-flto flag makes clang to produce binary llvm code which causes 'Module format not recognized' error

[SebWouters]

Can you please provide all specs (chemps2 commit, clang version, cmake version, setup options, etc.) as well as the full configuration input, configuration output, and build output?

I'm using

• ubuntu 17.10,
• cmake 3.9.1,
• clang 4.0.1-6, and
• chemps2 d2852d7.

The relevant lines on -flto are master/CMakeLists.txt lines 87-90:

check_cxx_compiler_flag (-flto HAS_FLTO)
if (HAS_FLTO)
    set (CMAKE_CXX_FLAGS "-flto ${CMAKE_CXX_FLAGS}")
endif()

My configuration yields:

-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Failed

and the build does not use -flto.

[yurivict]

FreeBSD 11.1 clang-4.0.0 cmake-3.9.4

[SebWouters]

I would also need the rest of the info:

• chemps2 version
• configuration input
• configuration output
• build output

to say something meaningful. Can you provide it?

[yurivict]

The error:

CMakeFiles/CMakeError.log:CMakeFiles/cmTC_b0020.dir/src.cxx.o: file not recognized: File format not recognized

• chemps2 version

1.8.4-12-55d6b381

• configuration input

configure environment:

F77="gfortran6" FC="gfortran6" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc6" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc6" XDG_DATA_HOME=/usr/ports/science/chemps2/work  XDG_CONFIG_HOME=/usr/ports/science/chemps2/work  HOME=/usr/ports/science/chemps2/work PATH=/usr/ports/science/chemps2/work/.bin:.:/home/yuri/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh

• configuration output

-- The C compiler identification is Clang 4.0.0
-- The CXX compiler identification is Clang 4.0.0
-- 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
-- The CMake build type is Release
-- Performing Test HAS_IPO
-- Performing Test HAS_IPO - Success
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Failed
-- LAPACK detection suppressed.
-- Found TargetLAPACK: Found LAPACK: -lopenblas  
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- HDF5 detected.
-- Found TargetHDF5: Found HDF5: /usr/local/lib/libhdf5.so;/usr/local/lib/libsz.so;/usr/lib/libz.so;/usr/lib/libm.so (found version 1.10.1) (found version "1.10.1") 
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_CXX_FLAGS_DEBUG
    CMAKE_C_FLAGS_DEBUG
    CMAKE_C_FLAGS_RELEASE
    CMAKE_MODULE_LINKER_FLAGS
    THREADS_HAVE_PTHREAD_ARG

build output

[  1%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/CASPT2.cpp.o
[  3%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/CASSCFnewtonraphson.cpp.o
[  4%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/ConjugateGradient.cpp.o
[  6%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/CASSCFpt2.cpp.o
[  7%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/ConvergenceScheme.cpp.o
[  9%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/CASSCFdebug.cpp.o
[ 11%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Correlations.cpp.o
[ 12%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/CASSCF.cpp.o
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
[ 14%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Cumulant.cpp.o
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
[ 15%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Davidson.cpp.o
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
[ 17%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DIIS.cpp.o
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
[ 19%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRG.cpp.o
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
[ 20%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGfock.cpp.o
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
[ 22%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGmpsio.cpp.o
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
[ 23%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGoperators.cpp.o
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
[ 25%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGoperators3RDM.cpp.o
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
[ 26%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGSCFindices.cpp.o
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
[ 28%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGSCFintegrals.cpp.o
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]
[ 30%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGSCFmatrix.cpp.o
c++: warning: argument unused during compilation: '-ipo' [-Wunused-command-line-argument]

[SebWouters]

@yurivict,

Your configuration clearly states:

-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Failed

So I assume, if you would build with

make VERBOSE=1

that no "-flto" flag is used. Can you confirm?

In any case, can you please provide the full build output up to and including the error which you obtain with "make VERBOSE=1"? It currently seems to me that "-flto" cannot be the cause of the problem...

Thanks, Seb

[yurivict]

-flto only fails in configure stage. I must have created this bug by mistake.

-ipo is the flag that causes many warnings, not -flto.