Segmentation Errors while doing root install with python

alexantony.arokiaraj · November 24, 2023, 4:07pm

I am installing root 6.18.04 with python 3.7.

My python installation is fine and it works without any problems.

At the end of the installation I get this crazy segmentation errors, which I am unable to troubleshoot.

In file included from input_line_12:18:
In file included from ./etc/dictpch/allHeaders.h:658:
./include/ROOT/RVec.hxx:46:10: fatal error: ‘vdt/vdtMath.h’ file not found
#include <vdt/vdtMath.h>
^~~~~~~~~~~~~~~
#0 0x00007f2c1064657f PrintStackTraceSignalHandler(void*) (./lib/libCling.so+0x22dc57f)
#1 0x00007f2c1064470e llvm::sys::RunSignalHandlers() (./lib/libCling.so+0x22da70e)
#2 0x00007f2c1064484a SignalHandler(int) (./lib/libCling.so+0x22da84a)
#3 0x00007f2c0d8af050 __restore_rt (/lib64/libpthread.so.0+0x14050)
#4 0x00007f2c0fd98697 NoteIndirectBases(clang::ASTContext&, llvm::SmallPtrSet<clang::QualType, 4u>&, clang::QualType const&) (./lib/libCling.so+0x1a2e697)
#5 0x00007f2c0fd98f30 clang::Sema::AttachBaseSpecifiers(clang::CXXRecordDecl*, llvm::MutableArrayRefclang::CXXBaseSpecifier*) (./lib/libCling.so+0x1a2ef30)
#6 0x00007f2c0fd9947e clang::Sema::ActOnBaseSpecifiers(clang::Decl*, llvm::MutableArrayRefclang::CXXBaseSpecifier*) (./lib/libCling.so+0x1a2f47e)
#7 0x00007f2c0fb71062 clang::Parser::ParseBaseClause(clang::Decl*) (./lib/libCling.so+0x1807062)
#8 0x00007f2c0fb719eb clang::Parser::ParseCXXMemberSpecification(clang::SourceLocation, clang::SourceLocation, clang::Parser::ParsedAttributesWithRange&, unsigned int, clang::Decl*) (./lib/libCling.so+0x18079eb)
#9 0x00007f2c0fb73e65 clang::Parser::ParseClassSpecifier(clang::tok::TokenKind, clang::SourceLocation, clang::DeclSpec&, clang::Parser::ParsedTemplateInfo const&, clang::AccessSpecifier, bool, clang::Parser::DeclSpecContext, clang::Parser::ParsedAttributesWithRange&) (./lib/libCling.so+0x1809e65)
#10 0x00007f2c0fb55217 clang::Parser::ParseDeclarationSpecifiers(clang::DeclSpec&, clang::Parser::ParsedTemplateInfo const&, clang::AccessSpecifier, clang::Parser::DeclSpecContext, clang::Parser::LateParsedAttrList*) (./lib/libCling.so+0x17eb217)
#11 0x00007f2c0fb5f18b clang::Parser::ParseSimpleDeclaration(unsigned int, clang::SourceLocation&, clang::Parser::ParsedAttributesWithRange&, bool, clang::Parser::ForRangeInit*) (./lib/libCling.so+0x17f518b)
#12 0x00007f2c0fb5f4fe clang::Parser::ParseDeclaration(unsigned int, clang::SourceLocation&, clang::Parser::ParsedAttributesWithRange&) (./lib/libCling.so+0x17f54fe)
#13 0x00007f2c0fbb711d clang::Parser::ParseStatementOrDeclarationAfterAttributes(llvm::SmallVector<clang::Stmt*, 32u>&, clang::Parser::AllowedConstructsKind, clang::SourceLocation*, clang::Parser::ParsedAttributesWithRange&) (./lib/libCling.so+0x184d11d)
#14 0x00007f2c0fbb7313 clang::Parser::ParseStatementOrDeclaration(llvm::SmallVector<clang::Stmt*, 32u>&, clang::Parser::AllowedConstructsKind, clang::SourceLocation*) (./lib/libCling.so+0x184d313)
#15 0x00007f2c0fbb7b91 clang::Parser::ParseCompoundStatementBody(bool) (./lib/libCling.so+0x184db91)
#16 0x00007f2c0fbb9b49 clang::Parser::ParseFunctionStatementBody(clang::Decl*, clang::Parser::ParseScope&) (./lib/libCling.so+0x184fb49)
#17 0x00007f2c0fbd9de3 clang::Parser::ParseFunctionDefinition(clang::ParsingDeclarator&, clang::Parser::ParsedTemplateInfo const&, clang::Parser::LateParsedAttrList*) (./lib/libCling.so+0x186fde3)
#18 0x00007f2c0fbc926b clang::Parser::ParseSingleDeclarationAfterTemplate(unsigned int, clang::Parser::ParsedTemplateInfo const&, clang::ParsingDeclRAIIObject&, clang::SourceLocation&, clang::AccessSpecifier, clang::AttributeList*) (./lib/libCling.so+0x185f26b)
#19 0x00007f2c0fbc9eb1 clang::Parser::ParseTemplateDeclarationOrSpecialization(unsigned int, clang::SourceLocation&, clang::AccessSpecifier, clang::AttributeList*) (./lib/libCling.so+0x185feb1)
#20 0x00007f2c0fbca1ab clang::Parser::ParseDeclarationStartingWithTemplate(unsigned int, clang::SourceLocation&, clang::AccessSpecifier, clang::AttributeList*) (./lib/libCling.so+0x18601ab)
#21 0x00007f2c0fb5f74a clang::Parser::ParseDeclaration(unsigned int, clang::SourceLocation&, clang::Parser::ParsedAttributesWithRange&) (./lib/libCling.so+0x17f574a)
#22 0x00007f2c0fbd7b0a clang::Parser::ParseExternalDeclaration(clang::Parser::ParsedAttributesWithRange&, clang::ParsingDeclSpec*) (./lib/libCling.so+0x186db0a)
#23 0x00007f2c0fb6fb11 clang::Parser::ParseInnerNamespace(std::vector<clang::SourceLocation, std::allocatorclang::SourceLocation >&, std::vector<clang::IdentifierInfo*, std::allocatorclang::IdentifierInfo* >&, std::vector<clang::SourceLocation, std::allocatorclang::SourceLocation >&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) (./lib/libCling.so+0x1805b11)
#24 0x00007f2c0fb703a8 clang::Parser::ParseNamespace(unsigned int, clang::SourceLocation&, clang::SourceLocation) (./lib/libCling.so+0x18063a8)
#25 0x00007f2c0fb5f824 clang::Parser::ParseDeclaration(unsigned int, clang::SourceLocation&, clang::Parser::ParsedAttributesWithRange&) (./lib/libCling.so+0x17f5824)
#26 0x00007f2c0fbd7b0a clang::Parser::ParseExternalDeclaration(clang::Parser::ParsedAttributesWithRange&, clang::ParsingDeclSpec*) (./lib/libCling.so+0x186db0a)
#27 0x00007f2c0fb6fb11 clang::Parser::ParseInnerNamespace(std::vector<clang::SourceLocation, std::allocatorclang::SourceLocation >&, std::vector<clang::IdentifierInfo*, std::allocatorclang::IdentifierInfo* >&, std::vector<clang::SourceLocation, std::allocatorclang::SourceLocation >&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) (./lib/libCling.so+0x1805b11)
#28 0x00007f2c0fb703a8 clang::Parser::ParseNamespace(unsigned int, clang::SourceLocation&, clang::SourceLocation) (./lib/libCling.so+0x18063a8)
#29 0x00007f2c0fb5f824 clang::Parser::ParseDeclaration(unsigned int, clang::SourceLocation&, clang::Parser::ParsedAttributesWithRange&) (./lib/libCling.so+0x17f5824)
#30 0x00007f2c0fbd7b0a clang::Parser::ParseExternalDeclaration(clang::Parser::ParsedAttributesWithRange&, clang::ParsingDeclSpec*) (./lib/libCling.so+0x186db0a)
#31 0x00007f2c0fbd8d31 clang::Parser::ParseTopLevelDecl(clang::OpaquePtrclang::DeclGroupRef&) (./lib/libCling.so+0x186ed31)
#32 0x00007f2c0e909160 cling::IncrementalParser::ParseInternal(llvm::StringRef) (./lib/libCling.so+0x59f160)
#33 0x00007f2c0e909fec cling::IncrementalParser::Compile(llvm::StringRef, cling::CompilationOptions const&) (./lib/libCling.so+0x59ffec)
#34 0x00007f2c0e8a4b8c cling::Interpreter::DeclareInternal(std::string const&, cling::CompilationOptions const&, cling::Transaction**) const (./lib/libCling.so+0x53ab8c)
#35 0x00007f2c0e8a4cce cling::Interpreter::declare(std::string const&, cling::Transaction**) (./lib/libCling.so+0x53acce)
#36 0x00007f2c0e7e44ed InjectModuleUtilHeader(char const*, ROOT::TModuleGenerator&, cling::Interpreter&, bool) /mnt/ksf2/H1/user/u0100486/linux/doctorate/software/root-6.18.04/core/dictgen/src/rootcling_impl.cxx:2046:0
#37 0x00007f2c0e7e7e31 RootClingMain(int, char**, bool, bool) /mnt/ksf2/H1/user/u0100486/linux/doctorate/software/root-6.18.04/core/dictgen/src/rootcling_impl.cxx:4534:0
#38 0x00007f2c0e7f0dec ROOT_rootcling_Driver /mnt/ksf2/H1/user/u0100486/linux/doctorate/software/root-6.18.04/core/dictgen/src/rootcling_impl.cxx:6090:0
#39 0x0000000000400c22 main /mnt/ksf2/H1/user/u0100486/linux/doctorate/software/root-6.18.04/main/src/rootcling.cxx:45:0
#40 0x00007f2c0cb7e34d _libc_start_main (/lib64/libc.so.6+0x2534d)
#41 0x0000000000400c6a start /home/abuild/rpmbuild/BUILD/glibc-2.31/csu/…/sysdeps/x86_64/start.S:122:0
Stack dump:
0. Program arguments: ./bin/rootcling -rootbuild -1 -f allDict.cxx -noDictSelection -c -D__CLING -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -DROOT_PCH -fsigned-char -I./include -I./etc -I./etc/dictpch -I./etc/cling -I/mnt/ksf2/H1/user/u0100486/linux/.local/lib/python3.7/site-packages/numpy/core/include -I/mnt/ksf2/H1/user/u0100486/linux/doctorate/software/python/include/python3.7m -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -std=c++11 -pipe -fsigned-char -pthread -DSYSTEM_TYPE_unix -I/mnt/ksf2/H1/user/u0100486/linux/doctorate/software/root-6.18.04/root_build/include etc/dictpch/allHeaders.h etc/dictpch/allLinkDefs.h
 ./include/ROOT/RLazyDS.hxx:18:1: parsing namespace 'ROOT'
 ./include/ROOT/RLazyDS.hxx:20:1: parsing namespace 'ROOT::RDF'
 ./include/ROOT/RLazyDS.hxx:29:1: parsing function body 'ROOT::RDF::MakeLazyDataFrame'
 ./include/ROOT/RLazyDS.hxx:29:1: in compound statement ('{}')
 ./include/TVirtualPad.h:49:1: parsing struct/union/class body 'TVirtualPad'
*** Break *** segmentation violation
if sys.flags.utf8_mode:
gmake[2]: *** [CMakeFiles/onepcm.dir/build.make:82: etc/allDict.cxx.pch] Error 139
gmake[1]: *** [CMakeFiles/Makefile2:6962: CMakeFiles/onepcm.dir/all] Error 2
gmake[1]: *** Waiting for unfinished jobs…
[100%] Linking CXX shared library …/…/lib/libHistFactory.so
[100%] Built target HistFactory
gmake: *** [Makefile:169: all] Error 2

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Danilo · November 25, 2023, 2:30pm

Hi Alexantony,

I am sorry to hear that your build process fails at the end so cryptically while building the pch.
I am not sure what linux distributuon you are using, however, you are using a ROOT version which is 4 years old and a python version which is 5 years old.

My suggestion would be to try, if possible, to build a more recent ROOT, compatibly with the constraints of your working environment.

I hope this help.

Best,
D

system · December 9, 2023, 2:30pm

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