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FairRoot installation fails on Mac [message #18647]

Thu, 05 November 2015 08:32

Valerii
Messages: 3
Registered: November 2015
Location: Japan

occasional visitor

From: *riken.go.jp

Hi,

I am trying to install FairRoot-v-15.07 on my Mac (Os X El Captain 10.11.1), following the instructions on https://www.r3broot.gsi.de/fairroot-installation
The FairSoft-jul15p1 has been successfully installed before, after fixing the problem as explained in another post:
https://forum.gsi.de/index.php?t=tree&th=4709&start=0&

While executing 'make' command I get the following error:

...
Scanning dependencies of target fileSinkBoost
[ 69%] Building CXX object example/Tutorial3/CMakeFiles/fileSinkBoost.dir/run/runFileSinkBoost.cxx. o
[ 69%] Linking CXX executable ../../bin/fileSinkBoost
Undefined symbols for architecture x86_64:
"boost::archive::basic_binary_iarchive<boost::archive::binary_iarchive>::load_override(boost::archive::class_name_type&) ", referenced from:
boost::archive::detail::common_iarchive<boost::archive::binary_iarchive >::vload(boost::archive::class_name_type&) in runFileSinkBoost.cxx.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [bin/fileSinkBoost] Error 1
make[1]: *** [example/Tutorial3/CMakeFiles/fileSinkBoost.dir/all] Error 2
make: *** [all] Error 2

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Re: FairRoot installation fails on Mac [message #18648 is a reply to message #18647]

Thu, 05 November 2015 09:17

Dmytro Kresan
Messages: 166
Registered: June 2004

first-grade participant

From: *gsi.de

Hi Valerii,

It is recommended to use the latest releases / patches. So, I would suggest to try with following versions, and see if error remains.

FairSoft jul15p2 https://github.com/FairRootGroup/FairSoft/releases/tag/jul15p2 (the same patch for Geant4 with Xcode 7 is needed)

FairRoot v-15.07a https://github.com/FairRootGroup/FairRoot/releases/tag/v-15.07a

Please report back.

Cheers,
Dima

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Re: FairRoot installation fails on Mac [message #18650 is a reply to message #18647]

Thu, 05 November 2015 15:18

Valerii
Messages: 3
Registered: November 2015
Location: Japan

occasional visitor

From: *dynamic.ppp.asahi-net.or.jp

Hi Dima,

I have tried with the FairSoft and FairRoot versions which you suggested and I still get exactly the same error. Any ideas?
V

[Updated on: Thu, 05 November 2015 15:19]

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Re: FairRoot installation fails on Mac [message #18651 is a reply to message #18650]

Thu, 05 November 2015 15:29

Dmytro Kresan
Messages: 166
Registered: June 2004

first-grade participant

From: *gsi.de

Please post here (or attach a file) with the output of configuration (output before the actual building starts) of both FairSoft and FairRoot on your machine.

Dima

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Re: FairRoot installation fails on Mac [message #18652 is a reply to message #18651]

Thu, 05 November 2015 15:46

Valerii
Messages: 3
Registered: November 2015
Location: Japan

occasional visitor

From: *dynamic.ppp.asahi-net.or.jp

Below, is the configuration output for FairSoft (see FairRoot configuration in the attached file)

The build process for the external packages for the FairRoot Project was started at 051115_190310

Use these cached settings:

compiler=Clang
debug=no
optimize=no
geant4_download_install_data_automatic=yes
geant4_install_data_from_dir=no
build_root6=no
build_python=no
install_sim=yes
SIMPATH_INSTALL=/Users/vpanin/Desktop/Soft/R3Bsim/FairSoft/build-jul15p2
platform=macosx

Ok [Y/n]: Y
*** Compiling the external packages with the Clang compiler
*** Building the libraries with optimization
----------------- Install FairSoft ---------------
-- The C compiler identification is AppleClang 7.0.0.7000176
-- The CXX compiler identification is AppleClang 7.0.0.7000176
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoo lchain/usr/bin/clang
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoo lchain/usr/bin/clang -- 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: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoo lchain/usr/bin/clang++
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoo lchain/usr/bin/clang++ -- 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 5.0.0
-- Checking whether Fortran compiler has -isysroot
-- Checking whether Fortran compiler has -isysroot - yes
-- Checking whether Fortran compiler supports OSX deployment target flag
-- Checking whether Fortran compiler supports OSX deployment target flag - yes
-- Check for working Fortran compiler: /usr/local/bin/gfortran
-- Check for working Fortran compiler: /usr/local/bin/gfortran -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/local/bin/gfortran supports Fortran 90
-- Checking whether /usr/local/bin/gfortran supports Fortran 90 -- yes
-- Found Clang Version >= 3.4
-- Found all necessary compilers.
-- Looking for XOpenDisplay in /opt/local/lib/libX11.dylib;/opt/local/lib/libXext.dylib
-- Looking for XOpenDisplay in /opt/local/lib/libX11.dylib;/opt/local/lib/libXext.dylib - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
-- Found X11: /opt/local/lib/libX11.dylib
-- Found all necessary X11 features.
-- Found OpenGL: /System/Library/Frameworks/OpenGL.framework
-- Found all necessary OpenGL features.
-- Found CURL: /opt/local/lib/libcurl.dylib (found version "7.45.0")
-- Found OpenSSL: /opt/local/lib/libssl.dylib;/opt/local/lib/libcrypto.dylib (found version "1.0.2d")
-- Found all necessary programs in PATH.
-- Performing Test HAS_CXX11
-- Performing Test HAS_CXX11 - Success
-- Current compiler does suppport -std=c++11 option.
-- Performing Test HAS_LIBCXX
-- Performing Test HAS_LIBCXX - Success
-- Current compiler does suppport -stdlib=libc++
-- Found Subversion: /Applications/Xcode.app/Contents/Developer/usr/bin/svn (found version "1.7.20")
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/vpanin/Desktop/Soft/R3Bsim/FairSoft/FairSoft-jul15p2/test/build
The following parameters are set.
System : 64bit
C++ compiler : clang++
C compiler : clang
Fortran compiler : gfortran
CXXFLAGS : -O2 -std=c++11 -stdlib=libc++
CFLAGS : -O2
FFLAGS : -O2
Compiler : Clang
Fortran compiler : gfortran
Debug : no
Optimization : no
Platform : macosx
Architecture : macosx64
G4System : Darwin-g++
g4_data_files :
g4_get_data :
Number of parallel
processes for build : 4
Installation Directory: /Users/vpanin/Desktop/Soft/R3Bsim/FairSoft/build-jul15p2
Found cmake version 3.3.2 which is newer than the
required version 3.1.0 in PATH
This version is okay. Don't install cmake as external package.
*** Package gtest is OK ***
*** Package gsl is OK ***
*** Package Boost is OK ***
*** Package Pythia6 is OK ***
*** Package hepmc is OK ***
*** Package pythia8 is OK ***
*** Compiling Geant4-lib ................
The patch geant4.10.00_clang_osx.patch is already applied.
The patch geant4.10.00.p02_cmake.patch is already applied.
*** Package Geant4-build is OK ***
-- Clang version : 7.0.0
-- Found EXPAT: /opt/local/lib/libexpat.dylib (found version "2.1.0")
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of off64_t
-- Check size of off64_t - failed
-- Looking for fseeko
-- Looking for fseeko - found
-- Looking for unistd.h
-- Looking for unistd.h - found
-- Configuring download of missing dataset G4NDL (4.5)
-- Configuring download of missing dataset G4EMLOW (6.41)
-- Configuring download of missing dataset PhotonEvaporation (3.1)
-- Configuring download of missing dataset RadioactiveDecay (4.2)
-- Configuring download of missing dataset G4NEUTRONXS (1.4)
-- Configuring download of missing dataset G4PII (1.3)
-- Configuring download of missing dataset RealSurface (1.0)
-- Configuring download of missing dataset G4SAIDDATA (1.1)
-- Configuring download of missing dataset G4ABLA (3.0)
-- Configuring download of missing dataset G4ENSDFSTATE (1.0)
-- The following Geant4 features are enabled:
GEANT4_BUILD_CXXSTD: Compiling against C++ Standard 'c++11'
GEANT4_USE_SYSTEM_EXPAT: Using system EXPAT library
GEANT4_USE_G3TOG4: Building Geant3 ASCII call list reader library

-- Configuring done
-- Generating done

Attachment: FairRoot_config.txt
(Size: 9.01KB, Downloaded 269 times)

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Re: FairRoot installation fails on Mac [message #18653 is a reply to message #18652]

Thu, 05 November 2015 15:58

Dmytro Kresan
Messages: 166
Registered: June 2004

first-grade participant

From: *gsi.de

In case you use macports. Try to disable it:
1. Comment out setting of $PATH in your .bash_profile
2. Temporary move /opt/local to different location (or rename)

Try out homebrew

1. ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
2. brew install openssl
3. export OPENSSL_ROOT_DIR= path to your OpenSSL installation in /usr/local/
4. Reinstall everything. Sad

Should work.

Dima

[Updated on: Thu, 05 November 2015 16:18]

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