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new T0 Calib for adjust time exactly in 0
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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"
0f389141 24#include "TEnv.h"
7c2cd90a 25#include "TBits.h"
0f389141 26#include "TError.h"
c57f56b7 27#include "TROOT.h"
28#include "TSystem.h"
29#include "TFile.h"
830acc4c 30#include "TFileCollection.h"
3bdcb562 31#include "TChain.h"
c57f56b7 32#include "TObjString.h"
33#include "TObjArray.h"
34#include "TGrid.h"
35#include "TGridResult.h"
36#include "TGridCollection.h"
37#include "TGridJDL.h"
d2a409b2 38#include "TGridJobStatusList.h"
39#include "TGridJobStatus.h"
c57f56b7 40#include "TFileMerger.h"
41#include "AliAnalysisManager.h"
bb885a9e 42#include "AliVEventHandler.h"
43#include "AliAnalysisDataContainer.h"
c57f56b7 44#include "AliAnalysisAlien.h"
45
46ClassImp(AliAnalysisAlien)
47
48//______________________________________________________________________________
49AliAnalysisAlien::AliAnalysisAlien()
50 :AliAnalysisGrid(),
51 fGridJDL(NULL),
0f389141 52 fMergingJDL(NULL),
c57f56b7 53 fPrice(0),
54 fTTL(0),
55 fSplitMaxInputFileNumber(0),
56 fMaxInitFailed(0),
57 fMasterResubmitThreshold(0),
bb885a9e 58 fNtestFiles(0),
319593fb 59 fNrunsPerMaster(0),
16a4353c 60 fMaxMergeFiles(0),
d2a409b2 61 fNsubmitted(0),
a3e84053 62 fProductionMode(0),
cd11251e 63 fOutputToRunNo(0),
0f389141 64 fMergeViaJDL(0),
65 fFastReadOption(0),
e1c22e21 66 fOverwriteMode(1),
149d288c 67 fNreplicas(2),
3bdcb562 68 fNproofWorkers(0),
27734f0e 69 fNproofWorkersPerSlave(0),
3bdcb562 70 fProofReset(0),
c57f56b7 71 fRunNumbers(),
72 fExecutable(),
0a1c1f7f 73 fExecutableCommand(),
c57f56b7 74 fArguments(),
631c0b05 75 fExecutableArgs(),
c57f56b7 76 fAnalysisMacro(),
77 fAnalysisSource(),
d3b18c4c 78 fValidationScript(),
d5c6455a 79 fAdditionalRootLibs(),
c57f56b7 80 fAdditionalLibs(),
81 fSplitMode(),
82 fAPIVersion(),
83 fROOTVersion(),
84 fAliROOTVersion(),
648174cf 85 fExternalPackages(),
c57f56b7 86 fUser(),
87 fGridWorkingDir(),
88 fGridDataDir(),
89 fDataPattern(),
90 fGridOutputDir(),
91 fOutputArchive(),
92 fOutputFiles(),
93 fInputFormat(),
e7c71df0 94 fDatasetName(),
c57f56b7 95 fJDLName(),
d3b18c4c 96 fTerminateFiles(),
bb885a9e 97 fMergeExcludes(),
f965131e 98 fIncludePath(),
bb885a9e 99 fCloseSE(),
0df6ccf2 100 fFriendChainName(),
c6cb3634 101 fJobTag(),
648174cf 102 fOutputSingle(),
5fce53f4 103 fRunPrefix(),
3bdcb562 104 fProofCluster(),
105 fProofDataSet(),
106 fFileForTestMode(),
107 fRootVersionForProof(),
108 fAliRootMode(),
4e5c5506 109 fInputFiles(0),
110 fPackages(0)
c57f56b7 111{
112// Dummy ctor.
113 SetDefaults();
114}
115
116//______________________________________________________________________________
117AliAnalysisAlien::AliAnalysisAlien(const char *name)
118 :AliAnalysisGrid(name),
119 fGridJDL(NULL),
0f389141 120 fMergingJDL(NULL),
c57f56b7 121 fPrice(0),
122 fTTL(0),
123 fSplitMaxInputFileNumber(0),
124 fMaxInitFailed(0),
125 fMasterResubmitThreshold(0),
bb885a9e 126 fNtestFiles(0),
319593fb 127 fNrunsPerMaster(0),
16a4353c 128 fMaxMergeFiles(0),
d2a409b2 129 fNsubmitted(0),
a3e84053 130 fProductionMode(0),
cd11251e 131 fOutputToRunNo(0),
0f389141 132 fMergeViaJDL(0),
133 fFastReadOption(0),
e1c22e21 134 fOverwriteMode(1),
149d288c 135 fNreplicas(2),
3bdcb562 136 fNproofWorkers(0),
27734f0e 137 fNproofWorkersPerSlave(0),
3bdcb562 138 fProofReset(0),
c57f56b7 139 fRunNumbers(),
140 fExecutable(),
0a1c1f7f 141 fExecutableCommand(),
c57f56b7 142 fArguments(),
631c0b05 143 fExecutableArgs(),
c57f56b7 144 fAnalysisMacro(),
145 fAnalysisSource(),
d3b18c4c 146 fValidationScript(),
d5c6455a 147 fAdditionalRootLibs(),
c57f56b7 148 fAdditionalLibs(),
149 fSplitMode(),
150 fAPIVersion(),
151 fROOTVersion(),
152 fAliROOTVersion(),
648174cf 153 fExternalPackages(),
c57f56b7 154 fUser(),
155 fGridWorkingDir(),
156 fGridDataDir(),
157 fDataPattern(),
158 fGridOutputDir(),
159 fOutputArchive(),
160 fOutputFiles(),
161 fInputFormat(),
e7c71df0 162 fDatasetName(),
c57f56b7 163 fJDLName(),
d3b18c4c 164 fTerminateFiles(),
bb885a9e 165 fMergeExcludes(),
f965131e 166 fIncludePath(),
bb885a9e 167 fCloseSE(),
0df6ccf2 168 fFriendChainName(),
c6cb3634 169 fJobTag(),
648174cf 170 fOutputSingle(),
5fce53f4 171 fRunPrefix(),
3bdcb562 172 fProofCluster(),
173 fProofDataSet(),
174 fFileForTestMode(),
175 fRootVersionForProof(),
176 fAliRootMode(),
4e5c5506 177 fInputFiles(0),
178 fPackages(0)
c57f56b7 179{
180// Default ctor.
181 SetDefaults();
182}
183
184//______________________________________________________________________________
185AliAnalysisAlien::AliAnalysisAlien(const AliAnalysisAlien& other)
186 :AliAnalysisGrid(other),
187 fGridJDL(NULL),
0f389141 188 fMergingJDL(NULL),
c57f56b7 189 fPrice(other.fPrice),
190 fTTL(other.fTTL),
191 fSplitMaxInputFileNumber(other.fSplitMaxInputFileNumber),
192 fMaxInitFailed(other.fMaxInitFailed),
193 fMasterResubmitThreshold(other.fMasterResubmitThreshold),
bb885a9e 194 fNtestFiles(other.fNtestFiles),
319593fb 195 fNrunsPerMaster(other.fNrunsPerMaster),
16a4353c 196 fMaxMergeFiles(other.fMaxMergeFiles),
d2a409b2 197 fNsubmitted(other.fNsubmitted),
a3e84053 198 fProductionMode(other.fProductionMode),
cd11251e 199 fOutputToRunNo(other.fOutputToRunNo),
0f389141 200 fMergeViaJDL(other.fMergeViaJDL),
201 fFastReadOption(other.fFastReadOption),
202 fOverwriteMode(other.fOverwriteMode),
149d288c 203 fNreplicas(other.fNreplicas),
3bdcb562 204 fNproofWorkers(other.fNproofWorkers),
27734f0e 205 fNproofWorkersPerSlave(other.fNproofWorkersPerSlave),
3bdcb562 206 fProofReset(other.fProofReset),
c57f56b7 207 fRunNumbers(other.fRunNumbers),
208 fExecutable(other.fExecutable),
0a1c1f7f 209 fExecutableCommand(other.fExecutableCommand),
c57f56b7 210 fArguments(other.fArguments),
631c0b05 211 fExecutableArgs(other.fExecutableArgs),
c57f56b7 212 fAnalysisMacro(other.fAnalysisMacro),
213 fAnalysisSource(other.fAnalysisSource),
d3b18c4c 214 fValidationScript(other.fValidationScript),
d5c6455a 215 fAdditionalRootLibs(other.fAdditionalRootLibs),
c57f56b7 216 fAdditionalLibs(other.fAdditionalLibs),
217 fSplitMode(other.fSplitMode),
218 fAPIVersion(other.fAPIVersion),
219 fROOTVersion(other.fROOTVersion),
220 fAliROOTVersion(other.fAliROOTVersion),
648174cf 221 fExternalPackages(other.fExternalPackages),
c57f56b7 222 fUser(other.fUser),
223 fGridWorkingDir(other.fGridWorkingDir),
224 fGridDataDir(other.fGridDataDir),
225 fDataPattern(other.fDataPattern),
226 fGridOutputDir(other.fGridOutputDir),
227 fOutputArchive(other.fOutputArchive),
228 fOutputFiles(other.fOutputFiles),
229 fInputFormat(other.fInputFormat),
e7c71df0 230 fDatasetName(other.fDatasetName),
c57f56b7 231 fJDLName(other.fJDLName),
d3b18c4c 232 fTerminateFiles(other.fTerminateFiles),
bb885a9e 233 fMergeExcludes(other.fMergeExcludes),
f965131e 234 fIncludePath(other.fIncludePath),
bb885a9e 235 fCloseSE(other.fCloseSE),
0df6ccf2 236 fFriendChainName(other.fFriendChainName),
c6cb3634 237 fJobTag(other.fJobTag),
648174cf 238 fOutputSingle(other.fOutputSingle),
5fce53f4 239 fRunPrefix(other.fRunPrefix),
3bdcb562 240 fProofCluster(other.fProofCluster),
241 fProofDataSet(other.fProofDataSet),
242 fFileForTestMode(other.fFileForTestMode),
243 fRootVersionForProof(other.fRootVersionForProof),
244 fAliRootMode(other.fAliRootMode),
4e5c5506 245 fInputFiles(0),
246 fPackages(0)
c57f56b7 247{
248// Copy ctor.
249 fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
0f389141 250 fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
a8739e8a 251 fRunRange[0] = other.fRunRange[0];
252 fRunRange[1] = other.fRunRange[1];
c57f56b7 253 if (other.fInputFiles) {
254 fInputFiles = new TObjArray();
255 TIter next(other.fInputFiles);
256 TObject *obj;
257 while ((obj=next())) fInputFiles->Add(new TObjString(obj->GetName()));
258 fInputFiles->SetOwner();
259 }
4e5c5506 260 if (other.fPackages) {
261 fPackages = new TObjArray();
262 TIter next(other.fPackages);
263 TObject *obj;
264 while ((obj=next())) fPackages->Add(new TObjString(obj->GetName()));
265 fPackages->SetOwner();
266 }
c57f56b7 267}
268
269//______________________________________________________________________________
270AliAnalysisAlien::~AliAnalysisAlien()
271{
272// Destructor.
273 if (fGridJDL) delete fGridJDL;
0f389141 274 if (fMergingJDL) delete fMergingJDL;
c57f56b7 275 if (fInputFiles) delete fInputFiles;
4e5c5506 276 if (fPackages) delete fPackages;
c57f56b7 277}
278
279//______________________________________________________________________________
280AliAnalysisAlien &AliAnalysisAlien::operator=(const AliAnalysisAlien& other)
281{
282// Assignment.
283 if (this != &other) {
284 AliAnalysisGrid::operator=(other);
285 fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
0f389141 286 fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
c57f56b7 287 fPrice = other.fPrice;
288 fTTL = other.fTTL;
289 fSplitMaxInputFileNumber = other.fSplitMaxInputFileNumber;
290 fMaxInitFailed = other.fMaxInitFailed;
291 fMasterResubmitThreshold = other.fMasterResubmitThreshold;
bb885a9e 292 fNtestFiles = other.fNtestFiles;
a3e84053 293 fNrunsPerMaster = other.fNrunsPerMaster;
294 fMaxMergeFiles = other.fMaxMergeFiles;
295 fNsubmitted = other.fNsubmitted;
296 fProductionMode = other.fProductionMode;
cd11251e 297 fOutputToRunNo = other.fOutputToRunNo;
0f389141 298 fMergeViaJDL = other.fMergeViaJDL;
299 fFastReadOption = other.fFastReadOption;
300 fOverwriteMode = other.fOverwriteMode;
149d288c 301 fNreplicas = other.fNreplicas;
3bdcb562 302 fNproofWorkers = other.fNproofWorkers;
27734f0e 303 fNproofWorkersPerSlave = other.fNproofWorkersPerSlave;
3bdcb562 304 fProofReset = other.fProofReset;
c57f56b7 305 fRunNumbers = other.fRunNumbers;
306 fExecutable = other.fExecutable;
0a1c1f7f 307 fExecutableCommand = other.fExecutableCommand;
c57f56b7 308 fArguments = other.fArguments;
631c0b05 309 fExecutableArgs = other.fExecutableArgs;
c57f56b7 310 fAnalysisMacro = other.fAnalysisMacro;
311 fAnalysisSource = other.fAnalysisSource;
d3b18c4c 312 fValidationScript = other.fValidationScript;
d5c6455a 313 fAdditionalRootLibs = other.fAdditionalRootLibs;
c57f56b7 314 fAdditionalLibs = other.fAdditionalLibs;
315 fSplitMode = other.fSplitMode;
316 fAPIVersion = other.fAPIVersion;
317 fROOTVersion = other.fROOTVersion;
318 fAliROOTVersion = other.fAliROOTVersion;
648174cf 319 fExternalPackages = other.fExternalPackages;
c57f56b7 320 fUser = other.fUser;
321 fGridWorkingDir = other.fGridWorkingDir;
322 fGridDataDir = other.fGridDataDir;
323 fDataPattern = other.fDataPattern;
324 fGridOutputDir = other.fGridOutputDir;
325 fOutputArchive = other.fOutputArchive;
326 fOutputFiles = other.fOutputFiles;
327 fInputFormat = other.fInputFormat;
e7c71df0 328 fDatasetName = other.fDatasetName;
c57f56b7 329 fJDLName = other.fJDLName;
d3b18c4c 330 fTerminateFiles = other.fTerminateFiles;
bb885a9e 331 fMergeExcludes = other.fMergeExcludes;
f965131e 332 fIncludePath = other.fIncludePath;
bb885a9e 333 fCloseSE = other.fCloseSE;
0df6ccf2 334 fFriendChainName = other.fFriendChainName;
c6cb3634 335 fJobTag = other.fJobTag;
648174cf 336 fOutputSingle = other.fOutputSingle;
5fce53f4 337 fRunPrefix = other.fRunPrefix;
3bdcb562 338 fProofCluster = other.fProofCluster;
339 fProofDataSet = other.fProofDataSet;
340 fFileForTestMode = other.fFileForTestMode;
341 fRootVersionForProof = other.fRootVersionForProof;
342 fAliRootMode = other.fAliRootMode;
c57f56b7 343 if (other.fInputFiles) {
344 fInputFiles = new TObjArray();
345 TIter next(other.fInputFiles);
346 TObject *obj;
347 while ((obj=next())) fInputFiles->Add(new TObjString(obj->GetName()));
348 fInputFiles->SetOwner();
349 }
4e5c5506 350 if (other.fPackages) {
351 fPackages = new TObjArray();
352 TIter next(other.fPackages);
353 TObject *obj;
354 while ((obj=next())) fPackages->Add(new TObjString(obj->GetName()));
355 fPackages->SetOwner();
356 }
c57f56b7 357 }
358 return *this;
359}
360
f965131e 361//______________________________________________________________________________
362void AliAnalysisAlien::AddIncludePath(const char *path)
363{
364// Add include path in the remote analysis macro.
365 TString p(path);
366 if (p.Contains("-I")) fIncludePath += Form("%s ", path);
367 else fIncludePath += Form("-I%s ", path);
368}
369
c57f56b7 370//______________________________________________________________________________
371void AliAnalysisAlien::AddRunNumber(Int_t run)
372{
373// Add a run number to the list of runs to be processed.
374 if (fRunNumbers.Length()) fRunNumbers += " ";
5fce53f4 375 fRunNumbers += Form("%s%d", fRunPrefix.Data(), run);
c57f56b7 376}
377
ee75cfc3 378//______________________________________________________________________________
379void AliAnalysisAlien::AddRunNumber(const char* run)
380{
381// Add a run number to the list of runs to be processed.
382 if (fRunNumbers.Length()) fRunNumbers += " ";
383 fRunNumbers += run;
384}
385
c57f56b7 386//______________________________________________________________________________
387void AliAnalysisAlien::AddDataFile(const char *lfn)
388{
389// Adds a data file to the input to be analysed. The file should be a valid LFN
390// or point to an existing file in the alien workdir.
391 if (!fInputFiles) fInputFiles = new TObjArray();
392 fInputFiles->Add(new TObjString(lfn));
393}
648174cf 394
395//______________________________________________________________________________
396void AliAnalysisAlien::AddExternalPackage(const char *package)
397{
398// Adds external packages w.r.t to the default ones (root,aliroot and gapi)
399 if (fExternalPackages) fExternalPackages += " ";
400 fExternalPackages += package;
401}
402
c57f56b7 403//______________________________________________________________________________
404Bool_t AliAnalysisAlien::Connect()
405{
406// Try to connect to AliEn. User needs a valid token and /tmp/gclient_env_$UID sourced.
407 if (gGrid && gGrid->IsConnected()) return kTRUE;
d3b18c4c 408 if (fProductionMode) return kTRUE;
c57f56b7 409 if (!gGrid) {
410 Info("Connect", "Trying to connect to AliEn ...");
411 TGrid::Connect("alien://");
412 }
413 if (!gGrid || !gGrid->IsConnected()) {
414 Error("Connect", "Did not managed to connect to AliEn. Make sure you have a valid token.");
415 return kFALSE;
416 }
417 fUser = gGrid->GetUser();
418 Info("Connect", "\n##### Connected to AliEn as user %s. Setting analysis user to <%s>", fUser.Data(), fUser.Data());
419 return kTRUE;
420}
421
422//______________________________________________________________________________
423void AliAnalysisAlien::CdWork()
424{
425// Check validity of alien workspace. Create directory if possible.
426 if (!Connect()) {
427 Error("CdWork", "Alien connection required");
428 return;
429 }
430 TString homedir = gGrid->GetHomeDirectory();
431 TString workdir = homedir + fGridWorkingDir;
923e2ca5 432 if (DirectoryExists(workdir)) {
433 gGrid->Cd(workdir);
434 return;
435 }
436 // Work directory not existing - create it
437 gGrid->Cd(homedir);
b93f8109 438 if (gGrid->Mkdir(workdir, "-p")) {
923e2ca5 439 gGrid->Cd(fGridWorkingDir);
d3b18c4c 440 Info("CdWork", "\n##### Created alien working directory %s", fGridWorkingDir.Data());
923e2ca5 441 } else {
d3b18c4c 442 Warning("CdWork", "Working directory %s cannot be created.\n Using %s instead.",
923e2ca5 443 workdir.Data(), homedir.Data());
444 fGridWorkingDir = "";
445 }
c57f56b7 446}
447
348be253 448//______________________________________________________________________________
449Bool_t AliAnalysisAlien::CheckFileCopy(const char *alienpath)
450{
451// Check if file copying is possible.
d3b18c4c 452 if (fProductionMode) return kTRUE;
348be253 453 if (!Connect()) {
454 Error("CheckFileCopy", "Not connected to AliEn. File copying cannot be tested.");
455 return kFALSE;
456 }
d3339be3 457 Info("CheckFileCopy", "Checking possibility to copy files to your AliEn home directory... \
458 \n +++ NOTE: You can disable this via: plugin->SetCheckCopy(kFALSE);");
348be253 459 // Check if alien_CLOSE_SE is defined
460 TString closeSE = gSystem->Getenv("alien_CLOSE_SE");
461 if (!closeSE.IsNull()) {
462 Info("CheckFileCopy", "Your current close storage is pointing to: \
463 \n alien_CLOSE_SE = \"%s\"", closeSE.Data());
464 } else {
465 Warning("CheckFileCopy", "Your current close storage is empty ! Depending on your location, file copying may fail.");
466 }
467 // Check if grid directory exists.
468 if (!DirectoryExists(alienpath)) {
469 Error("CheckFileCopy", "Alien path %s does not seem to exist", alienpath);
470 return kFALSE;
471 }
d3339be3 472 TFile f("plugin_test_copy", "RECREATE");
348be253 473 // User may not have write permissions to current directory
474 if (f.IsZombie()) {
475 Error("CheckFileCopy", "Cannot create local test file. Do you have write access to current directory: <%s> ?",
476 gSystem->WorkingDirectory());
477 return kFALSE;
478 }
479 f.Close();
d3339be3 480 if (FileExists(Form("alien://%s/%s",alienpath, f.GetName()))) gGrid->Rm(Form("alien://%s/%s",alienpath, f.GetName()));
481 if (!TFile::Cp(f.GetName(), Form("alien://%s/%s",alienpath, f.GetName()))) {
482 Error("CheckFileCopy", "Cannot copy files to Alien destination: <%s> This may be temporary, or: \
348be253 483 \n# 1. Make sure you have write permissions there. If this is the case: \
484 \n# 2. Check the storage availability at: http://alimonitor.cern.ch/stats?page=SE/table \
485 \n# Do: export alien_CLOSE_SE=\"working_disk_SE\" \
486 \n# To make this permanent put in in your .bashrc (in .alienshrc is not enough) \
487 \n# Redo token: rm /tmp/x509up_u$UID then: alien-token-init <username>", alienpath);
488 gSystem->Unlink(f.GetName());
489 return kFALSE;
490 }
491 gSystem->Unlink(f.GetName());
d3339be3 492 gGrid->Rm(Form("%s%s",alienpath,f.GetName()));
493 Info("CheckFileCopy", "### ...SUCCESS ###");
348be253 494 return kTRUE;
495}
496
c57f56b7 497//______________________________________________________________________________
498Bool_t AliAnalysisAlien::CheckInputData()
499{
500// Check validity of input data. If necessary, create xml files.
d3b18c4c 501 if (fProductionMode) return kTRUE;
a8739e8a 502 if (!fInputFiles && !fRunNumbers.Length() && !fRunRange[0]) {
d2a409b2 503 if (!fGridDataDir.Length()) {
504 Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
505 return kFALSE;
506 }
507 Info("CheckInputData", "Analysis will make a single xml for base data directory %s",fGridDataDir.Data());
23329835 508 if (fDataPattern.Contains("tag") && TestBit(AliAnalysisGrid::kTest))
509 TObject::SetBit(AliAnalysisGrid::kUseTags, kTRUE); // ADDED (fix problem in determining the tag usage in test mode)
d2a409b2 510 return kTRUE;
c57f56b7 511 }
512 // Process declared files
a2f5fc01 513 Bool_t isCollection = kFALSE;
514 Bool_t isXml = kFALSE;
515 Bool_t useTags = kFALSE;
c57f56b7 516 Bool_t checked = kFALSE;
d3b18c4c 517 if (!TestBit(AliAnalysisGrid::kTest)) CdWork();
c57f56b7 518 TString file;
519 TString workdir = gGrid->GetHomeDirectory();
520 workdir += fGridWorkingDir;
521 if (fInputFiles) {
522 TObjString *objstr;
523 TIter next(fInputFiles);
524 while ((objstr=(TObjString*)next())) {
525 file = workdir;
526 file += "/";
527 file += objstr->GetString();
528 // Store full lfn path
529 if (FileExists(file)) objstr->SetString(file);
530 else {
531 file = objstr->GetName();
532 if (!FileExists(objstr->GetName())) {
533 Error("CheckInputData", "Data file %s not found or not in your working dir: %s",
534 objstr->GetName(), workdir.Data());
535 return kFALSE;
536 }
537 }
538 Bool_t iscoll, isxml, usetags;
539 CheckDataType(file, iscoll, isxml, usetags);
540 if (!checked) {
541 checked = kTRUE;
a2f5fc01 542 isCollection = iscoll;
543 isXml = isxml;
544 useTags = usetags;
545 TObject::SetBit(AliAnalysisGrid::kUseTags, useTags);
c57f56b7 546 } else {
a2f5fc01 547 if ((iscoll != isCollection) || (isxml != isXml) || (usetags != useTags)) {
c57f56b7 548 Error("CheckInputData", "Some conflict was found in the types of inputs");
549 return kFALSE;
550 }
551 }
552 }
553 }
554 // Process requested run numbers
a8739e8a 555 if (!fRunNumbers.Length() && !fRunRange[0]) return kTRUE;
c57f56b7 556 // Check validity of alien data directory
557 if (!fGridDataDir.Length()) {
558 Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
559 return kFALSE;
560 }
923e2ca5 561 if (!DirectoryExists(fGridDataDir)) {
c57f56b7 562 Error("CheckInputData", "Data directory %s not existing.", fGridDataDir.Data());
563 return kFALSE;
564 }
a2f5fc01 565 if (isCollection) {
c57f56b7 566 Error("CheckInputData", "You are using raw AliEn collections as input. Cannot process run numbers.");
567 return kFALSE;
568 }
569
a2f5fc01 570 if (checked && !isXml) {
c57f56b7 571 Error("CheckInputData", "Cannot mix processing of full runs with non-xml files");
572 return kFALSE;
573 }
574 // Check validity of run number(s)
575 TObjArray *arr;
576 TObjString *os;
319593fb 577 Int_t nruns = 0;
904f9f5f 578 TString schunk, schunk2;
c57f56b7 579 TString path;
580 if (!checked) {
581 checked = kTRUE;
a2f5fc01 582 useTags = fDataPattern.Contains("tag");
583 TObject::SetBit(AliAnalysisGrid::kUseTags, useTags);
c57f56b7 584 }
a2f5fc01 585 if (useTags != fDataPattern.Contains("tag")) {
c57f56b7 586 Error("CheckInputData", "Cannot mix input files using/not using tags");
587 return kFALSE;
588 }
589 if (fRunNumbers.Length()) {
a8739e8a 590 Info("CheckDataType", "Using supplied run numbers (run ranges are ignored)");
c57f56b7 591 arr = fRunNumbers.Tokenize(" ");
592 TIter next(arr);
593 while ((os=(TObjString*)next())) {
594 path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data());
923e2ca5 595 if (!DirectoryExists(path)) {
596 Warning("CheckInputData", "Run number %s not found in path: <%s>", os->GetString().Data(), path.Data());
a8739e8a 597 continue;
c57f56b7 598 }
599 path = Form("%s/%s.xml", workdir.Data(),os->GetString().Data());
600 TString msg = "\n##### file: ";
601 msg += path;
602 msg += " type: xml_collection;";
a2f5fc01 603 if (useTags) msg += " using_tags: Yes";
c57f56b7 604 else msg += " using_tags: No";
23329835 605 Info("CheckDataType", "%s", msg.Data());
319593fb 606 if (fNrunsPerMaster<2) {
d2a409b2 607 AddDataFile(Form("%s.xml", os->GetString().Data()));
319593fb 608 } else {
609 nruns++;
610 if (((nruns-1)%fNrunsPerMaster) == 0) {
611 schunk = os->GetString();
612 }
613 if ((nruns%fNrunsPerMaster)!=0 && os!=arr->Last()) continue;
614 schunk += Form("_%s.xml", os->GetString().Data());
d2a409b2 615 AddDataFile(schunk);
319593fb 616 }
c57f56b7 617 }
618 delete arr;
a8739e8a 619 } else {
620 Info("CheckDataType", "Using run range [%d, %d]", fRunRange[0], fRunRange[1]);
621 for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
5fce53f4 622 path = Form("%s/%s%d ", fGridDataDir.Data(), fRunPrefix.Data(), irun);
923e2ca5 623 if (!DirectoryExists(path)) {
624// Warning("CheckInputData", "Run number %d not found in path: <%s>", irun, path.Data());
a8739e8a 625 continue;
626 }
5fce53f4 627 path = Form("%s/%s%d.xml", workdir.Data(),fRunPrefix.Data(),irun);
a8739e8a 628 TString msg = "\n##### file: ";
629 msg += path;
630 msg += " type: xml_collection;";
a2f5fc01 631 if (useTags) msg += " using_tags: Yes";
a8739e8a 632 else msg += " using_tags: No";
23329835 633 Info("CheckDataType", "%s", msg.Data());
319593fb 634 if (fNrunsPerMaster<2) {
5fce53f4 635 AddDataFile(Form("%s%d.xml",fRunPrefix.Data(),irun));
319593fb 636 } else {
637 nruns++;
638 if (((nruns-1)%fNrunsPerMaster) == 0) {
5fce53f4 639 schunk = Form("%s%d", fRunPrefix.Data(),irun);
319593fb 640 }
904f9f5f 641 schunk2 = Form("_%s%d.xml", fRunPrefix.Data(), irun);
319593fb 642 if ((nruns%fNrunsPerMaster)!=0 && irun != fRunRange[1]) continue;
904f9f5f 643 schunk += schunk2;
d2a409b2 644 AddDataFile(schunk);
319593fb 645 }
a8739e8a 646 }
904f9f5f 647 if (!fInputFiles) {
648 schunk += schunk2;
649 AddDataFile(schunk);
650 }
c57f56b7 651 }
652 return kTRUE;
653}
654
655//______________________________________________________________________________
656Bool_t AliAnalysisAlien::CreateDataset(const char *pattern)
657{
658// Create dataset for the grid data directory + run number.
d3b18c4c 659 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline)) return kTRUE;
c57f56b7 660 if (!Connect()) {
661 Error("CreateDataset", "Cannot create dataset with no grid connection");
662 return kFALSE;
663 }
664
665 // Cd workspace
d3b18c4c 666 if (!TestBit(AliAnalysisGrid::kTest)) CdWork();
c57f56b7 667 TString workdir = gGrid->GetHomeDirectory();
668 workdir += fGridWorkingDir;
669
670 // Compose the 'find' command arguments
671 TString command;
672 TString options = "-x collection ";
bb885a9e 673 if (TestBit(AliAnalysisGrid::kTest)) options += Form("-l %d ", fNtestFiles);
c57f56b7 674 TString conditions = "";
675
676 TString file;
677 TString path;
319593fb 678 Int_t nruns = 0;
904f9f5f 679 TString schunk, schunk2;
ab254fd1 680 TGridCollection *cbase=0, *cadd=0;
d2a409b2 681 if (!fRunNumbers.Length() && !fRunRange[0]) {
682 if (fInputFiles && fInputFiles->GetEntries()) return kTRUE;
683 // Make a single data collection from data directory.
684 path = fGridDataDir;
923e2ca5 685 if (!DirectoryExists(path)) {
d2a409b2 686 Error("CreateDataset", "Path to data directory %s not valid",fGridDataDir.Data());
687 return kFALSE;
688 }
923e2ca5 689// CdWork();
d2a409b2 690 if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
691 else file = Form("%s.xml", gSystem->BaseName(path));
0f389141 692 if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
d2a409b2 693 command = "find ";
694 command += options;
695 command += path;
696 command += " ";
697 command += pattern;
698 command += conditions;
84fcd93f 699 printf("command: %s\n", command.Data());
d2a409b2 700 TGridResult *res = gGrid->Command(command);
701 if (res) delete res;
702 // Write standard output to file
703 gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
a2f5fc01 704 Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE;
705 Bool_t nullFile = kFALSE;
706 if (!hasGrep) {
d3339be3 707 Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command");
708 } else {
a2f5fc01 709 nullFile = (gSystem->Exec(Form("grep /event %s 2>/dev/null > /dev/null",file.Data()))==0)?kFALSE:kTRUE;
710 if (nullFile) {
defd7a3a 711 Error("CreateDataset","Dataset %s produced by the previous find command is empty !", file.Data());
712 return kFALSE;
713 }
d3339be3 714 }
0f389141 715 }
716 Bool_t fileExists = FileExists(file);
717 if (!TestBit(AliAnalysisGrid::kTest) && (!fileExists || fOverwriteMode)) {
d2a409b2 718 // Copy xml file to alien space
0f389141 719 if (fileExists) gGrid->Rm(file);
d2a409b2 720 TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
721 if (!FileExists(file)) {
722 Error("CreateDataset", "Command %s did NOT succeed", command.Data());
723 return kFALSE;
724 }
725 // Update list of files to be processed.
726 }
727 AddDataFile(Form("%s/%s", workdir.Data(), file.Data()));
728 return kTRUE;
729 }
c57f56b7 730 // Several runs
a2f5fc01 731 Bool_t nullResult = kTRUE;
a8739e8a 732 if (fRunNumbers.Length()) {
733 TObjArray *arr = fRunNumbers.Tokenize(" ");
734 TObjString *os;
735 TIter next(arr);
736 while ((os=(TObjString*)next())) {
737 path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data());
923e2ca5 738 if (!DirectoryExists(path)) continue;
739// CdWork();
a8739e8a 740 if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
741 else file = Form("%s.xml", os->GetString().Data());
319593fb 742 // If local collection file does not exist, create it via 'find' command.
d3339be3 743 if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
319593fb 744 command = "find ";
745 command += options;
746 command += path;
747 command += pattern;
748 command += conditions;
749 TGridResult *res = gGrid->Command(command);
750 if (res) delete res;
751 // Write standard output to file
752 gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
a2f5fc01 753 Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE;
754 Bool_t nullFile = kFALSE;
755 if (!hasGrep) {
d3339be3 756 Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command");
757 } else {
a2f5fc01 758 nullFile = (gSystem->Exec(Form("grep /event %s 2>/dev/null > /dev/null",file.Data()))==0)?kFALSE:kTRUE;
759 if (nullFile) {
defd7a3a 760 Warning("CreateDataset","Dataset %s produced by: <%s> is empty !", file.Data(), command.Data());
761 fRunNumbers.ReplaceAll(os->GetString().Data(), "");
762 continue;
763 }
d3339be3 764 }
a2f5fc01 765 nullResult = kFALSE;
d3339be3 766 }
a8739e8a 767 if (TestBit(AliAnalysisGrid::kTest)) break;
319593fb 768 // Check if there is one run per master job.
769 if (fNrunsPerMaster<2) {
770 if (FileExists(file)) {
0f389141 771 if (fOverwriteMode) gGrid->Rm(file);
772 else {
773 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
774 continue;
775 }
319593fb 776 }
777 // Copy xml file to alien space
778 TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
779 if (!FileExists(file)) {
780 Error("CreateDataset", "Command %s did NOT succeed", command.Data());
781 delete arr;
782 return kFALSE;
783 }
784 } else {
785 nruns++;
786 if (((nruns-1)%fNrunsPerMaster) == 0) {
787 schunk = os->GetString();
788 cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
789 } else {
790 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
84fcd93f 791 printf(" Merging collection <%s> into masterjob input...\n", file.Data());
319593fb 792 cbase->Add(cadd);
793 delete cadd;
794 }
795 if ((nruns%fNrunsPerMaster)!=0 && os!=arr->Last()) {
796 continue;
797 }
798 schunk += Form("_%s.xml", os->GetString().Data());
0f389141 799 if (FileExists(schunk)) {
800 if (fOverwriteMode) gGrid->Rm(file);
801 else {
802 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
803 continue;
804 }
319593fb 805 }
84fcd93f 806 printf("Exporting merged collection <%s> and copying to AliEn\n", schunk.Data());
319593fb 807 cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs");
e95434bc 808 TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data()));
319593fb 809 if (!FileExists(schunk)) {
810 Error("CreateDataset", "Copy command did NOT succeed for %s", schunk.Data());
811 delete arr;
812 return kFALSE;
813 }
d3339be3 814 }
a8739e8a 815 }
816 delete arr;
a2f5fc01 817 if (nullResult) {
d3339be3 818 Error("CreateDataset", "No valid dataset corresponding to the query!");
819 return kFALSE;
820 }
a8739e8a 821 } else {
822 // Process a full run range.
823 for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
5fce53f4 824 path = Form("%s/%s%d ", fGridDataDir.Data(), fRunPrefix.Data(), irun);
923e2ca5 825 if (!DirectoryExists(path)) continue;
826// CdWork();
a8739e8a 827 if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
5fce53f4 828 else file = Form("%s%d.xml", fRunPrefix.Data(), irun);
0f389141 829 if (FileExists(file) && fNrunsPerMaster<2 && !TestBit(AliAnalysisGrid::kTest)) {
830 if (fOverwriteMode) gGrid->Rm(file);
831 else {
832 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
833 continue;
834 }
a8739e8a 835 }
319593fb 836 // If local collection file does not exist, create it via 'find' command.
d3339be3 837 if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
319593fb 838 command = "find ";
839 command += options;
840 command += path;
841 command += pattern;
842 command += conditions;
843 TGridResult *res = gGrid->Command(command);
844 if (res) delete res;
845 // Write standard output to file
846 gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
a2f5fc01 847 Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE;
848 Bool_t nullFile = kFALSE;
849 if (!hasGrep) {
d3339be3 850 Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command");
851 } else {
a2f5fc01 852 nullFile = (gSystem->Exec(Form("grep /event %s 2>/dev/null > /dev/null",file.Data()))==0)?kFALSE:kTRUE;
853 if (nullFile) {
defd7a3a 854 Warning("CreateDataset","Dataset %s produced by: <%s> is empty !", file.Data(), command.Data());
855 continue;
856 }
d3339be3 857 }
a2f5fc01 858 nullResult = kFALSE;
319593fb 859 }
a8739e8a 860 if (TestBit(AliAnalysisGrid::kTest)) break;
319593fb 861 // Check if there is one run per master job.
862 if (fNrunsPerMaster<2) {
863 if (FileExists(file)) {
0f389141 864 if (fOverwriteMode) gGrid->Rm(file);
865 else {
866 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
867 continue;
868 }
319593fb 869 }
870 // Copy xml file to alien space
871 TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
872 if (!FileExists(file)) {
873 Error("CreateDataset", "Command %s did NOT succeed", command.Data());
874 return kFALSE;
875 }
876 } else {
877 nruns++;
95e5b448 878 // Check if the collection for the chunk exist locally.
879 Int_t nchunk = (nruns-1)/fNrunsPerMaster;
0f389141 880 if (FileExists(fInputFiles->At(nchunk)->GetName())) {
881 if (fOverwriteMode) gGrid->Rm(fInputFiles->At(nchunk)->GetName());
882 else continue;
883 }
84fcd93f 884 printf(" Merging collection <%s> into %d runs chunk...\n",file.Data(),fNrunsPerMaster);
319593fb 885 if (((nruns-1)%fNrunsPerMaster) == 0) {
904f9f5f 886 schunk = Form("%s%d", fRunPrefix.Data(), irun);
319593fb 887 cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
888 } else {
889 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
890 cbase->Add(cadd);
891 delete cadd;
892 }
904f9f5f 893 schunk2 = Form("%s_%s%d.xml", schunk.Data(), fRunPrefix.Data(), irun);
894 if ((nruns%fNrunsPerMaster)!=0 && irun!=fRunRange[1] && schunk2 != fInputFiles->Last()->GetName()) {
319593fb 895 continue;
896 }
904f9f5f 897 schunk = schunk2;
319593fb 898 if (FileExists(schunk)) {
0f389141 899 if (fOverwriteMode) gGrid->Rm(schunk);
900 else {
901 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
902 continue;
903 }
319593fb 904 }
84fcd93f 905 printf("Exporting merged collection <%s> and copying to AliEn.\n", schunk.Data());
319593fb 906 cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs");
95e5b448 907 if (FileExists(schunk)) {
0f389141 908 if (fOverwriteMode) gGrid->Rm(schunk);
909 else {
910 Info("CreateDataset", "\n##### Dataset %s exist. Skipping copy...", schunk.Data());
911 continue;
912 }
95e5b448 913 }
319593fb 914 TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data()));
915 if (!FileExists(schunk)) {
916 Error("CreateDataset", "Copy command did NOT succeed for %s", schunk.Data());
917 return kFALSE;
918 }
919 }
c57f56b7 920 }
a2f5fc01 921 if (nullResult) {
d3339be3 922 Error("CreateDataset", "No valid dataset corresponding to the query!");
923 return kFALSE;
924 }
a8739e8a 925 }
c57f56b7 926 return kTRUE;
927}
928
929//______________________________________________________________________________
930Bool_t AliAnalysisAlien::CreateJDL()
931{
932// Generate a JDL file according to current settings. The name of the file is
933// specified by fJDLName.
934 Bool_t error = kFALSE;
935 TObjArray *arr = 0;
936 Bool_t copy = kTRUE;
d3b18c4c 937 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
c57f56b7 938 Bool_t generate = kTRUE;
939 if (TestBit(AliAnalysisGrid::kTest) || TestBit(AliAnalysisGrid::kSubmit)) generate = kFALSE;
940 if (!Connect()) {
941 Error("CreateJDL", "Alien connection required");
942 return kFALSE;
943 }
944 // Check validity of alien workspace
d3b18c4c 945 TString workdir;
946 if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice")) workdir = gGrid->GetHomeDirectory();
947 if (!fProductionMode && !TestBit(AliAnalysisGrid::kTest)) CdWork();
c57f56b7 948 workdir += fGridWorkingDir;
949 if (generate) {
950 TObjString *os;
951 if (!fInputFiles) {
952 Error("CreateJDL()", "Define some input files for your analysis.");
953 error = kTRUE;
954 }
955 // Compose list of input files
956 // Check if output files were defined
957 if (!fOutputFiles.Length()) {
958 Error("CreateJDL", "You must define at least one output file");
959 error = kTRUE;
960 }
961 // Check if an output directory was defined and valid
962 if (!fGridOutputDir.Length()) {
963 Error("CreateJDL", "You must define AliEn output directory");
964 error = kTRUE;
965 } else {
d3b18c4c 966 if (!fProductionMode) {
967 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
968 if (!DirectoryExists(fGridOutputDir)) {
969 if (gGrid->Mkdir(fGridOutputDir,"-p")) {
970 Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
971 } else {
972 Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
973 // error = kTRUE;
974 }
975 }
976 gGrid->Cd(workdir);
977 }
c57f56b7 978 }
979 // Exit if any error up to now
980 if (error) return kFALSE;
981 // Set JDL fields
0f389141 982 if (!fUser.IsNull()) {
983 fGridJDL->SetValue("User", Form("\"%s\"", fUser.Data()));
984 fMergingJDL->SetValue("User", Form("\"%s\"", fUser.Data()));
985 }
986 fGridJDL->SetExecutable(fExecutable, "This is the startup script");
987 TString mergeExec = fExecutable;
988 mergeExec.ReplaceAll(".sh", "_merge.sh");
989 fMergingJDL->SetExecutable(mergeExec, "This is the startup script");
990 mergeExec.ReplaceAll(".sh", ".C");
991 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),mergeExec.Data()), "List of input files to be uploaded to workers");
b5b9dee8 992 if (!fArguments.IsNull())
993 fGridJDL->SetArguments(fArguments, "Arguments for the executable command");
d3b18c4c 994 if (IsOneStageMerging()) fMergingJDL->SetArguments(fGridOutputDir);
995 else fMergingJDL->SetArguments("$1 $2 $3");
1f0d1ca2 996 fGridJDL->SetValue("TTL", Form("\"%d\"",fTTL));
997 fGridJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60));
998 fMergingJDL->SetValue("TTL", Form("\"%d\"",fTTL));
999 fMergingJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60));
1000
0f389141 1001 if (fMaxInitFailed > 0) {
c57f56b7 1002 fGridJDL->SetValue("MaxInitFailed", Form("\"%d\"",fMaxInitFailed));
0f389141 1003 fGridJDL->SetDescription("MaxInitFailed", "Maximum number of first failing jobs to abort the master job");
1004 }
1005 if (fSplitMaxInputFileNumber > 0) {
c57f56b7 1006 fGridJDL->SetValue("SplitMaxInputFileNumber", Form("\"%d\"", fSplitMaxInputFileNumber));
0f389141 1007 fGridJDL->SetDescription("SplitMaxInputFileNumber", "Maximum number of input files to be processed per subjob");
1008 }
1009 if (fSplitMode.Length()) {
c57f56b7 1010 fGridJDL->SetValue("Split", Form("\"%s\"", fSplitMode.Data()));
0f389141 1011 fGridJDL->SetDescription("Split", "We split per SE or file");
1012 }
1013 if (!fAliROOTVersion.IsNull()) {
1014 fGridJDL->AddToPackages("AliRoot", fAliROOTVersion,"VO_ALICE", "List of requested packages");
1015 fMergingJDL->AddToPackages("AliRoot", fAliROOTVersion, "VO_ALICE", "List of requested packages");
1016 }
1017 if (!fROOTVersion.IsNull()) {
c57f56b7 1018 fGridJDL->AddToPackages("ROOT", fROOTVersion);
0f389141 1019 fMergingJDL->AddToPackages("ROOT", fROOTVersion);
1020 }
1021 if (!fAPIVersion.IsNull()) {
c57f56b7 1022 fGridJDL->AddToPackages("APISCONFIG", fAPIVersion);
0f389141 1023 fMergingJDL->AddToPackages("APISCONFIG", fAPIVersion);
1024 }
648174cf 1025 if (!fExternalPackages.IsNull()) {
1026 arr = fExternalPackages.Tokenize(" ");
1027 TIter next(arr);
1028 while ((os=(TObjString*)next())) {
1029 TString pkgname = os->GetString();
1030 Int_t index = pkgname.Index("::");
1031 TString pkgversion = pkgname(index+2, pkgname.Length());
1032 pkgname.Remove(index);
1033 fGridJDL->AddToPackages(pkgname, pkgversion);
0f389141 1034 fMergingJDL->AddToPackages(pkgname, pkgversion);
648174cf 1035 }
1036 delete arr;
1037 }
0f389141 1038 fGridJDL->SetInputDataListFormat(fInputFormat, "Format of input data");
1039 fGridJDL->SetInputDataList("wn.xml", "Collection name to be processed on each worker node");
1040 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), fAnalysisMacro.Data()), "List of input files to be uploaded to workers");
f10e8481 1041 TString analysisFile = fExecutable;
1042 analysisFile.ReplaceAll(".sh", ".root");
1043 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),analysisFile.Data()));
f866cba5 1044 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),analysisFile.Data()));
c57f56b7 1045 if (IsUsingTags() && !gSystem->AccessPathName("ConfigureCuts.C"))
1046 fGridJDL->AddToInputSandbox(Form("LF:%s/ConfigureCuts.C", workdir.Data()));
1047 if (fAdditionalLibs.Length()) {
1048 arr = fAdditionalLibs.Tokenize(" ");
1049 TIter next(arr);
1050 while ((os=(TObjString*)next())) {
1051 if (os->GetString().Contains(".so")) continue;
1052 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), os->GetString().Data()));
0f389141 1053 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), os->GetString().Data()));
c57f56b7 1054 }
1055 delete arr;
1056 }
4e5c5506 1057 if (fPackages) {
1058 TIter next(fPackages);
1059 TObject *obj;
0f389141 1060 while ((obj=next())) {
4e5c5506 1061 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName()));
0f389141 1062 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName()));
1063 }
4e5c5506 1064 }
c57f56b7 1065 if (fOutputArchive.Length()) {
1066 arr = fOutputArchive.Tokenize(" ");
1067 TIter next(arr);
0f389141 1068 Bool_t first = kTRUE;
1069 const char *comment = "Files to be archived";
1070 const char *comment1 = comment;
1071 while ((os=(TObjString*)next())) {
1072 if (!first) comment = NULL;
1073 if (!os->GetString().Contains("@") && fCloseSE.Length())
1074 fGridJDL->AddToOutputArchive(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
1075 else
1076 fGridJDL->AddToOutputArchive(os->GetString(), comment);
1077 first = kFALSE;
1078 }
c57f56b7 1079 delete arr;
f790bc1b 1080 // Output archive for the merging jdl
1081 TString outputArchive;
1082 if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
7acc5b9d 1083 outputArchive = "log_archive.zip:std*,*.stat@disk=1 ";
f790bc1b 1084 // Add normal output files, extra files + terminate files
1085 TString files = GetListOfFiles("outextter");
1086 // Do not register merge excludes
1087 if (!fMergeExcludes.IsNull()) {
1088 arr = fMergeExcludes.Tokenize(" ");
1089 TIter next1(arr);
1090 while ((os=(TObjString*)next1())) {
1091 files.ReplaceAll(Form("%s,",os->GetString().Data()),"");
1092 files.ReplaceAll(os->GetString(),"");
1093 }
66d71516 1094 delete arr;
0f389141 1095 }
f790bc1b 1096 files.ReplaceAll(".root", "*.root");
7acc5b9d 1097 outputArchive += Form("root_archive.zip:%s@disk=%d",files.Data(),fNreplicas);
f790bc1b 1098 } else {
95f84779 1099 TString files = fOutputArchive;
1100 files.ReplaceAll(".root", "*.root"); // nreplicas etc should be already atttached by use
1101 outputArchive = files;
f790bc1b 1102 }
0f389141 1103 arr = outputArchive.Tokenize(" ");
705adb3e 1104 TIter next2(arr);
0f389141 1105 comment = comment1;
1106 first = kTRUE;
705adb3e 1107 while ((os=(TObjString*)next2())) {
0f389141 1108 if (!first) comment = NULL;
0cdf65a8 1109 TString currentfile = os->GetString();
d3b18c4c 1110 if (!IsOneStageMerging()) currentfile.ReplaceAll(".zip", "-Stage$2_$3.zip");
0cdf65a8 1111 if (!currentfile.Contains("@") && fCloseSE.Length())
d3b18c4c 1112 fMergingJDL->AddToOutputArchive(Form("%s@%s",currentfile.Data(), fCloseSE.Data()), comment);
0f389141 1113 else
0cdf65a8 1114 fMergingJDL->AddToOutputArchive(currentfile, comment);
0f389141 1115 first = kFALSE;
1116 }
1117 delete arr;
c57f56b7 1118 }
149d288c 1119 arr = fOutputFiles.Tokenize(",");
c57f56b7 1120 TIter next(arr);
0f389141 1121 Bool_t first = kTRUE;
f790bc1b 1122 const char *comment = "Files to be saved";
43da816a 1123 while ((os=(TObjString*)next())) {
e1eaf596 1124 // Ignore ouputs in jdl that are also in outputarchive
1125 TString sout = os->GetString();
f790bc1b 1126 sout.ReplaceAll("*", "");
1127 sout.ReplaceAll(".root", "");
e1eaf596 1128 if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
1129 if (fOutputArchive.Contains(sout)) continue;
0f389141 1130 if (!first) comment = NULL;
43da816a 1131 if (!os->GetString().Contains("@") && fCloseSE.Length())
0f389141 1132 fGridJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
43da816a 1133 else
0f389141 1134 fGridJDL->AddToOutputSandbox(os->GetString(), comment);
1135 first = kFALSE;
f790bc1b 1136 if (fMergeExcludes.Contains(sout)) continue;
1137 if (!os->GetString().Contains("@") && fCloseSE.Length())
1138 fMergingJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
1139 else
1140 fMergingJDL->AddToOutputSandbox(os->GetString(), comment);
43da816a 1141 }
c57f56b7 1142 delete arr;
0f389141 1143 fGridJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
1144 fMergingJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
d3b18c4c 1145 TString validationScript = fValidationScript;
0f389141 1146 fGridJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
d3b18c4c 1147 validationScript.ReplaceAll(".sh", "_merge.sh");
0f389141 1148 fMergingJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
1149 if (fMasterResubmitThreshold) {
1150 fGridJDL->SetValue("MasterResubmitThreshold", Form("\"%d%%\"", fMasterResubmitThreshold));
1151 fGridJDL->SetDescription("MasterResubmitThreshold", "Resubmit failed jobs until DONE rate reaches this percentage");
1152 }
d2a409b2 1153 // Write a jdl with 2 input parameters: collection name and output dir name.
1154 WriteJDL(copy);
c57f56b7 1155 }
1156 // Copy jdl to grid workspace
a8739e8a 1157 if (copy) {
b5e4aaa7 1158 // Check if an output directory was defined and valid
1159 if (!fGridOutputDir.Length()) {
1160 Error("CreateJDL", "You must define AliEn output directory");
1161 return kFALSE;
1162 } else {
1163 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
bb2e67a0 1164 if (!fProductionMode && !DirectoryExists(fGridOutputDir)) {
b93f8109 1165 if (gGrid->Mkdir(fGridOutputDir,"-p")) {
b5e4aaa7 1166 Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
1167 } else {
1168 Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
1169 return kFALSE;
1170 }
1171 }
1172 gGrid->Cd(workdir);
1173 }
648174cf 1174 if (TestBit(AliAnalysisGrid::kSubmit)) {
0f389141 1175 TString mergeJDLName = fExecutable;
1176 mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
648174cf 1177 TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
0f389141 1178 TString locjdl1 = Form("%s/%s", fGridOutputDir.Data(),mergeJDLName.Data());
1179 if (fProductionMode) {
648174cf 1180 locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
0f389141 1181 locjdl1 = Form("%s/%s", workdir.Data(),mergeJDLName.Data());
1182 }
648174cf 1183 if (FileExists(locjdl)) gGrid->Rm(locjdl);
0f389141 1184 if (FileExists(locjdl1)) gGrid->Rm(locjdl1);
1185 Info("CreateJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
648174cf 1186 TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
0f389141 1187 if (fMergeViaJDL) {
1188 Info("CreateJDL", "\n##### Copying merging JDL file <%s> to your AliEn output directory", mergeJDLName.Data());
1189 TFile::Cp(Form("file:%s",mergeJDLName.Data()), Form("alien://%s", locjdl1.Data()));
1190 }
648174cf 1191 }
c57f56b7 1192 if (fAdditionalLibs.Length()) {
e7c71df0 1193 arr = fAdditionalLibs.Tokenize(" ");
c57f56b7 1194 TObjString *os;
1195 TIter next(arr);
1196 while ((os=(TObjString*)next())) {
c57f56b7 1197 if (os->GetString().Contains(".so")) continue;
4e5c5506 1198 Info("CreateJDL", "\n##### Copying dependency: <%s> to your alien workspace", os->GetString().Data());
c57f56b7 1199 if (FileExists(os->GetString())) gGrid->Rm(os->GetString());
1200 TFile::Cp(Form("file:%s",os->GetString().Data()), Form("alien://%s/%s", workdir.Data(), os->GetString().Data()));
1201 }
1202 delete arr;
1203 }
4e5c5506 1204 if (fPackages) {
1205 TIter next(fPackages);
1206 TObject *obj;
1207 while ((obj=next())) {
fdbbc7be 1208 if (FileExists(obj->GetName())) gGrid->Rm(obj->GetName());
4e5c5506 1209 Info("CreateJDL", "\n##### Copying dependency: <%s> to your alien workspace", obj->GetName());
1210 TFile::Cp(Form("file:%s",obj->GetName()), Form("alien://%s/%s", workdir.Data(), obj->GetName()));
1211 }
1212 }
c57f56b7 1213 }
1214 return kTRUE;
1215}
1216
a8739e8a 1217//______________________________________________________________________________
d2a409b2 1218Bool_t AliAnalysisAlien::WriteJDL(Bool_t copy)
a8739e8a 1219{
1220// Writes one or more JDL's corresponding to findex. If findex is negative,
1221// all run numbers are considered in one go (jdl). For non-negative indices
1222// they correspond to the indices in the array fInputFiles.
1223 if (!fInputFiles) return kFALSE;
d3b18c4c 1224 TObject *os;
1225 TString workdir;
1226 if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice")) workdir = gGrid->GetHomeDirectory();
a8739e8a 1227 workdir += fGridWorkingDir;
d2a409b2 1228
d3b18c4c 1229 if (fProductionMode) {
a8739e8a 1230 TIter next(fInputFiles);
d3b18c4c 1231 while ((os=next()))
1232 fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetName()), "Input xml collections");
1233 fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_04i#", fGridOutputDir.Data()));
1234 fMergingJDL->SetOutputDirectory(fGridOutputDir);
1235 } else {
1236 if (!fRunNumbers.Length() && !fRunRange[0]) {
1237 // One jdl with no parameters in case input data is specified by name.
1238 TIter next(fInputFiles);
1239 while ((os=next()))
1240 fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetName()), "Input xml collections");
1241 if (!fOutputSingle.IsNull())
1242 fGridJDL->SetOutputDirectory(Form("#alienfulldir#/../%s",fOutputSingle.Data()), "Output directory");
1243 else {
1244 fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
1245 fMergingJDL->SetOutputDirectory(fGridOutputDir);
1246 }
1247 } else {
1248 // One jdl to be submitted with 2 input parameters: data collection name and output dir prefix
1249 fGridJDL->AddToInputDataCollection(Form("LF:%s/$1,nodownload", workdir.Data()), "Input xml collections");
1250 if (!fOutputSingle.IsNull()) {
1251 if (!fOutputToRunNo) fGridJDL->SetOutputDirectory(Form("#alienfulldir#/%s",fOutputSingle.Data()), "Output directory");
1252 else fGridJDL->SetOutputDirectory(Form("%s/$2",fGridOutputDir.Data()), "Output directory");
1253 } else {
1254 fGridJDL->SetOutputDirectory(Form("%s/$2/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
1255 fMergingJDL->SetOutputDirectory("$1", "Output directory");
1256 }
1257 }
a8739e8a 1258 }
1259
a8739e8a 1260 // Generate the JDL as a string
1261 TString sjdl = fGridJDL->Generate();
0f389141 1262 TString sjdl1 = fMergingJDL->Generate();
a8739e8a 1263 Int_t index;
a8739e8a 1264 sjdl.ReplaceAll("\"LF:", "\n \"LF:");
1265 sjdl.ReplaceAll("(member", "\n (member");
1266 sjdl.ReplaceAll("\",\"VO_", "\",\n \"VO_");
1267 sjdl.ReplaceAll("{", "{\n ");
1268 sjdl.ReplaceAll("};", "\n};");
1269 sjdl.ReplaceAll("{\n \n", "{\n");
1270 sjdl.ReplaceAll("\n\n", "\n");
1271 sjdl.ReplaceAll("OutputDirectory", "OutputDir");
0f389141 1272 sjdl1.ReplaceAll("\"LF:", "\n \"LF:");
1273 sjdl1.ReplaceAll("(member", "\n (member");
1274 sjdl1.ReplaceAll("\",\"VO_", "\",\n \"VO_");
1275 sjdl1.ReplaceAll("{", "{\n ");
1276 sjdl1.ReplaceAll("};", "\n};");
1277 sjdl1.ReplaceAll("{\n \n", "{\n");
1278 sjdl1.ReplaceAll("\n\n", "\n");
1279 sjdl1.ReplaceAll("OutputDirectory", "OutputDir");
a8739e8a 1280 sjdl += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
f60ef0ba 1281 sjdl.Prepend(Form("Jobtag = {\n \"comment:%s\"\n};\n", fJobTag.Data()));
a8739e8a 1282 index = sjdl.Index("JDLVariables");
1283 if (index >= 0) sjdl.Insert(index, "\n# JDL variables\n");
4739b2aa 1284 sjdl += "Workdirectorysize = {\"5000MB\"};";
0f389141 1285 sjdl1 += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
d3b18c4c 1286 index = fJobTag.Index(":");
1287 if (index < 0) index = fJobTag.Length();
1288 TString jobTag = fJobTag;
1289 jobTag.Insert(index, "_Merging");
1290 sjdl1.Prepend(Form("Jobtag = {\n \"comment:%s_Merging\"\n};\n", jobTag.Data()));
7c2cd90a 1291 sjdl1.Prepend("# Generated merging jdl\n# $1 = full alien path to output directory to be merged\n# $2 = merging stage\n# $3 = merged chunk\n");
0f389141 1292 index = sjdl1.Index("JDLVariables");
1293 if (index >= 0) sjdl1.Insert(index, "\n# JDL variables\n");
4739b2aa 1294 sjdl1 += "Workdirectorysize = {\"5000MB\"};";
a8739e8a 1295 // Write jdl to file
a8739e8a 1296 ofstream out;
d2a409b2 1297 out.open(fJDLName.Data(), ios::out);
a8739e8a 1298 if (out.bad()) {
d3b18c4c 1299 Error("WriteJDL", "Bad file name: %s", fJDLName.Data());
a8739e8a 1300 return kFALSE;
1301 }
1302 out << sjdl << endl;
0f389141 1303 TString mergeJDLName = fExecutable;
1304 mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
1305 if (fMergeViaJDL) {
1306 ofstream out1;
1307 out1.open(mergeJDLName.Data(), ios::out);
1308 if (out.bad()) {
d3b18c4c 1309 Error("WriteJDL", "Bad file name: %s", mergeJDLName.Data());
0f389141 1310 return kFALSE;
1311 }
1312 out1 << sjdl1 << endl;
1313 }
a8739e8a 1314
1315 // Copy jdl to grid workspace
1316 if (!copy) {
d3b18c4c 1317 Info("WriteJDL", "\n##### You may want to review jdl:%s and analysis macro:%s before running in <submit> mode", fJDLName.Data(), fAnalysisMacro.Data());
a8739e8a 1318 } else {
d2a409b2 1319 TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
0f389141 1320 TString locjdl1 = Form("%s/%s", fGridOutputDir.Data(),mergeJDLName.Data());
1321 if (fProductionMode) {
b5fe9cba 1322 locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
0f389141 1323 locjdl1 = Form("%s/%s", workdir.Data(),mergeJDLName.Data());
1324 }
d2a409b2 1325 if (FileExists(locjdl)) gGrid->Rm(locjdl);
0f389141 1326 if (FileExists(locjdl1)) gGrid->Rm(locjdl1);
d3b18c4c 1327 Info("WriteJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
5513444a 1328 TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
0f389141 1329 if (fMergeViaJDL) {
d3b18c4c 1330 Info("WriteJDL", "\n##### Copying merging JDL file <%s> to your AliEn output directory", mergeJDLName.Data());
0f389141 1331 TFile::Cp(Form("file:%s",mergeJDLName.Data()), Form("alien://%s", locjdl1.Data()));
1332 }
a8739e8a 1333 }
1334 return kTRUE;
1335}
1336
c57f56b7 1337//______________________________________________________________________________
5513444a 1338Bool_t AliAnalysisAlien::FileExists(const char *lfn)
c57f56b7 1339{
1340// Returns true if file exists.
5513444a 1341 if (!gGrid) return kFALSE;
2ea55496 1342 TString slfn = lfn;
1343 slfn.ReplaceAll("alien://","");
1344 TGridResult *res = gGrid->Ls(slfn);
c57f56b7 1345 if (!res) return kFALSE;
1346 TMap *map = dynamic_cast<TMap*>(res->At(0));
1347 if (!map) {
1348 delete res;
1349 return kFALSE;
1350 }
1351 TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("name"));
1352 if (!objs || !objs->GetString().Length()) {
1353 delete res;
1354 return kFALSE;
1355 }
1356 delete res;
1357 return kTRUE;
1358}
1359
923e2ca5 1360//______________________________________________________________________________
1361Bool_t AliAnalysisAlien::DirectoryExists(const char *dirname)
1362{
1363// Returns true if directory exists. Can be also a path.
1364 if (!gGrid) return kFALSE;
1365 // Check if dirname is a path
1366 TString dirstripped = dirname;
1367 dirstripped = dirstripped.Strip();
1368 dirstripped = dirstripped.Strip(TString::kTrailing, '/');
1369 TString dir = gSystem->BaseName(dirstripped);
1370 dir += "/";
1371 TString path = gSystem->DirName(dirstripped);
1372 TGridResult *res = gGrid->Ls(path, "-F");
1373 if (!res) return kFALSE;
1374 TIter next(res);
1375 TMap *map;
1376 TObject *obj;
1377 while ((map=dynamic_cast<TMap*>(next()))) {
1378 obj = map->GetValue("name");
1379 if (!obj) break;
1380 if (dir == obj->GetName()) {
1381 delete res;
1382 return kTRUE;
1383 }
1384 }
1385 delete res;
1386 return kFALSE;
1387}
1388
c57f56b7 1389//______________________________________________________________________________
a2f5fc01 1390void AliAnalysisAlien::CheckDataType(const char *lfn, Bool_t &isCollection, Bool_t &isXml, Bool_t &useTags)
c57f56b7 1391{
1392// Check input data type.
a2f5fc01 1393 isCollection = kFALSE;
1394 isXml = kFALSE;
1395 useTags = kFALSE;
c57f56b7 1396 if (!gGrid) {
1397 Error("CheckDataType", "No connection to grid");
1398 return;
1399 }
a2f5fc01 1400 isCollection = IsCollection(lfn);
c57f56b7 1401 TString msg = "\n##### file: ";
1402 msg += lfn;
a2f5fc01 1403 if (isCollection) {
c57f56b7 1404 msg += " type: raw_collection;";
1405 // special treatment for collections
a2f5fc01 1406 isXml = kFALSE;
c57f56b7 1407 // check for tag files in the collection
1408 TGridResult *res = gGrid->Command(Form("listFilesFromCollection -z -v %s",lfn), kFALSE);
1409 if (!res) {
1410 msg += " using_tags: No (unknown)";
23329835 1411 Info("CheckDataType", "%s", msg.Data());
c57f56b7 1412 return;
1413 }
1414 const char* typeStr = res->GetKey(0, "origLFN");
1415 if (!typeStr || !strlen(typeStr)) {
1416 msg += " using_tags: No (unknown)";
23329835 1417 Info("CheckDataType", "%s", msg.Data());
c57f56b7 1418 return;
1419 }
1420 TString file = typeStr;
a2f5fc01 1421 useTags = file.Contains(".tag");
1422 if (useTags) msg += " using_tags: Yes";
c57f56b7 1423 else msg += " using_tags: No";
23329835 1424 Info("CheckDataType", "%s", msg.Data());
c57f56b7 1425 return;
1426 }
1427 TString slfn(lfn);
1428 slfn.ToLower();
a2f5fc01 1429 isXml = slfn.Contains(".xml");
1430 if (isXml) {
c57f56b7 1431 // Open xml collection and check if there are tag files inside
1432 msg += " type: xml_collection;";
1433 TGridCollection *coll = (TGridCollection*)gROOT->ProcessLine(Form("TAlienCollection::Open(\"alien://%s\",1);",lfn));
1434 if (!coll) {
1435 msg += " using_tags: No (unknown)";
23329835 1436 Info("CheckDataType", "%s", msg.Data());
c57f56b7 1437 return;
1438 }
1439 TMap *map = coll->Next();
1440 if (!map) {
1441 msg += " using_tags: No (unknown)";
23329835 1442 Info("CheckDataType", "%s", msg.Data());
c57f56b7 1443 return;
1444 }
1445 map = (TMap*)map->GetValue("");
1446 TString file;
1447 if (map && map->GetValue("name")) file = map->GetValue("name")->GetName();
a2f5fc01 1448 useTags = file.Contains(".tag");
c57f56b7 1449 delete coll;
a2f5fc01 1450 if (useTags) msg += " using_tags: Yes";
c57f56b7 1451 else msg += " using_tags: No";
23329835 1452 Info("CheckDataType", "%s", msg.Data());
c57f56b7 1453 return;
1454 }
a2f5fc01 1455 useTags = slfn.Contains(".tag");
c57f56b7 1456 if (slfn.Contains(".root")) msg += " type: root file;";
f866cba5 1457 else msg += " type: unknown file;";
a2f5fc01 1458 if (useTags) msg += " using_tags: Yes";
c57f56b7 1459 else msg += " using_tags: No";
23329835 1460 Info("CheckDataType", "%s", msg.Data());
c57f56b7 1461}
1462
4e5c5506 1463//______________________________________________________________________________
1464void AliAnalysisAlien::EnablePackage(const char *package)
1465{
1466// Enables a par file supposed to exist in the current directory.
1467 TString pkg(package);
1468 pkg.ReplaceAll(".par", "");
1469 pkg += ".par";
1470 if (gSystem->AccessPathName(pkg)) {
ebcdf05e 1471 Fatal("EnablePackage", "Package %s not found", pkg.Data());
4e5c5506 1472 return;
1473 }
1474 if (!TObject::TestBit(AliAnalysisGrid::kUsePars))
1475 Info("EnablePackage", "AliEn plugin will use .par packages");
1476 TObject::SetBit(AliAnalysisGrid::kUsePars, kTRUE);
1477 if (!fPackages) {
1478 fPackages = new TObjArray();
1479 fPackages->SetOwner();
1480 }
1481 fPackages->Add(new TObjString(pkg));
1482}
1483
3bdcb562 1484//______________________________________________________________________________
1485TChain *AliAnalysisAlien::GetChainForTestMode(const char *treeName) const
1486{
1487// Make a tree from files having the location specified in fFileForTestMode.
1488// Inspired from JF's CreateESDChain.
1489 if (fFileForTestMode.IsNull()) {
1490 Error("GetChainForTestMode", "For proof test mode please use SetFileForTestMode() pointing to a file that contains data file locations.");
1491 return NULL;
1492 }
1493 if (gSystem->AccessPathName(fFileForTestMode)) {
1494 Error("GetChainForTestMode", "File not found: %s", fFileForTestMode.Data());
1495 return NULL;
1496 }
1497 // Open the file
1498 ifstream in;
1499 in.open(fFileForTestMode);
1500 Int_t count = 0;
1501 // Read the input list of files and add them to the chain
1502 TString line;
1503 TChain *chain = new TChain(treeName);
1504 while (in.good())
1505 {
1506 in >> line;
1507 if (line.IsNull()) continue;
1508 if (count++ == fNtestFiles) break;
1509 TString esdFile(line);
1510 TFile *file = TFile::Open(esdFile);
1511 if (file) {
1512 if (!file->IsZombie()) chain->Add(esdFile);
1513 file->Close();
1514 } else {
1515 Error("GetChainforTestMode", "Skipping un-openable file: %s", esdFile.Data());
1516 }
1517 }
1518 in.close();
1519 if (!chain->GetListOfFiles()->GetEntries()) {
1520 Error("GetChainForTestMode", "No file from %s could be opened", fFileForTestMode.Data());
1521 delete chain;
1522 return NULL;
1523 }
1524// chain->ls();
1525 return chain;
1526}
1527
d2a409b2 1528//______________________________________________________________________________
1529const char *AliAnalysisAlien::GetJobStatus(Int_t jobidstart, Int_t lastid, Int_t &nrunning, Int_t &nwaiting, Int_t &nerror, Int_t &ndone)
1530{
1531// Get job status for all jobs with jobid>jobidstart.
1532 static char mstatus[20];
1533 mstatus[0] = '\0';
1534 nrunning = 0;
1535 nwaiting = 0;
1536 nerror = 0;
1537 ndone = 0;
1538 TGridJobStatusList *list = gGrid->Ps("");
1539 if (!list) return mstatus;
1540 Int_t nentries = list->GetSize();
1541 TGridJobStatus *status;
1542 Int_t pid;
1543 for (Int_t ijob=0; ijob<nentries; ijob++) {
1544 status = (TGridJobStatus *)list->At(ijob);
1545 pid = gROOT->ProcessLine(Form("atoi(((TAlienJobStatus*)0x%lx)->GetKey(\"queueId\"));", (ULong_t)status));
1546 if (pid<jobidstart) continue;
1547 if (pid == lastid) {
1548 gROOT->ProcessLine(Form("sprintf((char*)0x%lx,((TAlienJobStatus*)0x%lx)->GetKey(\"status\"));",(ULong_t)mstatus, (ULong_t)status));
1549 }
1550 switch (status->GetStatus()) {
1551 case TGridJobStatus::kWAITING:
1552 nwaiting++; break;
1553 case TGridJobStatus::kRUNNING:
1554 nrunning++; break;
1555 case TGridJobStatus::kABORTED:
1556 case TGridJobStatus::kFAIL:
1557 case TGridJobStatus::kUNKNOWN:
1558 nerror++; break;
1559 case TGridJobStatus::kDONE:
1560 ndone++;
1561 }
1562 }
1563 list->Delete();
1564 delete list;
1565 return mstatus;
1566}
1567
c57f56b7 1568//______________________________________________________________________________
1569Bool_t AliAnalysisAlien::IsCollection(const char *lfn) const
1570{
1571// Returns true if file is a collection. Functionality duplicated from
1572// TAlien::Type() because we don't want to directly depend on TAlien.
1573 if (!gGrid) {
1574 Error("IsCollection", "No connection to grid");
1575 return kFALSE;
1576 }
1577 TGridResult *res = gGrid->Command(Form("type -z %s",lfn),kFALSE);
1578 if (!res) return kFALSE;
1579 const char* typeStr = res->GetKey(0, "type");
1580 if (!typeStr || !strlen(typeStr)) return kFALSE;
1581 if (!strcmp(typeStr, "collection")) return kTRUE;
1582 delete res;
1583 return kFALSE;
1584}
1585
fe2d7fc2 1586//______________________________________________________________________________
1587Bool_t AliAnalysisAlien::IsSingleOutput() const
1588{
1589// Check if single-ouput option is on.
1590 return (!fOutputSingle.IsNull());
1591}
1592
16a4353c 1593//______________________________________________________________________________
1594void AliAnalysisAlien::Print(Option_t *) const
1595{
1596// Print current plugin settings.
84fcd93f 1597 printf("### AliEn analysis plugin current settings ###\n");
d3b18c4c 1598 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
1599 if (mgr && mgr->IsProofMode()) {
1600 TString proofType = "= PLUGIN IN PROOF MODE ON CLUSTER:_________________";
1601 if (TestBit(AliAnalysisGrid::kTest))
1602 proofType = "= PLUGIN IN PROOF LITE MODE ON CLUSTER:____________";
1603 printf("%s %s\n", proofType.Data(), fProofCluster.Data());
1604 if (!fProofDataSet.IsNull())
1605 printf("= Requested data set:___________________________ %s\n", fProofDataSet.Data());
1606 if (fProofReset==1)
1607 printf("= Soft reset signal will be send to master______ CHANGE BEHAVIOR AFTER COMPLETION\n");
1608 if (fProofReset>1)
1609 printf("= Hard reset signal will be send to master______ CHANGE BEHAVIOR AFTER COMPLETION\n");
1610 if (!fRootVersionForProof.IsNull())
1611 printf("= ROOT version requested________________________ %s\n", fRootVersionForProof.Data());
1612 else
1613 printf("= ROOT version requested________________________ default\n");
1614 printf("= AliRoot version requested_____________________ %s\n", fAliROOTVersion.Data());
1615 if (!fAliRootMode.IsNull())
1616 printf("= Requested AliRoot mode________________________ %s\n", fAliRootMode.Data());
1617 if (fNproofWorkers)
1618 printf("= Number of PROOF workers limited to____________ %d\n", fNproofWorkers);
1619 if (fNproofWorkersPerSlave)
1620 printf("= Maximum number of workers per slave___________ %d\n", fNproofWorkersPerSlave);
1621 if (TestSpecialBit(kClearPackages))
1622 printf("= ClearPackages requested...\n");
1623 if (fIncludePath.Data())
1624 printf("= Include path for runtime task compilation: ___ %s\n", fIncludePath.Data());
1625 printf("= Additional libs to be loaded or souces to be compiled runtime: <%s>\n",fAdditionalLibs.Data());
1626 if (fPackages && fPackages->GetEntries()) {
1627 TIter next(fPackages);
1628 TObject *obj;
1629 TString list;
1630 while ((obj=next())) list += obj->GetName();
1631 printf("= Par files to be used: ________________________ %s\n", list.Data());
1632 }
1633 if (TestSpecialBit(kProofConnectGrid))
1634 printf("= Requested PROOF connection to grid\n");
1635 return;
1636 }
e1c22e21 1637 printf("= OverwriteMode:________________________________ %d\n", fOverwriteMode);
1638 if (fOverwriteMode) {
1639 printf("***** NOTE: Overwrite mode will overwrite the input generated datasets and partial results from previous analysis. \
1640 \n***** To disable, use: plugin->SetOverwriteMode(kFALSE);\n");
1641 }
348be253 1642 printf("= Copy files to grid: __________________________ %s\n", (IsUseCopy())?"YES":"NO");
1643 printf("= Check if files can be copied to grid: ________ %s\n", (IsCheckCopy())?"YES":"NO");
84fcd93f 1644 printf("= Production mode:______________________________ %d\n", fProductionMode);
1645 printf("= Version of API requested: ____________________ %s\n", fAPIVersion.Data());
1646 printf("= Version of ROOT requested: ___________________ %s\n", fROOTVersion.Data());
1647 printf("= Version of AliRoot requested: ________________ %s\n", fAliROOTVersion.Data());
16a4353c 1648 if (fUser.Length())
84fcd93f 1649 printf("= User running the plugin: _____________________ %s\n", fUser.Data());
1650 printf("= Grid workdir relative to user $HOME: _________ %s\n", fGridWorkingDir.Data());
1651 printf("= Grid output directory relative to workdir: ___ %s\n", fGridOutputDir.Data());
1652 printf("= Data base directory path requested: __________ %s\n", fGridDataDir.Data());
1653 printf("= Data search pattern: _________________________ %s\n", fDataPattern.Data());
1654 printf("= Input data format: ___________________________ %s\n", fInputFormat.Data());
16a4353c 1655 if (fRunNumbers.Length())
84fcd93f 1656 printf("= Run numbers to be processed: _________________ %s\n", fRunNumbers.Data());
16a4353c 1657 if (fRunRange[0])
5fce53f4 1658 printf("= Run range to be processed: ___________________ %s%d-%s%d\n", fRunPrefix.Data(), fRunRange[0], fRunPrefix.Data(), fRunRange[1]);
16a4353c 1659 if (!fRunRange[0] && !fRunNumbers.Length()) {
1660 TIter next(fInputFiles);
1661 TObject *obj;
1662 TString list;
1663 while ((obj=next())) list += obj->GetName();
84fcd93f 1664 printf("= Input files to be processed: _________________ %s\n", list.Data());
16a4353c 1665 }
1666 if (TestBit(AliAnalysisGrid::kTest))
84fcd93f 1667 printf("= Number of input files used in test mode: _____ %d\n", fNtestFiles);
1668 printf("= List of output files to be registered: _______ %s\n", fOutputFiles.Data());
1669 printf("= List of outputs going to be archived: ________ %s\n", fOutputArchive.Data());
1670 printf("= List of outputs that should not be merged: ___ %s\n", fMergeExcludes.Data());
d3b18c4c 1671 printf("= List of outputs produced during Terminate: ___ %s\n", fTerminateFiles.Data());
84fcd93f 1672 printf("=====================================================================\n");
1673 printf("= Job price: ___________________________________ %d\n", fPrice);
1674 printf("= Time to live (TTL): __________________________ %d\n", fTTL);
1675 printf("= Max files per subjob: ________________________ %d\n", fSplitMaxInputFileNumber);
16a4353c 1676 if (fMaxInitFailed>0)
84fcd93f 1677 printf("= Max number of subjob fails to kill: __________ %d\n", fMaxInitFailed);
16a4353c 1678 if (fMasterResubmitThreshold>0)
84fcd93f 1679 printf("= Resubmit master job if failed subjobs >_______ %d\n", fMasterResubmitThreshold);
149d288c 1680 printf("= Number of replicas for the output files_______ %d\n", fNreplicas);
319593fb 1681 if (fNrunsPerMaster>0)
84fcd93f 1682 printf("= Number of runs per master job: _______________ %d\n", fNrunsPerMaster);
1683 printf("= Number of files in one chunk to be merged: ___ %d\n", fMaxMergeFiles);
b5b9dee8 1684 printf("= Name of the generated execution script: ______ %s\n", fExecutable.Data());
1685 printf("= Executable command: __________________________ %s\n", fExecutableCommand.Data());
16a4353c 1686 if (fArguments.Length())
84fcd93f 1687 printf("= Arguments for the execution script: __________ %s\n",fArguments.Data());
631c0b05 1688 if (fExecutableArgs.Length())
1689 printf("= Arguments after macro name in executable______ %s\n",fExecutableArgs.Data());
84fcd93f 1690 printf("= Name of the generated analysis macro: ________ %s\n",fAnalysisMacro.Data());
1691 printf("= User analysis files to be deployed: __________ %s\n",fAnalysisSource.Data());
1692 printf("= Additional libs to be loaded or souces to be compiled runtime: <%s>\n",fAdditionalLibs.Data());
1693 printf("= Master jobs split mode: ______________________ %s\n",fSplitMode.Data());
16a4353c 1694 if (fDatasetName)
84fcd93f 1695 printf("= Custom name for the dataset to be created: ___ %s\n", fDatasetName.Data());
1696 printf("= Name of the generated JDL: ___________________ %s\n", fJDLName.Data());
16a4353c 1697 if (fIncludePath.Data())
84fcd93f 1698 printf("= Include path for runtime task compilation: ___ %s\n", fIncludePath.Data());
16a4353c 1699 if (fCloseSE.Length())
84fcd93f 1700 printf("= Force job outputs to storage element: ________ %s\n", fCloseSE.Data());
16a4353c 1701 if (fFriendChainName.Length())
84fcd93f 1702 printf("= Open friend chain file on worker: ____________ %s\n", fFriendChainName.Data());
d3b18c4c 1703 if (fPackages && fPackages->GetEntries()) {
16a4353c 1704 TIter next(fPackages);
1705 TObject *obj;
1706 TString list;
1707 while ((obj=next())) list += obj->GetName();
84fcd93f 1708 printf("= Par files to be used: ________________________ %s\n", list.Data());
16a4353c 1709 }
1710}
1711
c57f56b7 1712//______________________________________________________________________________
1713void AliAnalysisAlien::SetDefaults()
1714{
1715// Set default values for everything. What cannot be filled will be left empty.
1716 if (fGridJDL) delete fGridJDL;
1717 fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
0f389141 1718 fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
c57f56b7 1719 fPrice = 1;
1720 fTTL = 30000;
1721 fSplitMaxInputFileNumber = 100;
1722 fMaxInitFailed = 0;
1723 fMasterResubmitThreshold = 0;
bb885a9e 1724 fNtestFiles = 10;
149d288c 1725 fNreplicas = 2;
a8739e8a 1726 fRunRange[0] = 0;
1727 fRunRange[1] = 0;
319593fb 1728 fNrunsPerMaster = 1;
16a4353c 1729 fMaxMergeFiles = 100;
c57f56b7 1730 fRunNumbers = "";
1731 fExecutable = "analysis.sh";
0a1c1f7f 1732 fExecutableCommand = "root -b -q";
c57f56b7 1733 fArguments = "";
631c0b05 1734 fExecutableArgs = "";
c57f56b7 1735 fAnalysisMacro = "myAnalysis.C";
1736 fAnalysisSource = "";
1737 fAdditionalLibs = "";
1738 fSplitMode = "se";
1739 fAPIVersion = "";
1740 fROOTVersion = "";
1741 fAliROOTVersion = "";
1742 fUser = ""; // Your alien user name
1743 fGridWorkingDir = "";
1744 fGridDataDir = ""; // Can be like: /alice/sim/PDC_08a/LHC08c9/
1745 fDataPattern = "*AliESDs.root"; // Can be like: *AliESDs.root, */pass1/*AliESDs.root, ...
0df6ccf2 1746 fFriendChainName = "";
c57f56b7 1747 fGridOutputDir = "output";
7acc5b9d 1748 fOutputArchive = "log_archive.zip:std*,*.stat@disk=1 root_archive.zip:*.root@disk=2";
c57f56b7 1749 fOutputFiles = ""; // Like "AliAODs.root histos.root"
1750 fInputFormat = "xml-single";
1751 fJDLName = "analysis.jdl";
c6cb3634 1752 fJobTag = "Automatically generated analysis JDL";
bb885a9e 1753 fMergeExcludes = "";
0f389141 1754 fMergeViaJDL = 0;
348be253 1755 SetUseCopy(kTRUE);
1756 SetCheckCopy(kTRUE);
149d288c 1757 SetDefaultOutputs(kTRUE);
e1c22e21 1758 fOverwriteMode = 1;
c57f56b7 1759}
1760
0f389141 1761//______________________________________________________________________________
7c2cd90a 1762Bool_t AliAnalysisAlien::CheckMergedFiles(const char *filename, const char *aliendir, Int_t nperchunk, Bool_t submit, const char *jdl)
0f389141 1763{
7c2cd90a 1764// Static method that checks the status of merging. This can submit merging jobs that did not produced the expected
1765// output. If <submit> is false (checking) returns true only when the final merged file was found. If submit is true returns
1766// true if the jobs were successfully submitted.
1767 Int_t countOrig = 0;
1768 Int_t countStage = 0;
1769 Int_t stage = 0;
1770 Int_t i;
1771 Bool_t doneFinal = kFALSE;
1772 TBits chunksDone;
1773 TString saliendir(aliendir);
1774 TString sfilename, stmp;
1775 saliendir.ReplaceAll("//","/");
1776 saliendir = saliendir.Strip(TString::kTrailing, '/');
1777 if (!gGrid) {
1778 ::Error("GetNregisteredFiles", "You need to be connected to AliEn.");
1779 return kFALSE;
1780 }
0cdf65a8 1781 sfilename = filename;
1782 sfilename.ReplaceAll(".root", "*.root");
1783 printf("Checking directory <%s> for merged files <%s> ...\n", aliendir, sfilename.Data());
1784 TString command = Form("find %s/ *%s", saliendir.Data(), sfilename.Data());
7c2cd90a 1785 TGridResult *res = gGrid->Command(command);
1786 if (!res) {
1787 ::Error("GetNregisteredFiles","Error: No result for the find command\n");
1788 return kFALSE;
1789 }
1790 TIter nextmap(res);
1791 TMap *map = 0;
1792 while ((map=(TMap*)nextmap())) {
1793 TString turl = map->GetValue("turl")->GetName();
1794 if (!turl.Length()) {
1795 // Nothing found
1796 delete res;
1797 return kFALSE;
1798 }
1799 turl.ReplaceAll("alien://", "");
1800 turl.ReplaceAll(saliendir, "");
1801 sfilename = gSystem->BaseName(turl);
0cdf65a8 1802 turl = turl.Strip(TString::kLeading, '/');
7c2cd90a 1803 // Now check to what the file corresponds to:
1804 // original output - aliendir/%03d/filename
1805 // merged file (which stage) - aliendir/filename-Stage%02d_%04d
1806 // final merged file - aliendir/filename
1807 if (sfilename == turl) {
1808 if (sfilename == filename) {
1809 doneFinal = kTRUE;
1810 } else {
1811 // check stage
1812 Int_t index = sfilename.Index("Stage");
1813 if (index<0) continue;
1814 stmp = sfilename(index+5,2);
1815 Int_t istage = atoi(stmp);
1816 stmp = sfilename(index+8,4);
1817 Int_t ijob = atoi(stmp);
1818 if (istage<stage) continue; // Ignore lower stages
1819 if (istage>stage) {
1820 countStage = 0;
1821 chunksDone.ResetAllBits();
1822 stage = istage;
1823 }
1824 countStage++;
1825 chunksDone.SetBitNumber(ijob);
1826 }
1827 } else {
1828 countOrig++;
1829 }
1830 if (doneFinal) {
1831 delete res;
0cdf65a8 1832 printf("=> Removing files from previous stages...\n");
1833 gGrid->Rm(Form("%s/*Stage*.root", aliendir));
7a62d541 1834 for (i=1; i<stage; i++)
1835 gGrid->Rm(Form("%s/*Stage%d*.zip", aliendir, i));
7c2cd90a 1836 return kTRUE;
1837 }
1838 }
1839 delete res;
1840 // Compute number of jobs that were submitted for the current stage
1841 Int_t ntotstage = countOrig;
7ae54d70 1842 for (i=1; i<=stage; i++) {
1843 if (ntotstage%nperchunk) ntotstage = (ntotstage/nperchunk)+1;
1844 else ntotstage = (ntotstage/nperchunk);
1845 }
7c2cd90a 1846 // Now compare with the number of set bits in the chunksDone array
1847 Int_t nmissing = (stage>0)?(ntotstage - countStage):0;
1848 // Print the info
1849 printf("*** Found %d original files\n", countOrig);
1850 if (stage==0) printf("*** No merging completed so far.\n");
1851 else printf("*** Found %d out of %d files merged for stage %d\n", countStage, ntotstage, stage);
1852 if (nmissing) printf("*** Number of merged files missing for this stage: %d -> check merging job completion\n", nmissing);
7c2cd90a 1853 if (!submit) return doneFinal;
1854 // Sumbit merging jobs for all missing chunks for the current stage.
1855 TString query = Form("submit %s %s", jdl, aliendir);
1856 Int_t ichunk = -1;
95f84779 1857 chunksDone.SetBitNumber(ntotstage); // expand the array to the maximum number of chunks
7c2cd90a 1858 if (nmissing) {
1859 for (i=0; i<nmissing; i++) {
1860 ichunk = chunksDone.FirstNullBit(ichunk+1);
1861 Int_t jobId = SubmitSingleJob(Form("%s %d %d", query.Data(), stage, ichunk));
1862 if (!jobId) return kFALSE;
1863 }
1864 return kTRUE;
1865 }
1866 // Submit next stage of merging
1867 if (stage==0) countStage = countOrig;
7ae54d70 1868 Int_t nchunks = (countStage/nperchunk);
1869 if (countStage%nperchunk) nchunks += 1;
7c2cd90a 1870 for (i=0; i<nchunks; i++) {
1871 Int_t jobId = SubmitSingleJob(Form("%s %d %d", query.Data(), stage+1, i));
1872 if (!jobId) return kFALSE;
1873 }
1874 return kTRUE;
1875}
1876
1877//______________________________________________________________________________
1878Int_t AliAnalysisAlien::SubmitSingleJob(const char *query)
1879{
1880// Submits a single job corresponding to the query and returns job id. If 0 submission failed.
1881 if (!gGrid) return 0;
1882 printf("=> %s ------> ",query);
1883 TGridResult *res = gGrid->Command(query);
1884 if (!res) return 0;
1885 TString jobId = res->GetKey(0,"jobId");
1886 delete res;
1887 if (jobId.IsNull()) {
1888 printf("submission failed. Reason:\n");
1889 gGrid->Stdout();
1890 gGrid->Stderr();
1891 ::Error("SubmitSingleJob", "Your query %s could not be submitted", query);
1892 return 0;
1893 }
1894 printf(" Job id: %s\n", jobId.Data());
1895 return atoi(jobId);
1896}
1897
1898//______________________________________________________________________________
1899Bool_t AliAnalysisAlien::MergeOutput(const char *output, const char *basedir, Int_t nmaxmerge, Int_t stage, Int_t ichunk)
1900{
1901// Merge given output files from basedir. The file merger will merge nmaxmerge
1902// files in a group. Merging can be done in stages:
1903// stage=0 : will merge all existing files in a single stage
1904// stage=1 : does a find command for all files that do NOT contain the string "Stage".
1905// If their number is bigger that nmaxmerge, only the files from
1906// ichunk*nmaxmerge to ichunk*(nmaxmerge+1)-1 will get merged as output_stage_<ichunk>
1907// stage=n : does a find command for files named <output>Stage<stage-1>_*. If their number is bigger than
1908// nmaxmerge, merge just the chunk ichunk, otherwise write the merged output to the file
1909// named <output>.
a2f5fc01 1910 TString outputFile = output;
0f389141 1911 TString command;
a2f5fc01 1912 TString outputChunk;
1913 TString previousChunk = "";
1914 Int_t countChunk = 0;
1915 Int_t countZero = nmaxmerge;
0f389141 1916 Bool_t merged = kTRUE;
a2f5fc01 1917 Int_t index = outputFile.Index("@");
1918 if (index > 0) outputFile.Remove(index);
7c2cd90a 1919 TString inputFile = outputFile;
1920 if (stage>1) inputFile.ReplaceAll(".root", Form("-Stage%02d_*.root", stage-1));
1921 command = Form("find %s/ *%s", basedir, inputFile.Data());
0f389141 1922 printf("command: %s\n", command.Data());
1923 TGridResult *res = gGrid->Command(command);
1924 if (!res) {
7c2cd90a 1925 ::Error("MergeOutput","No result for the find command\n");
0f389141 1926 return kFALSE;
1927 }
1928
1929 TFileMerger *fm = 0;
1930 TIter nextmap(res);
1931 TMap *map = 0;
7c2cd90a 1932 // Check if there is a merge operation to resume. Works only for stage 0 or 1.
a2f5fc01 1933 outputChunk = outputFile;
1934 outputChunk.ReplaceAll(".root", "_*.root");
0f389141 1935 // Check for existent temporary merge files
e1c22e21 1936 // Check overwrite mode and remove previous partial results if needed
7c2cd90a 1937 // Preserve old merging functionality for stage 0.
1938 if (stage==0) {
2ea55496 1939 Int_t countChar = 0;
7c2cd90a 1940 if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
1941 while (1) {
1942 // Skip as many input files as in a chunk
2ea55496 1943 for (Int_t counter=0; counter<nmaxmerge; counter++) {
1944 map = (TMap*)nextmap();
1945 if (!map) {
1946 ::Error("MergeOutput", "Mismatch found. Please remove partial merged files from local dir.");
1947 delete res;
1948 return kFALSE;
1949 }
1950 TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl"));
1951 // Count the '/' characters in the path to the current file.
1952 Int_t crtCount = objs->GetString().CountChar('/');
1953 if (!countChar) {
1954 countChar = crtCount;
1955 // Make sure we check if the same file in the parent dir exists
1956 if (FileExists(Form("%s/../%s", basedir, output))) countChar--;
1957 }
1958 if (crtCount > countChar) counter--;
1959 }
7c2cd90a 1960 if (!map) {
1961 ::Error("MergeOutput", "Cannot resume merging for <%s>, nentries=%d", outputFile.Data(), res->GetSize());
1962 delete res;
1963 return kFALSE;
1964 }
1965 outputChunk = outputFile;
1966 outputChunk.ReplaceAll(".root", Form("_%04d.root", countChunk));
1967 countChunk++;
1968 if (gSystem->AccessPathName(outputChunk)) continue;
1969 // Merged file with chunks up to <countChunk> found
1970 ::Info("MergeOutput", "Resume merging of <%s> from <%s>\n", outputFile.Data(), outputChunk.Data());
1971 previousChunk = outputChunk;
1972 break;
1973 }
1974 }
1975 countZero = nmaxmerge;
1976
1977 while ((map=(TMap*)nextmap())) {
2ea55496 1978 TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl"));
1979 if (!objs || !objs->GetString().Length()) {
1980 // Nothing found - skip this output
1981 delete res;
1982 delete fm;
1983 return kFALSE;
1984 }
1985 // Make sure this is a good file and not one from a subjob directory in case we merge runs
1986 // Count the '/' characters in the path to the current file.
1987 Int_t crtCount = objs->GetString().CountChar('/');
1988 if (!countChar) {
1989 countChar = crtCount;
1990 // Make sure we check if the same file in the parent dir exists
1991 if (FileExists(Form("%s/../%s", basedir, output))) countChar--;
1992 }
1993 if (crtCount > countChar) continue;
1994 // Loop 'find' results and get next LFN
7c2cd90a 1995 if (countZero == nmaxmerge) {
1996 // First file in chunk - create file merger and add previous chunk if any.
1997 fm = new TFileMerger(kFALSE);
1998 fm->SetFastMethod(kTRUE);
1999 if (previousChunk.Length()) fm->AddFile(previousChunk.Data());
2000 outputChunk = outputFile;
2001 outputChunk.ReplaceAll(".root", Form("_%04d.root", countChunk));
2002 }
2003 // If last file found, put merged results in the output file
2004 if (map == res->Last()) outputChunk = outputFile;
7c2cd90a 2005 // Add file to be merged and decrement chunk counter.
2006 fm->AddFile(objs->GetString());
2007 countZero--;
2008 if (countZero==0 || map == res->Last()) {
2009 if (!fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
2010 // Nothing found - skip this output
2011 ::Warning("MergeOutput", "No <%s> files found.", inputFile.Data());
2012 delete res;
2013 delete fm;
2014 return kFALSE;
2015 }
2016 fm->OutputFile(outputChunk);
2017 // Merge the outputs, then go to next chunk
2018 if (!fm->Merge()) {
2019 ::Error("MergeOutput", "Could not merge all <%s> files", outputFile.Data());
2020 delete res;
2021 delete fm;
2022 return kFALSE;
2023 } else {
2024 ::Info("MergeOutputs", "\n##### Merged %d output files to <%s>", fm->GetMergeList()->GetSize(), outputChunk.Data());
2025 gSystem->Unlink(previousChunk);
2026 }
2027 if (map == res->Last()) {
2028 delete res;
2029 delete fm;
2030 break;
2031 }
2032 countChunk++;
2033 countZero = nmaxmerge;
2034 previousChunk = outputChunk;
0f389141 2035 }
0f389141 2036 }
7c2cd90a 2037 return merged;
2038 }
2039 // Merging stage different than 0.
2040 // Move to the begining of the requested chunk.
2041 outputChunk = outputFile;
2042 if (nmaxmerge < res->GetSize()) {
2043 if (ichunk*nmaxmerge >= res->GetSize()) {
2044 ::Error("MergeOutput", "Cannot merge merge chunk %d grouping %d files from %d total.", ichunk, nmaxmerge, res->GetSize());
2045 delete res;
2046 return kFALSE;
2047 }
8a8f17bb 2048 for (Int_t counter=0; counter<ichunk*nmaxmerge; counter++) nextmap();
7c2cd90a 2049 outputChunk.ReplaceAll(".root", Form("-Stage%02d_%04d.root", stage, ichunk));
2050 }
2051 countZero = nmaxmerge;
2052 fm = new TFileMerger(kFALSE);
2053 fm->SetFastMethod(kTRUE);
0f389141 2054 while ((map=(TMap*)nextmap())) {
7c2cd90a 2055 // Loop 'find' results and get next LFN
0f389141 2056 TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl"));
2057 if (!objs || !objs->GetString().Length()) {
2058 // Nothing found - skip this output
2059 delete res;
2060 delete fm;
2061 return kFALSE;
2062 }
2063 // Add file to be merged and decrement chunk counter.
2064 fm->AddFile(objs->GetString());
a2f5fc01 2065 countZero--;
7c2cd90a 2066 if (countZero==0) break;
2067 }
2068 delete res;
2069 if (!fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
2070 // Nothing found - skip this output
2071 ::Warning("MergeOutput", "No <%s> files found.", inputFile.Data());
2072 delete fm;
2073 return kFALSE;
2074 }
2075 fm->OutputFile(outputChunk);
2076 // Merge the outputs
2077 if (!fm->Merge()) {
2078 ::Error("MergeOutput", "Could not merge all <%s> files", outputFile.Data());
2079 delete fm;
2080 return kFALSE;
2081 } else {
2082 ::Info("MergeOutput", "\n##### Merged %d output files to <%s>", fm->GetMergeList()->GetSize(), outputChunk.Data());
0f389141 2083 }
7c2cd90a 2084 delete fm;
2085 return kTRUE;
0f389141 2086}
2087
c57f56b7 2088//______________________________________________________________________________
2089Bool_t AliAnalysisAlien::MergeOutputs()
2090{
2091// Merge analysis outputs existing in the AliEn space.
2092 if (TestBit(AliAnalysisGrid::kTest)) return kTRUE;
2093 if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
2094 if (!Connect()) {
2095 Error("MergeOutputs", "Cannot merge outputs without grid connection. Terminate will NOT be executed");
2096 return kFALSE;
0f389141 2097 }
c9e8f7fd 2098 if (fMergeViaJDL) {
2099 if (!TestBit(AliAnalysisGrid::kMerge)) {
2100 Info("MergeOutputs", "### Re-run with <MergeViaJDL> option in terminate mode of the plugin to submit merging jobs ###");
2101 return kFALSE;
2102 }
2103 if (fProductionMode) {
2104 Info("MergeOutputs", "### Merging will be submitted by LPM manager... ###");
2105 return kFALSE;
2106 }
0f389141 2107 Info("MergeOutputs", "Submitting merging JDL");
a03be957 2108 if (!SubmitMerging()) return kFALSE;
0f389141 2109 Info("MergeOutputs", "### Re-run with <MergeViaJDL> off to collect results after merging jobs are done ###");
c9e8f7fd 2110 Info("MergeOutputs", "### The Terminate() method is executed by the merging jobs");
001cb79e 2111 return kFALSE;
c57f56b7 2112 }
2113 // Get the output path
d2a409b2 2114 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
923e2ca5 2115 if (!DirectoryExists(fGridOutputDir)) {
c57f56b7 2116 Error("MergeOutputs", "Grid output directory %s not found. Terminate() will NOT be executed", fGridOutputDir.Data());
2117 return kFALSE;
2118 }
2119 if (!fOutputFiles.Length()) {
2120 Error("MergeOutputs", "No output file names defined. Are you running the right AliAnalysisAlien configuration ?");
2121 return kFALSE;
0f389141 2122 }
2123 // Check if fast read option was requested
e1c22e21 2124 Info("MergeOutputs", "Started local merging of output files from: alien://%s \
2125 \n======= overwrite mode = %d", fGridOutputDir.Data(), (Int_t)fOverwriteMode);
0f389141 2126 if (fFastReadOption) {
d3339be3 2127 Warning("MergeOutputs", "You requested FastRead option. Using xrootd flags to reduce timeouts. This may skip some files that could be accessed ! \
2128 \n+++ NOTE: To disable this option, use: plugin->SetFastReadOption(kFALSE)");
2129 gEnv->SetValue("XNet.ConnectTimeout",10);
2130 gEnv->SetValue("XNet.RequestTimeout",10);
0f389141 2131 gEnv->SetValue("XNet.MaxRedirectCount",2);
d3339be3 2132 gEnv->SetValue("XNet.ReconnectTimeout",10);
0f389141 2133 gEnv->SetValue("XNet.FirstConnectMaxCnt",1);
c57f56b7 2134 }
e8b839ab 2135 // Make sure we change the temporary directory
2136 gSystem->Setenv("TMPDIR", gSystem->pwd());
149d288c 2137 TObjArray *list = fOutputFiles.Tokenize(",");
c57f56b7 2138 TIter next(list);
2139 TObjString *str;
a2f5fc01 2140 TString outputFile;
c57f56b7 2141 Bool_t merged = kTRUE;
2142 while((str=(TObjString*)next())) {
a2f5fc01 2143 outputFile = str->GetString();
2144 Int_t index = outputFile.Index("@");
2145 if (index > 0) outputFile.Remove(index);
2146 TString outputChunk = outputFile;
2147 outputChunk.ReplaceAll(".root", "_*.root");
319593fb 2148 // Skip already merged outputs
a2f5fc01 2149 if (!gSystem->AccessPathName(outputFile)) {
e1c22e21 2150 if (fOverwriteMode) {
a2f5fc01 2151 Info("MergeOutputs", "Overwrite mode. Existing file %s was deleted.", outputFile.Data());
2152 gSystem->Unlink(outputFile);
2153 if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
e1c22e21 2154 Info("MergeOutput", "Overwrite mode: partial merged files %s will removed",
a2f5fc01 2155 outputChunk.Data());
2156 gSystem->Exec(Form("rm -f %s", outputChunk.Data()));
e1c22e21 2157 }
2158 } else {
a2f5fc01 2159 Info("MergeOutputs", "Output file <%s> found. Not merging again.", outputFile.Data());
e1c22e21 2160 continue;
2161 }
2162 } else {
a2f5fc01 2163 if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
e1c22e21 2164 Info("MergeOutput", "Overwrite mode: partial merged files %s will removed",
a2f5fc01 2165 outputChunk.Data());
2166 gSystem->Exec(Form("rm -f %s", outputChunk.Data()));
e1c22e21 2167 }
2168 }
bb885a9e 2169 if (fMergeExcludes.Length() &&
a2f5fc01 2170 fMergeExcludes.Contains(outputFile.Data())) continue;
16a4353c 2171 // Perform a 'find' command in the output directory, looking for registered outputs
a2f5fc01 2172 merged = MergeOutput(outputFile, fGridOutputDir, fMaxMergeFiles);
0f389141 2173 if (!merged) {
2174 Error("MergeOutputs", "Terminate() will NOT be executed");
2175 return kFALSE;
ff07ec61 2176 }
2177 TFile *fileOpened = (TFile*)gROOT->GetListOfFiles()->FindObject(outputFile);
2178 if (fileOpened) fileOpened->Close();
c57f56b7 2179 }
0f389141 2180 return kTRUE;
c57f56b7 2181}
2182
bb885a9e 2183//______________________________________________________________________________
2184void AliAnalysisAlien::SetDefaultOutputs(Bool_t flag)
2185{
2186// Use the output files connected to output containers from the analysis manager
2187// rather than the files defined by SetOutputFiles
2188 if (flag && !TObject::TestBit(AliAnalysisGrid::kDefaultOutputs))
205b201f 2189 Info("SetDefaultOutputs", "Plugin will use the output files taken from analysis manager");
bb885a9e 2190 TObject::SetBit(AliAnalysisGrid::kDefaultOutputs, flag);
2191}
2192
149d288c 2193//______________________________________________________________________________
2194void AliAnalysisAlien::SetOutputFiles(const char *list)
2195{
2196// Manually set the output files list.
2197// Removes duplicates. Not allowed if default outputs are not disabled.
2198 if (TObject::TestBit(AliAnalysisGrid::kDefaultOutputs)) {
2199 Fatal("SetOutputFiles", "You have to explicitly call SetDefaultOutputs(kFALSE) to manually set output files.");
2200 return;
2201 }
2202 Info("SetOutputFiles", "Output file list is set manually - you are on your own.");
2203 fOutputFiles = "";
2204 TString slist = list;
2205 if (slist.Contains("@")) Warning("SetOutputFiles","The plugin does not allow explicit SE's. Please use: SetNumberOfReplicas() instead.");
2206 TObjArray *arr = slist.Tokenize(" ");
2207 TObjString *os;
2208 TIter next(arr);
2209 TString sout;
2210 while ((os=(TObjString*)next())) {
2211 sout = os->GetString();
2212 if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
2213 if (fOutputFiles.Contains(sout)) continue;
2214 if (!fOutputFiles.IsNull()) fOutputFiles += ",";
2215 fOutputFiles += sout;
2216 }
2217 delete arr;
f790bc1b 2218}
149d288c 2219
2220//______________________________________________________________________________
2221void AliAnalysisAlien::SetOutputArchive(const char *list)
2222{
2223// Manually set the output archive list. Free text - you are on your own...
2224// Not allowed if default outputs are not disabled.
2225 if (TObject::TestBit(AliAnalysisGrid::kDefaultOutputs)) {
2226 Fatal("SetOutputArchive", "You have to explicitly call SetDefaultOutputs(kFALSE) to manually set the output archives.");
2227 return;
2228 }
2229 Info("SetOutputArchive", "Output archive is set manually - you are on your own.");
2230 fOutputArchive = list;
2231}
2232
2233//______________________________________________________________________________
2234void AliAnalysisAlien::SetPreferedSE(const char */*se*/)
2235{
2236// Setting a prefered output SE is not allowed anymore.
2237 Warning("SetPreferedSE", "Setting a preferential SE is not allowed anymore via the plugin. Use SetNumberOfReplicas() and SetDefaultOutputs()");
2238}
2239
5513444a 2240//______________________________________________________________________________
2241Bool_t AliAnalysisAlien::StartAnalysis(Long64_t /*nentries*/, Long64_t /*firstEntry*/)
c57f56b7 2242{
2243// Start remote grid analysis.
3bdcb562 2244 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
2245 Bool_t testMode = TestBit(AliAnalysisGrid::kTest);
2246 if (!mgr || !mgr->IsInitialized()) {
2247 Error("StartAnalysis", "You need an initialized analysis manager for this");
2248 return kFALSE;
2249 }
2250 // Are we in PROOF mode ?
2251 if (mgr->IsProofMode()) {
90d50a8c 2252 Info("StartAnalysis", "##### Starting PROOF analysis on cluster <%s> via the plugin #####", fProofCluster.Data());
3bdcb562 2253 if (fProofCluster.IsNull()) {
2254 Error("StartAnalysis", "You need to specify the proof cluster name via SetProofCluster");
2255 return kFALSE;
2256 }
2257 if (fProofDataSet.IsNull() && !testMode) {
2258 Error("StartAnalysis", "You need to specify a dataset using SetProofDataSet()");
2259 return kFALSE;
2260 }
2261 // Set the needed environment
2262 gEnv->SetValue("XSec.GSI.DelegProxy","2");
2263 // Do we need to reset PROOF ? The success of the Reset operation cannot be checked
2264 if (fProofReset && !testMode) {
2265 if (fProofReset==1) {
2266 Info("StartAnalysis", "Sending soft reset signal to proof cluster %s", fProofCluster.Data());
2267 gROOT->ProcessLine(Form("TProof::Reset(\"%s\", kFALSE);", fProofCluster.Data()));
2268 } else {
2269 Info("StartAnalysis", "Sending hard reset signal to proof cluster %s", fProofCluster.Data());
2270 gROOT->ProcessLine(Form("TProof::Reset(\"%s\", kTRUE);", fProofCluster.Data()));
2271 }
2272 Info("StartAnalysis", "Stopping the analysis. Please use SetProofReset(0) to resume.");
2273 return kFALSE;
2274 }
2275 // Do we need to change the ROOT version ? The success of this cannot be checked.
2276 if (!fRootVersionForProof.IsNull() && !testMode) {
2277 gROOT->ProcessLine(Form("TProof::Mgr(\"%s\")->SetROOTVersion(\"%s\");",
2278 fProofCluster.Data(), fRootVersionForProof.Data()));
2279 }
2280 // Connect to PROOF and check the status
2281 Long_t proof = 0;
27734f0e 2282 TString sworkers;
2283 if (fNproofWorkersPerSlave) sworkers = Form("workers=%dx", fNproofWorkersPerSlave);
2284 else if (fNproofWorkers) sworkers = Form("workers=%d", fNproofWorkers);
3bdcb562 2285 if (!testMode) {
27734f0e 2286 if (!sworkers.IsNull())
2287 proof = gROOT->ProcessLine(Form("TProof::Open(\"%s\", \"%s\");", fProofCluster.Data(), sworkers.Data()));
3bdcb562 2288 else
2289 proof = gROOT->ProcessLine(Form("TProof::Open(\"%s\");", fProofCluster.Data()));
2290 } else {
2291 proof = gROOT->ProcessLine("TProof::Open(\"\");");
2292 if (!proof) {
2293 Error("StartAnalysis", "Could not start PROOF in test mode");
2294 return kFALSE;
2295 }
2296 }
2297 if (!proof) {
2298 Error("StartAnalysis", "Could not connect to PROOF cluster <%s>", fProofCluster.Data());
2299 return kFALSE;
2300 }
27734f0e 2301 if (fNproofWorkersPerSlave*fNproofWorkers > 0)
2302 gROOT->ProcessLine(Form("gProof->SetParallel(%d);", fNproofWorkers));
3bdcb562 2303 // Is dataset existing ?
2304 if (!testMode) {
2305 TString dataset = fProofDataSet;
2306 Int_t index = dataset.Index("#");
2307 if (index>=0) dataset.Remove(index);
830acc4c 2308// if (!gROOT->ProcessLine(Form("gProof->ExistsDataSet(\"%s\");",fProofDataSet.Data()))) {
2309// Error("StartAnalysis", "Dataset %s not existing", fProofDataSet.Data());
2310// return kFALSE;
2311// }
2312// Info("StartAnalysis", "Dataset %s found", dataset.Data());
3bdcb562 2313 }
2314 // Is ClearPackages() needed ?
2315 if (TestSpecialBit(kClearPackages)) {
2316 Info("StartAnalysis", "ClearPackages signal sent to PROOF. Use SetClearPackages(kFALSE) to reset this.");
2317 gROOT->ProcessLine("gProof->ClearPackages();");
2318 }
2319 // Is a given aliroot mode requested ?
2320 TList optionsList;
1ac846e9 2321 TString parLibs;
830acc4c 2322 if (!fAliRootMode.IsNull()) {
3bdcb562 2323 TString alirootMode = fAliRootMode;
2324 if (alirootMode == "default") alirootMode = "";
2325 Info("StartAnalysis", "You are requesting AliRoot mode: %s", fAliRootMode.Data());
2326 optionsList.SetOwner();
2327 optionsList.Add(new TNamed("ALIROOT_MODE", alirootMode.Data()));
2328 // Check the additional libs to be loaded
2329 TString extraLibs;
1ac846e9 2330 Bool_t parMode = kFALSE;
3bdcb562 2331 if (!alirootMode.IsNull()) extraLibs = "ANALYSIS:ANALYSISalice";
2332 // Parse the extra libs for .so
2333 if (fAdditionalLibs.Length()) {
2334 TObjArray *list = fAdditionalLibs.Tokenize(" ");
2335 TIter next(list);
2336 TObjString *str;
1ac846e9 2337 while((str=(TObjString*)next())) {
2338 if (str->GetString().Contains(".so")) {
2339 if (parMode) {
2340 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());
2341 break;
2342 }
2343 TString stmp = str->GetName();
2344 if (stmp.BeginsWith("lib")) stmp.Remove(0,3);
2345 stmp.ReplaceAll(".so","");
2346 if (!extraLibs.IsNull()) extraLibs += ":";
2347 extraLibs += stmp;
2348 continue;
2349 }
2350 if (str->GetString().Contains(".par")) {
2351 // The first par file found in the list will not allow any further .so
2352 parMode = kTRUE;
2353 if (!parLibs.IsNull()) parLibs += ":";
2354 parLibs += str->GetName();
2355 continue;
2356 }
3bdcb562 2357 }
2358 if (list) delete list;
2359 }
2360 if (!extraLibs.IsNull()) optionsList.Add(new TNamed("ALIROOT_EXTRA_LIBS",extraLibs.Data()));
830acc4c 2361 // Check extra includes
2362 if (!fIncludePath.IsNull()) {
2363 TString includePath = fIncludePath;
2364 includePath.ReplaceAll(" ",":");
2365 includePath.Strip(TString::kTrailing, ':');
2366 Info("StartAnalysis", "Adding extra includes: %s",includePath.Data());
2367 optionsList.Add(new TNamed("ALIROOT_EXTRA_INCLUDES",includePath.Data()));
2368 }
27734f0e 2369 // Check if connection to grid is requested
2370 if (TestSpecialBit(kProofConnectGrid))
2371 optionsList.Add(new TNamed("ALIROOT_ENABLE_ALIEN", "1"));
830acc4c 2372 // Enable AliRoot par
2373 if (testMode) {
2374 // Enable proof lite package
2375 TString alirootLite = gSystem->ExpandPathName("$ALICE_ROOT/ANALYSIS/macros/AliRootProofLite.par");
2376 for (Int_t i=0; i<optionsList.GetSize(); i++) {
2377 TNamed *obj = (TNamed*)optionsList.At(i);
2378 printf("%s %s\n", obj->GetName(), obj->GetTitle());
2379 }
2380 if (!gROOT->ProcessLine(Form("gProof->UploadPackage(\"%s\");",alirootLite.Data()))
2381 && !gROOT->ProcessLine(Form("gProof->EnablePackage(\"%s\", (TList*)0x%lx);",alirootLite.Data(),(ULong_t)&optionsList))) {
2382 Info("StartAnalysis", "AliRootProofLite enabled");
2383 } else {
2384 Error("StartAnalysis", "There was an error trying to enable package AliRootProofLite.par");
2385 return kFALSE;
2386 }
2387 } else {
2388 if (gROOT->ProcessLine(Form("gProof->EnablePackage(\"VO_ALICE@AliRoot::%s\", (TList*)0x%lx);",
2389 fAliROOTVersion.Data(), (ULong_t)&optionsList))) {
2390 Error("StartAnalysis", "There was an error trying to enable package VO_ALICE@AliRoot::%s", fAliROOTVersion.Data());
2391 return kFALSE;
2392 }
27734f0e 2393 }
1ac846e9 2394 // Enable first par files from fAdditionalLibs
2395 if (!parLibs.IsNull()) {
2396 TObjArray *list = parLibs.Tokenize(":");
2397 TIter next(list);
2398 TObjString *package;
2399 while((package=(TObjString*)next())) {
40501bb7 2400 TString spkg = package->GetName();
2401 spkg.ReplaceAll(".par", "");
2402 gSystem->Exec(TString::Format("rm -rf %s", spkg.Data()));
b50a41c3 2403 if (!gROOT->ProcessLine(Form("gProof->UploadPackage(\"%s\");", package->GetName()))) {
4f136f18 2404 TString enablePackage = (testMode)?Form("gProof->EnablePackage(\"%s\",kFALSE);", package->GetName()):Form("gProof->EnablePackage(\"%s\",kTRUE);", package->GetName());
2405 if (gROOT->ProcessLine(enablePackage)) {
1ac846e9 2406 Error("StartAnalysis", "There was an error trying to enable package %s", package->GetName());
2407 return kFALSE;
2408 }
2409 } else {
2410 Error("StartAnalysis", "There was an error trying to upload package %s", package->GetName());
2411 return kFALSE;
2412 }
2413 }
2414 if (list) delete list;
2415 }
3bdcb562 2416 } else {
2417 if (fAdditionalLibs.Contains(".so") && !testMode) {
2418 Error("StartAnalysis", "You request additional libs to be loaded but did not enabled any AliRoot mode. Please refer to: \
2419 \n http://aaf.cern.ch/node/83 and use a parameter for SetAliRootMode()");
2420 return kFALSE;
2421 }
2422 }
2423 // Enable par files if requested
2424 if (fPackages && fPackages->GetEntries()) {
2425 TIter next(fPackages);
2426 TObject *package;
2427 while ((package=next())) {
1ac846e9 2428 // Skip packages already enabled
2429 if (parLibs.Contains(package->GetName())) continue;
40501bb7 2430 TString spkg = package->GetName();
2431 spkg.ReplaceAll(".par", "");
2432 gSystem->Exec(TString::Format("rm -rf %s", spkg.Data()));
3bdcb562 2433 if (gROOT->ProcessLine(Form("gProof->UploadPackage(\"%s\");", package->GetName()))) {
27734f0e 2434 if (gROOT->ProcessLine(Form("gProof->EnablePackage(\"%s\",kTRUE);", package->GetName()))) {
3bdcb562 2435 Error("StartAnalysis", "There was an error trying to enable package %s", package->GetName());
2436 return kFALSE;
2437 }
2438 } else {
2439 Error("StartAnalysis", "There was an error trying to upload package %s", package->GetName());
2440 return kFALSE;
2441 }
2442 }
2443 }
2444 // Do we need to load analysis source files ?
2445 // NOTE: don't load on client since this is anyway done by the user to attach his task.
2446 if (fAnalysisSource.Length()) {
2447 TObjArray *list = fAnalysisSource.Tokenize(" ");
2448 TIter next(list);
2449 TObjString *str;
2450 while((str=(TObjString*)next())) {
2451 gROOT->ProcessLine(Form("gProof->Load(\"%s+g\", kTRUE);", str->GetName()));
2452 }
2453 if (list) delete list;
2454 }
830acc4c 2455 if (testMode) {
2456 // Register dataset to proof lite.
2457 if (fFileForTestMode.IsNull()) {
2458 Error("GetChainForTestMode", "For proof test mode please use SetFileForTestMode() pointing to a file that contains data file locations.");
2459 return kFALSE;
2460 }
2461 if (gSystem->AccessPathName(fFileForTestMode)) {
2462 Error("GetChainForTestMode", "File not found: %s", fFileForTestMode.Data());
2463 return kFALSE;
2464 }
2465 TFileCollection *coll = new TFileCollection();
2466 coll->AddFromFile(fFileForTestMode);
27734f0e 2467 gROOT->ProcessLine(Form("gProof->RegisterDataSet(\"test_collection\", (TFileCollection*)0x%lx, \"OV\");", (ULong_t)coll));
2468 gROOT->ProcessLine("gProof->ShowDataSets()");
830acc4c 2469 }
3bdcb562 2470 return kTRUE;
2471 }
c57f56b7 2472
43da816a 2473 // Check if output files have to be taken from the analysis manager
2474 if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
f790bc1b 2475 // Add output files and AOD files
2476 fOutputFiles = GetListOfFiles("outaod");
c07b9ce2 2477 // Add extra files registered to the analysis manager
f790bc1b 2478 TString extra = GetListOfFiles("ext");
2479 if (!extra.IsNull()) {
149d288c 2480 extra.ReplaceAll(".root", "*.root");
f790bc1b 2481 if (!fOutputFiles.IsNull()) fOutputFiles += ",";
149d288c 2482 fOutputFiles += extra;
84fcd93f 2483 }
149d288c 2484 // Compose the output archive.
7acc5b9d 2485 fOutputArchive = "log_archive.zip:std*,*.stat@disk=1 ";
149d288c 2486 fOutputArchive += Form("root_archive.zip:%s@disk=%d",fOutputFiles.Data(),fNreplicas);
43da816a 2487 }
f7b1cbc2 2488// if (!fCloseSE.Length()) fCloseSE = gSystem->Getenv("alien_CLOSE_SE");
c57f56b7 2489 if (TestBit(AliAnalysisGrid::kOffline)) {
2490 Info("StartAnalysis","\n##### OFFLINE MODE ##### Files to be used in GRID are produced but not copied \
2491 \n there nor any job run. You can revise the JDL and analysis \
2492 \n macro then run the same in \"submit\" mode.");
2493 } else if (TestBit(AliAnalysisGrid::kTest)) {
2494 Info("StartAnalysis","\n##### LOCAL MODE ##### Your analysis will be run locally on a subset of the requested \
2495 \n dataset.");
2496 } else if (TestBit(AliAnalysisGrid::kSubmit)) {
2497 Info("StartAnalysis","\n##### SUBMIT MODE ##### Files required by your analysis are copied to your grid working \
2498 \n space and job submitted.");
2499 } else if (TestBit(AliAnalysisGrid::kMerge)) {
2500 Info("StartAnalysis","\n##### MERGE MODE ##### The registered outputs of the analysis will be merged");
0f389141 2501 if (fMergeViaJDL) CheckInputData();
5513444a 2502 return kTRUE;
c57f56b7 2503 } else {
2504 Info("StartAnalysis","\n##### FULL ANALYSIS MODE ##### Producing needed files and submitting your analysis job...");
2505 }
2506
348be253 2507 Print();
c57f56b7 2508 if (!Connect()) {
2509 Error("StartAnalysis", "Cannot start grid analysis without grid connection");
5513444a 2510 return kFALSE;
16a4353c 2511 }
d3b18c4c 2512 if (IsCheckCopy() && gGrid) CheckFileCopy(gGrid->GetHomeDirectory());
c57f56b7 2513 if (!CheckInputData()) {
2514 Error("StartAnalysis", "There was an error in preprocessing your requested input data");
5513444a 2515 return kFALSE;
c57f56b7 2516 }
d3339be3 2517 if (!CreateDataset(fDataPattern)) {
2518 TString serror;
2519 if (!fRunNumbers.Length() && !fRunRange[0]) serror = Form("path to data directory: <%s>", fGridDataDir.Data());
2520 if (fRunNumbers.Length()) serror = "run numbers";
2521 if (fRunRange[0]) serror = Form("run range [%d, %d]", fRunRange[0], fRunRange[1]);
2522 serror += Form("\n or data pattern <%s>", fDataPattern.Data());
2523 Error("StartAnalysis", "No data to process. Please fix %s in your plugin configuration.", serror.Data());
2524 return kFALSE;
2525 }
c57f56b7 2526 WriteAnalysisFile();
2527 WriteAnalysisMacro();
2528 WriteExecutable();
2529 WriteValidationScript();
0f389141 2530 if (fMergeViaJDL) {
2531 WriteMergingMacro();
2532 WriteMergeExecutable();
2533 WriteValidationScript(kTRUE);
2534 }
5513444a 2535 if (!CreateJDL()) return kFALSE;
2536 if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
3bdcb562 2537 if (testMode) {
c57f56b7 2538 // Locally testing the analysis
2539 Info("StartAnalysis", "\n_______________________________________________________________________ \
2540 \n Running analysis script in a daughter shell as on a worker node \
2541 \n_______________________________________________________________________");
149d288c 2542 TObjArray *list = fOutputFiles.Tokenize(",");
c57f56b7 2543 TIter next(list);
2544 TObjString *str;
a2f5fc01 2545 TString outputFile;
c57f56b7 2546 while((str=(TObjString*)next())) {
a2f5fc01 2547 outputFile = str->GetString();
2548 Int_t index = outputFile.Index("@");
2549 if (index > 0) outputFile.Remove(index);
2550 if (!gSystem->AccessPathName(outputFile)) gSystem->Exec(Form("rm %s", outputFile.Data()));
c57f56b7 2551 }
2552 delete list;
2553 gSystem->Exec(Form("bash %s 2>stderr", fExecutable.Data()));
f50e4bc8 2554 gSystem->Exec(Form("bash %s",fValidationScript.Data()));
c57f56b7 2555// gSystem->Exec("cat stdout");
5513444a 2556 return kFALSE;
c57f56b7 2557 }
5513444a 2558 // Check if submitting is managed by LPM manager
a3e84053 2559 if (fProductionMode) {
5513444a 2560 TString prodfile = fJDLName;
2561 prodfile.ReplaceAll(".jdl", ".prod");
2562 WriteProductionFile(prodfile);
2563 Info("StartAnalysis", "Job submitting is managed by LPM. Rerun in terminate mode after jobs finished.");
2564 return kFALSE;
2565 }
a8739e8a 2566 // Submit AliEn job(s)
d2a409b2 2567 gGrid->Cd(fGridOutputDir);
a8739e8a 2568 TGridResult *res;
c57f56b7 2569 TString jobID = "";
d2a409b2 2570 if (!fRunNumbers.Length() && !fRunRange[0]) {
dd74a515 2571 // Submit a given xml or a set of runs
a8739e8a 2572 res = gGrid->Command(Form("submit %s", fJDLName.Data()));
84fcd93f 2573 printf("*************************** %s\n",Form("submit %s", fJDLName.Data()));
a8739e8a 2574 if (res) {
2575 const char *cjobId = res->GetKey(0,"jobId");
2576 if (!cjobId) {
a03be957 2577 gGrid->Stdout();
2578 gGrid->Stderr();
a8739e8a 2579 Error("StartAnalysis", "Your JDL %s could not be submitted", fJDLName.Data());
5513444a 2580 return kFALSE;
a8739e8a 2581 } else {
2582 Info("StartAnalysis", "\n_______________________________________________________________________ \
2583 \n##### Your JDL %s was successfully submitted. \nTHE JOB ID IS: %s \
2584 \n_______________________________________________________________________",
2585 fJDLName.Data(), cjobId);
2586 jobID = cjobId;
2587 }
2588 delete res;
a03be957 2589 } else {
2590 Error("StartAnalysis", "No grid result after submission !!! Bailing out...");
2591 return kFALSE;
a8739e8a 2592 }
2593 } else {
d2a409b2 2594 // Submit for a range of enumeration of runs.
a03be957 2595 if (!Submit()) return kFALSE;
c57f56b7 2596 }
a8739e8a 2597
c57f56b7 2598 Info("StartAnalysis", "\n#### STARTING AN ALIEN SHELL FOR YOU. EXIT WHEN YOUR JOB %s HAS FINISHED. #### \
2599 \n You may exit at any time and terminate the job later using the option <terminate> \
2600 \n ##################################################################################", jobID.Data());
bb885a9e 2601 gSystem->Exec("aliensh");
5513444a 2602 return kTRUE;
c57f56b7 2603}
2604
f790bc1b 2605//______________________________________________________________________________
2606const char *AliAnalysisAlien::GetListOfFiles(const char *type)
2607{
2608// Get a comma-separated list of output files of the requested type.
2609// Type can be (case unsensitive):
2610// aod - list of aod files (std, extensions and filters)
2611// out - list of output files connected to containers (but not aod's or extras)
2612// ext - list of extra files registered to the manager
2613// ter - list of files produced in terminate
2614 static TString files;
2615 files = "";
2616 TString stype = type;
2617 stype.ToLower();
2618 TString aodfiles, extra;
2619 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
2620 if (!mgr) {
2621 ::Error("GetListOfFiles", "Cannot call this without analysis manager");
2622 return files.Data();
2623 }
2624 if (mgr->GetOutputEventHandler()) {
2625 aodfiles = mgr->GetOutputEventHandler()->GetOutputFileName();
2626 TString extraaod = mgr->GetOutputEventHandler()->GetExtraOutputs();
2627 if (!extraaod.IsNull()) {
2628 aodfiles += ",";
2629 aodfiles += extraaod;
2630 }
2631 }
2632 if (stype.Contains("aod")) {
2633 files = aodfiles;
2634 if (stype == "aod") return files.Data();
2635 }
2636 // Add output files that are not in the list of AOD files
2637 TString outputfiles = "";
2638 TIter next(mgr->GetOutputs());
2639 AliAnalysisDataContainer *output;
2640 const char *filename = 0;
2641 while ((output=(AliAnalysisDataContainer*)next())) {
2642 filename = output->GetFileName();
2643 if (!(strcmp(filename, "default"))) continue;
2644 if (outputfiles.Contains(filename)) continue;
2645 if (aodfiles.Contains(filename)) continue;
2646 if (!outputfiles.IsNull()) outputfiles += ",";
2647 outputfiles += filename;
2648 }
2649 if (stype.Contains("out")) {
2650 if (!files.IsNull()) files += ",";
2651 files += outputfiles;
2652 if (stype == "out") return files.Data();
2653 }
2654 // Add extra files registered to the analysis manager
2655 TString sextra;
2656 extra = mgr->GetExtraFiles();
2657 if (!extra.IsNull()) {
2658 extra.Strip();
2659 extra.ReplaceAll(" ", ",");
2660 TObjArray *fextra = extra.Tokenize(",");
2661 TIter nextx(fextra);
2662 TObject *obj;
2663 while ((obj=nextx())) {
2664 if (aodfiles.Contains(obj->GetName())) continue;
2665 if (outputfiles.Contains(obj->GetName())) continue;
2666 if (sextra.Contains(obj->GetName())) continue;
2667 if (!sextra.IsNull()) sextra += ",";
2668 sextra += obj->GetName();
2669 }
2670 delete fextra;
2671 if (stype.Contains("ext")) {
2672 if (!files.IsNull()) files += ",";
2673 files += sextra;
2674 }
2675 }
2676 if (stype == "ext") return files.Data();
2677 TString termfiles;
2678 if (!fTerminateFiles.IsNull()) {
2679 fTerminateFiles.Strip();
2680 fTerminateFiles.ReplaceAll(" ",",");
9c939f2b 2681 TObjArray *fextra = fTerminateFiles.Tokenize(",");
f790bc1b 2682 TIter nextx(fextra);
2683 TObject *obj;
2684 while ((obj=nextx())) {
2685 if (aodfiles.Contains(obj->GetName())) continue;
2686 if (outputfiles.Contains(obj->GetName())) continue;
2687 if (termfiles.Contains(obj->GetName())) continue;
2688 if (sextra.Contains(obj->GetName())) continue;
2689 if (!termfiles.IsNull()) termfiles += ",";
2690 termfiles += obj->GetName();
2691 }
2692 delete fextra;
2693 }
2694 if (stype.Contains("ter")) {
2695 if (!files.IsNull() && !termfiles.IsNull()) {
2696 files += ",";
2697 files += termfiles;
2698 }
2699 }
2700 return files.Data();
2701}
2702
d2a409b2 2703//______________________________________________________________________________
a03be957 2704Bool_t AliAnalysisAlien::Submit()
d2a409b2 2705{
2706// Submit all master jobs.
2707 Int_t nmasterjobs = fInputFiles->GetEntries();
2708 Long_t tshoot = gSystem->Now();
a03be957 2709 if (!fNsubmitted && !SubmitNext()) return kFALSE;
d2a409b2 2710 while (fNsubmitted < nmasterjobs) {
2711 Long_t now = gSystem->Now();
2712 if ((now-tshoot)>30000) {
2713 tshoot = now;
a03be957 2714 if (!SubmitNext()) return kFALSE;
d2a409b2 2715 }
2716 }
a03be957 2717 return kTRUE;
d2a409b2 2718}
2719
0f389141 2720//______________________________________________________________________________
a03be957 2721Bool_t AliAnalysisAlien::SubmitMerging()
0f389141 2722{
2723// Submit all merging jobs.
2724 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
2725 gGrid->Cd(fGridOutputDir);
2726 TString mergeJDLName = fExecutable;
2727 mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
2728 Int_t ntosubmit = fInputFiles->GetEntries();
0f389141 2729 for (Int_t i=0; i<ntosubmit; i++) {
f866cba5 2730 TString runOutDir = gSystem->BaseName(fInputFiles->At(i)->GetName());
2731 runOutDir.ReplaceAll(".xml", "");
7c2cd90a 2732 if (fOutputToRunNo) {
2733 // The output directory is the run number
2734 printf("### Submitting merging job for run <%s>\n", runOutDir.Data());
2735 runOutDir = Form("%s/%s", fGridOutputDir.Data(), runOutDir.Data());
2736 } else {
2737 // The output directory is the master number in 3 digits format
2738 printf("### Submitting merging job for master <%03d>\n", i);
2739 runOutDir = Form("%s/%03d",fGridOutputDir.Data(), i);
2740 }
2741 // Check now the number of merging stages.
2b222f7c 2742 TObjArray *list = fOutputFiles.Tokenize(",");
2743 TIter next(list);
2744 TObjString *str;
2745 TString outputFile;
2746 while((str=(TObjString*)next())) {
2747 outputFile = str->GetString();
2748 Int_t index = outputFile.Index("@");
2749 if (index > 0) outputFile.Remove(index);
2750 if (!fMergeExcludes.Contains(outputFile)) break;
2751 }
2752 delete list;
7c2cd90a 2753 Bool_t done = CheckMergedFiles(outputFile, runOutDir, fMaxMergeFiles, kTRUE, mergeJDLName);
2754 if (!done) return kFALSE;
0f389141 2755 }
a03be957 2756 if (!ntosubmit) return kTRUE;
0f389141 2757 Info("StartAnalysis", "\n#### STARTING AN ALIEN SHELL FOR YOU. EXIT WHEN YOUR MERGING JOBS HAVE FINISHED. #### \
2758 \n You may exit at any time and terminate the job later using the option <terminate> but disabling SetMergeViaJDL\
2759 \n ##################################################################################");
2760 gSystem->Exec("aliensh");
a03be957 2761 return kTRUE;
0f389141 2762}
2763
d2a409b2 2764//______________________________________________________________________________
a03be957 2765Bool_t AliAnalysisAlien::SubmitNext()
d2a409b2 2766{
08d5b699 2767// Submit next bunch of master jobs if the queue is free. The first master job is
2768// submitted right away, while the next will not be unless the previous was split.
2769// The plugin will not submit new master jobs if there are more that 500 jobs in
2770// waiting phase.
d2a409b2 2771 static Bool_t iscalled = kFALSE;
2772 static Int_t firstmaster = 0;
2773 static Int_t lastmaster = 0;
2774 static Int_t npermaster = 0;
a03be957 2775 if (iscalled) return kTRUE;
d2a409b2 2776 iscalled = kTRUE;
2777 Int_t nrunning=0, nwaiting=0, nerror=0, ndone=0;
2778 Int_t ntosubmit = 0;
2779 TGridResult *res;
2780 TString jobID = "";
3bdcb562 2781 Int_t nmasterjobs = fInputFiles->GetEntries();
2782 if (!fNsubmitted) {
2783 ntosubmit = 1;
2784 if (!IsUseSubmitPolicy()) {
90d50a8c 2785 if (nmasterjobs>5)
3bdcb562 2786 Info("SubmitNext","### Warning submit policy not used ! Submitting too many jobs at a time may be prohibitted. \
2787 \n### You can use SetUseSubmitPolicy() to enable if you have problems.");
2788 ntosubmit = nmasterjobs;
2789 }
2790 } else {
d2a409b2 2791 TString status = GetJobStatus(firstmaster, lastmaster, nrunning, nwaiting, nerror, ndone);
84fcd93f 2792 printf("=== master %d: %s\n", lastmaster, status.Data());
d2a409b2 2793 // If last master not split, just return
a03be957 2794 if (status != "SPLIT") {iscalled = kFALSE; return kTRUE;}
d2a409b2 2795 // No more than 100 waiting jobs
08d5b699 2796 if (nwaiting>500) {iscalled = kFALSE; return kTRUE;}
d2a409b2 2797 npermaster = (nrunning+nwaiting+nerror+ndone)/fNsubmitted;
08d5b699 2798 if (npermaster) ntosubmit = (500-nwaiting)/npermaster;
7586eedc 2799 if (!ntosubmit) ntosubmit = 1;
84fcd93f 2800 printf("=== WAITING(%d) RUNNING(%d) DONE(%d) OTHER(%d) NperMaster=%d => to submit %d jobs\n",
d2a409b2 2801 nwaiting, nrunning, ndone, nerror, npermaster, ntosubmit);
2802 }
d2a409b2 2803 for (Int_t i=0; i<ntosubmit; i++) {
2804 // Submit for a range of enumeration of runs.
a03be957 2805 if (fNsubmitted>=nmasterjobs) {iscalled = kFALSE; return kTRUE;}
d2a409b2 2806 TString query;
cd11251e 2807 TString runOutDir = gSystem->BaseName(fInputFiles->At(fNsubmitted)->GetName());
2808 runOutDir.ReplaceAll(".xml", "");
2809 if (fOutputToRunNo)
2810 query = Form("submit %s %s %s", fJDLName.Data(), fInputFiles->At(fNsubmitted)->GetName(), runOutDir.Data());
2811 else
2812 query = Form("submit %s %s %03d", fJDLName.Data(), fInputFiles->At(fNsubmitted)->GetName(), fNsubmitted);
84fcd93f 2813 printf("********* %s\n",query.Data());
d2a409b2 2814 res = gGrid->Command(query);
2815 if (res) {
98ca124f 2816 TString cjobId1 = res->GetKey(0,"jobId");
2817 if (!cjobId1.Length()) {
d2a409b2 2818 iscalled = kFALSE;
a03be957 2819 gGrid->Stdout();
2820 gGrid->Stderr();
2821 Error("StartAnalysis", "Your JDL %s could not be submitted. The message was:", fJDLName.Data());
2822 return kFALSE;
d2a409b2 2823 } else {
2824 Info("StartAnalysis", "\n_______________________________________________________________________ \
2825 \n##### Your JDL %s submitted (%d to go). \nTHE JOB ID IS: %s \
2826 \n_______________________________________________________________________",
98ca124f 2827 fJDLName.Data(), nmasterjobs-fNsubmitted-1, cjobId1.Data());
d2a409b2 2828 jobID += cjobId1;
2829 jobID += " ";
98ca124f 2830 lastmaster = cjobId1.Atoi();
d2a409b2 2831 if (!firstmaster) firstmaster = lastmaster;
2832 fNsubmitted++;
2833 }
2834 delete res;
a03be957 2835 } else {
2836 Error("StartAnalysis", "No grid result after submission !!! Bailing out...");
2837 return kFALSE;
d2a409b2 2838 }
2839 }
2840 iscalled = kFALSE;
a03be957 2841 return kTRUE;
d2a409b2 2842}
2843
c57f56b7 2844//______________________________________________________________________________
2845void AliAnalysisAlien::WriteAnalysisFile()
2846{
f10e8481 2847// Write current analysis manager into the file <analysisFile>
2848 TString analysisFile = fExecutable;
2849 analysisFile.ReplaceAll(".sh", ".root");
c57f56b7 2850 if (!TestBit(AliAnalysisGrid::kSubmit)) {
2851 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
2852 if (!mgr || !mgr->IsInitialized()) {
2853 Error("WriteAnalysisFile", "You need an initialized analysis manager for this");
2854 return;
2855 }
2856 // Check analysis type
2857 TObject *handler;
2858 if (mgr->GetMCtruthEventHandler()) TObject::SetBit(AliAnalysisGrid::kUseMC);
2859 handler = (TObject*)mgr->GetInputEventHandler();
2860 if (handler) {
2861 if (handler->InheritsFrom("AliESDInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseESD);
2862 if (handler->InheritsFrom("AliAODInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseAOD);
2863 }
2864 TDirectory *cdir = gDirectory;
f10e8481 2865 TFile *file = TFile::Open(analysisFile, "RECREATE");
c57f56b7 2866 if (file) {
e16a394c 2867 // Skip task Terminate calls for the grid job (but not in test mode, where we want to check also the terminate mode
2868 if (!TestBit(AliAnalysisGrid::kTest)) mgr->SetSkipTerminate(kTRUE);
fe2d7fc2 2869 // Unless merging makes no sense
2870 if (IsSingleOutput()) mgr->SetSkipTerminate(kFALSE);
c57f56b7 2871 mgr->Write();
2872 delete file;
fe2d7fc2 2873 // Enable termination for local jobs
2874 mgr->SetSkipTerminate(kFALSE);
c57f56b7 2875 }
2876 if (cdir) cdir->cd();
f10e8481 2877 Info("WriteAnalysisFile", "\n##### Analysis manager: %s wrote to file <%s>\n", mgr->GetName(),analysisFile.Data());
c57f56b7 2878 }
2879 Bool_t copy = kTRUE;
d3b18c4c 2880 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
c57f56b7 2881 if (copy) {
2882 CdWork();
2883 TString workdir = gGrid->GetHomeDirectory();
2884 workdir += fGridWorkingDir;
d3b18c4c 2885 Info("WriteAnalysisFile", "\n##### Copying file <%s> containing your initialized analysis manager to your alien workspace", analysisFile.Data());
f10e8481 2886 if (FileExists(analysisFile)) gGrid->Rm(analysisFile);
2887 TFile::Cp(Form("file:%s",analysisFile.Data()), Form("alien://%s/%s", workdir.Data(),analysisFile.Data()));
c57f56b7 2888 }
2889}
2890
2891//______________________________________________________________________________
2892void AliAnalysisAlien::WriteAnalysisMacro()
2893{
2894// Write the analysis macro that will steer the analysis in grid mode.
2895 if (!TestBit(AliAnalysisGrid::kSubmit)) {
2896 ofstream out;
2897 out.open(fAnalysisMacro.Data(), ios::out);
2898 if (!out.good()) {
2899 Error("WriteAnalysisMacro", "could not open file %s for writing", fAnalysisMacro.Data());
2900 return;
2901 }
5b273635 2902 Bool_t hasSTEERBase = kFALSE;
2903 Bool_t hasESD = kFALSE;
2904 Bool_t hasAOD = kFALSE;
2905 Bool_t hasANALYSIS = kFALSE;
2906 Bool_t hasANALYSISalice = kFALSE;
2907 Bool_t hasCORRFW = kFALSE;
c57f56b7 2908 TString func = fAnalysisMacro;
2909 TString type = "ESD";
2910 TString comment = "// Analysis using ";
2911 if (TObject::TestBit(AliAnalysisGrid::kUseESD)) comment += "ESD";
2912 if (TObject::TestBit(AliAnalysisGrid::kUseAOD)) {
2913 type = "AOD";
2914 comment += "AOD";
2915 }
0df6ccf2 2916 if (type!="AOD" && fFriendChainName!="") {
2917 Error("WriteAnalysisMacro", "Friend chain can be attached only to AOD");
2918 return;
2919 }
c57f56b7 2920 if (TObject::TestBit(AliAnalysisGrid::kUseMC)) comment += "/MC";
2921 else comment += " data";
2922 out << "const char *anatype = \"" << type.Data() << "\";" << endl << endl;
2923 func.ReplaceAll(".C", "");
2924 out << "void " << func.Data() << "()" << endl;
2925 out << "{" << endl;
2926 out << comment.Data() << endl;
2927 out << "// Automatically generated analysis steering macro executed in grid subjobs" << endl << endl;
f7498086 2928 out << " TStopwatch timer;" << endl;
2929 out << " timer.Start();" << endl << endl;
13f0c00b 2930 // Change temp directory to current one
2931 out << "// Set temporary merging directory to current one" << endl;
2932 out << " gSystem->Setenv(\"TMPDIR\", gSystem->pwd());" << endl << endl;
f790bc1b 2933 if (!fExecutableCommand.Contains("aliroot")) {
2934 out << "// load base root libraries" << endl;
2935 out << " gSystem->Load(\"libTree\");" << endl;
2936 out << " gSystem->Load(\"libGeom\");" << endl;
2937 out << " gSystem->Load(\"libVMC\");" << endl;
2938 out << " gSystem->Load(\"libPhysics\");" << endl << endl;
2939 out << " gSystem->Load(\"libMinuit\");" << endl << endl;
2940 }
d5c6455a 2941 if (fAdditionalRootLibs.Length()) {
47a4137d 2942 // in principle libtree /lib geom libvmc etc. can go into this list, too
2943 out << "// Add aditional libraries" << endl;
2944 TObjArray *list = fAdditionalRootLibs.Tokenize(" ");
2945 TIter next(list);
2946 TObjString *str;
2947 while((str=(TObjString*)next())) {
2948 if (str->GetString().Contains(".so"))
2949 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
d5c6455a 2950 }
47a4137d 2951 if (list) delete list;
d5c6455a 2952 }
47a4137d 2953 out << "// include path" << endl;
2954 if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
2955 out << " gSystem->AddIncludePath(\"-I$ALICE_ROOT/include\");" << endl << endl;
57377eb5 2956 out << "// Load analysis framework libraries" << endl;
652561d5 2957 TString setupPar = "AliAnalysisAlien::SetupPar";
4e5c5506 2958 if (!fPackages) {
f790bc1b 2959 if (!fExecutableCommand.Contains("aliroot")) {
2960 out << " gSystem->Load(\"libSTEERBase\");" << endl;
2961 out << " gSystem->Load(\"libESD\");" << endl;
2962 out << " gSystem->Load(\"libAOD\");" << endl;
2963 }
4e5c5506 2964 out << " gSystem->Load(\"libANALYSIS\");" << endl;
57377eb5 2965 out << " gSystem->Load(\"libANALYSISalice\");" << endl;
2966 out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
4e5c5506 2967 } else {
4e5c5506 2968 TIter next(fPackages);
2969 TObject *obj;
57377eb5 2970 TString pkgname;
57377eb5 2971 while ((obj=next())) {
2972 pkgname = obj->GetName();
4478e6f1 2973 if (pkgname == "STEERBase" ||
2974 pkgname == "STEERBase.par") hasSTEERBase = kTRUE;
2975 if (pkgname == "ESD" ||
2976 pkgname == "ESD.par") hasESD = kTRUE;
2977 if (pkgname == "AOD" ||
2978 pkgname == "AOD.par") hasAOD = kTRUE;
2979 if (pkgname == "ANALYSIS" ||
2980 pkgname == "ANALYSIS.par") hasANALYSIS = kTRUE;
2981 if (pkgname == "ANALYSISalice" ||
2982 pkgname == "ANALYSISalice.par") hasANALYSISalice = kTRUE;
2983 if (pkgname == "CORRFW" ||
2984 pkgname == "CORRFW.par") hasCORRFW = kTRUE;
5b273635 2985 }
2986 if (hasANALYSISalice) setupPar = "SetupPar";
57377eb5 2987 if (!hasSTEERBase) out << " gSystem->Load(\"libSTEERBase\");" << endl;
5b273635 2988 else out << " if (!" << setupPar << "(\"STEERBase\")) return;" << endl;
57377eb5 2989 if (!hasESD) out << " gSystem->Load(\"libESD\");" << endl;
5b273635 2990 else out << " if (!" << setupPar << "(\"ESD\")) return;" << endl;
57377eb5 2991 if (!hasAOD) out << " gSystem->Load(\"libAOD\");" << endl;
5b273635 2992 else out << " if (!" << setupPar << "(\"AOD\")) return;" << endl;
57377eb5 2993 if (!hasANALYSIS) out << " gSystem->Load(\"libANALYSIS\");" << endl;
5b273635 2994 else out << " if (!" << setupPar << "(\"ANALYSIS\")) return;" << endl;
57377eb5 2995 if (!hasANALYSISalice) out << " gSystem->Load(\"libANALYSISalice\");" << endl;
5b273635 2996 else out << " if (!" << setupPar << "(\"ANALYSISalice\")) return;" << endl;
57377eb5 2997 if (!hasCORRFW) out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
5b273635 2998 else out << " if (!" << setupPar << "(\"CORRFW\")) return;" << endl << endl;
57377eb5 2999 out << "// Compile other par packages" << endl;
3000 next.Reset();
fcc9bb6f 3001 while ((obj=next())) {
3002 pkgname = obj->GetName();
4478e6f1 3003 if (pkgname == "STEERBase" ||
3004 pkgname == "STEERBase.par" ||
3005 pkgname == "ESD" ||
3006 pkgname == "ESD.par" ||
3007 pkgname == "AOD" ||
3008 pkgname == "AOD.par" ||
3009 pkgname == "ANALYSIS" ||
3010 pkgname == "ANALYSIS.par" ||
3011 pkgname == "ANALYSISalice" ||
3012 pkgname == "ANALYSISalice.par" ||
3013 pkgname == "CORRFW" ||
3014 pkgname == "CORRFW.par") continue;
5b273635 3015 out << " if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
fcc9bb6f 3016 }
4e5c5506 3017 }
6da75e0b 3018 if (fAdditionalLibs.Length()) {
3019 out << "// Add aditional AliRoot libraries" << endl;
3020 TObjArray *list = fAdditionalLibs.Tokenize(" ");
3021 TIter next(list);
3022 TObjString *str;
3023 while((str=(TObjString*)next())) {
3024 if (str->GetString().Contains(".so"))
3025 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
652561d5 3026 if (str->GetString().Contains(".par"))
3027 out << " if (!" << setupPar << "(\"" << str->GetString() << "\")) return;" << endl;
6da75e0b 3028 }
3029 if (list) delete list;
3030 }
3031 out << endl;
c57f56b7 3032 out << "// analysis source to be compiled at runtime (if any)" << endl;
3033 if (fAnalysisSource.Length()) {
3034 TObjArray *list = fAnalysisSource.Tokenize(" ");
3035 TIter next(list);
3036 TObjString *str;
3037 while((str=(TObjString*)next())) {
3038 out << " gROOT->ProcessLine(\".L " << str->GetString().Data() << "+g\");" << endl;
3039 }
3040 if (list) delete list;
3041 }
3042 out << endl;
0f389141 3043 if (fFastReadOption) {
d3339be3 3044 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 !!! \
3045 \n+++ NOTE: To disable this option, use: plugin->SetFastReadOption(kFALSE)");
0f389141 3046 out << "// fast xrootd reading enabled" << endl;
3047 out << " printf(\"!!! You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !!!\");" << endl;
d3339be3 3048 out << " gEnv->SetValue(\"XNet.ConnectTimeout\",10);" << endl;
f790bc1b 3049 out << " gEnv->SetValue(\"XNet.RequestTimeout\",10);" << endl;
0f389141 3050 out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
f790bc1b 3051 out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",10);" << endl;
0f389141 3052 out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
3053 }
c57f56b7 3054 out << "// connect to AliEn and make the chain" << endl;
3055 out << " if (!TGrid::Connect(\"alien://\")) return;" << endl;
c57f56b7 3056 out << "// read the analysis manager from file" << endl;
f10e8481 3057 TString analysisFile = fExecutable;
3058 analysisFile.ReplaceAll(".sh", ".root");
3059 out << " TFile *file = TFile::Open(\"" << analysisFile << "\");" << endl;
c57f56b7 3060 out << " if (!file) return;" << endl;
3061 out << " TIter nextkey(file->GetListOfKeys());" << endl;
3062 out << " AliAnalysisManager *mgr = 0;" << endl;
3063 out << " TKey *key;" << endl;
3064 out << " while ((key=(TKey*)nextkey())) {" << endl;
3065 out << " if (!strcmp(key->GetClassName(), \"AliAnalysisManager\"))" << endl;
3066 out << " mgr = (AliAnalysisManager*)file->Get(key->GetName());" << endl;
3067 out << " };" << endl;
3068 out << " if (!mgr) {" << endl;
205b201f 3069 out << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file " << analysisFile <<"\");" << endl;
c57f56b7 3070 out << " return;" << endl;
3071 out << " }" << endl << endl;
3072 out << " mgr->PrintStatus();" << endl;
52b6a92b 3073 if (AliAnalysisManager::GetAnalysisManager()) {
f866cba5 3074 if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) {
52b6a92b 3075 out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
de52b69c 3076 } else {
9a8288ff 3077 if (TestBit(AliAnalysisGrid::kTest))
3078 out << " AliLog::SetGlobalLogLevel(AliLog::kWarning);" << endl;
3079 else
3080 out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
52b6a92b 3081 }
3082 }
242accb2 3083 if (IsUsingTags()) {
3084 out << " TChain *chain = CreateChainFromTags(\"wn.xml\", anatype);" << endl << endl;
3085 } else {
3086 out << " TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl;
3087 }
c57f56b7 3088 out << " mgr->StartAnalysis(\"localfile\", chain);" << endl;
f7498086 3089 out << " timer.Stop();" << endl;
3090 out << " timer.Print();" << endl;
c57f56b7 3091 out << "}" << endl << endl;
3092 if (IsUsingTags()) {
3093 out << "TChain* CreateChainFromTags(const char *xmlfile, const char *type=\"ESD\")" << endl;
3094 out << "{" << endl;
3095 out << "// Create a chain using tags from the xml file." << endl;
3096 out << " TAlienCollection* coll = TAlienCollection::Open(xmlfile);" << endl;
3097 out << " if (!coll) {" << endl;
3098 out << " ::Error(\"CreateChainFromTags\", \"Cannot create an AliEn collection from %s\", xmlfile);" << endl;
3099 out << " return NULL;" << endl;
3100 out << " }" << endl;
3101 out << " TGridResult* tagResult = coll->GetGridResult(\"\",kFALSE,kFALSE);" << endl;
3102 out << " AliTagAnalysis *tagAna = new AliTagAnalysis(type);" << endl;
3103 out << " tagAna->ChainGridTags(tagResult);" << endl << endl;
3104 out << " AliRunTagCuts *runCuts = new AliRunTagCuts();" << endl;
3105 out << " AliLHCTagCuts *lhcCuts = new AliLHCTagCuts();" << endl;
3106 out << " AliDetectorTagCuts *detCuts = new AliDetectorTagCuts();" << endl;
3107 out << " AliEventTagCuts *evCuts = new AliEventTagCuts();" << endl;
3108 out << " // Check if the cuts configuration file was provided" << endl;
3109 out << " if (!gSystem->AccessPathName(\"ConfigureCuts.C\")) {" << endl;
3110 out << " gROOT->LoadMacro(\"ConfigureCuts.C\");" << endl;
3111 out << " ConfigureCuts(runCuts, lhcCuts, detCuts, evCuts);" << endl;
3112 out << " }" << endl;
0df6ccf2 3113 if (fFriendChainName=="") {
3114 out << " TChain *chain = tagAna->QueryTags(runCuts, lhcCuts, detCuts, evCuts);" << endl;
3115 } else {
3116 out << " TString tmpColl=\"tmpCollection.xml\";" << endl;
3117 out << " tagAna->CreateXMLCollection(tmpColl.Data(),runCuts, lhcCuts, detCuts, evCuts);" << endl;
3118 out << " TChain *chain = CreateChain(tmpColl.Data(),type);" << endl;
3119 }
c57f56b7 3120 out << " if (!chain || !chain->GetNtrees()) return NULL;" << endl;
3121 out << " chain->ls();" << endl;
3122 out << " return chain;" << endl;
fcc9bb6f 3123 out << "}" << endl << endl;
c57f56b7 3124 if (gSystem->AccessPathName("ConfigureCuts.C")) {
3125 TString msg = "\n##### You may want to provide a macro ConfigureCuts.C with a method:\n";
3126 msg += " void ConfigureCuts(AliRunTagCuts *runCuts,\n";
3127 msg += " AliLHCTagCuts *lhcCuts,\n";
3128 msg += " AliDetectorTagCuts *detCuts,\n";
3129 msg += " AliEventTagCuts *evCuts)";
23329835 3130 Info("WriteAnalysisMacro", "%s", msg.Data());
c57f56b7 3131 }
0df6ccf2 3132 }
3133 if (!IsUsingTags() || fFriendChainName!="") {
fcc9bb6f 3134 out <<"//________________________________________________________________________________" << endl;
c57f56b7 3135 out << "TChain* CreateChain(const char *xmlfile, const char *type=\"ESD\")" << endl;
3136 out << "{" << endl;
3137 out << "// Create a chain using url's from xml file" << endl;
242accb2 3138 out << " TString filename;" << endl;
3139 out << " Int_t run = 0;" << endl;
c57f56b7 3140 out << " TString treename = type;" << endl;
3141 out << " treename.ToLower();" << endl;
3142 out << " treename += \"Tree\";" << endl;
e02fee64 3143 out << " printf(\"***************************************\\n\");" << endl;
3144 out << " printf(\" Getting chain of trees %s\\n\", treename.Data());" << endl;
3145 out << " printf(\"***************************************\\n\");" << endl;
c57f56b7 3146 out << " TAlienCollection *coll = TAlienCollection::Open(xmlfile);" << endl;
3147 out << " if (!coll) {" << endl;
3148 out << " ::Error(\"CreateChain\", \"Cannot create an AliEn collection from %s\", xmlfile);" << endl;
3149 out << " return NULL;" << endl;
3150 out << " }" << endl;
242accb2 3151 out << " AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();" << endl;
c57f56b7 3152 out << " TChain *chain = new TChain(treename);" << endl;
0df6ccf2 3153 if(fFriendChainName!="") {
3154 out << " TChain *chainFriend = new TChain(treename);" << endl;
3155 }
c57f56b7 3156 out << " coll->Reset();" << endl;
0df6ccf2 3157 out << " while (coll->Next()) {" << endl;
242accb2 3158 out << " filename = coll->GetTURL("");" << endl;
3159 out << " if (mgr) {" << endl;
3160 out << " Int_t nrun = AliAnalysisManager::GetRunFromAlienPath(filename);" << endl;
3161 out << " if (nrun && nrun != run) {" << endl;
3162 out << " printf(\"### Run number detected from chain: %d\\n\", nrun);" << endl;
3163 out << " mgr->SetRunFromPath(nrun);" << endl;
3164 out << " run = nrun;" << endl;
3165 out << " }" << endl;
3166 out << " }" << endl;
3167 out << " chain->Add(filename);" << endl;
0df6ccf2 3168 if(fFriendChainName!="") {
3169 out << " TString fileFriend=coll->GetTURL(\"\");" << endl;
3170 out << " fileFriend.ReplaceAll(\"AliAOD.root\",\""<<fFriendChainName.Data()<<"\");" << endl;
3171 out << " fileFriend.ReplaceAll(\"AliAODs.root\",\""<<fFriendChainName.Data()<<"\");" << endl;
3172 out << " chainFriend->Add(fileFriend.Data());" << endl;
3173 }
3174 out << " }" << endl;
c57f56b7 3175 out << " if (!chain->GetNtrees()) {" << endl;
3176 out << " ::Error(\"CreateChain\", \"No tree found from collection %s\", xmlfile);" << endl;
3177 out << " return NULL;" << endl;
3178 out << " }" << endl;
0df6ccf2 3179 if(fFriendChainName!="") {
3180 out << " chain->AddFriend(chainFriend);" << endl;
3181 }
c57f56b7 3182 out << " return chain;" << endl;
fcc9bb6f 3183 out << "}" << endl << endl;
c57f56b7 3184 }
5b273635 3185 if (hasANALYSISalice) {
3186 out <<"//________________________________________________________________________________" << endl;
3187 out << "Bool_t SetupPar(const char *package) {" << endl;
3188 out << "// Compile the package and set it up." << endl;
3189 out << " TString pkgdir = package;" << endl;
3190 out << " pkgdir.ReplaceAll(\".par\",\"\");" << endl;
b50a41c3 3191 out << " gSystem->Exec(TString::Format(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
5b273635 3192 out << " TString cdir = gSystem->WorkingDirectory();" << endl;
3193 out << " gSystem->ChangeDirectory(pkgdir);" << endl;
3194 out << " // Check for BUILD.sh and execute" << endl;
3195 out << " if (!gSystem->AccessPathName(\"PROOF-INF/BUILD.sh\")) {" << endl;
3196 out << " printf(\"*******************************\\n\");" << endl;
3197 out << " printf(\"*** Building PAR archive ***\\n\");" << endl;
3198 out << " printf(\"*******************************\\n\");" << endl;
3199 out << " if (gSystem->Exec(\"PROOF-INF/BUILD.sh\")) {" << endl;
3200 out << " ::Error(\"SetupPar\", \"Cannot build par archive %s\", pkgdir.Data());" << endl;
3201 out << " gSystem->ChangeDirectory(cdir);" << endl;
3202 out << " return kFALSE;" << endl;
3203 out << " }" << endl;
3204 out << " } else {" << endl;
3205 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/BUILD.sh for package %s\", pkgdir.Data());" << endl;
3206 out << " gSystem->ChangeDirectory(cdir);" << endl;
3207 out << " return kFALSE;" << endl;
3208 out << " }" << endl;
3209 out << " // Check for SETUP.C and execute" << endl;
3210 out << " if (!gSystem->AccessPathName(\"PROOF-INF/SETUP.C\")) {" << endl;
3211 out << " printf(\"*******************************\\n\");" << endl;
3212 out << " printf(\"*** Setup PAR archive ***\\n\");" << endl;
3213 out << " printf(\"*******************************\\n\");" << endl;
3214 out << " gROOT->Macro(\"PROOF-INF/SETUP.C\");" << endl;
3215 out << " } else {" << endl;
3216 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/SETUP.C for package %s\", pkgdir.Data());" << endl;
3217 out << " gSystem->ChangeDirectory(cdir);" << endl;
3218 out << " return kFALSE;" << endl;
3219 out << " }" << endl;
3220 out << " // Restore original workdir" << endl;
3221 out << " gSystem->ChangeDirectory(cdir);" << endl;
3222 out << " return kTRUE;" << endl;
3223 out << "}" << endl;
3224 }
c57f56b7 3225 Info("WriteAnalysisMacro", "\n##### Analysis macro to run on worker nodes <%s> written",fAnalysisMacro.Data());
3226 }
3227 Bool_t copy = kTRUE;
d3b18c4c 3228 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
c57f56b7 3229 if (copy) {
3230 CdWork();
3231 TString workdir = gGrid->GetHomeDirectory();
3232 workdir += fGridWorkingDir;
3233 if (FileExists(fAnalysisMacro)) gGrid->Rm(fAnalysisMacro);
3234 if (IsUsingTags() && !gSystem->AccessPathName("ConfigureCuts.C")) {
3235 if (FileExists("ConfigureCuts.C")) gGrid->Rm("ConfigureCuts.C");
3236 Info("WriteAnalysisMacro", "\n##### Copying cuts configuration macro: <ConfigureCuts.C> to your alien workspace");
3237 TFile::Cp("file:ConfigureCuts.C", Form("alien://%s/ConfigureCuts.C", workdir.Data()));
3238 }
3239 Info("WriteAnalysisMacro", "\n##### Copying analysis macro: <%s> to your alien workspace", fAnalysisMacro.Data());
3240 TFile::Cp(Form("file:%s",fAnalysisMacro.Data()), Form("alien://%s/%s", workdir.Data(), fAnalysisMacro.Data()));
3241 }
3242}
3243
0f389141 3244//______________________________________________________________________________
3245void AliAnalysisAlien::WriteMergingMacro()
3246{
3247// Write a macro to merge the outputs per master job.
3248 if (!fMergeViaJDL) return;
3249 if (!fOutputFiles.Length()) {
3250 Error("WriteMergingMacro", "No output file names defined. Are you running the right AliAnalysisAlien configuration ?");
3251 return;
3252 }
3253 TString mergingMacro = fExecutable;
3254 mergingMacro.ReplaceAll(".sh","_merge.C");
3255 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
3256 if (!TestBit(AliAnalysisGrid::kSubmit)) {
3257 ofstream out;
3258 out.open(mergingMacro.Data(), ios::out);
3259 if (!out.good()) {
3260 Error("WriteMergingMacro", "could not open file %s for writing", fAnalysisMacro.Data());
3261 return;
3262 }
5b273635 3263 Bool_t hasSTEERBase = kFALSE;
3264 Bool_t hasESD = kFALSE;
3265 Bool_t hasAOD = kFALSE;
3266 Bool_t hasANALYSIS = kFALSE;
3267 Bool_t hasANALYSISalice = kFALSE;
3268 Bool_t hasCORRFW = kFALSE;
0f389141 3269 TString func = mergingMacro;
3270 TString comment;
3271 func.ReplaceAll(".C", "");
7c2cd90a 3272 out << "void " << func.Data() << "(const char *dir, Int_t stage=0, Int_t ichunk=0)" << endl;
0f389141 3273 out << "{" << endl;
3274 out << "// Automatically generated merging macro executed in grid subjobs" << endl << endl;
3275 out << " TStopwatch timer;" << endl;
3276 out << " timer.Start();" << endl << endl;
7c2cd90a 3277 if (!fExecutableCommand.Contains("aliroot")) {
3278 out << "// load base root libraries" << endl;
3279 out << " gSystem->Load(\"libTree\");" << endl;
3280 out << " gSystem->Load(\"libGeom\");" << endl;
3281 out << " gSystem->Load(\"libVMC\");" << endl;
3282 out << " gSystem->Load(\"libPhysics\");" << endl << endl;
3283 out << " gSystem->Load(\"libMinuit\");" << endl << endl;
3284 }
0f389141 3285 if (fAdditionalRootLibs.Length()) {
3286 // in principle libtree /lib geom libvmc etc. can go into this list, too
3287 out << "// Add aditional libraries" << endl;
3288 TObjArray *list = fAdditionalRootLibs.Tokenize(" ");
3289 TIter next(list);
3290 TObjString *str;
3291 while((str=(TObjString*)next())) {
3292 if (str->GetString().Contains(".so"))
3293 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
3294 }
3295 if (list) delete list;
3296 }
3297 out << "// include path" << endl;
3298 if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
3299 out << " gSystem->AddIncludePath(\"-I$ALICE_ROOT/include\");" << endl << endl;
3300 out << "// Load analysis framework libraries" << endl;
3301 if (!fPackages) {
7c2cd90a 3302 if (!fExecutableCommand.Contains("aliroot")) {
3303 out << " gSystem->Load(\"libSTEERBase\");" << endl;
3304 out << " gSystem->Load(\"libESD\");" << endl;
3305 out << " gSystem->Load(\"libAOD\");" << endl;
3306 }
0f389141 3307 out << " gSystem->Load(\"libANALYSIS\");" << endl;
3308 out << " gSystem->Load(\"libANALYSISalice\");" << endl;
3309 out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
3310 } else {
3311 TIter next(fPackages);
3312 TObject *obj;
3313 TString pkgname;
5b273635 3314 TString setupPar = "AliAnalysisAlien::SetupPar";
0f389141 3315 while ((obj=next())) {
3316 pkgname = obj->GetName();
3317 if (pkgname == "STEERBase" ||
3318 pkgname == "STEERBase.par") hasSTEERBase = kTRUE;
3319 if (pkgname == "ESD" ||
3320 pkgname == "ESD.par") hasESD = kTRUE;
3321 if (pkgname == "AOD" ||
3322 pkgname == "AOD.par") hasAOD = kTRUE;
3323 if (pkgname == "ANALYSIS" ||
3324 pkgname == "ANALYSIS.par") hasANALYSIS = kTRUE;
3325 if (pkgname == "ANALYSISalice" ||
3326 pkgname == "ANALYSISalice.par") hasANALYSISalice = kTRUE;
3327 if (pkgname == "CORRFW" ||
3328 pkgname == "CORRFW.par") hasCORRFW = kTRUE;
3329 }
5b273635 3330 if (hasANALYSISalice) setupPar = "SetupPar";
0f389141 3331 if (!hasSTEERBase) out << " gSystem->Load(\"libSTEERBase\");" << endl;
5b273635 3332 else out << " if (!" << setupPar << "(\"STEERBase\")) return;" << endl;
0f389141 3333 if (!hasESD) out << " gSystem->Load(\"libESD\");" << endl;
5b273635 3334 else out << " if (!" << setupPar << "(\"ESD\")) return;" << endl;
0f389141 3335 if (!hasAOD) out << " gSystem->Load(\"libAOD\");" << endl;
5b273635 3336 else out << " if (!" << setupPar << "(\"AOD\")) return;" << endl;
0f389141 3337 if (!hasANALYSIS) out << " gSystem->Load(\"libANALYSIS\");" << endl;
5b273635 3338 else out << " if (!" << setupPar << "(\"ANALYSIS\")) return;" << endl;
0f389141 3339 if (!hasANALYSISalice) out << " gSystem->Load(\"libANALYSISalice\");" << endl;
5b273635 3340 else out << " if (!" << setupPar << "(\"ANALYSISalice\")) return;" << endl;
0f389141 3341 if (!hasCORRFW) out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
5b273635 3342 else out << " if (!" << setupPar << "(\"CORRFW\")) return;" << endl << endl;
0f389141 3343 out << "// Compile other par packages" << endl;
3344 next.Reset();
3345 while ((obj=next())) {
3346 pkgname = obj->GetName();
3347 if (pkgname == "STEERBase" ||
3348 pkgname == "STEERBase.par" ||
3349 pkgname == "ESD" ||
3350 pkgname == "ESD.par" ||
3351 pkgname == "AOD" ||
3352 pkgname == "AOD.par" ||
3353 pkgname == "ANALYSIS" ||
3354 pkgname == "ANALYSIS.par" ||
3355 pkgname == "ANALYSISalice" ||
3356 pkgname == "ANALYSISalice.par" ||
3357 pkgname == "CORRFW" ||
3358 pkgname == "CORRFW.par") continue;
5b273635 3359 out << " if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
0f389141 3360 }
3361 }
3362 if (fAdditionalLibs.Length()) {
3363 out << "// Add aditional AliRoot libraries" << endl;
3364 TObjArray *list = fAdditionalLibs.Tokenize(" ");
3365 TIter next(list);
3366 TObjString *str;
3367 while((str=(TObjString*)next())) {
3368 if (str->GetString().Contains(".so"))
3369 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
3370 }
3371 if (list) delete list;
3372 }
3373 out << endl;
3374 out << "// Analysis source to be compiled at runtime (if any)" << endl;
3375 if (fAnalysisSource.Length()) {
3376 TObjArray *list = fAnalysisSource.Tokenize(" ");
3377 TIter next(list);
3378 TObjString *str;
3379 while((str=(TObjString*)next())) {
3380 out << " gROOT->ProcessLine(\".L " << str->GetString().Data() << "+g\");" << endl;
3381 }
3382 if (list) delete list;
3383 }
149d288c 3384 out << endl;
3385
0f389141 3386 if (fFastReadOption) {
3387 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 !!!");
3388 out << "// fast xrootd reading enabled" << endl;
3389 out << " printf(\"!!! You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !!!\");" << endl;
d3339be3 3390 out << " gEnv->SetValue(\"XNet.ConnectTimeout\",10);" << endl;
f790bc1b 3391 out << " gEnv->SetValue(\"XNet.RequestTimeout\",10);" << endl;
0f389141 3392 out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
f790bc1b 3393 out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",10);" << endl;
0f389141 3394 out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
e8b839ab 3395 }
3396 // Change temp directory to current one
3397 out << "// Set temporary merging directory to current one" << endl;
3398 out << " gSystem->Setenv(\"TMPDIR\", gSystem->pwd());" << endl << endl;
0f389141 3399 out << "// Connect to AliEn" << endl;
3400 out << " if (!TGrid::Connect(\"alien://\")) return;" << endl;
0cdf65a8 3401 out << " Bool_t laststage = kFALSE;" << endl;
7c2cd90a 3402 out << " TString outputDir = dir;" << endl;
f790bc1b 3403 out << " TString outputFiles = \"" << GetListOfFiles("out") << "\";" << endl;
0f389141 3404 out << " TString mergeExcludes = \"" << fMergeExcludes << "\";" << endl;
58268c13 3405 out << " TObjArray *list = outputFiles.Tokenize(\",\");" << endl;
0f389141 3406 out << " TIter *iter = new TIter(list);" << endl;
3407 out << " TObjString *str;" << endl;
a2f5fc01 3408 out << " TString outputFile;" << endl;
0f389141 3409 out << " Bool_t merged = kTRUE;" << endl;
3410 out << " while((str=(TObjString*)iter->Next())) {" << endl;
a2f5fc01 3411 out << " outputFile = str->GetString();" << endl;
7c2cd90a 3412 out << " if (outputFile.Contains(\"*\")) continue;" << endl;
a2f5fc01 3413 out << " Int_t index = outputFile.Index(\"@\");" << endl;
3414 out << " if (index > 0) outputFile.Remove(index);" << endl;
0f389141 3415 out << " // Skip already merged outputs" << endl;
a2f5fc01 3416 out << " if (!gSystem->AccessPathName(outputFile)) {" << endl;
3417 out << " printf(\"Output file <%s> found. Not merging again.\",outputFile.Data());" << endl;
0f389141 3418 out << " continue;" << endl;
3419 out << " }" << endl;
a2f5fc01 3420 out << " if (mergeExcludes.Contains(outputFile.Data())) continue;" << endl;
7c2cd90a 3421 out << " merged = AliAnalysisAlien::MergeOutput(outputFile, outputDir, " << fMaxMergeFiles << ", stage, ichunk);" << endl;
0f389141 3422 out << " if (!merged) {" << endl;
a2f5fc01 3423 out << " printf(\"ERROR: Cannot merge %s\\n\", outputFile.Data());" << endl;
7c2cd90a 3424 out << " return;" << endl;
0f389141 3425 out << " }" << endl;
7c2cd90a 3426 out << " // Check if this was the last stage. If yes, run terminate for the tasks." << endl;
3427 out << " if (!gSystem->AccessPathName(outputFile)) laststage = kTRUE;" << endl;
0f389141 3428 out << " }" << endl;
7c2cd90a 3429 out << " // all outputs merged, validate" << endl;
3430 out << " ofstream out;" << endl;
3431 out << " out.open(\"outputs_valid\", ios::out);" << endl;
3432 out << " out.close();" << endl;
3433 out << " // read the analysis manager from file" << endl;
f866cba5 3434 TString analysisFile = fExecutable;
3435 analysisFile.ReplaceAll(".sh", ".root");
7c2cd90a 3436 out << " if (!laststage) return;" << endl;
f866cba5 3437 out << " TFile *file = TFile::Open(\"" << analysisFile << "\");" << endl;
7c2cd90a 3438 out << " if (!file) return;" << endl;
f866cba5 3439 out << " TIter nextkey(file->GetListOfKeys());" << endl;
3440 out << " AliAnalysisManager *mgr = 0;" << endl;
3441 out << " TKey *key;" << endl;
3442 out << " while ((key=(TKey*)nextkey())) {" << endl;
3443 out << " if (!strcmp(key->GetClassName(), \"AliAnalysisManager\"))" << endl;
3444 out << " mgr = (AliAnalysisManager*)file->Get(key->GetName());" << endl;
3445 out << " };" << endl;
3446 out << " if (!mgr) {" << endl;
3447 out << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file" << analysisFile <<"\");" << endl;
3448 out << " return;" << endl;
3449 out << " }" << endl << endl;
5c4250fc 3450 out << " mgr->SetRunFromPath(mgr->GetRunFromAlienPath(dir));" << endl;
b385fec0 3451 out << " mgr->SetSkipTerminate(kFALSE);" << endl;
f866cba5 3452 out << " mgr->PrintStatus();" << endl;
3453 if (AliAnalysisManager::GetAnalysisManager()) {
3454 if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) {
3455 out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
3456 } else {
9a8288ff 3457 if (TestBit(AliAnalysisGrid::kTest))
3458 out << " AliLog::SetGlobalLogLevel(AliLog::kWarning);" << endl;
3459 else
3460 out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
f866cba5 3461 }
3462 }
9a8288ff 3463 out << " TTree *tree = NULL;" << endl;
3464 out << " mgr->StartAnalysis(\"gridterminate\", tree);" << endl;
0f389141 3465 out << "}" << endl << endl;
5b273635 3466 if (hasANALYSISalice) {
3467 out <<"//________________________________________________________________________________" << endl;
3468 out << "Bool_t SetupPar(const char *package) {" << endl;
3469 out << "// Compile the package and set it up." << endl;
3470 out << " TString pkgdir = package;" << endl;
3471 out << " pkgdir.ReplaceAll(\".par\",\"\");" << endl;
b50a41c3 3472 out << " gSystem->Exec(TString::Format(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
5b273635 3473 out << " TString cdir = gSystem->WorkingDirectory();" << endl;
3474 out << " gSystem->ChangeDirectory(pkgdir);" << endl;
3475 out << " // Check for BUILD.sh and execute" << endl;
3476 out << " if (!gSystem->AccessPathName(\"PROOF-INF/BUILD.sh\")) {" << endl;
3477 out << " printf(\"*******************************\\n\");" << endl;
3478 out << " printf(\"*** Building PAR archive ***\\n\");" << endl;
3479 out << " printf(\"*******************************\\n\");" << endl;
3480 out << " if (gSystem->Exec(\"PROOF-INF/BUILD.sh\")) {" << endl;
3481 out << " ::Error(\"SetupPar\", \"Cannot build par archive %s\", pkgdir.Data());" << endl;
3482 out << " gSystem->ChangeDirectory(cdir);" << endl;
3483 out << " return kFALSE;" << endl;
3484 out << " }" << endl;
3485 out << " } else {" << endl;
3486 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/BUILD.sh for package %s\", pkgdir.Data());" << endl;
3487 out << " gSystem->ChangeDirectory(cdir);" << endl;
3488 out << " return kFALSE;" << endl;
3489 out << " }" << endl;
3490 out << " // Check for SETUP.C and execute" << endl;
3491 out << " if (!gSystem->AccessPathName(\"PROOF-INF/SETUP.C\")) {" << endl;
3492 out << " printf(\"*******************************\\n\");" << endl;
3493 out << " printf(\"*** Setup PAR archive ***\\n\");" << endl;
3494 out << " printf(\"*******************************\\n\");" << endl;
3495 out << " gROOT->Macro(\"PROOF-INF/SETUP.C\");" << endl;
3496 out << " } else {" << endl;
3497 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/SETUP.C for package %s\", pkgdir.Data());" << endl;
3498 out << " gSystem->ChangeDirectory(cdir);" << endl;
3499 out << " return kFALSE;" << endl;
3500 out << " }" << endl;
3501 out << " // Restore original workdir" << endl;
3502 out << " gSystem->ChangeDirectory(cdir);" << endl;
3503 out << " return kTRUE;" << endl;
3504 out << "}" << endl;
3505 }
0f389141 3506 }
3507 Bool_t copy = kTRUE;
d3b18c4c 3508 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
0f389141 3509 if (copy) {
3510 CdWork();
3511 TString workdir = gGrid->GetHomeDirectory();
3512 workdir += fGridWorkingDir;
3513 if (FileExists(mergingMacro)) gGrid->Rm(mergingMacro);
3514 Info("WriteMergingMacro", "\n##### Copying merging macro: <%s> to your alien workspace", mergingMacro.Data());
3515 TFile::Cp(Form("file:%s",mergingMacro.Data()), Form("alien://%s/%s", workdir.Data(), mergingMacro.Data()));
3516 }
3517}
3518
3519//______________________________________________________________________________
3520Bool_t AliAnalysisAlien::SetupPar(const char *package)
3521{
205b201f 3522// Compile the par file archive pointed by <package>. This must be present in the current directory.
0f389141 3523// Note that for loading the compiled library. The current directory should have precedence in
3524// LD_LIBRARY_PATH
3525 TString pkgdir = package;
3526 pkgdir.ReplaceAll(".par","");
b50a41c3 3527 gSystem->Exec(TString::Format("tar xzf %s.par", pkgdir.Data()));
0f389141 3528 TString cdir = gSystem->WorkingDirectory();
3529 gSystem->ChangeDirectory(pkgdir);
3530 // Check for BUILD.sh and execute
3531 if (!gSystem->AccessPathName("PROOF-INF/BUILD.sh")) {
3532 printf("**************************************************\n");
3533 printf("*** Building PAR archive %s\n", package);
3534 printf("**************************************************\n");
3535 if (gSystem->Exec("PROOF-INF/BUILD.sh")) {
3536 ::Error("SetupPar", "Cannot build par archive %s", pkgdir.Data());
3537 gSystem->ChangeDirectory(cdir);
3538 return kFALSE;
3539 }
3540 } else {
3541 ::Error("SetupPar","Cannot access PROOF-INF/BUILD.sh for package %s", pkgdir.Data());
3542 gSystem->ChangeDirectory(cdir);
3543 return kFALSE;
3544 }
3545 // Check for SETUP.C and execute
3546 if (!gSystem->AccessPathName("PROOF-INF/SETUP.C")) {
3547 printf("**************************************************\n");
3548 printf("*** Setup PAR archive %s\n", package);
3549 printf("**************************************************\n");
3550 gROOT->Macro("PROOF-INF/SETUP.C");
3551 printf("*** Loaded library: %s\n", gSystem->GetLibraries(pkgdir,"",kFALSE));
3552 } else {
3553 ::Error("SetupPar","Cannot access PROOF-INF/SETUP.C for package %s", pkgdir.Data());
3554 gSystem->ChangeDirectory(cdir);
3555 return kFALSE;
3556 }
3557 // Restore original workdir
3558 gSystem->ChangeDirectory(cdir);
3559 return kTRUE;
3560}
3561
c57f56b7 3562//______________________________________________________________________________
3563void AliAnalysisAlien::WriteExecutable()
3564{
3565// Generate the alien executable script.
3566 if (!TestBit(AliAnalysisGrid::kSubmit)) {
3567 ofstream out;
3568 out.open(fExecutable.Data(), ios::out);
3569 if (out.bad()) {
5513444a 3570 Error("WriteExecutable", "Bad file name for executable: %s", fExecutable.Data());
c57f56b7 3571 return;
3572 }
3573 out << "#!/bin/bash" << endl;
c57f56b7 3574 out << "echo \"=========================================\"" << endl;
3575 out << "echo \"############## PATH : ##############\"" << endl;
3576 out << "echo $PATH" << endl;
3577 out << "echo \"############## LD_LIBRARY_PATH : ##############\"" << endl;
3578 out << "echo $LD_LIBRARY_PATH" << endl;
3579 out << "echo \"############## ROOTSYS : ##############\"" << endl;
3580 out << "echo $ROOTSYS" << endl;
3581 out << "echo \"############## which root : ##############\"" << endl;
3582 out << "which root" << endl;
3583 out << "echo \"############## ALICE_ROOT : ##############\"" << endl;
3584 out << "echo $ALICE_ROOT" << endl;
3585 out << "echo \"############## which aliroot : ##############\"" << endl;
3586 out << "which aliroot" << endl;
9c5ddadc 3587 out << "echo \"############## system limits : ##############\"" << endl;
3588 out << "ulimit -a" << endl;
3589 out << "echo \"############## memory : ##############\"" << endl;
3590 out << "free -m" << endl;
c57f56b7 3591 out << "echo \"=========================================\"" << endl << endl;
74a53467 3592 // Make sure we can properly compile par files
3593 if (TObject::TestBit(AliAnalysisGrid::kUsePars)) out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
0a1c1f7f 3594 out << fExecutableCommand << " ";
631c0b05 3595 out << fAnalysisMacro.Data() << " " << fExecutableArgs.Data() << endl << endl;
9c5ddadc 3596 out << "echo \"======== " << fAnalysisMacro.Data() << " finished with exit code: $? ========\"" << endl;
3597 out << "echo \"############## memory after: ##############\"" << endl;
3598 out << "free -m" << endl;
c57f56b7 3599 }
3600 Bool_t copy = kTRUE;
d3b18c4c 3601 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
c57f56b7 3602 if (copy) {
3603 CdWork();
3604 TString workdir = gGrid->GetHomeDirectory();
923e2ca5 3605 TString bindir = Form("%s/bin", workdir.Data());
b93f8109 3606 if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir,"-p");
c57f56b7 3607 workdir += fGridWorkingDir;
3608 TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), fExecutable.Data());
3609 if (FileExists(executable)) gGrid->Rm(executable);
d3b18c4c 3610 Info("WriteExecutable", "\n##### Copying executable file <%s> to your AliEn bin directory", fExecutable.Data());
c57f56b7 3611 TFile::Cp(Form("file:%s",fExecutable.Data()), Form("alien://%s", executable.Data()));
3612 }
3613}
3614
0f389141 3615//______________________________________________________________________________
3616void AliAnalysisAlien::WriteMergeExecutable()
3617{
3618// Generate the alien executable script for the merging job.
3619 if (!fMergeViaJDL) return;
3620 TString mergeExec = fExecutable;
3621 mergeExec.ReplaceAll(".sh", "_merge.sh");
3622 if (!TestBit(AliAnalysisGrid::kSubmit)) {
3623 ofstream out;
3624 out.open(mergeExec.Data(), ios::out);
3625 if (out.bad()) {
3626 Error("WriteMergingExecutable", "Bad file name for executable: %s", mergeExec.Data());
3627 return;
3628 }
3629 out << "#!/bin/bash" << endl;
3630 out << "echo \"=========================================\"" << endl;
3631 out << "echo \"############## PATH : ##############\"" << endl;
3632 out << "echo $PATH" << endl;
3633 out << "echo \"############## LD_LIBRARY_PATH : ##############\"" << endl;
3634 out << "echo $LD_LIBRARY_PATH" << endl;
3635 out << "echo \"############## ROOTSYS : ##############\"" << endl;
3636 out << "echo $ROOTSYS" << endl;
3637 out << "echo \"############## which root : ##############\"" << endl;
3638 out << "which root" << endl;
3639 out << "echo \"############## ALICE_ROOT : ##############\"" << endl;
3640 out << "echo $ALICE_ROOT" << endl;
3641 out << "echo \"############## which aliroot : ##############\"" << endl;
3642 out << "which aliroot" << endl;
3643 out << "echo \"############## system limits : ##############\"" << endl;
3644 out << "ulimit -a" << endl;
3645 out << "echo \"############## memory : ##############\"" << endl;
3646 out << "free -m" << endl;
3647 out << "echo \"=========================================\"" << endl << endl;
3648 // Make sure we can properly compile par files
3649 if (TObject::TestBit(AliAnalysisGrid::kUsePars)) out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
3650 TString mergeMacro = fExecutable;
3651 mergeMacro.ReplaceAll(".sh", "_merge.C");
f790bc1b 3652 if (IsOneStageMerging())
3653 out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\")\"" << endl;
3654 else
3655 out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\",$2,$3)\"" << endl;
0f389141 3656 out << fExecutableCommand << " " << "$ARG" << endl;
3657 out << "echo \"======== " << mergeMacro.Data() << " finished with exit code: $? ========\"" << endl;
3658 out << "echo \"############## memory after: ##############\"" << endl;
3659 out << "free -m" << endl;
0f389141 3660 }
3661 Bool_t copy = kTRUE;
d3b18c4c 3662 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
0f389141 3663 if (copy) {
3664 CdWork();
3665 TString workdir = gGrid->GetHomeDirectory();
3666 TString bindir = Form("%s/bin", workdir.Data());
b93f8109 3667 if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir,"-p");
0f389141 3668 workdir += fGridWorkingDir;
3669 TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), mergeExec.Data());
3670 if (FileExists(executable)) gGrid->Rm(executable);
d3b18c4c 3671 Info("WriteMergeExecutable", "\n##### Copying executable file <%s> to your AliEn bin directory", mergeExec.Data());
0f389141 3672 TFile::Cp(Form("file:%s",mergeExec.Data()), Form("alien://%s", executable.Data()));
3673 }
3674}
3675
c57f56b7 3676//______________________________________________________________________________
5513444a 3677void AliAnalysisAlien::WriteProductionFile(const char *filename) const
3678{
3679// Write the production file to be submitted by LPM manager. The format is:
f5e8c702 3680// First line: full_path_to_jdl estimated_no_subjobs_per_master
5513444a 3681// Next lines: full_path_to_dataset XXX (XXX is a string)
3682// To submit, one has to: submit jdl XXX for all lines
3683 ofstream out;
3684 out.open(filename, ios::out);
3685 if (out.bad()) {
3686 Error("WriteProductionFile", "Bad file name: %s", filename);
3687 return;
3688 }
d3b18c4c 3689 TString workdir;
3690 if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice"))
3691 workdir = gGrid->GetHomeDirectory();
5513444a 3692 workdir += fGridWorkingDir;
f5e8c702 3693 Int_t njobspermaster = 1000*fNrunsPerMaster/fSplitMaxInputFileNumber;
5513444a 3694 TString locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
f5e8c702 3695 out << locjdl << " " << njobspermaster << endl;
5513444a 3696 Int_t nmasterjobs = fInputFiles->GetEntries();
3697 for (Int_t i=0; i<nmasterjobs; i++) {
409b4ada 3698 TString runOutDir = gSystem->BaseName(fInputFiles->At(i)->GetName());
3699 runOutDir.ReplaceAll(".xml", "");
3700 if (fOutputToRunNo)
3701 out << Form("%s", fInputFiles->At(i)->GetName()) << " " << runOutDir << endl;
3702 else
3703 out << Form("%s", fInputFiles->At(i)->GetName()) << " " << Form("%03d", i) << endl;
5513444a 3704 }
d3b18c4c 3705 if (gGrid) {
3706 Info("WriteProductionFile", "\n##### Copying production file <%s> to your work directory", filename);
3707 if (FileExists(filename)) gGrid->Rm(filename);
3708 TFile::Cp(Form("file:%s",filename), Form("alien://%s/%s", workdir.Data(),filename));
3709 }
5513444a 3710}
3711
3712//______________________________________________________________________________
0f389141 3713void AliAnalysisAlien::WriteValidationScript(Bool_t merge)
c57f56b7 3714{
3715// Generate the alien validation script.
3716 // Generate the validation script
3717 TObjString *os;
d3b18c4c 3718 if (fValidationScript.IsNull()) {
3719 fValidationScript = fExecutable;
3720 fValidationScript.ReplaceAll(".sh", "_validation.sh");
3721 }
3722 TString validationScript = fValidationScript;
3723 if (merge) validationScript.ReplaceAll(".sh", "_merge.sh");
c57f56b7 3724 if (!Connect()) {
3725 Error("WriteValidationScript", "Alien connection required");
3726 return;
3727 }
d3b18c4c 3728 if (!fTerminateFiles.IsNull()) {
3729 fTerminateFiles.Strip();
3730 fTerminateFiles.ReplaceAll(" ",",");
3731 }
a2f5fc01 3732 TString outStream = "";
3733 if (!TestBit(AliAnalysisGrid::kTest)) outStream = " >> stdout";
c57f56b7 3734 if (!TestBit(AliAnalysisGrid::kSubmit)) {
3735 ofstream out;
0d5d317c 3736 out.open(validationScript, ios::out);
c57f56b7 3737 out << "#!/bin/bash" << endl;
3738 out << "##################################################" << endl;
3739 out << "validateout=`dirname $0`" << endl;
3740 out << "validatetime=`date`" << endl;
3741 out << "validated=\"0\";" << endl;
3742 out << "error=0" << endl;
3743 out << "if [ -z $validateout ]" << endl;
3744 out << "then" << endl;
3745 out << " validateout=\".\"" << endl;
3746 out << "fi" << endl << endl;
3747 out << "cd $validateout;" << endl;
3748 out << "validateworkdir=`pwd`;" << endl << endl;
a2f5fc01 3749 out << "echo \"*******************************************************\"" << outStream << endl;
3750 out << "echo \"* Automatically generated validation script *\"" << outStream << endl;
c57f56b7 3751 out << "" << endl;
a2f5fc01 3752 out << "echo \"* Time: $validatetime \"" << outStream << endl;
3753 out << "echo \"* Dir: $validateout\"" << outStream << endl;
3754 out << "echo \"* Workdir: $validateworkdir\"" << outStream << endl;
3755 out << "echo \"* ----------------------------------------------------*\"" << outStream << endl;
3756 out << "ls -la ./" << outStream << endl;
3757 out << "echo \"* ----------------------------------------------------*\"" << outStream << endl << endl;
c57f56b7 3758 out << "##################################################" << endl;
ebec370a 3759 out << "" << endl;
3760
3761 out << "if [ ! -f stderr ] ; then" << endl;
3762 out << " error=1" << endl;
a2f5fc01 3763 out << " echo \"* ########## Job not validated - no stderr ###\" " << outStream << endl;
3764 out << " echo \"Error = $error\" " << outStream << endl;
ebec370a 3765 out << "fi" << endl;
3766
b34c9f51 3767 out << "parArch=`grep -Ei \"Cannot Build the PAR Archive\" stderr`" << endl;
3768 out << "segViol=`grep -Ei \"Segmentation violation\" stderr`" << endl;
3769 out << "segFault=`grep -Ei \"Segmentation fault\" stderr`" << endl;
3770 out << "glibcErr=`grep -Ei \"*** glibc detected ***\" stderr`" << endl;
3771 out << "" << endl;
3772
ebec370a 3773 out << "if [ \"$parArch\" != \"\" ] ; then" << endl;
3774 out << " error=1" << endl;
a2f5fc01 3775 out << " echo \"* ########## Job not validated - PAR archive not built ###\" " << outStream << endl;
3776 out << " echo \"$parArch\" " << outStream << endl;
3777 out << " echo \"Error = $error\" " << outStream << endl;
ebec370a 3778 out << "fi" << endl;
3779
3780 out << "if [ \"$segViol\" != \"\" ] ; then" << endl;
3781 out << " error=1" << endl;
a2f5fc01 3782 out << " echo \"* ########## Job not validated - Segment. violation ###\" " << outStream << endl;
3783 out << " echo \"$segViol\" " << outStream << endl;
3784 out << " echo \"Error = $error\" " << outStream << endl;
ebec370a 3785 out << "fi" << endl;
3786
3787 out << "if [ \"$segFault\" != \"\" ] ; then" << endl;
3788 out << " error=1" << endl;
a2f5fc01 3789 out << " echo \"* ########## Job not validated - Segment. fault ###\" " << outStream << endl;
3790 out << " echo \"$segFault\" " << outStream << endl;
3791 out << " echo \"Error = $error\" " << outStream << endl;
ebec370a 3792 out << "fi" << endl;
3793
b34c9f51 3794 out << "if [ \"$glibcErr\" != \"\" ] ; then" << endl;
3795 out << " error=1" << endl;
a2f5fc01 3796 out << " echo \"* ########## Job not validated - *** glibc detected *** ###\" " << outStream << endl;
3797 out << " echo \"$glibcErr\" " << outStream << endl;
3798 out << " echo \"Error = $error\" " << outStream << endl;
b34c9f51 3799 out << "fi" << endl;
3800
ebec370a 3801 // Part dedicated to the specific analyses running into the train
3802
d3b18c4c 3803 TString outputFiles = fOutputFiles;
3804 if (merge && !fTerminateFiles.IsNull()) {
3805 outputFiles += ",";
3806 outputFiles += fTerminateFiles;
3807 }
3808 TObjArray *arr = outputFiles.Tokenize(",");
c57f56b7 3809 TIter next1(arr);
a2f5fc01 3810 TString outputFile;
bbd88db8 3811 while (!merge && (os=(TObjString*)next1())) {
3812 // No need to validate outputs produced by merging since the merging macro does this
a2f5fc01 3813 outputFile = os->GetString();
3814 Int_t index = outputFile.Index("@");
3815 if (index > 0) outputFile.Remove(index);
bbd88db8 3816 if (fTerminateFiles.Contains(outputFile)) continue;
a2f5fc01 3817 if (outputFile.Contains("*")) continue;
3818 out << "if ! [ -f " << outputFile.Data() << " ] ; then" << endl;
c57f56b7 3819 out << " error=1" << endl;
7c2cd90a 3820 out << " echo \"Output file " << outputFile << " not found. Job FAILED !\"" << outStream << endl;
3821 out << " echo \"Output file " << outputFile << " not found. Job FAILED !\" >> stderr" << endl;
c57f56b7 3822 out << "fi" << endl;
3823 }
3824 delete arr;
7c2cd90a 3825 out << "if ! [ -f outputs_valid ] ; then" << endl;
3826 out << " error=1" << endl;
3827 out << " echo \"Output files were not validated by the analysis manager\" >> stdout" << endl;
3828 out << " echo \"Output files were not validated by the analysis manager\" >> stderr" << endl;
3829 out << "fi" << endl;
923e2ca5 3830
c57f56b7 3831 out << "if [ $error = 0 ] ; then" << endl;
a2f5fc01 3832 out << " echo \"* ---------------- Job Validated ------------------*\"" << outStream << endl;
149d288c 3833 if (!IsKeepLogs()) {
3834 out << " echo \"* === Logs std* will be deleted === \"" << endl;
a2f5fc01 3835 outStream = "";
149d288c 3836 out << " rm -f std*" << endl;
3837 }
c57f56b7 3838 out << "fi" << endl;
3839
a2f5fc01 3840 out << "echo \"* ----------------------------------------------------*\"" << outStream << endl;
3841 out << "echo \"*******************************************************\"" << outStream << endl;
c57f56b7 3842 out << "cd -" << endl;
3843 out << "exit $error" << endl;
3844 }
3845 Bool_t copy = kTRUE;
d3b18c4c 3846 if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
c57f56b7 3847 if (copy) {
3848 CdWork();
3849 TString workdir = gGrid->GetHomeDirectory();
3850 workdir += fGridWorkingDir;
d3b18c4c 3851 Info("WriteValidationScript", "\n##### Copying validation script <%s> to your AliEn working space", validationScript.Data());
0d5d317c 3852 if (FileExists(validationScript)) gGrid->Rm(validationScript);
3853 TFile::Cp(Form("file:%s",validationScript.Data()), Form("alien://%s/%s", workdir.Data(),validationScript.Data()));
c57f56b7 3854 }
3855}