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c57f56b7 | 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 "Riostream.h" | |
24 | #include "TROOT.h" | |
25 | #include "TSystem.h" | |
26 | #include "TFile.h" | |
27 | #include "TObjString.h" | |
28 | #include "TObjArray.h" | |
29 | #include "TGrid.h" | |
30 | #include "TGridResult.h" | |
31 | #include "TGridCollection.h" | |
32 | #include "TGridJDL.h" | |
33 | #include "TFileMerger.h" | |
34 | #include "AliAnalysisManager.h" | |
35 | #include "AliAnalysisAlien.h" | |
36 | ||
37 | ClassImp(AliAnalysisAlien) | |
38 | ||
39 | //______________________________________________________________________________ | |
40 | AliAnalysisAlien::AliAnalysisAlien() | |
41 | :AliAnalysisGrid(), | |
42 | fGridJDL(NULL), | |
43 | fPrice(0), | |
44 | fTTL(0), | |
45 | fSplitMaxInputFileNumber(0), | |
46 | fMaxInitFailed(0), | |
47 | fMasterResubmitThreshold(0), | |
48 | fRunNumbers(), | |
49 | fExecutable(), | |
50 | fArguments(), | |
51 | fAnalysisMacro(), | |
52 | fAnalysisSource(), | |
53 | fAdditionalLibs(), | |
54 | fSplitMode(), | |
55 | fAPIVersion(), | |
56 | fROOTVersion(), | |
57 | fAliROOTVersion(), | |
58 | fUser(), | |
59 | fGridWorkingDir(), | |
60 | fGridDataDir(), | |
61 | fDataPattern(), | |
62 | fGridOutputDir(), | |
63 | fOutputArchive(), | |
64 | fOutputFiles(), | |
65 | fInputFormat(), | |
e7c71df0 | 66 | fDatasetName(), |
c57f56b7 | 67 | fJDLName(), |
4e5c5506 | 68 | fInputFiles(0), |
69 | fPackages(0) | |
c57f56b7 | 70 | { |
71 | // Dummy ctor. | |
72 | SetDefaults(); | |
73 | } | |
74 | ||
75 | //______________________________________________________________________________ | |
76 | AliAnalysisAlien::AliAnalysisAlien(const char *name) | |
77 | :AliAnalysisGrid(name), | |
78 | fGridJDL(NULL), | |
79 | fPrice(0), | |
80 | fTTL(0), | |
81 | fSplitMaxInputFileNumber(0), | |
82 | fMaxInitFailed(0), | |
83 | fMasterResubmitThreshold(0), | |
84 | fRunNumbers(), | |
85 | fExecutable(), | |
86 | fArguments(), | |
87 | fAnalysisMacro(), | |
88 | fAnalysisSource(), | |
89 | fAdditionalLibs(), | |
90 | fSplitMode(), | |
91 | fAPIVersion(), | |
92 | fROOTVersion(), | |
93 | fAliROOTVersion(), | |
94 | fUser(), | |
95 | fGridWorkingDir(), | |
96 | fGridDataDir(), | |
97 | fDataPattern(), | |
98 | fGridOutputDir(), | |
99 | fOutputArchive(), | |
100 | fOutputFiles(), | |
101 | fInputFormat(), | |
e7c71df0 | 102 | fDatasetName(), |
c57f56b7 | 103 | fJDLName(), |
4e5c5506 | 104 | fInputFiles(0), |
105 | fPackages(0) | |
c57f56b7 | 106 | { |
107 | // Default ctor. | |
108 | SetDefaults(); | |
109 | } | |
110 | ||
111 | //______________________________________________________________________________ | |
112 | AliAnalysisAlien::AliAnalysisAlien(const AliAnalysisAlien& other) | |
113 | :AliAnalysisGrid(other), | |
114 | fGridJDL(NULL), | |
115 | fPrice(other.fPrice), | |
116 | fTTL(other.fTTL), | |
117 | fSplitMaxInputFileNumber(other.fSplitMaxInputFileNumber), | |
118 | fMaxInitFailed(other.fMaxInitFailed), | |
119 | fMasterResubmitThreshold(other.fMasterResubmitThreshold), | |
120 | fRunNumbers(other.fRunNumbers), | |
121 | fExecutable(other.fExecutable), | |
122 | fArguments(other.fArguments), | |
123 | fAnalysisMacro(other.fAnalysisMacro), | |
124 | fAnalysisSource(other.fAnalysisSource), | |
125 | fAdditionalLibs(other.fAdditionalLibs), | |
126 | fSplitMode(other.fSplitMode), | |
127 | fAPIVersion(other.fAPIVersion), | |
128 | fROOTVersion(other.fROOTVersion), | |
129 | fAliROOTVersion(other.fAliROOTVersion), | |
130 | fUser(other.fUser), | |
131 | fGridWorkingDir(other.fGridWorkingDir), | |
132 | fGridDataDir(other.fGridDataDir), | |
133 | fDataPattern(other.fDataPattern), | |
134 | fGridOutputDir(other.fGridOutputDir), | |
135 | fOutputArchive(other.fOutputArchive), | |
136 | fOutputFiles(other.fOutputFiles), | |
137 | fInputFormat(other.fInputFormat), | |
e7c71df0 | 138 | fDatasetName(other.fDatasetName), |
c57f56b7 | 139 | fJDLName(other.fJDLName), |
4e5c5506 | 140 | fInputFiles(0), |
141 | fPackages(0) | |
c57f56b7 | 142 | { |
143 | // Copy ctor. | |
144 | fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()"); | |
145 | if (other.fInputFiles) { | |
146 | fInputFiles = new TObjArray(); | |
147 | TIter next(other.fInputFiles); | |
148 | TObject *obj; | |
149 | while ((obj=next())) fInputFiles->Add(new TObjString(obj->GetName())); | |
150 | fInputFiles->SetOwner(); | |
151 | } | |
4e5c5506 | 152 | if (other.fPackages) { |
153 | fPackages = new TObjArray(); | |
154 | TIter next(other.fPackages); | |
155 | TObject *obj; | |
156 | while ((obj=next())) fPackages->Add(new TObjString(obj->GetName())); | |
157 | fPackages->SetOwner(); | |
158 | } | |
c57f56b7 | 159 | } |
160 | ||
161 | //______________________________________________________________________________ | |
162 | AliAnalysisAlien::~AliAnalysisAlien() | |
163 | { | |
164 | // Destructor. | |
165 | if (fGridJDL) delete fGridJDL; | |
166 | if (fInputFiles) delete fInputFiles; | |
4e5c5506 | 167 | if (fPackages) delete fPackages; |
c57f56b7 | 168 | } |
169 | ||
170 | //______________________________________________________________________________ | |
171 | AliAnalysisAlien &AliAnalysisAlien::operator=(const AliAnalysisAlien& other) | |
172 | { | |
173 | // Assignment. | |
174 | if (this != &other) { | |
175 | AliAnalysisGrid::operator=(other); | |
176 | fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()"); | |
177 | fPrice = other.fPrice; | |
178 | fTTL = other.fTTL; | |
179 | fSplitMaxInputFileNumber = other.fSplitMaxInputFileNumber; | |
180 | fMaxInitFailed = other.fMaxInitFailed; | |
181 | fMasterResubmitThreshold = other.fMasterResubmitThreshold; | |
182 | fRunNumbers = other.fRunNumbers; | |
183 | fExecutable = other.fExecutable; | |
184 | fArguments = other.fArguments; | |
185 | fAnalysisMacro = other.fAnalysisMacro; | |
186 | fAnalysisSource = other.fAnalysisSource; | |
187 | fAdditionalLibs = other.fAdditionalLibs; | |
188 | fSplitMode = other.fSplitMode; | |
189 | fAPIVersion = other.fAPIVersion; | |
190 | fROOTVersion = other.fROOTVersion; | |
191 | fAliROOTVersion = other.fAliROOTVersion; | |
192 | fUser = other.fUser; | |
193 | fGridWorkingDir = other.fGridWorkingDir; | |
194 | fGridDataDir = other.fGridDataDir; | |
195 | fDataPattern = other.fDataPattern; | |
196 | fGridOutputDir = other.fGridOutputDir; | |
197 | fOutputArchive = other.fOutputArchive; | |
198 | fOutputFiles = other.fOutputFiles; | |
199 | fInputFormat = other.fInputFormat; | |
e7c71df0 | 200 | fDatasetName = other.fDatasetName; |
c57f56b7 | 201 | fJDLName = other.fJDLName; |
202 | if (other.fInputFiles) { | |
203 | fInputFiles = new TObjArray(); | |
204 | TIter next(other.fInputFiles); | |
205 | TObject *obj; | |
206 | while ((obj=next())) fInputFiles->Add(new TObjString(obj->GetName())); | |
207 | fInputFiles->SetOwner(); | |
208 | } | |
4e5c5506 | 209 | if (other.fPackages) { |
210 | fPackages = new TObjArray(); | |
211 | TIter next(other.fPackages); | |
212 | TObject *obj; | |
213 | while ((obj=next())) fPackages->Add(new TObjString(obj->GetName())); | |
214 | fPackages->SetOwner(); | |
215 | } | |
c57f56b7 | 216 | } |
217 | return *this; | |
218 | } | |
219 | ||
220 | //______________________________________________________________________________ | |
221 | void AliAnalysisAlien::AddRunNumber(Int_t run) | |
222 | { | |
223 | // Add a run number to the list of runs to be processed. | |
224 | if (fRunNumbers.Length()) fRunNumbers += " "; | |
225 | fRunNumbers += Form("%d", run); | |
226 | } | |
227 | ||
228 | //______________________________________________________________________________ | |
229 | void AliAnalysisAlien::AddDataFile(const char *lfn) | |
230 | { | |
231 | // Adds a data file to the input to be analysed. The file should be a valid LFN | |
232 | // or point to an existing file in the alien workdir. | |
233 | if (!fInputFiles) fInputFiles = new TObjArray(); | |
234 | fInputFiles->Add(new TObjString(lfn)); | |
235 | } | |
236 | ||
237 | //______________________________________________________________________________ | |
238 | Bool_t AliAnalysisAlien::Connect() | |
239 | { | |
240 | // Try to connect to AliEn. User needs a valid token and /tmp/gclient_env_$UID sourced. | |
241 | if (gGrid && gGrid->IsConnected()) return kTRUE; | |
242 | if (!gSystem->Getenv("alien_API_USER")) { | |
243 | Error("Connect", "Make sure you:\n 1. Have called: alien-token-init <username> today\n 2. Have sourced /tmp/gclient_env_%s", | |
244 | gSystem->Getenv("UID")); | |
245 | return kFALSE; | |
246 | } | |
247 | if (!gGrid) { | |
248 | Info("Connect", "Trying to connect to AliEn ..."); | |
249 | TGrid::Connect("alien://"); | |
250 | } | |
251 | if (!gGrid || !gGrid->IsConnected()) { | |
252 | Error("Connect", "Did not managed to connect to AliEn. Make sure you have a valid token."); | |
253 | return kFALSE; | |
254 | } | |
255 | fUser = gGrid->GetUser(); | |
256 | Info("Connect", "\n##### Connected to AliEn as user %s. Setting analysis user to <%s>", fUser.Data(), fUser.Data()); | |
257 | return kTRUE; | |
258 | } | |
259 | ||
260 | //______________________________________________________________________________ | |
261 | void AliAnalysisAlien::CdWork() | |
262 | { | |
263 | // Check validity of alien workspace. Create directory if possible. | |
264 | if (!Connect()) { | |
265 | Error("CdWork", "Alien connection required"); | |
266 | return; | |
267 | } | |
268 | TString homedir = gGrid->GetHomeDirectory(); | |
269 | TString workdir = homedir + fGridWorkingDir; | |
270 | if (!gGrid->Cd(workdir)) { | |
271 | gGrid->Cd(homedir); | |
272 | if (gGrid->Mkdir(workdir)) { | |
273 | gGrid->Cd(fGridWorkingDir); | |
274 | Info("CreateJDL", "\n##### Created alien working directory %s", fGridWorkingDir.Data()); | |
275 | } else { | |
276 | Warning("CreateJDL", "Working directory %s cannot be created.\n Using %s instead.", | |
277 | workdir.Data(), homedir.Data()); | |
278 | fGridWorkingDir = ""; | |
279 | } | |
280 | } | |
281 | } | |
282 | ||
283 | //______________________________________________________________________________ | |
284 | Bool_t AliAnalysisAlien::CheckInputData() | |
285 | { | |
286 | // Check validity of input data. If necessary, create xml files. | |
287 | if (!fInputFiles && !fRunNumbers.Length()) { | |
288 | Error("CheckInputData", "You have to specify either a set of run numbers or some existing grid files. Use AddRunNumber()/AddDataFile()."); | |
289 | return kFALSE; | |
290 | } | |
291 | // Process declared files | |
292 | Bool_t is_collection = kFALSE; | |
293 | Bool_t is_xml = kFALSE; | |
294 | Bool_t use_tags = kFALSE; | |
295 | Bool_t checked = kFALSE; | |
296 | CdWork(); | |
297 | TString file; | |
298 | TString workdir = gGrid->GetHomeDirectory(); | |
299 | workdir += fGridWorkingDir; | |
300 | if (fInputFiles) { | |
301 | TObjString *objstr; | |
302 | TIter next(fInputFiles); | |
303 | while ((objstr=(TObjString*)next())) { | |
304 | file = workdir; | |
305 | file += "/"; | |
306 | file += objstr->GetString(); | |
307 | // Store full lfn path | |
308 | if (FileExists(file)) objstr->SetString(file); | |
309 | else { | |
310 | file = objstr->GetName(); | |
311 | if (!FileExists(objstr->GetName())) { | |
312 | Error("CheckInputData", "Data file %s not found or not in your working dir: %s", | |
313 | objstr->GetName(), workdir.Data()); | |
314 | return kFALSE; | |
315 | } | |
316 | } | |
317 | Bool_t iscoll, isxml, usetags; | |
318 | CheckDataType(file, iscoll, isxml, usetags); | |
319 | if (!checked) { | |
320 | checked = kTRUE; | |
321 | is_collection = iscoll; | |
322 | is_xml = isxml; | |
323 | use_tags = usetags; | |
324 | TObject::SetBit(AliAnalysisGrid::kUseTags, use_tags); | |
325 | } else { | |
326 | if ((iscoll != is_collection) || (isxml != is_xml) || (usetags != use_tags)) { | |
327 | Error("CheckInputData", "Some conflict was found in the types of inputs"); | |
328 | return kFALSE; | |
329 | } | |
330 | } | |
331 | } | |
332 | } | |
333 | // Process requested run numbers | |
334 | if (!fRunNumbers.Length()) return kTRUE; | |
335 | // Check validity of alien data directory | |
336 | if (!fGridDataDir.Length()) { | |
337 | Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()"); | |
338 | return kFALSE; | |
339 | } | |
340 | if (!gGrid->Cd(fGridDataDir)) { | |
341 | Error("CheckInputData", "Data directory %s not existing.", fGridDataDir.Data()); | |
342 | return kFALSE; | |
343 | } | |
344 | if (is_collection) { | |
345 | Error("CheckInputData", "You are using raw AliEn collections as input. Cannot process run numbers."); | |
346 | return kFALSE; | |
347 | } | |
348 | ||
349 | if (checked && !is_xml) { | |
350 | Error("CheckInputData", "Cannot mix processing of full runs with non-xml files"); | |
351 | return kFALSE; | |
352 | } | |
353 | // Check validity of run number(s) | |
354 | TObjArray *arr; | |
355 | TObjString *os; | |
356 | TString path; | |
357 | if (!checked) { | |
358 | checked = kTRUE; | |
359 | use_tags = fDataPattern.Contains("tag"); | |
360 | TObject::SetBit(AliAnalysisGrid::kUseTags, use_tags); | |
361 | } | |
362 | if (use_tags != fDataPattern.Contains("tag")) { | |
363 | Error("CheckInputData", "Cannot mix input files using/not using tags"); | |
364 | return kFALSE; | |
365 | } | |
366 | if (fRunNumbers.Length()) { | |
367 | arr = fRunNumbers.Tokenize(" "); | |
368 | TIter next(arr); | |
369 | while ((os=(TObjString*)next())) { | |
370 | path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data()); | |
371 | if (!gGrid->Cd(path)) { | |
372 | Error("CheckInputData", "Run number %s not found in path: %s", os->GetString().Data(), path.Data()); | |
373 | return kFALSE; | |
374 | } | |
375 | path = Form("%s/%s.xml", workdir.Data(),os->GetString().Data()); | |
376 | TString msg = "\n##### file: "; | |
377 | msg += path; | |
378 | msg += " type: xml_collection;"; | |
379 | if (use_tags) msg += " using_tags: Yes"; | |
380 | else msg += " using_tags: No"; | |
381 | Info("CheckDataType", msg.Data()); | |
382 | AddDataFile(path); | |
383 | } | |
384 | delete arr; | |
385 | } | |
386 | return kTRUE; | |
387 | } | |
388 | ||
389 | //______________________________________________________________________________ | |
390 | Bool_t AliAnalysisAlien::CreateDataset(const char *pattern) | |
391 | { | |
392 | // Create dataset for the grid data directory + run number. | |
393 | if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE; | |
394 | if (!Connect()) { | |
395 | Error("CreateDataset", "Cannot create dataset with no grid connection"); | |
396 | return kFALSE; | |
397 | } | |
398 | ||
399 | // Cd workspace | |
400 | CdWork(); | |
401 | TString workdir = gGrid->GetHomeDirectory(); | |
402 | workdir += fGridWorkingDir; | |
403 | ||
404 | // Compose the 'find' command arguments | |
405 | TString command; | |
406 | TString options = "-x collection "; | |
6da75e0b | 407 | if (TestBit(AliAnalysisGrid::kTest)) options += "-l 100 "; |
c57f56b7 | 408 | TString conditions = ""; |
409 | ||
410 | TString file; | |
411 | TString path; | |
412 | if (!fRunNumbers.Length()) return kTRUE; | |
413 | // Several runs | |
414 | TObjArray *arr = fRunNumbers.Tokenize(" "); | |
415 | TObjString *os; | |
416 | TIter next(arr); | |
417 | while ((os=(TObjString*)next())) { | |
418 | path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data()); | |
1535db97 | 419 | if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml"; |
420 | else file = Form("%s.xml", os->GetString().Data()); | |
421 | if (FileExists(file) && !TestBit(AliAnalysisGrid::kTest)) { | |
c57f56b7 | 422 | Info("CreateDataset", "\n##### Removing previous dataset %s", file.Data()); |
423 | gGrid->Rm(file); | |
424 | } | |
425 | command = "find "; | |
426 | command += options; | |
427 | command += path; | |
428 | command += pattern; | |
1535db97 | 429 | // conditions = Form(" > %s", file.Data()); |
c57f56b7 | 430 | command += conditions; |
431 | TGridResult *res = gGrid->Command(command); | |
432 | if (res) delete res; | |
1535db97 | 433 | // Write standard output to file |
434 | gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data())); | |
435 | if (TestBit(AliAnalysisGrid::kTest)) break; | |
436 | // Copy xml file to alien space | |
437 | TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data())); | |
c57f56b7 | 438 | if (!FileExists(file)) { |
439 | Error("CreateDataset", "Command %s did NOT succeed", command.Data()); | |
440 | delete arr; | |
441 | return kFALSE; | |
442 | } | |
c57f56b7 | 443 | } |
444 | delete arr; | |
c57f56b7 | 445 | return kTRUE; |
446 | } | |
447 | ||
448 | //______________________________________________________________________________ | |
449 | Bool_t AliAnalysisAlien::CreateJDL() | |
450 | { | |
451 | // Generate a JDL file according to current settings. The name of the file is | |
452 | // specified by fJDLName. | |
453 | Bool_t error = kFALSE; | |
454 | TObjArray *arr = 0; | |
455 | Bool_t copy = kTRUE; | |
456 | if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE; | |
457 | Bool_t generate = kTRUE; | |
458 | if (TestBit(AliAnalysisGrid::kTest) || TestBit(AliAnalysisGrid::kSubmit)) generate = kFALSE; | |
459 | if (!Connect()) { | |
460 | Error("CreateJDL", "Alien connection required"); | |
461 | return kFALSE; | |
462 | } | |
463 | // Check validity of alien workspace | |
464 | CdWork(); | |
465 | TString workdir = gGrid->GetHomeDirectory(); | |
466 | workdir += fGridWorkingDir; | |
467 | if (generate) { | |
468 | TObjString *os; | |
469 | if (!fInputFiles) { | |
470 | Error("CreateJDL()", "Define some input files for your analysis."); | |
471 | error = kTRUE; | |
472 | } | |
473 | // Compose list of input files | |
474 | // Check if output files were defined | |
475 | if (!fOutputFiles.Length()) { | |
476 | Error("CreateJDL", "You must define at least one output file"); | |
477 | error = kTRUE; | |
478 | } | |
479 | // Check if an output directory was defined and valid | |
480 | if (!fGridOutputDir.Length()) { | |
481 | Error("CreateJDL", "You must define AliEn output directory"); | |
482 | error = kTRUE; | |
483 | } else { | |
484 | if (!gGrid->Cd(fGridOutputDir)) { | |
485 | if (gGrid->Mkdir(fGridOutputDir)) { | |
486 | Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data()); | |
487 | } else { | |
488 | Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data()); | |
489 | error = kTRUE; | |
490 | } | |
491 | } | |
492 | gGrid->Cd(workdir); | |
493 | } | |
494 | // Exit if any error up to now | |
495 | if (error) return kFALSE; | |
496 | // Set JDL fields | |
497 | fGridJDL->SetValue("User", Form("\"%s\"", fUser.Data())); | |
498 | fGridJDL->SetExecutable(fExecutable); | |
499 | // fGridJDL->SetTTL((UInt_t)fTTL); | |
500 | fGridJDL->SetValue("TTL", Form("\"%d\"", fTTL)); | |
501 | if (fMaxInitFailed > 0) | |
502 | fGridJDL->SetValue("MaxInitFailed", Form("\"%d\"",fMaxInitFailed)); | |
503 | if (fSplitMaxInputFileNumber > 0) | |
504 | fGridJDL->SetValue("SplitMaxInputFileNumber", Form("\"%d\"", fSplitMaxInputFileNumber)); | |
505 | if (fSplitMode.Length()) | |
506 | fGridJDL->SetValue("Split", Form("\"%s\"", fSplitMode.Data())); | |
507 | // fGridJDL->SetSplitMode(fSplitMode, (UInt_t)fSplitMaxInputFileNumber); | |
508 | if (fAliROOTVersion.Length()) | |
509 | fGridJDL->AddToPackages("AliRoot", fAliROOTVersion); | |
510 | if (fROOTVersion.Length()) | |
511 | fGridJDL->AddToPackages("ROOT", fROOTVersion); | |
512 | if (fAPIVersion.Length()) | |
513 | fGridJDL->AddToPackages("APISCONFIG", fAPIVersion); | |
514 | fGridJDL->SetInputDataListFormat(fInputFormat); | |
515 | fGridJDL->SetInputDataList("wn.xml"); | |
516 | if (fInputFiles) { | |
517 | TIter next(fInputFiles); | |
518 | while ((os=(TObjString*)next())) | |
519 | fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetString().Data())); | |
520 | } | |
521 | fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), fAnalysisMacro.Data())); | |
522 | fGridJDL->AddToInputSandbox(Form("LF:%s/analysis.root", workdir.Data())); | |
523 | if (IsUsingTags() && !gSystem->AccessPathName("ConfigureCuts.C")) | |
524 | fGridJDL->AddToInputSandbox(Form("LF:%s/ConfigureCuts.C", workdir.Data())); | |
525 | if (fAdditionalLibs.Length()) { | |
526 | arr = fAdditionalLibs.Tokenize(" "); | |
527 | TIter next(arr); | |
528 | while ((os=(TObjString*)next())) { | |
529 | if (os->GetString().Contains(".so")) continue; | |
530 | fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), os->GetString().Data())); | |
531 | } | |
532 | delete arr; | |
533 | } | |
4e5c5506 | 534 | if (fPackages) { |
535 | TIter next(fPackages); | |
536 | TObject *obj; | |
537 | while ((obj=next())) | |
538 | fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName())); | |
539 | } | |
c57f56b7 | 540 | if (fOutputArchive.Length()) { |
541 | arr = fOutputArchive.Tokenize(" "); | |
542 | TIter next(arr); | |
543 | while ((os=(TObjString*)next())) | |
544 | fGridJDL->AddToOutputArchive(os->GetString().Data()); | |
545 | delete arr; | |
546 | } | |
547 | fGridJDL->SetOutputDirectory(Form("%s/%s/#alien_counter_03i#", workdir.Data(), fGridOutputDir.Data())); | |
548 | arr = fOutputFiles.Tokenize(" "); | |
549 | TIter next(arr); | |
550 | while ((os=(TObjString*)next())) fGridJDL->AddToOutputSandbox(os->GetString()); | |
551 | delete arr; | |
552 | // fGridJDL->SetPrice((UInt_t)fPrice); | |
553 | fGridJDL->SetValue("Price", Form("\"%d\"", fPrice)); | |
554 | fGridJDL->SetValidationCommand(Form("%s/validate.sh", workdir.Data())); | |
555 | if (fMasterResubmitThreshold) fGridJDL->SetValue("MasterResubmitThreshold", Form("\"%d%%\"", fMasterResubmitThreshold)); | |
556 | // Generate the JDL as a string | |
557 | TString sjdl = fGridJDL->Generate(); | |
558 | Int_t index; | |
559 | index = sjdl.Index("Executable"); | |
560 | if (index >= 0) sjdl.Insert(index, "\n# This is the startup script\n"); | |
561 | index = sjdl.Index("Split "); | |
562 | if (index >= 0) sjdl.Insert(index, "\n# We split per storage element\n"); | |
563 | index = sjdl.Index("SplitMaxInputFileNumber"); | |
564 | if (index >= 0) sjdl.Insert(index, "\n# We want each subjob to get maximum this number of input files\n"); | |
565 | index = sjdl.Index("InputDataCollection"); | |
566 | if (index >= 0) sjdl.Insert(index, "# Input xml collections\n"); | |
567 | index = sjdl.Index("InputFile"); | |
568 | if (index >= 0) sjdl.Insert(index, "\n# List of input files to be uploaded to wn's\n"); | |
569 | index = sjdl.Index("InputDataList "); | |
570 | if (index >= 0) sjdl.Insert(index, "\n# Collection to be processed on wn\n"); | |
571 | index = sjdl.Index("InputDataListFormat"); | |
572 | if (index >= 0) sjdl.Insert(index, "\n# Format of input data\n"); | |
573 | index = sjdl.Index("Price"); | |
574 | if (index >= 0) sjdl.Insert(index, "\n# AliEn price for this job\n"); | |
575 | index = sjdl.Index("Requirements"); | |
576 | if (index >= 0) sjdl.Insert(index, "\n# Additional requirements for the computing element\n"); | |
577 | index = sjdl.Index("Packages"); | |
578 | if (index >= 0) sjdl.Insert(index, "\n# Packages to be used\n"); | |
579 | index = sjdl.Index("User"); | |
580 | if (index >= 0) sjdl.Insert(index, "\n# AliEn user\n"); | |
581 | index = sjdl.Index("TTL"); | |
582 | if (index >= 0) sjdl.Insert(index, "\n# Time to live for the job\n"); | |
583 | index = sjdl.Index("OutputFile"); | |
584 | if (index >= 0) sjdl.Insert(index, "\n# List of output files to be registered\n"); | |
585 | index = sjdl.Index("OutputDir"); | |
586 | if (index >= 0) sjdl.Insert(index, "\n# Output directory\n"); | |
587 | index = sjdl.Index("OutputArchive"); | |
588 | if (index >= 0) sjdl.Insert(index, "\n# Files to be archived\n"); | |
589 | index = sjdl.Index("MaxInitFailed"); | |
590 | if (index >= 0) sjdl.Insert(index, "\n# Maximum number of first failing jobs to abort the master job\n"); | |
591 | index = sjdl.Index("MasterResubmitThreshold"); | |
592 | if (index >= 0) sjdl.Insert(index, "\n# Resubmit failed jobs until DONE rate reaches this percentage\n"); | |
593 | sjdl.ReplaceAll("ValidationCommand", "Validationcommand"); | |
594 | index = sjdl.Index("Validationcommand"); | |
595 | if (index >= 0) sjdl.Insert(index, "\n# Validation script to be run for each subjob\n"); | |
596 | sjdl.ReplaceAll("\"LF:", "\n \"LF:"); | |
597 | sjdl.ReplaceAll("(member", "\n (member"); | |
598 | sjdl.ReplaceAll("\",\"VO_", "\",\n \"VO_"); | |
599 | sjdl.ReplaceAll("{", "{\n "); | |
600 | sjdl.ReplaceAll("};", "\n};"); | |
601 | sjdl.ReplaceAll("{\n \n", "{\n"); | |
602 | sjdl.ReplaceAll("\n\n", "\n"); | |
603 | sjdl.ReplaceAll("OutputDirectory", "OutputDir"); | |
604 | sjdl += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n"; | |
605 | sjdl.Prepend("JobTag = \"Automatically generated analysis JDL\";\n"); | |
606 | index = sjdl.Index("JDLVariables"); | |
607 | if (index >= 0) sjdl.Insert(index, "\n# JDL variables\n"); | |
608 | // Write jdl to file | |
609 | ofstream out; | |
610 | out.open(fJDLName.Data(), ios::out); | |
611 | if (out.bad()) { | |
612 | Error("CreateJDL", "Bad file name: %s", fJDLName.Data()); | |
613 | return kFALSE; | |
614 | } | |
615 | out << sjdl << endl; | |
616 | } | |
617 | // Copy jdl to grid workspace | |
618 | if (!copy) { | |
619 | Info("CreateJDL", "\n##### You may want to review jdl:%s and analysis macro:%s before running in <submit> mode", fJDLName.Data(), fAnalysisMacro.Data()); | |
620 | } else { | |
621 | Info("CreateJDL", "\n##### Copying JDL file <%s> to your AliEn working space", fJDLName.Data()); | |
622 | if (FileExists(fJDLName)) gGrid->Rm(fJDLName); | |
623 | TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s/%s", workdir.Data(), fJDLName.Data())); | |
624 | if (fAdditionalLibs.Length()) { | |
e7c71df0 | 625 | arr = fAdditionalLibs.Tokenize(" "); |
c57f56b7 | 626 | TObjString *os; |
627 | TIter next(arr); | |
628 | while ((os=(TObjString*)next())) { | |
c57f56b7 | 629 | if (os->GetString().Contains(".so")) continue; |
4e5c5506 | 630 | Info("CreateJDL", "\n##### Copying dependency: <%s> to your alien workspace", os->GetString().Data()); |
c57f56b7 | 631 | if (FileExists(os->GetString())) gGrid->Rm(os->GetString()); |
632 | TFile::Cp(Form("file:%s",os->GetString().Data()), Form("alien://%s/%s", workdir.Data(), os->GetString().Data())); | |
633 | } | |
634 | delete arr; | |
635 | } | |
4e5c5506 | 636 | if (fPackages) { |
637 | TIter next(fPackages); | |
638 | TObject *obj; | |
639 | while ((obj=next())) { | |
640 | Info("CreateJDL", "\n##### Copying dependency: <%s> to your alien workspace", obj->GetName()); | |
641 | TFile::Cp(Form("file:%s",obj->GetName()), Form("alien://%s/%s", workdir.Data(), obj->GetName())); | |
642 | } | |
643 | } | |
c57f56b7 | 644 | } |
645 | return kTRUE; | |
646 | } | |
647 | ||
648 | //______________________________________________________________________________ | |
649 | Bool_t AliAnalysisAlien::FileExists(const char *lfn) const | |
650 | { | |
651 | // Returns true if file exists. | |
652 | if (!gGrid) { | |
653 | Error("FileExists", "No connection to grid"); | |
654 | return kFALSE; | |
655 | } | |
656 | TGridResult *res = gGrid->Ls(lfn); | |
657 | if (!res) return kFALSE; | |
658 | TMap *map = dynamic_cast<TMap*>(res->At(0)); | |
659 | if (!map) { | |
660 | delete res; | |
661 | return kFALSE; | |
662 | } | |
663 | TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("name")); | |
664 | if (!objs || !objs->GetString().Length()) { | |
665 | delete res; | |
666 | return kFALSE; | |
667 | } | |
668 | delete res; | |
669 | return kTRUE; | |
670 | } | |
671 | ||
672 | //______________________________________________________________________________ | |
673 | void AliAnalysisAlien::CheckDataType(const char *lfn, Bool_t &is_collection, Bool_t &is_xml, Bool_t &use_tags) | |
674 | { | |
675 | // Check input data type. | |
676 | is_collection = kFALSE; | |
677 | is_xml = kFALSE; | |
678 | use_tags = kFALSE; | |
679 | if (!gGrid) { | |
680 | Error("CheckDataType", "No connection to grid"); | |
681 | return; | |
682 | } | |
683 | is_collection = IsCollection(lfn); | |
684 | TString msg = "\n##### file: "; | |
685 | msg += lfn; | |
686 | if (is_collection) { | |
687 | msg += " type: raw_collection;"; | |
688 | // special treatment for collections | |
689 | is_xml = kFALSE; | |
690 | // check for tag files in the collection | |
691 | TGridResult *res = gGrid->Command(Form("listFilesFromCollection -z -v %s",lfn), kFALSE); | |
692 | if (!res) { | |
693 | msg += " using_tags: No (unknown)"; | |
694 | Info("CheckDataType", msg.Data()); | |
695 | return; | |
696 | } | |
697 | const char* typeStr = res->GetKey(0, "origLFN"); | |
698 | if (!typeStr || !strlen(typeStr)) { | |
699 | msg += " using_tags: No (unknown)"; | |
700 | Info("CheckDataType", msg.Data()); | |
701 | return; | |
702 | } | |
703 | TString file = typeStr; | |
704 | use_tags = file.Contains(".tag"); | |
705 | if (use_tags) msg += " using_tags: Yes"; | |
706 | else msg += " using_tags: No"; | |
707 | Info("CheckDataType", msg.Data()); | |
708 | return; | |
709 | } | |
710 | TString slfn(lfn); | |
711 | slfn.ToLower(); | |
712 | is_xml = slfn.Contains(".xml"); | |
713 | if (is_xml) { | |
714 | // Open xml collection and check if there are tag files inside | |
715 | msg += " type: xml_collection;"; | |
716 | TGridCollection *coll = (TGridCollection*)gROOT->ProcessLine(Form("TAlienCollection::Open(\"alien://%s\",1);",lfn)); | |
717 | if (!coll) { | |
718 | msg += " using_tags: No (unknown)"; | |
719 | Info("CheckDataType", msg.Data()); | |
720 | return; | |
721 | } | |
722 | TMap *map = coll->Next(); | |
723 | if (!map) { | |
724 | msg += " using_tags: No (unknown)"; | |
725 | Info("CheckDataType", msg.Data()); | |
726 | return; | |
727 | } | |
728 | map = (TMap*)map->GetValue(""); | |
729 | TString file; | |
730 | if (map && map->GetValue("name")) file = map->GetValue("name")->GetName(); | |
731 | use_tags = file.Contains(".tag"); | |
732 | delete coll; | |
733 | if (use_tags) msg += " using_tags: Yes"; | |
734 | else msg += " using_tags: No"; | |
735 | Info("CheckDataType", msg.Data()); | |
736 | return; | |
737 | } | |
738 | use_tags = slfn.Contains(".tag"); | |
739 | if (slfn.Contains(".root")) msg += " type: root file;"; | |
740 | else msg += " type: unhnown file;"; | |
741 | if (use_tags) msg += " using_tags: Yes"; | |
742 | else msg += " using_tags: No"; | |
743 | Info("CheckDataType", msg.Data()); | |
744 | } | |
745 | ||
4e5c5506 | 746 | //______________________________________________________________________________ |
747 | void AliAnalysisAlien::EnablePackage(const char *package) | |
748 | { | |
749 | // Enables a par file supposed to exist in the current directory. | |
750 | TString pkg(package); | |
751 | pkg.ReplaceAll(".par", ""); | |
752 | pkg += ".par"; | |
753 | if (gSystem->AccessPathName(pkg)) { | |
754 | Error("EnablePackage", "Package %s not found", pkg.Data()); | |
755 | return; | |
756 | } | |
757 | if (!TObject::TestBit(AliAnalysisGrid::kUsePars)) | |
758 | Info("EnablePackage", "AliEn plugin will use .par packages"); | |
759 | TObject::SetBit(AliAnalysisGrid::kUsePars, kTRUE); | |
760 | if (!fPackages) { | |
761 | fPackages = new TObjArray(); | |
762 | fPackages->SetOwner(); | |
763 | } | |
764 | fPackages->Add(new TObjString(pkg)); | |
765 | } | |
766 | ||
c57f56b7 | 767 | //______________________________________________________________________________ |
768 | Bool_t AliAnalysisAlien::IsCollection(const char *lfn) const | |
769 | { | |
770 | // Returns true if file is a collection. Functionality duplicated from | |
771 | // TAlien::Type() because we don't want to directly depend on TAlien. | |
772 | if (!gGrid) { | |
773 | Error("IsCollection", "No connection to grid"); | |
774 | return kFALSE; | |
775 | } | |
776 | TGridResult *res = gGrid->Command(Form("type -z %s",lfn),kFALSE); | |
777 | if (!res) return kFALSE; | |
778 | const char* typeStr = res->GetKey(0, "type"); | |
779 | if (!typeStr || !strlen(typeStr)) return kFALSE; | |
780 | if (!strcmp(typeStr, "collection")) return kTRUE; | |
781 | delete res; | |
782 | return kFALSE; | |
783 | } | |
784 | ||
785 | //______________________________________________________________________________ | |
786 | void AliAnalysisAlien::SetDefaults() | |
787 | { | |
788 | // Set default values for everything. What cannot be filled will be left empty. | |
789 | if (fGridJDL) delete fGridJDL; | |
790 | fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()"); | |
791 | fPrice = 1; | |
792 | fTTL = 30000; | |
793 | fSplitMaxInputFileNumber = 100; | |
794 | fMaxInitFailed = 0; | |
795 | fMasterResubmitThreshold = 0; | |
796 | fRunNumbers = ""; | |
797 | fExecutable = "analysis.sh"; | |
798 | fArguments = ""; | |
799 | fAnalysisMacro = "myAnalysis.C"; | |
800 | fAnalysisSource = ""; | |
801 | fAdditionalLibs = ""; | |
802 | fSplitMode = "se"; | |
803 | fAPIVersion = ""; | |
804 | fROOTVersion = ""; | |
805 | fAliROOTVersion = ""; | |
806 | fUser = ""; // Your alien user name | |
807 | fGridWorkingDir = ""; | |
808 | fGridDataDir = ""; // Can be like: /alice/sim/PDC_08a/LHC08c9/ | |
809 | fDataPattern = "*AliESDs.root"; // Can be like: *AliESDs.root, */pass1/*AliESDs.root, ... | |
810 | fGridOutputDir = "output"; | |
811 | fOutputArchive = "log_archive.zip:stdout,stderr root_archive.zip:*.root"; | |
812 | fOutputFiles = ""; // Like "AliAODs.root histos.root" | |
813 | fInputFormat = "xml-single"; | |
814 | fJDLName = "analysis.jdl"; | |
815 | } | |
816 | ||
817 | //______________________________________________________________________________ | |
818 | Bool_t AliAnalysisAlien::MergeOutputs() | |
819 | { | |
820 | // Merge analysis outputs existing in the AliEn space. | |
821 | if (TestBit(AliAnalysisGrid::kTest)) return kTRUE; | |
822 | if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE; | |
823 | if (!Connect()) { | |
824 | Error("MergeOutputs", "Cannot merge outputs without grid connection. Terminate will NOT be executed"); | |
825 | return kFALSE; | |
826 | } | |
827 | // Get the output path | |
828 | TString output = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data()); | |
829 | if (!gGrid->Cd(output)) output = Form("/%s/%s", gGrid->GetHomeDirectory(), fGridOutputDir.Data()); | |
830 | if (!gGrid->Cd(output)) { | |
831 | Error("MergeOutputs", "Grid output directory %s not found. Terminate() will NOT be executed", fGridOutputDir.Data()); | |
832 | return kFALSE; | |
833 | } | |
834 | if (!fOutputFiles.Length()) { | |
835 | Error("MergeOutputs", "No output file names defined. Are you running the right AliAnalysisAlien configuration ?"); | |
836 | return kFALSE; | |
837 | } | |
838 | TObjArray *list = fOutputFiles.Tokenize(" "); | |
839 | TIter next(list); | |
840 | TObjString *str; | |
841 | TString command; | |
842 | TString output_file; | |
843 | Bool_t merged = kTRUE; | |
844 | while((str=(TObjString*)next())) { | |
845 | output_file = str->GetString(); | |
846 | Int_t index = output_file.Index("@"); | |
847 | if (index > 0) output_file.Remove(index); | |
848 | command = Form("find %s/ *%s", output.Data(), output_file.Data()); | |
849 | printf("command: %s\n", command.Data()); | |
850 | TGridResult *res = gGrid->Command(command); | |
851 | if (!res) continue; | |
852 | TFileMerger *fm = 0; | |
853 | TIter nextmap(res); | |
854 | TMap *map; | |
855 | while ((map=(TMap*)nextmap())) { | |
856 | TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl")); | |
857 | if (!objs || !objs->GetString().Length()) { | |
858 | delete res; | |
859 | continue; | |
860 | } | |
861 | if (!fm) { | |
862 | fm = new TFileMerger(kFALSE); | |
863 | fm->SetFastMethod(kTRUE); | |
864 | fm->OutputFile(output_file); | |
865 | } | |
866 | fm->AddFile(objs->GetString()); | |
867 | } | |
868 | if (!fm || !fm->GetMergeList() || !fm->GetMergeList()->GetSize()) { | |
869 | Warning("MergeOutputs", "No <%s> files found.", output_file.Data()); | |
870 | merged = kFALSE; | |
871 | delete res; | |
872 | continue; | |
873 | } | |
874 | if (!fm->Merge()) { | |
875 | Error("MergeOutputs", "Could not merge all <%s> files", output_file.Data()); | |
876 | merged = kFALSE; | |
877 | } else { | |
878 | Info("MergeOutputs", "\n##### Merged %d output files <%s>", fm->GetMergeList()->GetSize(), output_file.Data()); | |
879 | } | |
880 | delete fm; | |
881 | delete res; | |
882 | } | |
883 | if (!merged) { | |
884 | Error("MergeOutputs", "Terminate() will NOT be executed"); | |
885 | } | |
886 | return merged; | |
887 | } | |
888 | ||
889 | //______________________________________________________________________________ | |
890 | void AliAnalysisAlien::StartAnalysis(Long64_t /*nentries*/, Long64_t /*firstEntry*/) | |
891 | { | |
892 | // Start remote grid analysis. | |
893 | ||
894 | if (TestBit(AliAnalysisGrid::kOffline)) { | |
895 | Info("StartAnalysis","\n##### OFFLINE MODE ##### Files to be used in GRID are produced but not copied \ | |
896 | \n there nor any job run. You can revise the JDL and analysis \ | |
897 | \n macro then run the same in \"submit\" mode."); | |
898 | } else if (TestBit(AliAnalysisGrid::kTest)) { | |
899 | Info("StartAnalysis","\n##### LOCAL MODE ##### Your analysis will be run locally on a subset of the requested \ | |
900 | \n dataset."); | |
901 | } else if (TestBit(AliAnalysisGrid::kSubmit)) { | |
902 | Info("StartAnalysis","\n##### SUBMIT MODE ##### Files required by your analysis are copied to your grid working \ | |
903 | \n space and job submitted."); | |
904 | } else if (TestBit(AliAnalysisGrid::kMerge)) { | |
905 | Info("StartAnalysis","\n##### MERGE MODE ##### The registered outputs of the analysis will be merged"); | |
906 | return; | |
907 | } else { | |
908 | Info("StartAnalysis","\n##### FULL ANALYSIS MODE ##### Producing needed files and submitting your analysis job..."); | |
909 | } | |
910 | ||
911 | if (!Connect()) { | |
912 | Error("StartAnalysis", "Cannot start grid analysis without grid connection"); | |
913 | return; | |
914 | } | |
915 | if (!CheckInputData()) { | |
916 | Error("StartAnalysis", "There was an error in preprocessing your requested input data"); | |
917 | return; | |
918 | } | |
919 | CreateDataset(fDataPattern); | |
920 | WriteAnalysisFile(); | |
921 | WriteAnalysisMacro(); | |
922 | WriteExecutable(); | |
923 | WriteValidationScript(); | |
924 | if (!CreateJDL()) return; | |
925 | if (TestBit(AliAnalysisGrid::kOffline)) return; | |
926 | if (TestBit(AliAnalysisGrid::kTest)) { | |
927 | // Locally testing the analysis | |
928 | Info("StartAnalysis", "\n_______________________________________________________________________ \ | |
929 | \n Running analysis script in a daughter shell as on a worker node \ | |
930 | \n_______________________________________________________________________"); | |
931 | TObjArray *list = fOutputFiles.Tokenize(" "); | |
932 | TIter next(list); | |
933 | TObjString *str; | |
934 | TString output_file; | |
935 | while((str=(TObjString*)next())) { | |
936 | output_file = str->GetString(); | |
937 | Int_t index = output_file.Index("@"); | |
938 | if (index > 0) output_file.Remove(index); | |
939 | gSystem->Exec(Form("rm %s", output_file.Data())); | |
940 | } | |
941 | delete list; | |
942 | gSystem->Exec(Form("bash %s 2>stderr", fExecutable.Data())); | |
943 | gSystem->Exec("bash validate.sh"); | |
944 | // gSystem->Exec("cat stdout"); | |
945 | return; | |
946 | } | |
947 | // Submit AliEn job | |
948 | CdWork(); | |
949 | TGridResult *res = gGrid->Command(Form("submit %s", fJDLName.Data())); | |
950 | TString jobID = ""; | |
951 | if (res) { | |
952 | const char *cjobId = res->GetKey(0,"jobId"); | |
953 | if (!cjobId) { | |
954 | Error("StartAnalysis", "Your JDL %s could not be submitted", fJDLName.Data()); | |
955 | return; | |
956 | } else { | |
957 | Info("StartAnalysis", "\n_______________________________________________________________________ \ | |
958 | \n##### Your JDL %s was successfully submitted. \nTHE JOB ID IS: %s \ | |
959 | \n_______________________________________________________________________", | |
960 | fJDLName.Data(), cjobId); | |
961 | jobID = cjobId; | |
962 | } | |
963 | delete res; | |
964 | } | |
965 | Info("StartAnalysis", "\n#### STARTING AN ALIEN SHELL FOR YOU. EXIT WHEN YOUR JOB %s HAS FINISHED. #### \ | |
966 | \n You may exit at any time and terminate the job later using the option <terminate> \ | |
967 | \n ##################################################################################", jobID.Data()); | |
968 | gGrid->Shell(); | |
969 | } | |
970 | ||
971 | //______________________________________________________________________________ | |
972 | void AliAnalysisAlien::WriteAnalysisFile() | |
973 | { | |
974 | // Write current analysis manager into the file analysis.root | |
975 | if (!TestBit(AliAnalysisGrid::kSubmit)) { | |
976 | AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager(); | |
977 | if (!mgr || !mgr->IsInitialized()) { | |
978 | Error("WriteAnalysisFile", "You need an initialized analysis manager for this"); | |
979 | return; | |
980 | } | |
981 | // Check analysis type | |
982 | TObject *handler; | |
983 | if (mgr->GetMCtruthEventHandler()) TObject::SetBit(AliAnalysisGrid::kUseMC); | |
984 | handler = (TObject*)mgr->GetInputEventHandler(); | |
985 | if (handler) { | |
986 | if (handler->InheritsFrom("AliESDInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseESD); | |
987 | if (handler->InheritsFrom("AliAODInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseAOD); | |
988 | } | |
989 | TDirectory *cdir = gDirectory; | |
990 | TFile *file = TFile::Open("analysis.root", "RECREATE"); | |
991 | if (file) { | |
992 | mgr->Write(); | |
993 | delete file; | |
994 | } | |
995 | if (cdir) cdir->cd(); | |
996 | Info("WriteAnalysisFile", "\n##### Analysis manager: %s wrote to file <analysis.root>\n", mgr->GetName()); | |
997 | } | |
998 | Bool_t copy = kTRUE; | |
999 | if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE; | |
1000 | if (copy) { | |
1001 | CdWork(); | |
1002 | TString workdir = gGrid->GetHomeDirectory(); | |
1003 | workdir += fGridWorkingDir; | |
1004 | Info("CreateJDL", "\n##### Copying file <analysis.root> containing your initialized analysis manager to your alien workspace"); | |
1005 | if (FileExists("analysis.root")) gGrid->Rm("analysis.root"); | |
1006 | TFile::Cp("file:analysis.root", Form("alien://%s/analysis.root", workdir.Data())); | |
1007 | } | |
1008 | } | |
1009 | ||
1010 | //______________________________________________________________________________ | |
1011 | void AliAnalysisAlien::WriteAnalysisMacro() | |
1012 | { | |
1013 | // Write the analysis macro that will steer the analysis in grid mode. | |
1014 | if (!TestBit(AliAnalysisGrid::kSubmit)) { | |
1015 | ofstream out; | |
1016 | out.open(fAnalysisMacro.Data(), ios::out); | |
1017 | if (!out.good()) { | |
1018 | Error("WriteAnalysisMacro", "could not open file %s for writing", fAnalysisMacro.Data()); | |
1019 | return; | |
1020 | } | |
1021 | TString func = fAnalysisMacro; | |
1022 | TString type = "ESD"; | |
1023 | TString comment = "// Analysis using "; | |
1024 | if (TObject::TestBit(AliAnalysisGrid::kUseESD)) comment += "ESD"; | |
1025 | if (TObject::TestBit(AliAnalysisGrid::kUseAOD)) { | |
1026 | type = "AOD"; | |
1027 | comment += "AOD"; | |
1028 | } | |
1029 | if (TObject::TestBit(AliAnalysisGrid::kUseMC)) comment += "/MC"; | |
1030 | else comment += " data"; | |
1031 | out << "const char *anatype = \"" << type.Data() << "\";" << endl << endl; | |
1032 | func.ReplaceAll(".C", ""); | |
1033 | out << "void " << func.Data() << "()" << endl; | |
1034 | out << "{" << endl; | |
1035 | out << comment.Data() << endl; | |
1036 | out << "// Automatically generated analysis steering macro executed in grid subjobs" << endl << endl; | |
1037 | out << "// load base root libraries" << endl; | |
1038 | out << " gSystem->Load(\"libTree\");" << endl; | |
1039 | out << " gSystem->Load(\"libGeom\");" << endl; | |
1040 | out << " gSystem->Load(\"libVMC\");" << endl; | |
1041 | out << " gSystem->Load(\"libPhysics\");" << endl << endl; | |
4e5c5506 | 1042 | if (!fPackages) { |
1043 | out << "// Load analysis framework libraries" << endl; | |
1044 | out << " gSystem->Load(\"libSTEERBase\");" << endl; | |
1045 | out << " gSystem->Load(\"libESD\");" << endl; | |
1046 | out << " gSystem->Load(\"libAOD\");" << endl; | |
1047 | out << " gSystem->Load(\"libANALYSIS\");" << endl; | |
1048 | out << " gSystem->Load(\"libANALYSISalice\");" << endl << endl; | |
1049 | out << "// include path (remove if using par files)" << endl; | |
1050 | out << " gROOT->ProcessLine(\".include $ALICE_ROOT/include\");" << endl << endl; | |
1051 | } else { | |
1052 | out << "// Compile all par packages" << endl; | |
1053 | TIter next(fPackages); | |
1054 | TObject *obj; | |
1055 | while ((obj=next())) | |
1056 | out << " if (!SetupPar(\"" << obj->GetName() << "\")) return;" << endl; | |
1057 | } | |
6da75e0b | 1058 | if (fAdditionalLibs.Length()) { |
1059 | out << "// Add aditional AliRoot libraries" << endl; | |
1060 | TObjArray *list = fAdditionalLibs.Tokenize(" "); | |
1061 | TIter next(list); | |
1062 | TObjString *str; | |
1063 | while((str=(TObjString*)next())) { | |
1064 | if (str->GetString().Contains(".so")) | |
1065 | out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl; | |
1066 | } | |
1067 | if (list) delete list; | |
1068 | } | |
1069 | out << endl; | |
c57f56b7 | 1070 | out << "// analysis source to be compiled at runtime (if any)" << endl; |
1071 | if (fAnalysisSource.Length()) { | |
1072 | TObjArray *list = fAnalysisSource.Tokenize(" "); | |
1073 | TIter next(list); | |
1074 | TObjString *str; | |
1075 | while((str=(TObjString*)next())) { | |
1076 | out << " gROOT->ProcessLine(\".L " << str->GetString().Data() << "+g\");" << endl; | |
1077 | } | |
1078 | if (list) delete list; | |
1079 | } | |
1080 | out << endl; | |
1081 | out << "// connect to AliEn and make the chain" << endl; | |
1082 | out << " if (!TGrid::Connect(\"alien://\")) return;" << endl; | |
1083 | if (IsUsingTags()) { | |
1084 | out << " TChain *chain = CreateChainFromTags(\"wn.xml\", anatype);" << endl << endl; | |
1085 | } else { | |
1086 | out << " TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl; | |
1087 | } | |
1088 | out << "// read the analysis manager from file" << endl; | |
1089 | out << " TFile *file = TFile::Open(\"analysis.root\");" << endl; | |
1090 | out << " if (!file) return;" << endl; | |
1091 | out << " TIter nextkey(file->GetListOfKeys());" << endl; | |
1092 | out << " AliAnalysisManager *mgr = 0;" << endl; | |
1093 | out << " TKey *key;" << endl; | |
1094 | out << " while ((key=(TKey*)nextkey())) {" << endl; | |
1095 | out << " if (!strcmp(key->GetClassName(), \"AliAnalysisManager\"))" << endl; | |
1096 | out << " mgr = (AliAnalysisManager*)file->Get(key->GetName());" << endl; | |
1097 | out << " };" << endl; | |
1098 | out << " if (!mgr) {" << endl; | |
1099 | out << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file analysis.root\");" << endl; | |
1100 | out << " return;" << endl; | |
1101 | out << " }" << endl << endl; | |
1102 | out << " mgr->PrintStatus();" << endl; | |
1103 | out << " mgr->StartAnalysis(\"localfile\", chain);" << endl; | |
1104 | out << "}" << endl << endl; | |
1105 | if (IsUsingTags()) { | |
1106 | out << "TChain* CreateChainFromTags(const char *xmlfile, const char *type=\"ESD\")" << endl; | |
1107 | out << "{" << endl; | |
1108 | out << "// Create a chain using tags from the xml file." << endl; | |
1109 | out << " TAlienCollection* coll = TAlienCollection::Open(xmlfile);" << endl; | |
1110 | out << " if (!coll) {" << endl; | |
1111 | out << " ::Error(\"CreateChainFromTags\", \"Cannot create an AliEn collection from %s\", xmlfile);" << endl; | |
1112 | out << " return NULL;" << endl; | |
1113 | out << " }" << endl; | |
1114 | out << " TGridResult* tagResult = coll->GetGridResult(\"\",kFALSE,kFALSE);" << endl; | |
1115 | out << " AliTagAnalysis *tagAna = new AliTagAnalysis(type);" << endl; | |
1116 | out << " tagAna->ChainGridTags(tagResult);" << endl << endl; | |
1117 | out << " AliRunTagCuts *runCuts = new AliRunTagCuts();" << endl; | |
1118 | out << " AliLHCTagCuts *lhcCuts = new AliLHCTagCuts();" << endl; | |
1119 | out << " AliDetectorTagCuts *detCuts = new AliDetectorTagCuts();" << endl; | |
1120 | out << " AliEventTagCuts *evCuts = new AliEventTagCuts();" << endl; | |
1121 | out << " // Check if the cuts configuration file was provided" << endl; | |
1122 | out << " if (!gSystem->AccessPathName(\"ConfigureCuts.C\")) {" << endl; | |
1123 | out << " gROOT->LoadMacro(\"ConfigureCuts.C\");" << endl; | |
1124 | out << " ConfigureCuts(runCuts, lhcCuts, detCuts, evCuts);" << endl; | |
1125 | out << " }" << endl; | |
1126 | out << " TChain *chain = tagAna->QueryTags(runCuts, lhcCuts, detCuts, evCuts);" << endl; | |
1127 | out << " if (!chain || !chain->GetNtrees()) return NULL;" << endl; | |
1128 | out << " chain->ls();" << endl; | |
1129 | out << " return chain;" << endl; | |
1130 | out << "}" << endl; | |
1131 | if (gSystem->AccessPathName("ConfigureCuts.C")) { | |
1132 | TString msg = "\n##### You may want to provide a macro ConfigureCuts.C with a method:\n"; | |
1133 | msg += " void ConfigureCuts(AliRunTagCuts *runCuts,\n"; | |
1134 | msg += " AliLHCTagCuts *lhcCuts,\n"; | |
1135 | msg += " AliDetectorTagCuts *detCuts,\n"; | |
1136 | msg += " AliEventTagCuts *evCuts)"; | |
1137 | Info("WriteAnalysisMacro", msg.Data()); | |
1138 | } | |
1139 | } else { | |
1140 | out << "TChain* CreateChain(const char *xmlfile, const char *type=\"ESD\")" << endl; | |
1141 | out << "{" << endl; | |
1142 | out << "// Create a chain using url's from xml file" << endl; | |
1143 | out << " TString treename = type;" << endl; | |
1144 | out << " treename.ToLower();" << endl; | |
1145 | out << " treename += \"Tree\";" << endl; | |
1146 | out << " printf(\"***************************************\");" << endl; | |
1147 | out << " printf(\" Getting chain of trees %s\\n\", treename);" << endl; | |
1148 | out << " printf(\"***************************************\");" << endl; | |
1149 | out << " TAlienCollection *coll = TAlienCollection::Open(xmlfile);" << endl; | |
1150 | out << " if (!coll) {" << endl; | |
1151 | out << " ::Error(\"CreateChain\", \"Cannot create an AliEn collection from %s\", xmlfile);" << endl; | |
1152 | out << " return NULL;" << endl; | |
1153 | out << " }" << endl; | |
1154 | out << " TChain *chain = new TChain(treename);" << endl; | |
1155 | out << " coll->Reset();" << endl; | |
1156 | out << " while (coll->Next()) chain->Add(coll->GetTURL(\"\"));" << endl; | |
1157 | out << " if (!chain->GetNtrees()) {" << endl; | |
1158 | out << " ::Error(\"CreateChain\", \"No tree found from collection %s\", xmlfile);" << endl; | |
1159 | out << " return NULL;" << endl; | |
1160 | out << " }" << endl; | |
1161 | out << " return chain;" << endl; | |
1162 | out << "}" << endl; | |
1163 | } | |
4e5c5506 | 1164 | if (fPackages) { |
1165 | out << "Bool_t SetupPar(const char *package) {" << endl; | |
1166 | out << "// Compile the package and set it up." << endl; | |
1167 | out << " TString pkgdir = package;" << endl; | |
1168 | out << " pkgdir.ReplaceAll(\".par\",\"\");" << endl; | |
1169 | out << " gSystem->Exec(Form(\"tar xvzf %s\", package));" << endl; | |
1170 | out << " TString cdir = gSystem->WorkingDirectory();" << endl; | |
1171 | out << " gSystem->ChangeDirectory(pkgdir);" << endl; | |
1172 | out << " // Check for BUILD.sh and execute" << endl; | |
1173 | out << " if (!gSystem->AccessPathName(\"PROOF-INF/BUILD.sh\")) {" << endl; | |
1174 | out << " printf(\"*******************************\\n\");" << endl; | |
1175 | out << " printf(\"*** Building PAR archive ***\\n\");" << endl; | |
1176 | out << " printf(\"*******************************\\n\");" << endl; | |
1177 | out << " if (gSystem->Exec(\"PROOF-INF/BUILD.sh\")) {" << endl; | |
1178 | out << " ::Error(\"SetupPar\", \"Cannot build par archive %s\", package);" << endl; | |
1179 | out << " gSystem->ChangeDirectory(cdir);" << endl; | |
1180 | out << " return kFALSE;" << endl; | |
1181 | out << " }" << endl; | |
1182 | out << " } else {" << endl; | |
1183 | out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/BUILD.sh for package %s\", package);" << endl; | |
1184 | out << " gSystem->ChangeDirectory(cdir);" << endl; | |
1185 | out << " return kFALSE;" << endl; | |
1186 | out << " }" << endl; | |
1187 | out << " // Check for SETUP.C and execute" << endl; | |
1188 | out << " if (!gSystem->AccessPathName(\"PROOF-INF/SETUP.C\")) {" << endl; | |
1189 | out << " printf(\"*******************************\\n\");" << endl; | |
1190 | out << " printf(\"*** Setup PAR archive ***\\n\");" << endl; | |
1191 | out << " printf(\"*******************************\\n\");" << endl; | |
1192 | out << " gROOT->Macro(\"PROOF-INF/SETUP.C\");" << endl; | |
1193 | out << " } else {" << endl; | |
1194 | out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/SETUP.C for package %s\", package);" << endl; | |
1195 | out << " gSystem->ChangeDirectory(cdir);" << endl; | |
1196 | out << " return kFALSE;" << endl; | |
1197 | out << " }" << endl; | |
1198 | out << " // Restore original workdir" << endl; | |
1199 | out << " gSystem->ChangeDirectory(cdir);" << endl; | |
1200 | out << " return kTRUE;" << endl; | |
1201 | out << "}" << endl; | |
1202 | } | |
c57f56b7 | 1203 | Info("WriteAnalysisMacro", "\n##### Analysis macro to run on worker nodes <%s> written",fAnalysisMacro.Data()); |
1204 | } | |
1205 | Bool_t copy = kTRUE; | |
1206 | if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE; | |
1207 | if (copy) { | |
1208 | CdWork(); | |
1209 | TString workdir = gGrid->GetHomeDirectory(); | |
1210 | workdir += fGridWorkingDir; | |
1211 | if (FileExists(fAnalysisMacro)) gGrid->Rm(fAnalysisMacro); | |
1212 | if (IsUsingTags() && !gSystem->AccessPathName("ConfigureCuts.C")) { | |
1213 | if (FileExists("ConfigureCuts.C")) gGrid->Rm("ConfigureCuts.C"); | |
1214 | Info("WriteAnalysisMacro", "\n##### Copying cuts configuration macro: <ConfigureCuts.C> to your alien workspace"); | |
1215 | TFile::Cp("file:ConfigureCuts.C", Form("alien://%s/ConfigureCuts.C", workdir.Data())); | |
1216 | } | |
1217 | Info("WriteAnalysisMacro", "\n##### Copying analysis macro: <%s> to your alien workspace", fAnalysisMacro.Data()); | |
1218 | TFile::Cp(Form("file:%s",fAnalysisMacro.Data()), Form("alien://%s/%s", workdir.Data(), fAnalysisMacro.Data())); | |
1219 | } | |
1220 | } | |
1221 | ||
1222 | //______________________________________________________________________________ | |
1223 | void AliAnalysisAlien::WriteExecutable() | |
1224 | { | |
1225 | // Generate the alien executable script. | |
1226 | if (!TestBit(AliAnalysisGrid::kSubmit)) { | |
1227 | ofstream out; | |
1228 | out.open(fExecutable.Data(), ios::out); | |
1229 | if (out.bad()) { | |
1230 | Error("CreateJDL", "Bad file name for executable: %s", fExecutable.Data()); | |
1231 | return; | |
1232 | } | |
1233 | out << "#!/bin/bash" << endl; | |
1234 | out << "export GCLIENT_SERVER_LIST=\"pcapiserv04.cern.ch:10000|pcapiserv05.cern.ch:10000|pcapiserv06.cern.ch:10000|pcapiserv07.cern.ch:10000\"" << endl; | |
1235 | out << "echo \"=========================================\"" << endl; | |
1236 | out << "echo \"############## PATH : ##############\"" << endl; | |
1237 | out << "echo $PATH" << endl; | |
1238 | out << "echo \"############## LD_LIBRARY_PATH : ##############\"" << endl; | |
1239 | out << "echo $LD_LIBRARY_PATH" << endl; | |
1240 | out << "echo \"############## ROOTSYS : ##############\"" << endl; | |
1241 | out << "echo $ROOTSYS" << endl; | |
1242 | out << "echo \"############## which root : ##############\"" << endl; | |
1243 | out << "which root" << endl; | |
1244 | out << "echo \"############## ALICE_ROOT : ##############\"" << endl; | |
1245 | out << "echo $ALICE_ROOT" << endl; | |
1246 | out << "echo \"############## which aliroot : ##############\"" << endl; | |
1247 | out << "which aliroot" << endl; | |
1248 | out << "echo \"=========================================\"" << endl << endl; | |
1249 | // if (TestBit(AliAnalysisGrid::kTest)) out << "root "; | |
1250 | out << "root -b -q "; | |
1251 | out << fAnalysisMacro.Data() << endl << endl; | |
1252 | out << "echo \"======== " << fAnalysisMacro.Data() << " finished ========\"" << endl; | |
1253 | } | |
1254 | Bool_t copy = kTRUE; | |
1255 | if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE; | |
1256 | if (copy) { | |
1257 | CdWork(); | |
1258 | TString workdir = gGrid->GetHomeDirectory(); | |
1259 | workdir += fGridWorkingDir; | |
1260 | TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), fExecutable.Data()); | |
1261 | if (FileExists(executable)) gGrid->Rm(executable); | |
1262 | Info("CreateJDL", "\n##### Copying executable file <%s> to your AliEn bin directory", fExecutable.Data()); | |
1263 | TFile::Cp(Form("file:%s",fExecutable.Data()), Form("alien://%s", executable.Data())); | |
1264 | } | |
1265 | } | |
1266 | ||
1267 | //______________________________________________________________________________ | |
1268 | void AliAnalysisAlien::WriteValidationScript() | |
1269 | { | |
1270 | // Generate the alien validation script. | |
1271 | // Generate the validation script | |
1272 | TObjString *os; | |
1273 | if (!Connect()) { | |
1274 | Error("WriteValidationScript", "Alien connection required"); | |
1275 | return; | |
1276 | } | |
1277 | TString out_stream = ""; | |
1278 | if (!TestBit(AliAnalysisGrid::kTest)) out_stream = " >> stdout"; | |
1279 | if (!TestBit(AliAnalysisGrid::kSubmit)) { | |
1280 | ofstream out; | |
1281 | out.open("validate.sh", ios::out); | |
1282 | out << "#!/bin/bash" << endl; | |
1283 | out << "##################################################" << endl; | |
1284 | out << "validateout=`dirname $0`" << endl; | |
1285 | out << "validatetime=`date`" << endl; | |
1286 | out << "validated=\"0\";" << endl; | |
1287 | out << "error=0" << endl; | |
1288 | out << "if [ -z $validateout ]" << endl; | |
1289 | out << "then" << endl; | |
1290 | out << " validateout=\".\"" << endl; | |
1291 | out << "fi" << endl << endl; | |
1292 | out << "cd $validateout;" << endl; | |
1293 | out << "validateworkdir=`pwd`;" << endl << endl; | |
1294 | out << "echo \"*******************************************************\"" << out_stream << endl; | |
1295 | out << "echo \"* Automatically generated validation script *\"" << out_stream << endl; | |
1296 | out << "" << endl; | |
1297 | out << "echo \"* Time: $validatetime \"" << out_stream << endl; | |
1298 | out << "echo \"* Dir: $validateout\"" << out_stream << endl; | |
1299 | out << "echo \"* Workdir: $validateworkdir\"" << out_stream << endl; | |
1300 | out << "echo \"* ----------------------------------------------------*\"" << out_stream << endl; | |
1301 | out << "ls -la ./" << out_stream << endl; | |
1302 | out << "echo \"* ----------------------------------------------------*\"" << out_stream << endl << endl; | |
1303 | out << "##################################################" << endl; | |
1304 | TObjArray *arr = fOutputFiles.Tokenize(" "); | |
1305 | TIter next1(arr); | |
1306 | TString output_file; | |
1307 | while ((os=(TObjString*)next1())) { | |
1308 | output_file = os->GetString(); | |
1309 | Int_t index = output_file.Index("@"); | |
1310 | if (index > 0) output_file.Remove(index); | |
1311 | out << "if ! [ -f " << output_file.Data() << " ] ; then" << endl; | |
1312 | out << " error=1" << endl; | |
1313 | out << " echo \"Output file(s) not found. Job FAILED !\"" << out_stream << endl; | |
1314 | out << " echo \"Output file(s) not found. Job FAILED !\" >> stderr" << endl; | |
1315 | out << "fi" << endl; | |
1316 | } | |
1317 | delete arr; | |
1318 | out << "if [ $error = 0 ] ; then" << endl; | |
1319 | out << " echo \"* ---------------- Job Validated ------------------*\"" << out_stream << endl; | |
1320 | out << "fi" << endl; | |
1321 | ||
1322 | out << "echo \"* ----------------------------------------------------*\"" << out_stream << endl; | |
1323 | out << "echo \"*******************************************************\"" << out_stream << endl; | |
1324 | out << "cd -" << endl; | |
1325 | out << "exit $error" << endl; | |
1326 | } | |
1327 | Bool_t copy = kTRUE; | |
1328 | if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE; | |
1329 | if (copy) { | |
1330 | CdWork(); | |
1331 | TString workdir = gGrid->GetHomeDirectory(); | |
1332 | workdir += fGridWorkingDir; | |
1333 | Info("CreateJDL", "\n##### Copying validation script <validate.sh> to your AliEn working space"); | |
1334 | if (FileExists("validate.sh")) gGrid->Rm("validate.sh"); | |
1335 | TFile::Cp("file:validate.sh", Form("alien://%s/validate.sh", workdir.Data())); | |
1336 | } | |
1337 | } |