ROOT build failed for v6.14.06

Debjyoti · May 28, 2019, 8:33am

_ROOT Version: 6.14.06
Platform: Scientific Linux release 7.5 (Nitrogen)
Compiler: GCC

I am trying to get ROOT installed on a scientific cluster. I go through the usual procedure. Configure works fine, but CMake of the build fails at 95%. Here’s what I get:

[ 95%] Built target root
Scanning dependencies of target hsimple
[ 95%] Generating tutorials/hsimple.root
Warning in cling::IncrementalParser::CheckABICompatibility():
  Possible C++ standard library mismatch, compiled with __GLIBCXX__ '20150623'
  Extraction of runtime standard library version was: '20190222'
IncrementalExecutor::executeFunction: symbol '_ZN5cling10printValueB5cxx11EPKb' unresolved while linking symbol 'atexit'!
You are probably missing the definition of cling::printValue[abi:cxx11](bool const*)
Maybe you need to load the corresponding shared library?
atexit not defined
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)

Processing hsimple.C...
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)
Error in <TInterpreter::TCling::AutoLoad>: failure loading library libTree.so for TNtuple.h
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)
Error in <TInterpreter::TCling::AutoLoad>: failure loading library libHist.so for TH2.h
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)
Error in <TInterpreter::TCling::AutoLoad>: failure loading library libHist.so for TProfile.h
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)
Error in <TInterpreter::TCling::AutoLoad>: failure loading library libGpad.so for TCanvas.h
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)
Error in <TInterpreter::TCling::AutoLoad>: failure loading library libGraf.so for TFrame.h
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)
Error in <TInterpreter::TCling::AutoLoad>: failure loading library libMathCore.so for TRandom3.h
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-install/lib/libtbb.so.2)
IncrementalExecutor::executeFunction: symbol '_ZN7TRandom6RannorERfS0_' unresolved while linking [cling interface function]!
You are probably missing the definition of TRandom::Rannor(float&, float&)
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN4TH1FC1EPKcS1_idd' unresolved while linking [cling interface function]!
You are probably missing the definition of TH1F::TH1F(char const*, char const*, int, double, double)
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN8TRandom3D1Ev' unresolved while linking [cling interface function]!
You are probably missing the definition of TRandom3::~TRandom3()
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN7TCanvasC1EPKcS1_iiii' unresolved while linking [cling interface function]!
You are probably missing the definition of TCanvas::TCanvas(char const*, char const*, int, int, int, int)
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN7TNtupleC1EPKcS1_S1_i' unresolved while linking [cling interface function]!
You are probably missing the definition of TNtuple::TNtuple(char const*, char const*, char const*, int)
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN4TH2FC1EPKcS1_iddidd' unresolved while linking [cling interface function]!
You are probably missing the definition of TH2F::TH2F(char const*, char const*, int, double, double, int, double, double)
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN8TRandom3C1Ej' unresolved while linking [cling interface function]!
You are probably missing the definition of TRandom3::TRandom3(unsigned int)
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN8TProfileC1EPKcS1_iddddS1_' unresolved while linking [cling interface function]!
You are probably missing the definition of TProfile::TProfile(char const*, char const*, int, double, double, double, double, char const*)
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN8TRandom34RndmEv' unresolved while linking [cling interface function]!
You are probably missing the definition of TRandom3::Rndm()
Maybe you need to load the corresponding shared library?
gmake[2]: *** [tutorials/hsimple.root] Error 1
gmake[1]: *** [CMakeFiles/hsimple.dir/all] Error 2
gmake: *** [all] Error 2

How can I fix this problem?

StephanH · May 28, 2019, 8:54am

The first error looks like an old version of a root library has been loaded, which was compiled with a gcc from 2015. Could it be that an old installation is lingering around on the system?

Which gcc version are you compiling with?

Debjyoti · May 28, 2019, 9:35am

Hello,
Thanks for your reply.

I’m building root into a directory I specify, which was created only for this build. Plus, there was no other ROOT system anyway before the installation.

The GCC version on my system is gcc (GCC) 8.3.0. In addition I might add that the CMake version is 3.14.4.

Thanks.

StephanH · May 28, 2019, 4:47pm

Ok, thanks for the infos. I invite @amadio or @Axel to help here.

Axel · May 28, 2019, 7:01pm

The compiler use to build ROOT was newer than the compiler found when running ROOT. That doesn’t work, for any C++ program.

Now the curious thing is that this happens during the build! Could you share your CMakeCache.txt?

Debjyoti · May 29, 2019, 4:31am

The CMakeCache.txt file is attached. CMakeCache.txt (133.0 KB)

Also, about the C++ compiler version issue you mentioned, which compiler do I need to upgrade?

Axel · May 29, 2019, 6:12am

You seem to have two ROOT builds, one at /fastspace/projects/kats/Bardhan/root-install and the other at /fastspace/projects/kats/Bardhan/root-6.14.06/?

Don’t upgrade your compiler - I’m just trying to figure out what’s special in your environment that causes the build to fail.

Can you send the output of the following commands:

echo $LD_LIBRARY_PATH
echo $PATH
which root
root.exe -l -b -q

Debjyoti · May 29, 2019, 6:21am

I don’t really have any root builds at the moment. The one in folder /fastspace/projects/kats/Bardhan/root-6.14.06/ is simply the untarred root directory. My preferred build directory is /fastspace/projects/kats/Bardhan/root-install.

The output of the commands is pasted below (clearly showing that I have no root build):

bardhan@sge212:/fastspace/projects/kats/Bardhan->echo $LD_LIBRARY_PATH

/gpfs0/kats/projects/lib:/usr/openwin/lib:/usr/local/lib:/storage/intel/lib/intel64:/storage/SGE6U8/lib/lx24-amd64:/usr/lib:/usr/lib64:/storage/openmpi_1.5/lib:/usr/lib64/lam/lib:/fastspace/projects/sivan/COMSOL5.2a/comsol52a/multiphysics/lib/glnxa64:/opt/lumerical/fdtd/lib:/fastspace/projects/tamyr/fsl/lib:/fastspace/projects/ymiller/lib64

bardhan@sge212:/fastspace/projects/kats/Bardhan->echo $PATH

/gpfs0/kats/projects/bin:/bin:/sbin:/usr/sbin:/usr/bin:/usr/local/bin:/usr/X11R6/bin:/storage/SGE6U8/bin/lx24-amd64:/storage/intel/bin:/usr/openwin/bin:/usr/openwin/bin/xview:/fastspace/matlab/bin:/storage/LOQO:/usr/licenses:/storage/openmpi_1.5/bin:/storage/Wolfram/Mathematica/10.0.2/Executables:/usr/lib64/lam/bin:/storage/scripts:/gpfs0/fluent/projects/Ansys19/v190/fluent/bin:/usr/bin/AMPL/linux64:/fastspace/projects/sivan/COMSOL5.3/comsol53/multiphysics/bin:/opt/lumerical/fdtd/bin:/fastspace/projects/tamyr/fsl/bin:/fastspace/projects/ymiller/bin:.

bardhan@sge212:/fastspace/projects/kats/Bardhan->which root

root: Command not found.

bardhan@sge212:/fastspace/projects/kats/Bardhan-&gt;root.exe -l -b -q

root.exe: Command not found.

Axel · May 29, 2019, 6:36am

Which tar file did you untar? Could you give the exact file name of the tar.gz file?

Debjyoti · May 29, 2019, 6:42am

The root source: root_v6.14.06.source.tar.gz

My file structure is this:
root-6.14.06 is the name of the directory created after untarring the source. I created a separate directory called root-install outside of the untarred root directory. I wanted to install root in this directory. I used the following commands to do this:

bardhan@sge212:/fastspace/projects/kats/Bardhan/root-install->cmake /fastspace/projects/kats/Bardhan/root-6.14.06
bardhan@sge212:/fastspace/projects/kats/Bardhan/root-install->cmake --build .

Axel · May 29, 2019, 6:48am

Sounds perfect!

Can you delete the build directory and re-run these steps? Somewhere something must have gone wrong - I cannot imagine how this can fail unless there were some stale build products in the build directory…

Debjyoti · May 29, 2019, 6:50am

Will do! Posting after the CMake.

Debjyoti · May 29, 2019, 12:02pm

I deleted both my root-install folder and the untarring folder, downloaded a fresh source file, untarred it and followed the same procedure as I had done earlier. And I come up with the same error as last time.

Scanning dependencies of target hsimple
[ 95%] Generating tutorials/hsimple.root
Warning in cling::IncrementalParser::CheckABICompatibility():
  Possible C++ standard library mismatch, compiled with __GLIBCXX__ '20150623'
  Extraction of runtime standard library version was: '20190222'
IncrementalExecutor::executeFunction: symbol '_ZN5cling10printValueB5cxx11EPKb' unresolved while linking symbol 'atexit'!
You are probably missing the definition of cling::printValue[abi:cxx11](bool const*)
Maybe you need to load the corresponding shared library?
atexit not defined
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)

Processing hsimple.C...
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)
Error in <TInterpreter::TCling::AutoLoad>: failure loading library libTree.so for TNtuple.h
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)
Error in <TInterpreter::TCling::AutoLoad>: failure loading library libHist.so for TH2.h
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)
Error in <TInterpreter::TCling::AutoLoad>: failure loading library libHist.so for TProfile.h
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)
Error in <TInterpreter::TCling::AutoLoad>: failure loading library libGpad.so for TCanvas.h
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)
Error in <TInterpreter::TCling::AutoLoad>: failure loading library libGraf.so for TFrame.h
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)
Error in <TInterpreter::TCling::AutoLoad>: failure loading library libMathCore.so for TRandom3.h
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)
cling::DynamicLibraryManager::loadLibrary(): /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /fastspace/projects/kats/Bardhan/root-build/lib/libtbb.so.2)
IncrementalExecutor::executeFunction: symbol '_ZN7TRandom6RannorERfS0_' unresolved while linking [cling interface function]!
You are probably missing the definition of TRandom::Rannor(float&, float&)
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN4TH1FC1EPKcS1_idd' unresolved while linking [cling interface function]!
You are probably missing the definition of TH1F::TH1F(char const*, char const*, int, double, double)
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN8TRandom3D1Ev' unresolved while linking [cling interface function]!
You are probably missing the definition of TRandom3::~TRandom3()
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN7TCanvasC1EPKcS1_iiii' unresolved while linking [cling interface function]!
You are probably missing the definition of TCanvas::TCanvas(char const*, char const*, int, int, int, int)
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN7TNtupleC1EPKcS1_S1_i' unresolved while linking [cling interface function]!
You are probably missing the definition of TNtuple::TNtuple(char const*, char const*, char const*, int)
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN4TH2FC1EPKcS1_iddidd' unresolved while linking [cling interface function]!
You are probably missing the definition of TH2F::TH2F(char const*, char const*, int, double, double, int, double, double)
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN8TRandom3C1Ej' unresolved while linking [cling interface function]!
You are probably missing the definition of TRandom3::TRandom3(unsigned int)
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN8TProfileC1EPKcS1_iddddS1_' unresolved while linking [cling interface function]!
You are probably missing the definition of TProfile::TProfile(char const*, char const*, int, double, double, double, double, char const*)
Maybe you need to load the corresponding shared library?
IncrementalExecutor::executeFunction: symbol '_ZN8TRandom34RndmEv' unresolved while linking [cling interface function]!
You are probably missing the definition of TRandom3::Rndm()
Maybe you need to load the corresponding shared library?
gmake[2]: *** [tutorials/hsimple.root] Error 1
gmake[1]: *** [CMakeFiles/hsimple.dir/all] Error 2
gmake: *** [all] Error 2

Axel · May 29, 2019, 1:18pm

OK this is absurd

I see two problems; they might be related: wrong libstdc++.so and wrong C++ standard. Can you attach TBB-prefix/src/TBB-stamp/TBB-build-RelWithDebInfo.cmake? Do you have a custom compiler?

Can you put the following code into testme.cxx:

#include <vector>
#include <string>
std::vector<std::string> v;
int main(int argc, char* argv[]) {
  v.push_back(argv[0]);
  return v.size() - 1;
}

Then run:

/usr/bin/c++ -o testme testme.cxx
./testme

Does that work?

Debjyoti · May 30, 2019, 6:10am

The requested file is here: TBB-build-RelWithDebInfo_cmake.txt (2.0 KB)

(Please note: I had to change the extension of the file because I cannot upload a .cmake over here.)

The code snippet you sent compiles and runs smoothly, but doesn’t produce an output.

Debjyoti · May 30, 2019, 1:24pm

Additionally, when I tried to install ROOT v6.14.00, the build of that failed as well. It wasn’t at 95% and with the same error messages. Is this a problem with the platform I’m using?

Axel · May 30, 2019, 2:12pm

Sorry, I’m out of ideas, I have never seen anything like that. Maybe you have the environment variable $CXXFLAGS set? This is really, really unique and weird. @pcanal maybe you have a hint?

@Debjyoti my best workaround for now is that you simply download a binary release. You can simply take https://root.cern/download/root_v6.16.00.Linux-centos7-x86_64-gcc4.8.tar.gz

Debjyoti · May 30, 2019, 2:32pm

Do I build it in the usual way?

pcanal · May 30, 2019, 4:17pm

Since it is a ‘binary’ release you ‘just’ need to install it, no need to build it.

pcanal · May 30, 2019, 4:19pm

To debug your original issue can provide the output of

echo $ROOTSYS
ldd `$ROOTSYS/bin/root.exe`
ldd `$ROOTSYS/lib/libCling.so`
ldd `$ROOTSYS/lib/libCore.so`
which gcc