Compile errors with Delphes and ExRootAnalysis

Newbie
1

Please read tips for efficient and successful posting and posting code

_ROOT Version:6
_Platform: UBUNTU 20.04
_Compiler:g++

The cluster I’m working on recently updated to ubuntu20.04 and I’m trying to get everything to work again. When I tried to compile Delphes and ExRootAnalysis, I get this respectively

(venv1) dkennedy_umass_edu@login2:~/LNV/MG5_aMC_v3_5_4/Delphes$ make
>> Generating tmp/classes/ClassesDict.cc
ERROR in cling::CIFactory::createCI(): cannot extract standard library include paths!
Invoking:
  LC_ALL=C x86_64-linux-gnu-g++-9   -xc++ -E -v /dev/null 2>&1 | sed -n -e '/^.include/,${' -e '/^ \/.*++/p' -e '}'
Results was:
With exit code 0
input_line_1:1:10: fatal error: 'new' file not found
#include <new>
         ^~~~~
Warning in cling::IncrementalParser::CheckABICompatibility():
  Failed to extract C++ standard library version.
In file included from input_line_3:1:
/home/dkennedy_umass_edu/root/include/RtypesCore.h:28:10: fatal error: 'cstddef' file not found
#include <cstddef> // size_t, NULL
         ^~~~~~~~~
In file included from input_line_4:2:
In file included from /home/dkennedy_umass_edu/root/include/Rtypes.h:23:
/home/dkennedy_umass_edu/root/include/RtypesCore.h:28:10: fatal error: 'cstddef' file not found
#include <cstddef> // size_t, NULL
         ^~~~~~~~~
Error: Error loading the default rootcling header files.
make: *** [Makefile:2520: tmp/classes/ClassesDict.cc] Error 1

>> Generating tmp/src/ExRootAnalysisDict.cc
ERROR in cling::CIFactory::createCI(): cannot extract standard library include paths!
Invoking:
  LC_ALL=C x86_64-linux-gnu-g++-9   -xc++ -E -v /dev/null 2>&1 | sed -n -e '/^.include/,${' -e '/^ \/.*++/p' -e '}'
Results was:
With exit code 0
input_line_1:1:10: fatal error: 'new' file not found
#include <new>
         ^~~~~
Warning in cling::IncrementalParser::CheckABICompatibility():
  Failed to extract C++ standard library version.
In file included from input_line_3:1:
/home/dkennedy_umass_edu/root/include/RtypesCore.h:28:10: fatal error: 'cstddef' file not found
#include <cstddef> // size_t, NULL
         ^~~~~~~~~
In file included from input_line_4:2:
In file included from /home/dkennedy_umass_edu/root/include/Rtypes.h:23:
/home/dkennedy_umass_edu/root/include/RtypesCore.h:28:10: fatal error: 'cstddef' file not found
#include <cstddef> // size_t, NULL
         ^~~~~~~~~
Error: Error loading the default rootcling header files.
make: *** [Makefile:204: tmp/src/ExRootAnalysisDict.cc] Error 1

Nearly the same error.
Then when I try to run root:

(venv1) dkennedy_umass_edu@login2:~/root$ root
ERROR in cling::CIFactory::createCI(): cannot extract standard library include paths!
Invoking:
  LC_ALL=C x86_64-linux-gnu-g++-9   -xc++ -E -v /dev/null 2>&1 | sed -n -e '/^.include/,${' -e '/^ \/.*++/p' -e '}'
Results was:
With exit code 0
error: entry with relative path at the root level is not discoverable
{ 'name': '', 'type': 'directory',
          ^~
Error in modulemap.overlay!

 *** Break *** segmentation violation



===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x0000799c799107a7 in __GI___wait4 (pid=1305854, stat_loc=stat_loc
entry=0x7ffe5c0f70d8, options=options
entry=0, usage=usage
entry=0x0) at ../sysdeps/unix/sysv/linux/wait4.c:30
#1  0x0000799c799108eb in __GI___waitpid (pid=<optimized out>, stat_loc=stat_loc
entry=0x7ffe5c0f70d8, options=options
entry=0) at ./posix/waitpid.c:38
#2  0x0000799c798585ab in do_system (line=<optimized out>) at ../sysdeps/posix/system.c:172
#3  0x0000799c7a2cd00e in TUnixSystem::StackTrace() () from /home/dkennedy_umass_edu/root/lib/libCore.so
#4  0x0000799c7a2c9eb5 in TUnixSystem::DispatchSignals(ESignals) () from /home/dkennedy_umass_edu/root/lib/libCore.so
#5  <signal handler called>
#6  0x0000799c77ee2ba8 in llvm::vfs::OverlayFileSystem::pushOverlay(llvm::IntrusiveRefCntPtr<llvm::vfs::FileSystem>) () from /home/dkennedy_umass_edu/root/lib/libCling.so
#7  0x0000799c741e4b84 in (anonymous namespace)::collectModuleMaps(clang::CompilerInstance&, llvm::SmallVectorImpl<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >&) [clone .constprop.0] () from /home/dkennedy_umass_edu/root/lib/libCling.so
#8  0x0000799c741e56ed in (anonymous namespace)::setupCxxModules(clang::CompilerInstance&) () from /home/dkennedy_umass_edu/root/lib/libCling.so
#9  0x0000799c741e7c20 in (anonymous namespace)::createCIImpl(std::unique_ptr<llvm::MemoryBuffer, std::default_delete<llvm::MemoryBuffer> >, cling::CompilerOptions const&, char const*, std::unique_ptr<clang::ASTConsumer, std::default_delete<clang::ASTConsumer> >, std::vector<std::shared_ptr<clang::ModuleFileExtension>, std::allocator<std::shared_ptr<clang::ModuleFileExtension> > > const&, bool, bool) () from /home/dkennedy_umass_edu/root/lib/libCling.so
#10 0x0000799c741e9dca in cling::CIFactory::createCI(llvm::StringRef, cling::InvocationOptions const&, char const*, std::unique_ptr<clang::ASTConsumer, std::default_delete<clang::ASTConsumer> >, std::vector<std::shared_ptr<clang::ModuleFileExtension>, std::allocator<std::shared_ptr<clang::ModuleFileExtension> > > const&) () from /home/dkennedy_umass_edu/root/lib/libCling.so
#11 0x0000799c742c4eca in cling::IncrementalParser::IncrementalParser(cling::Interpreter*, char const*, std::vector<std::shared_ptr<clang::ModuleFileExtension>, std::allocator<std::shared_ptr<clang::ModuleFileExtension> > > const&) () from /home/dkennedy_umass_edu/root/lib/libCling.so
#12 0x0000799c742360bd in cling::Interpreter::Interpreter(int, char const* const*, char const*, std::vector<std::shared_ptr<clang::ModuleFileExtension>, std::allocator<std::shared_ptr<clang::ModuleFileExtension> > > const&, void*, bool, cling::Interpreter const*) () from /home/dkennedy_umass_edu/root/lib/libCling.so
#13 0x0000799c7413f1a6 in TCling::TCling(char const*, char const*, char const* const*, void*) () from /home/dkennedy_umass_edu/root/lib/libCling.so
#14 0x0000799c74141208 in CreateInterpreter () from /home/dkennedy_umass_edu/root/lib/libCling.so
#15 0x0000799c7a1bd543 in TROOT::InitInterpreter() () from /home/dkennedy_umass_edu/root/lib/libCore.so
#16 0x0000799c7a1bda3f in ROOT::Internal::GetROOT2() () from /home/dkennedy_umass_edu/root/lib/libCore.so
#17 0x0000799c7a16b49d in TApplication::TApplication(char const*, int*, char**, void*, int) () from /home/dkennedy_umass_edu/root/lib/libCore.so
#18 0x0000799c7a4893da in TRint::TRint(char const*, int*, char**, void*, int, bool, bool) () from /home/dkennedy_umass_edu/root/lib/libRint.so
#19 0x000056501cabd2c7 in main ()
===========================================================


The lines below might hint at the cause of the crash. If you see question
marks as part of the stack trace, try to recompile with debugging information
enabled and export CLING_DEBUG=1 environment variable before running.
You may get help by asking at the ROOT forum https://root.cern/forum
preferably using the command (.forum bug) in the ROOT prompt.
Only if you are really convinced it is a bug in ROOT then please submit a
report at https://root.cern/bugs or (preferably) using the command (.gh bug) in
the ROOT prompt. Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#6  0x0000799c77ee2ba8 in llvm::vfs::OverlayFileSystem::pushOverlay(llvm::IntrusiveRefCntPtr<llvm::vfs::FileSystem>) () from /home/dkennedy_umass_edu/root/lib/libCling.so
#7  0x0000799c741e4b84 in (anonymous namespace)::collectModuleMaps(clang::CompilerInstance&, llvm::SmallVectorImpl<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >&) [clone .constprop.0] () from /home/dkennedy_umass_edu/root/lib/libCling.so
#8  0x0000799c741e56ed in (anonymous namespace)::setupCxxModules(clang::CompilerInstance&) () from /home/dkennedy_umass_edu/root/lib/libCling.so
#9  0x0000799c741e7c20 in (anonymous namespace)::createCIImpl(std::unique_ptr<llvm::MemoryBuffer, std::default_delete<llvm::MemoryBuffer> >, cling::CompilerOptions const&, char const*, std::unique_ptr<clang::ASTConsumer, std::default_delete<clang::ASTConsumer> >, std::vector<std::shared_ptr<clang::ModuleFileExtension>, std::allocator<std::shared_ptr<clang::ModuleFileExtension> > > const&, bool, bool) () from /home/dkennedy_umass_edu/root/lib/libCling.so
#10 0x0000799c741e9dca in cling::CIFactory::createCI(llvm::StringRef, cling::InvocationOptions const&, char const*, std::unique_ptr<clang::ASTConsumer, std::default_delete<clang::ASTConsumer> >, std::vector<std::shared_ptr<clang::ModuleFileExtension>, std::allocator<std::shared_ptr<clang::ModuleFileExtension> > > const&) () from /home/dkennedy_umass_edu/root/lib/libCling.so
#11 0x0000799c742c4eca in cling::IncrementalParser::IncrementalParser(cling::Interpreter*, char const*, std::vector<std::shared_ptr<clang::ModuleFileExtension>, std::allocator<std::shared_ptr<clang::ModuleFileExtension> > > const&) () from /home/dkennedy_umass_edu/root/lib/libCling.so
#12 0x0000799c742360bd in cling::Interpreter::Interpreter(int, char const* const*, char const*, std::vector<std::shared_ptr<clang::ModuleFileExtension>, std::allocator<std::shared_ptr<clang::ModuleFileExtension> > > const&, void*, bool, cling::Interpreter const*) () from /home/dkennedy_umass_edu/root/lib/libCling.so
#13 0x0000799c7413f1a6 in TCling::TCling(char const*, char const*, char const* const*, void*) () from /home/dkennedy_umass_edu/root/lib/libCling.so
#14 0x0000799c74141208 in CreateInterpreter () from /home/dkennedy_umass_edu/root/lib/libCling.so
#15 0x0000799c7a1bd543 in TROOT::InitInterpreter() () from /home/dkennedy_umass_edu/root/lib/libCore.so
#16 0x0000799c7a1bda3f in ROOT::Internal::GetROOT2() () from /home/dkennedy_umass_edu/root/lib/libCore.so
#17 0x0000799c7a16b49d in TApplication::TApplication(char const*, int*, char**, void*, int) () from /home/dkennedy_umass_edu/root/lib/libCore.so
#18 0x0000799c7a4893da in TRint::TRint(char const*, int*, char**, void*, int, bool, bool) () from /home/dkennedy_umass_edu/root/lib/libRint.so
#19 0x000056501cabd2c7 in main ()
===========================================================
2

Did you try to search the forum for the same kind of error? For example: Search results for 'ERROR in cling::CIFactory::createCI(): cannot extract standard library include paths! order:latest' - ROOT Forum

3

Hi,
I did some more searching and this Error in modulemap.overlay! ...on Compute Nodes - #5 by Jimmy seems to be the closest to my issue. However, i can’t follow it. I don’t know how to edit the modulemap.overlay as suggested to get details.

4

I built it from source a while back because I had been using conda but that was causing issues with madgraph. I think I need to recompile, but I don’t know which part of the process that is. I most recently tried this:

(venv1) dkennedy_umass_edu@login2:~/root_build$ cmake -DCMAKE_INSTALLL_PREFIX=~/root_install ~/root/tutorials/
-- The C compiler identification is GNU 13.2.0
-- The CXX compiler identification is GNU 13.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Vdt: /home/dkennedy_umass_edu/root/include (found version "0.4")
-- 529/847 C++ tutorials have been activated.
CMake Error at CMakeLists.txt:742 (if):
  if given arguments:

    "NOT" "dataframe" "OR" "VERSION_LESS_EQUAL" "2.7.5" "OR" "(" "DEFINED" "ENV{ROOTTEST_IGNORE_NUMBA_PY2}" "AND" "PYTHON_VERSION_MAJOR_Development_Main" "EQUAL" "2" ")" "OR" "(" "DEFINED" "ENV{ROOTTEST_IGNORE_NUMBA_PY3}" "AND" "PYTHON_VERSION_MAJOR_Development_Main" "EQUAL" "3" ")" "OR" "(" "MSVC" "AND" "NOT" "win_broken_tests" ")"

  Unknown arguments specified


-- Configuring incomplete, errors occurred!