search

pnlbwh / ukftractography

Other
25 stars 27 forks source link

DBOOST_ROOT may not be set properly #111

Closed tashrifbillah closed 5 years ago

tashrifbillah commented 5 years ago

Trying to find a fix for the following:

[ 55%] Performing update step for 'Eigen'
-- Eigen update command succeeded.  See also /home/tb571/Downloads/ukftractography/build/Eigen-prefix/src/Eigen-stamp/Eigen-update-*.log
[ 57%] Performing configure step for 'Eigen'
Not searching for unused variables given on the command line.
loading initial cache file /home/tb571/Downloads/ukftractography/build/Eigen-prefix/tmp/Eigen-cache-Release.cmake
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/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: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test standard_math_library_linked_to_automatically
-- Performing Test standard_math_library_linked_to_automatically - Success
-- Standard libraries to link to explicitly: none
-- Performing Test COMPILER_SUPPORT_WERROR
-- Performing Test COMPILER_SUPPORT_WERROR - Success
-- Performing Test COMPILER_SUPPORT_pedantic
-- Performing Test COMPILER_SUPPORT_pedantic - Success
-- Performing Test COMPILER_SUPPORT_Wall
-- Performing Test COMPILER_SUPPORT_Wall - Success
-- Performing Test COMPILER_SUPPORT_Wextra
-- Performing Test COMPILER_SUPPORT_Wextra - Success
-- Performing Test COMPILER_SUPPORT_Wundef
-- Performing Test COMPILER_SUPPORT_Wundef - Success
-- Performing Test COMPILER_SUPPORT_Wcastalign
-- Performing Test COMPILER_SUPPORT_Wcastalign - Success
-- Performing Test COMPILER_SUPPORT_Wcharsubscripts
-- Performing Test COMPILER_SUPPORT_Wcharsubscripts - Success
-- Performing Test COMPILER_SUPPORT_Wnonvirtualdtor
-- Performing Test COMPILER_SUPPORT_Wnonvirtualdtor - Success
-- Performing Test COMPILER_SUPPORT_Wunusedlocaltypedefs
-- Performing Test COMPILER_SUPPORT_Wunusedlocaltypedefs - Failed
-- Performing Test COMPILER_SUPPORT_Wpointerarith
-- Performing Test COMPILER_SUPPORT_Wpointerarith - Success
-- Performing Test COMPILER_SUPPORT_Wwritestrings
-- Performing Test COMPILER_SUPPORT_Wwritestrings - Success
-- Performing Test COMPILER_SUPPORT_Wformatsecurity
-- Performing Test COMPILER_SUPPORT_Wformatsecurity - Success
-- Performing Test COMPILER_SUPPORT_Wshorten64to32
-- Performing Test COMPILER_SUPPORT_Wshorten64to32 - Failed
-- Performing Test COMPILER_SUPPORT_Wlogicalop
-- Performing Test COMPILER_SUPPORT_Wlogicalop - Success
-- Performing Test COMPILER_SUPPORT_Wenumconversion
-- Performing Test COMPILER_SUPPORT_Wenumconversion - Failed
-- Performing Test COMPILER_SUPPORT_Wcpp11extensions
-- Performing Test COMPILER_SUPPORT_Wcpp11extensions - Failed
-- Performing Test COMPILER_SUPPORT_Wdoublepromotion
-- Performing Test COMPILER_SUPPORT_Wdoublepromotion - Failed
-- Performing Test COMPILER_SUPPORT_Wnopsabi
-- Performing Test COMPILER_SUPPORT_Wnopsabi - Success
-- Performing Test COMPILER_SUPPORT_Wnovariadicmacros
-- Performing Test COMPILER_SUPPORT_Wnovariadicmacros - Success
-- Performing Test COMPILER_SUPPORT_Wnolonglong
-- Performing Test COMPILER_SUPPORT_Wnolonglong - Success
-- Performing Test COMPILER_SUPPORT_fnochecknew
-- Performing Test COMPILER_SUPPORT_fnochecknew - Success
-- Performing Test COMPILER_SUPPORT_fnocommon
-- Performing Test COMPILER_SUPPORT_fnocommon - Success
-- Performing Test COMPILER_SUPPORT_fstrictaliasing
-- Performing Test COMPILER_SUPPORT_fstrictaliasing - Success
-- Performing Test COMPILER_SUPPORT_wd981
-- Performing Test COMPILER_SUPPORT_wd981 - Failed
-- Performing Test COMPILER_SUPPORT_wd2304
-- Performing Test COMPILER_SUPPORT_wd2304 - Failed
-- Performing Test COMPILER_SUPPORT_STRICTANSI
-- Performing Test COMPILER_SUPPORT_STRICTANSI - Failed
-- Performing Test COMPILER_SUPPORT_Qunusedarguments
-- Performing Test COMPILER_SUPPORT_Qunusedarguments - Failed
-- Performing Test COMPILER_SUPPORT_ansi
-- Performing Test COMPILER_SUPPORT_ansi - Success
-- Performing Test COMPILER_SUPPORT_OPENMP
-- Performing Test COMPILER_SUPPORT_OPENMP - Success
-- Performing Test EIGEN_COMPILER_SUPPORT_CPP11
-- Performing Test EIGEN_COMPILER_SUPPORT_CPP11 - Failed
-- Performing Test EIGEN_COMPILER_SUPPORT_CXX11
-- Performing Test EIGEN_COMPILER_SUPPORT_CXX11 - Failed
-- The Fortran compiler identification is GNU 4.4.7
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- Could NOT find CHOLMOD (missing: CHOLMOD_INCLUDES CHOLMOD_LIBRARIES) 
-- Could NOT find UMFPACK (missing: UMFPACK_INCLUDES UMFPACK_LIBRARIES) 
-- Could NOT find SUPERLU (missing: SUPERLU_INCLUDES SUPERLU_LIBRARIES SUPERLU_VERSION_OK) 
-- A version of Pastix has been found but pastix_nompi.h does not exist in the include directory. Because Eigen tests require a version without MPI, we disable the Pastix backend.
-- Could NOT find SPQR (missing: SPQR_INCLUDES SPQR_LIBRARIES) 
-- Performing Test COMPILER_SUPPORT_FASTMATH
-- Performing Test COMPILER_SUPPORT_FASTMATH - Success
CMake Error at /usr/lib64/boost/Boost.cmake:536 (message):
  The imported target "boost_date_time-static" references the file

     "/usr/lib64/lib64/libboost_date_time.a"

  but this file does not exist.  Possible reasons include:

  * The file was deleted, renamed, or moved to another location.

  * An install or uninstall procedure did not complete successfully.

  * The installation package was faulty and contained

     "/usr/lib64/boost/Boost.cmake"

  but not all the files it references.

Call Stack (most recent call first):
  /usr/lib64/boost/BoostConfig.cmake:28 (include)
  /home/tb571/cmake-3.11.4-Linux-x86_64/share/cmake-3.11/Modules/FindBoost.cmake:261 (find_package)
  test/CMakeLists.txt:342 (find_package)

-- Configuring incomplete, errors occurred!
See also "/home/tb571/Downloads/ukftractography/build/Eigen-build/CMakeFiles/CMakeOutput.log".
See also "/home/tb571/Downloads/ukftractography/build/Eigen-build/CMakeFiles/CMakeError.log".
make[2]: *** [Eigen-prefix/src/Eigen-stamp/Eigen-configure] Error 1
make[1]: *** [CMakeFiles/Eigen.dir/all] Error 2
make: *** [all] Error 2
tashrifbillah commented 5 years ago

I have been able to install UKFTractography on Centos6 machines. The error we saw before was related to broken cmake files in /usr/lib64/boost/ directory. Although, we were loading an advanced version of boost, since Eigen wasn't doing a version check, the new one was not being found.

I encountered the above by forcing Eigen to find a minimum boost version 1.53 while our clusters have versions>=1.54.

Fixed by https://github.com/tashrifbillah/eigen-git-mirror/commit/6f584de8d2e5615411edfb3d611fdc932c19f905 and https://github.com/pnlbwh/ukftractography/commit/256d2b394e2fd818ce677950d5a469ac35d728b5