fix calculation versus multiplicity
[u/mrichter/AliRoot.git] / ANALYSIS / AliAnalysisAlien.cxx
CommitLineData
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"
30#include "TObjString.h"
31#include "TObjArray.h"
32#include "TGrid.h"
33#include "TGridResult.h"
34#include "TGridCollection.h"
35#include "TGridJDL.h"
d2a409b2 36#include "TGridJobStatusList.h"
37#include "TGridJobStatus.h"
c57f56b7 38#include "TFileMerger.h"
39#include "AliAnalysisManager.h"
bb885a9e 40#include "AliVEventHandler.h"
41#include "AliAnalysisDataContainer.h"
c57f56b7 42#include "AliAnalysisAlien.h"
43
44ClassImp(AliAnalysisAlien)
45
46//______________________________________________________________________________
47AliAnalysisAlien::AliAnalysisAlien()
48 :AliAnalysisGrid(),
49 fGridJDL(NULL),
0f389141 50 fMergingJDL(NULL),
c57f56b7 51 fPrice(0),
52 fTTL(0),
53 fSplitMaxInputFileNumber(0),
54 fMaxInitFailed(0),
55 fMasterResubmitThreshold(0),
bb885a9e 56 fNtestFiles(0),
319593fb 57 fNrunsPerMaster(0),
16a4353c 58 fMaxMergeFiles(0),
d2a409b2 59 fNsubmitted(0),
a3e84053 60 fProductionMode(0),
cd11251e 61 fOutputToRunNo(0),
0f389141 62 fMergeViaJDL(0),
63 fFastReadOption(0),
e1c22e21 64 fOverwriteMode(1),
149d288c 65 fNreplicas(2),
c57f56b7 66 fRunNumbers(),
67 fExecutable(),
0a1c1f7f 68 fExecutableCommand(),
c57f56b7 69 fArguments(),
631c0b05 70 fExecutableArgs(),
c57f56b7 71 fAnalysisMacro(),
72 fAnalysisSource(),
d5c6455a 73 fAdditionalRootLibs(),
c57f56b7 74 fAdditionalLibs(),
75 fSplitMode(),
76 fAPIVersion(),
77 fROOTVersion(),
78 fAliROOTVersion(),
648174cf 79 fExternalPackages(),
c57f56b7 80 fUser(),
81 fGridWorkingDir(),
82 fGridDataDir(),
83 fDataPattern(),
84 fGridOutputDir(),
85 fOutputArchive(),
86 fOutputFiles(),
87 fInputFormat(),
e7c71df0 88 fDatasetName(),
c57f56b7 89 fJDLName(),
bb885a9e 90 fMergeExcludes(),
f965131e 91 fIncludePath(),
bb885a9e 92 fCloseSE(),
0df6ccf2 93 fFriendChainName(),
c6cb3634 94 fJobTag(),
648174cf 95 fOutputSingle(),
5fce53f4 96 fRunPrefix(),
4e5c5506 97 fInputFiles(0),
98 fPackages(0)
c57f56b7 99{
100// Dummy ctor.
101 SetDefaults();
102}
103
104//______________________________________________________________________________
105AliAnalysisAlien::AliAnalysisAlien(const char *name)
106 :AliAnalysisGrid(name),
107 fGridJDL(NULL),
0f389141 108 fMergingJDL(NULL),
c57f56b7 109 fPrice(0),
110 fTTL(0),
111 fSplitMaxInputFileNumber(0),
112 fMaxInitFailed(0),
113 fMasterResubmitThreshold(0),
bb885a9e 114 fNtestFiles(0),
319593fb 115 fNrunsPerMaster(0),
16a4353c 116 fMaxMergeFiles(0),
d2a409b2 117 fNsubmitted(0),
a3e84053 118 fProductionMode(0),
cd11251e 119 fOutputToRunNo(0),
0f389141 120 fMergeViaJDL(0),
121 fFastReadOption(0),
e1c22e21 122 fOverwriteMode(1),
149d288c 123 fNreplicas(2),
c57f56b7 124 fRunNumbers(),
125 fExecutable(),
0a1c1f7f 126 fExecutableCommand(),
c57f56b7 127 fArguments(),
631c0b05 128 fExecutableArgs(),
c57f56b7 129 fAnalysisMacro(),
130 fAnalysisSource(),
d5c6455a 131 fAdditionalRootLibs(),
c57f56b7 132 fAdditionalLibs(),
133 fSplitMode(),
134 fAPIVersion(),
135 fROOTVersion(),
136 fAliROOTVersion(),
648174cf 137 fExternalPackages(),
c57f56b7 138 fUser(),
139 fGridWorkingDir(),
140 fGridDataDir(),
141 fDataPattern(),
142 fGridOutputDir(),
143 fOutputArchive(),
144 fOutputFiles(),
145 fInputFormat(),
e7c71df0 146 fDatasetName(),
c57f56b7 147 fJDLName(),
bb885a9e 148 fMergeExcludes(),
f965131e 149 fIncludePath(),
bb885a9e 150 fCloseSE(),
0df6ccf2 151 fFriendChainName(),
c6cb3634 152 fJobTag(),
648174cf 153 fOutputSingle(),
5fce53f4 154 fRunPrefix(),
4e5c5506 155 fInputFiles(0),
156 fPackages(0)
c57f56b7 157{
158// Default ctor.
159 SetDefaults();
160}
161
162//______________________________________________________________________________
163AliAnalysisAlien::AliAnalysisAlien(const AliAnalysisAlien& other)
164 :AliAnalysisGrid(other),
165 fGridJDL(NULL),
0f389141 166 fMergingJDL(NULL),
c57f56b7 167 fPrice(other.fPrice),
168 fTTL(other.fTTL),
169 fSplitMaxInputFileNumber(other.fSplitMaxInputFileNumber),
170 fMaxInitFailed(other.fMaxInitFailed),
171 fMasterResubmitThreshold(other.fMasterResubmitThreshold),
bb885a9e 172 fNtestFiles(other.fNtestFiles),
319593fb 173 fNrunsPerMaster(other.fNrunsPerMaster),
16a4353c 174 fMaxMergeFiles(other.fMaxMergeFiles),
d2a409b2 175 fNsubmitted(other.fNsubmitted),
a3e84053 176 fProductionMode(other.fProductionMode),
cd11251e 177 fOutputToRunNo(other.fOutputToRunNo),
0f389141 178 fMergeViaJDL(other.fMergeViaJDL),
179 fFastReadOption(other.fFastReadOption),
180 fOverwriteMode(other.fOverwriteMode),
149d288c 181 fNreplicas(other.fNreplicas),
c57f56b7 182 fRunNumbers(other.fRunNumbers),
183 fExecutable(other.fExecutable),
0a1c1f7f 184 fExecutableCommand(other.fExecutableCommand),
c57f56b7 185 fArguments(other.fArguments),
631c0b05 186 fExecutableArgs(other.fExecutableArgs),
c57f56b7 187 fAnalysisMacro(other.fAnalysisMacro),
188 fAnalysisSource(other.fAnalysisSource),
d5c6455a 189 fAdditionalRootLibs(other.fAdditionalRootLibs),
c57f56b7 190 fAdditionalLibs(other.fAdditionalLibs),
191 fSplitMode(other.fSplitMode),
192 fAPIVersion(other.fAPIVersion),
193 fROOTVersion(other.fROOTVersion),
194 fAliROOTVersion(other.fAliROOTVersion),
648174cf 195 fExternalPackages(other.fExternalPackages),
c57f56b7 196 fUser(other.fUser),
197 fGridWorkingDir(other.fGridWorkingDir),
198 fGridDataDir(other.fGridDataDir),
199 fDataPattern(other.fDataPattern),
200 fGridOutputDir(other.fGridOutputDir),
201 fOutputArchive(other.fOutputArchive),
202 fOutputFiles(other.fOutputFiles),
203 fInputFormat(other.fInputFormat),
e7c71df0 204 fDatasetName(other.fDatasetName),
c57f56b7 205 fJDLName(other.fJDLName),
bb885a9e 206 fMergeExcludes(other.fMergeExcludes),
f965131e 207 fIncludePath(other.fIncludePath),
bb885a9e 208 fCloseSE(other.fCloseSE),
0df6ccf2 209 fFriendChainName(other.fFriendChainName),
c6cb3634 210 fJobTag(other.fJobTag),
648174cf 211 fOutputSingle(other.fOutputSingle),
5fce53f4 212 fRunPrefix(other.fRunPrefix),
4e5c5506 213 fInputFiles(0),
214 fPackages(0)
c57f56b7 215{
216// Copy ctor.
217 fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
0f389141 218 fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
a8739e8a 219 fRunRange[0] = other.fRunRange[0];
220 fRunRange[1] = other.fRunRange[1];
c57f56b7 221 if (other.fInputFiles) {
222 fInputFiles = new TObjArray();
223 TIter next(other.fInputFiles);
224 TObject *obj;
225 while ((obj=next())) fInputFiles->Add(new TObjString(obj->GetName()));
226 fInputFiles->SetOwner();
227 }
4e5c5506 228 if (other.fPackages) {
229 fPackages = new TObjArray();
230 TIter next(other.fPackages);
231 TObject *obj;
232 while ((obj=next())) fPackages->Add(new TObjString(obj->GetName()));
233 fPackages->SetOwner();
234 }
c57f56b7 235}
236
237//______________________________________________________________________________
238AliAnalysisAlien::~AliAnalysisAlien()
239{
240// Destructor.
241 if (fGridJDL) delete fGridJDL;
0f389141 242 if (fMergingJDL) delete fMergingJDL;
c57f56b7 243 if (fInputFiles) delete fInputFiles;
4e5c5506 244 if (fPackages) delete fPackages;
c57f56b7 245}
246
247//______________________________________________________________________________
248AliAnalysisAlien &AliAnalysisAlien::operator=(const AliAnalysisAlien& other)
249{
250// Assignment.
251 if (this != &other) {
252 AliAnalysisGrid::operator=(other);
253 fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
0f389141 254 fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
c57f56b7 255 fPrice = other.fPrice;
256 fTTL = other.fTTL;
257 fSplitMaxInputFileNumber = other.fSplitMaxInputFileNumber;
258 fMaxInitFailed = other.fMaxInitFailed;
259 fMasterResubmitThreshold = other.fMasterResubmitThreshold;
bb885a9e 260 fNtestFiles = other.fNtestFiles;
a3e84053 261 fNrunsPerMaster = other.fNrunsPerMaster;
262 fMaxMergeFiles = other.fMaxMergeFiles;
263 fNsubmitted = other.fNsubmitted;
264 fProductionMode = other.fProductionMode;
cd11251e 265 fOutputToRunNo = other.fOutputToRunNo;
0f389141 266 fMergeViaJDL = other.fMergeViaJDL;
267 fFastReadOption = other.fFastReadOption;
268 fOverwriteMode = other.fOverwriteMode;
149d288c 269 fNreplicas = other.fNreplicas;
c57f56b7 270 fRunNumbers = other.fRunNumbers;
271 fExecutable = other.fExecutable;
0a1c1f7f 272 fExecutableCommand = other.fExecutableCommand;
c57f56b7 273 fArguments = other.fArguments;
631c0b05 274 fExecutableArgs = other.fExecutableArgs;
c57f56b7 275 fAnalysisMacro = other.fAnalysisMacro;
276 fAnalysisSource = other.fAnalysisSource;
d5c6455a 277 fAdditionalRootLibs = other.fAdditionalRootLibs;
c57f56b7 278 fAdditionalLibs = other.fAdditionalLibs;
279 fSplitMode = other.fSplitMode;
280 fAPIVersion = other.fAPIVersion;
281 fROOTVersion = other.fROOTVersion;
282 fAliROOTVersion = other.fAliROOTVersion;
648174cf 283 fExternalPackages = other.fExternalPackages;
c57f56b7 284 fUser = other.fUser;
285 fGridWorkingDir = other.fGridWorkingDir;
286 fGridDataDir = other.fGridDataDir;
287 fDataPattern = other.fDataPattern;
288 fGridOutputDir = other.fGridOutputDir;
289 fOutputArchive = other.fOutputArchive;
290 fOutputFiles = other.fOutputFiles;
291 fInputFormat = other.fInputFormat;
e7c71df0 292 fDatasetName = other.fDatasetName;
c57f56b7 293 fJDLName = other.fJDLName;
bb885a9e 294 fMergeExcludes = other.fMergeExcludes;
f965131e 295 fIncludePath = other.fIncludePath;
bb885a9e 296 fCloseSE = other.fCloseSE;
0df6ccf2 297 fFriendChainName = other.fFriendChainName;
c6cb3634 298 fJobTag = other.fJobTag;
648174cf 299 fOutputSingle = other.fOutputSingle;
5fce53f4 300 fRunPrefix = other.fRunPrefix;
c57f56b7 301 if (other.fInputFiles) {
302 fInputFiles = new TObjArray();
303 TIter next(other.fInputFiles);
304 TObject *obj;
305 while ((obj=next())) fInputFiles->Add(new TObjString(obj->GetName()));
306 fInputFiles->SetOwner();
307 }
4e5c5506 308 if (other.fPackages) {
309 fPackages = new TObjArray();
310 TIter next(other.fPackages);
311 TObject *obj;
312 while ((obj=next())) fPackages->Add(new TObjString(obj->GetName()));
313 fPackages->SetOwner();
314 }
c57f56b7 315 }
316 return *this;
317}
318
319//______________________________________________________________________________
f965131e 320void AliAnalysisAlien::AddIncludePath(const char *path)
321{
322// Add include path in the remote analysis macro.
323 TString p(path);
324 if (p.Contains("-I")) fIncludePath += Form("%s ", path);
325 else fIncludePath += Form("-I%s ", path);
326}
327
328//______________________________________________________________________________
c57f56b7 329void AliAnalysisAlien::AddRunNumber(Int_t run)
330{
331// Add a run number to the list of runs to be processed.
332 if (fRunNumbers.Length()) fRunNumbers += " ";
5fce53f4 333 fRunNumbers += Form("%s%d", fRunPrefix.Data(), run);
c57f56b7 334}
335
336//______________________________________________________________________________
ee75cfc3 337void AliAnalysisAlien::AddRunNumber(const char* run)
338{
339// Add a run number to the list of runs to be processed.
340 if (fRunNumbers.Length()) fRunNumbers += " ";
341 fRunNumbers += run;
342}
343
344//______________________________________________________________________________
c57f56b7 345void AliAnalysisAlien::AddDataFile(const char *lfn)
346{
347// Adds a data file to the input to be analysed. The file should be a valid LFN
348// or point to an existing file in the alien workdir.
349 if (!fInputFiles) fInputFiles = new TObjArray();
350 fInputFiles->Add(new TObjString(lfn));
351}
648174cf 352
353//______________________________________________________________________________
354void AliAnalysisAlien::AddExternalPackage(const char *package)
355{
356// Adds external packages w.r.t to the default ones (root,aliroot and gapi)
357 if (fExternalPackages) fExternalPackages += " ";
358 fExternalPackages += package;
359}
360
c57f56b7 361//______________________________________________________________________________
362Bool_t AliAnalysisAlien::Connect()
363{
364// Try to connect to AliEn. User needs a valid token and /tmp/gclient_env_$UID sourced.
365 if (gGrid && gGrid->IsConnected()) return kTRUE;
c57f56b7 366 if (!gGrid) {
367 Info("Connect", "Trying to connect to AliEn ...");
368 TGrid::Connect("alien://");
369 }
370 if (!gGrid || !gGrid->IsConnected()) {
371 Error("Connect", "Did not managed to connect to AliEn. Make sure you have a valid token.");
372 return kFALSE;
373 }
374 fUser = gGrid->GetUser();
375 Info("Connect", "\n##### Connected to AliEn as user %s. Setting analysis user to <%s>", fUser.Data(), fUser.Data());
376 return kTRUE;
377}
378
379//______________________________________________________________________________
380void AliAnalysisAlien::CdWork()
381{
382// Check validity of alien workspace. Create directory if possible.
383 if (!Connect()) {
384 Error("CdWork", "Alien connection required");
385 return;
386 }
387 TString homedir = gGrid->GetHomeDirectory();
388 TString workdir = homedir + fGridWorkingDir;
923e2ca5 389 if (DirectoryExists(workdir)) {
390 gGrid->Cd(workdir);
391 return;
392 }
393 // Work directory not existing - create it
394 gGrid->Cd(homedir);
b93f8109 395 if (gGrid->Mkdir(workdir, "-p")) {
923e2ca5 396 gGrid->Cd(fGridWorkingDir);
397 Info("CreateJDL", "\n##### Created alien working directory %s", fGridWorkingDir.Data());
398 } else {
399 Warning("CreateJDL", "Working directory %s cannot be created.\n Using %s instead.",
400 workdir.Data(), homedir.Data());
401 fGridWorkingDir = "";
402 }
c57f56b7 403}
404
405//______________________________________________________________________________
348be253 406Bool_t AliAnalysisAlien::CheckFileCopy(const char *alienpath)
407{
408// Check if file copying is possible.
409 if (!Connect()) {
410 Error("CheckFileCopy", "Not connected to AliEn. File copying cannot be tested.");
411 return kFALSE;
412 }
d3339be3 413 Info("CheckFileCopy", "Checking possibility to copy files to your AliEn home directory... \
414 \n +++ NOTE: You can disable this via: plugin->SetCheckCopy(kFALSE);");
348be253 415 // Check if alien_CLOSE_SE is defined
416 TString closeSE = gSystem->Getenv("alien_CLOSE_SE");
417 if (!closeSE.IsNull()) {
418 Info("CheckFileCopy", "Your current close storage is pointing to: \
419 \n alien_CLOSE_SE = \"%s\"", closeSE.Data());
420 } else {
421 Warning("CheckFileCopy", "Your current close storage is empty ! Depending on your location, file copying may fail.");
422 }
423 // Check if grid directory exists.
424 if (!DirectoryExists(alienpath)) {
425 Error("CheckFileCopy", "Alien path %s does not seem to exist", alienpath);
426 return kFALSE;
427 }
d3339be3 428 TFile f("plugin_test_copy", "RECREATE");
348be253 429 // User may not have write permissions to current directory
430 if (f.IsZombie()) {
431 Error("CheckFileCopy", "Cannot create local test file. Do you have write access to current directory: <%s> ?",
432 gSystem->WorkingDirectory());
433 return kFALSE;
434 }
435 f.Close();
d3339be3 436 if (FileExists(Form("alien://%s/%s",alienpath, f.GetName()))) gGrid->Rm(Form("alien://%s/%s",alienpath, f.GetName()));
437 if (!TFile::Cp(f.GetName(), Form("alien://%s/%s",alienpath, f.GetName()))) {
438 Error("CheckFileCopy", "Cannot copy files to Alien destination: <%s> This may be temporary, or: \
348be253 439 \n# 1. Make sure you have write permissions there. If this is the case: \
440 \n# 2. Check the storage availability at: http://alimonitor.cern.ch/stats?page=SE/table \
441 \n# Do: export alien_CLOSE_SE=\"working_disk_SE\" \
442 \n# To make this permanent put in in your .bashrc (in .alienshrc is not enough) \
443 \n# Redo token: rm /tmp/x509up_u$UID then: alien-token-init <username>", alienpath);
444 gSystem->Unlink(f.GetName());
445 return kFALSE;
446 }
447 gSystem->Unlink(f.GetName());
d3339be3 448 gGrid->Rm(Form("%s%s",alienpath,f.GetName()));
449 Info("CheckFileCopy", "### ...SUCCESS ###");
348be253 450 return kTRUE;
451}
452
453//______________________________________________________________________________
c57f56b7 454Bool_t AliAnalysisAlien::CheckInputData()
455{
456// Check validity of input data. If necessary, create xml files.
a8739e8a 457 if (!fInputFiles && !fRunNumbers.Length() && !fRunRange[0]) {
d2a409b2 458 if (!fGridDataDir.Length()) {
459 Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
460 return kFALSE;
461 }
462 Info("CheckInputData", "Analysis will make a single xml for base data directory %s",fGridDataDir.Data());
23329835 463 if (fDataPattern.Contains("tag") && TestBit(AliAnalysisGrid::kTest))
464 TObject::SetBit(AliAnalysisGrid::kUseTags, kTRUE); // ADDED (fix problem in determining the tag usage in test mode)
d2a409b2 465 return kTRUE;
c57f56b7 466 }
467 // Process declared files
a2f5fc01 468 Bool_t isCollection = kFALSE;
469 Bool_t isXml = kFALSE;
470 Bool_t useTags = kFALSE;
c57f56b7 471 Bool_t checked = kFALSE;
472 CdWork();
473 TString file;
474 TString workdir = gGrid->GetHomeDirectory();
475 workdir += fGridWorkingDir;
476 if (fInputFiles) {
477 TObjString *objstr;
478 TIter next(fInputFiles);
479 while ((objstr=(TObjString*)next())) {
480 file = workdir;
481 file += "/";
482 file += objstr->GetString();
483 // Store full lfn path
484 if (FileExists(file)) objstr->SetString(file);
485 else {
486 file = objstr->GetName();
487 if (!FileExists(objstr->GetName())) {
488 Error("CheckInputData", "Data file %s not found or not in your working dir: %s",
489 objstr->GetName(), workdir.Data());
490 return kFALSE;
491 }
492 }
493 Bool_t iscoll, isxml, usetags;
494 CheckDataType(file, iscoll, isxml, usetags);
495 if (!checked) {
496 checked = kTRUE;
a2f5fc01 497 isCollection = iscoll;
498 isXml = isxml;
499 useTags = usetags;
500 TObject::SetBit(AliAnalysisGrid::kUseTags, useTags);
c57f56b7 501 } else {
a2f5fc01 502 if ((iscoll != isCollection) || (isxml != isXml) || (usetags != useTags)) {
c57f56b7 503 Error("CheckInputData", "Some conflict was found in the types of inputs");
504 return kFALSE;
505 }
506 }
507 }
508 }
509 // Process requested run numbers
a8739e8a 510 if (!fRunNumbers.Length() && !fRunRange[0]) return kTRUE;
c57f56b7 511 // Check validity of alien data directory
512 if (!fGridDataDir.Length()) {
513 Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
514 return kFALSE;
515 }
923e2ca5 516 if (!DirectoryExists(fGridDataDir)) {
c57f56b7 517 Error("CheckInputData", "Data directory %s not existing.", fGridDataDir.Data());
518 return kFALSE;
519 }
a2f5fc01 520 if (isCollection) {
c57f56b7 521 Error("CheckInputData", "You are using raw AliEn collections as input. Cannot process run numbers.");
522 return kFALSE;
523 }
524
a2f5fc01 525 if (checked && !isXml) {
c57f56b7 526 Error("CheckInputData", "Cannot mix processing of full runs with non-xml files");
527 return kFALSE;
528 }
529 // Check validity of run number(s)
530 TObjArray *arr;
531 TObjString *os;
319593fb 532 Int_t nruns = 0;
904f9f5f 533 TString schunk, schunk2;
c57f56b7 534 TString path;
535 if (!checked) {
536 checked = kTRUE;
a2f5fc01 537 useTags = fDataPattern.Contains("tag");
538 TObject::SetBit(AliAnalysisGrid::kUseTags, useTags);
c57f56b7 539 }
a2f5fc01 540 if (useTags != fDataPattern.Contains("tag")) {
c57f56b7 541 Error("CheckInputData", "Cannot mix input files using/not using tags");
542 return kFALSE;
543 }
544 if (fRunNumbers.Length()) {
a8739e8a 545 Info("CheckDataType", "Using supplied run numbers (run ranges are ignored)");
c57f56b7 546 arr = fRunNumbers.Tokenize(" ");
547 TIter next(arr);
548 while ((os=(TObjString*)next())) {
549 path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data());
923e2ca5 550 if (!DirectoryExists(path)) {
551 Warning("CheckInputData", "Run number %s not found in path: <%s>", os->GetString().Data(), path.Data());
a8739e8a 552 continue;
c57f56b7 553 }
554 path = Form("%s/%s.xml", workdir.Data(),os->GetString().Data());
555 TString msg = "\n##### file: ";
556 msg += path;
557 msg += " type: xml_collection;";
a2f5fc01 558 if (useTags) msg += " using_tags: Yes";
c57f56b7 559 else msg += " using_tags: No";
23329835 560 Info("CheckDataType", "%s", msg.Data());
319593fb 561 if (fNrunsPerMaster<2) {
d2a409b2 562 AddDataFile(Form("%s.xml", os->GetString().Data()));
319593fb 563 } else {
564 nruns++;
565 if (((nruns-1)%fNrunsPerMaster) == 0) {
566 schunk = os->GetString();
567 }
568 if ((nruns%fNrunsPerMaster)!=0 && os!=arr->Last()) continue;
569 schunk += Form("_%s.xml", os->GetString().Data());
d2a409b2 570 AddDataFile(schunk);
319593fb 571 }
c57f56b7 572 }
573 delete arr;
a8739e8a 574 } else {
575 Info("CheckDataType", "Using run range [%d, %d]", fRunRange[0], fRunRange[1]);
576 for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
5fce53f4 577 path = Form("%s/%s%d ", fGridDataDir.Data(), fRunPrefix.Data(), irun);
923e2ca5 578 if (!DirectoryExists(path)) {
579// Warning("CheckInputData", "Run number %d not found in path: <%s>", irun, path.Data());
a8739e8a 580 continue;
581 }
5fce53f4 582 path = Form("%s/%s%d.xml", workdir.Data(),fRunPrefix.Data(),irun);
a8739e8a 583 TString msg = "\n##### file: ";
584 msg += path;
585 msg += " type: xml_collection;";
a2f5fc01 586 if (useTags) msg += " using_tags: Yes";
a8739e8a 587 else msg += " using_tags: No";
23329835 588 Info("CheckDataType", "%s", msg.Data());
319593fb 589 if (fNrunsPerMaster<2) {
5fce53f4 590 AddDataFile(Form("%s%d.xml",fRunPrefix.Data(),irun));
319593fb 591 } else {
592 nruns++;
593 if (((nruns-1)%fNrunsPerMaster) == 0) {
5fce53f4 594 schunk = Form("%s%d", fRunPrefix.Data(),irun);
319593fb 595 }
904f9f5f 596 schunk2 = Form("_%s%d.xml", fRunPrefix.Data(), irun);
319593fb 597 if ((nruns%fNrunsPerMaster)!=0 && irun != fRunRange[1]) continue;
904f9f5f 598 schunk += schunk2;
d2a409b2 599 AddDataFile(schunk);
319593fb 600 }
a8739e8a 601 }
904f9f5f 602 if (!fInputFiles) {
603 schunk += schunk2;
604 AddDataFile(schunk);
605 }
c57f56b7 606 }
607 return kTRUE;
608}
609
610//______________________________________________________________________________
611Bool_t AliAnalysisAlien::CreateDataset(const char *pattern)
612{
613// Create dataset for the grid data directory + run number.
f9e1936d 614 if (TestBit(AliAnalysisGrid::kOffline)) return kTRUE;
c57f56b7 615 if (!Connect()) {
616 Error("CreateDataset", "Cannot create dataset with no grid connection");
617 return kFALSE;
618 }
619
620 // Cd workspace
621 CdWork();
622 TString workdir = gGrid->GetHomeDirectory();
623 workdir += fGridWorkingDir;
624
625 // Compose the 'find' command arguments
626 TString command;
627 TString options = "-x collection ";
bb885a9e 628 if (TestBit(AliAnalysisGrid::kTest)) options += Form("-l %d ", fNtestFiles);
c57f56b7 629 TString conditions = "";
630
631 TString file;
632 TString path;
319593fb 633 Int_t nruns = 0;
904f9f5f 634 TString schunk, schunk2;
ab254fd1 635 TGridCollection *cbase=0, *cadd=0;
d2a409b2 636 if (!fRunNumbers.Length() && !fRunRange[0]) {
637 if (fInputFiles && fInputFiles->GetEntries()) return kTRUE;
638 // Make a single data collection from data directory.
639 path = fGridDataDir;
923e2ca5 640 if (!DirectoryExists(path)) {
d2a409b2 641 Error("CreateDataset", "Path to data directory %s not valid",fGridDataDir.Data());
642 return kFALSE;
643 }
923e2ca5 644// CdWork();
d2a409b2 645 if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
646 else file = Form("%s.xml", gSystem->BaseName(path));
0f389141 647 if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
d2a409b2 648 command = "find ";
649 command += options;
650 command += path;
651 command += " ";
652 command += pattern;
653 command += conditions;
84fcd93f 654 printf("command: %s\n", command.Data());
d2a409b2 655 TGridResult *res = gGrid->Command(command);
656 if (res) delete res;
657 // Write standard output to file
658 gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
a2f5fc01 659 Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE;
660 Bool_t nullFile = kFALSE;
661 if (!hasGrep) {
d3339be3 662 Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command");
663 } else {
a2f5fc01 664 nullFile = (gSystem->Exec(Form("grep /event %s 2>/dev/null > /dev/null",file.Data()))==0)?kFALSE:kTRUE;
665 if (nullFile) {
defd7a3a 666 Error("CreateDataset","Dataset %s produced by the previous find command is empty !", file.Data());
667 return kFALSE;
668 }
d3339be3 669 }
0f389141 670 }
671 Bool_t fileExists = FileExists(file);
672 if (!TestBit(AliAnalysisGrid::kTest) && (!fileExists || fOverwriteMode)) {
d2a409b2 673 // Copy xml file to alien space
0f389141 674 if (fileExists) gGrid->Rm(file);
d2a409b2 675 TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
676 if (!FileExists(file)) {
677 Error("CreateDataset", "Command %s did NOT succeed", command.Data());
678 return kFALSE;
679 }
680 // Update list of files to be processed.
681 }
682 AddDataFile(Form("%s/%s", workdir.Data(), file.Data()));
683 return kTRUE;
684 }
c57f56b7 685 // Several runs
a2f5fc01 686 Bool_t nullResult = kTRUE;
a8739e8a 687 if (fRunNumbers.Length()) {
688 TObjArray *arr = fRunNumbers.Tokenize(" ");
689 TObjString *os;
690 TIter next(arr);
691 while ((os=(TObjString*)next())) {
692 path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data());
923e2ca5 693 if (!DirectoryExists(path)) continue;
694// CdWork();
a8739e8a 695 if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
696 else file = Form("%s.xml", os->GetString().Data());
319593fb 697 // If local collection file does not exist, create it via 'find' command.
d3339be3 698 if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
319593fb 699 command = "find ";
700 command += options;
701 command += path;
702 command += pattern;
703 command += conditions;
704 TGridResult *res = gGrid->Command(command);
705 if (res) delete res;
706 // Write standard output to file
707 gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
a2f5fc01 708 Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE;
709 Bool_t nullFile = kFALSE;
710 if (!hasGrep) {
d3339be3 711 Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command");
712 } else {
a2f5fc01 713 nullFile = (gSystem->Exec(Form("grep /event %s 2>/dev/null > /dev/null",file.Data()))==0)?kFALSE:kTRUE;
714 if (nullFile) {
defd7a3a 715 Warning("CreateDataset","Dataset %s produced by: <%s> is empty !", file.Data(), command.Data());
716 fRunNumbers.ReplaceAll(os->GetString().Data(), "");
717 continue;
718 }
d3339be3 719 }
a2f5fc01 720 nullResult = kFALSE;
d3339be3 721 }
a8739e8a 722 if (TestBit(AliAnalysisGrid::kTest)) break;
319593fb 723 // Check if there is one run per master job.
724 if (fNrunsPerMaster<2) {
725 if (FileExists(file)) {
0f389141 726 if (fOverwriteMode) gGrid->Rm(file);
727 else {
728 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
729 continue;
730 }
319593fb 731 }
732 // Copy xml file to alien space
733 TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
734 if (!FileExists(file)) {
735 Error("CreateDataset", "Command %s did NOT succeed", command.Data());
736 delete arr;
737 return kFALSE;
738 }
739 } else {
740 nruns++;
741 if (((nruns-1)%fNrunsPerMaster) == 0) {
742 schunk = os->GetString();
743 cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
744 } else {
745 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
84fcd93f 746 printf(" Merging collection <%s> into masterjob input...\n", file.Data());
319593fb 747 cbase->Add(cadd);
748 delete cadd;
749 }
750 if ((nruns%fNrunsPerMaster)!=0 && os!=arr->Last()) {
751 continue;
752 }
753 schunk += Form("_%s.xml", os->GetString().Data());
0f389141 754 if (FileExists(schunk)) {
755 if (fOverwriteMode) gGrid->Rm(file);
756 else {
757 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
758 continue;
759 }
319593fb 760 }
84fcd93f 761 printf("Exporting merged collection <%s> and copying to AliEn\n", schunk.Data());
319593fb 762 cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs");
e95434bc 763 TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data()));
319593fb 764 if (!FileExists(schunk)) {
765 Error("CreateDataset", "Copy command did NOT succeed for %s", schunk.Data());
766 delete arr;
767 return kFALSE;
768 }
d3339be3 769 }
a8739e8a 770 }
771 delete arr;
a2f5fc01 772 if (nullResult) {
d3339be3 773 Error("CreateDataset", "No valid dataset corresponding to the query!");
774 return kFALSE;
775 }
a8739e8a 776 } else {
777 // Process a full run range.
778 for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
5fce53f4 779 path = Form("%s/%s%d ", fGridDataDir.Data(), fRunPrefix.Data(), irun);
923e2ca5 780 if (!DirectoryExists(path)) continue;
781// CdWork();
a8739e8a 782 if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
5fce53f4 783 else file = Form("%s%d.xml", fRunPrefix.Data(), irun);
0f389141 784 if (FileExists(file) && fNrunsPerMaster<2 && !TestBit(AliAnalysisGrid::kTest)) {
785 if (fOverwriteMode) gGrid->Rm(file);
786 else {
787 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
788 continue;
789 }
a8739e8a 790 }
319593fb 791 // If local collection file does not exist, create it via 'find' command.
d3339be3 792 if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
319593fb 793 command = "find ";
794 command += options;
795 command += path;
796 command += pattern;
797 command += conditions;
798 TGridResult *res = gGrid->Command(command);
799 if (res) delete res;
800 // Write standard output to file
801 gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
a2f5fc01 802 Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE;
803 Bool_t nullFile = kFALSE;
804 if (!hasGrep) {
d3339be3 805 Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command");
806 } else {
a2f5fc01 807 nullFile = (gSystem->Exec(Form("grep /event %s 2>/dev/null > /dev/null",file.Data()))==0)?kFALSE:kTRUE;
808 if (nullFile) {
defd7a3a 809 Warning("CreateDataset","Dataset %s produced by: <%s> is empty !", file.Data(), command.Data());
810 continue;
811 }
d3339be3 812 }
a2f5fc01 813 nullResult = kFALSE;
319593fb 814 }
a8739e8a 815 if (TestBit(AliAnalysisGrid::kTest)) break;
319593fb 816 // Check if there is one run per master job.
817 if (fNrunsPerMaster<2) {
818 if (FileExists(file)) {
0f389141 819 if (fOverwriteMode) gGrid->Rm(file);
820 else {
821 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
822 continue;
823 }
319593fb 824 }
825 // Copy xml file to alien space
826 TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
827 if (!FileExists(file)) {
828 Error("CreateDataset", "Command %s did NOT succeed", command.Data());
829 return kFALSE;
830 }
831 } else {
832 nruns++;
95e5b448 833 // Check if the collection for the chunk exist locally.
834 Int_t nchunk = (nruns-1)/fNrunsPerMaster;
0f389141 835 if (FileExists(fInputFiles->At(nchunk)->GetName())) {
836 if (fOverwriteMode) gGrid->Rm(fInputFiles->At(nchunk)->GetName());
837 else continue;
838 }
84fcd93f 839 printf(" Merging collection <%s> into %d runs chunk...\n",file.Data(),fNrunsPerMaster);
319593fb 840 if (((nruns-1)%fNrunsPerMaster) == 0) {
904f9f5f 841 schunk = Form("%s%d", fRunPrefix.Data(), irun);
319593fb 842 cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
843 } else {
844 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
845 cbase->Add(cadd);
846 delete cadd;
847 }
904f9f5f 848 schunk2 = Form("%s_%s%d.xml", schunk.Data(), fRunPrefix.Data(), irun);
849 if ((nruns%fNrunsPerMaster)!=0 && irun!=fRunRange[1] && schunk2 != fInputFiles->Last()->GetName()) {
319593fb 850 continue;
851 }
904f9f5f 852 schunk = schunk2;
319593fb 853 if (FileExists(schunk)) {
0f389141 854 if (fOverwriteMode) gGrid->Rm(schunk);
855 else {
856 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
857 continue;
858 }
319593fb 859 }
84fcd93f 860 printf("Exporting merged collection <%s> and copying to AliEn.\n", schunk.Data());
319593fb 861 cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs");
95e5b448 862 if (FileExists(schunk)) {
0f389141 863 if (fOverwriteMode) gGrid->Rm(schunk);
864 else {
865 Info("CreateDataset", "\n##### Dataset %s exist. Skipping copy...", schunk.Data());
866 continue;
867 }
95e5b448 868 }
319593fb 869 TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data()));
870 if (!FileExists(schunk)) {
871 Error("CreateDataset", "Copy command did NOT succeed for %s", schunk.Data());
872 return kFALSE;
873 }
874 }
c57f56b7 875 }
a2f5fc01 876 if (nullResult) {
d3339be3 877 Error("CreateDataset", "No valid dataset corresponding to the query!");
878 return kFALSE;
879 }
a8739e8a 880 }
c57f56b7 881 return kTRUE;
882}
883
884//______________________________________________________________________________
885Bool_t AliAnalysisAlien::CreateJDL()
886{
887// Generate a JDL file according to current settings. The name of the file is
888// specified by fJDLName.
889 Bool_t error = kFALSE;
890 TObjArray *arr = 0;
891 Bool_t copy = kTRUE;
892 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
893 Bool_t generate = kTRUE;
894 if (TestBit(AliAnalysisGrid::kTest) || TestBit(AliAnalysisGrid::kSubmit)) generate = kFALSE;
895 if (!Connect()) {
896 Error("CreateJDL", "Alien connection required");
897 return kFALSE;
898 }
899 // Check validity of alien workspace
900 CdWork();
901 TString workdir = gGrid->GetHomeDirectory();
902 workdir += fGridWorkingDir;
903 if (generate) {
904 TObjString *os;
905 if (!fInputFiles) {
906 Error("CreateJDL()", "Define some input files for your analysis.");
907 error = kTRUE;
908 }
909 // Compose list of input files
910 // Check if output files were defined
911 if (!fOutputFiles.Length()) {
912 Error("CreateJDL", "You must define at least one output file");
913 error = kTRUE;
914 }
915 // Check if an output directory was defined and valid
916 if (!fGridOutputDir.Length()) {
917 Error("CreateJDL", "You must define AliEn output directory");
918 error = kTRUE;
919 } else {
d2a409b2 920 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
923e2ca5 921 if (!DirectoryExists(fGridOutputDir)) {
b93f8109 922 if (gGrid->Mkdir(fGridOutputDir,"-p")) {
c57f56b7 923 Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
924 } else {
925 Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
5513444a 926 // error = kTRUE;
c57f56b7 927 }
928 }
929 gGrid->Cd(workdir);
930 }
931 // Exit if any error up to now
932 if (error) return kFALSE;
933 // Set JDL fields
0f389141 934 if (!fUser.IsNull()) {
935 fGridJDL->SetValue("User", Form("\"%s\"", fUser.Data()));
936 fMergingJDL->SetValue("User", Form("\"%s\"", fUser.Data()));
937 }
938 fGridJDL->SetExecutable(fExecutable, "This is the startup script");
939 TString mergeExec = fExecutable;
940 mergeExec.ReplaceAll(".sh", "_merge.sh");
941 fMergingJDL->SetExecutable(mergeExec, "This is the startup script");
942 mergeExec.ReplaceAll(".sh", ".C");
943 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),mergeExec.Data()), "List of input files to be uploaded to workers");
b5b9dee8 944 if (!fArguments.IsNull())
945 fGridJDL->SetArguments(fArguments, "Arguments for the executable command");
7c2cd90a 946 fMergingJDL->SetArguments("$1 $2 $3");
1f0d1ca2 947 fGridJDL->SetValue("TTL", Form("\"%d\"",fTTL));
948 fGridJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60));
949 fMergingJDL->SetValue("TTL", Form("\"%d\"",fTTL));
950 fMergingJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60));
951
0f389141 952 if (fMaxInitFailed > 0) {
c57f56b7 953 fGridJDL->SetValue("MaxInitFailed", Form("\"%d\"",fMaxInitFailed));
0f389141 954 fGridJDL->SetDescription("MaxInitFailed", "Maximum number of first failing jobs to abort the master job");
955 }
956 if (fSplitMaxInputFileNumber > 0) {
c57f56b7 957 fGridJDL->SetValue("SplitMaxInputFileNumber", Form("\"%d\"", fSplitMaxInputFileNumber));
0f389141 958 fGridJDL->SetDescription("SplitMaxInputFileNumber", "Maximum number of input files to be processed per subjob");
959 }
960 if (fSplitMode.Length()) {
c57f56b7 961 fGridJDL->SetValue("Split", Form("\"%s\"", fSplitMode.Data()));
0f389141 962 fGridJDL->SetDescription("Split", "We split per SE or file");
963 }
964 if (!fAliROOTVersion.IsNull()) {
965 fGridJDL->AddToPackages("AliRoot", fAliROOTVersion,"VO_ALICE", "List of requested packages");
966 fMergingJDL->AddToPackages("AliRoot", fAliROOTVersion, "VO_ALICE", "List of requested packages");
967 }
968 if (!fROOTVersion.IsNull()) {
c57f56b7 969 fGridJDL->AddToPackages("ROOT", fROOTVersion);
0f389141 970 fMergingJDL->AddToPackages("ROOT", fROOTVersion);
971 }
972 if (!fAPIVersion.IsNull()) {
c57f56b7 973 fGridJDL->AddToPackages("APISCONFIG", fAPIVersion);
0f389141 974 fMergingJDL->AddToPackages("APISCONFIG", fAPIVersion);
975 }
648174cf 976 if (!fExternalPackages.IsNull()) {
977 arr = fExternalPackages.Tokenize(" ");
978 TIter next(arr);
979 while ((os=(TObjString*)next())) {
980 TString pkgname = os->GetString();
981 Int_t index = pkgname.Index("::");
982 TString pkgversion = pkgname(index+2, pkgname.Length());
983 pkgname.Remove(index);
984 fGridJDL->AddToPackages(pkgname, pkgversion);
0f389141 985 fMergingJDL->AddToPackages(pkgname, pkgversion);
648174cf 986 }
987 delete arr;
988 }
0f389141 989 fGridJDL->SetInputDataListFormat(fInputFormat, "Format of input data");
990 fGridJDL->SetInputDataList("wn.xml", "Collection name to be processed on each worker node");
991 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), fAnalysisMacro.Data()), "List of input files to be uploaded to workers");
f10e8481 992 TString analysisFile = fExecutable;
993 analysisFile.ReplaceAll(".sh", ".root");
994 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),analysisFile.Data()));
f866cba5 995 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),analysisFile.Data()));
c57f56b7 996 if (IsUsingTags() && !gSystem->AccessPathName("ConfigureCuts.C"))
997 fGridJDL->AddToInputSandbox(Form("LF:%s/ConfigureCuts.C", workdir.Data()));
998 if (fAdditionalLibs.Length()) {
999 arr = fAdditionalLibs.Tokenize(" ");
1000 TIter next(arr);
1001 while ((os=(TObjString*)next())) {
1002 if (os->GetString().Contains(".so")) continue;
1003 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), os->GetString().Data()));
0f389141 1004 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), os->GetString().Data()));
c57f56b7 1005 }
1006 delete arr;
1007 }
4e5c5506 1008 if (fPackages) {
1009 TIter next(fPackages);
1010 TObject *obj;
0f389141 1011 while ((obj=next())) {
4e5c5506 1012 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName()));
0f389141 1013 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName()));
1014 }
4e5c5506 1015 }
c57f56b7 1016 if (fOutputArchive.Length()) {
1017 arr = fOutputArchive.Tokenize(" ");
1018 TIter next(arr);
0f389141 1019 Bool_t first = kTRUE;
1020 const char *comment = "Files to be archived";
1021 const char *comment1 = comment;
1022 while ((os=(TObjString*)next())) {
1023 if (!first) comment = NULL;
1024 if (!os->GetString().Contains("@") && fCloseSE.Length())
1025 fGridJDL->AddToOutputArchive(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
1026 else
1027 fGridJDL->AddToOutputArchive(os->GetString(), comment);
1028 first = kFALSE;
1029 }
c57f56b7 1030 delete arr;
0f389141 1031 TString outputArchive = fOutputArchive;
1032 if (!fMergeExcludes.IsNull()) {
1033 arr = fMergeExcludes.Tokenize(" ");
705adb3e 1034 TIter next1(arr);
1035 while ((os=(TObjString*)next1())) {
0f389141 1036 outputArchive.ReplaceAll(Form("%s,",os->GetString().Data()),"");
1037 outputArchive.ReplaceAll(os->GetString(),"");
1038 }
1039 delete arr;
1040 }
1041 arr = outputArchive.Tokenize(" ");
705adb3e 1042 TIter next2(arr);
0f389141 1043 comment = comment1;
1044 first = kTRUE;
705adb3e 1045 while ((os=(TObjString*)next2())) {
0f389141 1046 if (!first) comment = NULL;
0cdf65a8 1047 TString currentfile = os->GetString();
1048 currentfile.ReplaceAll(".root", "*.root");
1049 currentfile.ReplaceAll(".zip", "-Stage$2_$3.zip");
1050 if (!currentfile.Contains("@") && fCloseSE.Length())
1051 fMergingJDL->AddToOutputArchive(Form("%s@%s",currentfile.Data(), fCloseSE.Data()), comment);
0f389141 1052 else
0cdf65a8 1053 fMergingJDL->AddToOutputArchive(currentfile, comment);
0f389141 1054 first = kFALSE;
1055 }
1056 delete arr;
c57f56b7 1057 }
149d288c 1058 arr = fOutputFiles.Tokenize(",");
c57f56b7 1059 TIter next(arr);
0f389141 1060 Bool_t first = kTRUE;
1061 const char *comment = "Files to be archived";
1062 const char *comment1 = comment;
43da816a 1063 while ((os=(TObjString*)next())) {
e1eaf596 1064 // Ignore ouputs in jdl that are also in outputarchive
1065 TString sout = os->GetString();
1066 if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
1067 if (fOutputArchive.Contains(sout)) continue;
0f389141 1068 if (!first) comment = NULL;
43da816a 1069 if (!os->GetString().Contains("@") && fCloseSE.Length())
0f389141 1070 fGridJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
43da816a 1071 else
0f389141 1072 fGridJDL->AddToOutputSandbox(os->GetString(), comment);
1073 first = kFALSE;
43da816a 1074 }
c57f56b7 1075 delete arr;
0f389141 1076 if (fOutputFiles.Length()) {
1077 TString outputFiles = fOutputFiles;
1078 if (!fMergeExcludes.IsNull()) {
1079 arr = fMergeExcludes.Tokenize(" ");
705adb3e 1080 TIter next1(arr);
1081 while ((os=(TObjString*)next1())) {
0f389141 1082 outputFiles.ReplaceAll(Form("%s,",os->GetString().Data()),"");
1083 outputFiles.ReplaceAll(os->GetString(),"");
1084 }
1085 delete arr;
1086 }
1087 arr = outputFiles.Tokenize(" ");
705adb3e 1088 TIter next2(arr);
0f389141 1089 comment = comment1;
1090 first = kTRUE;
705adb3e 1091 while ((os=(TObjString*)next2())) {
0f389141 1092 // Ignore ouputs in jdl that are also in outputarchive
1093 TString sout = os->GetString();
1094 if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
1095 if (fOutputArchive.Contains(sout)) continue;
1096 if (!first) comment = NULL;
1097 if (!os->GetString().Contains("@") && fCloseSE.Length())
1098 fMergingJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
1099 else
1100 fMergingJDL->AddToOutputSandbox(os->GetString(), comment);
020d7c04 1101 first = kFALSE;
0f389141 1102 }
1103 delete arr;
1104 }
1105 fGridJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
1106 fMergingJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
0d5d317c 1107 TString validationScript = fExecutable;
1108 validationScript.ReplaceAll(".sh", "_validation.sh");
0f389141 1109 fGridJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
1110 validationScript = fExecutable;
1111 validationScript.ReplaceAll(".sh", "_mergevalidation.sh");
1112 fMergingJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
1113 if (fMasterResubmitThreshold) {
1114 fGridJDL->SetValue("MasterResubmitThreshold", Form("\"%d%%\"", fMasterResubmitThreshold));
1115 fGridJDL->SetDescription("MasterResubmitThreshold", "Resubmit failed jobs until DONE rate reaches this percentage");
1116 }
d2a409b2 1117 // Write a jdl with 2 input parameters: collection name and output dir name.
1118 WriteJDL(copy);
c57f56b7 1119 }
1120 // Copy jdl to grid workspace
a8739e8a 1121 if (copy) {
b5e4aaa7 1122 // Check if an output directory was defined and valid
1123 if (!fGridOutputDir.Length()) {
1124 Error("CreateJDL", "You must define AliEn output directory");
1125 return kFALSE;
1126 } else {
1127 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
bb2e67a0 1128 if (!fProductionMode && !DirectoryExists(fGridOutputDir)) {
b93f8109 1129 if (gGrid->Mkdir(fGridOutputDir,"-p")) {
b5e4aaa7 1130 Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
1131 } else {
1132 Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
1133 return kFALSE;
1134 }
1135 }
1136 gGrid->Cd(workdir);
1137 }
648174cf 1138 if (TestBit(AliAnalysisGrid::kSubmit)) {
0f389141 1139 TString mergeJDLName = fExecutable;
1140 mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
648174cf 1141 TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
0f389141 1142 TString locjdl1 = Form("%s/%s", fGridOutputDir.Data(),mergeJDLName.Data());
1143 if (fProductionMode) {
648174cf 1144 locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
0f389141 1145 locjdl1 = Form("%s/%s", workdir.Data(),mergeJDLName.Data());
1146 }
648174cf 1147 if (FileExists(locjdl)) gGrid->Rm(locjdl);
0f389141 1148 if (FileExists(locjdl1)) gGrid->Rm(locjdl1);
1149 Info("CreateJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
648174cf 1150 TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
0f389141 1151 if (fMergeViaJDL) {
1152 Info("CreateJDL", "\n##### Copying merging JDL file <%s> to your AliEn output directory", mergeJDLName.Data());
1153 TFile::Cp(Form("file:%s",mergeJDLName.Data()), Form("alien://%s", locjdl1.Data()));
1154 }
648174cf 1155 }
c57f56b7 1156 if (fAdditionalLibs.Length()) {
e7c71df0 1157 arr = fAdditionalLibs.Tokenize(" ");
c57f56b7 1158 TObjString *os;
1159 TIter next(arr);
1160 while ((os=(TObjString*)next())) {
c57f56b7 1161 if (os->GetString().Contains(".so")) continue;
4e5c5506 1162 Info("CreateJDL", "\n##### Copying dependency: <%s> to your alien workspace", os->GetString().Data());
c57f56b7 1163 if (FileExists(os->GetString())) gGrid->Rm(os->GetString());
1164 TFile::Cp(Form("file:%s",os->GetString().Data()), Form("alien://%s/%s", workdir.Data(), os->GetString().Data()));
1165 }
1166 delete arr;
1167 }
4e5c5506 1168 if (fPackages) {
1169 TIter next(fPackages);
1170 TObject *obj;
1171 while ((obj=next())) {
fdbbc7be 1172 if (FileExists(obj->GetName())) gGrid->Rm(obj->GetName());
4e5c5506 1173 Info("CreateJDL", "\n##### Copying dependency: <%s> to your alien workspace", obj->GetName());
1174 TFile::Cp(Form("file:%s",obj->GetName()), Form("alien://%s/%s", workdir.Data(), obj->GetName()));
1175 }
1176 }
c57f56b7 1177 }
1178 return kTRUE;
1179}
1180
1181//______________________________________________________________________________
d2a409b2 1182Bool_t AliAnalysisAlien::WriteJDL(Bool_t copy)
a8739e8a 1183{
1184// Writes one or more JDL's corresponding to findex. If findex is negative,
1185// all run numbers are considered in one go (jdl). For non-negative indices
1186// they correspond to the indices in the array fInputFiles.
1187 if (!fInputFiles) return kFALSE;
1188 TObjString *os;
a8739e8a 1189 TString workdir = gGrid->GetHomeDirectory();
1190 workdir += fGridWorkingDir;
d2a409b2 1191
1192 if (!fRunNumbers.Length() && !fRunRange[0]) {
1193 // One jdl with no parameters in case input data is specified by name.
a8739e8a 1194 TIter next(fInputFiles);
1195 while ((os=(TObjString*)next()))
0f389141 1196 fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetString().Data()), "Input xml collections");
648174cf 1197 if (!fOutputSingle.IsNull())
0f389141 1198 fGridJDL->SetOutputDirectory(Form("#alienfulldir#/../%s",fOutputSingle.Data()), "Output directory");
1199 else {
1200 fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
1201 fMergingJDL->SetOutputDirectory(fGridOutputDir);
1202 }
a8739e8a 1203 } else {
d2a409b2 1204 // One jdl to be submitted with 2 input parameters: data collection name and output dir prefix
0f389141 1205 fGridJDL->AddToInputDataCollection(Form("LF:%s/$1,nodownload", workdir.Data()), "Input xml collections");
cd11251e 1206 if (!fOutputSingle.IsNull()) {
0f389141 1207 if (!fOutputToRunNo) fGridJDL->SetOutputDirectory(Form("#alienfulldir#/%s",fOutputSingle.Data()), "Output directory");
1208 else fGridJDL->SetOutputDirectory(Form("%s/$2",fGridOutputDir.Data()), "Output directory");
cd11251e 1209 } else {
0f389141 1210 fGridJDL->SetOutputDirectory(Form("%s/$2/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
23329835 1211 fMergingJDL->SetOutputDirectory("$1", "Output directory");
cd11251e 1212 }
a8739e8a 1213 }
1214
1215
1216 // Generate the JDL as a string
1217 TString sjdl = fGridJDL->Generate();
0f389141 1218 TString sjdl1 = fMergingJDL->Generate();
a8739e8a 1219 Int_t index;
a8739e8a 1220 sjdl.ReplaceAll("\"LF:", "\n \"LF:");
1221 sjdl.ReplaceAll("(member", "\n (member");
1222 sjdl.ReplaceAll("\",\"VO_", "\",\n \"VO_");
1223 sjdl.ReplaceAll("{", "{\n ");
1224 sjdl.ReplaceAll("};", "\n};");
1225 sjdl.ReplaceAll("{\n \n", "{\n");
1226 sjdl.ReplaceAll("\n\n", "\n");
1227 sjdl.ReplaceAll("OutputDirectory", "OutputDir");
0f389141 1228 sjdl1.ReplaceAll("\"LF:", "\n \"LF:");
1229 sjdl1.ReplaceAll("(member", "\n (member");
1230 sjdl1.ReplaceAll("\",\"VO_", "\",\n \"VO_");
1231 sjdl1.ReplaceAll("{", "{\n ");
1232 sjdl1.ReplaceAll("};", "\n};");
1233 sjdl1.ReplaceAll("{\n \n", "{\n");
1234 sjdl1.ReplaceAll("\n\n", "\n");
1235 sjdl1.ReplaceAll("OutputDirectory", "OutputDir");
a8739e8a 1236 sjdl += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
f60ef0ba 1237 sjdl.Prepend(Form("Jobtag = {\n \"comment:%s\"\n};\n", fJobTag.Data()));
a8739e8a 1238 index = sjdl.Index("JDLVariables");
1239 if (index >= 0) sjdl.Insert(index, "\n# JDL variables\n");
4739b2aa 1240 sjdl += "Workdirectorysize = {\"5000MB\"};";
0f389141 1241 sjdl1 += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
7c2cd90a 1242 sjdl1.Prepend(Form("Jobtag = {\n \"comment:%s_Merging\"\n};\n", fJobTag.Data()));
1243 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 1244 index = sjdl1.Index("JDLVariables");
1245 if (index >= 0) sjdl1.Insert(index, "\n# JDL variables\n");
4739b2aa 1246 sjdl1 += "Workdirectorysize = {\"5000MB\"};";
a8739e8a 1247 // Write jdl to file
a8739e8a 1248 ofstream out;
d2a409b2 1249 out.open(fJDLName.Data(), ios::out);
a8739e8a 1250 if (out.bad()) {
d2a409b2 1251 Error("CreateJDL", "Bad file name: %s", fJDLName.Data());
a8739e8a 1252 return kFALSE;
1253 }
1254 out << sjdl << endl;
0f389141 1255 TString mergeJDLName = fExecutable;
1256 mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
1257 if (fMergeViaJDL) {
1258 ofstream out1;
1259 out1.open(mergeJDLName.Data(), ios::out);
1260 if (out.bad()) {
1261 Error("CreateJDL", "Bad file name: %s", mergeJDLName.Data());
1262 return kFALSE;
1263 }
1264 out1 << sjdl1 << endl;
1265 }
a8739e8a 1266
1267 // Copy jdl to grid workspace
1268 if (!copy) {
1269 Info("CreateJDL", "\n##### You may want to review jdl:%s and analysis macro:%s before running in <submit> mode", fJDLName.Data(), fAnalysisMacro.Data());
1270 } else {
d2a409b2 1271 TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
0f389141 1272 TString locjdl1 = Form("%s/%s", fGridOutputDir.Data(),mergeJDLName.Data());
1273 if (fProductionMode) {
b5fe9cba 1274 locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
0f389141 1275 locjdl1 = Form("%s/%s", workdir.Data(),mergeJDLName.Data());
1276 }
d2a409b2 1277 if (FileExists(locjdl)) gGrid->Rm(locjdl);
0f389141 1278 if (FileExists(locjdl1)) gGrid->Rm(locjdl1);
1279 Info("CreateJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
5513444a 1280 TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
0f389141 1281 if (fMergeViaJDL) {
1282 Info("CreateJDL", "\n##### Copying merging JDL file <%s> to your AliEn output directory", mergeJDLName.Data());
1283 TFile::Cp(Form("file:%s",mergeJDLName.Data()), Form("alien://%s", locjdl1.Data()));
1284 }
a8739e8a 1285 }
1286 return kTRUE;
1287}
1288
1289//______________________________________________________________________________
5513444a 1290Bool_t AliAnalysisAlien::FileExists(const char *lfn)
c57f56b7 1291{
1292// Returns true if file exists.
5513444a 1293 if (!gGrid) return kFALSE;
c57f56b7 1294 TGridResult *res = gGrid->Ls(lfn);
1295 if (!res) return kFALSE;
1296 TMap *map = dynamic_cast<TMap*>(res->At(0));
1297 if (!map) {
1298 delete res;
1299 return kFALSE;
1300 }
1301 TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("name"));
1302 if (!objs || !objs->GetString().Length()) {
1303 delete res;
1304 return kFALSE;
1305 }
1306 delete res;
1307 return kTRUE;
1308}
1309
1310//______________________________________________________________________________
923e2ca5 1311Bool_t AliAnalysisAlien::DirectoryExists(const char *dirname)
1312{
1313// Returns true if directory exists. Can be also a path.
1314 if (!gGrid) return kFALSE;
1315 // Check if dirname is a path
1316 TString dirstripped = dirname;
1317 dirstripped = dirstripped.Strip();
1318 dirstripped = dirstripped.Strip(TString::kTrailing, '/');
1319 TString dir = gSystem->BaseName(dirstripped);
1320 dir += "/";
1321 TString path = gSystem->DirName(dirstripped);
1322 TGridResult *res = gGrid->Ls(path, "-F");
1323 if (!res) return kFALSE;
1324 TIter next(res);
1325 TMap *map;
1326 TObject *obj;
1327 while ((map=dynamic_cast<TMap*>(next()))) {
1328 obj = map->GetValue("name");
1329 if (!obj) break;
1330 if (dir == obj->GetName()) {
1331 delete res;
1332 return kTRUE;
1333 }
1334 }
1335 delete res;
1336 return kFALSE;
1337}
1338
1339//______________________________________________________________________________
a2f5fc01 1340void AliAnalysisAlien::CheckDataType(const char *lfn, Bool_t &isCollection, Bool_t &isXml, Bool_t &useTags)
c57f56b7 1341{
1342// Check input data type.
a2f5fc01 1343 isCollection = kFALSE;
1344 isXml = kFALSE;
1345 useTags = kFALSE;
c57f56b7 1346 if (!gGrid) {
1347 Error("CheckDataType", "No connection to grid");
1348 return;
1349 }
a2f5fc01 1350 isCollection = IsCollection(lfn);
c57f56b7 1351 TString msg = "\n##### file: ";
1352 msg += lfn;
a2f5fc01 1353 if (isCollection) {
c57f56b7 1354 msg += " type: raw_collection;";
1355 // special treatment for collections
a2f5fc01 1356 isXml = kFALSE;
c57f56b7 1357 // check for tag files in the collection
1358 TGridResult *res = gGrid->Command(Form("listFilesFromCollection -z -v %s",lfn), kFALSE);
1359 if (!res) {
1360 msg += " using_tags: No (unknown)";
23329835 1361 Info("CheckDataType", "%s", msg.Data());
c57f56b7 1362 return;
1363 }
1364 const char* typeStr = res->GetKey(0, "origLFN");
1365 if (!typeStr || !strlen(typeStr)) {
1366 msg += " using_tags: No (unknown)";
23329835 1367 Info("CheckDataType", "%s", msg.Data());
c57f56b7 1368 return;
1369 }
1370 TString file = typeStr;
a2f5fc01 1371 useTags = file.Contains(".tag");
1372 if (useTags) msg += " using_tags: Yes";
c57f56b7 1373 else msg += " using_tags: No";
23329835 1374 Info("CheckDataType", "%s", msg.Data());
c57f56b7 1375 return;
1376 }
1377 TString slfn(lfn);
1378 slfn.ToLower();
a2f5fc01 1379 isXml = slfn.Contains(".xml");
1380 if (isXml) {
c57f56b7 1381 // Open xml collection and check if there are tag files inside
1382 msg += " type: xml_collection;";
1383 TGridCollection *coll = (TGridCollection*)gROOT->ProcessLine(Form("TAlienCollection::Open(\"alien://%s\",1);",lfn));
1384 if (!coll) {
1385 msg += " using_tags: No (unknown)";
23329835 1386 Info("CheckDataType", "%s", msg.Data());
c57f56b7 1387 return;
1388 }
1389 TMap *map = coll->Next();
1390 if (!map) {
1391 msg += " using_tags: No (unknown)";
23329835 1392 Info("CheckDataType", "%s", msg.Data());
c57f56b7 1393 return;
1394 }
1395 map = (TMap*)map->GetValue("");
1396 TString file;
1397 if (map && map->GetValue("name")) file = map->GetValue("name")->GetName();
a2f5fc01 1398 useTags = file.Contains(".tag");
c57f56b7 1399 delete coll;
a2f5fc01 1400 if (useTags) msg += " using_tags: Yes";
c57f56b7 1401 else msg += " using_tags: No";
23329835 1402 Info("CheckDataType", "%s", msg.Data());
c57f56b7 1403 return;
1404 }
a2f5fc01 1405 useTags = slfn.Contains(".tag");
c57f56b7 1406 if (slfn.Contains(".root")) msg += " type: root file;";
f866cba5 1407 else msg += " type: unknown file;";
a2f5fc01 1408 if (useTags) msg += " using_tags: Yes";
c57f56b7 1409 else msg += " using_tags: No";
23329835 1410 Info("CheckDataType", "%s", msg.Data());
c57f56b7 1411}
1412
1413//______________________________________________________________________________
4e5c5506 1414void AliAnalysisAlien::EnablePackage(const char *package)
1415{
1416// Enables a par file supposed to exist in the current directory.
1417 TString pkg(package);
1418 pkg.ReplaceAll(".par", "");
1419 pkg += ".par";
1420 if (gSystem->AccessPathName(pkg)) {
ebcdf05e 1421 Fatal("EnablePackage", "Package %s not found", pkg.Data());
4e5c5506 1422 return;
1423 }
1424 if (!TObject::TestBit(AliAnalysisGrid::kUsePars))
1425 Info("EnablePackage", "AliEn plugin will use .par packages");
1426 TObject::SetBit(AliAnalysisGrid::kUsePars, kTRUE);
1427 if (!fPackages) {
1428 fPackages = new TObjArray();
1429 fPackages->SetOwner();
1430 }
1431 fPackages->Add(new TObjString(pkg));
1432}
1433
1434//______________________________________________________________________________
d2a409b2 1435const char *AliAnalysisAlien::GetJobStatus(Int_t jobidstart, Int_t lastid, Int_t &nrunning, Int_t &nwaiting, Int_t &nerror, Int_t &ndone)
1436{
1437// Get job status for all jobs with jobid>jobidstart.
1438 static char mstatus[20];
1439 mstatus[0] = '\0';
1440 nrunning = 0;
1441 nwaiting = 0;
1442 nerror = 0;
1443 ndone = 0;
1444 TGridJobStatusList *list = gGrid->Ps("");
1445 if (!list) return mstatus;
1446 Int_t nentries = list->GetSize();
1447 TGridJobStatus *status;
1448 Int_t pid;
1449 for (Int_t ijob=0; ijob<nentries; ijob++) {
1450 status = (TGridJobStatus *)list->At(ijob);
1451 pid = gROOT->ProcessLine(Form("atoi(((TAlienJobStatus*)0x%lx)->GetKey(\"queueId\"));", (ULong_t)status));
1452 if (pid<jobidstart) continue;
1453 if (pid == lastid) {
1454 gROOT->ProcessLine(Form("sprintf((char*)0x%lx,((TAlienJobStatus*)0x%lx)->GetKey(\"status\"));",(ULong_t)mstatus, (ULong_t)status));
1455 }
1456 switch (status->GetStatus()) {
1457 case TGridJobStatus::kWAITING:
1458 nwaiting++; break;
1459 case TGridJobStatus::kRUNNING:
1460 nrunning++; break;
1461 case TGridJobStatus::kABORTED:
1462 case TGridJobStatus::kFAIL:
1463 case TGridJobStatus::kUNKNOWN:
1464 nerror++; break;
1465 case TGridJobStatus::kDONE:
1466 ndone++;
1467 }
1468 }
1469 list->Delete();
1470 delete list;
1471 return mstatus;
1472}
1473
1474//______________________________________________________________________________
c57f56b7 1475Bool_t AliAnalysisAlien::IsCollection(const char *lfn) const
1476{
1477// Returns true if file is a collection. Functionality duplicated from
1478// TAlien::Type() because we don't want to directly depend on TAlien.
1479 if (!gGrid) {
1480 Error("IsCollection", "No connection to grid");
1481 return kFALSE;
1482 }
1483 TGridResult *res = gGrid->Command(Form("type -z %s",lfn),kFALSE);
1484 if (!res) return kFALSE;
1485 const char* typeStr = res->GetKey(0, "type");
1486 if (!typeStr || !strlen(typeStr)) return kFALSE;
1487 if (!strcmp(typeStr, "collection")) return kTRUE;
1488 delete res;
1489 return kFALSE;
1490}
1491
1492//______________________________________________________________________________
fe2d7fc2 1493Bool_t AliAnalysisAlien::IsSingleOutput() const
1494{
1495// Check if single-ouput option is on.
1496 return (!fOutputSingle.IsNull());
1497}
1498
1499//______________________________________________________________________________
16a4353c 1500void AliAnalysisAlien::Print(Option_t *) const
1501{
1502// Print current plugin settings.
84fcd93f 1503 printf("### AliEn analysis plugin current settings ###\n");
e1c22e21 1504 printf("= OverwriteMode:________________________________ %d\n", fOverwriteMode);
1505 if (fOverwriteMode) {
1506 printf("***** NOTE: Overwrite mode will overwrite the input generated datasets and partial results from previous analysis. \
1507 \n***** To disable, use: plugin->SetOverwriteMode(kFALSE);\n");
1508 }
348be253 1509 printf("= Copy files to grid: __________________________ %s\n", (IsUseCopy())?"YES":"NO");
1510 printf("= Check if files can be copied to grid: ________ %s\n", (IsCheckCopy())?"YES":"NO");
84fcd93f 1511 printf("= Production mode:______________________________ %d\n", fProductionMode);
1512 printf("= Version of API requested: ____________________ %s\n", fAPIVersion.Data());
1513 printf("= Version of ROOT requested: ___________________ %s\n", fROOTVersion.Data());
1514 printf("= Version of AliRoot requested: ________________ %s\n", fAliROOTVersion.Data());
16a4353c 1515 if (fUser.Length())
84fcd93f 1516 printf("= User running the plugin: _____________________ %s\n", fUser.Data());
1517 printf("= Grid workdir relative to user $HOME: _________ %s\n", fGridWorkingDir.Data());
1518 printf("= Grid output directory relative to workdir: ___ %s\n", fGridOutputDir.Data());
1519 printf("= Data base directory path requested: __________ %s\n", fGridDataDir.Data());
1520 printf("= Data search pattern: _________________________ %s\n", fDataPattern.Data());
1521 printf("= Input data format: ___________________________ %s\n", fInputFormat.Data());
16a4353c 1522 if (fRunNumbers.Length())
84fcd93f 1523 printf("= Run numbers to be processed: _________________ %s\n", fRunNumbers.Data());
16a4353c 1524 if (fRunRange[0])
5fce53f4 1525 printf("= Run range to be processed: ___________________ %s%d-%s%d\n", fRunPrefix.Data(), fRunRange[0], fRunPrefix.Data(), fRunRange[1]);
16a4353c 1526 if (!fRunRange[0] && !fRunNumbers.Length()) {
1527 TIter next(fInputFiles);
1528 TObject *obj;
1529 TString list;
1530 while ((obj=next())) list += obj->GetName();
84fcd93f 1531 printf("= Input files to be processed: _________________ %s\n", list.Data());
16a4353c 1532 }
1533 if (TestBit(AliAnalysisGrid::kTest))
84fcd93f 1534 printf("= Number of input files used in test mode: _____ %d\n", fNtestFiles);
1535 printf("= List of output files to be registered: _______ %s\n", fOutputFiles.Data());
1536 printf("= List of outputs going to be archived: ________ %s\n", fOutputArchive.Data());
1537 printf("= List of outputs that should not be merged: ___ %s\n", fMergeExcludes.Data());
1538 printf("=====================================================================\n");
1539 printf("= Job price: ___________________________________ %d\n", fPrice);
1540 printf("= Time to live (TTL): __________________________ %d\n", fTTL);
1541 printf("= Max files per subjob: ________________________ %d\n", fSplitMaxInputFileNumber);
16a4353c 1542 if (fMaxInitFailed>0)
84fcd93f 1543 printf("= Max number of subjob fails to kill: __________ %d\n", fMaxInitFailed);
16a4353c 1544 if (fMasterResubmitThreshold>0)
84fcd93f 1545 printf("= Resubmit master job if failed subjobs >_______ %d\n", fMasterResubmitThreshold);
149d288c 1546 printf("= Number of replicas for the output files_______ %d\n", fNreplicas);
319593fb 1547 if (fNrunsPerMaster>0)
84fcd93f 1548 printf("= Number of runs per master job: _______________ %d\n", fNrunsPerMaster);
1549 printf("= Number of files in one chunk to be merged: ___ %d\n", fMaxMergeFiles);
b5b9dee8 1550 printf("= Name of the generated execution script: ______ %s\n", fExecutable.Data());
1551 printf("= Executable command: __________________________ %s\n", fExecutableCommand.Data());
16a4353c 1552 if (fArguments.Length())
84fcd93f 1553 printf("= Arguments for the execution script: __________ %s\n",fArguments.Data());
631c0b05 1554 if (fExecutableArgs.Length())
1555 printf("= Arguments after macro name in executable______ %s\n",fExecutableArgs.Data());
84fcd93f 1556 printf("= Name of the generated analysis macro: ________ %s\n",fAnalysisMacro.Data());
1557 printf("= User analysis files to be deployed: __________ %s\n",fAnalysisSource.Data());
1558 printf("= Additional libs to be loaded or souces to be compiled runtime: <%s>\n",fAdditionalLibs.Data());
1559 printf("= Master jobs split mode: ______________________ %s\n",fSplitMode.Data());
16a4353c 1560 if (fDatasetName)
84fcd93f 1561 printf("= Custom name for the dataset to be created: ___ %s\n", fDatasetName.Data());
1562 printf("= Name of the generated JDL: ___________________ %s\n", fJDLName.Data());
16a4353c 1563 if (fIncludePath.Data())
84fcd93f 1564 printf("= Include path for runtime task compilation: ___ %s\n", fIncludePath.Data());
16a4353c 1565 if (fCloseSE.Length())
84fcd93f 1566 printf("= Force job outputs to storage element: ________ %s\n", fCloseSE.Data());
16a4353c 1567 if (fFriendChainName.Length())
84fcd93f 1568 printf("= Open friend chain file on worker: ____________ %s\n", fFriendChainName.Data());
16a4353c 1569 if (fPackages) {
1570 TIter next(fPackages);
1571 TObject *obj;
1572 TString list;
1573 while ((obj=next())) list += obj->GetName();
84fcd93f 1574 printf("= Par files to be used: ________________________ %s\n", list.Data());
16a4353c 1575 }
1576}
1577
1578//______________________________________________________________________________
c57f56b7 1579void AliAnalysisAlien::SetDefaults()
1580{
1581// Set default values for everything. What cannot be filled will be left empty.
1582 if (fGridJDL) delete fGridJDL;
1583 fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
0f389141 1584 fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
c57f56b7 1585 fPrice = 1;
1586 fTTL = 30000;
1587 fSplitMaxInputFileNumber = 100;
1588 fMaxInitFailed = 0;
1589 fMasterResubmitThreshold = 0;
bb885a9e 1590 fNtestFiles = 10;
149d288c 1591 fNreplicas = 2;
a8739e8a 1592 fRunRange[0] = 0;
1593 fRunRange[1] = 0;
319593fb 1594 fNrunsPerMaster = 1;
16a4353c 1595 fMaxMergeFiles = 100;
c57f56b7 1596 fRunNumbers = "";
1597 fExecutable = "analysis.sh";
0a1c1f7f 1598 fExecutableCommand = "root -b -q";
c57f56b7 1599 fArguments = "";
631c0b05 1600 fExecutableArgs = "";
c57f56b7 1601 fAnalysisMacro = "myAnalysis.C";
1602 fAnalysisSource = "";
1603 fAdditionalLibs = "";
1604 fSplitMode = "se";
1605 fAPIVersion = "";
1606 fROOTVersion = "";
1607 fAliROOTVersion = "";
1608 fUser = ""; // Your alien user name
1609 fGridWorkingDir = "";
1610 fGridDataDir = ""; // Can be like: /alice/sim/PDC_08a/LHC08c9/
1611 fDataPattern = "*AliESDs.root"; // Can be like: *AliESDs.root, */pass1/*AliESDs.root, ...
0df6ccf2 1612 fFriendChainName = "";
c57f56b7 1613 fGridOutputDir = "output";
149d288c 1614 fOutputArchive = "log_archive.zip:std*@disk=1 root_archive.zip:*.root@disk=2";
c57f56b7 1615 fOutputFiles = ""; // Like "AliAODs.root histos.root"
1616 fInputFormat = "xml-single";
1617 fJDLName = "analysis.jdl";
c6cb3634 1618 fJobTag = "Automatically generated analysis JDL";
bb885a9e 1619 fMergeExcludes = "";
0f389141 1620 fMergeViaJDL = 0;
348be253 1621 SetUseCopy(kTRUE);
1622 SetCheckCopy(kTRUE);
149d288c 1623 SetDefaultOutputs(kTRUE);
e1c22e21 1624 fOverwriteMode = 1;
c57f56b7 1625}
1626
1627//______________________________________________________________________________
7c2cd90a 1628Bool_t AliAnalysisAlien::CheckMergedFiles(const char *filename, const char *aliendir, Int_t nperchunk, Bool_t submit, const char *jdl)
0f389141 1629{
7c2cd90a 1630// Static method that checks the status of merging. This can submit merging jobs that did not produced the expected
1631// output. If <submit> is false (checking) returns true only when the final merged file was found. If submit is true returns
1632// true if the jobs were successfully submitted.
1633 Int_t countOrig = 0;
1634 Int_t countStage = 0;
1635 Int_t stage = 0;
1636 Int_t i;
1637 Bool_t doneFinal = kFALSE;
1638 TBits chunksDone;
1639 TString saliendir(aliendir);
1640 TString sfilename, stmp;
1641 saliendir.ReplaceAll("//","/");
1642 saliendir = saliendir.Strip(TString::kTrailing, '/');
1643 if (!gGrid) {
1644 ::Error("GetNregisteredFiles", "You need to be connected to AliEn.");
1645 return kFALSE;
1646 }
0cdf65a8 1647 sfilename = filename;
1648 sfilename.ReplaceAll(".root", "*.root");
1649 printf("Checking directory <%s> for merged files <%s> ...\n", aliendir, sfilename.Data());
1650 TString command = Form("find %s/ *%s", saliendir.Data(), sfilename.Data());
7c2cd90a 1651 TGridResult *res = gGrid->Command(command);
1652 if (!res) {
1653 ::Error("GetNregisteredFiles","Error: No result for the find command\n");
1654 return kFALSE;
1655 }
1656 TIter nextmap(res);
1657 TMap *map = 0;
1658 while ((map=(TMap*)nextmap())) {
1659 TString turl = map->GetValue("turl")->GetName();
1660 if (!turl.Length()) {
1661 // Nothing found
1662 delete res;
1663 return kFALSE;
1664 }
1665 turl.ReplaceAll("alien://", "");
1666 turl.ReplaceAll(saliendir, "");
1667 sfilename = gSystem->BaseName(turl);
0cdf65a8 1668 turl = turl.Strip(TString::kLeading, '/');
7c2cd90a 1669 // Now check to what the file corresponds to:
1670 // original output - aliendir/%03d/filename
1671 // merged file (which stage) - aliendir/filename-Stage%02d_%04d
1672 // final merged file - aliendir/filename
1673 if (sfilename == turl) {
1674 if (sfilename == filename) {
1675 doneFinal = kTRUE;
1676 } else {
1677 // check stage
1678 Int_t index = sfilename.Index("Stage");
1679 if (index<0) continue;
1680 stmp = sfilename(index+5,2);
1681 Int_t istage = atoi(stmp);
1682 stmp = sfilename(index+8,4);
1683 Int_t ijob = atoi(stmp);
1684 if (istage<stage) continue; // Ignore lower stages
1685 if (istage>stage) {
1686 countStage = 0;
1687 chunksDone.ResetAllBits();
1688 stage = istage;
1689 }
1690 countStage++;
1691 chunksDone.SetBitNumber(ijob);
1692 }
1693 } else {
1694 countOrig++;
1695 }
1696 if (doneFinal) {
1697 delete res;
0cdf65a8 1698 printf("=> Removing files from previous stages...\n");
1699 gGrid->Rm(Form("%s/*Stage*.root", aliendir));
7a62d541 1700 for (i=1; i<stage; i++)
1701 gGrid->Rm(Form("%s/*Stage%d*.zip", aliendir, i));
7c2cd90a 1702 return kTRUE;
1703 }
1704 }
1705 delete res;
1706 // Compute number of jobs that were submitted for the current stage
1707 Int_t ntotstage = countOrig;
7ae54d70 1708 for (i=1; i<=stage; i++) {
1709 if (ntotstage%nperchunk) ntotstage = (ntotstage/nperchunk)+1;
1710 else ntotstage = (ntotstage/nperchunk);
1711 }
7c2cd90a 1712 // Now compare with the number of set bits in the chunksDone array
1713 Int_t nmissing = (stage>0)?(ntotstage - countStage):0;
1714 // Print the info
1715 printf("*** Found %d original files\n", countOrig);
1716 if (stage==0) printf("*** No merging completed so far.\n");
1717 else printf("*** Found %d out of %d files merged for stage %d\n", countStage, ntotstage, stage);
1718 if (nmissing) printf("*** Number of merged files missing for this stage: %d -> check merging job completion\n", nmissing);
7c2cd90a 1719 if (!submit) return doneFinal;
1720 // Sumbit merging jobs for all missing chunks for the current stage.
1721 TString query = Form("submit %s %s", jdl, aliendir);
1722 Int_t ichunk = -1;
1723 if (nmissing) {
1724 for (i=0; i<nmissing; i++) {
1725 ichunk = chunksDone.FirstNullBit(ichunk+1);
1726 Int_t jobId = SubmitSingleJob(Form("%s %d %d", query.Data(), stage, ichunk));
1727 if (!jobId) return kFALSE;
1728 }
1729 return kTRUE;
1730 }
1731 // Submit next stage of merging
1732 if (stage==0) countStage = countOrig;
7ae54d70 1733 Int_t nchunks = (countStage/nperchunk);
1734 if (countStage%nperchunk) nchunks += 1;
7c2cd90a 1735 for (i=0; i<nchunks; i++) {
1736 Int_t jobId = SubmitSingleJob(Form("%s %d %d", query.Data(), stage+1, i));
1737 if (!jobId) return kFALSE;
1738 }
1739 return kTRUE;
1740}
1741
1742//______________________________________________________________________________
1743Int_t AliAnalysisAlien::SubmitSingleJob(const char *query)
1744{
1745// Submits a single job corresponding to the query and returns job id. If 0 submission failed.
1746 if (!gGrid) return 0;
1747 printf("=> %s ------> ",query);
1748 TGridResult *res = gGrid->Command(query);
1749 if (!res) return 0;
1750 TString jobId = res->GetKey(0,"jobId");
1751 delete res;
1752 if (jobId.IsNull()) {
1753 printf("submission failed. Reason:\n");
1754 gGrid->Stdout();
1755 gGrid->Stderr();
1756 ::Error("SubmitSingleJob", "Your query %s could not be submitted", query);
1757 return 0;
1758 }
1759 printf(" Job id: %s\n", jobId.Data());
1760 return atoi(jobId);
1761}
1762
1763//______________________________________________________________________________
1764Bool_t AliAnalysisAlien::MergeOutput(const char *output, const char *basedir, Int_t nmaxmerge, Int_t stage, Int_t ichunk)
1765{
1766// Merge given output files from basedir. The file merger will merge nmaxmerge
1767// files in a group. Merging can be done in stages:
1768// stage=0 : will merge all existing files in a single stage
1769// stage=1 : does a find command for all files that do NOT contain the string "Stage".
1770// If their number is bigger that nmaxmerge, only the files from
1771// ichunk*nmaxmerge to ichunk*(nmaxmerge+1)-1 will get merged as output_stage_<ichunk>
1772// stage=n : does a find command for files named <output>Stage<stage-1>_*. If their number is bigger than
1773// nmaxmerge, merge just the chunk ichunk, otherwise write the merged output to the file
1774// named <output>.
a2f5fc01 1775 TString outputFile = output;
0f389141 1776 TString command;
a2f5fc01 1777 TString outputChunk;
1778 TString previousChunk = "";
1779 Int_t countChunk = 0;
1780 Int_t countZero = nmaxmerge;
0f389141 1781 Bool_t merged = kTRUE;
a2f5fc01 1782 Int_t index = outputFile.Index("@");
1783 if (index > 0) outputFile.Remove(index);
7c2cd90a 1784 TString inputFile = outputFile;
1785 if (stage>1) inputFile.ReplaceAll(".root", Form("-Stage%02d_*.root", stage-1));
1786 command = Form("find %s/ *%s", basedir, inputFile.Data());
0f389141 1787 printf("command: %s\n", command.Data());
1788 TGridResult *res = gGrid->Command(command);
1789 if (!res) {
7c2cd90a 1790 ::Error("MergeOutput","No result for the find command\n");
0f389141 1791 return kFALSE;
1792 }
1793
1794 TFileMerger *fm = 0;
1795 TIter nextmap(res);
1796 TMap *map = 0;
7c2cd90a 1797 // Check if there is a merge operation to resume. Works only for stage 0 or 1.
a2f5fc01 1798 outputChunk = outputFile;
1799 outputChunk.ReplaceAll(".root", "_*.root");
0f389141 1800 // Check for existent temporary merge files
e1c22e21 1801 // Check overwrite mode and remove previous partial results if needed
7c2cd90a 1802 // Preserve old merging functionality for stage 0.
1803 if (stage==0) {
1804 if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
1805 while (1) {
1806 // Skip as many input files as in a chunk
1807 for (Int_t counter=0; counter<nmaxmerge; counter++) map = (TMap*)nextmap();
1808 if (!map) {
1809 ::Error("MergeOutput", "Cannot resume merging for <%s>, nentries=%d", outputFile.Data(), res->GetSize());
1810 delete res;
1811 return kFALSE;
1812 }
1813 outputChunk = outputFile;
1814 outputChunk.ReplaceAll(".root", Form("_%04d.root", countChunk));
1815 countChunk++;
1816 if (gSystem->AccessPathName(outputChunk)) continue;
1817 // Merged file with chunks up to <countChunk> found
1818 ::Info("MergeOutput", "Resume merging of <%s> from <%s>\n", outputFile.Data(), outputChunk.Data());
1819 previousChunk = outputChunk;
1820 break;
1821 }
1822 }
1823 countZero = nmaxmerge;
1824
1825 while ((map=(TMap*)nextmap())) {
1826 // Loop 'find' results and get next LFN
1827 if (countZero == nmaxmerge) {
1828 // First file in chunk - create file merger and add previous chunk if any.
1829 fm = new TFileMerger(kFALSE);
1830 fm->SetFastMethod(kTRUE);
1831 if (previousChunk.Length()) fm->AddFile(previousChunk.Data());
1832 outputChunk = outputFile;
1833 outputChunk.ReplaceAll(".root", Form("_%04d.root", countChunk));
1834 }
1835 // If last file found, put merged results in the output file
1836 if (map == res->Last()) outputChunk = outputFile;
1837 TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl"));
1838 if (!objs || !objs->GetString().Length()) {
1839 // Nothing found - skip this output
0f389141 1840 delete res;
7c2cd90a 1841 delete fm;
0f389141 1842 return kFALSE;
7c2cd90a 1843 }
1844 // Add file to be merged and decrement chunk counter.
1845 fm->AddFile(objs->GetString());
1846 countZero--;
1847 if (countZero==0 || map == res->Last()) {
1848 if (!fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
1849 // Nothing found - skip this output
1850 ::Warning("MergeOutput", "No <%s> files found.", inputFile.Data());
1851 delete res;
1852 delete fm;
1853 return kFALSE;
1854 }
1855 fm->OutputFile(outputChunk);
1856 // Merge the outputs, then go to next chunk
1857 if (!fm->Merge()) {
1858 ::Error("MergeOutput", "Could not merge all <%s> files", outputFile.Data());
1859 delete res;
1860 delete fm;
1861 return kFALSE;
1862 } else {
1863 ::Info("MergeOutputs", "\n##### Merged %d output files to <%s>", fm->GetMergeList()->GetSize(), outputChunk.Data());
1864 gSystem->Unlink(previousChunk);
1865 }
1866 if (map == res->Last()) {
1867 delete res;
1868 delete fm;
1869 break;
1870 }
1871 countChunk++;
1872 countZero = nmaxmerge;
1873 previousChunk = outputChunk;
0f389141 1874 }
0f389141 1875 }
7c2cd90a 1876 return merged;
1877 }
1878 // Merging stage different than 0.
1879 // Move to the begining of the requested chunk.
1880 outputChunk = outputFile;
1881 if (nmaxmerge < res->GetSize()) {
1882 if (ichunk*nmaxmerge >= res->GetSize()) {
1883 ::Error("MergeOutput", "Cannot merge merge chunk %d grouping %d files from %d total.", ichunk, nmaxmerge, res->GetSize());
1884 delete res;
1885 return kFALSE;
1886 }
1887 for (Int_t counter=0; counter<ichunk*nmaxmerge; counter++) map = (TMap*)nextmap();
1888 outputChunk.ReplaceAll(".root", Form("-Stage%02d_%04d.root", stage, ichunk));
1889 }
1890 countZero = nmaxmerge;
1891 fm = new TFileMerger(kFALSE);
1892 fm->SetFastMethod(kTRUE);
0f389141 1893 while ((map=(TMap*)nextmap())) {
7c2cd90a 1894 // Loop 'find' results and get next LFN
0f389141 1895 TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl"));
1896 if (!objs || !objs->GetString().Length()) {
1897 // Nothing found - skip this output
1898 delete res;
1899 delete fm;
1900 return kFALSE;
1901 }
1902 // Add file to be merged and decrement chunk counter.
1903 fm->AddFile(objs->GetString());
a2f5fc01 1904 countZero--;
7c2cd90a 1905 if (countZero==0) break;
1906 }
1907 delete res;
1908 if (!fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
1909 // Nothing found - skip this output
1910 ::Warning("MergeOutput", "No <%s> files found.", inputFile.Data());
1911 delete fm;
1912 return kFALSE;
1913 }
1914 fm->OutputFile(outputChunk);
1915 // Merge the outputs
1916 if (!fm->Merge()) {
1917 ::Error("MergeOutput", "Could not merge all <%s> files", outputFile.Data());
1918 delete fm;
1919 return kFALSE;
1920 } else {
1921 ::Info("MergeOutput", "\n##### Merged %d output files to <%s>", fm->GetMergeList()->GetSize(), outputChunk.Data());
0f389141 1922 }
7c2cd90a 1923 delete fm;
1924 return kTRUE;
0f389141 1925}
1926
1927//______________________________________________________________________________
c57f56b7 1928Bool_t AliAnalysisAlien::MergeOutputs()
1929{
1930// Merge analysis outputs existing in the AliEn space.
1931 if (TestBit(AliAnalysisGrid::kTest)) return kTRUE;
1932 if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
1933 if (!Connect()) {
1934 Error("MergeOutputs", "Cannot merge outputs without grid connection. Terminate will NOT be executed");
1935 return kFALSE;
0f389141 1936 }
c9e8f7fd 1937 if (fMergeViaJDL) {
1938 if (!TestBit(AliAnalysisGrid::kMerge)) {
1939 Info("MergeOutputs", "### Re-run with <MergeViaJDL> option in terminate mode of the plugin to submit merging jobs ###");
1940 return kFALSE;
1941 }
1942 if (fProductionMode) {
1943 Info("MergeOutputs", "### Merging will be submitted by LPM manager... ###");
1944 return kFALSE;
1945 }
0f389141 1946 Info("MergeOutputs", "Submitting merging JDL");
a03be957 1947 if (!SubmitMerging()) return kFALSE;
0f389141 1948 Info("MergeOutputs", "### Re-run with <MergeViaJDL> off to collect results after merging jobs are done ###");
c9e8f7fd 1949 Info("MergeOutputs", "### The Terminate() method is executed by the merging jobs");
001cb79e 1950 return kFALSE;
c57f56b7 1951 }
1952 // Get the output path
d2a409b2 1953 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
923e2ca5 1954 if (!DirectoryExists(fGridOutputDir)) {
c57f56b7 1955 Error("MergeOutputs", "Grid output directory %s not found. Terminate() will NOT be executed", fGridOutputDir.Data());
1956 return kFALSE;
1957 }
1958 if (!fOutputFiles.Length()) {
1959 Error("MergeOutputs", "No output file names defined. Are you running the right AliAnalysisAlien configuration ?");
1960 return kFALSE;
0f389141 1961 }
1962 // Check if fast read option was requested
e1c22e21 1963 Info("MergeOutputs", "Started local merging of output files from: alien://%s \
1964 \n======= overwrite mode = %d", fGridOutputDir.Data(), (Int_t)fOverwriteMode);
0f389141 1965 if (fFastReadOption) {
d3339be3 1966 Warning("MergeOutputs", "You requested FastRead option. Using xrootd flags to reduce timeouts. This may skip some files that could be accessed ! \
1967 \n+++ NOTE: To disable this option, use: plugin->SetFastReadOption(kFALSE)");
1968 gEnv->SetValue("XNet.ConnectTimeout",10);
1969 gEnv->SetValue("XNet.RequestTimeout",10);
0f389141 1970 gEnv->SetValue("XNet.MaxRedirectCount",2);
d3339be3 1971 gEnv->SetValue("XNet.ReconnectTimeout",10);
0f389141 1972 gEnv->SetValue("XNet.FirstConnectMaxCnt",1);
c57f56b7 1973 }
e8b839ab 1974 // Make sure we change the temporary directory
1975 gSystem->Setenv("TMPDIR", gSystem->pwd());
149d288c 1976 TObjArray *list = fOutputFiles.Tokenize(",");
c57f56b7 1977 TIter next(list);
1978 TObjString *str;
a2f5fc01 1979 TString outputFile;
c57f56b7 1980 Bool_t merged = kTRUE;
1981 while((str=(TObjString*)next())) {
a2f5fc01 1982 outputFile = str->GetString();
1983 Int_t index = outputFile.Index("@");
1984 if (index > 0) outputFile.Remove(index);
1985 TString outputChunk = outputFile;
1986 outputChunk.ReplaceAll(".root", "_*.root");
319593fb 1987 // Skip already merged outputs
a2f5fc01 1988 if (!gSystem->AccessPathName(outputFile)) {
e1c22e21 1989 if (fOverwriteMode) {
a2f5fc01 1990 Info("MergeOutputs", "Overwrite mode. Existing file %s was deleted.", outputFile.Data());
1991 gSystem->Unlink(outputFile);
1992 if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
e1c22e21 1993 Info("MergeOutput", "Overwrite mode: partial merged files %s will removed",
a2f5fc01 1994 outputChunk.Data());
1995 gSystem->Exec(Form("rm -f %s", outputChunk.Data()));
e1c22e21 1996 }
1997 } else {
a2f5fc01 1998 Info("MergeOutputs", "Output file <%s> found. Not merging again.", outputFile.Data());
e1c22e21 1999 continue;
2000 }
2001 } else {
a2f5fc01 2002 if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
e1c22e21 2003 Info("MergeOutput", "Overwrite mode: partial merged files %s will removed",
a2f5fc01 2004 outputChunk.Data());
2005 gSystem->Exec(Form("rm -f %s", outputChunk.Data()));
e1c22e21 2006 }
2007 }
bb885a9e 2008 if (fMergeExcludes.Length() &&
a2f5fc01 2009 fMergeExcludes.Contains(outputFile.Data())) continue;
16a4353c 2010 // Perform a 'find' command in the output directory, looking for registered outputs
a2f5fc01 2011 merged = MergeOutput(outputFile, fGridOutputDir, fMaxMergeFiles);
0f389141 2012 if (!merged) {
2013 Error("MergeOutputs", "Terminate() will NOT be executed");
2014 return kFALSE;
ff07ec61 2015 }
2016 TFile *fileOpened = (TFile*)gROOT->GetListOfFiles()->FindObject(outputFile);
2017 if (fileOpened) fileOpened->Close();
c57f56b7 2018 }
0f389141 2019 return kTRUE;
c57f56b7 2020}
2021
2022//______________________________________________________________________________
bb885a9e 2023void AliAnalysisAlien::SetDefaultOutputs(Bool_t flag)
2024{
2025// Use the output files connected to output containers from the analysis manager
2026// rather than the files defined by SetOutputFiles
2027 if (flag && !TObject::TestBit(AliAnalysisGrid::kDefaultOutputs))
205b201f 2028 Info("SetDefaultOutputs", "Plugin will use the output files taken from analysis manager");
bb885a9e 2029 TObject::SetBit(AliAnalysisGrid::kDefaultOutputs, flag);
2030}
2031
2032//______________________________________________________________________________
149d288c 2033void AliAnalysisAlien::SetOutputFiles(const char *list)
2034{
2035// Manually set the output files list.
2036// Removes duplicates. Not allowed if default outputs are not disabled.
2037 if (TObject::TestBit(AliAnalysisGrid::kDefaultOutputs)) {
2038 Fatal("SetOutputFiles", "You have to explicitly call SetDefaultOutputs(kFALSE) to manually set output files.");
2039 return;
2040 }
2041 Info("SetOutputFiles", "Output file list is set manually - you are on your own.");
2042 fOutputFiles = "";
2043 TString slist = list;
2044 if (slist.Contains("@")) Warning("SetOutputFiles","The plugin does not allow explicit SE's. Please use: SetNumberOfReplicas() instead.");
2045 TObjArray *arr = slist.Tokenize(" ");
2046 TObjString *os;
2047 TIter next(arr);
2048 TString sout;
2049 while ((os=(TObjString*)next())) {
2050 sout = os->GetString();
2051 if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
2052 if (fOutputFiles.Contains(sout)) continue;
2053 if (!fOutputFiles.IsNull()) fOutputFiles += ",";
2054 fOutputFiles += sout;
2055 }
2056 delete arr;
2057}
2058
2059//______________________________________________________________________________
2060void AliAnalysisAlien::SetOutputArchive(const char *list)
2061{
2062// Manually set the output archive list. Free text - you are on your own...
2063// Not allowed if default outputs are not disabled.
2064 if (TObject::TestBit(AliAnalysisGrid::kDefaultOutputs)) {
2065 Fatal("SetOutputArchive", "You have to explicitly call SetDefaultOutputs(kFALSE) to manually set the output archives.");
2066 return;
2067 }
2068 Info("SetOutputArchive", "Output archive is set manually - you are on your own.");
2069 fOutputArchive = list;
2070}
2071
2072//______________________________________________________________________________
2073void AliAnalysisAlien::SetPreferedSE(const char */*se*/)
2074{
2075// Setting a prefered output SE is not allowed anymore.
2076 Warning("SetPreferedSE", "Setting a preferential SE is not allowed anymore via the plugin. Use SetNumberOfReplicas() and SetDefaultOutputs()");
2077}
2078
2079//______________________________________________________________________________
5513444a 2080Bool_t AliAnalysisAlien::StartAnalysis(Long64_t /*nentries*/, Long64_t /*firstEntry*/)
c57f56b7 2081{
2082// Start remote grid analysis.
2083
43da816a 2084 // Check if output files have to be taken from the analysis manager
2085 if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
2086 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
2087 if (!mgr || !mgr->IsInitialized()) {
2088 Error("StartAnalysis", "You need an initialized analysis manager for this");
5513444a 2089 return kFALSE;
43da816a 2090 }
2091 fOutputFiles = "";
2092 TIter next(mgr->GetOutputs());
2093 AliAnalysisDataContainer *output;
2094 while ((output=(AliAnalysisDataContainer*)next())) {
2095 const char *filename = output->GetFileName();
2096 if (!(strcmp(filename, "default"))) {
2097 if (!mgr->GetOutputEventHandler()) continue;
2098 filename = mgr->GetOutputEventHandler()->GetOutputFileName();
2099 }
84fcd93f 2100 if (fOutputFiles.Contains(filename)) continue;
149d288c 2101 if (fOutputFiles.Length()) fOutputFiles += ",";
43da816a 2102 fOutputFiles += filename;
2103 }
c07b9ce2 2104 // Add extra files registered to the analysis manager
2105 if (mgr->GetExtraFiles().Length()) {
149d288c 2106 if (fOutputFiles.Length()) fOutputFiles += ",";
2107 TString extra = mgr->GetExtraFiles();
2108 extra.ReplaceAll(" ", ",");
2109 // Protection in case extra files do not exist (will it work?)
2110 extra.ReplaceAll(".root", "*.root");
2111 fOutputFiles += extra;
84fcd93f 2112 }
149d288c 2113 // Compose the output archive.
2114 fOutputArchive = "log_archive.zip:std*@disk=1 ";
2115 fOutputArchive += Form("root_archive.zip:%s@disk=%d",fOutputFiles.Data(),fNreplicas);
43da816a 2116 }
f7b1cbc2 2117// if (!fCloseSE.Length()) fCloseSE = gSystem->Getenv("alien_CLOSE_SE");
c57f56b7 2118 if (TestBit(AliAnalysisGrid::kOffline)) {
2119 Info("StartAnalysis","\n##### OFFLINE MODE ##### Files to be used in GRID are produced but not copied \
2120 \n there nor any job run. You can revise the JDL and analysis \
2121 \n macro then run the same in \"submit\" mode.");
2122 } else if (TestBit(AliAnalysisGrid::kTest)) {
2123 Info("StartAnalysis","\n##### LOCAL MODE ##### Your analysis will be run locally on a subset of the requested \
2124 \n dataset.");
2125 } else if (TestBit(AliAnalysisGrid::kSubmit)) {
2126 Info("StartAnalysis","\n##### SUBMIT MODE ##### Files required by your analysis are copied to your grid working \
2127 \n space and job submitted.");
2128 } else if (TestBit(AliAnalysisGrid::kMerge)) {
2129 Info("StartAnalysis","\n##### MERGE MODE ##### The registered outputs of the analysis will be merged");
0f389141 2130 if (fMergeViaJDL) CheckInputData();
5513444a 2131 return kTRUE;
c57f56b7 2132 } else {
2133 Info("StartAnalysis","\n##### FULL ANALYSIS MODE ##### Producing needed files and submitting your analysis job...");
2134 }
2135
348be253 2136 Print();
c57f56b7 2137 if (!Connect()) {
2138 Error("StartAnalysis", "Cannot start grid analysis without grid connection");
5513444a 2139 return kFALSE;
16a4353c 2140 }
348be253 2141 if (IsCheckCopy()) CheckFileCopy(gGrid->GetHomeDirectory());
c57f56b7 2142 if (!CheckInputData()) {
2143 Error("StartAnalysis", "There was an error in preprocessing your requested input data");
5513444a 2144 return kFALSE;
c57f56b7 2145 }
d3339be3 2146 if (!CreateDataset(fDataPattern)) {
2147 TString serror;
2148 if (!fRunNumbers.Length() && !fRunRange[0]) serror = Form("path to data directory: <%s>", fGridDataDir.Data());
2149 if (fRunNumbers.Length()) serror = "run numbers";
2150 if (fRunRange[0]) serror = Form("run range [%d, %d]", fRunRange[0], fRunRange[1]);
2151 serror += Form("\n or data pattern <%s>", fDataPattern.Data());
2152 Error("StartAnalysis", "No data to process. Please fix %s in your plugin configuration.", serror.Data());
2153 return kFALSE;
2154 }
c57f56b7 2155 WriteAnalysisFile();
2156 WriteAnalysisMacro();
2157 WriteExecutable();
2158 WriteValidationScript();
0f389141 2159 if (fMergeViaJDL) {
2160 WriteMergingMacro();
2161 WriteMergeExecutable();
2162 WriteValidationScript(kTRUE);
2163 }
5513444a 2164 if (!CreateJDL()) return kFALSE;
2165 if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
c57f56b7 2166 if (TestBit(AliAnalysisGrid::kTest)) {
2167 // Locally testing the analysis
2168 Info("StartAnalysis", "\n_______________________________________________________________________ \
2169 \n Running analysis script in a daughter shell as on a worker node \
2170 \n_______________________________________________________________________");
149d288c 2171 TObjArray *list = fOutputFiles.Tokenize(",");
c57f56b7 2172 TIter next(list);
2173 TObjString *str;
a2f5fc01 2174 TString outputFile;
c57f56b7 2175 while((str=(TObjString*)next())) {
a2f5fc01 2176 outputFile = str->GetString();
2177 Int_t index = outputFile.Index("@");
2178 if (index > 0) outputFile.Remove(index);
2179 if (!gSystem->AccessPathName(outputFile)) gSystem->Exec(Form("rm %s", outputFile.Data()));
c57f56b7 2180 }
2181 delete list;
2182 gSystem->Exec(Form("bash %s 2>stderr", fExecutable.Data()));
0d5d317c 2183 TString validationScript = fExecutable;
2184 validationScript.ReplaceAll(".sh", "_validation.sh");
2185 gSystem->Exec(Form("bash %s",validationScript.Data()));
c57f56b7 2186// gSystem->Exec("cat stdout");
5513444a 2187 return kFALSE;
c57f56b7 2188 }
5513444a 2189 // Check if submitting is managed by LPM manager
a3e84053 2190 if (fProductionMode) {
5513444a 2191 TString prodfile = fJDLName;
2192 prodfile.ReplaceAll(".jdl", ".prod");
2193 WriteProductionFile(prodfile);
2194 Info("StartAnalysis", "Job submitting is managed by LPM. Rerun in terminate mode after jobs finished.");
2195 return kFALSE;
2196 }
a8739e8a 2197 // Submit AliEn job(s)
d2a409b2 2198 gGrid->Cd(fGridOutputDir);
a8739e8a 2199 TGridResult *res;
c57f56b7 2200 TString jobID = "";
d2a409b2 2201 if (!fRunNumbers.Length() && !fRunRange[0]) {
dd74a515 2202 // Submit a given xml or a set of runs
a8739e8a 2203 res = gGrid->Command(Form("submit %s", fJDLName.Data()));
84fcd93f 2204 printf("*************************** %s\n",Form("submit %s", fJDLName.Data()));
a8739e8a 2205 if (res) {
2206 const char *cjobId = res->GetKey(0,"jobId");
2207 if (!cjobId) {
a03be957 2208 gGrid->Stdout();
2209 gGrid->Stderr();
a8739e8a 2210 Error("StartAnalysis", "Your JDL %s could not be submitted", fJDLName.Data());
5513444a 2211 return kFALSE;
a8739e8a 2212 } else {
2213 Info("StartAnalysis", "\n_______________________________________________________________________ \
2214 \n##### Your JDL %s was successfully submitted. \nTHE JOB ID IS: %s \
2215 \n_______________________________________________________________________",
2216 fJDLName.Data(), cjobId);
2217 jobID = cjobId;
2218 }
2219 delete res;
a03be957 2220 } else {
2221 Error("StartAnalysis", "No grid result after submission !!! Bailing out...");
2222 return kFALSE;
a8739e8a 2223 }
2224 } else {
d2a409b2 2225 // Submit for a range of enumeration of runs.
a03be957 2226 if (!Submit()) return kFALSE;
c57f56b7 2227 }
a8739e8a 2228
c57f56b7 2229 Info("StartAnalysis", "\n#### STARTING AN ALIEN SHELL FOR YOU. EXIT WHEN YOUR JOB %s HAS FINISHED. #### \
2230 \n You may exit at any time and terminate the job later using the option <terminate> \
2231 \n ##################################################################################", jobID.Data());
bb885a9e 2232 gSystem->Exec("aliensh");
5513444a 2233 return kTRUE;
c57f56b7 2234}
2235
2236//______________________________________________________________________________
a03be957 2237Bool_t AliAnalysisAlien::Submit()
d2a409b2 2238{
2239// Submit all master jobs.
2240 Int_t nmasterjobs = fInputFiles->GetEntries();
2241 Long_t tshoot = gSystem->Now();
a03be957 2242 if (!fNsubmitted && !SubmitNext()) return kFALSE;
d2a409b2 2243 while (fNsubmitted < nmasterjobs) {
2244 Long_t now = gSystem->Now();
2245 if ((now-tshoot)>30000) {
2246 tshoot = now;
a03be957 2247 if (!SubmitNext()) return kFALSE;
d2a409b2 2248 }
2249 }
a03be957 2250 return kTRUE;
d2a409b2 2251}
2252
2253//______________________________________________________________________________
a03be957 2254Bool_t AliAnalysisAlien::SubmitMerging()
0f389141 2255{
2256// Submit all merging jobs.
2257 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
2258 gGrid->Cd(fGridOutputDir);
2259 TString mergeJDLName = fExecutable;
2260 mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
2261 Int_t ntosubmit = fInputFiles->GetEntries();
0f389141 2262 for (Int_t i=0; i<ntosubmit; i++) {
f866cba5 2263 TString runOutDir = gSystem->BaseName(fInputFiles->At(i)->GetName());
2264 runOutDir.ReplaceAll(".xml", "");
7c2cd90a 2265 if (fOutputToRunNo) {
2266 // The output directory is the run number
2267 printf("### Submitting merging job for run <%s>\n", runOutDir.Data());
2268 runOutDir = Form("%s/%s", fGridOutputDir.Data(), runOutDir.Data());
2269 } else {
2270 // The output directory is the master number in 3 digits format
2271 printf("### Submitting merging job for master <%03d>\n", i);
2272 runOutDir = Form("%s/%03d",fGridOutputDir.Data(), i);
2273 }
2274 // Check now the number of merging stages.
2b222f7c 2275 TObjArray *list = fOutputFiles.Tokenize(",");
2276 TIter next(list);
2277 TObjString *str;
2278 TString outputFile;
2279 while((str=(TObjString*)next())) {
2280 outputFile = str->GetString();
2281 Int_t index = outputFile.Index("@");
2282 if (index > 0) outputFile.Remove(index);
2283 if (!fMergeExcludes.Contains(outputFile)) break;
2284 }
2285 delete list;
7c2cd90a 2286 Bool_t done = CheckMergedFiles(outputFile, runOutDir, fMaxMergeFiles, kTRUE, mergeJDLName);
2287 if (!done) return kFALSE;
0f389141 2288 }
a03be957 2289 if (!ntosubmit) return kTRUE;
0f389141 2290 Info("StartAnalysis", "\n#### STARTING AN ALIEN SHELL FOR YOU. EXIT WHEN YOUR MERGING JOBS HAVE FINISHED. #### \
2291 \n You may exit at any time and terminate the job later using the option <terminate> but disabling SetMergeViaJDL\
2292 \n ##################################################################################");
2293 gSystem->Exec("aliensh");
a03be957 2294 return kTRUE;
0f389141 2295}
2296
2297//______________________________________________________________________________
a03be957 2298Bool_t AliAnalysisAlien::SubmitNext()
d2a409b2 2299{
08d5b699 2300// Submit next bunch of master jobs if the queue is free. The first master job is
2301// submitted right away, while the next will not be unless the previous was split.
2302// The plugin will not submit new master jobs if there are more that 500 jobs in
2303// waiting phase.
d2a409b2 2304 static Bool_t iscalled = kFALSE;
2305 static Int_t firstmaster = 0;
2306 static Int_t lastmaster = 0;
2307 static Int_t npermaster = 0;
a03be957 2308 if (iscalled) return kTRUE;
d2a409b2 2309 iscalled = kTRUE;
2310 Int_t nrunning=0, nwaiting=0, nerror=0, ndone=0;
2311 Int_t ntosubmit = 0;
2312 TGridResult *res;
2313 TString jobID = "";
2314 if (!fNsubmitted) ntosubmit = 1;
2315 else {
2316 TString status = GetJobStatus(firstmaster, lastmaster, nrunning, nwaiting, nerror, ndone);
84fcd93f 2317 printf("=== master %d: %s\n", lastmaster, status.Data());
d2a409b2 2318 // If last master not split, just return
a03be957 2319 if (status != "SPLIT") {iscalled = kFALSE; return kTRUE;}
d2a409b2 2320 // No more than 100 waiting jobs
08d5b699 2321 if (nwaiting>500) {iscalled = kFALSE; return kTRUE;}
d2a409b2 2322 npermaster = (nrunning+nwaiting+nerror+ndone)/fNsubmitted;
08d5b699 2323 if (npermaster) ntosubmit = (500-nwaiting)/npermaster;
7586eedc 2324 if (!ntosubmit) ntosubmit = 1;
84fcd93f 2325 printf("=== WAITING(%d) RUNNING(%d) DONE(%d) OTHER(%d) NperMaster=%d => to submit %d jobs\n",
d2a409b2 2326 nwaiting, nrunning, ndone, nerror, npermaster, ntosubmit);
2327 }
2328 Int_t nmasterjobs = fInputFiles->GetEntries();
2329 for (Int_t i=0; i<ntosubmit; i++) {
2330 // Submit for a range of enumeration of runs.
a03be957 2331 if (fNsubmitted>=nmasterjobs) {iscalled = kFALSE; return kTRUE;}
d2a409b2 2332 TString query;
cd11251e 2333 TString runOutDir = gSystem->BaseName(fInputFiles->At(fNsubmitted)->GetName());
2334 runOutDir.ReplaceAll(".xml", "");
2335 if (fOutputToRunNo)
2336 query = Form("submit %s %s %s", fJDLName.Data(), fInputFiles->At(fNsubmitted)->GetName(), runOutDir.Data());
2337 else
2338 query = Form("submit %s %s %03d", fJDLName.Data(), fInputFiles->At(fNsubmitted)->GetName(), fNsubmitted);
84fcd93f 2339 printf("********* %s\n",query.Data());
d2a409b2 2340 res = gGrid->Command(query);
2341 if (res) {
98ca124f 2342 TString cjobId1 = res->GetKey(0,"jobId");
2343 if (!cjobId1.Length()) {
d2a409b2 2344 iscalled = kFALSE;
a03be957 2345 gGrid->Stdout();
2346 gGrid->Stderr();
2347 Error("StartAnalysis", "Your JDL %s could not be submitted. The message was:", fJDLName.Data());
2348 return kFALSE;
d2a409b2 2349 } else {
2350 Info("StartAnalysis", "\n_______________________________________________________________________ \
2351 \n##### Your JDL %s submitted (%d to go). \nTHE JOB ID IS: %s \
2352 \n_______________________________________________________________________",
98ca124f 2353 fJDLName.Data(), nmasterjobs-fNsubmitted-1, cjobId1.Data());
d2a409b2 2354 jobID += cjobId1;
2355 jobID += " ";
98ca124f 2356 lastmaster = cjobId1.Atoi();
d2a409b2 2357 if (!firstmaster) firstmaster = lastmaster;
2358 fNsubmitted++;
2359 }
2360 delete res;
a03be957 2361 } else {
2362 Error("StartAnalysis", "No grid result after submission !!! Bailing out...");
2363 return kFALSE;
d2a409b2 2364 }
2365 }
2366 iscalled = kFALSE;
a03be957 2367 return kTRUE;
d2a409b2 2368}
2369
2370//______________________________________________________________________________
c57f56b7 2371void AliAnalysisAlien::WriteAnalysisFile()
2372{
f10e8481 2373// Write current analysis manager into the file <analysisFile>
2374 TString analysisFile = fExecutable;
2375 analysisFile.ReplaceAll(".sh", ".root");
c57f56b7 2376 if (!TestBit(AliAnalysisGrid::kSubmit)) {
2377 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
2378 if (!mgr || !mgr->IsInitialized()) {
2379 Error("WriteAnalysisFile", "You need an initialized analysis manager for this");
2380 return;
2381 }
2382 // Check analysis type
2383 TObject *handler;
2384 if (mgr->GetMCtruthEventHandler()) TObject::SetBit(AliAnalysisGrid::kUseMC);
2385 handler = (TObject*)mgr->GetInputEventHandler();
2386 if (handler) {
2387 if (handler->InheritsFrom("AliESDInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseESD);
2388 if (handler->InheritsFrom("AliAODInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseAOD);
2389 }
2390 TDirectory *cdir = gDirectory;
f10e8481 2391 TFile *file = TFile::Open(analysisFile, "RECREATE");
c57f56b7 2392 if (file) {
e16a394c 2393 // Skip task Terminate calls for the grid job (but not in test mode, where we want to check also the terminate mode
2394 if (!TestBit(AliAnalysisGrid::kTest)) mgr->SetSkipTerminate(kTRUE);
fe2d7fc2 2395 // Unless merging makes no sense
2396 if (IsSingleOutput()) mgr->SetSkipTerminate(kFALSE);
c57f56b7 2397 mgr->Write();
2398 delete file;
fe2d7fc2 2399 // Enable termination for local jobs
2400 mgr->SetSkipTerminate(kFALSE);
c57f56b7 2401 }
2402 if (cdir) cdir->cd();
f10e8481 2403 Info("WriteAnalysisFile", "\n##### Analysis manager: %s wrote to file <%s>\n", mgr->GetName(),analysisFile.Data());
c57f56b7 2404 }
2405 Bool_t copy = kTRUE;
2406 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
2407 if (copy) {
2408 CdWork();
2409 TString workdir = gGrid->GetHomeDirectory();
2410 workdir += fGridWorkingDir;
f10e8481 2411 Info("CreateJDL", "\n##### Copying file <%s> containing your initialized analysis manager to your alien workspace", analysisFile.Data());
2412 if (FileExists(analysisFile)) gGrid->Rm(analysisFile);
2413 TFile::Cp(Form("file:%s",analysisFile.Data()), Form("alien://%s/%s", workdir.Data(),analysisFile.Data()));
c57f56b7 2414 }
2415}
2416
2417//______________________________________________________________________________
2418void AliAnalysisAlien::WriteAnalysisMacro()
2419{
2420// Write the analysis macro that will steer the analysis in grid mode.
2421 if (!TestBit(AliAnalysisGrid::kSubmit)) {
2422 ofstream out;
2423 out.open(fAnalysisMacro.Data(), ios::out);
2424 if (!out.good()) {
2425 Error("WriteAnalysisMacro", "could not open file %s for writing", fAnalysisMacro.Data());
2426 return;
2427 }
5b273635 2428 Bool_t hasSTEERBase = kFALSE;
2429 Bool_t hasESD = kFALSE;
2430 Bool_t hasAOD = kFALSE;
2431 Bool_t hasANALYSIS = kFALSE;
2432 Bool_t hasANALYSISalice = kFALSE;
2433 Bool_t hasCORRFW = kFALSE;
c57f56b7 2434 TString func = fAnalysisMacro;
2435 TString type = "ESD";
2436 TString comment = "// Analysis using ";
2437 if (TObject::TestBit(AliAnalysisGrid::kUseESD)) comment += "ESD";
2438 if (TObject::TestBit(AliAnalysisGrid::kUseAOD)) {
2439 type = "AOD";
2440 comment += "AOD";
2441 }
0df6ccf2 2442 if (type!="AOD" && fFriendChainName!="") {
2443 Error("WriteAnalysisMacro", "Friend chain can be attached only to AOD");
2444 return;
2445 }
c57f56b7 2446 if (TObject::TestBit(AliAnalysisGrid::kUseMC)) comment += "/MC";
2447 else comment += " data";
2448 out << "const char *anatype = \"" << type.Data() << "\";" << endl << endl;
2449 func.ReplaceAll(".C", "");
2450 out << "void " << func.Data() << "()" << endl;
2451 out << "{" << endl;
2452 out << comment.Data() << endl;
2453 out << "// Automatically generated analysis steering macro executed in grid subjobs" << endl << endl;
f7498086 2454 out << " TStopwatch timer;" << endl;
2455 out << " timer.Start();" << endl << endl;
13f0c00b 2456 // Change temp directory to current one
2457 out << "// Set temporary merging directory to current one" << endl;
2458 out << " gSystem->Setenv(\"TMPDIR\", gSystem->pwd());" << endl << endl;
c57f56b7 2459 out << "// load base root libraries" << endl;
2460 out << " gSystem->Load(\"libTree\");" << endl;
2461 out << " gSystem->Load(\"libGeom\");" << endl;
2462 out << " gSystem->Load(\"libVMC\");" << endl;
2463 out << " gSystem->Load(\"libPhysics\");" << endl << endl;
648174cf 2464 out << " gSystem->Load(\"libMinuit\");" << endl << endl;
d5c6455a 2465 if (fAdditionalRootLibs.Length()) {
47a4137d 2466 // in principle libtree /lib geom libvmc etc. can go into this list, too
2467 out << "// Add aditional libraries" << endl;
2468 TObjArray *list = fAdditionalRootLibs.Tokenize(" ");
2469 TIter next(list);
2470 TObjString *str;
2471 while((str=(TObjString*)next())) {
2472 if (str->GetString().Contains(".so"))
2473 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
d5c6455a 2474 }
47a4137d 2475 if (list) delete list;
d5c6455a 2476 }
47a4137d 2477 out << "// include path" << endl;
2478 if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
2479 out << " gSystem->AddIncludePath(\"-I$ALICE_ROOT/include\");" << endl << endl;
57377eb5 2480 out << "// Load analysis framework libraries" << endl;
652561d5 2481 TString setupPar = "AliAnalysisAlien::SetupPar";
4e5c5506 2482 if (!fPackages) {
4e5c5506 2483 out << " gSystem->Load(\"libSTEERBase\");" << endl;
2484 out << " gSystem->Load(\"libESD\");" << endl;
2485 out << " gSystem->Load(\"libAOD\");" << endl;
2486 out << " gSystem->Load(\"libANALYSIS\");" << endl;
57377eb5 2487 out << " gSystem->Load(\"libANALYSISalice\");" << endl;
2488 out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
4e5c5506 2489 } else {
4e5c5506 2490 TIter next(fPackages);
2491 TObject *obj;
57377eb5 2492 TString pkgname;
57377eb5 2493 while ((obj=next())) {
2494 pkgname = obj->GetName();
4478e6f1 2495 if (pkgname == "STEERBase" ||
2496 pkgname == "STEERBase.par") hasSTEERBase = kTRUE;
2497 if (pkgname == "ESD" ||
2498 pkgname == "ESD.par") hasESD = kTRUE;
2499 if (pkgname == "AOD" ||
2500 pkgname == "AOD.par") hasAOD = kTRUE;
2501 if (pkgname == "ANALYSIS" ||
2502 pkgname == "ANALYSIS.par") hasANALYSIS = kTRUE;
2503 if (pkgname == "ANALYSISalice" ||
2504 pkgname == "ANALYSISalice.par") hasANALYSISalice = kTRUE;
2505 if (pkgname == "CORRFW" ||
2506 pkgname == "CORRFW.par") hasCORRFW = kTRUE;
5b273635 2507 }
2508 if (hasANALYSISalice) setupPar = "SetupPar";
57377eb5 2509 if (!hasSTEERBase) out << " gSystem->Load(\"libSTEERBase\");" << endl;
5b273635 2510 else out << " if (!" << setupPar << "(\"STEERBase\")) return;" << endl;
57377eb5 2511 if (!hasESD) out << " gSystem->Load(\"libESD\");" << endl;
5b273635 2512 else out << " if (!" << setupPar << "(\"ESD\")) return;" << endl;
57377eb5 2513 if (!hasAOD) out << " gSystem->Load(\"libAOD\");" << endl;
5b273635 2514 else out << " if (!" << setupPar << "(\"AOD\")) return;" << endl;
57377eb5 2515 if (!hasANALYSIS) out << " gSystem->Load(\"libANALYSIS\");" << endl;
5b273635 2516 else out << " if (!" << setupPar << "(\"ANALYSIS\")) return;" << endl;
57377eb5 2517 if (!hasANALYSISalice) out << " gSystem->Load(\"libANALYSISalice\");" << endl;
5b273635 2518 else out << " if (!" << setupPar << "(\"ANALYSISalice\")) return;" << endl;
57377eb5 2519 if (!hasCORRFW) out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
5b273635 2520 else out << " if (!" << setupPar << "(\"CORRFW\")) return;" << endl << endl;
57377eb5 2521 out << "// Compile other par packages" << endl;
2522 next.Reset();
fcc9bb6f 2523 while ((obj=next())) {
2524 pkgname = obj->GetName();
4478e6f1 2525 if (pkgname == "STEERBase" ||
2526 pkgname == "STEERBase.par" ||
2527 pkgname == "ESD" ||
2528 pkgname == "ESD.par" ||
2529 pkgname == "AOD" ||
2530 pkgname == "AOD.par" ||
2531 pkgname == "ANALYSIS" ||
2532 pkgname == "ANALYSIS.par" ||
2533 pkgname == "ANALYSISalice" ||
2534 pkgname == "ANALYSISalice.par" ||
2535 pkgname == "CORRFW" ||
2536 pkgname == "CORRFW.par") continue;
5b273635 2537 out << " if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
fcc9bb6f 2538 }
4e5c5506 2539 }
6da75e0b 2540 if (fAdditionalLibs.Length()) {
2541 out << "// Add aditional AliRoot libraries" << endl;
2542 TObjArray *list = fAdditionalLibs.Tokenize(" ");
2543 TIter next(list);
2544 TObjString *str;
2545 while((str=(TObjString*)next())) {
2546 if (str->GetString().Contains(".so"))
2547 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
652561d5 2548 if (str->GetString().Contains(".par"))
2549 out << " if (!" << setupPar << "(\"" << str->GetString() << "\")) return;" << endl;
6da75e0b 2550 }
2551 if (list) delete list;
2552 }
2553 out << endl;
c57f56b7 2554 out << "// analysis source to be compiled at runtime (if any)" << endl;
2555 if (fAnalysisSource.Length()) {
2556 TObjArray *list = fAnalysisSource.Tokenize(" ");
2557 TIter next(list);
2558 TObjString *str;
2559 while((str=(TObjString*)next())) {
2560 out << " gROOT->ProcessLine(\".L " << str->GetString().Data() << "+g\");" << endl;
2561 }
2562 if (list) delete list;
2563 }
2564 out << endl;
0f389141 2565 if (fFastReadOption) {
d3339be3 2566 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 !!! \
2567 \n+++ NOTE: To disable this option, use: plugin->SetFastReadOption(kFALSE)");
0f389141 2568 out << "// fast xrootd reading enabled" << endl;
2569 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 2570 out << " gEnv->SetValue(\"XNet.ConnectTimeout\",10);" << endl;
2571 out << " gEnv->SetValue(\"XNet.RequestTimeout\",10);" << endl;
0f389141 2572 out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
d3339be3 2573 out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",10);" << endl;
0f389141 2574 out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
2575 }
c57f56b7 2576 out << "// connect to AliEn and make the chain" << endl;
2577 out << " if (!TGrid::Connect(\"alien://\")) return;" << endl;
2578 if (IsUsingTags()) {
2579 out << " TChain *chain = CreateChainFromTags(\"wn.xml\", anatype);" << endl << endl;
2580 } else {
45e980c4 2581 out << " TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl;
c57f56b7 2582 }
2583 out << "// read the analysis manager from file" << endl;
f10e8481 2584 TString analysisFile = fExecutable;
2585 analysisFile.ReplaceAll(".sh", ".root");
2586 out << " TFile *file = TFile::Open(\"" << analysisFile << "\");" << endl;
c57f56b7 2587 out << " if (!file) return;" << endl;
2588 out << " TIter nextkey(file->GetListOfKeys());" << endl;
2589 out << " AliAnalysisManager *mgr = 0;" << endl;
2590 out << " TKey *key;" << endl;
2591 out << " while ((key=(TKey*)nextkey())) {" << endl;
2592 out << " if (!strcmp(key->GetClassName(), \"AliAnalysisManager\"))" << endl;
2593 out << " mgr = (AliAnalysisManager*)file->Get(key->GetName());" << endl;
2594 out << " };" << endl;
2595 out << " if (!mgr) {" << endl;
205b201f 2596 out << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file " << analysisFile <<"\");" << endl;
c57f56b7 2597 out << " return;" << endl;
2598 out << " }" << endl << endl;
2599 out << " mgr->PrintStatus();" << endl;
52b6a92b 2600 if (AliAnalysisManager::GetAnalysisManager()) {
f866cba5 2601 if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) {
52b6a92b 2602 out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
de52b69c 2603 } else {
2604 out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
52b6a92b 2605 }
2606 }
c57f56b7 2607 out << " mgr->StartAnalysis(\"localfile\", chain);" << endl;
f7498086 2608 out << " timer.Stop();" << endl;
2609 out << " timer.Print();" << endl;
c57f56b7 2610 out << "}" << endl << endl;
2611 if (IsUsingTags()) {
2612 out << "TChain* CreateChainFromTags(const char *xmlfile, const char *type=\"ESD\")" << endl;
2613 out << "{" << endl;
2614 out << "// Create a chain using tags from the xml file." << endl;
2615 out << " TAlienCollection* coll = TAlienCollection::Open(xmlfile);" << endl;
2616 out << " if (!coll) {" << endl;
2617 out << " ::Error(\"CreateChainFromTags\", \"Cannot create an AliEn collection from %s\", xmlfile);" << endl;
2618 out << " return NULL;" << endl;
2619 out << " }" << endl;
2620 out << " TGridResult* tagResult = coll->GetGridResult(\"\",kFALSE,kFALSE);" << endl;
2621 out << " AliTagAnalysis *tagAna = new AliTagAnalysis(type);" << endl;
2622 out << " tagAna->ChainGridTags(tagResult);" << endl << endl;
2623 out << " AliRunTagCuts *runCuts = new AliRunTagCuts();" << endl;
2624 out << " AliLHCTagCuts *lhcCuts = new AliLHCTagCuts();" << endl;
2625 out << " AliDetectorTagCuts *detCuts = new AliDetectorTagCuts();" << endl;
2626 out << " AliEventTagCuts *evCuts = new AliEventTagCuts();" << endl;
2627 out << " // Check if the cuts configuration file was provided" << endl;
2628 out << " if (!gSystem->AccessPathName(\"ConfigureCuts.C\")) {" << endl;
2629 out << " gROOT->LoadMacro(\"ConfigureCuts.C\");" << endl;
2630 out << " ConfigureCuts(runCuts, lhcCuts, detCuts, evCuts);" << endl;
2631 out << " }" << endl;
0df6ccf2 2632 if (fFriendChainName=="") {
2633 out << " TChain *chain = tagAna->QueryTags(runCuts, lhcCuts, detCuts, evCuts);" << endl;
2634 } else {
2635 out << " TString tmpColl=\"tmpCollection.xml\";" << endl;
2636 out << " tagAna->CreateXMLCollection(tmpColl.Data(),runCuts, lhcCuts, detCuts, evCuts);" << endl;
2637 out << " TChain *chain = CreateChain(tmpColl.Data(),type);" << endl;
2638 }
c57f56b7 2639 out << " if (!chain || !chain->GetNtrees()) return NULL;" << endl;
2640 out << " chain->ls();" << endl;
2641 out << " return chain;" << endl;
fcc9bb6f 2642 out << "}" << endl << endl;
c57f56b7 2643 if (gSystem->AccessPathName("ConfigureCuts.C")) {
2644 TString msg = "\n##### You may want to provide a macro ConfigureCuts.C with a method:\n";
2645 msg += " void ConfigureCuts(AliRunTagCuts *runCuts,\n";
2646 msg += " AliLHCTagCuts *lhcCuts,\n";
2647 msg += " AliDetectorTagCuts *detCuts,\n";
2648 msg += " AliEventTagCuts *evCuts)";
23329835 2649 Info("WriteAnalysisMacro", "%s", msg.Data());
c57f56b7 2650 }
0df6ccf2 2651 }
2652 if (!IsUsingTags() || fFriendChainName!="") {
fcc9bb6f 2653 out <<"//________________________________________________________________________________" << endl;
c57f56b7 2654 out << "TChain* CreateChain(const char *xmlfile, const char *type=\"ESD\")" << endl;
2655 out << "{" << endl;
2656 out << "// Create a chain using url's from xml file" << endl;
2657 out << " TString treename = type;" << endl;
2658 out << " treename.ToLower();" << endl;
2659 out << " treename += \"Tree\";" << endl;
e02fee64 2660 out << " printf(\"***************************************\\n\");" << endl;
2661 out << " printf(\" Getting chain of trees %s\\n\", treename.Data());" << endl;
2662 out << " printf(\"***************************************\\n\");" << endl;
c57f56b7 2663 out << " TAlienCollection *coll = TAlienCollection::Open(xmlfile);" << endl;
2664 out << " if (!coll) {" << endl;
2665 out << " ::Error(\"CreateChain\", \"Cannot create an AliEn collection from %s\", xmlfile);" << endl;
2666 out << " return NULL;" << endl;
2667 out << " }" << endl;
2668 out << " TChain *chain = new TChain(treename);" << endl;
0df6ccf2 2669 if(fFriendChainName!="") {
2670 out << " TChain *chainFriend = new TChain(treename);" << endl;
2671 }
c57f56b7 2672 out << " coll->Reset();" << endl;
0df6ccf2 2673 out << " while (coll->Next()) {" << endl;
2674 out << " chain->Add(coll->GetTURL(\"\"));" << endl;
2675 if(fFriendChainName!="") {
2676 out << " TString fileFriend=coll->GetTURL(\"\");" << endl;
2677 out << " fileFriend.ReplaceAll(\"AliAOD.root\",\""<<fFriendChainName.Data()<<"\");" << endl;
2678 out << " fileFriend.ReplaceAll(\"AliAODs.root\",\""<<fFriendChainName.Data()<<"\");" << endl;
2679 out << " chainFriend->Add(fileFriend.Data());" << endl;
2680 }
2681 out << " }" << endl;
c57f56b7 2682 out << " if (!chain->GetNtrees()) {" << endl;
2683 out << " ::Error(\"CreateChain\", \"No tree found from collection %s\", xmlfile);" << endl;
2684 out << " return NULL;" << endl;
2685 out << " }" << endl;
0df6ccf2 2686 if(fFriendChainName!="") {
2687 out << " chain->AddFriend(chainFriend);" << endl;
2688 }
c57f56b7 2689 out << " return chain;" << endl;
fcc9bb6f 2690 out << "}" << endl << endl;
c57f56b7 2691 }
5b273635 2692 if (hasANALYSISalice) {
2693 out <<"//________________________________________________________________________________" << endl;
2694 out << "Bool_t SetupPar(const char *package) {" << endl;
2695 out << "// Compile the package and set it up." << endl;
2696 out << " TString pkgdir = package;" << endl;
2697 out << " pkgdir.ReplaceAll(\".par\",\"\");" << endl;
2698 out << " gSystem->Exec(Form(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
2699 out << " TString cdir = gSystem->WorkingDirectory();" << endl;
2700 out << " gSystem->ChangeDirectory(pkgdir);" << endl;
2701 out << " // Check for BUILD.sh and execute" << endl;
2702 out << " if (!gSystem->AccessPathName(\"PROOF-INF/BUILD.sh\")) {" << endl;
2703 out << " printf(\"*******************************\\n\");" << endl;
2704 out << " printf(\"*** Building PAR archive ***\\n\");" << endl;
2705 out << " printf(\"*******************************\\n\");" << endl;
2706 out << " if (gSystem->Exec(\"PROOF-INF/BUILD.sh\")) {" << endl;
2707 out << " ::Error(\"SetupPar\", \"Cannot build par archive %s\", pkgdir.Data());" << endl;
2708 out << " gSystem->ChangeDirectory(cdir);" << endl;
2709 out << " return kFALSE;" << endl;
2710 out << " }" << endl;
2711 out << " } else {" << endl;
2712 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/BUILD.sh for package %s\", pkgdir.Data());" << endl;
2713 out << " gSystem->ChangeDirectory(cdir);" << endl;
2714 out << " return kFALSE;" << endl;
2715 out << " }" << endl;
2716 out << " // Check for SETUP.C and execute" << endl;
2717 out << " if (!gSystem->AccessPathName(\"PROOF-INF/SETUP.C\")) {" << endl;
2718 out << " printf(\"*******************************\\n\");" << endl;
2719 out << " printf(\"*** Setup PAR archive ***\\n\");" << endl;
2720 out << " printf(\"*******************************\\n\");" << endl;
2721 out << " gROOT->Macro(\"PROOF-INF/SETUP.C\");" << endl;
2722 out << " } else {" << endl;
2723 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/SETUP.C for package %s\", pkgdir.Data());" << endl;
2724 out << " gSystem->ChangeDirectory(cdir);" << endl;
2725 out << " return kFALSE;" << endl;
2726 out << " }" << endl;
2727 out << " // Restore original workdir" << endl;
2728 out << " gSystem->ChangeDirectory(cdir);" << endl;
2729 out << " return kTRUE;" << endl;
2730 out << "}" << endl;
2731 }
c57f56b7 2732 Info("WriteAnalysisMacro", "\n##### Analysis macro to run on worker nodes <%s> written",fAnalysisMacro.Data());
2733 }
2734 Bool_t copy = kTRUE;
2735 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
2736 if (copy) {
2737 CdWork();
2738 TString workdir = gGrid->GetHomeDirectory();
2739 workdir += fGridWorkingDir;
2740 if (FileExists(fAnalysisMacro)) gGrid->Rm(fAnalysisMacro);
2741 if (IsUsingTags() && !gSystem->AccessPathName("ConfigureCuts.C")) {
2742 if (FileExists("ConfigureCuts.C")) gGrid->Rm("ConfigureCuts.C");
2743 Info("WriteAnalysisMacro", "\n##### Copying cuts configuration macro: <ConfigureCuts.C> to your alien workspace");
2744 TFile::Cp("file:ConfigureCuts.C", Form("alien://%s/ConfigureCuts.C", workdir.Data()));
2745 }
2746 Info("WriteAnalysisMacro", "\n##### Copying analysis macro: <%s> to your alien workspace", fAnalysisMacro.Data());
2747 TFile::Cp(Form("file:%s",fAnalysisMacro.Data()), Form("alien://%s/%s", workdir.Data(), fAnalysisMacro.Data()));
2748 }
2749}
2750
2751//______________________________________________________________________________
0f389141 2752void AliAnalysisAlien::WriteMergingMacro()
2753{
2754// Write a macro to merge the outputs per master job.
2755 if (!fMergeViaJDL) return;
2756 if (!fOutputFiles.Length()) {
2757 Error("WriteMergingMacro", "No output file names defined. Are you running the right AliAnalysisAlien configuration ?");
2758 return;
2759 }
2760 TString mergingMacro = fExecutable;
2761 mergingMacro.ReplaceAll(".sh","_merge.C");
2762 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
2763 if (!TestBit(AliAnalysisGrid::kSubmit)) {
2764 ofstream out;
2765 out.open(mergingMacro.Data(), ios::out);
2766 if (!out.good()) {
2767 Error("WriteMergingMacro", "could not open file %s for writing", fAnalysisMacro.Data());
2768 return;
2769 }
5b273635 2770 Bool_t hasSTEERBase = kFALSE;
2771 Bool_t hasESD = kFALSE;
2772 Bool_t hasAOD = kFALSE;
2773 Bool_t hasANALYSIS = kFALSE;
2774 Bool_t hasANALYSISalice = kFALSE;
2775 Bool_t hasCORRFW = kFALSE;
0f389141 2776 TString func = mergingMacro;
2777 TString comment;
2778 func.ReplaceAll(".C", "");
7c2cd90a 2779 out << "void " << func.Data() << "(const char *dir, Int_t stage=0, Int_t ichunk=0)" << endl;
0f389141 2780 out << "{" << endl;
2781 out << "// Automatically generated merging macro executed in grid subjobs" << endl << endl;
2782 out << " TStopwatch timer;" << endl;
2783 out << " timer.Start();" << endl << endl;
7c2cd90a 2784 if (!fExecutableCommand.Contains("aliroot")) {
2785 out << "// load base root libraries" << endl;
2786 out << " gSystem->Load(\"libTree\");" << endl;
2787 out << " gSystem->Load(\"libGeom\");" << endl;
2788 out << " gSystem->Load(\"libVMC\");" << endl;
2789 out << " gSystem->Load(\"libPhysics\");" << endl << endl;
2790 out << " gSystem->Load(\"libMinuit\");" << endl << endl;
2791 }
0f389141 2792 if (fAdditionalRootLibs.Length()) {
2793 // in principle libtree /lib geom libvmc etc. can go into this list, too
2794 out << "// Add aditional libraries" << endl;
2795 TObjArray *list = fAdditionalRootLibs.Tokenize(" ");
2796 TIter next(list);
2797 TObjString *str;
2798 while((str=(TObjString*)next())) {
2799 if (str->GetString().Contains(".so"))
2800 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
2801 }
2802 if (list) delete list;
2803 }
2804 out << "// include path" << endl;
2805 if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
2806 out << " gSystem->AddIncludePath(\"-I$ALICE_ROOT/include\");" << endl << endl;
2807 out << "// Load analysis framework libraries" << endl;
2808 if (!fPackages) {
7c2cd90a 2809 if (!fExecutableCommand.Contains("aliroot")) {
2810 out << " gSystem->Load(\"libSTEERBase\");" << endl;
2811 out << " gSystem->Load(\"libESD\");" << endl;
2812 out << " gSystem->Load(\"libAOD\");" << endl;
2813 }
0f389141 2814 out << " gSystem->Load(\"libANALYSIS\");" << endl;
2815 out << " gSystem->Load(\"libANALYSISalice\");" << endl;
2816 out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
2817 } else {
2818 TIter next(fPackages);
2819 TObject *obj;
2820 TString pkgname;
5b273635 2821 TString setupPar = "AliAnalysisAlien::SetupPar";
0f389141 2822 while ((obj=next())) {
2823 pkgname = obj->GetName();
2824 if (pkgname == "STEERBase" ||
2825 pkgname == "STEERBase.par") hasSTEERBase = kTRUE;
2826 if (pkgname == "ESD" ||
2827 pkgname == "ESD.par") hasESD = kTRUE;
2828 if (pkgname == "AOD" ||
2829 pkgname == "AOD.par") hasAOD = kTRUE;
2830 if (pkgname == "ANALYSIS" ||
2831 pkgname == "ANALYSIS.par") hasANALYSIS = kTRUE;
2832 if (pkgname == "ANALYSISalice" ||
2833 pkgname == "ANALYSISalice.par") hasANALYSISalice = kTRUE;
2834 if (pkgname == "CORRFW" ||
2835 pkgname == "CORRFW.par") hasCORRFW = kTRUE;
2836 }
5b273635 2837 if (hasANALYSISalice) setupPar = "SetupPar";
0f389141 2838 if (!hasSTEERBase) out << " gSystem->Load(\"libSTEERBase\");" << endl;
5b273635 2839 else out << " if (!" << setupPar << "(\"STEERBase\")) return;" << endl;
0f389141 2840 if (!hasESD) out << " gSystem->Load(\"libESD\");" << endl;
5b273635 2841 else out << " if (!" << setupPar << "(\"ESD\")) return;" << endl;
0f389141 2842 if (!hasAOD) out << " gSystem->Load(\"libAOD\");" << endl;
5b273635 2843 else out << " if (!" << setupPar << "(\"AOD\")) return;" << endl;
0f389141 2844 if (!hasANALYSIS) out << " gSystem->Load(\"libANALYSIS\");" << endl;
5b273635 2845 else out << " if (!" << setupPar << "(\"ANALYSIS\")) return;" << endl;
0f389141 2846 if (!hasANALYSISalice) out << " gSystem->Load(\"libANALYSISalice\");" << endl;
5b273635 2847 else out << " if (!" << setupPar << "(\"ANALYSISalice\")) return;" << endl;
0f389141 2848 if (!hasCORRFW) out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
5b273635 2849 else out << " if (!" << setupPar << "(\"CORRFW\")) return;" << endl << endl;
0f389141 2850 out << "// Compile other par packages" << endl;
2851 next.Reset();
2852 while ((obj=next())) {
2853 pkgname = obj->GetName();
2854 if (pkgname == "STEERBase" ||
2855 pkgname == "STEERBase.par" ||
2856 pkgname == "ESD" ||
2857 pkgname == "ESD.par" ||
2858 pkgname == "AOD" ||
2859 pkgname == "AOD.par" ||
2860 pkgname == "ANALYSIS" ||
2861 pkgname == "ANALYSIS.par" ||
2862 pkgname == "ANALYSISalice" ||
2863 pkgname == "ANALYSISalice.par" ||
2864 pkgname == "CORRFW" ||
2865 pkgname == "CORRFW.par") continue;
5b273635 2866 out << " if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
0f389141 2867 }
2868 }
2869 if (fAdditionalLibs.Length()) {
2870 out << "// Add aditional AliRoot libraries" << endl;
2871 TObjArray *list = fAdditionalLibs.Tokenize(" ");
2872 TIter next(list);
2873 TObjString *str;
2874 while((str=(TObjString*)next())) {
2875 if (str->GetString().Contains(".so"))
2876 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
2877 }
2878 if (list) delete list;
2879 }
2880 out << endl;
2881 out << "// Analysis source to be compiled at runtime (if any)" << endl;
2882 if (fAnalysisSource.Length()) {
2883 TObjArray *list = fAnalysisSource.Tokenize(" ");
2884 TIter next(list);
2885 TObjString *str;
2886 while((str=(TObjString*)next())) {
2887 out << " gROOT->ProcessLine(\".L " << str->GetString().Data() << "+g\");" << endl;
2888 }
2889 if (list) delete list;
2890 }
149d288c 2891 out << endl;
2892
0f389141 2893 if (fFastReadOption) {
2894 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 !!!");
2895 out << "// fast xrootd reading enabled" << endl;
2896 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 2897 out << " gEnv->SetValue(\"XNet.ConnectTimeout\",10);" << endl;
2898 out << " gEnv->SetValue(\"XNet.RequestTimeout\",10);" << endl;
0f389141 2899 out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
d3339be3 2900 out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",10);" << endl;
0f389141 2901 out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
e8b839ab 2902 }
2903 // Change temp directory to current one
2904 out << "// Set temporary merging directory to current one" << endl;
2905 out << " gSystem->Setenv(\"TMPDIR\", gSystem->pwd());" << endl << endl;
0f389141 2906 out << "// Connect to AliEn" << endl;
2907 out << " if (!TGrid::Connect(\"alien://\")) return;" << endl;
0cdf65a8 2908 out << " Bool_t laststage = kFALSE;" << endl;
7c2cd90a 2909 out << " TString outputDir = dir;" << endl;
0f389141 2910 out << " TString outputFiles = \"" << fOutputFiles << "\";" << endl;
2911 out << " TString mergeExcludes = \"" << fMergeExcludes << "\";" << endl;
1f0d1ca2 2912 out << " mergeExcludes += \"" << AliAnalysisManager::GetAnalysisManager()->GetExtraFiles() << "\";" << endl;
58268c13 2913 out << " TObjArray *list = outputFiles.Tokenize(\",\");" << endl;
0f389141 2914 out << " TIter *iter = new TIter(list);" << endl;
2915 out << " TObjString *str;" << endl;
a2f5fc01 2916 out << " TString outputFile;" << endl;
0f389141 2917 out << " Bool_t merged = kTRUE;" << endl;
2918 out << " while((str=(TObjString*)iter->Next())) {" << endl;
a2f5fc01 2919 out << " outputFile = str->GetString();" << endl;
7c2cd90a 2920 out << " if (outputFile.Contains(\"*\")) continue;" << endl;
a2f5fc01 2921 out << " Int_t index = outputFile.Index(\"@\");" << endl;
2922 out << " if (index > 0) outputFile.Remove(index);" << endl;
0f389141 2923 out << " // Skip already merged outputs" << endl;
a2f5fc01 2924 out << " if (!gSystem->AccessPathName(outputFile)) {" << endl;
2925 out << " printf(\"Output file <%s> found. Not merging again.\",outputFile.Data());" << endl;
0f389141 2926 out << " continue;" << endl;
2927 out << " }" << endl;