archivefile) > 0) {
1181// TODO here the archive in which the file resides should be determined
1182// however whereis returns only a guid, and guid2lfn does not work
1183// Therefore we use the one provided as argument for now
1184 source = Form("%s/%s", gSystem->DirName(source.Data()), archivefile);
1185 targetFileName = archivefile;
1186 }
1187 if (TFile::Cp(source, Form("file:./%s/%s", dirname.Data(), targetFileName.Data()))) {
1188 Bool_t success = kTRUE;
1189 if (additionalArchives) {
1190 for (Int_t j=0; j<additionalArchives->GetEntriesFast(); j++) {
1191 TString target;
1192 target.Form("./%s/%s", dirname.Data(), additionalArchives->At(j)->GetName());
1193 gSystem->MakeDirectory(gSystem->DirName(target));
1194 success &= TFile::Cp(Form("%s/%s", gSystem->DirName(source.Data()), additionalArchives->At(j)->GetName()), Form("file:%s", target.Data()));
1195 }
1196 }
1197
1198 if (success) {
1199 if (strlen(archivefile) > 0) targetFileName = Form("%s#%s", targetFileName.Data(), gSystem->BaseName(turl.Data()));
1200 out << cdir << Form("/%s/%s/%s", outputdir, dirname.Data(), targetFileName.Data()) << endl;
1201 ncopied++;
1202 }
1203 }
1204 }
1205 gSystem->ChangeDirectory(cdir);
1206 delete res;
1207 delete additionalArchives;
1208 return ncopied;
1209}
1210
1211//______________________________________________________________________________
1212Bool_t AliAnalysisAlien::CreateDataset(const char *pattern)
1213{
1214// Create dataset for the grid data directory + run number.
1215 const Int_t gMaxEntries = 15000;
1216 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline)) return kTRUE;
1217 if (!Connect()) {
1218 Error("CreateDataset", "Cannot create dataset with no grid connection");
1219 return kFALSE;
1220 }
1221
1222 // Cd workspace
1223 if (!TestBit(AliAnalysisGrid::kTest)) CdWork();
1224 TString workdir = gGrid->GetHomeDirectory();
1225 workdir += fGridWorkingDir;
1226
1227 // Compose the 'find' command arguments
1228 TString format;
1229 TString command;
1230 TString delimiter = pattern;
1231 delimiter.Strip();
1232 if (delimiter.Contains(" ")) delimiter = "";
1233 else delimiter = " ";
1234 TString options = "-x collection ";
1235 if (TestBit(AliAnalysisGrid::kTest)) options += Form("-l %d ", fNtestFiles);
1236 else options += Form("-l %d ", gMaxEntries); // Protection for the find command
1237 TString conditions = "";
1238 Int_t nstart = 0;
1239 Int_t ncount = 0;
1240 Int_t stage = 0;
1241 TString file;
1242 TString path;
1243 Int_t nruns = 0;
1244 TString schunk, schunk2;
1245 TGridCollection *cbase=0, *cadd=0;
1246 if (!fRunNumbers.Length() && !fRunRange[0]) {
1247 if (fInputFiles && fInputFiles->GetEntries()) return kTRUE;
1248 // Make a single data collection from data directory.
1249 path = fGridDataDir;
1250 if (!DirectoryExists(path)) {
1251 Error("CreateDataset", "Path to data directory %s not valid",fGridDataDir.Data());
1252 return kFALSE;
1253 }
1254// CdWork();
1255 if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
1256 else file = Form("%s.xml", gSystem->BaseName(path));
1257 while (1) {
1258 ncount = 0;
1259 stage++;
1260 if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
1261 command = "find ";
1262 command += Form("%s -o %d ",options.Data(), nstart);
1263 command += path;
1264 command += delimiter;
1265 command += pattern;
1266 command += conditions;
1267 printf("command: %s\n", command.Data());
1268 TGridResult *res = gGrid->Command(command);
1269 if (res) delete res;
1270 // Write standard output to file
1271 gROOT->ProcessLine(Form("gGrid->Stdout(); > __tmp%d__%s", stage, file.Data()));
1272 Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE;
1273 Bool_t nullFile = kFALSE;
1274 if (!hasGrep) {
1275 Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command");
1276 } else {
1277 nullFile = (gSystem->Exec(Form("grep -c /event __tmp%d__%s 2>/dev/null > __tmp__",stage,file.Data()))==0)?kFALSE:kTRUE;
1278 if (nullFile) {
1279 Error("CreateDataset","Dataset %s produced by the previous find command is empty !", file.Data());
1280 gSystem->Exec("rm -f __tmp*");
1281 return kFALSE;
1282 }
1283 TString line;
1284 ifstream in;
1285 in.open("__tmp__");
1286 in >> line;
1287 in.close();
1288 gSystem->Exec("rm -f __tmp__");
1289 ncount = line.Atoi();
1290 }
1291 }
1292 if (ncount == gMaxEntries) {
1293 Info("CreateDataset", "Dataset %s has more than 15K entries. Trying to merge...", file.Data());
1294 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"__tmp%d__%s\", 1000000);",stage,file.Data()));
1295 if (!cbase) cbase = cadd;
1296 else {
1297 cbase->Add(cadd);
1298 delete cadd;
1299 }
1300 nstart += ncount;
1301 } else {
1302 if (cbase) {
1303 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"__tmp%d__%s\", 1000000);",stage,file.Data()));
1304 printf("... please wait - TAlienCollection::Add() scales badly...\n");
1305 cbase->Add(cadd);
1306 delete cadd;
1307 cbase->ExportXML(Form("file://%s", file.Data()),kFALSE,kFALSE, file, "Merged entries for a run");
1308 delete cbase; cbase = 0;
1309 } else {
1310 TFile::Cp(Form("__tmp%d__%s",stage, file.Data()), file.Data());
1311 }
1312 gSystem->Exec("rm -f __tmp*");
1313 Info("CreateDataset", "Created dataset %s with %d files", file.Data(), nstart+ncount);
1314 break;
1315 }
1316 }
1317 Bool_t fileExists = FileExists(file);
1318 if (!TestBit(AliAnalysisGrid::kTest) && (!fileExists || fOverwriteMode)) {
1319 // Copy xml file to alien space
1320 if (fileExists) gGrid->Rm(file);
1321 TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
1322 if (!FileExists(file)) {
1323 Error("CreateDataset", "Command %s did NOT succeed", command.Data());
1324 return kFALSE;
1325 }
1326 // Update list of files to be processed.
1327 }
1328 AddDataFile(Form("%s/%s", workdir.Data(), file.Data()));
1329 return kTRUE;
1330 }
1331 // Several runs
1332 Bool_t nullResult = kTRUE;
1333 if (fRunNumbers.Length()) {
1334 TObjArray *arr = fRunNumbers.Tokenize(" ");
1335 TObjString *os;
1336 TIter next(arr);
1337 while ((os=(TObjString*)next())) {
1338 nstart = 0;
1339 stage = 0;
1340 path = Form("%s/%s", fGridDataDir.Data(), os->GetString().Data());
1341 if (!DirectoryExists(path)) continue;
1342// CdWork();
1343 if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
1344 else file = Form("%s.xml", os->GetString().Data());
1345 // If local collection file does not exist, create it via 'find' command.
1346 while (1) {
1347 ncount = 0;
1348 stage++;
1349 if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
1350 command = "find ";
1351 command += Form("%s -o %d ",options.Data(), nstart);
1352 command += path;
1353 command += delimiter;
1354 command += pattern;
1355 command += conditions;
1356 TGridResult *res = gGrid->Command(command);
1357 if (res) delete res;
1358 // Write standard output to file
1359 gROOT->ProcessLine(Form("gGrid->Stdout(); > __tmp%d__%s", stage,file.Data()));
1360 Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE;
1361 Bool_t nullFile = kFALSE;
1362 if (!hasGrep) {
1363 Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command");
1364 } else {
1365 nullFile = (gSystem->Exec(Form("grep -c /event __tmp%d__%s 2>/dev/null > __tmp__",stage,file.Data()))==0)?kFALSE:kTRUE;
1366 if (nullFile) {
1367 Warning("CreateDataset","Dataset %s produced by: <%s> is empty !", file.Data(), command.Data());
1368 gSystem->Exec("rm -f __tmp*");
1369 fRunNumbers.ReplaceAll(os->GetString().Data(), "");
1370 break;
1371 }
1372 TString line;
1373 ifstream in;
1374 in.open("__tmp__");
1375 in >> line;
1376 in.close();
1377 gSystem->Exec("rm -f __tmp__");
1378 ncount = line.Atoi();
1379 }
1380 nullResult = kFALSE;
1381 }
1382 if (ncount == gMaxEntries) {
1383 Info("CreateDataset", "Dataset %s has more than 15K entries. Trying to merge...", file.Data());
1384 if (fNrunsPerMaster > 1) {
1385 Error("CreateDataset", "File %s has more than %d entries. Please set the number of runs per master to 1 !",
1386 file.Data(),gMaxEntries);
1387 return kFALSE;
1388 }
1389 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"__tmp%d__%s\", 1000000);",stage,file.Data()));
1390 if (!cbase) cbase = cadd;
1391 else {
1392 cbase->Add(cadd);
1393 delete cadd;
1394 }
1395 nstart += ncount;
1396 } else {
1397 if (cbase && fNrunsPerMaster<2) {
1398 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"__tmp%d__%s\", 1000000);",stage,file.Data()));
1399 printf("... please wait - TAlienCollection::Add() scales badly...\n");
1400 cbase->Add(cadd);
1401 delete cadd;
1402 cbase->ExportXML(Form("file://%s", file.Data()),kFALSE,kFALSE, file, "Merged entries for a run");
1403 delete cbase; cbase = 0;
1404 } else {
1405 TFile::Cp(Form("__tmp%d__%s",stage, file.Data()), file.Data());
1406 }
1407 gSystem->Exec("rm -f __tmp*");
1408 Info("CreateDataset", "Created dataset %s with %d files", file.Data(), nstart+ncount);
1409 break;
1410 }
1411 }
1412 if (TestBit(AliAnalysisGrid::kTest)) break;
1413 // Check if there is one run per master job.
1414 if (fNrunsPerMaster<2) {
1415 if (FileExists(file)) {
1416 if (fOverwriteMode) gGrid->Rm(file);
1417 else {
1418 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
1419 continue;
1420 }
1421 }
1422 // Copy xml file to alien space
1423 TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
1424 if (!FileExists(file)) {
1425 Error("CreateDataset", "Command %s did NOT succeed", command.Data());
1426 delete arr;
1427 return kFALSE;
1428 }
1429 } else {
1430 nruns++;
1431 if (((nruns-1)%fNrunsPerMaster) == 0) {
1432 schunk = os->GetString();
1433 cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
1434 } else {
1435 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
1436 printf(" Merging collection <%s> into masterjob input...\n", file.Data());
1437 cbase->Add(cadd);
1438 delete cadd;
1439 }
1440 if ((nruns%fNrunsPerMaster)!=0 && os!=arr->Last()) {
1441 continue;
1442 }
1443 schunk += Form("_%s.xml", os->GetString().Data());
1444 if (FileExists(schunk)) {
1445 if (fOverwriteMode) gGrid->Rm(file);
1446 else {
1447 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
1448 continue;
1449 }
1450 }
1451 printf("Exporting merged collection <%s> and copying to AliEn\n", schunk.Data());
1452 cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs");
1453 TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data()));
1454 if (!FileExists(schunk)) {
1455 Error("CreateDataset", "Copy command did NOT succeed for %s", schunk.Data());
1456 delete arr;
1457 return kFALSE;
1458 }
1459 }
1460 }
1461 delete arr;
1462 if (nullResult) {
1463 Error("CreateDataset", "No valid dataset corresponding to the query!");
1464 return kFALSE;
1465 }
1466 } else {
1467 // Process a full run range.
1468 for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
1469 format = Form("%%s/%s", fRunPrefix.Data());
1470 nstart = 0;
1471 stage = 0;
1472 path = Form(format.Data(), fGridDataDir.Data(), irun);
1473 if (!DirectoryExists(path)) continue;
1474// CdWork();
1475 format = Form("%s.xml", fRunPrefix.Data());
1476 if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
1477 else file = Form(format.Data(), irun);
1478 if (FileExists(file) && fNrunsPerMaster<2 && !TestBit(AliAnalysisGrid::kTest)) {
1479 if (fOverwriteMode) gGrid->Rm(file);
1480 else {
1481 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
1482 continue;
1483 }
1484 }
1485 // If local collection file does not exist, create it via 'find' command.
1486 while (1) {
1487 ncount = 0;
1488 stage++;
1489 if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
1490 command = "find ";
1491 command += Form("%s -o %d ",options.Data(), nstart);
1492 command += path;
1493 command += delimiter;
1494 command += pattern;
1495 command += conditions;
1496 TGridResult *res = gGrid->Command(command);
1497 if (res) delete res;
1498 // Write standard output to file
1499 gROOT->ProcessLine(Form("gGrid->Stdout(); > __tmp%d__%s", stage,file.Data()));
1500 Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE;
1501 Bool_t nullFile = kFALSE;
1502 if (!hasGrep) {
1503 Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command");
1504 } else {
1505 nullFile = (gSystem->Exec(Form("grep -c /event __tmp%d__%s 2>/dev/null > __tmp__",stage,file.Data()))==0)?kFALSE:kTRUE;
1506 if (nullFile) {
1507 Warning("CreateDataset","Dataset %s produced by: <%s> is empty !", file.Data(), command.Data());
1508 gSystem->Exec("rm -f __tmp*");
1509 break;
1510 }
1511 TString line;
1512 ifstream in;
1513 in.open("__tmp__");
1514 in >> line;
1515 in.close();
1516 gSystem->Exec("rm -f __tmp__");
1517 ncount = line.Atoi();
1518 }
1519 nullResult = kFALSE;
1520 }
1521 if (ncount == gMaxEntries) {
1522 Info("CreateDataset", "Dataset %s has more than 15K entries. Trying to merge...", file.Data());
1523 if (fNrunsPerMaster > 1) {
1524 Error("CreateDataset", "File %s has more than %d entries. Please set the number of runs per master to 1 !",
1525 file.Data(),gMaxEntries);
1526 return kFALSE;
1527 }
1528 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"__tmp%d__%s\", 1000000);",stage,file.Data()));
1529 if (!cbase) cbase = cadd;
1530 else {
1531 cbase->Add(cadd);
1532 delete cadd;
1533 }
1534 nstart += ncount;
1535 } else {
1536 if (cbase && fNrunsPerMaster<2) {
1537 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"__tmp%d__%s\", 1000000);",stage,file.Data()));
1538 printf("... please wait - TAlienCollection::Add() scales badly...\n");
1539 cbase->Add(cadd);
1540 delete cadd;
1541 cbase->ExportXML(Form("file://%s", file.Data()),kFALSE,kFALSE, file, "Merged entries for a run");
1542 delete cbase; cbase = 0;
1543 } else {
1544 TFile::Cp(Form("__tmp%d__%s",stage, file.Data()), file.Data());
1545 }
1546 Info("CreateDataset", "Created dataset %s with %d files", file.Data(), nstart+ncount);
1547 break;
1548 }
1549 }
1550 if (TestBit(AliAnalysisGrid::kTest)) break;
1551 // Check if there is one run per master job.
1552 if (fNrunsPerMaster<2) {
1553 if (FileExists(file)) {
1554 if (fOverwriteMode) gGrid->Rm(file);
1555 else {
1556 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
1557 continue;
1558 }
1559 }
1560 // Copy xml file to alien space
1561 TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
1562 if (!FileExists(file)) {
1563 Error("CreateDataset", "Command %s did NOT succeed", command.Data());
1564 return kFALSE;
1565 }
1566 } else {
1567 nruns++;
1568 // Check if the collection for the chunk exist locally.
1569 Int_t nchunk = (nruns-1)/fNrunsPerMaster;
1570 if (FileExists(fInputFiles->At(nchunk)->GetName())) {
1571 if (fOverwriteMode) gGrid->Rm(fInputFiles->At(nchunk)->GetName());
1572 else continue;
1573 }
1574 printf(" Merging collection <%s> into %d runs chunk...\n",file.Data(),fNrunsPerMaster);
1575 if (((nruns-1)%fNrunsPerMaster) == 0) {
1576 schunk = Form(fRunPrefix.Data(), irun);
1577 cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
1578 } else {
1579 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
1580 cbase->Add(cadd);
1581 delete cadd;
1582 }
1583 format = Form("%%s_%s.xml", fRunPrefix.Data());
1584 schunk2 = Form(format.Data(), schunk.Data(), irun);
1585 if ((nruns%fNrunsPerMaster)!=0 && irun!=fRunRange[1] && schunk2 != fInputFiles->Last()->GetName()) {
1586 continue;
1587 }
1588 schunk = schunk2;
1589 if (FileExists(schunk)) {
1590 if (fOverwriteMode) gGrid->Rm(schunk);
1591 else {
1592 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
1593 continue;
1594 }
1595 }
1596 printf("Exporting merged collection <%s> and copying to AliEn.\n", schunk.Data());
1597 cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs");
1598 if (FileExists(schunk)) {
1599 if (fOverwriteMode) gGrid->Rm(schunk);
1600 else {
1601 Info("CreateDataset", "\n##### Dataset %s exist. Skipping copy...", schunk.Data());
1602 continue;
1603 }
1604 }
1605 TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data()));
1606 if (!FileExists(schunk)) {
1607 Error("CreateDataset", "Copy command did NOT succeed for %s", schunk.Data());
1608 return kFALSE;
1609 }
1610 }
1611 }
1612 if (nullResult) {
1613 Error("CreateDataset", "No valid dataset corresponding to the query!");
1614 return kFALSE;
1615 }
1616 }
1617 return kTRUE;
1618}
1619
1620//______________________________________________________________________________
1621Bool_t AliAnalysisAlien::CreateJDL()
1622{
1623// Generate a JDL file according to current settings. The name of the file is
1624// specified by fJDLName.
1625 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
1626 Bool_t error = kFALSE;
1627 TObjArray *arr = 0;
1628 Bool_t copy = kTRUE;
1629 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
1630 Bool_t generate = kTRUE;
1631 if (TestBit(AliAnalysisGrid::kTest) || TestBit(AliAnalysisGrid::kSubmit)) generate = kFALSE;
1632 if (!Connect()) {
1633 Error("CreateJDL", "Alien connection required");
1634 return kFALSE;
1635 }
1636 // Check validity of alien workspace
1637 TString workdir;
1638 if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice")) workdir = gGrid->GetHomeDirectory();
1639 if (!fProductionMode && !TestBit(AliAnalysisGrid::kTest)) CdWork();
1640 workdir += fGridWorkingDir;
1641 if (generate) {
1642 TObjString *os;
1643 if (!fInputFiles && !fMCLoop) {
1644 Error("CreateJDL()", "Define some input files for your analysis.");
1645 error = kTRUE;
1646 }
1647 // Compose list of input files
1648 // Check if output files were defined
1649 if (!fOutputFiles.Length()) {
1650 Error("CreateJDL", "You must define at least one output file");
1651 error = kTRUE;
1652 }
1653 // Check if an output directory was defined and valid
1654 if (!fGridOutputDir.Length()) {
1655 Error("CreateJDL", "You must define AliEn output directory");
1656 error = kTRUE;
1657 } else {
1658 if (!fProductionMode) {
1659 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
1660 if (!DirectoryExists(fGridOutputDir)) {
1661 if (gGrid->Mkdir(fGridOutputDir,"-p")) {
1662 Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
1663 } else {
1664 Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
1665 // error = kTRUE;
1666 }
1667 } else {
1668 Warning("CreateJDL", "#### Output directory %s exists! If this contains old data, jobs will fail with ERROR_SV !!! ###", fGridOutputDir.Data());
1669 }
1670 gGrid->Cd(workdir);
1671 }
1672 }
1673 // Exit if any error up to now
1674 if (error) return kFALSE;
1675 // Set JDL fields
1676 if (!fUser.IsNull()) {
1677 fGridJDL->SetValue("User", Form("\"%s\"", fUser.Data()));
1678 fMergingJDL->SetValue("User", Form("\"%s\"", fUser.Data()));
1679 }
1680 TString executable = fExecutable;
1681 if (!executable.BeginsWith("/"))
1682 executable.Prepend(Form("%s/", workdir.Data()));
1683 fGridJDL->SetExecutable(executable, "This is the startup script");
1684 TString mergeExec = executable;
1685 mergeExec.ReplaceAll(".sh", "_merge.sh");
1686 fMergingJDL->SetExecutable(mergeExec, "This is the startup script");
1687 mergeExec.ReplaceAll(".sh", ".C");
1688 fMergingJDL->AddToInputSandbox(Form("LF:%s", mergeExec.Data()), "List of input files to be uploaded to workers");
1689 if (!fArguments.IsNull())
1690 fGridJDL->SetArguments(fArguments, "Arguments for the executable command");
1691 if (IsOneStageMerging()) fMergingJDL->SetArguments(fGridOutputDir);
1692 else {
1693 if (fProductionMode) fMergingJDL->SetArguments("wn.xml $4"); // xml, stage
1694 else fMergingJDL->SetArguments("wn.xml $2"); // xml, stage
1695 }
1696
1697 fGridJDL->SetValue("TTL", Form("\"%d\"",fTTL));
1698 fGridJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60));
1699 fMergingJDL->SetValue("TTL", Form("\"%d\"",fTTL));
1700 fMergingJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60));
1701
1702 if (fMaxInitFailed > 0) {
1703 fGridJDL->SetValue("MaxInitFailed", Form("\"%d\"",fMaxInitFailed));
1704 fGridJDL->SetDescription("MaxInitFailed", "Maximum number of first failing jobs to abort the master job");
1705 }
1706 if (fSplitMaxInputFileNumber > 0 && !fMCLoop) {
1707 fGridJDL->SetValue("SplitMaxInputFileNumber", Form("\"%d\"", fSplitMaxInputFileNumber));
1708 fGridJDL->SetDescription("SplitMaxInputFileNumber", "Maximum number of input files to be processed per subjob");
1709 }
1710 if (!IsOneStageMerging()) {
1711 fMergingJDL->SetValue("SplitMaxInputFileNumber", Form("\"%d\"",fMaxMergeFiles));
1712 fMergingJDL->SetDescription("SplitMaxInputFileNumber", "Maximum number of input files to be merged in one go");
1713 }
1714 if (fSplitMode.Length()) {
1715 fGridJDL->SetValue("Split", Form("\"%s\"", fSplitMode.Data()));
1716 fGridJDL->SetDescription("Split", "We split per SE or file");
1717 }
1718 fMergingJDL->SetValue("Split", "\"se\"");
1719 fMergingJDL->SetDescription("Split", "We split per SE for merging in stages");
1720 if (!fAliROOTVersion.IsNull()) {
1721 fGridJDL->AddToPackages("AliRoot", fAliROOTVersion,"VO_ALICE", "List of requested packages");
1722 fMergingJDL->AddToPackages("AliRoot", fAliROOTVersion, "VO_ALICE", "List of requested packages");
1723 }
1724 if (!fROOTVersion.IsNull()) {
1725 fGridJDL->AddToPackages("ROOT", fROOTVersion);
1726 fMergingJDL->AddToPackages("ROOT", fROOTVersion);
1727 }
1728 if (!fAPIVersion.IsNull()) {
1729 fGridJDL->AddToPackages("APISCONFIG", fAPIVersion);
1730 fMergingJDL->AddToPackages("APISCONFIG", fAPIVersion);
1731 }
1732 if (!fExternalPackages.IsNull()) {
1733 arr = fExternalPackages.Tokenize(" ");
1734 TIter next(arr);
1735 while ((os=(TObjString*)next())) {
1736 TString pkgname = os->GetString();
1737 Int_t index = pkgname.Index("::");
1738 TString pkgversion = pkgname(index+2, pkgname.Length());
1739 pkgname.Remove(index);
1740 fGridJDL->AddToPackages(pkgname, pkgversion);
1741 fMergingJDL->AddToPackages(pkgname, pkgversion);
1742 }
1743 delete arr;
1744 }
1745 if (!fMCLoop) {
1746 fGridJDL->SetInputDataListFormat(fInputFormat, "Format of input data");
1747 fGridJDL->SetInputDataList("wn.xml", "Collection name to be processed on each worker node");
1748 }
1749 fMergingJDL->SetInputDataListFormat(fInputFormat, "Format of input data");
1750 fMergingJDL->SetInputDataList("wn.xml", "Collection name to be processed on each worker node");
1751 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), fAnalysisMacro.Data()), "List of input files to be uploaded to workers");
1752 TString analysisFile = fExecutable;
1753 analysisFile.ReplaceAll(".sh", ".root");
1754 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),analysisFile.Data()));
1755 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),analysisFile.Data()));
1756 if (fAdditionalLibs.Length()) {
1757 arr = fAdditionalLibs.Tokenize(" ");
1758 TIter next(arr);
1759 while ((os=(TObjString*)next())) {
1760 if (os->GetString().Contains(".so")) continue;
1761 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), os->GetString().Data()));
1762 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), os->GetString().Data()));
1763 }
1764 delete arr;
1765 }
1766 if (fPackages) {
1767 TIter next(fPackages);
1768 TObject *obj;
1769 while ((obj=next())) {
1770 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName()));
1771 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName()));
1772 }
1773 }
1774 const char *comment = "List of output files and archives";
1775 if (fOutputArchive.Length()) {
1776 TString outputArchive = fOutputArchive;
1777 if (!fRegisterExcludes.IsNull()) {
1778 arr = fRegisterExcludes.Tokenize(" ");
1779 TIter next1(arr);
1780 while ((os=(TObjString*)next1())) {
1781 outputArchive.ReplaceAll(Form("%s,",os->GetString().Data()),"");
1782 outputArchive.ReplaceAll(os->GetString(),"");
1783 }
1784 delete arr;
1785 }
1786 arr = outputArchive.Tokenize(" ");
1787 TIter next(arr);
1788 Bool_t first = kTRUE;
1789 while ((os=(TObjString*)next())) {
1790 if (!os->GetString().Contains("@") && fCloseSE.Length())
1791 fGridJDL->AddToSet("Output", Form("%s@%s",os->GetString().Data(), fCloseSE.Data()));
1792 else
1793 fGridJDL->AddToSet("Output", os->GetString());
1794 if (first) fGridJDL->AddToSetDescription("Output", comment);
1795 first = kFALSE;
1796 }
1797 delete arr;
1798 // Output archive for the merging jdl
1799 if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
1800 outputArchive = "log_archive.zip:std*@disk=1 ";
1801 // Add normal output files, extra files + terminate files
1802 TString files;
1803 if (IsMergeAOD()) files = GetListOfFiles("outaodextter");
1804 else files = GetListOfFiles("outextter");
1805 // Do not register files in fRegisterExcludes
1806 if (!fRegisterExcludes.IsNull()) {
1807 arr = fRegisterExcludes.Tokenize(" ");
1808 TIter next1(arr);
1809 while ((os=(TObjString*)next1())) {
1810 files.ReplaceAll(Form("%s,",os->GetString().Data()),"");
1811 files.ReplaceAll(os->GetString(),"");
1812 }
1813 delete arr;
1814 }
1815 files.ReplaceAll(".root", "*.root");
1816
1817 if (mgr->IsCollectThroughput())
1818 outputArchive += Form("root_archive.zip:%s,*.stat@disk=%d %s@disk=%d",files.Data(),fNreplicas, mgr->GetFileInfoLog(),fNreplicas);
1819 else
1820 outputArchive += Form("root_archive.zip:%s,*.stat@disk=%d",files.Data(),fNreplicas);
1821 } else {
1822 TString files = fOutputArchive;
1823 files.ReplaceAll(".root", "*.root"); // nreplicas etc should be already atttached by use
1824 outputArchive = files;
1825 }
1826 arr = outputArchive.Tokenize(" ");
1827 TIter next2(arr);
1828 first = kTRUE;
1829 while ((os=(TObjString*)next2())) {
1830 TString currentfile = os->GetString();
1831 if (!currentfile.Contains("@") && fCloseSE.Length())
1832 fMergingJDL->AddToSet("Output", Form("%s@%s",currentfile.Data(), fCloseSE.Data()));
1833 else
1834 fMergingJDL->AddToSet("Output", currentfile);
1835 if (first) fMergingJDL->AddToSetDescription("Output", comment);
1836 first = kFALSE;
1837 }
1838 delete arr;
1839 }
1840 arr = fOutputFiles.Tokenize(",");
1841 TIter next(arr);
1842 Bool_t first = kTRUE;
1843 while ((os=(TObjString*)next())) {
1844 // Ignore ouputs in jdl that are also in outputarchive
1845 TString sout = os->GetString();
1846 sout.ReplaceAll("*", "");
1847 sout.ReplaceAll(".root", "");
1848 if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
1849 if (fOutputArchive.Contains(sout)) continue;
1850 // Ignore fRegisterExcludes
1851 if (fRegisterExcludes.Contains(sout)) continue;
1852 if (!first) comment = NULL;
1853 if (!os->GetString().Contains("@") && fCloseSE.Length())
1854 fGridJDL->AddToSet("Output", Form("%s@%s",os->GetString().Data(), fCloseSE.Data()));
1855 else
1856 fGridJDL->AddToSet("Output", os->GetString());
1857 if (first) fGridJDL->AddToSetDescription("Output", comment);
1858 if (fMergeExcludes.Contains(sout)) continue;
1859 if (!os->GetString().Contains("@") && fCloseSE.Length())
1860 fMergingJDL->AddToSet("Output", Form("%s@%s",os->GetString().Data(), fCloseSE.Data()));
1861 else
1862 fMergingJDL->AddToSet("Output", os->GetString());
1863 if (first) fMergingJDL->AddToSetDescription("Output", comment);
1864 first = kFALSE;
1865 }
1866 delete arr;
1867 fGridJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
1868 fMergingJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
1869 TString validationScript = fValidationScript;
1870 fGridJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
1871 validationScript.ReplaceAll(".sh", "_merge.sh");
1872 fMergingJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
1873 if (fMasterResubmitThreshold) {
1874 fGridJDL->SetValue("MasterResubmitThreshold", Form("\"%d%%\"", fMasterResubmitThreshold));
1875 fGridJDL->SetDescription("MasterResubmitThreshold", "Resubmit failed jobs until DONE rate reaches this percentage");
1876 }
1877 // Write a jdl with 2 input parameters: collection name and output dir name.
1878 WriteJDL(copy);
1879 }
1880 // Copy jdl to grid workspace
1881 if (copy) {
1882 // Check if an output directory was defined and valid
1883 if (!fGridOutputDir.Length()) {
1884 Error("CreateJDL", "You must define AliEn output directory");
1885 return kFALSE;
1886 } else {
1887 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
1888 if (!fProductionMode && !DirectoryExists(fGridOutputDir)) {
1889 if (gGrid->Mkdir(fGridOutputDir,"-p")) {
1890 Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
1891 } else {
1892 Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
1893 return kFALSE;
1894 }
1895 }
1896 gGrid->Cd(workdir);
1897 }
1898 if (TestBit(AliAnalysisGrid::kSubmit)) {
1899 TString mergeJDLName = fExecutable;
1900 mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
1901 TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
1902 TString locjdl1 = Form("%s/%s", fGridOutputDir.Data(),mergeJDLName.Data());
1903 if (fProductionMode) {
1904 locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
1905 locjdl1 = Form("%s/%s", workdir.Data(),mergeJDLName.Data());
1906 }
1907 if (FileExists(locjdl)) gGrid->Rm(locjdl);
1908 if (FileExists(locjdl1)) gGrid->Rm(locjdl1);
1909 Info("CreateJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
1910 if (!copyLocal2Alien("CreateJDL", fJDLName, locjdl))
1911 Fatal("","Terminating");
1912// TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
1913 if (fMergeViaJDL) {
1914 Info("CreateJDL", "\n##### Copying merging JDL file <%s> to your AliEn output directory", mergeJDLName.Data());
1915// TFile::Cp(Form("file:%s",mergeJDLName.Data()), Form("alien://%s", locjdl1.Data()));
1916 if (!copyLocal2Alien("CreateJDL", mergeJDLName.Data(), locjdl1))
1917 Fatal("","Terminating");
1918 }
1919 }
1920 if (fAdditionalLibs.Length()) {
1921 arr = fAdditionalLibs.Tokenize(" ");
1922 TObjString *os;
1923 TIter next(arr);
1924 while ((os=(TObjString*)next())) {
1925 if (os->GetString().Contains(".so")) continue;
1926 Info("CreateJDL", "\n##### Copying dependency: <%s> to your alien workspace", os->GetString().Data());
1927 if (FileExists(os->GetString())) gGrid->Rm(os->GetString());
1928// TFile::Cp(Form("file:%s",os->GetString().Data()), Form("alien://%s/%s", workdir.Data(), os->GetString().Data()));
1929 if (!copyLocal2Alien("CreateJDL", os->GetString().Data(),
1930 Form("%s/%s", workdir.Data(), os->GetString().Data())))
1931 Fatal("","Terminating");
1932 }
1933 delete arr;
1934 }
1935 if (fPackages) {
1936 TIter next(fPackages);
1937 TObject *obj;
1938 while ((obj=next())) {
1939 if (FileExists(obj->GetName())) gGrid->Rm(obj->GetName());
1940 Info("CreateJDL", "\n##### Copying dependency: <%s> to your alien workspace", obj->GetName());
1941// TFile::Cp(Form("file:%s",obj->GetName()), Form("alien://%s/%s", workdir.Data(), obj->GetName()));
1942 if (!copyLocal2Alien("CreateJDL",obj->GetName(),
1943 Form("%s/%s", workdir.Data(), obj->GetName())))
1944 Fatal("","Terminating");
1945 }
1946 }
1947 }
1948 return kTRUE;
1949}
1950
1951//______________________________________________________________________________
1952Bool_t AliAnalysisAlien::WriteJDL(Bool_t copy)
1953{
1954// Writes one or more JDL's corresponding to findex. If findex is negative,
1955// all run numbers are considered in one go (jdl). For non-negative indices
1956// they correspond to the indices in the array fInputFiles.
1957 if (!fInputFiles && !fMCLoop) return kFALSE;
1958 TObject *os;
1959 TString workdir;
1960 if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice")) workdir = gGrid->GetHomeDirectory();
1961 workdir += fGridWorkingDir;
1962 TString stageName = "$2";
1963 if (fProductionMode) stageName = "$4";
1964 if (!fMergeDirName.IsNull()) {
1965 fMergingJDL->AddToInputDataCollection(Form("LF:$1/%s/Stage_%s.xml,nodownload",fMergeDirName.Data(),stageName.Data()), "Collection of files to be merged for current stage");
1966 fMergingJDL->SetOutputDirectory(Form("$1/%s/Stage_%s/#alien_counter_03i#",fMergeDirName.Data(),stageName.Data()), "Output directory");
1967 } else {
1968 fMergingJDL->AddToInputDataCollection(Form("LF:$1/Stage_%s.xml,nodownload",stageName.Data()), "Collection of files to be merged for current stage");
1969 fMergingJDL->SetOutputDirectory(Form("$1/Stage_%s/#alien_counter_03i#",stageName.Data()), "Output directory");
1970 }
1971 if (fProductionMode) {
1972 TIter next(fInputFiles);
1973 while ((os=next())) {
1974 fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetName()), "Input xml collections");
1975 }
1976 if (!fOutputToRunNo)
1977 fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_04i#", fGridOutputDir.Data()));
1978 else
1979 fGridJDL->SetOutputDirectory(fGridOutputDir);
1980 } else {
1981 if (!fRunNumbers.Length() && !fRunRange[0]) {
1982 // One jdl with no parameters in case input data is specified by name.
1983 TIter next(fInputFiles);
1984 while ((os=next()))
1985 fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetName()), "Input xml collections");
1986 if (!fOutputSingle.IsNull())
1987 fGridJDL->SetOutputDirectory(Form("#alienfulldir#/../%s",fOutputSingle.Data()), "Output directory");
1988 else {
1989 fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
1990// fMergingJDL->SetOutputDirectory(fGridOutputDir);
1991 }
1992 } else {
1993 // One jdl to be submitted with 2 input parameters: data collection name and output dir prefix
1994 fGridJDL->AddToInputDataCollection(Form("LF:%s/$1,nodownload", workdir.Data()), "Input xml collections");
1995 if (!fOutputSingle.IsNull()) {
1996 if (!fOutputToRunNo) fGridJDL->SetOutputDirectory(Form("#alienfulldir#/%s",fOutputSingle.Data()), "Output directory");
1997 else fGridJDL->SetOutputDirectory(Form("%s/$2",fGridOutputDir.Data()), "Output directory");
1998 } else {
1999 fGridJDL->SetOutputDirectory(Form("%s/$2/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
2000 }
2001 }
2002 }
2003
2004 // Generate the JDL as a string
2005 TString sjdl = fGridJDL->Generate();
2006 TString sjdl1 = fMergingJDL->Generate();
2007 // Final merge jdl
2008 if (!fMergeDirName.IsNull()) {
2009 fMergingJDL->SetOutputDirectory(Form("$1/%s",fMergeDirName.Data()), "Output directory");
2010 fMergingJDL->AddToInputSandbox(Form("LF:$1/%s/Stage_%s.xml",fMergeDirName.Data(),stageName.Data()));
2011 } else {
2012 fMergingJDL->SetOutputDirectory("$1", "Output directory");
2013 fMergingJDL->AddToInputSandbox(Form("LF:$1/Stage_%s.xml",stageName.Data()));
2014 }
2015 TString sjdl2 = fMergingJDL->Generate();
2016 Int_t index, index1;
2017 sjdl.ReplaceAll("\",\"", "\",\n \"");
2018 sjdl.ReplaceAll("(member", "\n (member");
2019 sjdl.ReplaceAll("\",\"VO_", "\",\n \"VO_");
2020 sjdl.ReplaceAll("{", "{\n ");
2021 sjdl.ReplaceAll("};", "\n};");
2022 sjdl.ReplaceAll("{\n \n", "{\n");
2023 sjdl.ReplaceAll("\n\n", "\n");
2024 sjdl.ReplaceAll("OutputDirectory", "OutputDir");
2025 sjdl1.ReplaceAll("\",\"", "\",\n \"");
2026 sjdl1.ReplaceAll("(member", "\n (member");
2027 sjdl1.ReplaceAll("\",\"VO_", "\",\n \"VO_");
2028 sjdl1.ReplaceAll("{", "{\n ");
2029 sjdl1.ReplaceAll("};", "\n};");
2030 sjdl1.ReplaceAll("{\n \n", "{\n");
2031 sjdl1.ReplaceAll("\n\n", "\n");
2032 sjdl1.ReplaceAll("OutputDirectory", "OutputDir");
2033 sjdl2.ReplaceAll("\",\"", "\",\n \"");
2034 sjdl2.ReplaceAll("(member", "\n (member");
2035 sjdl2.ReplaceAll("\",\"VO_", "\",\n \"VO_");
2036 sjdl2.ReplaceAll("{", "{\n ");
2037 sjdl2.ReplaceAll("};", "\n};");
2038 sjdl2.ReplaceAll("{\n \n", "{\n");
2039 sjdl2.ReplaceAll("\n\n", "\n");
2040 sjdl2.ReplaceAll("OutputDirectory", "OutputDir");
2041 sjdl += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
2042 sjdl.Prepend(Form("Jobtag = {\n \"comment:%s\"\n};\n", fJobTag.Data()));
2043 index = sjdl.Index("JDLVariables");
2044 if (index >= 0) sjdl.Insert(index, "\n# JDL variables\n");
2045 sjdl += "Workdirectorysize = {\"5000MB\"};";
2046 sjdl1 += "Workdirectorysize = {\"5000MB\"};";
2047 sjdl1 += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
2048 index = fJobTag.Index(":");
2049 if (index < 0) index = fJobTag.Length();
2050 TString jobTag = fJobTag;
2051 if (fProductionMode) jobTag.Insert(index,"_Stage$4");
2052 sjdl1.Prepend(Form("Jobtag = {\n \"comment:%s_Merging\"\n};\n", jobTag.Data()));
2053 if (fProductionMode) {
2054 sjdl1.Prepend("# Generated merging jdl (production mode) \
2055 \n# $1 = full alien path to output directory to be merged \
2056 \n# $2 = train number \
2057 \n# $3 = production (like LHC10b) \
2058 \n# $4 = merging stage \
2059 \n# Stage_<n>.xml made via: find <OutputDir> *Stage<n-1>/*root_archive.zip\n");
2060 sjdl2.Prepend(Form("Jobtag = {\n \"comment:%s_FinalMerging\"\n};\n", jobTag.Data()));
2061 sjdl2.Prepend("# Generated merging jdl \
2062 \n# $1 = full alien path to output directory to be merged \
2063 \n# $2 = train number \
2064 \n# $3 = production (like LHC10b) \
2065 \n# $4 = merging stage \
2066 \n# Stage_<n>.xml made via: find <OutputDir> *Stage<n-1>/*root_archive.zip\n");
2067 } else {
2068 sjdl1.Prepend("# Generated merging jdl \
2069 \n# $1 = full alien path to output directory to be merged \
2070 \n# $2 = merging stage \
2071 \n# xml made via: find <OutputDir> *Stage<n-1>/*root_archive.zip\n");
2072 sjdl2.Prepend(Form("Jobtag = {\n \"comment:%s_FinalMerging\"\n};\n", jobTag.Data()));
2073 sjdl2.Prepend("# Generated merging jdl \
2074 \n# $1 = full alien path to output directory to be merged \
2075 \n# $2 = merging stage \
2076 \n# xml made via: find <OutputDir> *Stage<n-1>/*root_archive.zip\n");
2077 }
2078 index = sjdl1.Index("JDLVariables");
2079 if (index >= 0) sjdl1.Insert(index, "\n# JDL variables\n");
2080 index = sjdl2.Index("JDLVariables");
2081 if (index >= 0) sjdl2.Insert(index, "\n# JDL variables\n");
2082 sjdl1 += "Workdirectorysize = {\"5000MB\"};";
2083 sjdl2 += "Workdirectorysize = {\"5000MB\"};";
2084 index = sjdl2.Index("Split =");
2085 if (index>=0) {
2086 index1 = sjdl2.Index("\n", index);
2087 sjdl2.Remove(index, index1-index+1);
2088 }
2089 index = sjdl2.Index("SplitMaxInputFileNumber");
2090 if (index>=0) {
2091 index1 = sjdl2.Index("\n", index);
2092 sjdl2.Remove(index, index1-index+1);
2093 }
2094 index = sjdl2.Index("InputDataCollection");
2095 if (index>=0) {
2096 index1 = sjdl2.Index(";", index);
2097 sjdl2.Remove(index, index1-index+1);
2098 }
2099 index = sjdl2.Index("InputDataListFormat");
2100 if (index>=0) {
2101 index1 = sjdl2.Index("\n", index);
2102 sjdl2.Remove(index, index1-index+1);
2103 }
2104 index = sjdl2.Index("InputDataList");
2105 if (index>=0) {
2106 index1 = sjdl2.Index("\n", index);
2107 sjdl2.Remove(index, index1-index+1);
2108 }
2109 sjdl2.ReplaceAll("wn.xml", Form("Stage_%s.xml",stageName.Data()));
2110 // Write jdl to file
2111 ofstream out;
2112 out.open(fJDLName.Data(), ios::out);
2113 if (out.bad()) {
2114 Error("WriteJDL", "Bad file name: %s", fJDLName.Data());
2115 return kFALSE;
2116 }
2117 out << sjdl << endl;
2118 out.close();
2119 TString mergeJDLName = fExecutable;
2120 mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
2121 if (fMergeViaJDL) {
2122 ofstream out1;
2123 out1.open(mergeJDLName.Data(), ios::out);
2124 if (out1.bad()) {
2125 Error("WriteJDL", "Bad file name: %s", mergeJDLName.Data());
2126 return kFALSE;
2127 }
2128 out1 << sjdl1 << endl;
2129 out1.close();
2130 ofstream out2;
2131 TString finalJDL = mergeJDLName;
2132 finalJDL.ReplaceAll(".jdl", "_final.jdl");
2133 out2.open(finalJDL.Data(), ios::out);
2134 if (out2.bad()) {
2135 Error("WriteJDL", "Bad file name: %s", finalJDL.Data());
2136 return kFALSE;
2137 }
2138 out2 << sjdl2 << endl;
2139 out2.close();
2140 }
2141
2142 // Copy jdl to grid workspace
2143 if (!copy) {
2144 Info("WriteJDL", "\n##### You may want to review jdl:%s and analysis macro:%s before running in <submit> mode", fJDLName.Data(), fAnalysisMacro.Data());
2145 } else {
2146 TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
2147 TString locjdl1 = Form("%s/%s", fGridOutputDir.Data(),mergeJDLName.Data());
2148 TString finalJDL = mergeJDLName;
2149 finalJDL.ReplaceAll(".jdl", "_final.jdl");
2150 TString locjdl2 = Form("%s/%s", fGridOutputDir.Data(),finalJDL.Data());
2151 if (fProductionMode) {
2152 locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
2153 locjdl1 = Form("%s/%s", workdir.Data(),mergeJDLName.Data());
2154 locjdl2 = Form("%s/%s", workdir.Data(),finalJDL.Data());
2155 }
2156 if (FileExists(locjdl)) gGrid->Rm(locjdl);
2157 if (FileExists(locjdl1)) gGrid->Rm(locjdl1);
2158 if (FileExists(locjdl2)) gGrid->Rm(locjdl2);
2159 Info("WriteJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
2160// TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
2161 if (!copyLocal2Alien("WriteJDL",fJDLName.Data(),locjdl.Data()))
2162 Fatal("","Terminating");
2163 if (fMergeViaJDL) {
2164 Info("WriteJDL", "\n##### Copying merging JDL files <%s> to your AliEn output directory", mergeJDLName.Data());
2165// TFile::Cp(Form("file:%s",mergeJDLName.Data()), Form("alien://%s", locjdl1.Data()));
2166// TFile::Cp(Form("file:%s",finalJDL.Data()), Form("alien://%s", locjdl2.Data()));
2167 if (!copyLocal2Alien("WriteJDL",mergeJDLName.Data(),locjdl1.Data()))
2168 Fatal("","Terminating");
2169 if (!copyLocal2Alien("WriteJDL",finalJDL.Data(),locjdl2.Data()))
2170 Fatal("","Terminating");
2171 }
2172 }
2173 return kTRUE;
2174}
2175
2176//______________________________________________________________________________
2177Bool_t AliAnalysisAlien::FileExists(const char *lfn)
2178{
2179// Returns true if file exists.
2180 if (!gGrid) return kFALSE;
2181 TString slfn = lfn;
2182 slfn.ReplaceAll("alien://","");
2183 TGridResult *res = gGrid->Ls(slfn);
2184 if (!res) return kFALSE;
2185 TMap *map = dynamic_cast<TMap*>(res->At(0));
2186 if (!map) {
2187 delete res;
2188 return kFALSE;
2189 }
2190 TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("name"));
2191 if (!objs || !objs->GetString().Length()) {
2192 delete res;
2193 return kFALSE;
2194 }
2195 delete res;
2196 return kTRUE;
2197}
2198
2199//______________________________________________________________________________
2200Bool_t AliAnalysisAlien::DirectoryExists(const char *dirname)
2201{
2202// Returns true if directory exists. Can be also a path.
2203 if (!gGrid) return kFALSE;
2204 // Check if dirname is a path
2205 TString dirstripped = dirname;
2206 dirstripped = dirstripped.Strip();
2207 dirstripped = dirstripped.Strip(TString::kTrailing, '/');
2208 TString dir = gSystem->BaseName(dirstripped);
2209 dir += "/";
2210 TString path = gSystem->DirName(dirstripped);
2211 TGridResult *res = gGrid->Ls(path, "-F");
2212 if (!res) return kFALSE;
2213 TIter next(res);
2214 TMap *map;
2215 TObject *obj;
2216 while ((map=dynamic_cast<TMap*>(next()))) {
2217 obj = map->GetValue("name");
2218 if (!obj) break;
2219 if (dir == obj->GetName()) {
2220 delete res;
2221 return kTRUE;
2222 }
2223 }
2224 delete res;
2225 return kFALSE;
2226}
2227
2228//______________________________________________________________________________
2229void AliAnalysisAlien::CheckDataType(const char *lfn, Bool_t &isCollection, Bool_t &isXml, Bool_t &useTags)
2230{
2231// Check input data type.
2232 isCollection = kFALSE;
2233 isXml = kFALSE;
2234 useTags = kFALSE;
2235 if (!gGrid) {
2236 Error("CheckDataType", "No connection to grid");
2237 return;
2238 }
2239 isCollection = IsCollection(lfn);
2240 TString msg = "\n##### file: ";
2241 msg += lfn;
2242 if (isCollection) {
2243 msg += " type: raw_collection;";
2244 // special treatment for collections
2245 isXml = kFALSE;
2246 // check for tag files in the collection
2247 TGridResult *res = gGrid->Command(Form("listFilesFromCollection -z -v %s",lfn), kFALSE);
2248 if (!res) {
2249 msg += " using_tags: No (unknown)";
2250 Info("CheckDataType", "%s", msg.Data());
2251 return;
2252 }
2253 const char* typeStr = res->GetKey(0, "origLFN");
2254 if (!typeStr || !strlen(typeStr)) {
2255 msg += " using_tags: No (unknown)";
2256 Info("CheckDataType", "%s", msg.Data());
2257 return;
2258 }
2259 TString file = typeStr;
2260 useTags = file.Contains(".tag");
2261 if (useTags) msg += " using_tags: Yes";
2262 else msg += " using_tags: No";
2263 Info("CheckDataType", "%s", msg.Data());
2264 return;
2265 }
2266 TString slfn(lfn);
2267 slfn.ToLower();
2268 isXml = slfn.Contains(".xml");
2269 if (isXml) {
2270 // Open xml collection and check if there are tag files inside
2271 msg += " type: xml_collection;";
2272 TGridCollection *coll = (TGridCollection*)gROOT->ProcessLine(Form("TAlienCollection::Open(\"alien://%s\",1);",lfn));
2273 if (!coll) {
2274 msg += " using_tags: No (unknown)";
2275 Info("CheckDataType", "%s", msg.Data());
2276 return;
2277 }
2278 TMap *map = coll->Next();
2279 if (!map) {
2280 msg += " using_tags: No (unknown)";
2281 Info("CheckDataType", "%s", msg.Data());
2282 return;
2283 }
2284 map = (TMap*)map->GetValue("");
2285 TString file;
2286 if (map && map->GetValue("name")) file = map->GetValue("name")->GetName();
2287 useTags = file.Contains(".tag");
2288 delete coll;
2289 if (useTags) msg += " using_tags: Yes";
2290 else msg += " using_tags: No";
2291 Info("CheckDataType", "%s", msg.Data());
2292 return;
2293 }
2294 useTags = slfn.Contains(".tag");
2295 if (slfn.Contains(".root")) msg += " type: root file;";
2296 else msg += " type: unknown file;";
2297 if (useTags) msg += " using_tags: Yes";
2298 else msg += " using_tags: No";
2299 Info("CheckDataType", "%s", msg.Data());
2300}
2301
2302//______________________________________________________________________________
2303void AliAnalysisAlien::EnablePackage(const char *package)
2304{
2305// Enables a par file supposed to exist in the current directory.
2306 TString pkg(package);
2307 pkg.ReplaceAll(".par", "");
2308 pkg += ".par";
2309 if (gSystem->AccessPathName(pkg)) {
2310 Fatal("EnablePackage", "Package %s not found", pkg.Data());
2311 return;
2312 }
2313 if (!TObject::TestBit(AliAnalysisGrid::kUsePars))
2314 Info("EnablePackage", "AliEn plugin will use .par packages");
2315 TObject::SetBit(AliAnalysisGrid::kUsePars, kTRUE);
2316 if (!fPackages) {
2317 fPackages = new TObjArray();
2318 fPackages->SetOwner();
2319 }
2320 fPackages->Add(new TObjString(pkg));
2321}
2322
2323//______________________________________________________________________________
2324TChain *AliAnalysisAlien::GetChainForTestMode(const char *treeName) const
2325{
2326// Make a tree from files having the location specified in fFileForTestMode.
2327// Inspired from JF's CreateESDChain.
2328 if (fFileForTestMode.IsNull()) {
2329 Error("GetChainForTestMode", "For proof test mode please use SetFileForTestMode() pointing to a file that contains data file locations.");
2330 return NULL;
2331 }
2332 if (gSystem->AccessPathName(fFileForTestMode)) {
2333 Error("GetChainForTestMode", "File not found: %s", fFileForTestMode.Data());
2334 return NULL;
2335 }
2336 // Open the file
2337 ifstream in;
2338 in.open(fFileForTestMode);
2339 Int_t count = 0;
2340 // Read the input list of files and add them to the chain
2341 TString line;
2342 TString streeName(treeName);
2343 if (IsUseMCchain()) streeName = "TE";
2344 TChain *chain = new TChain(streeName);
2345 TList *friends = new TList();
2346 TChain *cfriend = 0;
2347 if (!fFriendChainName.IsNull()) {
2348 TObjArray *list = fFriendChainName.Tokenize(" ");
2349 TIter next(list);
2350 TObjString *str;
2351 while((str=(TObjString*)next())) {
2352 cfriend = new TChain(streeName, str->GetName());
2353 friends->Add(cfriend);
2354 chain->AddFriend(cfriend);
2355 }
2356 delete list;
2357 }
2358 TString bpath;
2359 TIter nextfriend(friends);
2360 while (in.good())
2361 {
2362 in >> line;
2363 if (line.IsNull() || line.BeginsWith("#")) continue;
2364 if (count++ == fNtestFiles) break;
2365 TString esdFile(line);
2366 TFile *file = TFile::Open(esdFile);
2367 if (file && !file->IsZombie()) {
2368 chain->Add(esdFile);
2369 file->Close();
2370 if (!fFriendChainName.IsNull()) {
2371 if (esdFile.Index("#") > -1)
2372 esdFile.Remove(esdFile.Index("#"));
2373 bpath = gSystem->DirName(esdFile);
2374 bpath += "/";
2375 TString fileFriend;
2376 nextfriend.Reset();
2377 while ((cfriend=(TChain*)nextfriend())) {
2378 fileFriend = bpath;
2379 fileFriend += cfriend->GetTitle();
2380 file = TFile::Open(fileFriend);
2381 if (file && !file->IsZombie()) {
2382 file->Close();
2383 cfriend->Add(fileFriend);
2384 } else {
2385 Fatal("GetChainForTestMode", "Cannot open friend file: %s", fileFriend.Data());
2386 return 0;
2387 }
2388 }
2389 }
2390 } else {
2391 Error("GetChainforTestMode", "Skipping un-openable file: %s", esdFile.Data());
2392 }
2393 }
2394 in.close();
2395 if (!chain->GetListOfFiles()->GetEntries()) {
2396 Error("GetChainForTestMode", "No file from %s could be opened", fFileForTestMode.Data());
2397 delete chain;
2398 friends->Delete();
2399 delete friends;
2400 return NULL;
2401 }
2402 return chain;
2403}
2404
2405//______________________________________________________________________________
2406const char *AliAnalysisAlien::GetJobStatus(Int_t jobidstart, Int_t lastid, Int_t &nrunning, Int_t &nwaiting, Int_t &nerror, Int_t &ndone)
2407{
2408// Get job status for all jobs with jobid>jobidstart.
2409 static char mstatus[20];
2410 mstatus[0] = '\0';
2411 nrunning = 0;
2412 nwaiting = 0;
2413 nerror = 0;
2414 ndone = 0;
2415 TGridJobStatusList *list = gGrid->Ps("");
2416 if (!list) return mstatus;
2417 Int_t nentries = list->GetSize();
2418 TGridJobStatus *status;
2419 Int_t pid;
2420 for (Int_t ijob=0; ijob<nentries; ijob++) {
2421 status = (TGridJobStatus *)list->At(ijob);
2422 pid = gROOT->ProcessLine(Form("atoi(((TAlienJobStatus*)%p)->GetKey(\"queueId\"));", status));
2423 if (pid<jobidstart) continue;
2424 if (pid == lastid) {
2425 gROOT->ProcessLine(Form("sprintf((char*)%p,((TAlienJobStatus*)%p)->GetKey(\"status\"));",mstatus, status));
2426 }
2427 switch (status->GetStatus()) {
2428 case TGridJobStatus::kWAITING:
2429 nwaiting++; break;
2430 case TGridJobStatus::kRUNNING:
2431 nrunning++; break;
2432 case TGridJobStatus::kABORTED:
2433 case TGridJobStatus::kFAIL:
2434 case TGridJobStatus::kUNKNOWN:
2435 nerror++; break;
2436 case TGridJobStatus::kDONE:
2437 ndone++;
2438 }
2439 }
2440 list->Delete();
2441 delete list;
2442 return mstatus;
2443}
2444
2445//______________________________________________________________________________
2446Bool_t AliAnalysisAlien::IsCollection(const char *lfn) const
2447{
2448// Returns true if file is a collection. Functionality duplicated from
2449// TAlien::Type() because we don't want to directly depend on TAlien.
2450 if (!gGrid) {
2451 Error("IsCollection", "No connection to grid");
2452 return kFALSE;
2453 }
2454 TGridResult *res = gGrid->Command(Form("type -z %s",lfn),kFALSE);
2455 if (!res) return kFALSE;
2456 const char* typeStr = res->GetKey(0, "type");
2457 if (!typeStr || !strlen(typeStr)) return kFALSE;
2458 if (!strcmp(typeStr, "collection")) return kTRUE;
2459 delete res;
2460 return kFALSE;
2461}
2462
2463//______________________________________________________________________________
2464Bool_t AliAnalysisAlien::IsSingleOutput() const
2465{
2466// Check if single-ouput option is on.
2467 return (!fOutputSingle.IsNull());
2468}
2469
2470//______________________________________________________________________________
2471Long64_t AliAnalysisAlien::RunMacroAndExtractLibs(const char* macro, const char *args, TString &libs)
2472{
2473// Tries to run the specified macro and return the libraries that it loads.
2474 TString expname;
2475 if (strlen(macro)) expname = gSystem->ExpandPathName(macro);
2476 if (expname.IsNull() || gSystem->AccessPathName(expname)) {
2477 ::Error("RunMacroAndExtractLibs","Cannot find macro %s in current directory", macro);
2478 return -1;
2479 }
2480 TString oldlibs = gSystem->GetLibraries();
2481 TMacro m(expname);
2482 Int_t error = 0;
2483 Long64_t retval = m.Exec(args, &error);
2484 if (error != TInterpreter::kNoError)
2485 {
2486 ::Error("RunMacroAndExtractLibs", "Macro interpretation %s failed", macro);
2487 return -1;
2488 }
2489 libs = gSystem->GetLibraries();
2490 libs.ReplaceAll(oldlibs, "");
2491 libs.Strip(TString::kLeading);
2492 TObjArray *libTokens = libs.Tokenize(" ");
2493 libs = "";
2494 for (Int_t i=0; i<libTokens->GetEntries(); i++) {
2495 if (!libs.IsNull()) libs += " ";
2496 libs += gSystem->BaseName(libTokens->At(i)->GetName());
2497 }
2498 delete libTokens;
2499 return retval;
2500}
2501
2502//______________________________________________________________________________
2503void AliAnalysisAlien::Print(Option_t *) const
2504{
2505// Print current plugin settings.
2506 printf("### AliEn analysis plugin current settings ###\n");
2507 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
2508 if (mgr && mgr->IsProofMode()) {
2509 TString proofType = "= PLUGIN IN PROOF MODE ON CLUSTER:_________________";
2510 if (TestBit(AliAnalysisGrid::kTest))
2511 proofType = "= PLUGIN IN PROOF LITE MODE ON CLUSTER:____________";
2512 printf("%s %s\n", proofType.Data(), fProofCluster.Data());
2513 if (!fProofDataSet.IsNull())
2514 printf("= Requested data set:___________________________ %s\n", fProofDataSet.Data());
2515 if (fProofReset==1)
2516 printf("= Soft reset signal will be send to master______ CHANGE BEHAVIOR AFTER COMPLETION\n");
2517 if (fProofReset>1)
2518 printf("= Hard reset signal will be send to master______ CHANGE BEHAVIOR AFTER COMPLETION\n");
2519 if (!fROOTVersion.IsNull())
2520 printf("= ROOT version requested________________________ %s\n", fROOTVersion.Data());
2521 else
2522 printf("= ROOT version requested________________________ default\n");
2523 printf("= AliRoot version requested_____________________ %s\n", fAliROOTVersion.Data());
2524 if (!fAliRootMode.IsNull())
2525 printf("= Requested AliRoot mode________________________ %s\n", fAliRootMode.Data());
2526 if (fNproofWorkers)
2527 printf("= Number of PROOF workers limited to____________ %d\n", fNproofWorkers);
2528 if (fNproofWorkersPerSlave)
2529 printf("= Maximum number of workers per slave___________ %d\n", fNproofWorkersPerSlave);
2530 if (TestSpecialBit(kClearPackages))
2531 printf("= ClearPackages requested...\n");
2532 if (fIncludePath.Data())
2533 printf("= Include path for runtime task compilation: ___ %s\n", fIncludePath.Data());
2534 printf("= Additional libs to be loaded or souces to be compiled runtime: <%s>\n",fAdditionalLibs.Data());
2535 if (fPackages && fPackages->GetEntries()) {
2536 TIter next(fPackages);
2537 TObject *obj;
2538 TString list;
2539 while ((obj=next())) list += obj->GetName();
2540 printf("= Par files to be used: ________________________ %s\n", list.Data());
2541 }
2542 if (TestSpecialBit(kProofConnectGrid))
2543 printf("= Requested PROOF connection to grid\n");
2544 return;
2545 }
2546 printf("= OverwriteMode:________________________________ %d\n", fOverwriteMode);
2547 if (fOverwriteMode) {
2548 printf("***** NOTE: Overwrite mode will overwrite the input generated datasets and partial results from previous analysis. \
2549 \n***** To disable, use: plugin->SetOverwriteMode(kFALSE);\n");
2550 }
2551 printf("= Copy files to grid: __________________________ %s\n", (IsUseCopy())?"YES":"NO");
2552 printf("= Check if files can be copied to grid: ________ %s\n", (IsCheckCopy())?"YES":"NO:Print");
2553 printf("= Production mode:______________________________ %d\n", fProductionMode);
2554 printf("= Version of API requested: ____________________ %s\n", fAPIVersion.Data());
2555 printf("= Version of ROOT requested: ___________________ %s\n", fROOTVersion.Data());
2556 printf("= Version of AliRoot requested: ________________ %s\n", fAliROOTVersion.Data());
2557 if (fUser.Length())
2558 printf("= User running the plugin: _____________________ %s\n", fUser.Data());
2559 printf("= Grid workdir relative to user $HOME: _________ %s\n", fGridWorkingDir.Data());
2560 printf("= Grid output directory relative to workdir: ___ %s\n", fGridOutputDir.Data());
2561 TString basedatadir = fGridDataDir;
2562 TString pattern = fDataPattern;
2563 pattern.Strip();
2564 Int_t ind = pattern.Index(" ");
2565 if (ind>=0) {
2566 basedatadir += "/%run%/";
2567 basedatadir += pattern(0, ind);
2568 pattern = pattern(ind+1, pattern.Length());
2569 }
2570 printf("= Data base directory path requested: __________ %s\n", basedatadir.Data());
2571 printf("= Data search pattern: _________________________ %s\n", pattern.Data());
2572 printf("= Input data format: ___________________________ %s\n", fInputFormat.Data());
2573 if (fRunNumbers.Length())
2574 printf("= Run numbers to be processed: _________________ %s\n", fRunNumbers.Data());
2575 if (fRunRange[0])
2576 printf("= Run range to be processed: ___________________ %d-%d\n", fRunRange[0], fRunRange[1]);
2577 if (!fRunRange[0] && !fRunNumbers.Length()) {
2578 TIter next(fInputFiles);
2579 TObject *obj;
2580 TString list;
2581 while ((obj=next())) list += obj->GetName();
2582 printf("= Input files to be processed: _________________ %s\n", list.Data());
2583 }
2584 if (TestBit(AliAnalysisGrid::kTest))
2585 printf("= Number of input files used in test mode: _____ %d\n", fNtestFiles);
2586 printf("= List of output files to be registered: _______ %s\n", fOutputFiles.Data());
2587 printf("= List of outputs going to be archived: ________ %s\n", fOutputArchive.Data());
2588 printf("= List of outputs that should not be merged: ___ %s\n", fMergeExcludes.Data());
2589 printf("= List of outputs that should not be registered: %s\n", fRegisterExcludes.Data());
2590 printf("= List of outputs produced during Terminate: ___ %s\n", fTerminateFiles.Data());
2591 printf("=====================================================================\n");
2592 printf("= Job price: ___________________________________ %d\n", fPrice);
2593 printf("= Time to live (TTL): __________________________ %d\n", fTTL);
2594 printf("= Max files per subjob: ________________________ %d\n", fSplitMaxInputFileNumber);
2595 if (fMaxInitFailed>0)
2596 printf("= Max number of subjob fails to kill: __________ %d\n", fMaxInitFailed);
2597 if (fMasterResubmitThreshold>0)
2598 printf("= Resubmit master job if failed subjobs >_______ %d\n", fMasterResubmitThreshold);
2599 printf("= Number of replicas for the output files_______ %d\n", fNreplicas);
2600 if (fNrunsPerMaster>0)
2601 printf("= Number of runs per master job: _______________ %d\n", fNrunsPerMaster);
2602 printf("= Number of files in one chunk to be merged: ___ %d\n", fMaxMergeFiles);
2603 printf("= Name of the generated execution script: ______ %s\n", fExecutable.Data());
2604 printf("= Executable command: __________________________ %s\n", fExecutableCommand.Data());
2605 if (fArguments.Length())
2606 printf("= Arguments for the execution script: __________ %s\n",fArguments.Data());
2607 if (fExecutableArgs.Length())
2608 printf("= Arguments after macro name in executable______ %s\n",fExecutableArgs.Data());
2609 printf("= Name of the generated analysis macro: ________ %s\n",fAnalysisMacro.Data());
2610 printf("= User analysis files to be deployed: __________ %s\n",fAnalysisSource.Data());
2611 printf("= Additional libs to be loaded or souces to be compiled runtime: <%s>\n",fAdditionalLibs.Data());
2612 printf("= Master jobs split mode: ______________________ %s\n",fSplitMode.Data());
2613 if (fDatasetName)
2614 printf("= Custom name for the dataset to be created: ___ %s\n", fDatasetName.Data());
2615 printf("= Name of the generated JDL: ___________________ %s\n", fJDLName.Data());
2616 if (fIncludePath.Data())
2617 printf("= Include path for runtime task compilation: ___ %s\n", fIncludePath.Data());
2618 if (fCloseSE.Length())
2619 printf("= Force job outputs to storage element: ________ %s\n", fCloseSE.Data());
2620 if (fFriendChainName.Length())
2621 printf("= Open friend chain file on worker: ____________ %s\n", fFriendChainName.Data());
2622 if (fPackages && fPackages->GetEntries()) {
2623 TIter next(fPackages);
2624 TObject *obj;
2625 TString list;
2626 while ((obj=next())) list += obj->GetName();
2627 printf("= Par files to be used: ________________________ %s\n", list.Data());
2628 }
2629}
2630
2631//______________________________________________________________________________
2632void AliAnalysisAlien::SetDefaults()
2633{
2634// Set default values for everything. What cannot be filled will be left empty.
2635 if (fGridJDL) delete fGridJDL;
2636 fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
2637 fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
2638 fPrice = 1;
2639 fTTL = 30000;
2640 fSplitMaxInputFileNumber = 100;
2641 fMaxInitFailed = 0;
2642 fMasterResubmitThreshold = 0;
2643 fNtestFiles = 10;
2644 fNreplicas = 2;
2645 fRunRange[0] = 0;
2646 fRunRange[1] = 0;
2647 fRunPrefix = "%d";
2648 fNrunsPerMaster = 1;
2649 fMaxMergeFiles = 100;
2650 fRunNumbers = "";
2651 fExecutable = "analysis.sh";
2652 fExecutableCommand = "root -b -q -x";
2653 fArguments = "";
2654 fExecutableArgs = "";
2655 fAnalysisMacro = "myAnalysis.C";
2656 fAnalysisSource = "";
2657 fAdditionalLibs = "";
2658 fSplitMode = "se";
2659 fAPIVersion = "";
2660 fROOTVersion = "";
2661 fAliROOTVersion = "";
2662 fUser = ""; // Your alien user name
2663 fGridWorkingDir = "";
2664 fGridDataDir = ""; // Can be like: /alice/sim/PDC_08a/LHC08c9/
2665 fDataPattern = "*AliESDs.root"; // Can be like: *AliESDs.root, */pass1/*AliESDs.root, ...
2666 fFriendChainName = "";
2667 fGridOutputDir = "output";
2668 fOutputArchive = "log_archive.zip:std*@disk=1 root_archive.zip:*.root@disk=2";
2669 fOutputFiles = ""; // Like "AliAODs.root histos.root"
2670 fInputFormat = "xml-single";
2671 fJDLName = "analysis.jdl";
2672 fJobTag = "Automatically generated analysis JDL";
2673 fMergeExcludes = "";
2674 fMergeViaJDL = 0;
2675 SetUseCopy(kTRUE);
2676 SetCheckCopy(kTRUE);
2677 SetDefaultOutputs(kTRUE);
2678 fOverwriteMode = 1;
2679}
2680
2681//______________________________________________________________________________
2682void AliAnalysisAlien::SetFriendChainName(const char *name, const char *libnames)
2683{
2684 // Set file name for the chain of friends and optionally additional libs to be loaded.
2685 // Libs should be separated by blancs.
2686 fFriendChainName = name;
2687 fFriendChainName.ReplaceAll(",", " ");
2688 fFriendChainName.Strip();
2689 fFriendChainName.ReplaceAll(" ", " ");
2690
2691 fFriendLibs = libnames;
2692 if (fFriendLibs.Length()) {
2693 if(!fFriendLibs.Contains(".so"))
2694 Fatal("SetFriendChainName()", "You should provide explicit library names (with extension)");
2695 fFriendLibs.ReplaceAll(",", " ");
2696 fFriendLibs.Strip();
2697 fFriendLibs.ReplaceAll(" ", " ");
2698 }
2699}
2700
2701//______________________________________________________________________________
2702void AliAnalysisAlien::SetRootVersionForProof(const char *version)
2703{
2704// Obsolete method. Use SetROOTVersion instead
2705 Warning("SetRootVersionForProof", "Obsolete. Use SetROOTVersion instead");
2706 if (fROOTVersion.IsNull()) SetROOTVersion(version);
2707 else Error("SetRootVersionForProof", "ROOT version already set to %s", fROOTVersion.Data());
2708}
2709
2710//______________________________________________________________________________
2711Bool_t AliAnalysisAlien::CheckMergedFiles(const char *filename, const char *aliendir, Int_t nperchunk, const char *jdl)
2712{
2713// Checks current merge stage, makes xml for the next stage, counts number of files, submits next stage.
2714 // First check if the result is already in the output directory.
2715 if (FileExists(Form("%s/%s",aliendir,filename))) {
2716 printf("Final merged results found. Not merging again.\n");
2717 return kFALSE;
2718 }
2719 // Now check the last stage done.
2720 Int_t stage = 0;
2721 while (1) {
2722 if (!FileExists(Form("%s/Stage_%d.xml",aliendir, stage+1))) break;
2723 stage++;
2724 }
2725 // Next stage of merging
2726 stage++;
2727 TString pattern = "*root_archive.zip";
2728 if (stage>1) pattern = Form("Stage_%d/*root_archive.zip", stage-1);
2729 TGridResult *res = gGrid->Command(Form("find -x Stage_%d %s %s", stage, aliendir, pattern.Data()));
2730 if (res) delete res;
2731 // Write standard output to file
2732 gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", Form("Stage_%d.xml",stage)));
2733 // Count the number of files inside
2734 ifstream ifile;
2735 ifile.open(Form("Stage_%d.xml",stage));
2736 if (!ifile.good()) {
2737 ::Error("CheckMergedFiles", "Could not redirect result of the find command to file %s", Form("Stage_%d.xml",stage));
2738 return kFALSE;
2739 }
2740 TString line;
2741 Int_t nfiles = 0;
2742 while (!ifile.eof()) {
2743 ifile >> line;
2744 if (line.Contains("/event")) nfiles++;
2745 }
2746 ifile.close();
2747 if (!nfiles) {
2748 ::Error("CheckMergedFiles", "Cannot start Stage_%d merging since Stage_%d did not produced yet output", stage, stage-1);
2749 return kFALSE;
2750 } else {
2751 printf("=== Stage_%d produced %d files\n", stage-1, nfiles);
2752 }
2753 // Copy the file in the output directory
2754 printf("===> Copying collection %s in the output directory %s\n", Form("Stage_%d.xml",stage), aliendir);
2755// TFile::Cp(Form("Stage_%d.xml",stage), Form("alien://%s/Stage_%d.xml",aliendir,stage));
2756 if (!copyLocal2Alien("CheckMergedFiles", Form("Stage_%d.xml",stage),
2757 Form("%s/Stage_%d.xml",aliendir,stage))) Fatal("","Terminating");
2758 // Check if this is the last stage to be done.
2759 Bool_t laststage = (nfiles<nperchunk);
2760 if (fMaxMergeStages && stage>=fMaxMergeStages) laststage = kTRUE;
2761 Int_t jobId = 0;
2762 if (laststage) {
2763 printf("### Submiting final merging stage %d\n", stage);
2764 TString finalJDL = jdl;
2765 finalJDL.ReplaceAll(".jdl", "_final.jdl");
2766 TString query = Form("submit %s %s %d", finalJDL.Data(), aliendir, stage);
2767 jobId = SubmitSingleJob(query);
2768 } else {
2769 printf("### Submiting merging stage %d\n", stage);
2770 TString query = Form("submit %s %s %d", jdl, aliendir, stage);
2771 jobId = SubmitSingleJob(query);
2772 }
2773 if (!jobId) return kFALSE;
2774
2775 if (!fGridJobIDs.IsNull()) fGridJobIDs.Append(" ");
2776 fGridJobIDs.Append(Form("%d", jobId));
2777 if (!fGridStages.IsNull()) fGridStages.Append(" ");
2778 fGridStages.Append(Form("%s_merge_stage%d",
2779 laststage ? "final" : "partial", stage));
2780
2781 return kTRUE;
2782}
2783
2784//______________________________________________________________________________
2785AliAnalysisManager *AliAnalysisAlien::LoadAnalysisManager(const char *fname)
2786{
2787// Loat the analysis manager from a file.
2788 TFile *file = TFile::Open(fname);
2789 if (!file) {
2790 ::Error("LoadAnalysisManager", "Cannot open file %s", fname);
2791 return 0;
2792 }
2793 TIter nextkey(file->GetListOfKeys());
2794 AliAnalysisManager *mgr = 0;
2795 TKey *key;
2796 while ((key=(TKey*)nextkey())) {
2797 if (!strcmp(key->GetClassName(), "AliAnalysisManager"))
2798 mgr = (AliAnalysisManager*)file->Get(key->GetName());
2799 }
2800 if (!mgr)
2801 ::Error("LoadAnalysisManager", "No analysis manager found in file %s", fname);
2802 return mgr;
2803}
2804
2805//______________________________________________________________________________
2806Int_t AliAnalysisAlien::SubmitSingleJob(const char *query)
2807{
2808// Submits a single job corresponding to the query and returns job id. If 0 submission failed.
2809 if (!gGrid) return 0;
2810 printf("=> %s ------> ",query);
2811 TGridResult *res = gGrid->Command(query);
2812 if (!res) return 0;
2813 TString jobId = res->GetKey(0,"jobId");
2814 delete res;
2815 if (jobId.IsNull()) {
2816 printf("submission failed. Reason:\n");
2817 gGrid->Stdout();
2818 gGrid->Stderr();
2819 ::Error("SubmitSingleJob", "Your query %s could not be submitted", query);
2820 return 0;
2821 }
2822 Int_t ijobId = jobId.Atoi();
2823 printf(" Job id: '%s' (%d)\n", jobId.Data(), ijobId);
2824 return ijobId;
2825}
2826
2827//______________________________________________________________________________
2828Bool_t AliAnalysisAlien::MergeInfo(const char *output, const char *collection)
2829{
2830// Merges a collection of output files using concatenation.
2831 TString scoll(collection);
2832 if (!scoll.Contains(".xml")) return kFALSE;
2833 TGridCollection *coll = (TGridCollection*)gROOT->ProcessLine(Form("TAlienCollection::Open(\"%s\");", collection));
2834 if (!coll) {
2835 ::Error("MergeInfo", "Input XML %s collection empty.", collection);
2836 return kFALSE;
2837 }
2838 // Iterate grid collection
2839 TString outtmp;
2840 Bool_t merged = kFALSE;
2841 Int_t ifile = 0;
2842 while (coll->Next()) {
2843 TString fname = gSystem->DirName(coll->GetTURL());
2844 fname += "/";
2845 fname += output;
2846 outtmp = Form("%d_%s", ifile, output);
2847 if (!TFile::Cp(fname, outtmp)) {
2848 ::Error("MergeInfo", "Could not copy %s", fname.Data());
2849 continue;
2850 }
2851 ifile++;
2852 if (ifile<2) {
2853 gSystem->Exec(Form("cp %s lastmerged", outtmp.Data()));
2854 continue;
2855 }
2856 gSystem->Exec(Form("cat lastmerged %s > tempmerged", outtmp.Data()));
2857 gSystem->Exec("cp tempmerged lastmerged");
2858 }
2859 if (ifile) {
2860 gSystem->Exec(Form("cp lastmerged %s", output));
2861 gSystem->Exec(Form("rm tempmerged lastmerged *_%s", output));
2862 merged = kTRUE;
2863 }
2864 return merged;
2865}
2866
2867//______________________________________________________________________________
2868Bool_t AliAnalysisAlien::MergeOutput(const char *output, const char *basedir, Int_t nmaxmerge, Int_t stage)
2869{
2870// Merge given output files from basedir. Basedir can be an alien output directory
2871// but also an xml file with root_archive.zip locations. The file merger will merge nmaxmerge
2872// files in a group (ignored for xml input). Merging can be done in stages:
2873// stage=0 : will merge all existing files in a single stage, supporting resume if run locally
2874// stage=1 : works with an xml of all root_archive.zip in the output directory
2875// stage>1 : works with an xml of all root_archive.zip in the Stage_<n-1> directory
2876 TString outputFile = output;
2877 TString command;
2878 TString outputChunk;
2879 TString previousChunk = "";
2880 TObjArray *listoffiles = new TObjArray();
2881// listoffiles->SetOwner();
2882 Int_t countChunk = 0;
2883 Int_t countZero = nmaxmerge;
2884 Bool_t merged = kTRUE;
2885 Bool_t isGrid = kTRUE;
2886 Int_t index = outputFile.Index("@");
2887 if (index > 0) outputFile.Remove(index);
2888 TString inputFile = outputFile;
2889 TString sbasedir = basedir;
2890 if (sbasedir.Contains(".xml")) {
2891 // Merge files pointed by the xml - ignore nmaxmerge and set ichunk to 0
2892 nmaxmerge = 9999999;
2893 TGridCollection *coll = (TGridCollection*)gROOT->ProcessLine(Form("TAlienCollection::Open(\"%s\");", basedir));
2894 if (!coll) {
2895 ::Error("MergeOutput", "Input XML collection empty.");
2896 return kFALSE;
2897 }
2898 // Iterate grid collection
2899 while (coll->Next()) {
2900 TString fname = gSystem->DirName(coll->GetTURL());
2901 fname += "/";
2902 fname += inputFile;
2903 listoffiles->Add(new TNamed(fname.Data(),""));
2904 }
2905 } else if (sbasedir.Contains(".txt")) {
2906 // The file having the .txt extension is expected to contain a list of
2907 // folders where the output files will be looked. For alien folders,
2908 // the full folder LFN is expected (starting with alien://)
2909 // Assume lfn's on each line
2910 TString line;
2911 ifstream in;
2912 in.open(sbasedir);
2913 if (in.fail()) {
2914 ::Error("MergeOutput", "File %s cannot be opened. Merging stopped." ,sbasedir.Data());
2915 return kTRUE;
2916 }
2917 Int_t nfiles = 0;
2918 while (in.good()) {
2919 in >> line;
2920 if (line.IsNull() || line.BeginsWith("#")) continue;
2921 line.Strip();
2922 if (!line.Contains("alien:")) isGrid = kFALSE;
2923 line += "/";
2924 line += outputFile;
2925 nfiles++;
2926 listoffiles->Add(new TNamed(line.Data(),""));
2927 }
2928 in.close();
2929 if (!nfiles) {
2930 ::Error("MergeOutput","Input file %s contains no files to be merged\n", sbasedir.Data());
2931 delete listoffiles;
2932 return kFALSE;
2933 }
2934 } else {
2935 command = Form("find %s/ *%s", basedir, inputFile.Data());
2936 printf("command: %s\n", command.Data());
2937 TGridResult *res = gGrid->Command(command);
2938 if (!res) {
2939 ::Error("MergeOutput","No result for the find command\n");
2940 delete listoffiles;
2941 return kFALSE;
2942 }
2943 TIter nextmap(res);
2944 TMap *map = 0;
2945 while ((map=(TMap*)nextmap())) {
2946 TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl"));
2947 if (!objs || !objs->GetString().Length()) {
2948 // Nothing found - skip this output
2949 delete res;
2950 delete listoffiles;
2951 return kFALSE;
2952 }
2953 listoffiles->Add(new TNamed(objs->GetName(),""));
2954 }
2955 delete res;
2956 }
2957 if (!listoffiles->GetEntries()) {
2958 ::Error("MergeOutput","No result for the find command\n");
2959 delete listoffiles;
2960 return kFALSE;
2961 }
2962
2963 TFileMerger *fm = 0;
2964 TIter next0(listoffiles);
2965 TObjArray *listoffilestmp = new TObjArray();
2966 listoffilestmp->SetOwner();
2967 TObject *nextfile;
2968 TString snextfile;
2969 // Keep only the files at upper level
2970 Int_t countChar = 0;
2971 while ((nextfile=next0())) {
2972 snextfile = nextfile->GetName();
2973 Int_t crtCount = snextfile.CountChar('/');
2974 if (nextfile == listoffiles->First()) countChar = crtCount;
2975 if (crtCount < countChar) countChar = crtCount;
2976 }
2977 next0.Reset();
2978 while ((nextfile=next0())) {
2979 snextfile = nextfile->GetName();
2980 Int_t crtCount = snextfile.CountChar('/');
2981 if (crtCount > countChar) {
2982 delete nextfile;
2983 continue;
2984 }
2985 listoffilestmp->Add(nextfile);
2986 }
2987 delete listoffiles;
2988 listoffiles = listoffilestmp; // Now contains 'good' files
2989 listoffiles->Print();
2990 TIter next(listoffiles);
2991 // Check if there is a merge operation to resume. Works only for stage 0 or 1.
2992 outputChunk = outputFile;
2993 outputChunk.ReplaceAll(".root", "_*.root");
2994 // Check for existent temporary merge files
2995 // Check overwrite mode and remove previous partial results if needed
2996 // Preserve old merging functionality for stage 0.
2997 if (stage==0) {
2998 if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
2999 while (1) {
3000 // Skip as many input files as in a chunk
3001 for (Int_t counter=0; counter<nmaxmerge; counter++) {
3002 nextfile = next();
3003 if (!nextfile) {
3004 ::Error("MergeOutput", "Mismatch found. Please remove partial merged files from local dir.");
3005 delete listoffiles;
3006 return kFALSE;
3007 }
3008 snextfile = nextfile->GetName();
3009 }
3010 outputChunk = outputFile;
3011 outputChunk.ReplaceAll(".root", Form("_%04d.root", countChunk));
3012 countChunk++;
3013 if (gSystem->AccessPathName(outputChunk)) continue;
3014 // Merged file with chunks up to <countChunk> found
3015 ::Info("MergeOutput", "Resume merging of <%s> from <%s>\n", outputFile.Data(), outputChunk.Data());
3016 previousChunk = outputChunk;
3017 break;
3018 }
3019 }
3020 countZero = nmaxmerge;
3021
3022 while ((nextfile=next())) {
3023 snextfile = nextfile->GetName();
3024 // Loop 'find' results and get next LFN
3025 if (countZero == nmaxmerge) {
3026 // First file in chunk - create file merger and add previous chunk if any.
3027 fm = new TFileMerger(isGrid);
3028 fm->SetFastMethod(kTRUE);
3029 if (previousChunk.Length()) fm->AddFile(previousChunk.Data());
3030 outputChunk = outputFile;
3031 outputChunk.ReplaceAll(".root", Form("_%04d.root", countChunk));
3032 }
3033 // If last file found, put merged results in the output file
3034 if (nextfile == listoffiles->Last()) outputChunk = outputFile;
3035 // Add file to be merged and decrement chunk counter.
3036 fm->AddFile(snextfile);
3037 countZero--;
3038 if (countZero==0 || nextfile == listoffiles->Last()) {
3039 if (!fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
3040 // Nothing found - skip this output
3041 ::Warning("MergeOutput", "No <%s> files found.", inputFile.Data());
3042 merged = kFALSE;
3043 break;
3044 }
3045 fm->OutputFile(outputChunk);
3046 // Merge the outputs, then go to next chunk
3047 if (!fm->Merge()) {
3048 ::Error("MergeOutput", "Could not merge all <%s> files", outputFile.Data());
3049 merged = kFALSE;
3050 break;
3051 } else {
3052 ::Info("MergeOutputs", "\n##### Merged %d output files to <%s>", fm->GetMergeList()->GetSize(), outputChunk.Data());
3053 gSystem->Unlink(previousChunk);
3054 }
3055 if (nextfile == listoffiles->Last()) break;
3056 countChunk++;
3057 countZero = nmaxmerge;
3058 previousChunk = outputChunk;
3059 }
3060 }
3061 delete listoffiles;
3062 delete fm;
3063 return merged;
3064 }
3065 // Merging stage different than 0.
3066 // Move to the begining of the requested chunk.
3067 fm = new TFileMerger(isGrid);
3068 fm->SetFastMethod(kTRUE);
3069 while ((nextfile=next())) fm->AddFile(nextfile->GetName());
3070 delete listoffiles;
3071 if (!fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
3072 // Nothing found - skip this output
3073 ::Warning("MergeOutput", "No <%s> files found.", inputFile.Data());
3074 delete fm;
3075 return kFALSE;
3076 }
3077 fm->OutputFile(outputFile);
3078 // Merge the outputs
3079 if (!fm->Merge()) {
3080 ::Error("MergeOutput", "Could not merge all <%s> files", outputFile.Data());
3081 delete fm;
3082 return kFALSE;
3083 } else {
3084 ::Info("MergeOutput", "\n##### Merged %d output files to <%s>", fm->GetMergeList()->GetSize(), outputFile.Data());
3085 }
3086 delete fm;
3087 return kTRUE;
3088}
3089
3090//______________________________________________________________________________
3091Bool_t AliAnalysisAlien::MergeOutputs()
3092{
3093// Merge analysis outputs existing in the AliEn space.
3094 if (TestBit(AliAnalysisGrid::kTest)) return kTRUE;
3095 if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
3096 if (!Connect()) {
3097 Error("MergeOutputs", "Cannot merge outputs without grid connection. Terminate will NOT be executed");
3098 return kFALSE;
3099 }
3100 if (fMergeViaJDL) {
3101 if (!TestBit(AliAnalysisGrid::kMerge)) {
3102 Info("MergeOutputs", "### Re-run with <MergeViaJDL> option in terminate mode of the plugin to submit merging jobs ###");
3103 return kFALSE;
3104 }
3105 if (fProductionMode) {
3106 Info("MergeOutputs", "### Merging will be submitted by LPM manager... ###");
3107 return kFALSE;
3108 }
3109 Info("MergeOutputs", "Submitting merging JDL");
3110 if (!SubmitMerging()) return kFALSE;
3111 Info("MergeOutputs", "### Re-run with <MergeViaJDL> off to collect results after merging jobs are done ###");
3112 Info("MergeOutputs", "### The Terminate() method is executed by the merging jobs");
3113 return kFALSE;
3114 }
3115 // Get the output path
3116 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
3117 if (!DirectoryExists(fGridOutputDir)) {
3118 Error("MergeOutputs", "Grid output directory %s not found. Terminate() will NOT be executed", fGridOutputDir.Data());
3119 return kFALSE;
3120 }
3121 if (!fOutputFiles.Length()) {
3122 Error("MergeOutputs", "No output file names defined. Are you running the right AliAnalysisAlien configuration ?");
3123 return kFALSE;
3124 }
3125 // Check if fast read option was requested
3126 Info("MergeOutputs", "Started local merging of output files from: alien://%s \
3127 \n======= overwrite mode = %d", fGridOutputDir.Data(), (Int_t)fOverwriteMode);
3128 if (fFastReadOption) {
3129 Warning("MergeOutputs", "You requested FastRead option. Using xrootd flags to reduce timeouts. This may skip some files that could be accessed ! \
3130 \n+++ NOTE: To disable this option, use: plugin->SetFastReadOption(kFALSE)");
3131 gEnv->SetValue("XNet.ConnectTimeout",50);
3132 gEnv->SetValue("XNet.RequestTimeout",50);
3133 gEnv->SetValue("XNet.MaxRedirectCount",2);
3134 gEnv->SetValue("XNet.ReconnectTimeout",50);
3135 gEnv->SetValue("XNet.FirstConnectMaxCnt",1);
3136 }
3137 // Make sure we change the temporary directory
3138 gSystem->Setenv("TMPDIR", gSystem->pwd());
3139 // Set temporary compilation directory to current one
3140 gSystem->SetBuildDir(gSystem->pwd(), kTRUE);
3141 TObjArray *list = fOutputFiles.Tokenize(",");
3142 TIter next(list);
3143 TObjString *str;
3144 TString outputFile;
3145 Bool_t merged = kTRUE;
3146 while((str=(TObjString*)next())) {
3147 outputFile = str->GetString();
3148 Int_t index = outputFile.Index("@");
3149 if (index > 0) outputFile.Remove(index);
3150 TString outputChunk = outputFile;
3151 outputChunk.ReplaceAll(".root", "_*.root");
3152 // Skip already merged outputs
3153 if (!gSystem->AccessPathName(outputFile)) {
3154 if (fOverwriteMode) {
3155 Info("MergeOutputs", "Overwrite mode. Existing file %s was deleted.", outputFile.Data());
3156 gSystem->Unlink(outputFile);
3157 if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
3158 Info("MergeOutput", "Overwrite mode: partial merged files %s will removed",
3159 outputChunk.Data());
3160 gSystem->Exec(Form("rm -f %s", outputChunk.Data()));
3161 }
3162 } else {
3163 Info("MergeOutputs", "Output file <%s> found. Not merging again.", outputFile.Data());
3164 continue;
3165 }
3166 } else {
3167 if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
3168 Info("MergeOutput", "Overwrite mode: partial merged files %s will removed",
3169 outputChunk.Data());
3170 gSystem->Exec(Form("rm -f %s", outputChunk.Data()));
3171 }
3172 }
3173 if (fMergeExcludes.Contains(outputFile.Data()) ||
3174 fRegisterExcludes.Contains(outputFile.Data())) continue;
3175 // Perform a 'find' command in the output directory, looking for registered outputs
3176 merged = MergeOutput(outputFile, fGridOutputDir, fMaxMergeFiles);
3177 if (!merged) {
3178 Error("MergeOutputs", "Terminate() will NOT be executed");
3179 delete list;
3180 return kFALSE;
3181 }
3182 TFile *fileOpened = (TFile*)gROOT->GetListOfFiles()->FindObject(outputFile);
3183 if (fileOpened) fileOpened->Close();
3184 }
3185 delete list;
3186 return kTRUE;
3187}
3188
3189//______________________________________________________________________________
3190void AliAnalysisAlien::SetDefaultOutputs(Bool_t flag)
3191{
3192// Use the output files connected to output containers from the analysis manager
3193// rather than the files defined by SetOutputFiles
3194 if (flag && !TObject::TestBit(AliAnalysisGrid::kDefaultOutputs))
3195 Info("SetDefaultOutputs", "Plugin will use the output files taken from analysis manager");
3196 TObject::SetBit(AliAnalysisGrid::kDefaultOutputs, flag);
3197}
3198
3199//______________________________________________________________________________
3200void AliAnalysisAlien::SetOutputFiles(const char *list)
3201{
3202// Manually set the output files list.
3203// Removes duplicates. Not allowed if default outputs are not disabled.
3204 if (TObject::TestBit(AliAnalysisGrid::kDefaultOutputs)) {
3205 Fatal("SetOutputFiles", "You have to explicitly call SetDefaultOutputs(kFALSE) to manually set output files.");
3206 return;
3207 }
3208 Info("SetOutputFiles", "Output file list is set manually - you are on your own.");
3209 fOutputFiles = "";
3210 TString slist = list;
3211 if (slist.Contains("@")) Warning("SetOutputFiles","The plugin does not allow explicit SE's. Please use: SetNumberOfReplicas() instead.");
3212 TObjArray *arr = slist.Tokenize(" ");
3213 TObjString *os;
3214 TIter next(arr);
3215 TString sout;
3216 while ((os=(TObjString*)next())) {
3217 sout = os->GetString();
3218 if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
3219 if (fOutputFiles.Contains(sout)) continue;
3220 if (!fOutputFiles.IsNull()) fOutputFiles += ",";
3221 fOutputFiles += sout;
3222 }
3223 delete arr;
3224}
3225
3226//______________________________________________________________________________
3227void AliAnalysisAlien::SetOutputArchive(const char *list)
3228{
3229// Manually set the output archive list. Free text - you are on your own...
3230// Not allowed if default outputs are not disabled.
3231 if (TObject::TestBit(AliAnalysisGrid::kDefaultOutputs)) {
3232 Fatal("SetOutputArchive", "You have to explicitly call SetDefaultOutputs(kFALSE) to manually set the output archives.");
3233 return;
3234 }
3235 Info("SetOutputArchive", "Output archive is set manually - you are on your own.");
3236 fOutputArchive = list;
3237}
3238
3239//______________________________________________________________________________
3240void AliAnalysisAlien::SetPreferedSE(const char */*se*/)
3241{
3242// Setting a prefered output SE is not allowed anymore.
3243 Warning("SetPreferedSE", "Setting a preferential SE is not allowed anymore via the plugin. Use SetNumberOfReplicas() and SetDefaultOutputs()");
3244}
3245
3246//______________________________________________________________________________
3247void AliAnalysisAlien::SetProofParameter(const char *pname, const char *value)
3248{
3249// Set some PROOF special parameter.
3250 TPair *pair = dynamic_cast<TPair*>(fProofParam.FindObject(pname));
3251 if (pair) {
3252 TObject *old = pair->Key();
3253 TObject *val = pair->Value();
3254 fProofParam.Remove(old);
3255 delete old;
3256 delete val;
3257 }
3258 fProofParam.Add(new TObjString(pname), new TObjString(value));
3259}
3260
3261//______________________________________________________________________________
3262const char *AliAnalysisAlien::GetProofParameter(const char *pname) const
3263{
3264// Returns a special PROOF parameter.
3265 TPair *pair = dynamic_cast<TPair*>(fProofParam.FindObject(pname));
3266 if (!pair) return 0;
3267 return pair->Value()->GetName();
3268}
3269
3270//______________________________________________________________________________
3271Bool_t AliAnalysisAlien::StartAnalysis(Long64_t /*nentries*/, Long64_t /*firstEntry*/)
3272{
3273// Start remote grid analysis.
3274 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
3275 Bool_t testMode = TestBit(AliAnalysisGrid::kTest);
3276 if (!mgr || !mgr->IsInitialized()) {
3277 Error("StartAnalysis", "You need an initialized analysis manager for this");
3278 return kFALSE;
3279 }
3280 // Are we in PROOF mode ?
3281 if (mgr->IsProofMode()) {
3282 if (testMode) Info("StartAnalysis", "##### Starting PROOF analysis with Proof Lite via the plugin #####");
3283 else Info("StartAnalysis", "##### Starting PROOF analysis on cluster <%s> via the plugin #####", fProofCluster.Data());
3284 if (fProofCluster.IsNull()) {
3285 Error("StartAnalysis", "You need to specify the proof cluster name via SetProofCluster");
3286 return kFALSE;
3287 }
3288 if (fProofDataSet.IsNull() && !testMode) {
3289 Error("StartAnalysis", "You need to specify a dataset using SetProofDataSet()");
3290 return kFALSE;
3291 }
3292 // Set the needed environment
3293 gEnv->SetValue("XSec.GSI.DelegProxy","2");
3294 // Do we need to reset PROOF ? The success of the Reset operation cannot be checked
3295 if (fProofReset && !testMode) {
3296 if (fProofReset==1) {
3297 Info("StartAnalysis", "Sending soft reset signal to proof cluster %s", fProofCluster.Data());
3298 gROOT->ProcessLine(Form("TProof::Reset(\"%s\", kFALSE);", fProofCluster.Data()));
3299 } else {
3300 Info("StartAnalysis", "Sending hard reset signal to proof cluster %s", fProofCluster.Data());
3301 gROOT->ProcessLine(Form("TProof::Reset(\"%s\", kTRUE);", fProofCluster.Data()));
3302 }
3303 Info("StartAnalysis", "Stopping the analysis. Please use SetProofReset(0) to resume.");
3304 return kFALSE;
3305 }
3306
3307 if (!testMode) {
3308 // Check if there is an old active session
3309 Long_t nsessions = gROOT->ProcessLine(Form("TProof::Mgr(\"%s\")->QuerySessions(\"\")->GetEntries();", fProofCluster.Data()));
3310 if (nsessions) {
3311 Error("StartAnalysis","You have to reset your old session first\n");
3312 return kFALSE;
3313 }
3314 }
3315 // Do we need to change the ROOT version ? The success of this cannot be checked.
3316 if (!fROOTVersion.IsNull() && !testMode) {
3317 gROOT->ProcessLine(Form("TProof::Mgr(\"%s\")->SetROOTVersion(\"VO_ALICE@ROOT::%s\");",
3318 fProofCluster.Data(), fROOTVersion.Data()));
3319 }
3320 // Connect to PROOF and check the status
3321 Long_t proof = 0;
3322 TString sworkers;
3323 if (fNproofWorkersPerSlave) sworkers = Form("workers=%dx", fNproofWorkersPerSlave);
3324 else if (fNproofWorkers) sworkers = Form("workers=%d", fNproofWorkers);
3325 if (!testMode) {
3326 if (!sworkers.IsNull())
3327 proof = gROOT->ProcessLine(Form("TProof::Open(\"%s\", \"%s\");", fProofCluster.Data(), sworkers.Data()));
3328 else
3329 proof = gROOT->ProcessLine(Form("TProof::Open(\"%s\");", fProofCluster.Data()));
3330 } else {
3331 proof = gROOT->ProcessLine("TProof::Open(\"\");");
3332 if (!proof) {
3333 Error("StartAnalysis", "Could not start PROOF in test mode");
3334 return kFALSE;
3335 }
3336 }
3337 if (!proof) {
3338 Error("StartAnalysis", "Could not connect to PROOF cluster <%s>", fProofCluster.Data());
3339 return kFALSE;
3340 }
3341 if (fNproofWorkersPerSlave*fNproofWorkers > 0)
3342 gROOT->ProcessLine(Form("gProof->SetParallel(%d);", fNproofWorkers));
3343 // Set proof special parameters if any
3344 TIter nextpp(&fProofParam);
3345 TObject *proofparam;
3346 while ((proofparam=nextpp())) {
3347 TString svalue = GetProofParameter(proofparam->GetName());
3348 gROOT->ProcessLine(Form("gProof->SetParameter(\"%s\",%s);", proofparam->GetName(), svalue.Data()));
3349 }
3350 // Is dataset existing ?
3351 if (!testMode) {
3352 TString dataset = fProofDataSet;
3353 Int_t index = dataset.Index("#");
3354 if (index>=0) dataset.Remove(index);
3355// if (!gROOT->ProcessLine(Form("gProof->ExistsDataSet(\"%s\");",fProofDataSet.Data()))) {
3356// Error("StartAnalysis", "Dataset %s not existing", fProofDataSet.Data());
3357// return kFALSE;
3358// }
3359// Info("StartAnalysis", "Dataset %s found", dataset.Data());
3360 }
3361 // Is ClearPackages() needed ?
3362 if (TestSpecialBit(kClearPackages)) {
3363 Info("StartAnalysis", "ClearPackages signal sent to PROOF. Use SetClearPackages(kFALSE) to reset this.");
3364 gROOT->ProcessLine("gProof->ClearPackages();");
3365 }
3366 // Is a given aliroot mode requested ?
3367 TList optionsList;
3368 TString parLibs;
3369 if (!fAliRootMode.IsNull()) {
3370 TString alirootMode = fAliRootMode;
3371 if (alirootMode == "default") alirootMode = "";
3372 Info("StartAnalysis", "You are requesting AliRoot mode: %s", fAliRootMode.Data());
3373 optionsList.SetOwner();
3374 optionsList.Add(new TNamed("ALIROOT_MODE", alirootMode.Data()));
3375 // Check the additional libs to be loaded
3376 TString extraLibs;
3377 Bool_t parMode = kFALSE;
3378 if (!alirootMode.IsNull()) extraLibs = "ANALYSIS:OADB:ANALYSISalice";
3379 // Parse the extra libs for .so
3380 if (fAdditionalLibs.Length()) {
3381 TString additionalLibs = fAdditionalLibs;
3382 additionalLibs.Strip();
3383 if (additionalLibs.Length() && fFriendLibs.Length())
3384 additionalLibs += " ";
3385 additionalLibs += fFriendLibs;
3386 TObjArray *list = additionalLibs.Tokenize(" ");
3387 TIter next(list);
3388 TObjString *str;
3389 while((str=(TObjString*)next())) {
3390 if (str->GetString().Contains(".so")) {
3391 if (parMode) {
3392 Warning("StartAnalysis", "Plugin does not support loading libs after par files in PROOF mode. Library %s and following will not load on workers", str->GetName());
3393 break;
3394 }
3395 TString stmp = str->GetName();
3396 if (stmp.BeginsWith("lib")) stmp.Remove(0,3);
3397 stmp.ReplaceAll(".so","");
3398 if (!extraLibs.IsNull()) extraLibs += ":";
3399 extraLibs += stmp;
3400 continue;
3401 }
3402 if (str->GetString().Contains(".par")) {
3403 // The first par file found in the list will not allow any further .so
3404 parMode = kTRUE;
3405 if (!parLibs.IsNull()) parLibs += ":";
3406 parLibs += str->GetName();
3407 continue;
3408 }
3409 }
3410 if (list) delete list;
3411 }
3412 if (!extraLibs.IsNull()) {
3413 Info("StartAnalysis", "Adding extra libs: %s",extraLibs.Data());
3414 optionsList.Add(new TNamed("ALIROOT_EXTRA_LIBS",extraLibs.Data()));
3415 }
3416 // Check extra includes
3417 if (!fIncludePath.IsNull()) {
3418 TString includePath = fIncludePath;
3419 includePath.ReplaceAll(" ",":");
3420 includePath.ReplaceAll("$ALICE_ROOT/","");
3421 includePath.ReplaceAll("${ALICE_ROOT}/","");
3422 includePath.ReplaceAll("-I","");
3423 includePath.Remove(TString::kTrailing, ':');
3424 Info("StartAnalysis", "Adding extra includes: %s",includePath.Data());
3425 optionsList.Add(new TNamed("ALIROOT_EXTRA_INCLUDES",includePath.Data()));
3426 }
3427 // Check if connection to grid is requested
3428 if (TestSpecialBit(kProofConnectGrid))
3429 optionsList.Add(new TNamed("ALIROOT_ENABLE_ALIEN", "1"));
3430 // Enable AliRoot par
3431 if (testMode) {
3432 // Enable proof lite package
3433 TString alirootLite = gSystem->ExpandPathName("$ALICE_ROOT/ANALYSIS/macros/AliRootProofLite.par");
3434 for (Int_t i=0; i<optionsList.GetSize(); i++) {
3435 TNamed *obj = (TNamed*)optionsList.At(i);
3436 printf("%s %s\n", obj->GetName(), obj->GetTitle());
3437 }
3438 if (!gROOT->ProcessLine(Form("gProof->UploadPackage(\"%s\");",alirootLite.Data()))
3439 && !gROOT->ProcessLine(Form("gProof->EnablePackage(\"%s\", (TList*)%p);",alirootLite.Data(),&optionsList))) {
3440 Info("StartAnalysis", "AliRootProofLite enabled");
3441 } else {
3442 Error("StartAnalysis", "There was an error trying to enable package AliRootProofLite.par");
3443 return kFALSE;
3444 }
3445 } else {
3446 if ( ! fAliROOTVersion.IsNull() ) {
3447 if (gROOT->ProcessLine(Form("gProof->EnablePackage(\"VO_ALICE@AliRoot::%s\", (TList*)%p, kTRUE);",
3448 fAliROOTVersion.Data(), &optionsList))) {
3449 Error("StartAnalysis", "There was an error trying to enable package VO_ALICE@AliRoot::%s", fAliROOTVersion.Data());
3450 return kFALSE;
3451 }
3452 }
3453 }
3454 // Enable first par files from fAdditionalLibs
3455 if (!parLibs.IsNull()) {
3456 TObjArray *list = parLibs.Tokenize(":");
3457 TIter next(list);
3458 TObjString *package;
3459 while((package=(TObjString*)next())) {
3460 TString spkg = package->GetName();
3461 spkg.ReplaceAll(".par", "");
3462 gSystem->Exec(TString::Format("rm -rf %s", spkg.Data()));
3463 if (!gROOT->ProcessLine(Form("gProof->UploadPackage(\"%s\");", package->GetName()))) {
3464 TString enablePackage = (testMode)?Form("gProof->EnablePackage(\"%s\",kFALSE);", package->GetName()):Form("gProof->EnablePackage(\"%s\",kTRUE);", package->GetName());
3465 if (gROOT->ProcessLine(enablePackage)) {
3466 Error("StartAnalysis", "There was an error trying to enable package %s", package->GetName());
3467 return kFALSE;
3468 }
3469 } else {
3470 Error("StartAnalysis", "There was an error trying to upload package %s", package->GetName());
3471 return kFALSE;
3472 }
3473 }
3474 if (list) delete list;
3475 }
3476 } else {
3477 if (fAdditionalLibs.Contains(".so") && !testMode) {
3478 Error("StartAnalysis", "You request additional libs to be loaded but did not enabled any AliRoot mode. Please refer to: \
3479 \n http://aaf.cern.ch/node/83 and use a parameter for SetAliRootMode()");
3480 return kFALSE;
3481 }
3482 }
3483 // Enable par files if requested
3484 if (fPackages && fPackages->GetEntries()) {
3485 TIter next(fPackages);
3486 TObject *package;
3487 while ((package=next())) {
3488 // Skip packages already enabled
3489 if (parLibs.Contains(package->GetName())) continue;
3490 TString spkg = package->GetName();
3491 spkg.ReplaceAll(".par", "");
3492 gSystem->Exec(TString::Format("rm -rf %s", spkg.Data()));
3493 if (!gROOT->ProcessLine(Form("gProof->UploadPackage(\"%s\");", package->GetName()))) {
3494 if (gROOT->ProcessLine(Form("gProof->EnablePackage(\"%s\",kTRUE);", package->GetName()))) {
3495 Error("StartAnalysis", "There was an error trying to enable package %s", package->GetName());
3496 return kFALSE;
3497 }
3498 } else {
3499 Error("StartAnalysis", "There was an error trying to upload package %s", package->GetName());
3500 return kFALSE;
3501 }
3502 }
3503 }
3504 // Do we need to load analysis source files ?
3505 // NOTE: don't load on client since this is anyway done by the user to attach his task.
3506 if (fAnalysisSource.Length()) {
3507 TObjArray *list = fAnalysisSource.Tokenize(" ");
3508 TIter next(list);
3509 TObjString *str;
3510 while((str=(TObjString*)next())) {
3511 gROOT->ProcessLine(Form("gProof->Load(\"%s+g\", kTRUE);", str->GetName()));
3512 }
3513 if (list) delete list;
3514 }
3515 if (testMode) {
3516 // Register dataset to proof lite.
3517 if (fFileForTestMode.IsNull()) {
3518 Error("GetChainForTestMode", "For proof test mode please use SetFileForTestMode() pointing to a file that contains data file locations.");
3519 return kFALSE;
3520 }
3521 if (gSystem->AccessPathName(fFileForTestMode)) {
3522 Error("GetChainForTestMode", "File not found: %s", fFileForTestMode.Data());
3523 return kFALSE;
3524 }
3525 TFileCollection *coll = new TFileCollection();
3526 coll->AddFromFile(fFileForTestMode);
3527 gROOT->ProcessLine(Form("gProof->RegisterDataSet(\"test_collection\", (TFileCollection*)%p, \"OV\");", coll));
3528 gROOT->ProcessLine("gProof->ShowDataSets()");
3529 }
3530 return kTRUE;
3531 }
3532
3533 // Check if output files have to be taken from the analysis manager
3534 if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
3535 // Add output files and AOD files
3536 fOutputFiles = GetListOfFiles("outaod");
3537 // Add extra files registered to the analysis manager
3538 TString extra = GetListOfFiles("ext");
3539 if (!extra.IsNull()) {
3540 extra.ReplaceAll(".root", "*.root");
3541 if (!fOutputFiles.IsNull()) fOutputFiles += ",";
3542 fOutputFiles += extra;
3543 }
3544 // Compose the output archive.
3545 fOutputArchive = "log_archive.zip:std*@disk=1 ";
3546 if (mgr->IsCollectThroughput())
3547 fOutputArchive += Form("root_archive.zip:%s,*.stat@disk=%d %s@disk=%d",fOutputFiles.Data(),fNreplicas, mgr->GetFileInfoLog(),fNreplicas);
3548 else
3549 fOutputArchive += Form("root_archive.zip:%s,*.stat@disk=%d",fOutputFiles.Data(),fNreplicas);
3550 }
3551// if (!fCloseSE.Length()) fCloseSE = gSystem->Getenv("alien_CLOSE_SE");
3552 if (TestBit(AliAnalysisGrid::kOffline)) {
3553 Info("StartAnalysis","\n##### OFFLINE MODE ##### Files to be used in GRID are produced but not copied \
3554 \n there nor any job run. You can revise the JDL and analysis \
3555 \n macro then run the same in \"submit\" mode.");
3556 } else if (TestBit(AliAnalysisGrid::kTest)) {
3557 Info("StartAnalysis","\n##### LOCAL MODE ##### Your analysis will be run locally on a subset of the requested \
3558 \n dataset.");
3559 } else if (TestBit(AliAnalysisGrid::kSubmit)) {
3560 Info("StartAnalysis","\n##### SUBMIT MODE ##### Files required by your analysis are copied to your grid working \
3561 \n space and job submitted.");
3562 } else if (TestBit(AliAnalysisGrid::kMerge)) {
3563 Info("StartAnalysis","\n##### MERGE MODE ##### The registered outputs of the analysis will be merged");
3564 if (fMergeViaJDL) CheckInputData();
3565 return kTRUE;
3566 } else {
3567 Info("StartAnalysis","\n##### FULL ANALYSIS MODE ##### Producing needed files and submitting your analysis job...");
3568 }
3569
3570 Print();
3571 if (!Connect()) {
3572 Error("StartAnalysis", "Cannot start grid analysis without grid connection");
3573 return kFALSE;
3574 }
3575 if (IsCheckCopy() && gGrid) CheckFileCopy(gGrid->GetHomeDirectory());
3576 if (!CheckInputData()) {
3577 Error("StartAnalysis", "There was an error in preprocessing your requested input data");
3578 return kFALSE;
3579 }
3580 if (!CreateDataset(fDataPattern)) {
3581 TString serror;
3582 if (!fRunNumbers.Length() && !fRunRange[0]) serror = Form("path to data directory: <%s>", fGridDataDir.Data());
3583 if (fRunNumbers.Length()) serror = "run numbers";
3584 if (fRunRange[0]) serror = Form("run range [%d, %d]", fRunRange[0], fRunRange[1]);
3585 serror += Form("\n or data pattern <%s>", fDataPattern.Data());
3586 Error("StartAnalysis", "No data to process. Please fix %s in your plugin configuration.", serror.Data());
3587 return kFALSE;
3588 }
3589 WriteAnalysisFile();
3590 WriteAnalysisMacro();
3591 WriteExecutable();
3592 WriteValidationScript();
3593 if (fMergeViaJDL) {
3594 WriteMergingMacro();
3595 WriteMergeExecutable();
3596 WriteValidationScript(kTRUE);
3597 }
3598 if (!CreateJDL()) return kFALSE;
3599 if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
3600 if (testMode) {
3601 // Locally testing the analysis
3602 Info("StartAnalysis", "\n_______________________________________________________________________ \
3603 \n Running analysis script in a daughter shell as on a worker node \
3604 \n_______________________________________________________________________");
3605 TObjArray *list = fOutputFiles.Tokenize(",");
3606 TIter next(list);
3607 TObjString *str;
3608 TString outputFile;
3609 while((str=(TObjString*)next())) {
3610 outputFile = str->GetString();
3611 Int_t index = outputFile.Index("@");
3612 if (index > 0) outputFile.Remove(index);
3613 if (!gSystem->AccessPathName(outputFile)) gSystem->Exec(Form("rm %s", outputFile.Data()));
3614 }
3615 delete list;
3616 gSystem->Exec(Form("bash %s 2>stderr", fExecutable.Data()));
3617 gSystem->Exec(Form("bash %s",fValidationScript.Data()));
3618// gSystem->Exec("cat stdout");
3619 return kFALSE;
3620 }
3621 // Check if submitting is managed by LPM manager
3622 if (fProductionMode) {
3623 //TString prodfile = fJDLName;
3624 //prodfile.ReplaceAll(".jdl", ".prod");
3625 //WriteProductionFile(prodfile);
3626 Info("StartAnalysis", "Job submitting is managed by LPM. Rerun in terminate mode after jobs finished.");
3627 return kFALSE;
3628 }
3629 // Submit AliEn job(s)
3630 gGrid->Cd(fGridOutputDir);
3631 TGridResult *res;
3632 TString jobID = "";
3633 fGridJobIDs = "";
3634 fGridStages = "";
3635 if (!fRunNumbers.Length() && !fRunRange[0]) {
3636 // Submit a given xml or a set of runs
3637 res = gGrid->Command(Form("submit %s", fJDLName.Data()));
3638 printf("*************************** %s\n",Form("submit %s", fJDLName.Data()));
3639 if (res) {
3640 const char *cjobId = res->GetKey(0,"jobId");
3641 if (!cjobId) {
3642 gGrid->Stdout();
3643 gGrid->Stderr();
3644 Error("StartAnalysis", "Your JDL %s could not be submitted", fJDLName.Data());
3645 return kFALSE;
3646 } else {
3647 Info("StartAnalysis", "\n_______________________________________________________________________ \
3648 \n##### Your JDL %s was successfully submitted. \nTHE JOB ID IS: %s \
3649 \n_______________________________________________________________________",
3650 fJDLName.Data(), cjobId);
3651 jobID = cjobId;
3652 if (jobID.Atoi()) {
3653 if (!fGridJobIDs.IsNull()) fGridJobIDs.Append(" ");
3654 fGridJobIDs.Append(jobID);
3655 if (!fGridStages.IsNull()) fGridStages.Append(" ");
3656 fGridStages.Append("full");
3657 }
3658 }
3659 delete res;
3660 } else {
3661 Error("StartAnalysis", "No grid result after submission !!! Bailing out...");
3662 return kFALSE;
3663 }
3664 } else {
3665 // Submit for a range of enumeration of runs.
3666 if (!Submit()) return kFALSE;
3667 jobID = fGridJobIDs;
3668 }
3669
3670 if (fDropToShell) {
3671 Info("StartAnalysis", "\n#### STARTING AN ALIEN SHELL FOR YOU. EXIT WHEN YOUR JOB %s HAS FINISHED. #### \
3672 \n You may exit at any time and terminate the job later using the option <terminate> \
3673 \n ##################################################################################", jobID.Data());
3674 gSystem->Exec("aliensh");
3675 } else {
3676 Info("StartAnalysis", "\n#### SUBMITTED JOB %s TO ALIEN QUEUE #### \
3677 \n Remember to terminate the job later using the option <terminate> \
3678 \n ##################################################################################", jobID.Data());
3679 }
3680 return kTRUE;
3681}
3682
3683//______________________________________________________________________________
3684const char *AliAnalysisAlien::GetListOfFiles(const char *type)
3685{
3686// Get a comma-separated list of output files of the requested type.
3687// Type can be (case unsensitive):
3688// aod - list of aod files (std, extensions and filters)
3689// out - list of output files connected to containers (but not aod's or extras)
3690// ext - list of extra files registered to the manager
3691// ter - list of files produced in terminate
3692 static TString files;
3693 files = "";
3694 TString stype = type;
3695 stype.ToLower();
3696 TString aodfiles, extra;
3697 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
3698 if (!mgr) {
3699 ::Error("GetListOfFiles", "Cannot call this without analysis manager");
3700 return files.Data();
3701 }
3702 if (mgr->GetOutputEventHandler()) {
3703 aodfiles = "";
3704 if (mgr->GetOutputEventHandler()->GetFillAOD())
3705 aodfiles = mgr->GetOutputEventHandler()->GetOutputFileName();
3706 TString extraaod = mgr->GetOutputEventHandler()->GetExtraOutputs();
3707 if (!extraaod.IsNull() && mgr->GetOutputEventHandler()->GetFillExtension()) {
3708 if (!aodfiles.IsNull()) aodfiles += ",";
3709 aodfiles += extraaod;
3710 }
3711 }
3712 if (stype.Contains("aod")) {
3713 files = aodfiles;
3714 if (stype == "aod") return files.Data();
3715 }
3716 // Add output files that are not in the list of AOD files
3717 TString outputfiles = "";
3718 TIter next(mgr->GetOutputs());
3719 AliAnalysisDataContainer *output;
3720 const char *filename = 0;
3721 while ((output=(AliAnalysisDataContainer*)next())) {
3722 filename = output->GetFileName();
3723 if (!(strcmp(filename, "default"))) continue;
3724 if (outputfiles.Contains(filename)) continue;
3725 if (aodfiles.Contains(filename)) continue;
3726 if (!outputfiles.IsNull() && strlen(filename)) outputfiles += ",";
3727 outputfiles += filename;
3728 }
3729 if (stype.Contains("out")) {
3730 if (!files.IsNull() && !outputfiles.IsNull()) files += ",";
3731 files += outputfiles;
3732 if (stype == "out") return files.Data();
3733 }
3734 // Add extra files registered to the analysis manager
3735 TString sextra;
3736 extra = mgr->GetExtraFiles();
3737 if (!extra.IsNull()) {
3738 extra.Strip();
3739 extra.ReplaceAll(" ", ",");
3740 TObjArray *fextra = extra.Tokenize(",");
3741 TIter nextx(fextra);
3742 TObject *obj;
3743 while ((obj=nextx())) {
3744 if (aodfiles.Contains(obj->GetName())) continue;
3745 if (outputfiles.Contains(obj->GetName())) continue;
3746 if (sextra.Contains(obj->GetName())) continue;
3747 if (!sextra.IsNull()) sextra += ",";
3748 sextra += obj->GetName();
3749 }
3750 delete fextra;
3751 if (stype.Contains("ext")) {
3752 if (!files.IsNull() && !sextra.IsNull()) files += ",";
3753 files += sextra;
3754 }
3755 }
3756 if (stype == "ext") return files.Data();
3757 TString termfiles;
3758 if (!fTerminateFiles.IsNull()) {
3759 fTerminateFiles.Strip();
3760 fTerminateFiles.ReplaceAll(" ",",");
3761 TObjArray *fextra = fTerminateFiles.Tokenize(",");
3762 TIter nextx(fextra);
3763 TObject *obj;
3764 while ((obj=nextx())) {
3765 if (aodfiles.Contains(obj->GetName())) continue;
3766 if (outputfiles.Contains(obj->GetName())) continue;
3767 if (termfiles.Contains(obj->GetName())) continue;
3768 if (sextra.Contains(obj->GetName())) continue;
3769 if (!termfiles.IsNull()) termfiles += ",";
3770 termfiles += obj->GetName();
3771 }
3772 delete fextra;
3773 }
3774 if (stype.Contains("ter")) {
3775 if (!files.IsNull() && !termfiles.IsNull()) {
3776 files += ",";
3777 files += termfiles;
3778 }
3779 }
3780 return files.Data();
3781}
3782
3783//______________________________________________________________________________
3784Bool_t AliAnalysisAlien::Submit()
3785{
3786// Submit all master jobs.
3787 Int_t nmasterjobs = fInputFiles->GetEntries();
3788 Long_t tshoot = gSystem->Now();
3789 if (!fNsubmitted && !SubmitNext()) return kFALSE;
3790 while (fNsubmitted < nmasterjobs) {
3791 Long_t now = gSystem->Now();
3792 if ((now-tshoot)>30000) {
3793 tshoot = now;
3794 if (!SubmitNext()) return kFALSE;
3795 }
3796 }
3797 return kTRUE;
3798}
3799
3800//______________________________________________________________________________
3801Bool_t AliAnalysisAlien::SubmitMerging()
3802{
3803// Submit all merging jobs.
3804 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
3805 gGrid->Cd(fGridOutputDir);
3806 TString mergeJDLName = fExecutable;
3807 mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
3808 if (!fInputFiles) {
3809 Error("SubmitMerging", "You have to use explicit run numbers or run range to merge via JDL!");
3810 return kFALSE;
3811 }
3812 Int_t ntosubmit = fInputFiles->GetEntries();
3813 for (Int_t i=0; i<ntosubmit; i++) {
3814 TString runOutDir = gSystem->BaseName(fInputFiles->At(i)->GetName());
3815 runOutDir.ReplaceAll(".xml", "");
3816 if (fOutputToRunNo) {
3817 // The output directory is the run number
3818 printf("### Submitting merging job for run <%s>\n", runOutDir.Data());
3819 runOutDir = Form("%s/%s", fGridOutputDir.Data(), runOutDir.Data());
3820 } else {
3821 if (!fRunNumbers.Length() && !fRunRange[0]) {
3822 // The output directory is the grid outdir
3823 printf("### Submitting merging job for the full output directory %s.\n", fGridOutputDir.Data());
3824 runOutDir = fGridOutputDir;
3825 } else {
3826 // The output directory is the master number in 3 digits format
3827 printf("### Submitting merging job for master <%03d>\n", i);
3828 runOutDir = Form("%s/%03d",fGridOutputDir.Data(), i);
3829 }
3830 }
3831 // Check now the number of merging stages.
3832 TObjArray *list = fOutputFiles.Tokenize(",");
3833 TIter next(list);
3834 TObjString *str;
3835 TString outputFile;
3836 while((str=(TObjString*)next())) {
3837 outputFile = str->GetString();
3838 Int_t index = outputFile.Index("@");
3839 if (index > 0) outputFile.Remove(index);
3840 if (!fMergeExcludes.Contains(outputFile) &&
3841 !fRegisterExcludes.Contains(outputFile)) break;
3842 }
3843 delete list;
3844 Bool_t done = CheckMergedFiles(outputFile, runOutDir, fMaxMergeFiles, mergeJDLName);
3845 if (!done && (i==ntosubmit-1)) return kFALSE;
3846 if (!fRunNumbers.Length() && !fRunRange[0]) break;
3847 }
3848 if (!ntosubmit) return kTRUE;
3849 if (fDropToShell) {
3850 Info("StartAnalysis", "\n #### STARTING AN ALIEN SHELL FOR YOU. You can exit any time or inspect your jobs in a different shell.##########\
3851 \n Make sure your jobs are in a final state (you can resubmit failed ones via 'masterjob <id> resubmit ERROR_ALL')\
3852 \n Rerun in 'terminate' mode to submit all merging stages, each AFTER the previous one completed. The final merged \
3853 \n output will be written to your alien output directory, while separate stages in <Stage_n>. \
3854 \n ################################################################################################################");
3855 gSystem->Exec("aliensh");
3856 } else {
3857 Info("StartAnalysis", "\n #### STARTED MERGING JOBS FOR YOU #### \
3858 \n Make sure your jobs are in a final state (you can resubmit failed ones via 'masterjob <id> resubmit ERROR_ALL') \
3859 \n Rerun in 'terminate' mode to submit all merging stages, each AFTER the previous one completed. The final merged \
3860 \n output will be written to your alien output directory, while separate stages in <Stage_n>. \
3861 \n ################################################################################################################");
3862 }
3863 return kTRUE;
3864}
3865
3866//______________________________________________________________________________
3867Bool_t AliAnalysisAlien::SubmitNext()
3868{
3869// Submit next bunch of master jobs if the queue is free. The first master job is
3870// submitted right away, while the next will not be unless the previous was split.
3871// The plugin will not submit new master jobs if there are more that 500 jobs in
3872// waiting phase.
3873 static Bool_t iscalled = kFALSE;
3874 static Int_t firstmaster = 0;
3875 static Int_t lastmaster = 0;
3876 static Int_t npermaster = 0;
3877 if (iscalled) return kTRUE;
3878 iscalled = kTRUE;
3879 Int_t nrunning=0, nwaiting=0, nerror=0, ndone=0;
3880 Int_t ntosubmit = 0;
3881 TGridResult *res;
3882 TString jobID = "";
3883 Int_t nmasterjobs = fInputFiles->GetEntries();
3884 if (!fNsubmitted) {
3885 ntosubmit = 1;
3886 if (!IsUseSubmitPolicy()) {
3887 if (nmasterjobs>5)
3888 Info("SubmitNext","### Warning submit policy not used ! Submitting too many jobs at a time may be prohibitted. \
3889 \n### You can use SetUseSubmitPolicy() to enable if you have problems.");
3890 ntosubmit = nmasterjobs;
3891 }
3892 } else {
3893 TString status = GetJobStatus(firstmaster, lastmaster, nrunning, nwaiting, nerror, ndone);
3894 printf("=== master %d: %s\n", lastmaster, status.Data());
3895 // If last master not split, just return
3896 if (status != "SPLIT") {iscalled = kFALSE; return kTRUE;}
3897 // No more than 100 waiting jobs
3898 if (nwaiting>500) {iscalled = kFALSE; return kTRUE;}
3899 npermaster = (nrunning+nwaiting+nerror+ndone)/fNsubmitted;
3900 if (npermaster) ntosubmit = (500-nwaiting)/npermaster;
3901 if (!ntosubmit) ntosubmit = 1;
3902 printf("=== WAITING(%d) RUNNING(%d) DONE(%d) OTHER(%d) NperMaster=%d => to submit %d jobs\n",
3903 nwaiting, nrunning, ndone, nerror, npermaster, ntosubmit);
3904 }
3905 for (Int_t i=0; i<ntosubmit; i++) {
3906 // Submit for a range of enumeration of runs.
3907 if (fNsubmitted>=nmasterjobs) {iscalled = kFALSE; return kTRUE;}
3908 TString query;
3909 TString runOutDir = gSystem->BaseName(fInputFiles->At(fNsubmitted)->GetName());
3910 runOutDir.ReplaceAll(".xml", "");
3911 if (fOutputToRunNo)
3912 query = Form("submit %s %s %s", fJDLName.Data(), fInputFiles->At(fNsubmitted)->GetName(), runOutDir.Data());
3913 else
3914 query = Form("submit %s %s %03d", fJDLName.Data(), fInputFiles->At(fNsubmitted)->GetName(), fNsubmitted);
3915 printf("********* %s\n",query.Data());
3916 res = gGrid->Command(query);
3917 if (res) {
3918 TString cjobId1 = res->GetKey(0,"jobId");
3919 if (!cjobId1.Length()) {
3920 iscalled = kFALSE;
3921 gGrid->Stdout();
3922 gGrid->Stderr();
3923 Error("StartAnalysis", "Your JDL %s could not be submitted. The message was:", fJDLName.Data());
3924 return kFALSE;
3925 } else {
3926 Info("StartAnalysis", "\n_______________________________________________________________________ \
3927 \n##### Your JDL %s submitted (%d to go). \nTHE JOB ID IS: %s \
3928 \n_______________________________________________________________________",
3929 fJDLName.Data(), nmasterjobs-fNsubmitted-1, cjobId1.Data());
3930 if (!fGridJobIDs.IsNull()) fGridJobIDs.Append(" ");
3931 fGridJobIDs.Append(cjobId1);
3932 if (!fGridStages.IsNull()) fGridStages.Append(" ");
3933 fGridStages.Append("full");
3934 jobID += cjobId1;
3935 jobID += " ";
3936 lastmaster = cjobId1.Atoi();
3937 if (!firstmaster) firstmaster = lastmaster;
3938 fNsubmitted++;
3939 }
3940 delete res;
3941 } else {
3942 Error("StartAnalysis", "No grid result after submission !!! Bailing out...");
3943 return kFALSE;
3944 }
3945 }
3946 iscalled = kFALSE;
3947 return kTRUE;
3948}
3949
3950//______________________________________________________________________________
3951void AliAnalysisAlien::WriteAnalysisFile()
3952{
3953// Write current analysis manager into the file <analysisFile>
3954 TString analysisFile = fExecutable;
3955 analysisFile.ReplaceAll(".sh", ".root");
3956 if (!TestBit(AliAnalysisGrid::kSubmit)) {
3957 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
3958 if (!mgr || !mgr->IsInitialized()) {
3959 Error("WriteAnalysisFile", "You need an initialized analysis manager for this");
3960 return;
3961 }
3962 // Check analysis type
3963 TObject *handler;
3964 if (mgr->GetMCtruthEventHandler()) TObject::SetBit(AliAnalysisGrid::kUseMC);
3965 handler = (TObject*)mgr->GetInputEventHandler();
3966 if (handler) {
3967 if (handler->InheritsFrom("AliMultiInputEventHandler")) {
3968 AliMultiInputEventHandler *multiIH = (AliMultiInputEventHandler*)handler;
3969 if (multiIH->GetFirstInputEventHandler()->InheritsFrom("AliESDInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseESD);
3970 if (multiIH->GetFirstInputEventHandler()->InheritsFrom("AliAODInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseAOD);
3971 } else {
3972 if (handler->InheritsFrom("AliESDInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseESD);
3973 if (handler->InheritsFrom("AliAODInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseAOD);
3974 }
3975 }
3976 TDirectory *cdir = gDirectory;
3977 TFile *file = TFile::Open(analysisFile, "RECREATE");
3978 if (file) {
3979 // Skip task Terminate calls for the grid job (but not in test mode, where we want to check also the terminate mode
3980 if (!TestBit(AliAnalysisGrid::kTest)) mgr->SetSkipTerminate(kTRUE);
3981 // Unless merging makes no sense
3982 if (IsSingleOutput()) mgr->SetSkipTerminate(kFALSE);
3983 mgr->Write();
3984 delete file;
3985 // Enable termination for local jobs
3986 mgr->SetSkipTerminate(kFALSE);
3987 }
3988 if (cdir) cdir->cd();
3989 Info("WriteAnalysisFile", "\n##### Analysis manager: %s wrote to file <%s>\n", mgr->GetName(),analysisFile.Data());
3990 }
3991 Bool_t copy = kTRUE;
3992 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
3993 if (copy) {
3994 CdWork();
3995 TString workdir = gGrid->GetHomeDirectory();
3996 workdir += fGridWorkingDir;
3997 Info("WriteAnalysisFile", "\n##### Copying file <%s> containing your initialized analysis manager to your alien workspace", analysisFile.Data());
3998 if (FileExists(analysisFile)) gGrid->Rm(analysisFile);
3999 if (!copyLocal2Alien("WriteAnalysisFile",analysisFile.Data(),
4000 Form("%s/%s", workdir.Data(),analysisFile.Data()))) Fatal("","Terminating");
4001 }
4002}
4003
4004//______________________________________________________________________________
4005void AliAnalysisAlien::WriteAnalysisMacro()
4006{
4007// Write the analysis macro that will steer the analysis in grid mode.
4008 if (!TestBit(AliAnalysisGrid::kSubmit)) {
4009 ofstream out;
4010 out.open(fAnalysisMacro.Data(), ios::out);
4011 if (!out.good()) {
4012 Error("WriteAnalysisMacro", "could not open file %s for writing", fAnalysisMacro.Data());
4013 return;
4014 }
4015 Bool_t hasSTEERBase = kFALSE;
4016 Bool_t hasESD = kFALSE;
4017 Bool_t hasAOD = kFALSE;
4018 Bool_t hasANALYSIS = kFALSE;
4019 Bool_t hasOADB = kFALSE;
4020 Bool_t hasANALYSISalice = kFALSE;
4021 Bool_t hasCORRFW = kFALSE;
4022 TString func = fAnalysisMacro;
4023 TString type = "ESD";
4024 TString comment = "// Analysis using ";
4025 if (fMCLoop) {
4026 type = "MCGEN";
4027 comment += "MCGEN";
4028 } else {
4029 if (IsUseMCchain()) {
4030 type = "MC";
4031 comment += "MC";
4032 } else {
4033 if (TObject::TestBit(AliAnalysisGrid::kUseESD)) comment += "ESD";
4034 if (TObject::TestBit(AliAnalysisGrid::kUseAOD)) {
4035 type = "AOD";
4036 comment += "AOD";
4037 }
4038 }
4039 }
4040 if (type!="AOD" && fFriendChainName!="") {
4041 Error("WriteAnalysisMacro", "Friend chain can be attached only to AOD");
4042 return;
4043 }
4044 if (TObject::TestBit(AliAnalysisGrid::kUseMC)) comment += "/MC";
4045 else comment += " data";
4046 out << "const char *anatype = \"" << type.Data() << "\";" << endl << endl;
4047 func.ReplaceAll(".C", "");
4048 out << "void " << func.Data() << "()" << endl;
4049 out << "{" << endl;
4050 out << comment.Data() << endl;
4051 out << "// Automatically generated analysis steering macro executed in grid subjobs" << endl << endl;
4052 out << " TStopwatch timer;" << endl;
4053 out << " timer.Start();" << endl << endl;
4054 // Change temp directory to current one
4055 if (!IsLocalTest()) {
4056 out << "// connect to AliEn and make the chain" << endl;
4057 out << " if (!TGrid::Connect(\"alien://\")) return;" << endl;
4058 }
4059 out << "// Set temporary merging directory to current one" << endl;
4060 out << " gSystem->Setenv(\"TMPDIR\", gSystem->pwd());" << endl << endl;
4061 out << "// Set temporary compilation directory to current one" << endl;
4062 out << " gSystem->SetBuildDir(gSystem->pwd(), kTRUE);" << endl << endl;
4063 // Reset existing include path
4064 out << "// Reset existing include path and add current directory first in the search" << endl;
4065 out << " gSystem->SetIncludePath(\"-I.\");" << endl;
4066 if (!fExecutableCommand.Contains("aliroot")) {
4067 out << "// load base root libraries" << endl;
4068 out << " gSystem->Load(\"libTree\");" << endl;
4069 out << " gSystem->Load(\"libGeom\");" << endl;
4070 out << " gSystem->Load(\"libVMC\");" << endl;
4071 out << " gSystem->Load(\"libPhysics\");" << endl << endl;
4072 out << " gSystem->Load(\"libMinuit\");" << endl << endl;
4073 }
4074 if (fAdditionalRootLibs.Length()) {
4075 // in principle libtree /lib geom libvmc etc. can go into this list, too
4076 out << "// Add aditional libraries" << endl;
4077 TObjArray *list = fAdditionalRootLibs.Tokenize(" ");
4078 TIter next(list);
4079 TObjString *str;
4080 while((str=(TObjString*)next())) {
4081 if (str->GetString().Contains(".so"))
4082 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
4083 }
4084 if (list) delete list;
4085 }
4086 out << "// Load analysis framework libraries" << endl;
4087 TString setupPar = "AliAnalysisAlien::SetupPar";
4088 if (!fPackages) {
4089 if (!fExecutableCommand.Contains("aliroot")) {
4090 out << " gSystem->Load(\"libSTEERBase\");" << endl;
4091 out << " gSystem->Load(\"libESD\");" << endl;
4092 out << " gSystem->Load(\"libAOD\");" << endl;
4093 }
4094 out << " gSystem->Load(\"libANALYSIS\");" << endl;
4095 out << " gSystem->Load(\"libOADB\");" << endl;
4096 out << " gSystem->Load(\"libANALYSISalice\");" << endl;
4097 out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
4098 } else {
4099 TIter next(fPackages);
4100 TObject *obj;
4101 TString pkgname;
4102 while ((obj=next())) {
4103 pkgname = obj->GetName();
4104 if (pkgname == "STEERBase" ||
4105 pkgname == "STEERBase.par") hasSTEERBase = kTRUE;
4106 if (pkgname == "ESD" ||
4107 pkgname == "ESD.par") hasESD = kTRUE;
4108 if (pkgname == "AOD" ||
4109 pkgname == "AOD.par") hasAOD = kTRUE;
4110 if (pkgname == "ANALYSIS" ||
4111 pkgname == "ANALYSIS.par") hasANALYSIS = kTRUE;
4112 if (pkgname == "OADB" ||
4113 pkgname == "OADB.par") hasOADB = kTRUE;
4114 if (pkgname == "ANALYSISalice" ||
4115 pkgname == "ANALYSISalice.par") hasANALYSISalice = kTRUE;
4116 if (pkgname == "CORRFW" ||
4117 pkgname == "CORRFW.par") hasCORRFW = kTRUE;
4118 }
4119 if (hasANALYSISalice) setupPar = "SetupPar";
4120 if (!hasSTEERBase) out << " gSystem->Load(\"libSTEERBase\");" << endl;
4121 else out << " if (!" << setupPar << "(\"STEERBase\")) return;" << endl;
4122 if (!hasESD) out << " gSystem->Load(\"libESD\");" << endl;
4123 else out << " if (!" << setupPar << "(\"ESD\")) return;" << endl;
4124 if (!hasAOD) out << " gSystem->Load(\"libAOD\");" << endl;
4125 else out << " if (!" << setupPar << "(\"AOD\")) return;" << endl;
4126 if (!hasANALYSIS) out << " gSystem->Load(\"libANALYSIS\");" << endl;
4127 else out << " if (!" << setupPar << "(\"ANALYSIS\")) return;" << endl;
4128 if (!hasOADB) out << " gSystem->Load(\"libOADB\");" << endl;
4129 else out << " if (!" << setupPar << "(\"OADB\")) return;" << endl;
4130 if (!hasANALYSISalice) out << " gSystem->Load(\"libANALYSISalice\");" << endl;
4131 else out << " if (!" << setupPar << "(\"ANALYSISalice\")) return;" << endl;
4132 if (!hasCORRFW) out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
4133 else out << " if (!" << setupPar << "(\"CORRFW\")) return;" << endl << endl;
4134 out << "// Compile other par packages" << endl;
4135 next.Reset();
4136 while ((obj=next())) {
4137 pkgname = obj->GetName();
4138 if (pkgname == "STEERBase" ||
4139 pkgname == "STEERBase.par" ||
4140 pkgname == "ESD" ||
4141 pkgname == "ESD.par" ||
4142 pkgname == "AOD" ||
4143 pkgname == "AOD.par" ||
4144 pkgname == "ANALYSIS" ||
4145 pkgname == "ANALYSIS.par" ||
4146 pkgname == "OADB" ||
4147 pkgname == "OADB.par" ||
4148 pkgname == "ANALYSISalice" ||
4149 pkgname == "ANALYSISalice.par" ||
4150 pkgname == "CORRFW" ||
4151 pkgname == "CORRFW.par") continue;
4152 out << " if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
4153 }
4154 }
4155 out << "// include path" << endl;
4156 // Get the include path from the interpreter and remove entries pointing to AliRoot
4157 out << " TString intPath = gInterpreter->GetIncludePath();" << endl;
4158 out << " TObjArray *listpaths = intPath.Tokenize(\" \");" << endl;
4159 out << " TIter nextpath(listpaths);" << endl;
4160 out << " TObjString *pname;" << endl;
4161 out << " while ((pname=(TObjString*)nextpath())) {" << endl;
4162 out << " TString current = pname->GetName();" << endl;
4163 out << " if (current.Contains(\"AliRoot\") || current.Contains(\"ALICE_ROOT\")) continue;" << endl;
4164 out << " gSystem->AddIncludePath(current);" << endl;
4165 out << " }" << endl;
4166 out << " if (listpaths) delete listpaths;" << endl;
4167 if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
4168 out << " gROOT->ProcessLine(\".include $ALICE_ROOT/include\");" << endl;
4169 out << " printf(\"Include path: %s\\n\", gSystem->GetIncludePath());" << endl << endl;
4170 if (fMCLoop && !fGeneratorLibs.IsNull()) {
4171 out << "// MC generator libraries" << endl;
4172 TObjArray *list = fGeneratorLibs.Tokenize(" ");
4173 TIter next(list);
4174 TObjString *str;
4175 while((str=(TObjString*)next())) {
4176 out << " gSystem->Load(\"" << str->GetName() << "\");" << endl;
4177 }
4178 delete list;
4179 }
4180 if (fAdditionalLibs.Length()) {
4181 out << "// Add aditional AliRoot libraries" << endl;
4182 TString additionalLibs = fAdditionalLibs;
4183 additionalLibs.Strip();
4184 if (additionalLibs.Length() && fFriendLibs.Length())
4185 additionalLibs += " ";
4186 additionalLibs += fFriendLibs;
4187 TObjArray *list = additionalLibs.Tokenize(" ");
4188 TIter next(list);
4189 TObjString *str;
4190 while((str=(TObjString*)next())) {
4191 if (str->GetString().Contains(".so"))
4192 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
4193 if (str->GetString().Contains(".par"))
4194 out << " if (!" << setupPar << "(\"" << str->GetString() << "\")) return;" << endl;
4195 }
4196 delete list;
4197 }
4198 out << endl;
4199 out << "// analysis source to be compiled at runtime (if any)" << endl;
4200 if (fAnalysisSource.Length()) {
4201 TObjArray *list = fAnalysisSource.Tokenize(" ");
4202 TIter next(list);
4203 TObjString *str;
4204 while((str=(TObjString*)next())) {
4205 out << " gROOT->ProcessLine(\".L " << str->GetString().Data() << "+g\");" << endl;
4206 }
4207 if (list) delete list;
4208 }
4209 out << endl;
4210// out << " printf(\"Currently load libraries:\\n\");" << endl;
4211// out << " printf(\"%s\\n\", gSystem->GetLibraries());" << endl;
4212 if (fFastReadOption) {
4213 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 !!! \
4214 \n+++ NOTE: To disable this option, use: plugin->SetFastReadOption(kFALSE)");
4215 out << "// fast xrootd reading enabled" << endl;
4216 out << " printf(\"!!! You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !!!\");" << endl;
4217 out << " gEnv->SetValue(\"XNet.ConnectTimeout\",50);" << endl;
4218 out << " gEnv->SetValue(\"XNet.RequestTimeout\",50);" << endl;
4219 out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
4220 out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",50);" << endl;
4221 out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
4222 }
4223 out << "// read the analysis manager from file" << endl;
4224 TString analysisFile = fExecutable;
4225 analysisFile.ReplaceAll(".sh", ".root");
4226 out << " AliAnalysisManager *mgr = AliAnalysisAlien::LoadAnalysisManager(\""
4227 << analysisFile << "\");" << endl;
4228 out << " if (!mgr) return;" << endl;
4229 if (IsLocalTest()) {
4230 out << " AliAnalysisAlien *plugin = new AliAnalysisAlien();" << endl;
4231 out << " plugin->SetRunMode(\"test\");" << endl;
4232 if (fFileForTestMode.IsNull())
4233 out << " plugin->SetFileForTestMode(\"data.txt\");" << endl;
4234 else
4235 out << " plugin->SetFileForTestMode(\"" << fFileForTestMode << "\");" << endl;
4236 out << " plugin->SetNtestFiles(" << fNtestFiles << ");" << endl;
4237 if (!fFriendChainName.IsNull())
4238 out << " plugin->SetFriendChainName(\"" << fFriendChainName << "\",\"" << fFriendLibs << "\");" << endl;
4239 if (IsUseMCchain())
4240 out << " plugin->SetUseMCchain();" << endl;
4241 if (fMCLoop)
4242 out << " plugin->SetMCLoop(kTRUE);" << endl;
4243 out << " mgr->SetGridHandler(plugin);" << endl;
4244 if (AliAnalysisManager::GetAnalysisManager()) {
4245 out << " mgr->SetDebugLevel(" << AliAnalysisManager::GetAnalysisManager()->GetDebugLevel() << ");" << endl;
4246 out << " mgr->SetNSysInfo(" << AliAnalysisManager::GetAnalysisManager()->GetNsysInfo() << ");" << endl;
4247 } else {
4248 out << " mgr->SetDebugLevel(10);" << endl;
4249 out << " mgr->SetNSysInfo(100);" << endl;
4250 }
4251 }
4252 out << " mgr->PrintStatus();" << endl;
4253 if (AliAnalysisManager::GetAnalysisManager()) {
4254 if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) {
4255 out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
4256 } else {
4257 if (TestBit(AliAnalysisGrid::kTest))
4258 out << " AliLog::SetGlobalLogLevel(AliLog::kWarning);" << endl;
4259 else
4260 out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
4261 }
4262 }
4263 if (!IsLocalTest()) {
4264 if (fMCLoop) {
4265 out << " mgr->SetCacheSize(0);" << endl;
4266 out << " mgr->EventLoop(" << fNMCevents << ");" << endl;
4267 } else {
4268 out << " TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl;
4269 out << " mgr->StartAnalysis(\"localfile\", chain);" << endl;
4270 }
4271 } else {
4272 if (fMCLoop) {
4273 out << " mgr->SetCacheSize(0);" << endl;
4274 out << " mgr->EventLoop(" << fNMCevents << ");" << endl;
4275 } else {
4276 out << " mgr->StartAnalysis(\"localfile\");" << endl;
4277 }
4278 }
4279 out << " timer.Stop();" << endl;
4280 out << " timer.Print();" << endl;
4281 out << "}" << endl << endl;
4282 if (!IsLocalTest() && !fMCLoop) {
4283 out <<"//________________________________________________________________________________" << endl;
4284 out << "TChain* CreateChain(const char *xmlfile, const char *type=\"ESD\")" << endl;
4285 out << "{" << endl;
4286 out << "// Create a chain using url's from xml file" << endl;
4287 out << " TString filename;" << endl;
4288 out << " Int_t run = 0;" << endl;
4289 if (IsUseMCchain()) {
4290 out << " TString treename = \"TE\";" << endl;
4291 } else {
4292 if (!fTreeName.IsNull()) {
4293 out << " TString treename = \"" << fTreeName << "\";" << endl;
4294 } else {
4295 out << " TString treename = type;" << endl;
4296 out << " treename.ToLower();" << endl;
4297 out << " treename += \"Tree\";" << endl;
4298 }
4299 }
4300 out << " printf(\"***************************************\\n\");" << endl;
4301 out << " printf(\" Getting chain of trees %s\\n\", treename.Data());" << endl;
4302 out << " printf(\"***************************************\\n\");" << endl;
4303 out << " TAlienCollection *coll = TAlienCollection::Open(xmlfile);" << endl;
4304 out << " if (!coll) {" << endl;
4305 out << " ::Error(\"CreateChain\", \"Cannot create an AliEn collection from %s\", xmlfile);" << endl;
4306 out << " return NULL;" << endl;
4307 out << " }" << endl;
4308 out << " AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();" << endl;
4309 out << " TChain *chain = new TChain(treename);" << endl;
4310 if(!fFriendChainName.IsNull()) {
4311 out << " TList *friends = new TList();" << endl;
4312 out << " TIter nextfriend(friends);" << endl;
4313 out << " TChain *cfriend = 0;" << endl;
4314 TObjArray *list = fFriendChainName.Tokenize(" ");
4315 TIter next(list);
4316 TObjString *str;
4317 while((str=(TObjString*)next())) {
4318 out << " cfriend = new TChain(treename, \"" << str->GetName() << "\");" << endl;
4319 out << " friends->Add(cfriend);" << endl;
4320 out << " chain->AddFriend(cfriend);" << endl;
4321 }
4322 delete list;
4323// out << " TChain *chainFriend = new TChain(treename);" << endl;
4324 }
4325 out << " coll->Reset();" << endl;
4326 out << " while (coll->Next()) {" << endl;
4327 out << " filename = coll->GetTURL("");" << endl;
4328 out << " if (mgr) {" << endl;
4329 out << " Int_t nrun = AliAnalysisManager::GetRunFromAlienPath(filename);" << endl;
4330 out << " if (nrun && nrun != run) {" << endl;
4331 out << " printf(\"### Run number detected from chain: %d\\n\", nrun);" << endl;
4332 out << " mgr->SetRunFromPath(nrun);" << endl;
4333 out << " run = nrun;" << endl;
4334 out << " }" << endl;
4335 out << " }" << endl;
4336 out << " chain->Add(filename);" << endl;
4337 if(!fFriendChainName.IsNull()) {
4338 out << " TString bpath=coll->GetTURL(\"\");" << endl;
4339 out << " if (bpath.Index(\"#\") > -1) bpath.Remove(bpath.Index(\"#\"));" << endl;
4340 out << " bpath = gSystem->DirName(bpath);" << endl;
4341 out << " bpath += \"/\";" << endl;
4342 out << " TString fileFriend;" << endl;
4343 out << " nextfriend.Reset();" << endl;
4344 out << " while ((cfriend=(TChain*)nextfriend())) {" << endl;
4345 out << " fileFriend = bpath;" << endl;
4346 out << " fileFriend += cfriend->GetTitle();" << endl;
4347 out << " TFile *file = TFile::Open(fileFriend);" << endl;
4348 out << " if (file) {" << endl;
4349 out << " file->Close();" << endl;
4350 out << " cfriend->Add(fileFriend.Data());" << endl;
4351 out << " } else {" << endl;
4352 out << " ::Fatal(\"CreateChain\", \"Cannot open friend file: %s\", fileFriend.Data());" << endl;
4353 out << " return 0;" << endl;
4354 out << " }" << endl;
4355 out << " }" << endl;
4356 }
4357 out << " }" << endl;
4358 out << " if (!chain->GetNtrees()) {" << endl;
4359 out << " ::Error(\"CreateChain\", \"No tree found from collection %s\", xmlfile);" << endl;
4360 out << " return NULL;" << endl;
4361 out << " }" << endl;
4362 out << " return chain;" << endl;
4363 out << "}" << endl << endl;
4364 }
4365 if (hasANALYSISalice) {
4366 out <<"//________________________________________________________________________________" << endl;
4367 out << "Bool_t SetupPar(const char *package) {" << endl;
4368 out << "// Compile the package and set it up." << endl;
4369 out << " TString pkgdir = package;" << endl;
4370 out << " pkgdir.ReplaceAll(\".par\",\"\");" << endl;
4371 out << " gSystem->Exec(TString::Format(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
4372 out << " TString cdir = gSystem->WorkingDirectory();" << endl;
4373 out << " gSystem->ChangeDirectory(pkgdir);" << endl;
4374 out << " // Check for BUILD.sh and execute" << endl;
4375 out << " if (!gSystem->AccessPathName(\"PROOF-INF/BUILD.sh\")) {" << endl;
4376 out << " printf(\"*******************************\\n\");" << endl;
4377 out << " printf(\"*** Building PAR archive ***\\n\");" << endl;
4378 out << " printf(\"*******************************\\n\");" << endl;
4379 out << " if (gSystem->Exec(\"PROOF-INF/BUILD.sh\")) {" << endl;
4380 out << " ::Error(\"SetupPar\", \"Cannot build par archive %s\", pkgdir.Data());" << endl;
4381 out << " gSystem->ChangeDirectory(cdir);" << endl;
4382 out << " return kFALSE;" << endl;
4383 out << " }" << endl;
4384 out << " } else {" << endl;
4385 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/BUILD.sh for package %s\", pkgdir.Data());" << endl;
4386 out << " gSystem->ChangeDirectory(cdir);" << endl;
4387 out << " return kFALSE;" << endl;
4388 out << " }" << endl;
4389 out << " // Check for SETUP.C and execute" << endl;
4390 out << " if (!gSystem->AccessPathName(\"PROOF-INF/SETUP.C\")) {" << endl;
4391 out << " printf(\"*******************************\\n\");" << endl;
4392 out << " printf(\"*** Setup PAR archive ***\\n\");" << endl;
4393 out << " printf(\"*******************************\\n\");" << endl;
4394 out << " gROOT->Macro(\"PROOF-INF/SETUP.C\");" << endl;
4395 out << " } else {" << endl;
4396 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/SETUP.C for package %s\", pkgdir.Data());" << endl;
4397 out << " gSystem->ChangeDirectory(cdir);" << endl;
4398 out << " return kFALSE;" << endl;
4399 out << " }" << endl;
4400 out << " // Restore original workdir" << endl;
4401 out << " gSystem->ChangeDirectory(cdir);" << endl;
4402 out << " return kTRUE;" << endl;
4403 out << "}" << endl;
4404 }
4405 Info("WriteAnalysisMacro", "\n##### Analysis macro to run on worker nodes <%s> written",fAnalysisMacro.Data());
4406 }
4407 Bool_t copy = kTRUE;
4408 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
4409 if (copy) {
4410 CdWork();
4411 TString workdir = gGrid->GetHomeDirectory();
4412 workdir += fGridWorkingDir;
4413 if (FileExists(fAnalysisMacro)) gGrid->Rm(fAnalysisMacro);
4414 Info("WriteAnalysisMacro", "\n##### Copying analysis macro: <%s> to your alien workspace", fAnalysisMacro.Data());
4415// TFile::Cp(Form("file:%s",fAnalysisMacro.Data()), Form("alien://%s/%s", workdir.Data(), fAnalysisMacro.Data()));
4416 if (!copyLocal2Alien("WriteAnalysisMacro",fAnalysisMacro.Data(),
4417 Form("alien://%s/%s", workdir.Data(),
4418 fAnalysisMacro.Data()))) Fatal("","Terminating");
4419 }
4420}
4421
4422//______________________________________________________________________________
4423void AliAnalysisAlien::WriteMergingMacro()
4424{
4425// Write a macro to merge the outputs per master job.
4426 if (!fMergeViaJDL) return;
4427 if (!fOutputFiles.Length()) {
4428 Error("WriteMergingMacro", "No output file names defined. Are you running the right AliAnalysisAlien configuration ?");
4429 return;
4430 }
4431 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
4432 TString mergingMacro = fExecutable;
4433 mergingMacro.ReplaceAll(".sh","_merge.C");
4434 if (gGrid && !fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
4435 if (!TestBit(AliAnalysisGrid::kSubmit)) {
4436 ofstream out;
4437 out.open(mergingMacro.Data(), ios::out);
4438 if (!out.good()) {
4439 Error("WriteMergingMacro", "could not open file %s for writing", fAnalysisMacro.Data());
4440 return;
4441 }
4442 Bool_t hasSTEERBase = kFALSE;
4443 Bool_t hasESD = kFALSE;
4444 Bool_t hasAOD = kFALSE;
4445 Bool_t hasANALYSIS = kFALSE;
4446 Bool_t hasOADB = kFALSE;
4447 Bool_t hasANALYSISalice = kFALSE;
4448 Bool_t hasCORRFW = kFALSE;
4449 TString func = mergingMacro;
4450 TString comment;
4451 func.ReplaceAll(".C", "");
4452 out << "void " << func.Data() << "(const char *dir, Int_t stage=0)" << endl;
4453 out << "{" << endl;
4454 out << "// Automatically generated merging macro executed in grid subjobs" << endl << endl;
4455 out << " TStopwatch timer;" << endl;
4456 out << " timer.Start();" << endl << endl;
4457 // Reset existing include path
4458 out << "// Reset existing include path and add current directory first in the search" << endl;
4459 out << " gSystem->SetIncludePath(\"-I.\");" << endl;
4460 if (!fExecutableCommand.Contains("aliroot")) {
4461 out << "// load base root libraries" << endl;
4462 out << " gSystem->Load(\"libTree\");" << endl;
4463 out << " gSystem->Load(\"libGeom\");" << endl;
4464 out << " gSystem->Load(\"libVMC\");" << endl;
4465 out << " gSystem->Load(\"libPhysics\");" << endl << endl;
4466 out << " gSystem->Load(\"libMinuit\");" << endl << endl;
4467 }
4468 if (fAdditionalRootLibs.Length()) {
4469 // in principle libtree /lib geom libvmc etc. can go into this list, too
4470 out << "// Add aditional libraries" << endl;
4471 TObjArray *list = fAdditionalRootLibs.Tokenize(" ");
4472 TIter next(list);
4473 TObjString *str;
4474 while((str=(TObjString*)next())) {
4475 if (str->GetString().Contains(".so"))
4476 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
4477 }
4478 if (list) delete list;
4479 }
4480 out << "// Load analysis framework libraries" << endl;
4481 if (!fPackages) {
4482 if (!fExecutableCommand.Contains("aliroot")) {
4483 out << " gSystem->Load(\"libSTEERBase\");" << endl;
4484 out << " gSystem->Load(\"libESD\");" << endl;
4485 out << " gSystem->Load(\"libAOD\");" << endl;
4486 }
4487 out << " gSystem->Load(\"libANALYSIS\");" << endl;
4488 out << " gSystem->Load(\"libOADB\");" << endl;
4489 out << " gSystem->Load(\"libANALYSISalice\");" << endl;
4490 out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
4491 } else {
4492 TIter next(fPackages);
4493 TObject *obj;
4494 TString pkgname;
4495 TString setupPar = "AliAnalysisAlien::SetupPar";
4496 while ((obj=next())) {
4497 pkgname = obj->GetName();
4498 if (pkgname == "STEERBase" ||
4499 pkgname == "STEERBase.par") hasSTEERBase = kTRUE;
4500 if (pkgname == "ESD" ||
4501 pkgname == "ESD.par") hasESD = kTRUE;
4502 if (pkgname == "AOD" ||
4503 pkgname == "AOD.par") hasAOD = kTRUE;
4504 if (pkgname == "ANALYSIS" ||
4505 pkgname == "ANALYSIS.par") hasANALYSIS = kTRUE;
4506 if (pkgname == "OADB" ||
4507 pkgname == "OADB.par") hasOADB = kTRUE;
4508 if (pkgname == "ANALYSISalice" ||
4509 pkgname == "ANALYSISalice.par") hasANALYSISalice = kTRUE;
4510 if (pkgname == "CORRFW" ||
4511 pkgname == "CORRFW.par") hasCORRFW = kTRUE;
4512 }
4513 if (hasANALYSISalice) setupPar = "SetupPar";
4514 if (!hasSTEERBase) out << " gSystem->Load(\"libSTEERBase\");" << endl;
4515 else out << " if (!" << setupPar << "(\"STEERBase\")) return;" << endl;
4516 if (!hasESD) out << " gSystem->Load(\"libESD\");" << endl;
4517 else out << " if (!" << setupPar << "(\"ESD\")) return;" << endl;
4518 if (!hasAOD) out << " gSystem->Load(\"libAOD\");" << endl;
4519 else out << " if (!" << setupPar << "(\"AOD\")) return;" << endl;
4520 out << " gSystem->Load(\"libOADB\");" << endl;
4521 if (!hasANALYSIS) out << " gSystem->Load(\"libANALYSIS\");" << endl;
4522 else out << " if (!" << setupPar << "(\"ANALYSIS\")) return;" << endl;
4523 if (!hasOADB) out << " gSystem->Load(\"libOADB\");" << endl;
4524 else out << " if (!" << setupPar << "(\"OADB\")) return;" << endl;
4525 if (!hasANALYSISalice) out << " gSystem->Load(\"libANALYSISalice\");" << endl;
4526 else out << " if (!" << setupPar << "(\"ANALYSISalice\")) return;" << endl;
4527 if (!hasCORRFW) out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
4528 else out << " if (!" << setupPar << "(\"CORRFW\")) return;" << endl << endl;
4529 out << "// Compile other par packages" << endl;
4530 next.Reset();
4531 while ((obj=next())) {
4532 pkgname = obj->GetName();
4533 if (pkgname == "STEERBase" ||
4534 pkgname == "STEERBase.par" ||
4535 pkgname == "ESD" ||
4536 pkgname == "ESD.par" ||
4537 pkgname == "AOD" ||
4538 pkgname == "AOD.par" ||
4539 pkgname == "ANALYSIS" ||
4540 pkgname == "ANALYSIS.par" ||
4541 pkgname == "OADB" ||
4542 pkgname == "OADB.par" ||
4543 pkgname == "ANALYSISalice" ||
4544 pkgname == "ANALYSISalice.par" ||
4545 pkgname == "CORRFW" ||
4546 pkgname == "CORRFW.par") continue;
4547 out << " if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
4548 }
4549 }
4550 out << "// include path" << endl;
4551 // Get the include path from the interpreter and remove entries pointing to AliRoot
4552 out << " TString intPath = gInterpreter->GetIncludePath();" << endl;
4553 out << " TObjArray *listpaths = intPath.Tokenize(\" \");" << endl;
4554 out << " TIter nextpath(listpaths);" << endl;
4555 out << " TObjString *pname;" << endl;
4556 out << " while ((pname=(TObjString*)nextpath())) {" << endl;
4557 out << " TString current = pname->GetName();" << endl;
4558 out << " if (current.Contains(\"AliRoot\") || current.Contains(\"ALICE_ROOT\")) continue;" << endl;
4559 out << " gSystem->AddIncludePath(current);" << endl;
4560 out << " }" << endl;
4561 out << " if (listpaths) delete listpaths;" << endl;
4562 if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
4563 out << " gROOT->ProcessLine(\".include $ALICE_ROOT/include\");" << endl;
4564 out << " printf(\"Include path: %s\\n\", gSystem->GetIncludePath());" << endl << endl;
4565 if (fMCLoop && !fGeneratorLibs.IsNull()) {
4566 out << "// MC generator libraries" << endl;
4567 TObjArray *list = fGeneratorLibs.Tokenize(" ");
4568 TIter next(list);
4569 TObjString *str;
4570 while((str=(TObjString*)next())) {
4571 out << " gSystem->Load(\"" << str->GetName() << "\");" << endl;
4572 }
4573 delete list;
4574 }
4575 if (fAdditionalLibs.Length()) {
4576 out << "// Add aditional AliRoot libraries" << endl;
4577 TString additionalLibs = fAdditionalLibs;
4578 additionalLibs.Strip();
4579 if (additionalLibs.Length() && fFriendLibs.Length())
4580 additionalLibs += " ";
4581 additionalLibs += fFriendLibs;
4582 TObjArray *list = additionalLibs.Tokenize(" ");
4583 TIter next(list);
4584 TObjString *str;
4585 while((str=(TObjString*)next())) {
4586 if (str->GetString().Contains(".so"))
4587 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
4588 }
4589 if (list) delete list;
4590 }
4591 out << endl;
4592 out << "// Analysis source to be compiled at runtime (if any)" << endl;
4593 if (fAnalysisSource.Length()) {
4594 TObjArray *list = fAnalysisSource.Tokenize(" ");
4595 TIter next(list);
4596 TObjString *str;
4597 while((str=(TObjString*)next())) {
4598 out << " gROOT->ProcessLine(\".L " << str->GetString().Data() << "+g\");" << endl;
4599 }
4600 if (list) delete list;
4601 }
4602 out << endl;
4603
4604 if (fFastReadOption) {
4605 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 !!!");
4606 out << "// fast xrootd reading enabled" << endl;
4607 out << " printf(\"!!! You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !!!\");" << endl;
4608 out << " gEnv->SetValue(\"XNet.ConnectTimeout\",50);" << endl;
4609 out << " gEnv->SetValue(\"XNet.RequestTimeout\",50);" << endl;
4610 out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
4611 out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",50);" << endl;
4612 out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
4613 }
4614 // Change temp directory to current one
4615 out << "// Connect to AliEn" << endl;
4616 out << " if (!TGrid::Connect(\"alien://\")) return;" << endl;
4617 out << "// Set temporary merging directory to current one" << endl;
4618 out << " gSystem->Setenv(\"TMPDIR\", gSystem->pwd());" << endl << endl;
4619 out << "// Set temporary compilation directory to current one" << endl;
4620 out << " gSystem->SetBuildDir(gSystem->pwd(), kTRUE);" << endl << endl;
4621 out << " TString outputDir = dir;" << endl;
4622 if (IsMergeAOD())
4623 out << " TString outputFiles = \"" << GetListOfFiles("outaod") << "\";" << endl;
4624 else
4625 out << " TString outputFiles = \"" << GetListOfFiles("out") << "\";" << endl;
4626 out << " TString mergeExcludes = \"" << fMergeExcludes << " " << fRegisterExcludes << "\";" << endl;
4627 out << " TObjArray *list = outputFiles.Tokenize(\",\");" << endl;
4628 out << " TIter *iter = new TIter(list);" << endl;
4629 out << " TObjString *str;" << endl;
4630 out << " TString outputFile;" << endl;
4631 out << " Bool_t merged = kTRUE;" << endl;
4632 TString analysisFile = fExecutable;
4633 analysisFile.ReplaceAll(".sh", ".root");
4634 out << " AliAnalysisManager *mgr = AliAnalysisAlien::LoadAnalysisManager(\""
4635 << analysisFile << "\");" << endl;
4636 out << " if (!mgr) {" << endl;
4637 out << " printf(\"ERROR: Analysis manager could not be extracted from file \");" << endl;
4638 out << " return;" << endl;
4639 out << " }" << endl;
4640 if (IsLocalTest()) {
4641 out << " printf(\"===================================\\n\");" << endl;
4642 out << " printf(\"Testing merging...\\n\");" << endl;
4643 out << " printf(\"===================================\\n\");" << endl;
4644 }
4645 out << " while((str=(TObjString*)iter->Next())) {" << endl;
4646 out << " outputFile = str->GetString();" << endl;
4647 out << " if (outputFile.Contains(\"*\")) continue;" << endl;
4648 out << " Int_t index = outputFile.Index(\"@\");" << endl;
4649 out << " if (index > 0) outputFile.Remove(index);" << endl;
4650 out << " // Skip already merged outputs" << endl;
4651 out << " if (!gSystem->AccessPathName(outputFile)) {" << endl;
4652 out << " printf(\"Output file <%s> found. Not merging again.\\n\",outputFile.Data());" << endl;
4653 out << " continue;" << endl;
4654 out << " }" << endl;
4655 out << " if (mergeExcludes.Contains(outputFile.Data())) continue;" << endl;
4656 out << " merged = AliAnalysisAlien::MergeOutput(outputFile, outputDir, " << fMaxMergeFiles << ", stage);" << endl;
4657 out << " if (!merged) {" << endl;
4658 out << " printf(\"ERROR: Cannot merge %s\\n\", outputFile.Data());" << endl;
4659 out << " return;" << endl;
4660 out << " }" << endl;
4661 out << " }" << endl;
4662 if (mgr && mgr->IsCollectThroughput() && !IsLocalTest()) {
4663 out << " TString infolog = \"" << mgr->GetFileInfoLog() << "\";" << endl;
4664 out << " AliAnalysisAlien::MergeInfo(infolog, outputDir);" << endl;
4665 }
4666 out << " // all outputs merged, validate" << endl;
4667 out << " ofstream out;" << endl;
4668 out << " out.open(\"outputs_valid\", ios::out);" << endl;
4669 out << " out.close();" << endl;
4670 out << " // read the analysis manager from file" << endl;
4671 if (IsLocalTest()) {
4672 out << " printf(\"===================================\\n\");" << endl;
4673 out << " printf(\"Testing Terminate()...\\n\");" << endl;
4674 out << " printf(\"===================================\\n\");" << endl;
4675 } else {
4676 out << " if (!outputDir.Contains(\"Stage\")) return;" << endl;
4677 }
4678 out << " mgr->SetRunFromPath(mgr->GetRunFromAlienPath(dir));" << endl;
4679 out << " mgr->SetSkipTerminate(kFALSE);" << endl;
4680 out << " mgr->PrintStatus();" << endl;
4681 if (mgr) {
4682 if (mgr->GetDebugLevel()>3) {
4683 out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
4684 } else {
4685 if (TestBit(AliAnalysisGrid::kTest))
4686 out << " AliLog::SetGlobalLogLevel(AliLog::kWarning);" << endl;
4687 else
4688 out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
4689 }
4690 }
4691 out << " TTree *tree = NULL;" << endl;
4692 out << " mgr->StartAnalysis(\"gridterminate\", tree);" << endl;
4693 out << "}" << endl << endl;
4694 if (hasANALYSISalice) {
4695 out <<"//________________________________________________________________________________" << endl;
4696 out << "Bool_t SetupPar(const char *package) {" << endl;
4697 out << "// Compile the package and set it up." << endl;
4698 out << " TString pkgdir = package;" << endl;
4699 out << " pkgdir.ReplaceAll(\".par\",\"\");" << endl;
4700 out << " gSystem->Exec(TString::Format(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
4701 out << " TString cdir = gSystem->WorkingDirectory();" << endl;
4702 out << " gSystem->ChangeDirectory(pkgdir);" << endl;
4703 out << " // Check for BUILD.sh and execute" << endl;
4704 out << " if (!gSystem->AccessPathName(\"PROOF-INF/BUILD.sh\")) {" << endl;
4705 out << " printf(\"*******************************\\n\");" << endl;
4706 out << " printf(\"*** Building PAR archive ***\\n\");" << endl;
4707 out << " printf(\"*******************************\\n\");" << endl;
4708 out << " if (gSystem->Exec(\"PROOF-INF/BUILD.sh\")) {" << endl;
4709 out << " ::Error(\"SetupPar\", \"Cannot build par archive %s\", pkgdir.Data());" << endl;
4710 out << " gSystem->ChangeDirectory(cdir);" << endl;
4711 out << " return kFALSE;" << endl;
4712 out << " }" << endl;
4713 out << " } else {" << endl;
4714 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/BUILD.sh for package %s\", pkgdir.Data());" << endl;
4715 out << " gSystem->ChangeDirectory(cdir);" << endl;
4716 out << " return kFALSE;" << endl;
4717 out << " }" << endl;
4718 out << " // Check for SETUP.C and execute" << endl;
4719 out << " if (!gSystem->AccessPathName(\"PROOF-INF/SETUP.C\")) {" << endl;
4720 out << " printf(\"*******************************\\n\");" << endl;
4721 out << " printf(\"*** Setup PAR archive ***\\n\");" << endl;
4722 out << " printf(\"*******************************\\n\");" << endl;
4723 out << " gROOT->Macro(\"PROOF-INF/SETUP.C\");" << endl;
4724 out << " } else {" << endl;
4725 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/SETUP.C for package %s\", pkgdir.Data());" << endl;
4726 out << " gSystem->ChangeDirectory(cdir);" << endl;
4727 out << " return kFALSE;" << endl;
4728 out << " }" << endl;
4729 out << " // Restore original workdir" << endl;
4730 out << " gSystem->ChangeDirectory(cdir);" << endl;
4731 out << " return kTRUE;" << endl;
4732 out << "}" << endl;
4733 }
4734 }
4735 Bool_t copy = kTRUE;
4736 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
4737 if (copy) {
4738 CdWork();
4739 TString workdir = gGrid->GetHomeDirectory();
4740 workdir += fGridWorkingDir;
4741 if (FileExists(mergingMacro)) gGrid->Rm(mergingMacro);
4742 Info("WriteMergingMacro", "\n##### Copying merging macro: <%s> to your alien workspace", mergingMacro.Data());
4743// TFile::Cp(Form("file:%s",mergingMacro.Data()), Form("alien://%s/%s", workdir.Data(), mergingMacro.Data()));
4744 if (!copyLocal2Alien("WriteMergeMacro",mergingMacro.Data(),
4745 Form("%s/%s", workdir.Data(), mergingMacro.Data()))) Fatal("","Terminating");
4746 }
4747}
4748
4749//______________________________________________________________________________
4750Bool_t AliAnalysisAlien::SetupPar(const char *package)
4751{
4752// Compile the par file archive pointed by <package>. This must be present in the current directory.
4753// Note that for loading the compiled library. The current directory should have precedence in
4754// LD_LIBRARY_PATH
4755 TString pkgdir = package;
4756 pkgdir.ReplaceAll(".par","");
4757 gSystem->Exec(TString::Format("tar xzf %s.par", pkgdir.Data()));
4758 TString cdir = gSystem->WorkingDirectory();
4759 gSystem->ChangeDirectory(pkgdir);
4760 // Check for BUILD.sh and execute
4761 if (!gSystem->AccessPathName("PROOF-INF/BUILD.sh")) {
4762 printf("**************************************************\n");
4763 printf("*** Building PAR archive %s\n", package);
4764 printf("**************************************************\n");
4765 if (gSystem->Exec("PROOF-INF/BUILD.sh")) {
4766 ::Error("SetupPar", "Cannot build par archive %s", pkgdir.Data());
4767 gSystem->ChangeDirectory(cdir);
4768 return kFALSE;
4769 }
4770 } else {
4771 ::Error("SetupPar","Cannot access PROOF-INF/BUILD.sh for package %s", pkgdir.Data());
4772 gSystem->ChangeDirectory(cdir);
4773 return kFALSE;
4774 }
4775 // Check for SETUP.C and execute
4776 if (!gSystem->AccessPathName("PROOF-INF/SETUP.C")) {
4777 printf("**************************************************\n");
4778 printf("*** Setup PAR archive %s\n", package);
4779 printf("**************************************************\n");
4780 gROOT->Macro("PROOF-INF/SETUP.C");
4781 printf("*** Loaded library: %s\n", gSystem->GetLibraries(pkgdir,"",kFALSE));
4782 } else {
4783 ::Error("SetupPar","Cannot access PROOF-INF/SETUP.C for package %s", pkgdir.Data());
4784 gSystem->ChangeDirectory(cdir);
4785 return kFALSE;
4786 }
4787 // Restore original workdir
4788 gSystem->ChangeDirectory(cdir);
4789 return kTRUE;
4790}
4791
4792//______________________________________________________________________________
4793void AliAnalysisAlien::WriteExecutable()
4794{
4795// Generate the alien executable script.
4796 // Patch executable with -x to catch error code
4797 if (fExecutableCommand.Contains("root") &&
4798 fExecutableCommand.Contains("-q") &&
4799 !fExecutableCommand.Contains("-x")) fExecutableCommand += " -x";
4800 if (!TestBit(AliAnalysisGrid::kSubmit)) {
4801 ofstream out;
4802 out.open(fExecutable.Data(), ios::out);
4803 if (out.bad()) {
4804 Error("WriteExecutable", "Bad file name for executable: %s", fExecutable.Data());
4805 return;
4806 }
4807 out << "#!/bin/bash" << endl;
4808 // Make sure we can properly compile par files
4809 out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
4810 out << "echo \"=========================================\"" << endl;
4811 out << "echo \"############## PATH : ##############\"" << endl;
4812 out << "echo $PATH" << endl;
4813 out << "echo \"############## LD_LIBRARY_PATH : ##############\"" << endl;
4814 out << "echo $LD_LIBRARY_PATH" << endl;
4815 out << "echo \"############## ROOTSYS : ##############\"" << endl;
4816 out << "echo $ROOTSYS" << endl;
4817 out << "echo \"############## which root : ##############\"" << endl;
4818 out << "which root" << endl;
4819 out << "echo \"############## ALICE_ROOT : ##############\"" << endl;
4820 out << "echo $ALICE_ROOT" << endl;
4821 out << "echo \"############## which aliroot : ##############\"" << endl;
4822 out << "which aliroot" << endl;
4823 out << "echo \"############## system limits : ##############\"" << endl;
4824 out << "ulimit -a" << endl;
4825 out << "echo \"############## memory : ##############\"" << endl;
4826 out << "free -m" << endl;
4827 out << "echo \"=========================================\"" << endl << endl;
4828 out << fExecutableCommand << " ";
4829 out << fAnalysisMacro.Data() << " " << fExecutableArgs.Data() << endl;
4830 out << "RET=$?" << endl;
4831 out << "if [ \"$RET\" != \"0\" ];then" << endl;
4832 out << " echo \"======== ERROR : " << fAnalysisMacro.Data() << " finished with NON zero code: $RET ========\"" << endl;
4833 out << " if [ \"$RET\" -gt 128 ] && [ \"$RET\" -lt 160 ]; then"<<endl;
4834 out << " let sig=\"$RET - 128\""<<endl;
4835 out << " sigs='HUP INT QUIT ILL TRAP ABRT BUS FPE"<<endl;
4836 out << " KILL USR1 SEGV USR2 PIPE ALRM TERM STKFLT"<<endl;
4837 out << " CHLD CONT STOP TSTP TTIN TTOU URG XCPU"<<endl;
4838 out << " XFSZ VTALRM PROF WINCH IO PWR SYS'"<<endl;
4839 out << " sig=SIG`echo $sigs | awk '{ print $'\"$sig\"' }'`"<<endl;
4840 out << " echo \"======== it appears to have been killed with signal: $sig ========\""<<endl;
4841 out << " fi"<<endl;
4842 out << " exit $RET"<< endl;
4843 out << "fi" << endl << endl ;
4844 out << "echo \"======== " << fAnalysisMacro.Data() << " finished with exit code: $RET ========\"" << endl;
4845 out << "echo \"############## memory after: ##############\"" << endl;
4846 out << "free -m" << endl;
4847 }
4848 Bool_t copy = kTRUE;
4849 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
4850 if (copy) {
4851 CdWork();
4852 TString workdir = gGrid->GetHomeDirectory();
4853 workdir += fGridWorkingDir;
4854 TString executable = TString::Format("%s/%s", workdir.Data(), fExecutable.Data());
4855 if (FileExists(executable)) gGrid->Rm(executable);
4856 Info("WriteExecutable", "\n##### Copying executable file <%s> to your AliEn bin directory", fExecutable.Data());
4857 if (!copyLocal2Alien("WriteExecutable",fExecutable.Data(),
4858 executable.Data())) Fatal("","Terminating");
4859 }
4860}
4861
4862//______________________________________________________________________________
4863void AliAnalysisAlien::WriteMergeExecutable()
4864{
4865// Generate the alien executable script for the merging job.
4866 if (!fMergeViaJDL) return;
4867 TString mergeExec = fExecutable;
4868 mergeExec.ReplaceAll(".sh", "_merge.sh");
4869 if (!TestBit(AliAnalysisGrid::kSubmit)) {
4870 ofstream out;
4871 out.open(mergeExec.Data(), ios::out);
4872 if (out.bad()) {
4873 Error("WriteMergingExecutable", "Bad file name for executable: %s", mergeExec.Data());
4874 return;
4875 }
4876 out << "#!/bin/bash" << endl;
4877 // Make sure we can properly compile par files
4878 out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
4879 out << "echo \"=========================================\"" << endl;
4880 out << "echo \"############## PATH : ##############\"" << endl;
4881 out << "echo $PATH" << endl;
4882 out << "echo \"############## LD_LIBRARY_PATH : ##############\"" << endl;
4883 out << "echo $LD_LIBRARY_PATH" << endl;
4884 out << "echo \"############## ROOTSYS : ##############\"" << endl;
4885 out << "echo $ROOTSYS" << endl;
4886 out << "echo \"############## which root : ##############\"" << endl;
4887 out << "which root" << endl;
4888 out << "echo \"############## ALICE_ROOT : ##############\"" << endl;
4889 out << "echo $ALICE_ROOT" << endl;
4890 out << "echo \"############## which aliroot : ##############\"" << endl;
4891 out << "which aliroot" << endl;
4892 out << "echo \"############## system limits : ##############\"" << endl;
4893 out << "ulimit -a" << endl;
4894 out << "echo \"############## memory : ##############\"" << endl;
4895 out << "free -m" << endl;
4896 out << "echo \"=========================================\"" << endl << endl;
4897 TString mergeMacro = fExecutable;
4898 mergeMacro.ReplaceAll(".sh", "_merge.C");
4899 if (IsOneStageMerging())
4900 out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\")\"" << endl;
4901 else
4902 out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\",$2)\"" << endl;
4903 out << fExecutableCommand << " " << "$ARG" << endl;
4904 out << "RET=$?" << endl;
4905 out << "if [ \"$RET\" != \"0\" ];then" << endl;
4906 out << " echo \"======== ERROR : " << fAnalysisMacro.Data() << " finished with NON zero code: $RET ========\"" << endl;
4907 out << " if [ \"$RET\" -gt 128 ] && [ \"$RET\" -lt 160 ]; then"<<endl;
4908 out << " let sig=\"$RET - 128\""<<endl;
4909 out << " sigs='HUP INT QUIT ILL TRAP ABRT BUS FPE"<<endl;
4910 out << " KILL USR1 SEGV USR2 PIPE ALRM TERM STKFLT"<<endl;
4911 out << " CHLD CONT STOP TSTP TTIN TTOU URG XCPU"<<endl;
4912 out << " XFSZ VTALRM PROF WINCH IO PWR SYS'"<<endl;
4913 out << " sig=SIG`echo $sigs | awk '{ print $'\"$sig\"' }'`"<<endl;
4914 out << " echo \"======== it appears to have been killed with signal: $sig ========\""<<endl;
4915 out << " fi"<<endl;
4916 out << " exit $RET"<< endl;
4917 out << "fi" << endl << endl ;
4918 out << "echo \"======== " << mergeMacro.Data() << " finished with exit code: $? ========\"" << endl;
4919 out << "echo \"############## memory after: ##############\"" << endl;
4920 out << "free -m" << endl;
4921 }
4922 Bool_t copy = kTRUE;
4923 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
4924 if (copy) {
4925 CdWork();
4926 TString workdir = gGrid->GetHomeDirectory();
4927 workdir += fGridWorkingDir;
4928 TString executable = TString::Format("%s/%s", workdir.Data(), mergeExec.Data());
4929 if (FileExists(executable)) gGrid->Rm(executable);
4930 Info("WriteMergeExecutable", "\n##### Copying executable file <%s> to your AliEn bin directory", mergeExec.Data());
4931 if (!copyLocal2Alien("WriteMergeExecutable",mergeExec.Data(),
4932 executable.Data())) Fatal("","Terminating");
4933 }
4934}
4935
4936//______________________________________________________________________________
4937void AliAnalysisAlien::WriteProductionFile(const char *filename) const
4938{
4939// Write the production file to be submitted by LPM manager. The format is:
4940// First line: full_path_to_jdl estimated_no_subjobs_per_master
4941// Next lines: full_path_to_dataset XXX (XXX is a string)
4942// To submit, one has to: submit jdl XXX for all lines
4943 ofstream out;
4944 out.open(filename, ios::out);
4945 if (out.bad()) {
4946 Error("WriteProductionFile", "Bad file name: %s", filename);
4947 return;
4948 }
4949 TString workdir;
4950 if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice"))
4951 workdir = gGrid->GetHomeDirectory();
4952 workdir += fGridWorkingDir;
4953 Int_t njobspermaster = 1000*fNrunsPerMaster/fSplitMaxInputFileNumber;
4954 TString locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
4955 out << locjdl << " " << njobspermaster << endl;
4956 Int_t nmasterjobs = fInputFiles->GetEntries();
4957 for (Int_t i=0; i<nmasterjobs; i++) {
4958 TString runOutDir = gSystem->BaseName(fInputFiles->At(i)->GetName());
4959 runOutDir.ReplaceAll(".xml", "");
4960 if (fOutputToRunNo)
4961 out << Form("%s", fInputFiles->At(i)->GetName()) << " " << runOutDir << endl;
4962 else
4963 out << Form("%s", fInputFiles->At(i)->GetName()) << " " << Form("%03d", i) << endl;
4964 }
4965 if (gGrid) {
4966 Info("WriteProductionFile", "\n##### Copying production file <%s> to your work directory", filename);
4967 if (FileExists(filename)) gGrid->Rm(filename);
4968// TFile::Cp(Form("file:%s",filename), Form("alien://%s/%s", workdir.Data(),filename));
4969 if (!copyLocal2Alien("WriteProductionFile", filename,
4970 Form("%s/%s", workdir.Data(),filename))) Fatal("","Terminating");
4971 }
4972}
4973
4974//______________________________________________________________________________
4975void AliAnalysisAlien::WriteValidationScript(Bool_t merge)
4976{
4977// Generate the alien validation script.
4978 // Generate the validation script
4979 TObjString *os;
4980 if (fValidationScript.IsNull()) {
4981 fValidationScript = fExecutable;
4982 fValidationScript.ReplaceAll(".sh", "_validation.sh");
4983 }
4984 TString validationScript = fValidationScript;
4985 if (merge) validationScript.ReplaceAll(".sh", "_merge.sh");
4986 if (!Connect()) {
4987 Error("WriteValidationScript", "Alien connection required");
4988 return;
4989 }
4990 if (!fTerminateFiles.IsNull()) {
4991 fTerminateFiles.Strip();
4992 fTerminateFiles.ReplaceAll(" ",",");
4993 }
4994 TString outStream = "";
4995 if (!TestBit(AliAnalysisGrid::kTest)) outStream = " >> stdout";
4996 if (!TestBit(AliAnalysisGrid::kSubmit)) {
4997 ofstream out;
4998 out.open(validationScript, ios::out);
4999 out << "#!/bin/bash" << endl;
5000 out << "##################################################" << endl;
5001 out << "validateout=`dirname $0`" << endl;
5002 out << "validatetime=`date`" << endl;
5003 out << "validated=\"0\";" << endl;
5004 out << "error=0" << endl;
5005 out << "if [ -z $validateout ]" << endl;
5006 out << "then" << endl;
5007 out << " validateout=\".\"" << endl;
5008 out << "fi" << endl << endl;
5009 out << "cd $validateout;" << endl;
5010 out << "validateworkdir=`pwd`;" << endl << endl;
5011 out << "echo \"*******************************************************\"" << outStream << endl;
5012 out << "echo \"* Automatically generated validation script *\"" << outStream << endl;
5013 out << "" << endl;
5014 out << "echo \"* Time: $validatetime \"" << outStream << endl;
5015 out << "echo \"* Dir: $validateout\"" << outStream << endl;
5016 out << "echo \"* Workdir: $validateworkdir\"" << outStream << endl;
5017 out << "echo \"* ----------------------------------------------------*\"" << outStream << endl;
5018 out << "ls -la ./" << outStream << endl;
5019 out << "echo \"* ----------------------------------------------------*\"" << outStream << endl << endl;
5020 out << "##################################################" << endl;
5021 out << "" << endl;
5022
5023 out << "if [ ! -f stderr ] ; then" << endl;
5024 out << " error=1" << endl;
5025 out << " echo \"* ########## Job not validated - no stderr ###\" " << outStream << endl;
5026 out << " echo \"Error = $error\" " << outStream << endl;
5027 out << "fi" << endl;
5028
5029 out << "parArch=`grep -Ei \"Cannot Build the PAR Archive\" stderr`" << endl;
5030 out << "segViol=`grep -Ei \"Segmentation violation\" stderr`" << endl;
5031 out << "segFault=`grep -Ei \"Segmentation fault\" stderr`" << endl;
5032 out << "glibcErr=`grep -Ei \"*** glibc detected ***\" stderr`" << endl;
5033 out << "" << endl;
5034
5035 out << "if [ \"$parArch\" != \"\" ] ; then" << endl;
5036 out << " error=1" << endl;
5037 out << " echo \"* ########## Job not validated - PAR archive not built ###\" " << outStream << endl;
5038 out << " echo \"$parArch\" " << outStream << endl;
5039 out << " echo \"Error = $error\" " << outStream << endl;
5040 out << "fi" << endl;
5041
5042 out << "if [ \"$segViol\" != \"\" ] ; then" << endl;
5043 out << " error=1" << endl;
5044 out << " echo \"* ########## Job not validated - Segment. violation ###\" " << outStream << endl;
5045 out << " echo \"$segViol\" " << outStream << endl;
5046 out << " echo \"Error = $error\" " << outStream << endl;
5047 out << "fi" << endl;
5048
5049 out << "if [ \"$segFault\" != \"\" ] ; then" << endl;
5050 out << " error=1" << endl;
5051 out << " echo \"* ########## Job not validated - Segment. fault ###\" " << outStream << endl;
5052 out << " echo \"$segFault\" " << outStream << endl;
5053 out << " echo \"Error = $error\" " << outStream << endl;
5054 out << "fi" << endl;
5055
5056 out << "if [ \"$glibcErr\" != \"\" ] ; then" << endl;
5057 out << " error=1" << endl;
5058 out << " echo \"* ########## Job not validated - *** glibc detected *** ###\" " << outStream << endl;
5059 out << " echo \"$glibcErr\" " << outStream << endl;
5060 out << " echo \"Error = $error\" " << outStream << endl;
5061 out << "fi" << endl;
5062
5063 // Part dedicated to the specific analyses running into the train
5064
5065 TString outputFiles = fOutputFiles;
5066 if (merge && !fTerminateFiles.IsNull()) {
5067 if (!outputFiles.IsNull()) outputFiles += ",";
5068 outputFiles += fTerminateFiles;
5069 }
5070 TObjArray *arr = outputFiles.Tokenize(",");
5071 TIter next1(arr);
5072 TString outputFile;
5073 while (!merge && (os=(TObjString*)next1())) {
5074 // No need to validate outputs produced by merging since the merging macro does this
5075 outputFile = os->GetString();
5076 Int_t index = outputFile.Index("@");
5077 if (index > 0) outputFile.Remove(index);
5078 if (fTerminateFiles.Contains(outputFile)) continue;
5079 if (outputFile.Contains("*")) continue;
5080 out << "if ! [ -f " << outputFile.Data() << " ] ; then" << endl;
5081 out << " error=1" << endl;
5082 out << " echo \"Output file " << outputFile << " not found. Job FAILED !\"" << outStream << endl;
5083 out << " echo \"Output file " << outputFile << " not found. Job FAILED !\" >> stderr" << endl;
5084 out << "fi" << endl;
5085 }
5086 delete arr;
5087 out << "if ! [ -f outputs_valid ] ; then" << endl;
5088 out << " error=1" << endl;
5089 out << " echo \"Output files were not validated by the analysis manager\" >> stdout" << endl;
5090 out << " echo \"Output files were not validated by the analysis manager\" >> stderr" << endl;
5091 out << "fi" << endl;
5092
5093 out << "if [ $error = 0 ] ; then" << endl;
5094 out << " echo \"* ---------------- Job Validated ------------------*\"" << outStream << endl;
5095 if (!IsKeepLogs()) {
5096 out << " echo \"* === Logs std* will be deleted === \"" << endl;
5097 outStream = "";
5098 out << " rm -f std*" << endl;
5099 }
5100 out << "fi" << endl;
5101
5102 out << "echo \"* ----------------------------------------------------*\"" << outStream << endl;
5103 out << "echo \"*******************************************************\"" << outStream << endl;
5104 out << "cd -" << endl;
5105 out << "exit $error" << endl;
5106 }
5107 Bool_t copy = kTRUE;
5108 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
5109 if (copy) {
5110 CdWork();
5111 TString workdir = gGrid->GetHomeDirectory();
5112 workdir += fGridWorkingDir;
5113 Info("WriteValidationScript", "\n##### Copying validation script <%s> to your AliEn working space", validationScript.Data());
5114 if (FileExists(validationScript)) gGrid->Rm(validationScript);
5115// TFile::Cp(Form("file:%s",validationScript.Data()), Form("alien://%s/%s", workdir.Data(),validationScript.Data()));
5116 if (!copyLocal2Alien("WriteValidationScript", validationScript.Data(),
5117 Form("%s/%s",workdir.Data(), validationScript.Data()))) Fatal("","Terminating");
5118 }
5119}