#include "Riostream.h"
#include "TEnv.h"
+#include "TBits.h"
#include "TError.h"
#include "TROOT.h"
#include "TSystem.h"
#include "TFile.h"
+#include "TFileCollection.h"
+#include "TChain.h"
#include "TObjString.h"
#include "TObjArray.h"
#include "TGrid.h"
fNtestFiles(0),
fNrunsPerMaster(0),
fMaxMergeFiles(0),
+ fMaxMergeStages(0),
fNsubmitted(0),
fProductionMode(0),
fOutputToRunNo(0),
fMergeViaJDL(0),
fFastReadOption(0),
- fOverwriteMode(0),
+ fOverwriteMode(1),
+ fNreplicas(2),
+ fNproofWorkers(0),
+ fNproofWorkersPerSlave(0),
+ fProofReset(0),
fRunNumbers(),
fExecutable(),
fExecutableCommand(),
fExecutableArgs(),
fAnalysisMacro(),
fAnalysisSource(),
+ fValidationScript(),
fAdditionalRootLibs(),
fAdditionalLibs(),
fSplitMode(),
fInputFormat(),
fDatasetName(),
fJDLName(),
+ fTerminateFiles(),
fMergeExcludes(),
fIncludePath(),
fCloseSE(),
fJobTag(),
fOutputSingle(),
fRunPrefix(),
+ fProofCluster(),
+ fProofDataSet(),
+ fFileForTestMode(),
+ fRootVersionForProof(),
+ fAliRootMode(),
+ fMergeDirName(),
fInputFiles(0),
fPackages(0)
{
fNtestFiles(0),
fNrunsPerMaster(0),
fMaxMergeFiles(0),
+ fMaxMergeStages(0),
fNsubmitted(0),
fProductionMode(0),
fOutputToRunNo(0),
fMergeViaJDL(0),
fFastReadOption(0),
- fOverwriteMode(0),
+ fOverwriteMode(1),
+ fNreplicas(2),
+ fNproofWorkers(0),
+ fNproofWorkersPerSlave(0),
+ fProofReset(0),
fRunNumbers(),
fExecutable(),
fExecutableCommand(),
fExecutableArgs(),
fAnalysisMacro(),
fAnalysisSource(),
+ fValidationScript(),
fAdditionalRootLibs(),
fAdditionalLibs(),
fSplitMode(),
fInputFormat(),
fDatasetName(),
fJDLName(),
+ fTerminateFiles(),
fMergeExcludes(),
fIncludePath(),
fCloseSE(),
fJobTag(),
fOutputSingle(),
fRunPrefix(),
+ fProofCluster(),
+ fProofDataSet(),
+ fFileForTestMode(),
+ fRootVersionForProof(),
+ fAliRootMode(),
+ fMergeDirName(),
fInputFiles(0),
fPackages(0)
{
fNtestFiles(other.fNtestFiles),
fNrunsPerMaster(other.fNrunsPerMaster),
fMaxMergeFiles(other.fMaxMergeFiles),
+ fMaxMergeStages(other.fMaxMergeStages),
fNsubmitted(other.fNsubmitted),
fProductionMode(other.fProductionMode),
fOutputToRunNo(other.fOutputToRunNo),
fMergeViaJDL(other.fMergeViaJDL),
fFastReadOption(other.fFastReadOption),
fOverwriteMode(other.fOverwriteMode),
+ fNreplicas(other.fNreplicas),
+ fNproofWorkers(other.fNproofWorkers),
+ fNproofWorkersPerSlave(other.fNproofWorkersPerSlave),
+ fProofReset(other.fProofReset),
fRunNumbers(other.fRunNumbers),
fExecutable(other.fExecutable),
fExecutableCommand(other.fExecutableCommand),
fExecutableArgs(other.fExecutableArgs),
fAnalysisMacro(other.fAnalysisMacro),
fAnalysisSource(other.fAnalysisSource),
+ fValidationScript(other.fValidationScript),
fAdditionalRootLibs(other.fAdditionalRootLibs),
fAdditionalLibs(other.fAdditionalLibs),
fSplitMode(other.fSplitMode),
fInputFormat(other.fInputFormat),
fDatasetName(other.fDatasetName),
fJDLName(other.fJDLName),
+ fTerminateFiles(other.fTerminateFiles),
fMergeExcludes(other.fMergeExcludes),
fIncludePath(other.fIncludePath),
fCloseSE(other.fCloseSE),
fJobTag(other.fJobTag),
fOutputSingle(other.fOutputSingle),
fRunPrefix(other.fRunPrefix),
+ fProofCluster(other.fProofCluster),
+ fProofDataSet(other.fProofDataSet),
+ fFileForTestMode(other.fFileForTestMode),
+ fRootVersionForProof(other.fRootVersionForProof),
+ fAliRootMode(other.fAliRootMode),
+ fMergeDirName(other.fMergeDirName),
fInputFiles(0),
fPackages(0)
{
fNtestFiles = other.fNtestFiles;
fNrunsPerMaster = other.fNrunsPerMaster;
fMaxMergeFiles = other.fMaxMergeFiles;
+ fMaxMergeStages = other.fMaxMergeStages;
fNsubmitted = other.fNsubmitted;
fProductionMode = other.fProductionMode;
fOutputToRunNo = other.fOutputToRunNo;
fMergeViaJDL = other.fMergeViaJDL;
fFastReadOption = other.fFastReadOption;
fOverwriteMode = other.fOverwriteMode;
+ fNreplicas = other.fNreplicas;
+ fNproofWorkers = other.fNproofWorkers;
+ fNproofWorkersPerSlave = other.fNproofWorkersPerSlave;
+ fProofReset = other.fProofReset;
fRunNumbers = other.fRunNumbers;
fExecutable = other.fExecutable;
fExecutableCommand = other.fExecutableCommand;
fExecutableArgs = other.fExecutableArgs;
fAnalysisMacro = other.fAnalysisMacro;
fAnalysisSource = other.fAnalysisSource;
+ fValidationScript = other.fValidationScript;
fAdditionalRootLibs = other.fAdditionalRootLibs;
fAdditionalLibs = other.fAdditionalLibs;
fSplitMode = other.fSplitMode;
fInputFormat = other.fInputFormat;
fDatasetName = other.fDatasetName;
fJDLName = other.fJDLName;
+ fTerminateFiles = other.fTerminateFiles;
fMergeExcludes = other.fMergeExcludes;
fIncludePath = other.fIncludePath;
fCloseSE = other.fCloseSE;
fJobTag = other.fJobTag;
fOutputSingle = other.fOutputSingle;
fRunPrefix = other.fRunPrefix;
+ fProofCluster = other.fProofCluster;
+ fProofDataSet = other.fProofDataSet;
+ fFileForTestMode = other.fFileForTestMode;
+ fRootVersionForProof = other.fRootVersionForProof;
+ fAliRootMode = other.fAliRootMode;
+ fMergeDirName = other.fMergeDirName;
if (other.fInputFiles) {
fInputFiles = new TObjArray();
TIter next(other.fInputFiles);
return *this;
}
+//______________________________________________________________________________
+void AliAnalysisAlien::SetRunPrefix(const char *prefix)
+{
+// Set the run number format. Can be a prefix or a format like "%09d"
+ fRunPrefix = prefix;
+ if (!fRunPrefix.Contains("%")) fRunPrefix += "%d";
+}
+
//______________________________________________________________________________
void AliAnalysisAlien::AddIncludePath(const char *path)
{
{
// Add a run number to the list of runs to be processed.
if (fRunNumbers.Length()) fRunNumbers += " ";
- fRunNumbers += Form("%s%d", fRunPrefix.Data(), run);
+ fRunNumbers += Form(fRunPrefix.Data(), run);
}
+//______________________________________________________________________________
+void AliAnalysisAlien::AddRunList(const char* runList)
+{
+// Add several runs into the list of runs; they are expected to be separated by a blank character.
+ TString sList = runList;
+ TObjArray *list = sList.Tokenize(" ");
+ Int_t n = list->GetEntries();
+ for (Int_t i = 0; i < n; i++) {
+ TObjString *os = (TObjString*)list->At(i);
+ AddRunNumber(os->GetString().Atoi());
+ }
+ delete list;
+}
+
//______________________________________________________________________________
void AliAnalysisAlien::AddRunNumber(const char* run)
{
{
// Try to connect to AliEn. User needs a valid token and /tmp/gclient_env_$UID sourced.
if (gGrid && gGrid->IsConnected()) return kTRUE;
- if (!gSystem->Getenv("alien_API_USER")) {
- Error("Connect", "Make sure you:\n 1. Have called: alien-token-init <username> today\n 2. Have sourced /tmp/gclient_env_%s",
- gSystem->Getenv("UID"));
- return kFALSE;
- }
+ if (fProductionMode) return kTRUE;
if (!gGrid) {
Info("Connect", "Trying to connect to AliEn ...");
TGrid::Connect("alien://");
}
// Work directory not existing - create it
gGrid->Cd(homedir);
- if (gGrid->Mkdir(workdir)) {
+ if (gGrid->Mkdir(workdir, "-p")) {
gGrid->Cd(fGridWorkingDir);
- Info("CreateJDL", "\n##### Created alien working directory %s", fGridWorkingDir.Data());
+ Info("CdWork", "\n##### Created alien working directory %s", fGridWorkingDir.Data());
} else {
- Warning("CreateJDL", "Working directory %s cannot be created.\n Using %s instead.",
+ Warning("CdWork", "Working directory %s cannot be created.\n Using %s instead.",
workdir.Data(), homedir.Data());
fGridWorkingDir = "";
}
}
+//______________________________________________________________________________
+Bool_t AliAnalysisAlien::CheckFileCopy(const char *alienpath)
+{
+// Check if file copying is possible.
+ if (fProductionMode) return kTRUE;
+ if (!Connect()) {
+ Error("CheckFileCopy", "Not connected to AliEn. File copying cannot be tested.");
+ return kFALSE;
+ }
+ Info("CheckFileCopy", "Checking possibility to copy files to your AliEn home directory... \
+ \n +++ NOTE: You can disable this via: plugin->SetCheckCopy(kFALSE);");
+ // Check if alien_CLOSE_SE is defined
+ TString closeSE = gSystem->Getenv("alien_CLOSE_SE");
+ if (!closeSE.IsNull()) {
+ Info("CheckFileCopy", "Your current close storage is pointing to: \
+ \n alien_CLOSE_SE = \"%s\"", closeSE.Data());
+ } else {
+ Warning("CheckFileCopy", "Your current close storage is empty ! Depending on your location, file copying may fail.");
+ }
+ // Check if grid directory exists.
+ if (!DirectoryExists(alienpath)) {
+ Error("CheckFileCopy", "Alien path %s does not seem to exist", alienpath);
+ return kFALSE;
+ }
+ TFile f("plugin_test_copy", "RECREATE");
+ // User may not have write permissions to current directory
+ if (f.IsZombie()) {
+ Error("CheckFileCopy", "Cannot create local test file. Do you have write access to current directory: <%s> ?",
+ gSystem->WorkingDirectory());
+ return kFALSE;
+ }
+ f.Close();
+ if (FileExists(Form("alien://%s/%s",alienpath, f.GetName()))) gGrid->Rm(Form("alien://%s/%s",alienpath, f.GetName()));
+ if (!TFile::Cp(f.GetName(), Form("alien://%s/%s",alienpath, f.GetName()))) {
+ Error("CheckFileCopy", "Cannot copy files to Alien destination: <%s> This may be temporary, or: \
+ \n# 1. Make sure you have write permissions there. If this is the case: \
+ \n# 2. Check the storage availability at: http://alimonitor.cern.ch/stats?page=SE/table \
+ \n# Do: export alien_CLOSE_SE=\"working_disk_SE\" \
+ \n# To make this permanent put in in your .bashrc (in .alienshrc is not enough) \
+ \n# Redo token: rm /tmp/x509up_u$UID then: alien-token-init <username>", alienpath);
+ gSystem->Unlink(f.GetName());
+ return kFALSE;
+ }
+ gSystem->Unlink(f.GetName());
+ gGrid->Rm(Form("%s%s",alienpath,f.GetName()));
+ Info("CheckFileCopy", "### ...SUCCESS ###");
+ return kTRUE;
+}
+
//______________________________________________________________________________
Bool_t AliAnalysisAlien::CheckInputData()
{
// Check validity of input data. If necessary, create xml files.
+ if (fProductionMode) return kTRUE;
if (!fInputFiles && !fRunNumbers.Length() && !fRunRange[0]) {
if (!fGridDataDir.Length()) {
Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
return kFALSE;
}
+ if (fMergeViaJDL) {
+ Error("CheckInputData", "Merging via jdl works only with run numbers, run range or provided xml");
+ return kFALSE;
+ }
Info("CheckInputData", "Analysis will make a single xml for base data directory %s",fGridDataDir.Data());
+ if (fDataPattern.Contains("tag") && TestBit(AliAnalysisGrid::kTest))
+ TObject::SetBit(AliAnalysisGrid::kUseTags, kTRUE); // ADDED (fix problem in determining the tag usage in test mode)
return kTRUE;
}
// Process declared files
- Bool_t is_collection = kFALSE;
- Bool_t is_xml = kFALSE;
- Bool_t use_tags = kFALSE;
+ Bool_t isCollection = kFALSE;
+ Bool_t isXml = kFALSE;
+ Bool_t useTags = kFALSE;
Bool_t checked = kFALSE;
- CdWork();
+ if (!TestBit(AliAnalysisGrid::kTest)) CdWork();
TString file;
TString workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
CheckDataType(file, iscoll, isxml, usetags);
if (!checked) {
checked = kTRUE;
- is_collection = iscoll;
- is_xml = isxml;
- use_tags = usetags;
- TObject::SetBit(AliAnalysisGrid::kUseTags, use_tags);
+ isCollection = iscoll;
+ isXml = isxml;
+ useTags = usetags;
+ TObject::SetBit(AliAnalysisGrid::kUseTags, useTags);
} else {
- if ((iscoll != is_collection) || (isxml != is_xml) || (usetags != use_tags)) {
+ if ((iscoll != isCollection) || (isxml != isXml) || (usetags != useTags)) {
Error("CheckInputData", "Some conflict was found in the types of inputs");
return kFALSE;
}
Error("CheckInputData", "Data directory %s not existing.", fGridDataDir.Data());
return kFALSE;
}
- if (is_collection) {
+ if (isCollection) {
Error("CheckInputData", "You are using raw AliEn collections as input. Cannot process run numbers.");
return kFALSE;
}
- if (checked && !is_xml) {
+ if (checked && !isXml) {
Error("CheckInputData", "Cannot mix processing of full runs with non-xml files");
return kFALSE;
}
// Check validity of run number(s)
TObjArray *arr;
TObjString *os;
+ TString format;
Int_t nruns = 0;
TString schunk, schunk2;
TString path;
if (!checked) {
checked = kTRUE;
- use_tags = fDataPattern.Contains("tag");
- TObject::SetBit(AliAnalysisGrid::kUseTags, use_tags);
+ useTags = fDataPattern.Contains("tag");
+ TObject::SetBit(AliAnalysisGrid::kUseTags, useTags);
}
- if (use_tags != fDataPattern.Contains("tag")) {
+ if (useTags != fDataPattern.Contains("tag")) {
Error("CheckInputData", "Cannot mix input files using/not using tags");
return kFALSE;
}
TString msg = "\n##### file: ";
msg += path;
msg += " type: xml_collection;";
- if (use_tags) msg += " using_tags: Yes";
+ if (useTags) msg += " using_tags: Yes";
else msg += " using_tags: No";
- Info("CheckDataType", msg.Data());
+ Info("CheckDataType", "%s", msg.Data());
if (fNrunsPerMaster<2) {
AddDataFile(Form("%s.xml", os->GetString().Data()));
} else {
} else {
Info("CheckDataType", "Using run range [%d, %d]", fRunRange[0], fRunRange[1]);
for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
- path = Form("%s/%s%d ", fGridDataDir.Data(), fRunPrefix.Data(), irun);
+ format = Form("%%s/%s ", fRunPrefix.Data());
+ path = Form(format.Data(), fGridDataDir.Data(), irun);
if (!DirectoryExists(path)) {
-// Warning("CheckInputData", "Run number %d not found in path: <%s>", irun, path.Data());
continue;
}
- path = Form("%s/%s%d.xml", workdir.Data(),fRunPrefix.Data(),irun);
+ format = Form("%%s/%s.xml", fRunPrefix.Data());
+ path = Form(format.Data(), workdir.Data(),irun);
TString msg = "\n##### file: ";
msg += path;
msg += " type: xml_collection;";
- if (use_tags) msg += " using_tags: Yes";
+ if (useTags) msg += " using_tags: Yes";
else msg += " using_tags: No";
- Info("CheckDataType", msg.Data());
+ Info("CheckDataType", "%s", msg.Data());
if (fNrunsPerMaster<2) {
- AddDataFile(Form("%s%d.xml",fRunPrefix.Data(),irun));
+ format = Form("%s.xml", fRunPrefix.Data());
+ AddDataFile(Form(format.Data(),irun));
} else {
nruns++;
if (((nruns-1)%fNrunsPerMaster) == 0) {
- schunk = Form("%s%d", fRunPrefix.Data(),irun);
+ schunk = Form(fRunPrefix.Data(),irun);
}
- schunk2 = Form("_%s%d.xml", fRunPrefix.Data(), irun);
+ format = Form("_%s.xml", fRunPrefix.Data());
+ schunk2 = Form(format.Data(), irun);
if ((nruns%fNrunsPerMaster)!=0 && irun != fRunRange[1]) continue;
schunk += schunk2;
AddDataFile(schunk);
Bool_t AliAnalysisAlien::CreateDataset(const char *pattern)
{
// Create dataset for the grid data directory + run number.
- if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline)) return kTRUE;
if (!Connect()) {
Error("CreateDataset", "Cannot create dataset with no grid connection");
return kFALSE;
}
// Cd workspace
- CdWork();
+ if (!TestBit(AliAnalysisGrid::kTest)) CdWork();
TString workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
// Compose the 'find' command arguments
+ TString format;
TString command;
TString options = "-x collection ";
if (TestBit(AliAnalysisGrid::kTest)) options += Form("-l %d ", fNtestFiles);
if (res) delete res;
// Write standard output to file
gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
+ Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE;
+ Bool_t nullFile = kFALSE;
+ if (!hasGrep) {
+ Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command");
+ } else {
+ nullFile = (gSystem->Exec(Form("grep /event %s 2>/dev/null > /dev/null",file.Data()))==0)?kFALSE:kTRUE;
+ if (nullFile) {
+ Error("CreateDataset","Dataset %s produced by the previous find command is empty !", file.Data());
+ return kFALSE;
+ }
+ }
}
Bool_t fileExists = FileExists(file);
if (!TestBit(AliAnalysisGrid::kTest) && (!fileExists || fOverwriteMode)) {
return kTRUE;
}
// Several runs
+ Bool_t nullResult = kTRUE;
if (fRunNumbers.Length()) {
TObjArray *arr = fRunNumbers.Tokenize(" ");
TObjString *os;
if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
else file = Form("%s.xml", os->GetString().Data());
// If local collection file does not exist, create it via 'find' command.
- if (gSystem->AccessPathName(file)) {
+ if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
command = "find ";
command += options;
command += path;
if (res) delete res;
// Write standard output to file
gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
- }
+ Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE;
+ Bool_t nullFile = kFALSE;
+ if (!hasGrep) {
+ Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command");
+ } else {
+ nullFile = (gSystem->Exec(Form("grep /event %s 2>/dev/null > /dev/null",file.Data()))==0)?kFALSE:kTRUE;
+ if (nullFile) {
+ Warning("CreateDataset","Dataset %s produced by: <%s> is empty !", file.Data(), command.Data());
+ fRunNumbers.ReplaceAll(os->GetString().Data(), "");
+ continue;
+ }
+ }
+ nullResult = kFALSE;
+ }
if (TestBit(AliAnalysisGrid::kTest)) break;
// Check if there is one run per master job.
if (fNrunsPerMaster<2) {
delete arr;
return kFALSE;
}
- }
+ }
}
delete arr;
+ if (nullResult) {
+ Error("CreateDataset", "No valid dataset corresponding to the query!");
+ return kFALSE;
+ }
} else {
// Process a full run range.
for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
- path = Form("%s/%s%d ", fGridDataDir.Data(), fRunPrefix.Data(), irun);
+ format = Form("%%s/%s ", fRunPrefix.Data());
+ path = Form(format.Data(), fGridDataDir.Data(), irun);
if (!DirectoryExists(path)) continue;
// CdWork();
+ format = Form("%s.xml", fRunPrefix.Data());
if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
- else file = Form("%s%d.xml", fRunPrefix.Data(), irun);
+ else file = Form(format.Data(), irun);
if (FileExists(file) && fNrunsPerMaster<2 && !TestBit(AliAnalysisGrid::kTest)) {
if (fOverwriteMode) gGrid->Rm(file);
else {
}
}
// If local collection file does not exist, create it via 'find' command.
- if (gSystem->AccessPathName(file) || fOverwriteMode) {
+ if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
command = "find ";
command += options;
command += path;
if (res) delete res;
// Write standard output to file
gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
+ Bool_t hasGrep = (gSystem->Exec("grep --version 2>/dev/null > /dev/null")==0)?kTRUE:kFALSE;
+ Bool_t nullFile = kFALSE;
+ if (!hasGrep) {
+ Warning("CreateDataset", "'grep' command not available on this system - cannot validate the result of the grid 'find' command");
+ } else {
+ nullFile = (gSystem->Exec(Form("grep /event %s 2>/dev/null > /dev/null",file.Data()))==0)?kFALSE:kTRUE;
+ if (nullFile) {
+ Warning("CreateDataset","Dataset %s produced by: <%s> is empty !", file.Data(), command.Data());
+ continue;
+ }
+ }
+ nullResult = kFALSE;
}
if (TestBit(AliAnalysisGrid::kTest)) break;
// Check if there is one run per master job.
}
printf(" Merging collection <%s> into %d runs chunk...\n",file.Data(),fNrunsPerMaster);
if (((nruns-1)%fNrunsPerMaster) == 0) {
- schunk = Form("%s%d", fRunPrefix.Data(), irun);
+ schunk = Form(fRunPrefix.Data(), irun);
cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
} else {
cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
cbase->Add(cadd);
delete cadd;
}
- schunk2 = Form("%s_%s%d.xml", schunk.Data(), fRunPrefix.Data(), irun);
+ format = Form("%%s_%s.xml", fRunPrefix.Data());
+ schunk2 = Form(format.Data(), schunk.Data(), irun);
if ((nruns%fNrunsPerMaster)!=0 && irun!=fRunRange[1] && schunk2 != fInputFiles->Last()->GetName()) {
continue;
}
}
}
}
+ if (nullResult) {
+ Error("CreateDataset", "No valid dataset corresponding to the query!");
+ return kFALSE;
+ }
}
return kTRUE;
}
Bool_t error = kFALSE;
TObjArray *arr = 0;
Bool_t copy = kTRUE;
- if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
Bool_t generate = kTRUE;
if (TestBit(AliAnalysisGrid::kTest) || TestBit(AliAnalysisGrid::kSubmit)) generate = kFALSE;
if (!Connect()) {
return kFALSE;
}
// Check validity of alien workspace
- CdWork();
- TString workdir = gGrid->GetHomeDirectory();
+ TString workdir;
+ if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice")) workdir = gGrid->GetHomeDirectory();
+ if (!fProductionMode && !TestBit(AliAnalysisGrid::kTest)) CdWork();
workdir += fGridWorkingDir;
if (generate) {
TObjString *os;
Error("CreateJDL", "You must define AliEn output directory");
error = kTRUE;
} else {
- if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
- if (!DirectoryExists(fGridOutputDir)) {
- if (gGrid->Mkdir(fGridOutputDir)) {
- Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
+ if (!fProductionMode) {
+ if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
+ if (!DirectoryExists(fGridOutputDir)) {
+ if (gGrid->Mkdir(fGridOutputDir,"-p")) {
+ Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
+ } else {
+ Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
+ // error = kTRUE;
+ }
} else {
- Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
- // error = kTRUE;
- }
- }
- gGrid->Cd(workdir);
+ Warning("CreateJDL", "#### Output directory %s exists! If this contains old data, jobs will fail with ERROR_SV !!! ###", fGridOutputDir.Data());
+ }
+ gGrid->Cd(workdir);
+ }
}
// Exit if any error up to now
if (error) return kFALSE;
fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),mergeExec.Data()), "List of input files to be uploaded to workers");
if (!fArguments.IsNull())
fGridJDL->SetArguments(fArguments, "Arguments for the executable command");
- fMergingJDL->SetArguments("$1");
- fGridJDL->SetTTL((UInt_t)fTTL);
- fMergingJDL->SetTTL((UInt_t)fTTL);
+ if (IsOneStageMerging()) fMergingJDL->SetArguments(fGridOutputDir);
+ else {
+ if (fProductionMode) fMergingJDL->SetArguments("wn.xml $4"); // xml, stage
+ else fMergingJDL->SetArguments("wn.xml $2"); // xml, stage
+ }
+
+ fGridJDL->SetValue("TTL", Form("\"%d\"",fTTL));
+ fGridJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60));
+ fMergingJDL->SetValue("TTL", Form("\"%d\"",fTTL));
+ fMergingJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60));
+
if (fMaxInitFailed > 0) {
fGridJDL->SetValue("MaxInitFailed", Form("\"%d\"",fMaxInitFailed));
fGridJDL->SetDescription("MaxInitFailed", "Maximum number of first failing jobs to abort the master job");
if (fSplitMaxInputFileNumber > 0) {
fGridJDL->SetValue("SplitMaxInputFileNumber", Form("\"%d\"", fSplitMaxInputFileNumber));
fGridJDL->SetDescription("SplitMaxInputFileNumber", "Maximum number of input files to be processed per subjob");
+ }
+ if (!IsOneStageMerging()) {
+ fMergingJDL->SetValue("SplitMaxInputFileNumber", Form("\"%d\"",fMaxMergeFiles));
+ fMergingJDL->SetDescription("SplitMaxInputFileNumber", "Maximum number of input files to be merged in one go");
}
if (fSplitMode.Length()) {
fGridJDL->SetValue("Split", Form("\"%s\"", fSplitMode.Data()));
fGridJDL->SetDescription("Split", "We split per SE or file");
- }
+ }
+ fMergingJDL->SetValue("Split", "\"se\"");
+ fMergingJDL->SetDescription("Split", "We split per SE for merging in stages");
if (!fAliROOTVersion.IsNull()) {
fGridJDL->AddToPackages("AliRoot", fAliROOTVersion,"VO_ALICE", "List of requested packages");
fMergingJDL->AddToPackages("AliRoot", fAliROOTVersion, "VO_ALICE", "List of requested packages");
}
fGridJDL->SetInputDataListFormat(fInputFormat, "Format of input data");
fGridJDL->SetInputDataList("wn.xml", "Collection name to be processed on each worker node");
+ fMergingJDL->SetInputDataListFormat(fInputFormat, "Format of input data");
+ fMergingJDL->SetInputDataList("wn.xml", "Collection name to be processed on each worker node");
fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), fAnalysisMacro.Data()), "List of input files to be uploaded to workers");
TString analysisFile = fExecutable;
analysisFile.ReplaceAll(".sh", ".root");
first = kFALSE;
}
delete arr;
- TString outputArchive = fOutputArchive;
- if (!fMergeExcludes.IsNull()) {
- arr = fMergeExcludes.Tokenize(" ");
- TIter next1(arr);
- while ((os=(TObjString*)next1())) {
- outputArchive.ReplaceAll(Form("%s,",os->GetString().Data()),"");
- outputArchive.ReplaceAll(os->GetString(),"");
+ // Output archive for the merging jdl
+ TString outputArchive;
+ if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
+ outputArchive = "log_archive.zip:std*@disk=1 ";
+ // Add normal output files, extra files + terminate files
+ TString files = GetListOfFiles("outextter");
+ // Do not register merge excludes
+ if (!fMergeExcludes.IsNull()) {
+ arr = fMergeExcludes.Tokenize(" ");
+ TIter next1(arr);
+ while ((os=(TObjString*)next1())) {
+ files.ReplaceAll(Form("%s,",os->GetString().Data()),"");
+ files.ReplaceAll(os->GetString(),"");
+ }
+ delete arr;
}
- delete arr;
- }
+ files.ReplaceAll(".root", "*.root");
+ outputArchive += Form("root_archive.zip:%s,*.stat@disk=%d",files.Data(),fNreplicas);
+ } else {
+ TString files = fOutputArchive;
+ files.ReplaceAll(".root", "*.root"); // nreplicas etc should be already atttached by use
+ outputArchive = files;
+ }
arr = outputArchive.Tokenize(" ");
TIter next2(arr);
comment = comment1;
first = kTRUE;
while ((os=(TObjString*)next2())) {
if (!first) comment = NULL;
- if (!os->GetString().Contains("@") && fCloseSE.Length())
- fMergingJDL->AddToOutputArchive(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
+ TString currentfile = os->GetString();
+ if (!currentfile.Contains("@") && fCloseSE.Length())
+ fMergingJDL->AddToOutputArchive(Form("%s@%s",currentfile.Data(), fCloseSE.Data()), comment);
else
- fMergingJDL->AddToOutputArchive(os->GetString(), comment);
+ fMergingJDL->AddToOutputArchive(currentfile, comment);
first = kFALSE;
}
delete arr;
}
- arr = fOutputFiles.Tokenize(" ");
+ arr = fOutputFiles.Tokenize(",");
TIter next(arr);
Bool_t first = kTRUE;
- const char *comment = "Files to be archived";
- const char *comment1 = comment;
+ const char *comment = "Files to be saved";
while ((os=(TObjString*)next())) {
// Ignore ouputs in jdl that are also in outputarchive
TString sout = os->GetString();
+ sout.ReplaceAll("*", "");
+ sout.ReplaceAll(".root", "");
if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
if (fOutputArchive.Contains(sout)) continue;
if (!first) comment = NULL;
fGridJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
else
fGridJDL->AddToOutputSandbox(os->GetString(), comment);
- first = kFALSE;
+ first = kFALSE;
+ if (fMergeExcludes.Contains(sout)) continue;
+ if (!os->GetString().Contains("@") && fCloseSE.Length())
+ fMergingJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
+ else
+ fMergingJDL->AddToOutputSandbox(os->GetString(), comment);
}
delete arr;
- if (fOutputFiles.Length()) {
- TString outputFiles = fOutputFiles;
- if (!fMergeExcludes.IsNull()) {
- arr = fMergeExcludes.Tokenize(" ");
- TIter next1(arr);
- while ((os=(TObjString*)next1())) {
- outputFiles.ReplaceAll(Form("%s,",os->GetString().Data()),"");
- outputFiles.ReplaceAll(os->GetString(),"");
- }
- delete arr;
- }
- arr = outputFiles.Tokenize(" ");
- TIter next2(arr);
- comment = comment1;
- first = kTRUE;
- while ((os=(TObjString*)next2())) {
- // Ignore ouputs in jdl that are also in outputarchive
- TString sout = os->GetString();
- if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
- if (fOutputArchive.Contains(sout)) continue;
- if (!first) comment = NULL;
- if (!os->GetString().Contains("@") && fCloseSE.Length())
- fMergingJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
- else
- fMergingJDL->AddToOutputSandbox(os->GetString(), comment);
- }
- delete arr;
- }
fGridJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
fMergingJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
- TString validationScript = fExecutable;
- validationScript.ReplaceAll(".sh", "_validation.sh");
+ TString validationScript = fValidationScript;
fGridJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
- validationScript = fExecutable;
- validationScript.ReplaceAll(".sh", "_mergevalidation.sh");
+ validationScript.ReplaceAll(".sh", "_merge.sh");
fMergingJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
if (fMasterResubmitThreshold) {
fGridJDL->SetValue("MasterResubmitThreshold", Form("\"%d%%\"", fMasterResubmitThreshold));
} else {
if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
if (!fProductionMode && !DirectoryExists(fGridOutputDir)) {
- if (gGrid->Mkdir(fGridOutputDir)) {
+ if (gGrid->Mkdir(fGridOutputDir,"-p")) {
Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
} else {
Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
// all run numbers are considered in one go (jdl). For non-negative indices
// they correspond to the indices in the array fInputFiles.
if (!fInputFiles) return kFALSE;
- TObjString *os;
- TString workdir = gGrid->GetHomeDirectory();
+ TObject *os;
+ TString workdir;
+ if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice")) workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
-
- if (!fRunNumbers.Length() && !fRunRange[0]) {
- // One jdl with no parameters in case input data is specified by name.
- TIter next(fInputFiles);
- while ((os=(TObjString*)next()))
- fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetString().Data()), "Input xml collections");
- if (!fOutputSingle.IsNull())
- fGridJDL->SetOutputDirectory(Form("#alienfulldir#/../%s",fOutputSingle.Data()), "Output directory");
- else {
- fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
- fMergingJDL->SetOutputDirectory(fGridOutputDir);
- }
+ TString stageName = "$2";
+ if (fProductionMode) stageName = "$4";
+ if (!fMergeDirName.IsNull()) {
+ fMergingJDL->AddToInputDataCollection(Form("LF:$1/%s/Stage_%s.xml,nodownload",fMergeDirName.Data(),stageName.Data()), "Collection of files to be merged for current stage");
+ fMergingJDL->SetOutputDirectory(Form("$1/%s/Stage_%s/#alien_counter_03i#",fMergeDirName.Data(),stageName.Data()), "Output directory");
} else {
- // One jdl to be submitted with 2 input parameters: data collection name and output dir prefix
- fGridJDL->AddToInputDataCollection(Form("LF:%s/$1,nodownload", workdir.Data()), "Input xml collections");
- if (!fOutputSingle.IsNull()) {
- if (!fOutputToRunNo) fGridJDL->SetOutputDirectory(Form("#alienfulldir#/%s",fOutputSingle.Data()), "Output directory");
- else fGridJDL->SetOutputDirectory(Form("%s/$2",fGridOutputDir.Data()), "Output directory");
- } else {
- fGridJDL->SetOutputDirectory(Form("%s/$2/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
- fMergingJDL->SetOutputDirectory(Form("%s/$1", fGridOutputDir.Data()), "Output directory");
- }
+ fMergingJDL->AddToInputDataCollection(Form("LF:$1/Stage_%s.xml,nodownload",stageName.Data()), "Collection of files to be merged for current stage");
+ fMergingJDL->SetOutputDirectory(Form("$1/Stage_%s/#alien_counter_03i#",stageName.Data()), "Output directory");
+ }
+ if (fProductionMode) {
+ TIter next(fInputFiles);
+ while ((os=next())) {
+ fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetName()), "Input xml collections");
+ }
+ fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_04i#", fGridOutputDir.Data()));
+ } else {
+ if (!fRunNumbers.Length() && !fRunRange[0]) {
+ // One jdl with no parameters in case input data is specified by name.
+ TIter next(fInputFiles);
+ while ((os=next()))
+ fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetName()), "Input xml collections");
+ if (!fOutputSingle.IsNull())
+ fGridJDL->SetOutputDirectory(Form("#alienfulldir#/../%s",fOutputSingle.Data()), "Output directory");
+ else {
+ fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
+ fMergingJDL->SetOutputDirectory(fGridOutputDir);
+ }
+ } else {
+ // One jdl to be submitted with 2 input parameters: data collection name and output dir prefix
+ fGridJDL->AddToInputDataCollection(Form("LF:%s/$1,nodownload", workdir.Data()), "Input xml collections");
+ if (!fOutputSingle.IsNull()) {
+ if (!fOutputToRunNo) fGridJDL->SetOutputDirectory(Form("#alienfulldir#/%s",fOutputSingle.Data()), "Output directory");
+ else fGridJDL->SetOutputDirectory(Form("%s/$2",fGridOutputDir.Data()), "Output directory");
+ } else {
+ fGridJDL->SetOutputDirectory(Form("%s/$2/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
+ }
+ }
}
-
// Generate the JDL as a string
TString sjdl = fGridJDL->Generate();
TString sjdl1 = fMergingJDL->Generate();
- Int_t index;
+ // Final merge jdl
+ if (!fMergeDirName.IsNull()) {
+ fMergingJDL->SetOutputDirectory(Form("$1/%s",fMergeDirName.Data()), "Output directory");
+ fMergingJDL->AddToInputSandbox(Form("LF:$1/%s/Stage_%s.xml",fMergeDirName.Data(),stageName.Data()));
+ } else {
+ fMergingJDL->SetOutputDirectory("$1", "Output directory");
+ fMergingJDL->AddToInputSandbox(Form("LF:$1/Stage_%s.xml",stageName.Data()));
+ }
+ TString sjdl2 = fMergingJDL->Generate();
+ Int_t index, index1;
sjdl.ReplaceAll("\"LF:", "\n \"LF:");
sjdl.ReplaceAll("(member", "\n (member");
sjdl.ReplaceAll("\",\"VO_", "\",\n \"VO_");
sjdl1.ReplaceAll("{\n \n", "{\n");
sjdl1.ReplaceAll("\n\n", "\n");
sjdl1.ReplaceAll("OutputDirectory", "OutputDir");
+ sjdl2.ReplaceAll("\"LF:", "\n \"LF:");
+ sjdl2.ReplaceAll("(member", "\n (member");
+ sjdl2.ReplaceAll("\",\"VO_", "\",\n \"VO_");
+ sjdl2.ReplaceAll("{", "{\n ");
+ sjdl2.ReplaceAll("};", "\n};");
+ sjdl2.ReplaceAll("{\n \n", "{\n");
+ sjdl2.ReplaceAll("\n\n", "\n");
+ sjdl2.ReplaceAll("OutputDirectory", "OutputDir");
sjdl += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
sjdl.Prepend(Form("Jobtag = {\n \"comment:%s\"\n};\n", fJobTag.Data()));
index = sjdl.Index("JDLVariables");
if (index >= 0) sjdl.Insert(index, "\n# JDL variables\n");
+ sjdl += "Workdirectorysize = {\"5000MB\"};";
+ sjdl1 += "Workdirectorysize = {\"5000MB\"};";
sjdl1 += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
- sjdl1.Prepend(Form("Jobtag = {\n \"comment:Merging_%s\"\n};\n", fJobTag.Data()));
+ index = fJobTag.Index(":");
+ if (index < 0) index = fJobTag.Length();
+ TString jobTag = fJobTag;
+ if (fProductionMode) jobTag.Insert(index,"_Stage$4");
+ sjdl1.Prepend(Form("Jobtag = {\n \"comment:%s_Merging\"\n};\n", jobTag.Data()));
+ if (fProductionMode) {
+ sjdl1.Prepend("# Generated merging jdl (production mode) \
+ \n# $1 = full alien path to output directory to be merged \
+ \n# $2 = train number \
+ \n# $3 = production (like LHC10b) \
+ \n# $4 = merging stage \
+ \n# Stage_<n>.xml made via: find <OutputDir> *Stage<n-1>/*root_archive.zip\n");
+ sjdl2.Prepend(Form("Jobtag = {\n \"comment:%s_FinalMerging\"\n};\n", jobTag.Data()));
+ sjdl2.Prepend("# Generated merging jdl \
+ \n# $1 = full alien path to output directory to be merged \
+ \n# $2 = train number \
+ \n# $3 = production (like LHC10b) \
+ \n# $4 = merging stage \
+ \n# Stage_<n>.xml made via: find <OutputDir> *Stage<n-1>/*root_archive.zip\n");
+ } else {
+ sjdl1.Prepend("# Generated merging jdl \
+ \n# $1 = full alien path to output directory to be merged \
+ \n# $2 = merging stage \
+ \n# xml made via: find <OutputDir> *Stage<n-1>/*root_archive.zip\n");
+ sjdl2.Prepend(Form("Jobtag = {\n \"comment:%s_FinalMerging\"\n};\n", jobTag.Data()));
+ sjdl2.Prepend("# Generated merging jdl \
+ \n# $1 = full alien path to output directory to be merged \
+ \n# $2 = merging stage \
+ \n# xml made via: find <OutputDir> *Stage<n-1>/*root_archive.zip\n");
+ }
index = sjdl1.Index("JDLVariables");
if (index >= 0) sjdl1.Insert(index, "\n# JDL variables\n");
+ index = sjdl2.Index("JDLVariables");
+ if (index >= 0) sjdl2.Insert(index, "\n# JDL variables\n");
+ sjdl1 += "Workdirectorysize = {\"5000MB\"};";
+ sjdl2 += "Workdirectorysize = {\"5000MB\"};";
+ index = sjdl2.Index("Split =");
+ if (index>=0) {
+ index1 = sjdl2.Index("\n", index);
+ sjdl2.Remove(index, index1-index+1);
+ }
+ index = sjdl2.Index("SplitMaxInputFileNumber");
+ if (index>=0) {
+ index1 = sjdl2.Index("\n", index);
+ sjdl2.Remove(index, index1-index+1);
+ }
+ index = sjdl2.Index("InputDataCollection");
+ if (index>=0) {
+ index1 = sjdl2.Index(";", index);
+ sjdl2.Remove(index, index1-index+1);
+ }
+ index = sjdl2.Index("InputDataListFormat");
+ if (index>=0) {
+ index1 = sjdl2.Index("\n", index);
+ sjdl2.Remove(index, index1-index+1);
+ }
+ index = sjdl2.Index("InputDataList");
+ if (index>=0) {
+ index1 = sjdl2.Index("\n", index);
+ sjdl2.Remove(index, index1-index+1);
+ }
+ sjdl2.ReplaceAll("wn.xml", Form("Stage_%s.xml",stageName.Data()));
// Write jdl to file
ofstream out;
out.open(fJDLName.Data(), ios::out);
if (out.bad()) {
- Error("CreateJDL", "Bad file name: %s", fJDLName.Data());
+ Error("WriteJDL", "Bad file name: %s", fJDLName.Data());
return kFALSE;
}
out << sjdl << endl;
+ out.close();
TString mergeJDLName = fExecutable;
mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
if (fMergeViaJDL) {
ofstream out1;
out1.open(mergeJDLName.Data(), ios::out);
- if (out.bad()) {
- Error("CreateJDL", "Bad file name: %s", mergeJDLName.Data());
+ if (out1.bad()) {
+ Error("WriteJDL", "Bad file name: %s", mergeJDLName.Data());
return kFALSE;
}
out1 << sjdl1 << endl;
+ out1.close();
+ ofstream out2;
+ TString finalJDL = mergeJDLName;
+ finalJDL.ReplaceAll(".jdl", "_final.jdl");
+ out2.open(finalJDL.Data(), ios::out);
+ if (out2.bad()) {
+ Error("WriteJDL", "Bad file name: %s", finalJDL.Data());
+ return kFALSE;
+ }
+ out2 << sjdl2 << endl;
+ out2.close();
}
// Copy jdl to grid workspace
if (!copy) {
- Info("CreateJDL", "\n##### You may want to review jdl:%s and analysis macro:%s before running in <submit> mode", fJDLName.Data(), fAnalysisMacro.Data());
+ Info("WriteJDL", "\n##### You may want to review jdl:%s and analysis macro:%s before running in <submit> mode", fJDLName.Data(), fAnalysisMacro.Data());
} else {
TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
TString locjdl1 = Form("%s/%s", fGridOutputDir.Data(),mergeJDLName.Data());
+ TString finalJDL = mergeJDLName;
+ finalJDL.ReplaceAll(".jdl", "_final.jdl");
+ TString locjdl2 = Form("%s/%s", fGridOutputDir.Data(),finalJDL.Data());
if (fProductionMode) {
locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
locjdl1 = Form("%s/%s", workdir.Data(),mergeJDLName.Data());
+ locjdl2 = Form("%s/%s", workdir.Data(),finalJDL.Data());
}
if (FileExists(locjdl)) gGrid->Rm(locjdl);
if (FileExists(locjdl1)) gGrid->Rm(locjdl1);
- Info("CreateJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
+ if (FileExists(locjdl2)) gGrid->Rm(locjdl2);
+ Info("WriteJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
if (fMergeViaJDL) {
- Info("CreateJDL", "\n##### Copying merging JDL file <%s> to your AliEn output directory", mergeJDLName.Data());
+ Info("WriteJDL", "\n##### Copying merging JDL files <%s> to your AliEn output directory", mergeJDLName.Data());
TFile::Cp(Form("file:%s",mergeJDLName.Data()), Form("alien://%s", locjdl1.Data()));
+ TFile::Cp(Form("file:%s",finalJDL.Data()), Form("alien://%s", locjdl2.Data()));
}
}
return kTRUE;
{
// Returns true if file exists.
if (!gGrid) return kFALSE;
- TGridResult *res = gGrid->Ls(lfn);
+ TString slfn = lfn;
+ slfn.ReplaceAll("alien://","");
+ TGridResult *res = gGrid->Ls(slfn);
if (!res) return kFALSE;
TMap *map = dynamic_cast<TMap*>(res->At(0));
if (!map) {
}
//______________________________________________________________________________
-void AliAnalysisAlien::CheckDataType(const char *lfn, Bool_t &is_collection, Bool_t &is_xml, Bool_t &use_tags)
+void AliAnalysisAlien::CheckDataType(const char *lfn, Bool_t &isCollection, Bool_t &isXml, Bool_t &useTags)
{
// Check input data type.
- is_collection = kFALSE;
- is_xml = kFALSE;
- use_tags = kFALSE;
+ isCollection = kFALSE;
+ isXml = kFALSE;
+ useTags = kFALSE;
if (!gGrid) {
Error("CheckDataType", "No connection to grid");
return;
}
- is_collection = IsCollection(lfn);
+ isCollection = IsCollection(lfn);
TString msg = "\n##### file: ";
msg += lfn;
- if (is_collection) {
+ if (isCollection) {
msg += " type: raw_collection;";
// special treatment for collections
- is_xml = kFALSE;
+ isXml = kFALSE;
// check for tag files in the collection
TGridResult *res = gGrid->Command(Form("listFilesFromCollection -z -v %s",lfn), kFALSE);
if (!res) {
msg += " using_tags: No (unknown)";
- Info("CheckDataType", msg.Data());
+ Info("CheckDataType", "%s", msg.Data());
return;
}
const char* typeStr = res->GetKey(0, "origLFN");
if (!typeStr || !strlen(typeStr)) {
msg += " using_tags: No (unknown)";
- Info("CheckDataType", msg.Data());
+ Info("CheckDataType", "%s", msg.Data());
return;
}
TString file = typeStr;
- use_tags = file.Contains(".tag");
- if (use_tags) msg += " using_tags: Yes";
+ useTags = file.Contains(".tag");
+ if (useTags) msg += " using_tags: Yes";
else msg += " using_tags: No";
- Info("CheckDataType", msg.Data());
+ Info("CheckDataType", "%s", msg.Data());
return;
}
TString slfn(lfn);
slfn.ToLower();
- is_xml = slfn.Contains(".xml");
- if (is_xml) {
+ isXml = slfn.Contains(".xml");
+ if (isXml) {
// Open xml collection and check if there are tag files inside
msg += " type: xml_collection;";
TGridCollection *coll = (TGridCollection*)gROOT->ProcessLine(Form("TAlienCollection::Open(\"alien://%s\",1);",lfn));
if (!coll) {
msg += " using_tags: No (unknown)";
- Info("CheckDataType", msg.Data());
+ Info("CheckDataType", "%s", msg.Data());
return;
}
TMap *map = coll->Next();
if (!map) {
msg += " using_tags: No (unknown)";
- Info("CheckDataType", msg.Data());
+ Info("CheckDataType", "%s", msg.Data());
return;
}
map = (TMap*)map->GetValue("");
TString file;
if (map && map->GetValue("name")) file = map->GetValue("name")->GetName();
- use_tags = file.Contains(".tag");
+ useTags = file.Contains(".tag");
delete coll;
- if (use_tags) msg += " using_tags: Yes";
+ if (useTags) msg += " using_tags: Yes";
else msg += " using_tags: No";
- Info("CheckDataType", msg.Data());
+ Info("CheckDataType", "%s", msg.Data());
return;
}
- use_tags = slfn.Contains(".tag");
+ useTags = slfn.Contains(".tag");
if (slfn.Contains(".root")) msg += " type: root file;";
else msg += " type: unknown file;";
- if (use_tags) msg += " using_tags: Yes";
+ if (useTags) msg += " using_tags: Yes";
else msg += " using_tags: No";
- Info("CheckDataType", msg.Data());
+ Info("CheckDataType", "%s", msg.Data());
}
//______________________________________________________________________________
pkg.ReplaceAll(".par", "");
pkg += ".par";
if (gSystem->AccessPathName(pkg)) {
- Error("EnablePackage", "Package %s not found", pkg.Data());
+ Fatal("EnablePackage", "Package %s not found", pkg.Data());
return;
}
if (!TObject::TestBit(AliAnalysisGrid::kUsePars))
fPackages->Add(new TObjString(pkg));
}
+//______________________________________________________________________________
+TChain *AliAnalysisAlien::GetChainForTestMode(const char *treeName) const
+{
+// Make a tree from files having the location specified in fFileForTestMode.
+// Inspired from JF's CreateESDChain.
+ if (fFileForTestMode.IsNull()) {
+ Error("GetChainForTestMode", "For proof test mode please use SetFileForTestMode() pointing to a file that contains data file locations.");
+ return NULL;
+ }
+ if (gSystem->AccessPathName(fFileForTestMode)) {
+ Error("GetChainForTestMode", "File not found: %s", fFileForTestMode.Data());
+ return NULL;
+ }
+ // Open the file
+ ifstream in;
+ in.open(fFileForTestMode);
+ Int_t count = 0;
+ // Read the input list of files and add them to the chain
+ TString line;
+ TChain *chain = new TChain(treeName);
+ while (in.good())
+ {
+ in >> line;
+ if (line.IsNull()) continue;
+ if (count++ == fNtestFiles) break;
+ TString esdFile(line);
+ TFile *file = TFile::Open(esdFile);
+ if (file) {
+ if (!file->IsZombie()) chain->Add(esdFile);
+ file->Close();
+ } else {
+ Error("GetChainforTestMode", "Skipping un-openable file: %s", esdFile.Data());
+ }
+ }
+ in.close();
+ if (!chain->GetListOfFiles()->GetEntries()) {
+ Error("GetChainForTestMode", "No file from %s could be opened", fFileForTestMode.Data());
+ delete chain;
+ return NULL;
+ }
+// chain->ls();
+ return chain;
+}
+
//______________________________________________________________________________
const char *AliAnalysisAlien::GetJobStatus(Int_t jobidstart, Int_t lastid, Int_t &nrunning, Int_t &nwaiting, Int_t &nerror, Int_t &ndone)
{
Int_t pid;
for (Int_t ijob=0; ijob<nentries; ijob++) {
status = (TGridJobStatus *)list->At(ijob);
- pid = gROOT->ProcessLine(Form("atoi(((TAlienJobStatus*)0x%lx)->GetKey(\"queueId\"));", (ULong_t)status));
+ pid = gROOT->ProcessLine(Form("atoi(((TAlienJobStatus*)%p)->GetKey(\"queueId\"));", status));
if (pid<jobidstart) continue;
if (pid == lastid) {
- gROOT->ProcessLine(Form("sprintf((char*)0x%lx,((TAlienJobStatus*)0x%lx)->GetKey(\"status\"));",(ULong_t)mstatus, (ULong_t)status));
+ gROOT->ProcessLine(Form("sprintf((char*)%p,((TAlienJobStatus*)%p)->GetKey(\"status\"));",mstatus, status));
}
switch (status->GetStatus()) {
case TGridJobStatus::kWAITING:
{
// Print current plugin settings.
printf("### AliEn analysis plugin current settings ###\n");
+ AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
+ if (mgr && mgr->IsProofMode()) {
+ TString proofType = "= PLUGIN IN PROOF MODE ON CLUSTER:_________________";
+ if (TestBit(AliAnalysisGrid::kTest))
+ proofType = "= PLUGIN IN PROOF LITE MODE ON CLUSTER:____________";
+ printf("%s %s\n", proofType.Data(), fProofCluster.Data());
+ if (!fProofDataSet.IsNull())
+ printf("= Requested data set:___________________________ %s\n", fProofDataSet.Data());
+ if (fProofReset==1)
+ printf("= Soft reset signal will be send to master______ CHANGE BEHAVIOR AFTER COMPLETION\n");
+ if (fProofReset>1)
+ printf("= Hard reset signal will be send to master______ CHANGE BEHAVIOR AFTER COMPLETION\n");
+ if (!fRootVersionForProof.IsNull())
+ printf("= ROOT version requested________________________ %s\n", fRootVersionForProof.Data());
+ else
+ printf("= ROOT version requested________________________ default\n");
+ printf("= AliRoot version requested_____________________ %s\n", fAliROOTVersion.Data());
+ if (!fAliRootMode.IsNull())
+ printf("= Requested AliRoot mode________________________ %s\n", fAliRootMode.Data());
+ if (fNproofWorkers)
+ printf("= Number of PROOF workers limited to____________ %d\n", fNproofWorkers);
+ if (fNproofWorkersPerSlave)
+ printf("= Maximum number of workers per slave___________ %d\n", fNproofWorkersPerSlave);
+ if (TestSpecialBit(kClearPackages))
+ printf("= ClearPackages requested...\n");
+ if (fIncludePath.Data())
+ printf("= Include path for runtime task compilation: ___ %s\n", fIncludePath.Data());
+ printf("= Additional libs to be loaded or souces to be compiled runtime: <%s>\n",fAdditionalLibs.Data());
+ if (fPackages && fPackages->GetEntries()) {
+ TIter next(fPackages);
+ TObject *obj;
+ TString list;
+ while ((obj=next())) list += obj->GetName();
+ printf("= Par files to be used: ________________________ %s\n", list.Data());
+ }
+ if (TestSpecialBit(kProofConnectGrid))
+ printf("= Requested PROOF connection to grid\n");
+ return;
+ }
+ printf("= OverwriteMode:________________________________ %d\n", fOverwriteMode);
+ if (fOverwriteMode) {
+ printf("***** NOTE: Overwrite mode will overwrite the input generated datasets and partial results from previous analysis. \
+ \n***** To disable, use: plugin->SetOverwriteMode(kFALSE);\n");
+ }
+ printf("= Copy files to grid: __________________________ %s\n", (IsUseCopy())?"YES":"NO");
+ printf("= Check if files can be copied to grid: ________ %s\n", (IsCheckCopy())?"YES":"NO");
printf("= Production mode:______________________________ %d\n", fProductionMode);
printf("= Version of API requested: ____________________ %s\n", fAPIVersion.Data());
printf("= Version of ROOT requested: ___________________ %s\n", fROOTVersion.Data());
if (fRunNumbers.Length())
printf("= Run numbers to be processed: _________________ %s\n", fRunNumbers.Data());
if (fRunRange[0])
- printf("= Run range to be processed: ___________________ %s%d-%s%d\n", fRunPrefix.Data(), fRunRange[0], fRunPrefix.Data(), fRunRange[1]);
+ printf("= Run range to be processed: ___________________ %d-%d\n", fRunRange[0], fRunRange[1]);
if (!fRunRange[0] && !fRunNumbers.Length()) {
TIter next(fInputFiles);
TObject *obj;
printf("= List of output files to be registered: _______ %s\n", fOutputFiles.Data());
printf("= List of outputs going to be archived: ________ %s\n", fOutputArchive.Data());
printf("= List of outputs that should not be merged: ___ %s\n", fMergeExcludes.Data());
+ printf("= List of outputs produced during Terminate: ___ %s\n", fTerminateFiles.Data());
printf("=====================================================================\n");
printf("= Job price: ___________________________________ %d\n", fPrice);
printf("= Time to live (TTL): __________________________ %d\n", fTTL);
printf("= Max number of subjob fails to kill: __________ %d\n", fMaxInitFailed);
if (fMasterResubmitThreshold>0)
printf("= Resubmit master job if failed subjobs >_______ %d\n", fMasterResubmitThreshold);
+ printf("= Number of replicas for the output files_______ %d\n", fNreplicas);
if (fNrunsPerMaster>0)
printf("= Number of runs per master job: _______________ %d\n", fNrunsPerMaster);
printf("= Number of files in one chunk to be merged: ___ %d\n", fMaxMergeFiles);
printf("= Force job outputs to storage element: ________ %s\n", fCloseSE.Data());
if (fFriendChainName.Length())
printf("= Open friend chain file on worker: ____________ %s\n", fFriendChainName.Data());
- if (fPackages) {
+ if (fPackages && fPackages->GetEntries()) {
TIter next(fPackages);
TObject *obj;
TString list;
fMaxInitFailed = 0;
fMasterResubmitThreshold = 0;
fNtestFiles = 10;
+ fNreplicas = 2;
fRunRange[0] = 0;
fRunRange[1] = 0;
+ fRunPrefix = "%d";
fNrunsPerMaster = 1;
fMaxMergeFiles = 100;
fRunNumbers = "";
fDataPattern = "*AliESDs.root"; // Can be like: *AliESDs.root, */pass1/*AliESDs.root, ...
fFriendChainName = "";
fGridOutputDir = "output";
- fOutputArchive = "log_archive.zip:stdout,stderr root_archive.zip:*.root";
+ fOutputArchive = "log_archive.zip:std*@disk=1 root_archive.zip:*.root@disk=2";
fOutputFiles = ""; // Like "AliAODs.root histos.root"
fInputFormat = "xml-single";
fJDLName = "analysis.jdl";
fJobTag = "Automatically generated analysis JDL";
fMergeExcludes = "";
fMergeViaJDL = 0;
+ SetUseCopy(kTRUE);
+ SetCheckCopy(kTRUE);
+ SetDefaultOutputs(kTRUE);
+ fOverwriteMode = 1;
}
//______________________________________________________________________________
-Bool_t AliAnalysisAlien::MergeOutput(const char *output, const char *basedir, Int_t nmaxmerge)
+Bool_t AliAnalysisAlien::CheckMergedFiles(const char *filename, const char *aliendir, Int_t nperchunk, const char *jdl)
{
-// Merge all registered outputs from basedir.
- TString output_file = output;
+// Checks current merge stage, makes xml for the next stage, counts number of files, submits next stage.
+ // First check if the result is already in the output directory.
+ if (FileExists(Form("%s/%s",aliendir,filename))) {
+ printf("Final merged results found. Not merging again.\n");
+ return kFALSE;
+ }
+ // Now check the last stage done.
+ Int_t stage = 0;
+ while (1) {
+ if (!FileExists(Form("%s/Stage_%d.xml",aliendir, stage+1))) break;
+ stage++;
+ }
+ // Next stage of merging
+ stage++;
+ TString pattern = "*root_archive.zip";
+ if (stage>1) pattern = Form("Stage_%d/*root_archive.zip", stage-1);
+ TGridResult *res = gGrid->Command(Form("find -x Stage_%d %s %s", stage, aliendir, pattern.Data()));
+ if (res) delete res;
+ // Write standard output to file
+ gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", Form("Stage_%d.xml",stage)));
+ // Count the number of files inside
+ ifstream ifile;
+ ifile.open(Form("Stage_%d.xml",stage));
+ if (!ifile.good()) {
+ ::Error("CheckMergedFiles", "Could not redirect result of the find command to file %s", Form("Stage_%d.xml",stage));
+ return kFALSE;
+ }
+ TString line;
+ Int_t nfiles = 0;
+ while (!ifile.eof()) {
+ ifile >> line;
+ if (line.Contains("/event")) nfiles++;
+ }
+ ifile.close();
+ if (!nfiles) {
+ ::Error("CheckMergedFiles", "Cannot start Stage_%d merging since Stage_%d did not produced yet output", stage, stage-1);
+ return kFALSE;
+ } else {
+ printf("=== Stage_%d produced %d files\n", stage-1, nfiles);
+ }
+ // Copy the file in the output directory
+ printf("===> Copying collection %s in the output directory %s\n", Form("Stage_%d.xml",stage), aliendir);
+ TFile::Cp(Form("Stage_%d.xml",stage), Form("alien://%s/Stage_%d.xml",aliendir,stage));
+ // Check if this is the last stage to be done.
+ Bool_t laststage = (nfiles<nperchunk);
+ if (fMaxMergeStages && stage>=fMaxMergeStages) laststage = kTRUE;
+ if (laststage) {
+ printf("### Submiting final merging stage %d\n", stage);
+ TString finalJDL = jdl;
+ finalJDL.ReplaceAll(".jdl", "_final.jdl");
+ TString query = Form("submit %s %s %d", finalJDL.Data(), aliendir, stage);
+ Int_t jobId = SubmitSingleJob(query);
+ if (!jobId) return kFALSE;
+ } else {
+ printf("### Submiting merging stage %d\n", stage);
+ TString query = Form("submit %s %s %d", jdl, aliendir, stage);
+ Int_t jobId = SubmitSingleJob(query);
+ if (!jobId) return kFALSE;
+ }
+ return kTRUE;
+}
+
+//______________________________________________________________________________
+Int_t AliAnalysisAlien::SubmitSingleJob(const char *query)
+{
+// Submits a single job corresponding to the query and returns job id. If 0 submission failed.
+ if (!gGrid) return 0;
+ printf("=> %s ------> ",query);
+ TGridResult *res = gGrid->Command(query);
+ if (!res) return 0;
+ TString jobId = res->GetKey(0,"jobId");
+ delete res;
+ if (jobId.IsNull()) {
+ printf("submission failed. Reason:\n");
+ gGrid->Stdout();
+ gGrid->Stderr();
+ ::Error("SubmitSingleJob", "Your query %s could not be submitted", query);
+ return 0;
+ }
+ printf(" Job id: %s\n", jobId.Data());
+ return atoi(jobId);
+}
+
+//______________________________________________________________________________
+Bool_t AliAnalysisAlien::MergeOutput(const char *output, const char *basedir, Int_t nmaxmerge, Int_t stage)
+{
+// Merge given output files from basedir. Basedir can be an alien output directory
+// but also an xml file with root_archive.zip locations. The file merger will merge nmaxmerge
+// files in a group (ignored for xml input). Merging can be done in stages:
+// stage=0 : will merge all existing files in a single stage, supporting resume if run locally
+// stage=1 : works with an xml of all root_archive.zip in the output directory
+// stage>1 : works with an xml of all root_archive.zip in the Stage_<n-1> directory
+ TString outputFile = output;
TString command;
- TString output_chunk;
- TString previous_chunk = "";
- Int_t count_chunk = 0;
- Int_t count_zero = nmaxmerge;
+ TString outputChunk;
+ TString previousChunk = "";
+ TObjArray *listoffiles = new TObjArray();
+// listoffiles->SetOwner();
+ Int_t countChunk = 0;
+ Int_t countZero = nmaxmerge;
Bool_t merged = kTRUE;
- Int_t index = output_file.Index("@");
- if (index > 0) output_file.Remove(index);
- command = Form("find %s/ *%s", basedir, output_file.Data());
- printf("command: %s\n", command.Data());
- TGridResult *res = gGrid->Command(command);
- if (!res) {
- printf("Error: No result for the find command\n");
+ Int_t index = outputFile.Index("@");
+ if (index > 0) outputFile.Remove(index);
+ TString inputFile = outputFile;
+ TString sbasedir = basedir;
+ if (sbasedir.Contains(".xml")) {
+ // Merge files pointed by the xml - ignore nmaxmerge and set ichunk to 0
+ nmaxmerge = 9999999;
+ TGridCollection *coll = (TGridCollection*)gROOT->ProcessLine(Form("TAlienCollection::Open(\"%s\");", basedir));
+ if (!coll) {
+ ::Error("MergeOutput", "Input XML collection empty.");
+ return kFALSE;
+ }
+ // Iterate grid collection
+ while (coll->Next()) {
+ TString fname = gSystem->DirName(coll->GetTURL());
+ fname += "/";
+ fname += inputFile;
+ listoffiles->Add(new TNamed(fname.Data(),""));
+ }
+ } else {
+ command = Form("find %s/ *%s", basedir, inputFile.Data());
+ printf("command: %s\n", command.Data());
+ TGridResult *res = gGrid->Command(command);
+ if (!res) {
+ ::Error("MergeOutput","No result for the find command\n");
+ delete listoffiles;
+ return kFALSE;
+ }
+ TIter nextmap(res);
+ TMap *map = 0;
+ while ((map=(TMap*)nextmap())) {
+ TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl"));
+ if (!objs || !objs->GetString().Length()) {
+ // Nothing found - skip this output
+ delete res;
+ delete listoffiles;
+ return kFALSE;
+ }
+ listoffiles->Add(new TNamed(objs->GetName(),""));
+ }
+ delete res;
+ }
+ if (!listoffiles->GetEntries()) {
+ ::Error("MergeOutput","No result for the find command\n");
+ delete listoffiles;
return kFALSE;
}
TFileMerger *fm = 0;
- TIter nextmap(res);
- TMap *map = 0;
- // Check if there is a merge operation to resume
- output_chunk = output_file;
- output_chunk.ReplaceAll(".root", "_*.root");
+ TIter next0(listoffiles);
+ TObjArray *listoffilestmp = new TObjArray();
+ listoffilestmp->SetOwner();
+ TObject *nextfile;
+ TString snextfile;
+ // Keep only the files at upper level
+ Int_t countChar = 0;
+ while ((nextfile=next0())) {
+ snextfile = nextfile->GetName();
+ Int_t crtCount = snextfile.CountChar('/');
+ if (nextfile == listoffiles->First()) countChar = crtCount;
+ if (crtCount < countChar) countChar = crtCount;
+ }
+ next0.Reset();
+ while ((nextfile=next0())) {
+ snextfile = nextfile->GetName();
+ Int_t crtCount = snextfile.CountChar('/');
+ if (crtCount > countChar) {
+ delete nextfile;
+ continue;
+ }
+ listoffilestmp->Add(nextfile);
+ }
+ delete listoffiles;
+ listoffiles = listoffilestmp; // Now contains 'good' files
+ listoffiles->Print();
+ TIter next(listoffiles);
+ // Check if there is a merge operation to resume. Works only for stage 0 or 1.
+ outputChunk = outputFile;
+ outputChunk.ReplaceAll(".root", "_*.root");
// Check for existent temporary merge files
- if (!gSystem->Exec(Form("ls %s", output_chunk.Data()))) {
- while (1) {
- // Skip as many input files as in a chunk
- for (Int_t counter=0; counter<nmaxmerge; counter++) map = (TMap*)nextmap();
- if (!map) {
- ::Error("MergeOutputs", "Cannot resume merging for <%s>, nentries=%d", output_file.Data(), res->GetSize());
- delete res;
- return kFALSE;
+ // Check overwrite mode and remove previous partial results if needed
+ // Preserve old merging functionality for stage 0.
+ if (stage==0) {
+ if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
+ while (1) {
+ // Skip as many input files as in a chunk
+ for (Int_t counter=0; counter<nmaxmerge; counter++) {
+ nextfile = next();
+ if (!nextfile) {
+ ::Error("MergeOutput", "Mismatch found. Please remove partial merged files from local dir.");
+ delete listoffiles;
+ return kFALSE;
+ }
+ snextfile = nextfile->GetName();
+ }
+ outputChunk = outputFile;
+ outputChunk.ReplaceAll(".root", Form("_%04d.root", countChunk));
+ countChunk++;
+ if (gSystem->AccessPathName(outputChunk)) continue;
+ // Merged file with chunks up to <countChunk> found
+ ::Info("MergeOutput", "Resume merging of <%s> from <%s>\n", outputFile.Data(), outputChunk.Data());
+ previousChunk = outputChunk;
+ break;
}
- output_chunk = output_file;
- output_chunk.ReplaceAll(".root", Form("_%04d.root", count_chunk));
- count_chunk++;
- if (gSystem->AccessPathName(output_chunk)) continue;
- // Merged file with chunks up to <count_chunk> found
- printf("Resume merging of <%s> from <%s>\n", output_file.Data(), output_chunk.Data());
- previous_chunk = output_chunk;
- break;
- }
- }
- count_zero = nmaxmerge;
+ }
+ countZero = nmaxmerge;
- while ((map=(TMap*)nextmap())) {
- // Loop 'find' results and get next LFN
- if (count_zero == nmaxmerge) {
- // First file in chunk - create file merger and add previous chunk if any.
- fm = new TFileMerger(kFALSE);
- fm->SetFastMethod(kTRUE);
- if (previous_chunk.Length()) fm->AddFile(previous_chunk.Data());
- output_chunk = output_file;
- output_chunk.ReplaceAll(".root", Form("_%04d.root", count_chunk));
- }
- // If last file found, put merged results in the output file
- if (map == res->Last()) output_chunk = output_file;
- TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl"));
- if (!objs || !objs->GetString().Length()) {
- // Nothing found - skip this output
- delete res;
- delete fm;
- return kFALSE;
- }
- // Add file to be merged and decrement chunk counter.
- fm->AddFile(objs->GetString());
- count_zero--;
- if (count_zero==0 || map == res->Last()) {
- fm->OutputFile(output_chunk);
- if (!fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
- // Nothing found - skip this output
- ::Warning("MergeOutputs", "No <%s> files found.", output_file.Data());
- delete res;
- delete fm;
- return kFALSE;
+ while ((nextfile=next())) {
+ snextfile = nextfile->GetName();
+ // Loop 'find' results and get next LFN
+ if (countZero == nmaxmerge) {
+ // First file in chunk - create file merger and add previous chunk if any.
+ fm = new TFileMerger(kFALSE);
+ fm->SetFastMethod(kTRUE);
+ if (previousChunk.Length()) fm->AddFile(previousChunk.Data());
+ outputChunk = outputFile;
+ outputChunk.ReplaceAll(".root", Form("_%04d.root", countChunk));
}
- // Merge the outputs, then go to next chunk
- if (!fm->Merge()) {
- ::Error("MergeOutputs", "Could not merge all <%s> files", output_file.Data());
- delete res;
- delete fm;
- merged = kFALSE;
- return kFALSE;
- } else {
- ::Info("MergeOutputs", "\n##### Merged %d output files to <%s>", fm->GetMergeList()->GetSize(), output_chunk.Data());
- gSystem->Unlink(previous_chunk);
+ // If last file found, put merged results in the output file
+ if (nextfile == listoffiles->Last()) outputChunk = outputFile;
+ // Add file to be merged and decrement chunk counter.
+ fm->AddFile(snextfile);
+ countZero--;
+ if (countZero==0 || nextfile == listoffiles->Last()) {
+ if (!fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
+ // Nothing found - skip this output
+ ::Warning("MergeOutput", "No <%s> files found.", inputFile.Data());
+ merged = kFALSE;
+ break;
+ }
+ fm->OutputFile(outputChunk);
+ // Merge the outputs, then go to next chunk
+ if (!fm->Merge()) {
+ ::Error("MergeOutput", "Could not merge all <%s> files", outputFile.Data());
+ merged = kFALSE;
+ break;
+ } else {
+ ::Info("MergeOutputs", "\n##### Merged %d output files to <%s>", fm->GetMergeList()->GetSize(), outputChunk.Data());
+ gSystem->Unlink(previousChunk);
+ }
+ if (nextfile == listoffiles->Last()) break;
+ countChunk++;
+ countZero = nmaxmerge;
+ previousChunk = outputChunk;
}
- if (map == res->Last()) {
- delete res;
- delete fm;
- break;
- }
- count_chunk++;
- count_zero = nmaxmerge;
- previous_chunk = output_chunk;
}
+ delete listoffiles;
+ delete fm;
+ return merged;
+ }
+ // Merging stage different than 0.
+ // Move to the begining of the requested chunk.
+ fm = new TFileMerger(kFALSE);
+ fm->SetFastMethod(kTRUE);
+ while ((nextfile=next())) fm->AddFile(nextfile->GetName());
+ delete listoffiles;
+ if (!fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
+ // Nothing found - skip this output
+ ::Warning("MergeOutput", "No <%s> files found.", inputFile.Data());
+ delete fm;
+ return kFALSE;
+ }
+ fm->OutputFile(outputFile);
+ // Merge the outputs
+ if (!fm->Merge()) {
+ ::Error("MergeOutput", "Could not merge all <%s> files", outputFile.Data());
+ delete fm;
+ return kFALSE;
+ } else {
+ ::Info("MergeOutput", "\n##### Merged %d output files to <%s>", fm->GetMergeList()->GetSize(), outputFile.Data());
}
- return merged;
+ delete fm;
+ return kTRUE;
}
//______________________________________________________________________________
Error("MergeOutputs", "Cannot merge outputs without grid connection. Terminate will NOT be executed");
return kFALSE;
}
- if (fMergeViaJDL && !fProductionMode && TestBit(AliAnalysisGrid::kMerge)) {
+ if (fMergeViaJDL) {
+ if (!TestBit(AliAnalysisGrid::kMerge)) {
+ Info("MergeOutputs", "### Re-run with <MergeViaJDL> option in terminate mode of the plugin to submit merging jobs ###");
+ return kFALSE;
+ }
+ if (fProductionMode) {
+ Info("MergeOutputs", "### Merging will be submitted by LPM manager... ###");
+ return kFALSE;
+ }
Info("MergeOutputs", "Submitting merging JDL");
- SubmitMerging();
+ if (!SubmitMerging()) return kFALSE;
Info("MergeOutputs", "### Re-run with <MergeViaJDL> off to collect results after merging jobs are done ###");
- Info("MergeOutputs", "### Trying to continue merging ... (may fail if exited the shell prematurely)");
+ Info("MergeOutputs", "### The Terminate() method is executed by the merging jobs");
+ return kFALSE;
}
// Get the output path
if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
return kFALSE;
}
// Check if fast read option was requested
+ Info("MergeOutputs", "Started local merging of output files from: alien://%s \
+ \n======= overwrite mode = %d", fGridOutputDir.Data(), (Int_t)fOverwriteMode);
if (fFastReadOption) {
- Warning("MergeOutputs", "You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !");
- gEnv->SetValue("XNet.ConnectTimeout",5);
- gEnv->SetValue("XNet.RequestTimeout",5);
+ Warning("MergeOutputs", "You requested FastRead option. Using xrootd flags to reduce timeouts. This may skip some files that could be accessed ! \
+ \n+++ NOTE: To disable this option, use: plugin->SetFastReadOption(kFALSE)");
+ gEnv->SetValue("XNet.ConnectTimeout",50);
+ gEnv->SetValue("XNet.RequestTimeout",50);
gEnv->SetValue("XNet.MaxRedirectCount",2);
- gEnv->SetValue("XNet.ReconnectTimeout",5);
+ gEnv->SetValue("XNet.ReconnectTimeout",50);
gEnv->SetValue("XNet.FirstConnectMaxCnt",1);
}
- TObjArray *list = fOutputFiles.Tokenize(" ");
+ // Make sure we change the temporary directory
+ gSystem->Setenv("TMPDIR", gSystem->pwd());
+ TObjArray *list = fOutputFiles.Tokenize(",");
TIter next(list);
TObjString *str;
- TString output_file;
+ TString outputFile;
Bool_t merged = kTRUE;
while((str=(TObjString*)next())) {
- output_file = str->GetString();
- Int_t index = output_file.Index("@");
- if (index > 0) output_file.Remove(index);
+ outputFile = str->GetString();
+ Int_t index = outputFile.Index("@");
+ if (index > 0) outputFile.Remove(index);
+ TString outputChunk = outputFile;
+ outputChunk.ReplaceAll(".root", "_*.root");
// Skip already merged outputs
- if (!gSystem->AccessPathName(output_file)) {
- Info("MergeOutputs", "Output file <%s> found. Not merging again.", output_file.Data());
- continue;
- }
+ if (!gSystem->AccessPathName(outputFile)) {
+ if (fOverwriteMode) {
+ Info("MergeOutputs", "Overwrite mode. Existing file %s was deleted.", outputFile.Data());
+ gSystem->Unlink(outputFile);
+ if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
+ Info("MergeOutput", "Overwrite mode: partial merged files %s will removed",
+ outputChunk.Data());
+ gSystem->Exec(Form("rm -f %s", outputChunk.Data()));
+ }
+ } else {
+ Info("MergeOutputs", "Output file <%s> found. Not merging again.", outputFile.Data());
+ continue;
+ }
+ } else {
+ if (!gSystem->Exec(Form("ls %s 2>/dev/null", outputChunk.Data()))) {
+ Info("MergeOutput", "Overwrite mode: partial merged files %s will removed",
+ outputChunk.Data());
+ gSystem->Exec(Form("rm -f %s", outputChunk.Data()));
+ }
+ }
if (fMergeExcludes.Length() &&
- fMergeExcludes.Contains(output_file.Data())) continue;
+ fMergeExcludes.Contains(outputFile.Data())) continue;
// Perform a 'find' command in the output directory, looking for registered outputs
- merged = MergeOutput(output_file, fGridOutputDir, fMaxMergeFiles);
+ merged = MergeOutput(outputFile, fGridOutputDir, fMaxMergeFiles);
if (!merged) {
Error("MergeOutputs", "Terminate() will NOT be executed");
return kFALSE;
- }
+ }
+ TFile *fileOpened = (TFile*)gROOT->GetListOfFiles()->FindObject(outputFile);
+ if (fileOpened) fileOpened->Close();
}
return kTRUE;
}
// Use the output files connected to output containers from the analysis manager
// rather than the files defined by SetOutputFiles
if (flag && !TObject::TestBit(AliAnalysisGrid::kDefaultOutputs))
- Info("SetDefaultOutputs", "Plugin will use the output files taken from \
- analysis manager");
+ Info("SetDefaultOutputs", "Plugin will use the output files taken from analysis manager");
TObject::SetBit(AliAnalysisGrid::kDefaultOutputs, flag);
}
+//______________________________________________________________________________
+void AliAnalysisAlien::SetOutputFiles(const char *list)
+{
+// Manually set the output files list.
+// Removes duplicates. Not allowed if default outputs are not disabled.
+ if (TObject::TestBit(AliAnalysisGrid::kDefaultOutputs)) {
+ Fatal("SetOutputFiles", "You have to explicitly call SetDefaultOutputs(kFALSE) to manually set output files.");
+ return;
+ }
+ Info("SetOutputFiles", "Output file list is set manually - you are on your own.");
+ fOutputFiles = "";
+ TString slist = list;
+ if (slist.Contains("@")) Warning("SetOutputFiles","The plugin does not allow explicit SE's. Please use: SetNumberOfReplicas() instead.");
+ TObjArray *arr = slist.Tokenize(" ");
+ TObjString *os;
+ TIter next(arr);
+ TString sout;
+ while ((os=(TObjString*)next())) {
+ sout = os->GetString();
+ if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
+ if (fOutputFiles.Contains(sout)) continue;
+ if (!fOutputFiles.IsNull()) fOutputFiles += ",";
+ fOutputFiles += sout;
+ }
+ delete arr;
+}
+
+//______________________________________________________________________________
+void AliAnalysisAlien::SetOutputArchive(const char *list)
+{
+// Manually set the output archive list. Free text - you are on your own...
+// Not allowed if default outputs are not disabled.
+ if (TObject::TestBit(AliAnalysisGrid::kDefaultOutputs)) {
+ Fatal("SetOutputArchive", "You have to explicitly call SetDefaultOutputs(kFALSE) to manually set the output archives.");
+ return;
+ }
+ Info("SetOutputArchive", "Output archive is set manually - you are on your own.");
+ fOutputArchive = list;
+}
+
+//______________________________________________________________________________
+void AliAnalysisAlien::SetPreferedSE(const char */*se*/)
+{
+// Setting a prefered output SE is not allowed anymore.
+ Warning("SetPreferedSE", "Setting a preferential SE is not allowed anymore via the plugin. Use SetNumberOfReplicas() and SetDefaultOutputs()");
+}
+
//______________________________________________________________________________
Bool_t AliAnalysisAlien::StartAnalysis(Long64_t /*nentries*/, Long64_t /*firstEntry*/)
{
// Start remote grid analysis.
-
- // Check if output files have to be taken from the analysis manager
- if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
- AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
- if (!mgr || !mgr->IsInitialized()) {
- Error("StartAnalysis", "You need an initialized analysis manager for this");
+ AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
+ Bool_t testMode = TestBit(AliAnalysisGrid::kTest);
+ if (!mgr || !mgr->IsInitialized()) {
+ Error("StartAnalysis", "You need an initialized analysis manager for this");
+ return kFALSE;
+ }
+ // Are we in PROOF mode ?
+ if (mgr->IsProofMode()) {
+ Info("StartAnalysis", "##### Starting PROOF analysis on cluster <%s> via the plugin #####", fProofCluster.Data());
+ if (fProofCluster.IsNull()) {
+ Error("StartAnalysis", "You need to specify the proof cluster name via SetProofCluster");
return kFALSE;
+ }
+ if (fProofDataSet.IsNull() && !testMode) {
+ Error("StartAnalysis", "You need to specify a dataset using SetProofDataSet()");
+ return kFALSE;
+ }
+ // Set the needed environment
+ gEnv->SetValue("XSec.GSI.DelegProxy","2");
+ // Do we need to reset PROOF ? The success of the Reset operation cannot be checked
+ if (fProofReset && !testMode) {
+ if (fProofReset==1) {
+ Info("StartAnalysis", "Sending soft reset signal to proof cluster %s", fProofCluster.Data());
+ gROOT->ProcessLine(Form("TProof::Reset(\"%s\", kFALSE);", fProofCluster.Data()));
+ } else {
+ Info("StartAnalysis", "Sending hard reset signal to proof cluster %s", fProofCluster.Data());
+ gROOT->ProcessLine(Form("TProof::Reset(\"%s\", kTRUE);", fProofCluster.Data()));
+ }
+ Info("StartAnalysis", "Stopping the analysis. Please use SetProofReset(0) to resume.");
+ return kFALSE;
+ }
+ // Do we need to change the ROOT version ? The success of this cannot be checked.
+ if (!fRootVersionForProof.IsNull() && !testMode) {
+ gROOT->ProcessLine(Form("TProof::Mgr(\"%s\")->SetROOTVersion(\"%s\");",
+ fProofCluster.Data(), fRootVersionForProof.Data()));
+ }
+ // Connect to PROOF and check the status
+ Long_t proof = 0;
+ TString sworkers;
+ if (fNproofWorkersPerSlave) sworkers = Form("workers=%dx", fNproofWorkersPerSlave);
+ else if (fNproofWorkers) sworkers = Form("workers=%d", fNproofWorkers);
+ if (!testMode) {
+ if (!sworkers.IsNull())
+ proof = gROOT->ProcessLine(Form("TProof::Open(\"%s\", \"%s\");", fProofCluster.Data(), sworkers.Data()));
+ else
+ proof = gROOT->ProcessLine(Form("TProof::Open(\"%s\");", fProofCluster.Data()));
+ } else {
+ proof = gROOT->ProcessLine("TProof::Open(\"\");");
+ if (!proof) {
+ Error("StartAnalysis", "Could not start PROOF in test mode");
+ return kFALSE;
+ }
+ }
+ if (!proof) {
+ Error("StartAnalysis", "Could not connect to PROOF cluster <%s>", fProofCluster.Data());
+ return kFALSE;
+ }
+ if (fNproofWorkersPerSlave*fNproofWorkers > 0)
+ gROOT->ProcessLine(Form("gProof->SetParallel(%d);", fNproofWorkers));
+ // Is dataset existing ?
+ if (!testMode) {
+ TString dataset = fProofDataSet;
+ Int_t index = dataset.Index("#");
+ if (index>=0) dataset.Remove(index);
+// if (!gROOT->ProcessLine(Form("gProof->ExistsDataSet(\"%s\");",fProofDataSet.Data()))) {
+// Error("StartAnalysis", "Dataset %s not existing", fProofDataSet.Data());
+// return kFALSE;
+// }
+// Info("StartAnalysis", "Dataset %s found", dataset.Data());
+ }
+ // Is ClearPackages() needed ?
+ if (TestSpecialBit(kClearPackages)) {
+ Info("StartAnalysis", "ClearPackages signal sent to PROOF. Use SetClearPackages(kFALSE) to reset this.");
+ gROOT->ProcessLine("gProof->ClearPackages();");
+ }
+ // Is a given aliroot mode requested ?
+ TList optionsList;
+ TString parLibs;
+ if (!fAliRootMode.IsNull()) {
+ TString alirootMode = fAliRootMode;
+ if (alirootMode == "default") alirootMode = "";
+ Info("StartAnalysis", "You are requesting AliRoot mode: %s", fAliRootMode.Data());
+ optionsList.SetOwner();
+ optionsList.Add(new TNamed("ALIROOT_MODE", alirootMode.Data()));
+ // Check the additional libs to be loaded
+ TString extraLibs;
+ Bool_t parMode = kFALSE;
+ if (!alirootMode.IsNull()) extraLibs = "ANALYSIS:ANALYSISalice";
+ // Parse the extra libs for .so
+ if (fAdditionalLibs.Length()) {
+ TObjArray *list = fAdditionalLibs.Tokenize(" ");
+ TIter next(list);
+ TObjString *str;
+ while((str=(TObjString*)next())) {
+ if (str->GetString().Contains(".so")) {
+ if (parMode) {
+ Warning("StartAnalysis", "Plugin does not support loading libs after par files in PROOF mode. Library %s and following will not load on workers", str->GetName());
+ break;
+ }
+ TString stmp = str->GetName();
+ if (stmp.BeginsWith("lib")) stmp.Remove(0,3);
+ stmp.ReplaceAll(".so","");
+ if (!extraLibs.IsNull()) extraLibs += ":";
+ extraLibs += stmp;
+ continue;
+ }
+ if (str->GetString().Contains(".par")) {
+ // The first par file found in the list will not allow any further .so
+ parMode = kTRUE;
+ if (!parLibs.IsNull()) parLibs += ":";
+ parLibs += str->GetName();
+ continue;
+ }
+ }
+ if (list) delete list;
+ }
+ if (!extraLibs.IsNull()) optionsList.Add(new TNamed("ALIROOT_EXTRA_LIBS",extraLibs.Data()));
+ // Check extra includes
+ if (!fIncludePath.IsNull()) {
+ TString includePath = fIncludePath;
+ includePath.ReplaceAll(" ",":");
+ includePath.ReplaceAll("$ALICE_ROOT","");
+ includePath.ReplaceAll("${ALICE_ROOT}","");
+ includePath.ReplaceAll("-I","");
+ includePath.Strip(TString::kTrailing, ':');
+ Info("StartAnalysis", "Adding extra includes: %s",includePath.Data());
+ optionsList.Add(new TNamed("ALIROOT_EXTRA_INCLUDES",includePath.Data()));
+ }
+ // Check if connection to grid is requested
+ if (TestSpecialBit(kProofConnectGrid))
+ optionsList.Add(new TNamed("ALIROOT_ENABLE_ALIEN", "1"));
+ // Enable AliRoot par
+ if (testMode) {
+ // Enable proof lite package
+ TString alirootLite = gSystem->ExpandPathName("$ALICE_ROOT/ANALYSIS/macros/AliRootProofLite.par");
+ for (Int_t i=0; i<optionsList.GetSize(); i++) {
+ TNamed *obj = (TNamed*)optionsList.At(i);
+ printf("%s %s\n", obj->GetName(), obj->GetTitle());
+ }
+ if (!gROOT->ProcessLine(Form("gProof->UploadPackage(\"%s\");",alirootLite.Data()))
+ && !gROOT->ProcessLine(Form("gProof->EnablePackage(\"%s\", (TList*)%p);",alirootLite.Data(),&optionsList))) {
+ Info("StartAnalysis", "AliRootProofLite enabled");
+ } else {
+ Error("StartAnalysis", "There was an error trying to enable package AliRootProofLite.par");
+ return kFALSE;
+ }
+ } else {
+ if (gROOT->ProcessLine(Form("gProof->EnablePackage(\"VO_ALICE@AliRoot::%s\", (TList*)%p, kTRUE);",
+ fAliROOTVersion.Data(), &optionsList))) {
+ Error("StartAnalysis", "There was an error trying to enable package VO_ALICE@AliRoot::%s", fAliROOTVersion.Data());
+ return kFALSE;
+ }
+ }
+ // Enable first par files from fAdditionalLibs
+ if (!parLibs.IsNull()) {
+ TObjArray *list = parLibs.Tokenize(":");
+ TIter next(list);
+ TObjString *package;
+ while((package=(TObjString*)next())) {
+ TString spkg = package->GetName();
+ spkg.ReplaceAll(".par", "");
+ gSystem->Exec(TString::Format("rm -rf %s", spkg.Data()));
+ if (!gROOT->ProcessLine(Form("gProof->UploadPackage(\"%s\");", package->GetName()))) {
+ TString enablePackage = (testMode)?Form("gProof->EnablePackage(\"%s\",kFALSE);", package->GetName()):Form("gProof->EnablePackage(\"%s\",kTRUE);", package->GetName());
+ if (gROOT->ProcessLine(enablePackage)) {
+ Error("StartAnalysis", "There was an error trying to enable package %s", package->GetName());
+ return kFALSE;
+ }
+ } else {
+ Error("StartAnalysis", "There was an error trying to upload package %s", package->GetName());
+ return kFALSE;
+ }
+ }
+ if (list) delete list;
+ }
+ } else {
+ if (fAdditionalLibs.Contains(".so") && !testMode) {
+ Error("StartAnalysis", "You request additional libs to be loaded but did not enabled any AliRoot mode. Please refer to: \
+ \n http://aaf.cern.ch/node/83 and use a parameter for SetAliRootMode()");
+ return kFALSE;
+ }
+ }
+ // Enable par files if requested
+ if (fPackages && fPackages->GetEntries()) {
+ TIter next(fPackages);
+ TObject *package;
+ while ((package=next())) {
+ // Skip packages already enabled
+ if (parLibs.Contains(package->GetName())) continue;
+ TString spkg = package->GetName();
+ spkg.ReplaceAll(".par", "");
+ gSystem->Exec(TString::Format("rm -rf %s", spkg.Data()));
+ if (gROOT->ProcessLine(Form("gProof->UploadPackage(\"%s\");", package->GetName()))) {
+ if (gROOT->ProcessLine(Form("gProof->EnablePackage(\"%s\",kTRUE);", package->GetName()))) {
+ Error("StartAnalysis", "There was an error trying to enable package %s", package->GetName());
+ return kFALSE;
+ }
+ } else {
+ Error("StartAnalysis", "There was an error trying to upload package %s", package->GetName());
+ return kFALSE;
+ }
+ }
+ }
+ // Do we need to load analysis source files ?
+ // NOTE: don't load on client since this is anyway done by the user to attach his task.
+ if (fAnalysisSource.Length()) {
+ TObjArray *list = fAnalysisSource.Tokenize(" ");
+ TIter next(list);
+ TObjString *str;
+ while((str=(TObjString*)next())) {
+ gROOT->ProcessLine(Form("gProof->Load(\"%s+g\", kTRUE);", str->GetName()));
+ }
+ if (list) delete list;
}
- fOutputFiles = "";
- TIter next(mgr->GetOutputs());
- AliAnalysisDataContainer *output;
- while ((output=(AliAnalysisDataContainer*)next())) {
- const char *filename = output->GetFileName();
- if (!(strcmp(filename, "default"))) {
- if (!mgr->GetOutputEventHandler()) continue;
- filename = mgr->GetOutputEventHandler()->GetOutputFileName();
+ if (testMode) {
+ // Register dataset to proof lite.
+ if (fFileForTestMode.IsNull()) {
+ Error("GetChainForTestMode", "For proof test mode please use SetFileForTestMode() pointing to a file that contains data file locations.");
+ return kFALSE;
}
- if (fOutputFiles.Contains(filename)) continue;
- if (fOutputFiles.Length()) fOutputFiles += " ";
- fOutputFiles += filename;
+ if (gSystem->AccessPathName(fFileForTestMode)) {
+ Error("GetChainForTestMode", "File not found: %s", fFileForTestMode.Data());
+ return kFALSE;
+ }
+ TFileCollection *coll = new TFileCollection();
+ coll->AddFromFile(fFileForTestMode);
+ gROOT->ProcessLine(Form("gProof->RegisterDataSet(\"test_collection\", (TFileCollection*)%p, \"OV\");", coll));
+ gROOT->ProcessLine("gProof->ShowDataSets()");
}
+ return kTRUE;
+ }
+
+ // Check if output files have to be taken from the analysis manager
+ if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
+ // Add output files and AOD files
+ fOutputFiles = GetListOfFiles("outaod");
// Add extra files registered to the analysis manager
- if (mgr->GetExtraFiles().Length()) {
- if (fOutputFiles.Length()) fOutputFiles += " ";
- fOutputFiles += mgr->GetExtraFiles();
+ TString extra = GetListOfFiles("ext");
+ if (!extra.IsNull()) {
+ extra.ReplaceAll(".root", "*.root");
+ if (!fOutputFiles.IsNull()) fOutputFiles += ",";
+ fOutputFiles += extra;
}
+ // Compose the output archive.
+ fOutputArchive = "log_archive.zip:std*@disk=1 ";
+ fOutputArchive += Form("root_archive.zip:%s,*.stat@disk=%d",fOutputFiles.Data(),fNreplicas);
}
// if (!fCloseSE.Length()) fCloseSE = gSystem->Getenv("alien_CLOSE_SE");
if (TestBit(AliAnalysisGrid::kOffline)) {
Info("StartAnalysis","\n##### FULL ANALYSIS MODE ##### Producing needed files and submitting your analysis job...");
}
+ Print();
if (!Connect()) {
Error("StartAnalysis", "Cannot start grid analysis without grid connection");
return kFALSE;
}
- Print();
+ if (IsCheckCopy() && gGrid) CheckFileCopy(gGrid->GetHomeDirectory());
if (!CheckInputData()) {
Error("StartAnalysis", "There was an error in preprocessing your requested input data");
return kFALSE;
}
- CreateDataset(fDataPattern);
+ if (!CreateDataset(fDataPattern)) {
+ TString serror;
+ if (!fRunNumbers.Length() && !fRunRange[0]) serror = Form("path to data directory: <%s>", fGridDataDir.Data());
+ if (fRunNumbers.Length()) serror = "run numbers";
+ if (fRunRange[0]) serror = Form("run range [%d, %d]", fRunRange[0], fRunRange[1]);
+ serror += Form("\n or data pattern <%s>", fDataPattern.Data());
+ Error("StartAnalysis", "No data to process. Please fix %s in your plugin configuration.", serror.Data());
+ return kFALSE;
+ }
WriteAnalysisFile();
WriteAnalysisMacro();
WriteExecutable();
}
if (!CreateJDL()) return kFALSE;
if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
- if (TestBit(AliAnalysisGrid::kTest)) {
+ if (testMode) {
// Locally testing the analysis
Info("StartAnalysis", "\n_______________________________________________________________________ \
\n Running analysis script in a daughter shell as on a worker node \
\n_______________________________________________________________________");
- TObjArray *list = fOutputFiles.Tokenize(" ");
+ TObjArray *list = fOutputFiles.Tokenize(",");
TIter next(list);
TObjString *str;
- TString output_file;
+ TString outputFile;
while((str=(TObjString*)next())) {
- output_file = str->GetString();
- Int_t index = output_file.Index("@");
- if (index > 0) output_file.Remove(index);
- if (!gSystem->AccessPathName(output_file)) gSystem->Exec(Form("rm %s", output_file.Data()));
+ outputFile = str->GetString();
+ Int_t index = outputFile.Index("@");
+ if (index > 0) outputFile.Remove(index);
+ if (!gSystem->AccessPathName(outputFile)) gSystem->Exec(Form("rm %s", outputFile.Data()));
}
delete list;
gSystem->Exec(Form("bash %s 2>stderr", fExecutable.Data()));
- TString validationScript = fExecutable;
- validationScript.ReplaceAll(".sh", "_validation.sh");
- gSystem->Exec(Form("bash %s",validationScript.Data()));
+ gSystem->Exec(Form("bash %s",fValidationScript.Data()));
// gSystem->Exec("cat stdout");
return kFALSE;
}
if (res) {
const char *cjobId = res->GetKey(0,"jobId");
if (!cjobId) {
+ gGrid->Stdout();
+ gGrid->Stderr();
Error("StartAnalysis", "Your JDL %s could not be submitted", fJDLName.Data());
return kFALSE;
} else {
jobID = cjobId;
}
delete res;
+ } else {
+ Error("StartAnalysis", "No grid result after submission !!! Bailing out...");
+ return kFALSE;
}
} else {
// Submit for a range of enumeration of runs.
- Submit();
+ if (!Submit()) return kFALSE;
}
Info("StartAnalysis", "\n#### STARTING AN ALIEN SHELL FOR YOU. EXIT WHEN YOUR JOB %s HAS FINISHED. #### \
}
//______________________________________________________________________________
-void AliAnalysisAlien::Submit()
+const char *AliAnalysisAlien::GetListOfFiles(const char *type)
+{
+// Get a comma-separated list of output files of the requested type.
+// Type can be (case unsensitive):
+// aod - list of aod files (std, extensions and filters)
+// out - list of output files connected to containers (but not aod's or extras)
+// ext - list of extra files registered to the manager
+// ter - list of files produced in terminate
+ static TString files;
+ files = "";
+ TString stype = type;
+ stype.ToLower();
+ TString aodfiles, extra;
+ AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
+ if (!mgr) {
+ ::Error("GetListOfFiles", "Cannot call this without analysis manager");
+ return files.Data();
+ }
+ if (mgr->GetOutputEventHandler()) {
+ aodfiles = mgr->GetOutputEventHandler()->GetOutputFileName();
+ TString extraaod = mgr->GetOutputEventHandler()->GetExtraOutputs();
+ if (!extraaod.IsNull()) {
+ aodfiles += ",";
+ aodfiles += extraaod;
+ }
+ }
+ if (stype.Contains("aod")) {
+ files = aodfiles;
+ if (stype == "aod") return files.Data();
+ }
+ // Add output files that are not in the list of AOD files
+ TString outputfiles = "";
+ TIter next(mgr->GetOutputs());
+ AliAnalysisDataContainer *output;
+ const char *filename = 0;
+ while ((output=(AliAnalysisDataContainer*)next())) {
+ filename = output->GetFileName();
+ if (!(strcmp(filename, "default"))) continue;
+ if (outputfiles.Contains(filename)) continue;
+ if (aodfiles.Contains(filename)) continue;
+ if (!outputfiles.IsNull()) outputfiles += ",";
+ outputfiles += filename;
+ }
+ if (stype.Contains("out")) {
+ if (!files.IsNull()) files += ",";
+ files += outputfiles;
+ if (stype == "out") return files.Data();
+ }
+ // Add extra files registered to the analysis manager
+ TString sextra;
+ extra = mgr->GetExtraFiles();
+ if (!extra.IsNull()) {
+ extra.Strip();
+ extra.ReplaceAll(" ", ",");
+ TObjArray *fextra = extra.Tokenize(",");
+ TIter nextx(fextra);
+ TObject *obj;
+ while ((obj=nextx())) {
+ if (aodfiles.Contains(obj->GetName())) continue;
+ if (outputfiles.Contains(obj->GetName())) continue;
+ if (sextra.Contains(obj->GetName())) continue;
+ if (!sextra.IsNull()) sextra += ",";
+ sextra += obj->GetName();
+ }
+ delete fextra;
+ if (stype.Contains("ext")) {
+ if (!files.IsNull()) files += ",";
+ files += sextra;
+ }
+ }
+ if (stype == "ext") return files.Data();
+ TString termfiles;
+ if (!fTerminateFiles.IsNull()) {
+ fTerminateFiles.Strip();
+ fTerminateFiles.ReplaceAll(" ",",");
+ TObjArray *fextra = fTerminateFiles.Tokenize(",");
+ TIter nextx(fextra);
+ TObject *obj;
+ while ((obj=nextx())) {
+ if (aodfiles.Contains(obj->GetName())) continue;
+ if (outputfiles.Contains(obj->GetName())) continue;
+ if (termfiles.Contains(obj->GetName())) continue;
+ if (sextra.Contains(obj->GetName())) continue;
+ if (!termfiles.IsNull()) termfiles += ",";
+ termfiles += obj->GetName();
+ }
+ delete fextra;
+ }
+ if (stype.Contains("ter")) {
+ if (!files.IsNull() && !termfiles.IsNull()) {
+ files += ",";
+ files += termfiles;
+ }
+ }
+ return files.Data();
+}
+
+//______________________________________________________________________________
+Bool_t AliAnalysisAlien::Submit()
{
// Submit all master jobs.
Int_t nmasterjobs = fInputFiles->GetEntries();
Long_t tshoot = gSystem->Now();
- if (!fNsubmitted) SubmitNext();
+ if (!fNsubmitted && !SubmitNext()) return kFALSE;
while (fNsubmitted < nmasterjobs) {
Long_t now = gSystem->Now();
if ((now-tshoot)>30000) {
tshoot = now;
- SubmitNext();
+ if (!SubmitNext()) return kFALSE;
}
}
+ return kTRUE;
}
//______________________________________________________________________________
-void AliAnalysisAlien::SubmitMerging()
+Bool_t AliAnalysisAlien::SubmitMerging()
{
// Submit all merging jobs.
if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
gGrid->Cd(fGridOutputDir);
TString mergeJDLName = fExecutable;
mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
+ if (!fInputFiles) {
+ Error("SubmitMerging", "You have to use explicit run numbers or run range to merge via JDL!");
+ return kFALSE;
+ }
Int_t ntosubmit = fInputFiles->GetEntries();
- printf("### Submitting %d merging jobs...\n", ntosubmit);
for (Int_t i=0; i<ntosubmit; i++) {
- TString query;
TString runOutDir = gSystem->BaseName(fInputFiles->At(i)->GetName());
runOutDir.ReplaceAll(".xml", "");
- if (fOutputToRunNo)
- query = Form("submit %s %s", mergeJDLName.Data(), runOutDir.Data());
- else
- query = Form("submit %s %03d", mergeJDLName.Data(), i);
- printf("********* %s\n",query.Data());
- TGridResult *res = gGrid->Command(query);
- if (res) {
- const char *cjobId = res->GetKey(0,"jobId");
- if (!cjobId) {
- Error("StartAnalysis", "Your JDL %s could not be submitted", mergeJDLName.Data());
- return;
- } else {
- Info("StartAnalysis", "\n_______________________________________________________________________ \
- \n##### Your JDL %s was successfully submitted. \nTHE JOB ID IS: %s \
- \n_______________________________________________________________________",
- mergeJDLName.Data(), cjobId);
- }
- delete res;
- }
+ if (fOutputToRunNo) {
+ // The output directory is the run number
+ printf("### Submitting merging job for run <%s>\n", runOutDir.Data());
+ runOutDir = Form("%s/%s", fGridOutputDir.Data(), runOutDir.Data());
+ } else {
+ // The output directory is the master number in 3 digits format
+ printf("### Submitting merging job for master <%03d>\n", i);
+ runOutDir = Form("%s/%03d",fGridOutputDir.Data(), i);
+ }
+ // Check now the number of merging stages.
+ TObjArray *list = fOutputFiles.Tokenize(",");
+ TIter next(list);
+ TObjString *str;
+ TString outputFile;
+ while((str=(TObjString*)next())) {
+ outputFile = str->GetString();
+ Int_t index = outputFile.Index("@");
+ if (index > 0) outputFile.Remove(index);
+ if (!fMergeExcludes.Contains(outputFile)) break;
+ }
+ delete list;
+ Bool_t done = CheckMergedFiles(outputFile, runOutDir, fMaxMergeFiles, mergeJDLName);
+ if (!done && (i==ntosubmit-1)) return kFALSE;
}
- if (!ntosubmit) return;
- Info("StartAnalysis", "\n#### STARTING AN ALIEN SHELL FOR YOU. EXIT WHEN YOUR MERGING JOBS HAVE FINISHED. #### \
- \n You may exit at any time and terminate the job later using the option <terminate> but disabling SetMergeViaJDL\
- \n ##################################################################################");
+ if (!ntosubmit) return kTRUE;
+ Info("StartAnalysis", "\n #### STARTING AN ALIEN SHELL FOR YOU. You can exit any time or inspect your jobs in a different shell.##########\
+ \n Make sure your jobs are in a final state (you can resubmit failed ones via 'masterjob <id> resubmit ERROR_ALL')\
+ \n Rerun in 'terminate' mode to submit all merging stages, each AFTER the previous one completed. The final merged \
+ \n output will be written to your alien output directory, while separate stages in <Stage_n>. \
+ \n ################################################################################################################");
gSystem->Exec("aliensh");
+ return kTRUE;
}
//______________________________________________________________________________
-void AliAnalysisAlien::SubmitNext()
+Bool_t AliAnalysisAlien::SubmitNext()
{
-// Submit next bunch of master jobs if the queue is free.
+// Submit next bunch of master jobs if the queue is free. The first master job is
+// submitted right away, while the next will not be unless the previous was split.
+// The plugin will not submit new master jobs if there are more that 500 jobs in
+// waiting phase.
static Bool_t iscalled = kFALSE;
static Int_t firstmaster = 0;
static Int_t lastmaster = 0;
static Int_t npermaster = 0;
- if (iscalled) return;
+ if (iscalled) return kTRUE;
iscalled = kTRUE;
Int_t nrunning=0, nwaiting=0, nerror=0, ndone=0;
Int_t ntosubmit = 0;
TGridResult *res;
TString jobID = "";
- if (!fNsubmitted) ntosubmit = 1;
- else {
+ Int_t nmasterjobs = fInputFiles->GetEntries();
+ if (!fNsubmitted) {
+ ntosubmit = 1;
+ if (!IsUseSubmitPolicy()) {
+ if (nmasterjobs>5)
+ Info("SubmitNext","### Warning submit policy not used ! Submitting too many jobs at a time may be prohibitted. \
+ \n### You can use SetUseSubmitPolicy() to enable if you have problems.");
+ ntosubmit = nmasterjobs;
+ }
+ } else {
TString status = GetJobStatus(firstmaster, lastmaster, nrunning, nwaiting, nerror, ndone);
printf("=== master %d: %s\n", lastmaster, status.Data());
// If last master not split, just return
- if (status != "SPLIT") {iscalled = kFALSE; return;}
+ if (status != "SPLIT") {iscalled = kFALSE; return kTRUE;}
// No more than 100 waiting jobs
- if (nwaiting>100) {iscalled = kFALSE; return;}
+ if (nwaiting>500) {iscalled = kFALSE; return kTRUE;}
npermaster = (nrunning+nwaiting+nerror+ndone)/fNsubmitted;
- if (npermaster) ntosubmit = (100-nwaiting)/npermaster;
+ if (npermaster) ntosubmit = (500-nwaiting)/npermaster;
+ if (!ntosubmit) ntosubmit = 1;
printf("=== WAITING(%d) RUNNING(%d) DONE(%d) OTHER(%d) NperMaster=%d => to submit %d jobs\n",
nwaiting, nrunning, ndone, nerror, npermaster, ntosubmit);
}
- Int_t nmasterjobs = fInputFiles->GetEntries();
for (Int_t i=0; i<ntosubmit; i++) {
// Submit for a range of enumeration of runs.
- if (fNsubmitted>=nmasterjobs) {iscalled = kFALSE; return;}
+ if (fNsubmitted>=nmasterjobs) {iscalled = kFALSE; return kTRUE;}
TString query;
TString runOutDir = gSystem->BaseName(fInputFiles->At(fNsubmitted)->GetName());
runOutDir.ReplaceAll(".xml", "");
if (res) {
TString cjobId1 = res->GetKey(0,"jobId");
if (!cjobId1.Length()) {
- Error("StartAnalysis", "Your JDL %s could not be submitted", fJDLName.Data());
iscalled = kFALSE;
- return;
+ gGrid->Stdout();
+ gGrid->Stderr();
+ Error("StartAnalysis", "Your JDL %s could not be submitted. The message was:", fJDLName.Data());
+ return kFALSE;
} else {
Info("StartAnalysis", "\n_______________________________________________________________________ \
\n##### Your JDL %s submitted (%d to go). \nTHE JOB ID IS: %s \
fNsubmitted++;
}
delete res;
+ } else {
+ Error("StartAnalysis", "No grid result after submission !!! Bailing out...");
+ return kFALSE;
}
}
iscalled = kFALSE;
+ return kTRUE;
}
//______________________________________________________________________________
TDirectory *cdir = gDirectory;
TFile *file = TFile::Open(analysisFile, "RECREATE");
if (file) {
- // Skip task Terminate calls for the grid job
- mgr->SetSkipTerminate(kTRUE);
+ // Skip task Terminate calls for the grid job (but not in test mode, where we want to check also the terminate mode
+ if (!TestBit(AliAnalysisGrid::kTest)) mgr->SetSkipTerminate(kTRUE);
// Unless merging makes no sense
if (IsSingleOutput()) mgr->SetSkipTerminate(kFALSE);
mgr->Write();
Info("WriteAnalysisFile", "\n##### Analysis manager: %s wrote to file <%s>\n", mgr->GetName(),analysisFile.Data());
}
Bool_t copy = kTRUE;
- if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
- Info("CreateJDL", "\n##### Copying file <%s> containing your initialized analysis manager to your alien workspace", analysisFile.Data());
+ Info("WriteAnalysisFile", "\n##### Copying file <%s> containing your initialized analysis manager to your alien workspace", analysisFile.Data());
if (FileExists(analysisFile)) gGrid->Rm(analysisFile);
TFile::Cp(Form("file:%s",analysisFile.Data()), Form("alien://%s/%s", workdir.Data(),analysisFile.Data()));
}
out << "// Automatically generated analysis steering macro executed in grid subjobs" << endl << endl;
out << " TStopwatch timer;" << endl;
out << " timer.Start();" << endl << endl;
- out << "// load base root libraries" << endl;
- out << " gSystem->Load(\"libTree\");" << endl;
- out << " gSystem->Load(\"libGeom\");" << endl;
- out << " gSystem->Load(\"libVMC\");" << endl;
- out << " gSystem->Load(\"libPhysics\");" << endl << endl;
- out << " gSystem->Load(\"libMinuit\");" << endl << endl;
+ // Change temp directory to current one
+ out << "// Set temporary merging directory to current one" << endl;
+ out << " gSystem->Setenv(\"TMPDIR\", gSystem->pwd());" << endl << endl;
+ // Reset existing include path
+ out << "// Reset existing include path and add current directory first in the search" << endl;
+ out << " gSystem->SetIncludePath(\"-I.\");" << endl;
+ if (!fExecutableCommand.Contains("aliroot")) {
+ out << "// load base root libraries" << endl;
+ out << " gSystem->Load(\"libTree\");" << endl;
+ out << " gSystem->Load(\"libGeom\");" << endl;
+ out << " gSystem->Load(\"libVMC\");" << endl;
+ out << " gSystem->Load(\"libPhysics\");" << endl << endl;
+ out << " gSystem->Load(\"libMinuit\");" << endl << endl;
+ }
if (fAdditionalRootLibs.Length()) {
// in principle libtree /lib geom libvmc etc. can go into this list, too
out << "// Add aditional libraries" << endl;
}
if (list) delete list;
}
- out << "// include path" << endl;
- if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
- out << " gSystem->AddIncludePath(\"-I$ALICE_ROOT/include\");" << endl << endl;
out << "// Load analysis framework libraries" << endl;
+ TString setupPar = "AliAnalysisAlien::SetupPar";
if (!fPackages) {
- out << " gSystem->Load(\"libSTEERBase\");" << endl;
- out << " gSystem->Load(\"libESD\");" << endl;
- out << " gSystem->Load(\"libAOD\");" << endl;
+ if (!fExecutableCommand.Contains("aliroot")) {
+ out << " gSystem->Load(\"libSTEERBase\");" << endl;
+ out << " gSystem->Load(\"libESD\");" << endl;
+ out << " gSystem->Load(\"libAOD\");" << endl;
+ }
out << " gSystem->Load(\"libANALYSIS\");" << endl;
out << " gSystem->Load(\"libANALYSISalice\");" << endl;
out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
TIter next(fPackages);
TObject *obj;
TString pkgname;
- TString setupPar = "AliAnalysisAlien::SetupPar";
while ((obj=next())) {
pkgname = obj->GetName();
if (pkgname == "STEERBase" ||
out << " if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
}
}
+ out << "// include path" << endl;
+ // Get the include path from the interpreter and remove entries pointing to AliRoot
+ out << " TString intPath = gInterpreter->GetIncludePath();" << endl;
+ out << " TObjArray *listpaths = intPath.Tokenize(\" \");" << endl;
+ out << " TIter nextpath(listpaths);" << endl;
+ out << " TObjString *pname;" << endl;
+ out << " while ((pname=(TObjString*)nextpath())) {" << endl;
+ out << " TString current = pname->GetName();" << endl;
+ out << " if (current.Contains(\"AliRoot\") || current.Contains(\"ALICE_ROOT\")) continue;" << endl;
+ out << " gSystem->AddIncludePath(current);" << endl;
+ out << " }" << endl;
+ out << " if (listpaths) delete listpaths;" << endl;
+ if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
+ out << " gROOT->ProcessLine(\".include $ALICE_ROOT/include\");" << endl;
+ out << " printf(\"Include path: %s\\n\", gSystem->GetIncludePath());" << endl << endl;
if (fAdditionalLibs.Length()) {
out << "// Add aditional AliRoot libraries" << endl;
TObjArray *list = fAdditionalLibs.Tokenize(" ");
while((str=(TObjString*)next())) {
if (str->GetString().Contains(".so"))
out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
+ if (str->GetString().Contains(".par"))
+ out << " if (!" << setupPar << "(\"" << str->GetString() << "\")) return;" << endl;
}
if (list) delete list;
}
if (list) delete list;
}
out << endl;
+// out << " printf(\"Currently load libraries:\\n\");" << endl;
+// out << " printf(\"%s\\n\", gSystem->GetLibraries());" << endl;
if (fFastReadOption) {
- Warning("WriteAnalysisMacro", "!!! You requested FastRead option. Using xrootd flags to reduce timeouts in the grid jobs. Note that this may skip some files that could be accessed !!!");
+ 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 !!! \
+ \n+++ NOTE: To disable this option, use: plugin->SetFastReadOption(kFALSE)");
out << "// fast xrootd reading enabled" << endl;
out << " printf(\"!!! You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !!!\");" << endl;
- out << " gEnv->SetValue(\"XNet.ConnectTimeout\",5);" << endl;
- out << " gEnv->SetValue(\"XNet.RequestTimeout\",5);" << endl;
+ out << " gEnv->SetValue(\"XNet.ConnectTimeout\",50);" << endl;
+ out << " gEnv->SetValue(\"XNet.RequestTimeout\",50);" << endl;
out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
- out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",5);" << endl;
+ out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",50);" << endl;
out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
}
out << "// connect to AliEn and make the chain" << endl;
out << " if (!TGrid::Connect(\"alien://\")) return;" << endl;
- if (IsUsingTags()) {
- out << " TChain *chain = CreateChainFromTags(\"wn.xml\", anatype);" << endl << endl;
- } else {
- if(fFriendChainName!="AliAOD.VertexingHF.root") {
- out << " TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl;
- } else {
- out << " // Check if the macro to create the chain was provided" << endl;
- out << " if (gSystem->AccessPathName(\"MakeAODInputChain.C\")) {" << endl;
- out << " ::Error(\"" << func.Data() << "\", \"File MakeAODInputChain.C not provided. Aborting.\");" << endl;
- out << " return;" << endl;
- out << " }" << endl;
- out << " gROOT->LoadMacro(\"MakeAODInputChain.C\");" << endl;
- out << " TChain *chain = MakeAODInputChain(\"wn.xml\",\"none\");" << endl << endl;
- }
- }
out << "// read the analysis manager from file" << endl;
TString analysisFile = fExecutable;
analysisFile.ReplaceAll(".sh", ".root");
out << " mgr = (AliAnalysisManager*)file->Get(key->GetName());" << endl;
out << " };" << endl;
out << " if (!mgr) {" << endl;
- out << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file" << analysisFile <<"\");" << endl;
+ out << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file " << analysisFile <<"\");" << endl;
out << " return;" << endl;
out << " }" << endl << endl;
out << " mgr->PrintStatus();" << endl;
if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) {
out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
} else {
- out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
+ if (TestBit(AliAnalysisGrid::kTest))
+ out << " AliLog::SetGlobalLogLevel(AliLog::kWarning);" << endl;
+ else
+ out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
}
}
+ if (IsUsingTags()) {
+ out << " TChain *chain = CreateChainFromTags(\"wn.xml\", anatype);" << endl << endl;
+ } else {
+ out << " TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl;
+ }
out << " mgr->StartAnalysis(\"localfile\", chain);" << endl;
out << " timer.Stop();" << endl;
out << " timer.Print();" << endl;
msg += " AliLHCTagCuts *lhcCuts,\n";
msg += " AliDetectorTagCuts *detCuts,\n";
msg += " AliEventTagCuts *evCuts)";
- Info("WriteAnalysisMacro", msg.Data());
+ Info("WriteAnalysisMacro", "%s", msg.Data());
}
}
if (!IsUsingTags() || fFriendChainName!="") {
out << "TChain* CreateChain(const char *xmlfile, const char *type=\"ESD\")" << endl;
out << "{" << endl;
out << "// Create a chain using url's from xml file" << endl;
+ out << " TString filename;" << endl;
+ out << " Int_t run = 0;" << endl;
out << " TString treename = type;" << endl;
out << " treename.ToLower();" << endl;
out << " treename += \"Tree\";" << endl;
out << " ::Error(\"CreateChain\", \"Cannot create an AliEn collection from %s\", xmlfile);" << endl;
out << " return NULL;" << endl;
out << " }" << endl;
+ out << " AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();" << endl;
out << " TChain *chain = new TChain(treename);" << endl;
if(fFriendChainName!="") {
out << " TChain *chainFriend = new TChain(treename);" << endl;
}
out << " coll->Reset();" << endl;
out << " while (coll->Next()) {" << endl;
- out << " chain->Add(coll->GetTURL(\"\"));" << endl;
+ out << " filename = coll->GetTURL("");" << endl;
+ out << " if (mgr) {" << endl;
+ out << " Int_t nrun = AliAnalysisManager::GetRunFromAlienPath(filename);" << endl;
+ out << " if (nrun && nrun != run) {" << endl;
+ out << " printf(\"### Run number detected from chain: %d\\n\", nrun);" << endl;
+ out << " mgr->SetRunFromPath(nrun);" << endl;
+ out << " run = nrun;" << endl;
+ out << " }" << endl;
+ out << " }" << endl;
+ out << " chain->Add(filename);" << endl;
if(fFriendChainName!="") {
out << " TString fileFriend=coll->GetTURL(\"\");" << endl;
out << " fileFriend.ReplaceAll(\"AliAOD.root\",\""<<fFriendChainName.Data()<<"\");" << endl;
out << "// Compile the package and set it up." << endl;
out << " TString pkgdir = package;" << endl;
out << " pkgdir.ReplaceAll(\".par\",\"\");" << endl;
- out << " gSystem->Exec(Form(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
+ out << " gSystem->Exec(TString::Format(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
out << " TString cdir = gSystem->WorkingDirectory();" << endl;
out << " gSystem->ChangeDirectory(pkgdir);" << endl;
out << " // Check for BUILD.sh and execute" << endl;
Info("WriteAnalysisMacro", "\n##### Analysis macro to run on worker nodes <%s> written",fAnalysisMacro.Data());
}
Bool_t copy = kTRUE;
- if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
TString func = mergingMacro;
TString comment;
func.ReplaceAll(".C", "");
- out << "void " << func.Data() << "(const char *dir)" << endl;
+ out << "void " << func.Data() << "(const char *dir, Int_t stage=0)" << endl;
out << "{" << endl;
out << "// Automatically generated merging macro executed in grid subjobs" << endl << endl;
out << " TStopwatch timer;" << endl;
out << " timer.Start();" << endl << endl;
- out << "// load base root libraries" << endl;
- out << " gSystem->Load(\"libTree\");" << endl;
- out << " gSystem->Load(\"libGeom\");" << endl;
- out << " gSystem->Load(\"libVMC\");" << endl;
- out << " gSystem->Load(\"libPhysics\");" << endl << endl;
- out << " gSystem->Load(\"libMinuit\");" << endl << endl;
+ // Reset existing include path
+ out << "// Reset existing include path and add current directory first in the search" << endl;
+ out << " gSystem->SetIncludePath(\"-I.\");" << endl;
+ if (!fExecutableCommand.Contains("aliroot")) {
+ out << "// load base root libraries" << endl;
+ out << " gSystem->Load(\"libTree\");" << endl;
+ out << " gSystem->Load(\"libGeom\");" << endl;
+ out << " gSystem->Load(\"libVMC\");" << endl;
+ out << " gSystem->Load(\"libPhysics\");" << endl << endl;
+ out << " gSystem->Load(\"libMinuit\");" << endl << endl;
+ }
if (fAdditionalRootLibs.Length()) {
// in principle libtree /lib geom libvmc etc. can go into this list, too
out << "// Add aditional libraries" << endl;
}
if (list) delete list;
}
- out << "// include path" << endl;
- if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
- out << " gSystem->AddIncludePath(\"-I$ALICE_ROOT/include\");" << endl << endl;
out << "// Load analysis framework libraries" << endl;
if (!fPackages) {
- out << " gSystem->Load(\"libSTEERBase\");" << endl;
- out << " gSystem->Load(\"libESD\");" << endl;
- out << " gSystem->Load(\"libAOD\");" << endl;
+ if (!fExecutableCommand.Contains("aliroot")) {
+ out << " gSystem->Load(\"libSTEERBase\");" << endl;
+ out << " gSystem->Load(\"libESD\");" << endl;
+ out << " gSystem->Load(\"libAOD\");" << endl;
+ }
out << " gSystem->Load(\"libANALYSIS\");" << endl;
out << " gSystem->Load(\"libANALYSISalice\");" << endl;
out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
out << " if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
}
}
+ out << "// include path" << endl;
+ // Get the include path from the interpreter and remove entries pointing to AliRoot
+ out << " TString intPath = gInterpreter->GetIncludePath();" << endl;
+ out << " TObjArray *listpaths = intPath.Tokenize(\" \");" << endl;
+ out << " TIter nextpath(listpaths);" << endl;
+ out << " TObjString *pname;" << endl;
+ out << " while ((pname=(TObjString*)nextpath())) {" << endl;
+ out << " TString current = pname->GetName();" << endl;
+ out << " if (current.Contains(\"AliRoot\") || current.Contains(\"ALICE_ROOT\")) continue;" << endl;
+ out << " gSystem->AddIncludePath(current);" << endl;
+ out << " }" << endl;
+ out << " if (listpaths) delete listpaths;" << endl;
+ if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
+ out << " gROOT->ProcessLine(\".include $ALICE_ROOT/include\");" << endl;
+ out << " printf(\"Include path: %s\\n\", gSystem->GetIncludePath());" << endl << endl;
if (fAdditionalLibs.Length()) {
out << "// Add aditional AliRoot libraries" << endl;
TObjArray *list = fAdditionalLibs.Tokenize(" ");
}
if (list) delete list;
}
- out << endl;
+ out << endl;
+
if (fFastReadOption) {
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 !!!");
out << "// fast xrootd reading enabled" << endl;
out << " printf(\"!!! You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !!!\");" << endl;
- out << " gEnv->SetValue(\"XNet.ConnectTimeout\",5);" << endl;
- out << " gEnv->SetValue(\"XNet.RequestTimeout\",5);" << endl;
+ out << " gEnv->SetValue(\"XNet.ConnectTimeout\",50);" << endl;
+ out << " gEnv->SetValue(\"XNet.RequestTimeout\",50);" << endl;
out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
- out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",5);" << endl;
+ out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",50);" << endl;
out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
- }
+ }
+ // Change temp directory to current one
+ out << "// Set temporary merging directory to current one" << endl;
+ out << " gSystem->Setenv(\"TMPDIR\", gSystem->pwd());" << endl << endl;
out << "// Connect to AliEn" << endl;
out << " if (!TGrid::Connect(\"alien://\")) return;" << endl;
- out << " TString outputDir = \"" << fGridOutputDir << "/\";" << endl;
- out << " outputDir += dir;" << endl;
- out << " TString outputFiles = \"" << fOutputFiles << "\";" << endl;
+ out << " TString outputDir = dir;" << endl;
+ out << " TString outputFiles = \"" << GetListOfFiles("out") << "\";" << endl;
out << " TString mergeExcludes = \"" << fMergeExcludes << "\";" << endl;
- out << " TObjArray *list = outputFiles.Tokenize(\" \");" << endl;
+ out << " TObjArray *list = outputFiles.Tokenize(\",\");" << endl;
out << " TIter *iter = new TIter(list);" << endl;
out << " TObjString *str;" << endl;
- out << " TString output_file;" << endl;
+ out << " TString outputFile;" << endl;
out << " Bool_t merged = kTRUE;" << endl;
out << " while((str=(TObjString*)iter->Next())) {" << endl;
- out << " output_file = str->GetString();" << endl;
- out << " Int_t index = output_file.Index(\"@\");" << endl;
- out << " if (index > 0) output_file.Remove(index);" << endl;
+ out << " outputFile = str->GetString();" << endl;
+ out << " if (outputFile.Contains(\"*\")) continue;" << endl;
+ out << " Int_t index = outputFile.Index(\"@\");" << endl;
+ out << " if (index > 0) outputFile.Remove(index);" << endl;
out << " // Skip already merged outputs" << endl;
- out << " if (!gSystem->AccessPathName(output_file)) {" << endl;
- out << " printf(\"Output file <%s> found. Not merging again.\",output_file.Data());" << endl;
+ out << " if (!gSystem->AccessPathName(outputFile)) {" << endl;
+ out << " printf(\"Output file <%s> found. Not merging again.\",outputFile.Data());" << endl;
out << " continue;" << endl;
out << " }" << endl;
- out << " if (mergeExcludes.Contains(output_file.Data())) continue;" << endl;
- out << " merged = AliAnalysisAlien::MergeOutput(output_file, outputDir, " << fMaxMergeFiles << ");" << endl;
+ out << " if (mergeExcludes.Contains(outputFile.Data())) continue;" << endl;
+ out << " merged = AliAnalysisAlien::MergeOutput(outputFile, outputDir, " << fMaxMergeFiles << ", stage);" << endl;
out << " if (!merged) {" << endl;
- out << " printf(\"ERROR: Cannot merge %s\\n\", output_file.Data());" << endl;
+ out << " printf(\"ERROR: Cannot merge %s\\n\", outputFile.Data());" << endl;
out << " return;" << endl;
out << " }" << endl;
out << " }" << endl;
- out << "// read the analysis manager from file" << endl;
+ out << " // all outputs merged, validate" << endl;
+ out << " ofstream out;" << endl;
+ out << " out.open(\"outputs_valid\", ios::out);" << endl;
+ out << " out.close();" << endl;
+ out << " // read the analysis manager from file" << endl;
TString analysisFile = fExecutable;
analysisFile.ReplaceAll(".sh", ".root");
+ out << " if (!outputDir.Contains(\"Stage\")) return;" << endl;
out << " TFile *file = TFile::Open(\"" << analysisFile << "\");" << endl;
- out << " if (!file) return;" << endl;
+ out << " if (!file) return;" << endl;
out << " TIter nextkey(file->GetListOfKeys());" << endl;
out << " AliAnalysisManager *mgr = 0;" << endl;
out << " TKey *key;" << endl;
out << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file" << analysisFile <<"\");" << endl;
out << " return;" << endl;
out << " }" << endl << endl;
+ out << " mgr->SetRunFromPath(mgr->GetRunFromAlienPath(dir));" << endl;
+ out << " mgr->SetSkipTerminate(kFALSE);" << endl;
out << " mgr->PrintStatus();" << endl;
if (AliAnalysisManager::GetAnalysisManager()) {
if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) {
out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
} else {
- out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
+ if (TestBit(AliAnalysisGrid::kTest))
+ out << " AliLog::SetGlobalLogLevel(AliLog::kWarning);" << endl;
+ else
+ out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
}
}
- out << " mgr->StartAnalysis(\"gridterminate\");" << endl;
+ out << " TTree *tree = NULL;" << endl;
+ out << " mgr->StartAnalysis(\"gridterminate\", tree);" << endl;
out << "}" << endl << endl;
if (hasANALYSISalice) {
out <<"//________________________________________________________________________________" << endl;
out << "// Compile the package and set it up." << endl;
out << " TString pkgdir = package;" << endl;
out << " pkgdir.ReplaceAll(\".par\",\"\");" << endl;
- out << " gSystem->Exec(Form(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
+ out << " gSystem->Exec(TString::Format(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
out << " TString cdir = gSystem->WorkingDirectory();" << endl;
out << " gSystem->ChangeDirectory(pkgdir);" << endl;
out << " // Check for BUILD.sh and execute" << endl;
}
}
Bool_t copy = kTRUE;
- if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
//______________________________________________________________________________
Bool_t AliAnalysisAlien::SetupPar(const char *package)
{
-// Compile the par file archive pointed by <package>. This must be present in the current durectory.
+// Compile the par file archive pointed by <package>. This must be present in the current directory.
// Note that for loading the compiled library. The current directory should have precedence in
// LD_LIBRARY_PATH
TString pkgdir = package;
pkgdir.ReplaceAll(".par","");
- gSystem->Exec(Form("tar xvzf %s.par", pkgdir.Data()));
+ gSystem->Exec(TString::Format("tar xzf %s.par", pkgdir.Data()));
TString cdir = gSystem->WorkingDirectory();
gSystem->ChangeDirectory(pkgdir);
// Check for BUILD.sh and execute
return;
}
out << "#!/bin/bash" << endl;
+ // Make sure we can properly compile par files
+ out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
out << "echo \"=========================================\"" << endl;
out << "echo \"############## PATH : ##############\"" << endl;
out << "echo $PATH" << endl;
out << "echo \"############## memory : ##############\"" << endl;
out << "free -m" << endl;
out << "echo \"=========================================\"" << endl << endl;
- // Make sure we can properly compile par files
- if (TObject::TestBit(AliAnalysisGrid::kUsePars)) out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
out << fExecutableCommand << " ";
out << fAnalysisMacro.Data() << " " << fExecutableArgs.Data() << endl << endl;
out << "echo \"======== " << fAnalysisMacro.Data() << " finished with exit code: $? ========\"" << endl;
out << "echo \"############## memory after: ##############\"" << endl;
out << "free -m" << endl;
- out << "echo \"############## Last 10 lines from dmesg : ##############\"" << endl;
- out << "dmesg | tail -n 10" << endl;
}
Bool_t copy = kTRUE;
- if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
TString bindir = Form("%s/bin", workdir.Data());
- if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir);
+ if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir,"-p");
workdir += fGridWorkingDir;
TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), fExecutable.Data());
if (FileExists(executable)) gGrid->Rm(executable);
- Info("CreateJDL", "\n##### Copying executable file <%s> to your AliEn bin directory", fExecutable.Data());
+ Info("WriteExecutable", "\n##### Copying executable file <%s> to your AliEn bin directory", fExecutable.Data());
TFile::Cp(Form("file:%s",fExecutable.Data()), Form("alien://%s", executable.Data()));
}
}
return;
}
out << "#!/bin/bash" << endl;
+ // Make sure we can properly compile par files
+ out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
out << "echo \"=========================================\"" << endl;
out << "echo \"############## PATH : ##############\"" << endl;
out << "echo $PATH" << endl;
out << "echo \"############## memory : ##############\"" << endl;
out << "free -m" << endl;
out << "echo \"=========================================\"" << endl << endl;
- // Make sure we can properly compile par files
- if (TObject::TestBit(AliAnalysisGrid::kUsePars)) out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
TString mergeMacro = fExecutable;
mergeMacro.ReplaceAll(".sh", "_merge.C");
- out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\")\"" << endl;
+ if (IsOneStageMerging())
+ out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\")\"" << endl;
+ else
+ out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\",$2)\"" << endl;
out << fExecutableCommand << " " << "$ARG" << endl;
out << "echo \"======== " << mergeMacro.Data() << " finished with exit code: $? ========\"" << endl;
out << "echo \"############## memory after: ##############\"" << endl;
out << "free -m" << endl;
- out << "echo \"############## Last 10 lines from dmesg : ##############\"" << endl;
- out << "dmesg | tail -n 10" << endl;
}
Bool_t copy = kTRUE;
- if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
TString bindir = Form("%s/bin", workdir.Data());
- if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir);
+ if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir,"-p");
workdir += fGridWorkingDir;
TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), mergeExec.Data());
if (FileExists(executable)) gGrid->Rm(executable);
- Info("CreateJDL", "\n##### Copying executable file <%s> to your AliEn bin directory", mergeExec.Data());
+ Info("WriteMergeExecutable", "\n##### Copying executable file <%s> to your AliEn bin directory", mergeExec.Data());
TFile::Cp(Form("file:%s",mergeExec.Data()), Form("alien://%s", executable.Data()));
}
}
Error("WriteProductionFile", "Bad file name: %s", filename);
return;
}
- TString workdir = gGrid->GetHomeDirectory();
+ TString workdir;
+ if (!fProductionMode && !fGridWorkingDir.BeginsWith("/alice"))
+ workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
Int_t njobspermaster = 1000*fNrunsPerMaster/fSplitMaxInputFileNumber;
TString locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
else
out << Form("%s", fInputFiles->At(i)->GetName()) << " " << Form("%03d", i) << endl;
}
- Info("WriteProductionFile", "\n##### Copying production file <%s> to your work directory", filename);
- if (FileExists(filename)) gGrid->Rm(filename);
- TFile::Cp(Form("file:%s",filename), Form("alien://%s/%s", workdir.Data(),filename));
+ if (gGrid) {
+ Info("WriteProductionFile", "\n##### Copying production file <%s> to your work directory", filename);
+ if (FileExists(filename)) gGrid->Rm(filename);
+ TFile::Cp(Form("file:%s",filename), Form("alien://%s/%s", workdir.Data(),filename));
+ }
}
//______________________________________________________________________________
// Generate the alien validation script.
// Generate the validation script
TObjString *os;
- TString validationScript = fExecutable;
- if (merge) validationScript.ReplaceAll(".sh", "_mergevalidation.sh");
- else validationScript.ReplaceAll(".sh", "_validation.sh");
+ if (fValidationScript.IsNull()) {
+ fValidationScript = fExecutable;
+ fValidationScript.ReplaceAll(".sh", "_validation.sh");
+ }
+ TString validationScript = fValidationScript;
+ if (merge) validationScript.ReplaceAll(".sh", "_merge.sh");
if (!Connect()) {
Error("WriteValidationScript", "Alien connection required");
return;
}
- TString out_stream = "";
- if (!TestBit(AliAnalysisGrid::kTest)) out_stream = " >> stdout";
+ if (!fTerminateFiles.IsNull()) {
+ fTerminateFiles.Strip();
+ fTerminateFiles.ReplaceAll(" ",",");
+ }
+ TString outStream = "";
+ if (!TestBit(AliAnalysisGrid::kTest)) outStream = " >> stdout";
if (!TestBit(AliAnalysisGrid::kSubmit)) {
ofstream out;
out.open(validationScript, ios::out);
out << "fi" << endl << endl;
out << "cd $validateout;" << endl;
out << "validateworkdir=`pwd`;" << endl << endl;
- out << "echo \"*******************************************************\"" << out_stream << endl;
- out << "echo \"* Automatically generated validation script *\"" << out_stream << endl;
+ out << "echo \"*******************************************************\"" << outStream << endl;
+ out << "echo \"* Automatically generated validation script *\"" << outStream << endl;
out << "" << endl;
- out << "echo \"* Time: $validatetime \"" << out_stream << endl;
- out << "echo \"* Dir: $validateout\"" << out_stream << endl;
- out << "echo \"* Workdir: $validateworkdir\"" << out_stream << endl;
- out << "echo \"* ----------------------------------------------------*\"" << out_stream << endl;
- out << "ls -la ./" << out_stream << endl;
- out << "echo \"* ----------------------------------------------------*\"" << out_stream << endl << endl;
+ out << "echo \"* Time: $validatetime \"" << outStream << endl;
+ out << "echo \"* Dir: $validateout\"" << outStream << endl;
+ out << "echo \"* Workdir: $validateworkdir\"" << outStream << endl;
+ out << "echo \"* ----------------------------------------------------*\"" << outStream << endl;
+ out << "ls -la ./" << outStream << endl;
+ out << "echo \"* ----------------------------------------------------*\"" << outStream << endl << endl;
out << "##################################################" << endl;
-
- out << "" << endl;
- out << "parArch=`grep -Ei \"Cannot Build the PAR Archive\" stderr`" << endl;
- out << "segViol=`grep -Ei \"Segmentation violation\" stderr`" << endl;
- out << "segFault=`grep -Ei \"Segmentation fault\" stderr`" << endl;
out << "" << endl;
out << "if [ ! -f stderr ] ; then" << endl;
out << " error=1" << endl;
- out << " echo \"* ########## Job not validated - no stderr ###\" " << out_stream << endl;
- out << " echo \"Error = $error\" " << out_stream << endl;
+ out << " echo \"* ########## Job not validated - no stderr ###\" " << outStream << endl;
+ out << " echo \"Error = $error\" " << outStream << endl;
out << "fi" << endl;
+ out << "parArch=`grep -Ei \"Cannot Build the PAR Archive\" stderr`" << endl;
+ out << "segViol=`grep -Ei \"Segmentation violation\" stderr`" << endl;
+ out << "segFault=`grep -Ei \"Segmentation fault\" stderr`" << endl;
+ out << "glibcErr=`grep -Ei \"*** glibc detected ***\" stderr`" << endl;
+ out << "" << endl;
+
out << "if [ \"$parArch\" != \"\" ] ; then" << endl;
out << " error=1" << endl;
- out << " echo \"* ########## Job not validated - PAR archive not built ###\" " << out_stream << endl;
- out << " echo \"$parArch\" " << out_stream << endl;
- out << " echo \"Error = $error\" " << out_stream << endl;
+ out << " echo \"* ########## Job not validated - PAR archive not built ###\" " << outStream << endl;
+ out << " echo \"$parArch\" " << outStream << endl;
+ out << " echo \"Error = $error\" " << outStream << endl;
out << "fi" << endl;
out << "if [ \"$segViol\" != \"\" ] ; then" << endl;
out << " error=1" << endl;
- out << " echo \"* ########## Job not validated - Segment. violation ###\" " << out_stream << endl;
- out << " echo \"$segViol\" " << out_stream << endl;
- out << " echo \"Error = $error\" " << out_stream << endl;
+ out << " echo \"* ########## Job not validated - Segment. violation ###\" " << outStream << endl;
+ out << " echo \"$segViol\" " << outStream << endl;
+ out << " echo \"Error = $error\" " << outStream << endl;
out << "fi" << endl;
out << "if [ \"$segFault\" != \"\" ] ; then" << endl;
out << " error=1" << endl;
- out << " echo \"* ########## Job not validated - Segment. fault ###\" " << out_stream << endl;
- out << " echo \"$segFault\" " << out_stream << endl;
- out << " echo \"Error = $error\" " << out_stream << endl;
+ out << " echo \"* ########## Job not validated - Segment. fault ###\" " << outStream << endl;
+ out << " echo \"$segFault\" " << outStream << endl;
+ out << " echo \"Error = $error\" " << outStream << endl;
+ out << "fi" << endl;
+
+ out << "if [ \"$glibcErr\" != \"\" ] ; then" << endl;
+ out << " error=1" << endl;
+ out << " echo \"* ########## Job not validated - *** glibc detected *** ###\" " << outStream << endl;
+ out << " echo \"$glibcErr\" " << outStream << endl;
+ out << " echo \"Error = $error\" " << outStream << endl;
out << "fi" << endl;
// Part dedicated to the specific analyses running into the train
- TObjArray *arr = fOutputFiles.Tokenize(" ");
+ TString outputFiles = fOutputFiles;
+ if (merge && !fTerminateFiles.IsNull()) {
+ outputFiles += ",";
+ outputFiles += fTerminateFiles;
+ }
+ TObjArray *arr = outputFiles.Tokenize(",");
TIter next1(arr);
- TString output_file;
- while ((os=(TObjString*)next1())) {
- output_file = os->GetString();
- Int_t index = output_file.Index("@");
- if (index > 0) output_file.Remove(index);
- if (merge && fMergeExcludes.Contains(output_file)) continue;
- out << "if ! [ -f " << output_file.Data() << " ] ; then" << endl;
+ TString outputFile;
+ while (!merge && (os=(TObjString*)next1())) {
+ // No need to validate outputs produced by merging since the merging macro does this
+ outputFile = os->GetString();
+ Int_t index = outputFile.Index("@");
+ if (index > 0) outputFile.Remove(index);
+ if (fTerminateFiles.Contains(outputFile)) continue;
+ if (outputFile.Contains("*")) continue;
+ out << "if ! [ -f " << outputFile.Data() << " ] ; then" << endl;
out << " error=1" << endl;
- out << " echo \"Output file(s) not found. Job FAILED !\"" << out_stream << endl;
- out << " echo \"Output file(s) not found. Job FAILED !\" >> stderr" << endl;
+ out << " echo \"Output file " << outputFile << " not found. Job FAILED !\"" << outStream << endl;
+ out << " echo \"Output file " << outputFile << " not found. Job FAILED !\" >> stderr" << endl;
out << "fi" << endl;
}
delete arr;
- if (!merge) {
- out << "if ! [ -f outputs_valid ] ; then" << endl;
- out << " error=1" << endl;
- out << " echo \"Output files were not validated by the analysis manager\" >> stdout" << endl;
- out << " echo \"Output files were not validated by the analysis manager\" >> stderr" << endl;
- out << "fi" << endl;
- }
+ out << "if ! [ -f outputs_valid ] ; then" << endl;
+ out << " error=1" << endl;
+ out << " echo \"Output files were not validated by the analysis manager\" >> stdout" << endl;
+ out << " echo \"Output files were not validated by the analysis manager\" >> stderr" << endl;
+ out << "fi" << endl;
out << "if [ $error = 0 ] ; then" << endl;
- out << " echo \"* ---------------- Job Validated ------------------*\"" << out_stream << endl;
+ out << " echo \"* ---------------- Job Validated ------------------*\"" << outStream << endl;
+ if (!IsKeepLogs()) {
+ out << " echo \"* === Logs std* will be deleted === \"" << endl;
+ outStream = "";
+ out << " rm -f std*" << endl;
+ }
out << "fi" << endl;
- out << "echo \"* ----------------------------------------------------*\"" << out_stream << endl;
- out << "echo \"*******************************************************\"" << out_stream << endl;
+ out << "echo \"* ----------------------------------------------------*\"" << outStream << endl;
+ out << "echo \"*******************************************************\"" << outStream << endl;
out << "cd -" << endl;
out << "exit $error" << endl;
}
Bool_t copy = kTRUE;
- if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
+ if (fProductionMode || TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
if (copy) {
CdWork();
TString workdir = gGrid->GetHomeDirectory();
workdir += fGridWorkingDir;
- Info("CreateJDL", "\n##### Copying validation script <%s> to your AliEn working space", validationScript.Data());
+ Info("WriteValidationScript", "\n##### Copying validation script <%s> to your AliEn working space", validationScript.Data());
if (FileExists(validationScript)) gGrid->Rm(validationScript);
TFile::Cp(Form("file:%s",validationScript.Data()), Form("alien://%s/%s", workdir.Data(),validationScript.Data()));
}
git://git.uio.no / u / mrichter / AliRoot.git / blobdiff