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Question Segmentation Fault when using ROOT 6 to open output from TestEm5 

Forum: Analysis
Date: 09 Jan, 2015
From: Chris Howard <Chris Howard>

I've run the TestEm5 example under Geant4.10.1.0 and I used the pixe.mac macro. The program seemed to run fine and exit normally, creating the pixe.root output file. Now, if I open the file with ROOT 6.02 I get a segmentation violation.

See below for the output of the crash. So, is Geant4's root output not compatible with the new ROOT6 yet?

=========

chris{10:42:53}root pixe.root 
root [0] 
Attaching file pixe.root as _file0...
(class TFile *) 0xa1b5880
root [1] .ls
TFile**		pixe.root	
 TFile*		pixe.root	
  KEY: TH1D	h3;1	energy of neutral secondaries at creation
  KEY: TH1D	h5;1	energy of neutral at creation (log scale)
  KEY: TH1D	h17;1	energy of fluorescence gamma at creation
  KEY: TH1D	h19;1	energy of fluorescence gamma at creation (log scale)
  KEY: TH1D	h20;1	(transmit, neutral) : kinetic energy at exit
  KEY: TH1D	h40;1	(reflect , neutral) : kinetic energy at exit
  KEY: TH1D	h45;1	energy of PIXE gamma at creation
  KEY: TH1D	h47;1	energy of PIXE gamma at creation (log scale)
root [2] h3.Draw("HIST")

 *** Break *** segmentation violation

=========================================================== There was a crash (#8 0xb75f7f8b in SigHandler(ESignals) () from /home/choward/software/root/root-v6-02/lib/libCore.so). This is the entire stack trace of all threads: ===========================================================

#0  0xb773a424 in __kernel_vsyscall ()
#1  0xb7162ba3 in __waitpid_nocancel () at ../sysdeps/unix/syscall-template.S:81
#2  0xb70ecd1d in do_system (line=line
entry=0xa6d64e0 "/home/choward/software/root/root-v6-02/etc/gdb-backtrace.sh 30320 1>&2") at ../sysdeps/posix/system.c:148 #3 0xb70ed120 in __libc_system (line=line entry=0xa6d64e0 "/home/choward/software/root/root-v6-02/etc/gdb-backtrace.sh 30320 1>&2") at ../sysdeps/posix/system.c:184
#4  0xb726b10b in system (line=0xa6d64e0 "/home/choward/software/root/root-v6-02/etc/gdb-backtrace.sh 30320 1>&2") at pt-system.c:28
#5  0xb75f1a0b in TUnixSystem::Exec(char const*) () from /home/choward/software/root/root-v6-02/lib/libCore.so
#6  0xb75f4f72 in TUnixSystem::StackTrace() () from /home/choward/software/root/root-v6-02/lib/libCore.so
#7  0xb75f7e47 in TUnixSystem::DispatchSignals(ESignals) () from /home/choward/software/root/root-v6-02/lib/libCore.so
#8  0xb75f7f8b in SigHandler(ESignals) () from /home/choward/software/root/root-v6-02/lib/libCore.so
#9  0xb75f08a2 in sighandler(int) () from /home/choward/software/root/root-v6-02/lib/libCore.so
#10 0xb7629cb5 in textinput::TerminalConfigUnix::HandleSignal(int) () from /home/choward/software/root/root-v6-02/lib/libCore.so
#11 0xb7629d04 in (anonymous namespace)::TerminalConfigUnix__handleSignal(int) () from /home/choward/software/root/root-v6-02/lib/libCore.so
#12 <signal handler called>
#13 0xb75b5098 in TClass::IsStartingWithTObject() const () from /home/choward/software/root/root-v6-02/lib/libCore.so
#14 0xb4fa4636 in int TStreamerInfo::ReadBuffer<char**>(TBuffer&, char** const&, TStreamerInfo::TCompInfo* const*, int, int, int, int, int) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#15 0xb4e8909c in TStreamerInfoActions::GenericReadAction(TBuffer&, void*, TStreamerInfoActions::TConfiguration const*) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#16 0xb4e3a831 in TBufferFile::ApplySequence(TStreamerInfoActions::TActionSequence const&, void*) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#17 0xb4e38d8a in TBufferFile::ReadClassBuffer(TClass const*, void*, int, unsigned int, unsigned int, TClass const*) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#18 0xafc127a9 in TH1::Streamer(TBuffer&) () from /home/choward/software/root/root-v6-02/lib/libHist.so
#19 0xafcf81a3 in ROOT::streamer_TH1(TBuffer&, void*) () from /home/choward/software/root/root-v6-02/lib/libHist.so
#20 0xb75ea394 in TStreamerBase::ReadBuffer(TBuffer&, char*) () from /home/choward/software/root/root-v6-02/lib/libCore.so
#21 0xb4fa47ec in int TStreamerInfo::ReadBuffer<char**>(TBuffer&, char** const&, TStreamerInfo::TCompInfo* const*, int, int, int, int, int) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#22 0xb4e8909c in TStreamerInfoActions::GenericReadAction(TBuffer&, void*, TStreamerInfoActions::TConfiguration const*) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#23 0xb4e3a831 in TBufferFile::ApplySequence(TStreamerInfoActions::TActionSequence const&, void*) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#24 0xb4e391b5 in TBufferFile::ReadClassBuffer(TClass const*, void*, TClass const*) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#25 0xafcf42a4 in TH1D::Streamer(TBuffer&) () from /home/choward/software/root/root-v6-02/lib/libHist.so
#26 0xb4e7da60 in TKey::ReadObj() () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#27 0xb4e41e9b in TDirectoryFile::Get(char const*) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#28 0xb7552fbe in TROOT::FindSpecialObject(char const*, void*&) () from /home/choward/software/root/root-v6-02/lib/libCore.so
#29 0xb5472fdf in TCling__GetObjectAddress () from /home/choward/software/root/root-v6-02/lib/libCling.so
#30 0xb54ac2ff in TClingCallbacks::tryFindROOTSpecialInternal(clang::LookupResult&, clang::Scope*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#31 0xb54ad283 in TClingCallbacks::LookupObject(clang::LookupResult&, clang::Scope*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#32 0xb55734da in cling::MultiplexInterpreterCallbacks::LookupObject(clang::LookupResult&, clang::Scope*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#33 0xb556c038 in cling::InterpreterExternalSemaSource::LookupUnqualified(clang::LookupResult&, clang::Scope*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#34 0xb5d42d4a in clang::MultiplexExternalSemaSource::LookupUnqualified(clang::LookupResult&, clang::Scope*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#35 0xb5bda0ee in clang::Sema::LookupName(clang::LookupResult&, clang::Scope*, bool) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#36 0xb5bdaa92 in clang::Sema::LookupParsedName(clang::LookupResult&, clang::Scope*, clang::CXXScopeSpec*, bool, bool) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#37 0xb5a95d4d in clang::Sema::ClassifyName(clang::Scope*, clang::CXXScopeSpec&, clang::IdentifierInfo*&, clang::SourceLocation, clang::Token const&, bool, clang::CorrectionCandidateCallback*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#38 0xb59b4fe0 in clang::Parser::TryAnnotateName(bool, clang::CorrectionCandidateCallback*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#39 0xb599e4eb in clang::Parser::ParseStatementOrDeclarationAfterAttributes(llvm::SmallVector<clang::Stmt*, 32u>&, bool, clang::SourceLocation*, clang::Parser::ParsedAttributesWithRange&) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#40 0xb599e7cd in clang::Parser::ParseStatementOrDeclaration(llvm::SmallVector<clang::Stmt*, 32u>&, bool, clang::SourceLocation*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#41 0xb59a1670 in clang::Parser::ParseCompoundStatementBody(bool) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#42 0xb59a3a52 in clang::Parser::ParseFunctionStatementBody(clang::Decl*, clang::Parser::ParseScope&) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#43 0xb59ba857 in clang::Parser::ParseFunctionDefinition(clang::ParsingDeclarator&, clang::Parser::ParsedTemplateInfo const&, clang::Parser::LateParsedAttrList*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#44 0xb5952d34 in clang::Parser::ParseDeclGroup(clang::ParsingDeclSpec&, unsigned int, bool, clang::SourceLocation*, clang::Parser::ForRangeInit*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#45 0xb59b5883 in clang::Parser::ParseDeclOrFunctionDefInternal(clang::Parser::ParsedAttributesWithRange&, clang::ParsingDeclSpec&, clang::AccessSpecifier) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#46 0xb59b6041 in clang::Parser::ParseDeclarationOrFunctionDefinition(clang::Parser::ParsedAttributesWithRange&, clang::ParsingDeclSpec*, clang::AccessSpecifier) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#47 0xb59b8249 in clang::Parser::ParseExternalDeclaration(clang::Parser::ParsedAttributesWithRange&, clang::ParsingDeclSpec*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#48 0xb59b8c47 in clang::Parser::ParseTopLevelDecl(clang::OpaquePtr<clang::DeclGroupRef>&) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#49 0xb5569815 in cling::IncrementalParser::ParseInternal(llvm::StringRef) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#50 0xb556a81f in cling::IncrementalParser::Compile(llvm::StringRef, cling::CompilationOptions const&) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#51 0xb5572091 in cling::Interpreter::EvaluateInternal(std::string const&, cling::CompilationOptions const&, cling::Value*, cling::Transaction**) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#52 0xb5572332 in cling::Interpreter::process(std::string const&, cling::Value*, cling::Transaction**) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#53 0xb55b1678 in cling::MetaProcessor::process(char const*, cling::Interpreter::CompilationResult&, cling::Value*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#54 0xb5475b86 in TCling::ProcessLine(char const*, TInterpreter::EErrorCode*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#55 0xb750e015 in TApplication::ProcessLine(char const*, bool, int*) () from /home/choward/software/root/root-v6-02/lib/libCore.so
#56 0xb73a0c4f in TRint::ProcessLineNr(char const*, char const*, int*) () from /home/choward/software/root/root-v6-02/lib/libRint.so
#57 0xb73a0f98 in TRint::HandleTermInput() () from /home/choward/software/root/root-v6-02/lib/libRint.so
#58 0xb73a0372 in TTermInputHandler::Notify() () from /home/choward/software/root/root-v6-02/lib/libRint.so
#59 0xb73a2e52 in TTermInputHandler::ReadNotify() () from /home/choward/software/root/root-v6-02/lib/libRint.so
#60 0xb75f746b in TUnixSystem::CheckDescriptors() () from /home/choward/software/root/root-v6-02/lib/libCore.so
#61 0xb75f85d1 in TUnixSystem::DispatchOneEvent(bool) () from /home/choward/software/root/root-v6-02/lib/libCore.so
#62 0xb756dce2 in TSystem::InnerLoop() () from /home/choward/software/root/root-v6-02/lib/libCore.so
#63 0xb756eb80 in TSystem::Run() () from /home/choward/software/root/root-v6-02/lib/libCore.so
#64 0xb750bfd2 in TApplication::Run(bool) () from /home/choward/software/root/root-v6-02/lib/libCore.so
#65 0xb73a278f in TRint::Run(bool) () from /home/choward/software/root/root-v6-02/lib/libRint.so
#66 0x08048d20 in main ()
===========================================================

The lines below might hint at the cause of the crash. If they do not help you then please submit a bug report at http://root.cern.ch/bugs. Please post the ENTIRE stack trace from above as an attachment in addition to anything else that might help us fixing this issue. ===========================================================

#13 0xb75b5098 in TClass::IsStartingWithTObject() const () from /home/choward/software/root/root-v6-02/lib/libCore.so
#14 0xb4fa4636 in int TStreamerInfo::ReadBuffer<char**>(TBuffer&, char** const&, TStreamerInfo::TCompInfo* const*, int, int, int, int, int) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#15 0xb4e8909c in TStreamerInfoActions::GenericReadAction(TBuffer&, void*, TStreamerInfoActions::TConfiguration const*) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#16 0xb4e3a831 in TBufferFile::ApplySequence(TStreamerInfoActions::TActionSequence const&, void*) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#17 0xb4e38d8a in TBufferFile::ReadClassBuffer(TClass const*, void*, int, unsigned int, unsigned int, TClass const*) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#18 0xafc127a9 in TH1::Streamer(TBuffer&) () from /home/choward/software/root/root-v6-02/lib/libHist.so
#19 0xafcf81a3 in ROOT::streamer_TH1(TBuffer&, void*) () from /home/choward/software/root/root-v6-02/lib/libHist.so
#20 0xb75ea394 in TStreamerBase::ReadBuffer(TBuffer&, char*) () from /home/choward/software/root/root-v6-02/lib/libCore.so
#21 0xb4fa47ec in int TStreamerInfo::ReadBuffer<char**>(TBuffer&, char** const&, TStreamerInfo::TCompInfo* const*, int, int, int, int, int) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#22 0xb4e8909c in TStreamerInfoActions::GenericReadAction(TBuffer&, void*, TStreamerInfoActions::TConfiguration const*) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#23 0xb4e3a831 in TBufferFile::ApplySequence(TStreamerInfoActions::TActionSequence const&, void*) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#24 0xb4e391b5 in TBufferFile::ReadClassBuffer(TClass const*, void*, TClass const*) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#25 0xafcf42a4 in TH1D::Streamer(TBuffer&) () from /home/choward/software/root/root-v6-02/lib/libHist.so
#26 0xb4e7da60 in TKey::ReadObj() () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#27 0xb4e41e9b in TDirectoryFile::Get(char const*) () from /home/choward/software/root/root-v6-02/lib/libRIO.so
#28 0xb7552fbe in TROOT::FindSpecialObject(char const*, void*&) () from /home/choward/software/root/root-v6-02/lib/libCore.so
#29 0xb5472fdf in TCling__GetObjectAddress () from /home/choward/software/root/root-v6-02/lib/libCling.so
#30 0xb54ac2ff in TClingCallbacks::tryFindROOTSpecialInternal(clang::LookupResult&, clang::Scope*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#31 0xb54ad283 in TClingCallbacks::LookupObject(clang::LookupResult&, clang::Scope*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#32 0xb55734da in cling::MultiplexInterpreterCallbacks::LookupObject(clang::LookupResult&, clang::Scope*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#33 0xb556c038 in cling::InterpreterExternalSemaSource::LookupUnqualified(clang::LookupResult&, clang::Scope*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#34 0xb5d42d4a in clang::MultiplexExternalSemaSource::LookupUnqualified(clang::LookupResult&, clang::Scope*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#35 0xb5bda0ee in clang::Sema::LookupName(clang::LookupResult&, clang::Scope*, bool) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#36 0xb5bdaa92 in clang::Sema::LookupParsedName(clang::LookupResult&, clang::Scope*, clang::CXXScopeSpec*, bool, bool) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#37 0xb5a95d4d in clang::Sema::ClassifyName(clang::Scope*, clang::CXXScopeSpec&, clang::IdentifierInfo*&, clang::SourceLocation, clang::Token const&, bool, clang::CorrectionCandidateCallback*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#38 0xb59b4fe0 in clang::Parser::TryAnnotateName(bool, clang::CorrectionCandidateCallback*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#39 0xb599e4eb in clang::Parser::ParseStatementOrDeclarationAfterAttributes(llvm::SmallVector<clang::Stmt*, 32u>&, bool, clang::SourceLocation*, clang::Parser::ParsedAttributesWithRange&) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#40 0xb599e7cd in clang::Parser::ParseStatementOrDeclaration(llvm::SmallVector<clang::Stmt*, 32u>&, bool, clang::SourceLocation*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#41 0xb59a1670 in clang::Parser::ParseCompoundStatementBody(bool) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#42 0xb59a3a52 in clang::Parser::ParseFunctionStatementBody(clang::Decl*, clang::Parser::ParseScope&) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#43 0xb59ba857 in clang::Parser::ParseFunctionDefinition(clang::ParsingDeclarator&, clang::Parser::ParsedTemplateInfo const&, clang::Parser::LateParsedAttrList*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#44 0xb5952d34 in clang::Parser::ParseDeclGroup(clang::ParsingDeclSpec&, unsigned int, bool, clang::SourceLocation*, clang::Parser::ForRangeInit*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#45 0xb59b5883 in clang::Parser::ParseDeclOrFunctionDefInternal(clang::Parser::ParsedAttributesWithRange&, clang::ParsingDeclSpec&, clang::AccessSpecifier) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#46 0xb59b6041 in clang::Parser::ParseDeclarationOrFunctionDefinition(clang::Parser::ParsedAttributesWithRange&, clang::ParsingDeclSpec*, clang::AccessSpecifier) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#47 0xb59b8249 in clang::Parser::ParseExternalDeclaration(clang::Parser::ParsedAttributesWithRange&, clang::ParsingDeclSpec*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#48 0xb59b8c47 in clang::Parser::ParseTopLevelDecl(clang::OpaquePtr<clang::DeclGroupRef>&) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#49 0xb5569815 in cling::IncrementalParser::ParseInternal(llvm::StringRef) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#50 0xb556a81f in cling::IncrementalParser::Compile(llvm::StringRef, cling::CompilationOptions const&) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#51 0xb5572091 in cling::Interpreter::EvaluateInternal(std::string const&, cling::CompilationOptions const&, cling::Value*, cling::Transaction**) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#52 0xb5572332 in cling::Interpreter::process(std::string const&, cling::Value*, cling::Transaction**) () from /home/choward/software/root/root-v6-02/lib/libCling.so
#53 0xb55b1678 in cling::MetaProcessor::process(char const*, cling::Interpreter::CompilationResult&, cling::Value*) () from /home/choward/software/root/root-v6-02/lib/libCling.so
===========================================================

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1 None: Re: Segmentation Fault when using ROOT 6 to open output from TestEm5   (Guy Barrand - 18 Jan, 2015)
(_ None: Re: Segmentation Fault when using ROOT 6 to open output from TestEm5   (Guy Barrand - 20 Jan, 2015)
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