Segmentation Fault upon termination of program with ROOT 5.22/00b from Venkatesh Kaushik on 2009-06-01 (RootTalk)

From: Venkatesh Kaushik <venkat_at_hepmail.uta.edu>
Date: Mon, 1 Jun 2009 21:57:29 +0200

Hi,

I am using ATLAS software with ROOT v 5.22/00b /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/bin/root

I am not sure how to give a "simple" example of how to reproduce the crash I am getting without going into details about the program I am using, but I will certainly try. I should also mention that this crash did not occur
in earlier release (5.18/00f)

I am using a program (written in python) that creates a "transient tree" from an input data file. This memory resident tree is then accessed by my program.

Here's the python interface that calls this program and "creates" the transient
tree: (see attached ARATree.py)

I have a program in c++ which accesses the transient tree, does some analysis (the skeleton was written using TTree->MakeClass() using
this transient tree as input). The program runs fine. Upon termination of my program
I get a segmentation fault. The main program is given here (run.cxx)

I give also the stack trace ( stack_trace.txt if its of any help) for this: I have to mention that the
snippets I have provided are not sufficient (by themselves) to reproduce the crash.
Apologies. Any help is appreciated. I am willing to provide more information (other
package dependencies etc.)

# import libraries

import user
import ROOT
import PyCintex
import os
import sys
import AthenaROOTAccess.transientTree

# create a list of input files (local analysis)
def ReadFile(fileslist, nEvents) :

    namelist = []
    os.path.isfile(fileslist)
    FILE = open(fileslist,"r")
    for line in FILE :

        if type(line) == type("") :
            namelist.append(line.rstrip('\n'))

    FILE.close()
    print "--> reading " + str(len(namelist)) + " file(s) from " + os.path.dirname(namelist[0]) + "/"     shortlist = namelist
    if nEvents != -1 :

      print "--> determining number of files to open for " + str(nEvents) + " event(s)"
      shortlist = shortList(namelist, nEvents)
    for i in shortlist :
      print "--> " + os.path.basename(i)

return shortlist

# select files based on no. of events

def shortList(namelist, nEvents) :

    ntotal = 0
    ncount = 0
    for i in namelist :

      f = ROOT.TFile.Open (i)
      tree = f.Get ('CollectionTree')
      nentries = tree.GetEntries()
      ntotal += nentries
      ncount += 1
      if ntotal >= nEvents :
        break
    if ncount <= len(namelist) :
      namelist[ncount:len(namelist)] = []

print "--> found " + str(ntotal) + " event(s) in " + str(len(namelist)) + " file(s)" return namelist

# create a transient tree

def ARAtree(filelist, brNames = {}) :
  PyCintex.gbl.gEnv.SetValue("Root.ErrorIgnoreLevel", "Info")   chain = ROOT.AthenaROOTAccess.TChainROOTAccess('CollectionTree')   from glob import glob
  if type(filelist) is not list:
    filelist = glob(filelist)
  for i in filelist:
    chain.Add(i)
  tt = AthenaROOTAccess.transientTree.makeTree(chain, branchNames = brNames)   tt.chain = chain
  ROOT.SetOwnership(tt, True)
  return tt

#include <sstream>
#include <vector>
#include <cstdlib>

// local includes
#include "ARATopAnalysis/ARATree.h"
#include "ARATopAnalysis/TopAnalysis.h"

// ROOT includes
#include "TStopwatch.h"
#include "TPython.h"
#include "TTree.h"

// namespaces
using namespace std;

// helper function: event loop
void loop(int nEvents){

// define a top analysis object (one of the analysis objects) TopAnalysis *m_topAnalyser = new TopAnalysis("myTopAnalysis");

  // make a list of analysis objects
  std::vector<myAnalysis*> myAnalysers;
  myAnalysers.push_back(m_topAnalyser);

  // hook the transient tree to analysis   ARATree tree("myARATree");
  TStopwatch timer;
  timer.Start();
  // enter event loop with the list of analysers / number of events   int nEventsAnalysed = tree.Loop(nEvents,myAnalysers);   timer.Stop();

// finish analysis (save histograms etc.) m_topAnalyser->EndAnalysis();

Double_t rtime = timer.RealTime();
Double_t ctime = timer.CpuTime();

// print execution time

  std::cout << "Analysed events: " << nEventsAnalysed << std::endl;
  std::cout << "RealTime: " << rtime << " seconds. \t CpuTime: " << ctime << " seconds" << std::endl;
  std::cout << "Execution time: " << nEventsAnalysed/rtime << " events / RealTime second. \t";
  std::cout << nEventsAnalysed/ctime << " events / CpuTime second." << std::endl;

// delete all analysers
for(unsigned int i=0;i<myAnalysers.size();++i) delete myAnalysers[i];

// done
}

// helper function: make ARA transient tree TTree *MakeTree(string inputfilename) {

  static bool passOne = true;
  // import python modules to read list of input files   // and create transient tree
  if(passOne) {
    TPython::Exec( "from ARATopAnalysis.ARATree import ARAtree" );     TPython::Exec( "from ARATopAnalysis.ARATree import ReadFile" );     passOne = false;
  }

  // create a transient tree by invoking python module   std::ostringstream command;
  command << "ARAtree(ReadFile('" << inputfilename << "'))";   TTree* transTree = NULL;
  transTree = reinterpret_cast< TTree* >( ( void* ) TPython::Eval( command.str().c_str() ) );

  // exit if transient tree cannot be created   if( ! transTree ) {
    std::cout << "Couldn't create transient tree from persistent tree" << std::endl;     exit(1);
  }

// return transient tree to caller
return transTree;

// done
}

// main helper function: prepare transient tree and invoke event loop void analyzeSample(int nEvents, string sampleName, string program){

// run in batch mode by default
gROOT->SetBatch(kTRUE);

  TStopwatch timer;
  timer.Start();
  // make transient tree
  TTree *trTree = MakeTree(sampleName);
  timer.Stop();
  Double_t rtime = timer.RealTime();
  Double_t ctime = timer.CpuTime();

  // read number of entries in transient tree   int nEventS = nEvents;
  if(trTree) {
    Long64_t nentries = trTree->GetEntriesFast();     if(nEvents>nentries || nEvents == -1) nEventS = nentries;   }

// invoke event loop
loop(nEventS);
}

// main

int main(int argc, char ** argv){

  // set default number of events to process   // and the input file (in pwd)
  int nEvents = 1000;
  string sampleName = "filelist_top.txt";

  if(argc == 1) {
    printf("--> Usage: %s <nEvents> <sampleName>\n",argv[0]);     exit(1);
  }
  // get number of events to process and file list   // from command line
  if(argc>0) nEvents = atoi( argv[1]);
  if(argc>1) sampleName = argv[2];

// name of this program
string program = argv[0];

// invoke main analysis
analyzeSample(nEvents,sampleName,program);

// return success
return 0;

}

--> runProg.exe : switching to batch mode ... INFO runProg.exe : Initializing ARA transient tree. Could take a while, please wait...

--> reading 1 file(s) from /raid01/venkat/dataset/check/
--> determining number of files to open for 1 event(s)
--> found 250 event(s) in 1 file(s)
--> AOD.026357._00511.pool.root.1

Warning: Branch HLT_egamma renamed to HLT_egamma_1 to avoid duplicate name Types: egammaContainer egDetailContainer AthenaHitsVector DEBUG initialized.

 INFO    runProg.exe             : ARA Initialization: RealTime: 33.3378 s 	 CpuTime: 30.7 s
 INFO    runProg.exe             : Looping over events

...
...

 INFO    myTopAnalysis           : Event #: 0		20 kB
 INFO    runProg.exe             : RealTime: 0.746056 seconds. 	 CpuTime: 0.76 seconds
 INFO    runProg.exe             : Execution time: 1.34038 events / RealTime second. 	1.31579 events / CpuTime second.

Break *** segmentation violation
Break *** segmentation violation (no debugging symbols found) Using host libthread_db library "/lib/tls/libthread_db.so.1". Attaching to program: /proc/29258/exe, process 29258 (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. (no debugging symbols found)...done. [Thread debugging using libthread_db enabled] [New Thread -1209170240 (LWP 29258)]

0x005fd7a2 in _dl_sysinfo_int80 () from /lib/ld-linux.so.2
#1 0x0390e0f3 in __waitpid_nocancel () from /lib/tls/libc.so.6
#2 0x038b77b9 in do_system () from /lib/tls/libc.so.6
#3 0x02e9f387 in TUnixSystem::Exec ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#4 0x02ea501f in TUnixSystem::StackTrace ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#5 0x02ea1a1a in TUnixSystem::DispatchSignals ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#6 0x02ea1aa8 in SigHandler () from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#7 0x02ea0d25 in sighandler () from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#8 <signal handler called>
#9 0x05bb5004 in ?? ()
#10 0x04064bd7 in Cint::G__ExceptionWrapper ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCint.so
#11 0x0417c421 in G__callfunc0 () from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCint.so
#12 0x0417c4cb in G__calldtor () from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCint.so
#13 0x04097a5f in Cint::G__ClassInfo::Delete ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCint.so
#14 0x02e944f6 in TCint::ClassInfo_Delete ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#15 0x02e648f4 in TClass::Destructor ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#16 0x06754d6d in TBranchElement::ReleaseObject ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libTree.so
#17 0x06755a18 in TBranchElement::ResetAddress ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libTree.so
#18 0x0495c50d in TConvertingBranchElement::ResetAddress ()

from /afs/cern.ch/atlas/software/builds/AtlasCore/15.2.0/InstallArea/i686-slc4-gcc34-opt/lib/libRootConversions.so
#19 0x0495c76d in TConvertingBranchElement::~TConvertingBranchElement$delete ()

from /afs/cern.ch/atlas/software/builds/AtlasCore/15.2.0/InstallArea/i686-slc4-gcc34-opt/lib/libRootConversions.so
#20 0x02e4c3b0 in TCollection::GarbageCollect ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#21 0x02e53c0b in TObjArray::Delete ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#22 0x0679458a in TTree::~TTree$delete ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libTree.so
#23 0x02e4c3b0 in TCollection::GarbageCollect ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#24 0x02e507a5 in TList::Delete () from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#25 0x02e4e41c in THashList::Delete ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#26 0x061b3d37 in TDirectoryFile::Close ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libRIO.so
#27 0x061c22d9 in TFile::Close () from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libRIO.so
#28 0x061c270c in TFile::~TFile$delete ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libRIO.so
#29 0x02e4c3b0 in TCollection::GarbageCollect ()

   from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so


#30 0x02e507b5 in TList::Delete () from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so

#31 0x02e04f3a in TROOT::~TROOT () from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#32 0x02e0525b in __tcf_0 () from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#33 0x038ad868 in __cxa_finalize () from /lib/tls/libc.so.6
#34 0x02dc1cfa in __do_global_dtors_aux ()

from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#35 0x03143676 in _fini () from /afs/cern.ch/atlas/offline/external/LCGCMT/LCGCMT_56a/InstallArea/i686-slc4-gcc34-opt/lib/libCore.so
#36 0x00609e77 in _dl_fini () from /lib/ld-linux.so.2
#37 0x038ad5a7 in exit () from /lib/tls/libc.so.6
#38 0x03897dfd in __libc_start_main () from /lib/tls/libc.so.6
#39 0x08073651 in _start ()
Received on Mon Jun 01 2009 - 21:57:44 CEST

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