Install ROOT6, internal compiler error

Hi,

When I install ROOT 6 in the cluster (redhat) , I met some errors,

[ 85%] Building CXX object roofit/roofitcore/CMakeFiles/RooFitCore.dir/src/RooHashTable.cxx.o /home/huangli/tools/root/geom/geompainter/src/TGeoChecker.cxx: In member function 'Double_t TGeoChecker::TimingPerVolume(TGeoVolume*)': /home/huangli/tools/root/geom/geompainter/src/TGeoChecker.cxx:710:10: internal compiler error: Illegal instruction Double_t TGeoChecker::TimingPerVolume(TGeoVolume *vol) ^ [ 85%] Building CXX object roofit/roofitcore/CMakeFiles/RooFitCore.dir/src/RooHist.cxx.o Please submit a full bug report, with preprocessed source if appropriate. See <https://github.com/Homebrew/homebrew/issues> for instructions.

[code]/home/huangli/tools/root6/include/TInterpreter.h:236:7: note: in expansion of macro 'R__DEPRECATED' R__DEPRECATED(6,10, "CINT remnant, not applicable to cling") ^ make[2]: *** [geom/geompainter/CMakeFiles/GeomPainter.dir/build.make:105: geom/geompainter/CMakeFiles/GeomPainter.dir/src/TGeoChecker.cxx.o] Error 1 make[2]: *** Waiting for unfinished jobs.... [ 85%] Building CXX object roofit/roofitcore/CMakeFiles/RooFitCore.dir/src/RooHistFunc.cxx.o [ 85%] Building CXX object tree/treeplayer/CMakeFiles/TreePlayer.dir/src/TTreePlayer.cxx.o [ 85%] Building CXX object roofit/roofitcore/CMakeFiles/RooFitCore.dir/src/RooHistError.cxx.o [ 85%] Building CXX object gui/gui/CMakeFiles/Gui.dir/src/TGTextEntry.cxx.o [ 85%] Building CXX object tree/treeplayer/CMakeFiles/TreePlayer.dir/src/TTreeProxyGenerator.cxx.o [ 85%] Building CXX object tree/treeplayer/CMakeFiles/TreePlayer.dir/src/TTreeRe

/home/huangli/tools/root6/include/RConfig.h:439:30: note: in expansion of macro ‘NAME3

define R__JOIN3(F,X,Y) NAME3(F,X,Y)

                          ^

/home/huangli/tools/root6/include/RConfig.h:487:3: note: in expansion of macro R__JOIN3
R__JOIN3(R__DEPRECATED,MAJOR,MINOR)(“will be removed in ROOT v” #MAJOR “.” #MINOR ": " REASON)
^
/home/huangli/tools/root6/include/TInterpreter.h:236:7: note: in expansion of macro 'R__DEPRECATED’
R__DEPRECATED(6,10, “CINT remnant, not applicable to cling”)
^
[ 91%] Linking CXX shared library …/…/lib/libTreePlayer.so
[ 91%] Built target TreePlayer
[ 91%] Linking CXX shared library …/…/lib/libGui.so
[ 91%] Built target Gui
[ 91%] Linking CXX shared library …/…/lib/libRooFitCore.so
[ 91%] Built target RooFitCore
make: *** [Makefile:150: all] Error 2[/code]

I don’t understand the reason of the error. Can anybody help me?

I use commands,

cmake -D "CMAKE_PREFIX_PATH=/home/huangli/.linuxbrew/;/home/huangli/.linuxbrew/bin/;/home/huangli/.linuxbrew/lib/;/home/huangli/.linuxbrew/lib64/" -Dx11=OFF -Dopengl=OFF -Dminuit2=ON -Droofit=ON ~/tools/root

and my gcc is:

[huangli@login2 ~]$ gcc -v Reading specs from /home/huangli/.linuxbrew/Cellar/gcc/5.3.0/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.3.0/specs COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/home/huangli/.linuxbrew/Cellar/gcc/5.3.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.3.0/lto-wrapper Target: x86_64-unknown-linux-gnu Configured with: ../configure --prefix=/home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-5 --with-gmp=/home/linuxbrew/.linuxbrew/opt/gmp --with-mpfr=/home/linuxbrew/.linuxbrew/opt/mpfr --with-mpc=/home/linuxbrew/.linuxbrew/opt/libmpc --with-isl=/home/linuxbrew/.linuxbrew/opt/isl --with-system-zlib --enable-libstdcxx-time=yes --enable-stage1-checking --enable-checking=release --enable-lto --with-build-config=bootstrap-debug --disable-werror --with-pkgversion='Homebrew gcc 5.3.0' --with-bugurl=https://github.com/Homebrew/homebrew/issues --enable-plugin --disable-nls --disable-multilib Thread model: posix gcc version 5.3.0 (Homebrew gcc 5.3.0)

The full information of compile is too large, so I can’t put it in the attachment.

Hi,

Either your compiler is broken or you are running out of memory.

Cheers, Axel.

[quote=“Axel”]Hi,

Either your compiler is broken or you are running out of memory.

Cheers, Axel.[/quote]

Hi,

I will test my compiler, thanks!

Best,
Li

When I trying to use clang3.9.1,

I have added LINUXBREW/lib which contains a new version libc.so.6 when cmake (you may see my previous commands), and when I use gcc, I have no this problem.

What should I do to point to the new version glibc?

Hi,

I can help you with ROOT, but this looks like a system config issue to me. Maybe using a standard package tool (apt or whatever your distro is - I suppose it’s Linux, not MacOS?) instead of homebrew might help.

Cheers, Axel.

[quote=“Axel”]Hi,

I can help you with ROOT, but this looks like a system config issue to me. Maybe using a standard package tool (apt or whatever your distro is - I suppose it’s Linux, not MacOS?) instead of homebrew might help.

Cheers, Axel.[/quote]

Hi,
Maybe the best way for me is to wait a new version gcc…

I’d like to use standard packages without Homebrew, but the linux kernel is too old, so I have to use some third-party software manager…

The real problem maybe the Homebrew version gcc 5.3 has bug ( I tried to downgrade the version, but failed).

Thank anyway.

Best,
Li

Hi,

I guess the problem is when:

[ 92%] Built target GeomBuilder

Do you know this belongs to which packages so that I can disable it? I only enable the followings:

– Enabled support for: astiff builtin_afterimage builtin_ftgl builtin_gl2ps builtin_glew builtin_unuran builtin_llvm cxx11 cling exceptions explicitlink fortran genvector mathmore memstat minuit2 mysql pch python roofit shadowpw shared ssl thread tmva xml

Best,
Li

for more information,

The make information is:

[huangli@login2 root_install]$ make
[ 0%] Built target AFTERIMAGE
[ 0%] Built target move_header_roofit_histfactory
[ 0%] Built target move_header_core_clib
[ 0%] Built target move_header_core_clingutils
[ 0%] Built target move_header_core_cont
[ 0%] Built target move_header_core_foundation
[ 1%] Built target move_header_core_meta
[ 1%] Built target move_header_core_multiproc
[ 1%] Built target move_header_core_rint
[ 1%] Built target move_header_core_textinput
[ 1%] Built target move_header_core_thread
[ 1%] Built target move_header_core_zip
[ 1%] Built target move_header_core_lzma
[ 1%] Built target move_header_core_newdelete
[ 2%] Built target move_header_core_unix
[ 4%] Built target move_header_core_base
[ 5%] Built target move_header_math_mathcore
[ 6%] Built target move_header_math_matrix
[ 6%] Built target move_header_math_minuit
[ 8%] Built target move_header_math_minuit2
[ 8%] Built target move_header_math_fumili
[ 8%] Built target move_header_math_physics
[ 8%] Built target move_header_math_mlp
[ 8%] Built target move_header_math_quadp
[ 8%] Built target move_header_math_foam
[ 9%] Built target move_header_math_smatrix
[ 9%] Built target move_header_math_splot
[ 11%] Built target move_header_math_genvector
[ 11%] Built target move_header_math_genetic
[ 12%] Built target move_header_hist_hist
[ 12%] Built target move_header_hist_histpainter
[ 12%] Built target move_header_hist_spectrum
[ 12%] Built target move_header_hist_spectrumpainter
[ 13%] Built target move_header_hist_unfold
[ 13%] Built target move_header_hist_hbook
[ 15%] Built target move_header_tree_tree
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[ 16%] Built target move_header_io_xml
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[ 17%] Built target move_header_net_net
[ 17%] Built target move_header_net_auth
[ 17%] Built target move_header_net_krb5auth
[ 17%] Built target move_header_net_ldap
[ 17%] Built target move_header_graf2d_gpad
[ 17%] Built target move_header_graf2d_graf
[ 17%] Built target move_header_graf2d_postscript
[ 18%] Built target move_header_graf3d_g3d
[ 20%] Built target move_header_gui_gui
[ 20%] Built target move_header_gui_ged
[ 20%] Built target move_header_gui_fitpanel
[ 20%] Built target move_header_gui_guibuilder
[ 20%] Built target move_header_gui_guihtml
[ 20%] Built target move_header_gui_recorder
[ 20%] Built target move_header_gui_sessionviewer
[ 20%] Built target move_header_proof_proof
[ 21%] Built target move_header_proof_proofplayer
[ 21%] Built target move_header_proof_proofbench
[ 21%] Built target move_header_html
[ 21%] Built target move_header_montecarlo_eg
[ 21%] Built target move_header_montecarlo_vmc
[ 21%] Built target move_header_geom_geom
[ 22%] Built target move_header_geom_geombuilder
[ 22%] Built target move_header_geom_geompainter
[ 22%] Built target move_header_misc_memstat
[ 22%] Built target move_header_bindings_pyroot
[ 22%] Built target move_header_sql_mysql
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[ 25%] Built target move_header_tmva_tmva
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[ 25%] Built target move_header_tmva_pymva
[ 29%] Built target move_header_roofit_roofitcore
[ 30%] Built target move_header_roofit_roofit
[ 31%] Built target move_header_roofit_roostats
[ 31%] Built target move_headers
[ 31%] Built target Foundation_Stage1
[ 31%] Built target obj.clang-tblgen
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[ 32%] Built target LLVMTableGen
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[ 34%] Built target ClangAttrParsedAttrKinds
[ 34%] Built target ClangAttrParsedAttrImpl
[ 34%] Built target ClangAttrTemplateInstantiate
[ 34%] Built target ClangAttrPCHWrite
[ 34%] Built target ClangAttrPCHRead
[ 34%] Built target ClangSACheckers
[ 35%] Built target obj.clingUtils
[ 35%] Built target clingUtils
[ 35%] Built target ClangDriverOptions
[ 35%] Built target obj.clingInterpreter
[ 35%] Built target clingInterpreter
[ 35%] Built target obj.clingMetaProcessor
[ 35%] Built target clingMetaProcessor
[ 35%] Built target CLING
[ 35%] Built target AttributeCompatFuncTableGen
[ 35%] Built target LLVMCore
[ 35%] Built target LLVMIRReader
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[ 38%] Built target LLVMSelectionDAG
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[ 51%] Built target Dictgen
[ 51%] Built target rootcling_stage1
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[ 72%] Built target Zip
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[ 72%] Built target Unix
[ 72%] Built target gitcommit
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[ 72%] Built target Core
[ 72%] Built target G__Rint
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[ 72%] Built target root.exe
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Scanning dependencies of target hsimple
[ 78%] Generating tutorials/hsimple.root

Processing hsimple.C…
hsimple : Real Time = 0.24 seconds Cpu Time = 0.14 seconds
(TFile ) 0x1ad79e0
[ 78%] Built target hsimple
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[ 91%] Building CXX object geom/geombuilder/CMakeFiles/GeomBuilder.dir/src/TGeoVolumeEditor.cxx.o
[ 91%] Linking CXX shared library …/…/lib/libGeomBuilder.so
[ 92%] Built target GeomBuilder
[ 92%] Building CXX object geom/geompainter/CMakeFiles/GeomPainter.dir/src/TGeoChecker.cxx.o
/home/huangli/tools/root/geom/geompainter/src/TGeoChecker.cxx: In member function 'Double_t TGeoChecker::TimingPerVolume(TGeoVolume
)’:
/home/huangli/tools/root/geom/geompainter/src/TGeoChecker.cxx:710:10: internal compiler error: Illegal instruction
Double_t TGeoChecker::TimingPerVolume(TGeoVolume *vol)
^
Please submit a full bug report,
with preprocessed source if appropriate.
See https://github.com/Homebrew/homebrew/issues for instructions.
make[2]: *** [geom/geompainter/CMakeFiles/GeomPainter.dir/build.make:105: geom/geompainter/CMakeFiles/GeomPainter.dir/src/TGeoChecker.cxx.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:22037: geom/geompainter/CMakeFiles/GeomPainter.dir/all] Error 2
make: *** [Makefile:150: all] Error 2

Which clearly show the error comes from GeomBuilder. I have tested with gcc 5.3 ( the brew version ) and 4.8.5 (the conda version ) with the same bug report. ( and I am sure it’s not because of lack of memory).

So I think the easiest way for me is to disable GeomBuilder but I don’t find a way.

Or is there any necessary packages needed by GeomBuilder I missed? Or any possible reason?

Dose anyone has any idea?

Hi,

It’s extremely unlikely that you hit the same internal compiler error with two different versions in two different builds. It’s much more likely that you are not building with the GCC you thought you’re building with.

The package you cannot compile is GeomPainter, part of geom. You can do “make -k” to ignore build errors.

But I would not trust the result of a build if you hit compiler errors like that. Something is fishy in your environment.

Again - we can help with ROOT; I cannot really help with setting up your system to get a working compiler. You might be better off simply upgrading your OS.

Axel.

Hi,

Thanks very much, make -k skip the error well.

I am sure I use two different version, like,

– The C compiler identification is GNU 5.3.0
– The CXX compiler identification is GNU 5.3.0
– Check for working C compiler: /home/huangli/.linuxbrew/bin/cc
– Check for working C compiler: /home/huangli/.linuxbrew/bin/cc – works
– Detecting C compiler ABI info
– Detecting C compiler ABI info - done
– Detecting C compile features
– Detecting C compile features - done
– Check for working CXX compiler: /home/huangli/.linuxbrew/bin/c++
– Check for working CXX compiler: /home/huangli/.linuxbrew/bin/c++ – works
– Detecting CXX compiler ABI info
– Detecting CXX compiler ABI info - done
– Detecting CXX compile features
– Detecting CXX compile features - done
– The Fortran compiler identification is GNU 5.3.0
– Check for working Fortran compiler: /home/huangli/.linuxbrew/bin/gfortran
– Check for working Fortran compiler: /home/huangli/.linuxbrew/bin/gfortran – works
– Detecting Fortran compiler ABI info
– Detecting Fortran compiler ABI info - done
– Checking whether /home/huangli/.linuxbrew/bin/gfortran supports Fortran 90
– Checking whether /home/huangli/.linuxbrew/bin/gfortran supports Fortran 90 – yes

and,

– The C compiler identification is GNU 4.8.5
– The CXX compiler identification is GNU 4.8.5
– Check for working C compiler: /home/huangli/anaconda2/bin/cc
– Check for working C compiler: /home/huangli/anaconda2/bin/cc – works
– Detecting C compiler ABI info
– Checking if C linker supports --verbose
– Checking if C linker supports --verbose - yes
– Detecting C compiler ABI info - done
– Detecting C compile features
– Detecting C compile features - done
– Check for working CXX compiler: /home/huangli/anaconda2/bin/c++
– Check for working CXX compiler: /home/huangli/anaconda2/bin/c++ – works
– Detecting CXX compiler ABI info
– Checking if CXX linker supports --verbose
– Checking if CXX linker supports --verbose - yes
– Detecting CXX compiler ABI info - done
– Detecting CXX compile features
– Detecting CXX compile features - done
– The Fortran compiler identification is GNU 4.8.5
– Check for working Fortran compiler: /home/huangli/anaconda2/bin/gfortran
– Check for working Fortran compiler: /home/huangli/anaconda2/bin/gfortran – works
– Detecting Fortran compiler ABI info
– Checking if Fortran linker supports --verbose
– Checking if Fortran linker supports --verbose - yes
– Detecting Fortran compiler ABI info - done
– Checking whether /home/huangli/anaconda2/bin/gfortran supports Fortran 90
– Checking whether /home/huangli/anaconda2/bin/gfortran supports Fortran 90 – yes

But it’s ok now, I haven’t see any problem without GeomPainter yet.

Thanks again.

Best,
Li