help with compiling on Mac OS

[devonorourke]

Hi, I would greatly appreciate any suggestions on how I might be able to install the program on a Mac OS. I started by reviewing the very brief installation steps. Before cloning this repo, I first created a virtual environment using Conda as follows:

conda create -n w2rap_env python=2.7
conda activate w2rap_env 
conda install -c conda-forge cmake jemalloc llvm libgcc openmp

I then cloned the repo. Within the repo, I tried following your instructions, but received a series of error messages that largely amount to this:

Scanning dependencies of target specific_w2rap-contigger
Scanning dependencies of target hb_base_libs
Scanning dependencies of target base_libs
[  0%] Building CXX object CMakeFiles/specific_w2rap-contigger.dir/src/BasevectorTools.cc.o
[  0%] Building CXX object CMakeFiles/specific_w2rap-contigger.dir/src/CompressedSequence.cc.o
clang: error: unsupported option '-fopenmp'
clang: error: unsupported option '-fopenmp'
make[2]: *** [CMakeFiles/specific_w2rap-contigger.dir/src/CompressedSequence.cc.o] Error 1

As I understand it, my problem is not with your program at all, but my inability to specify to the Mac OS to use a compiler that isn't clang. I believe that even though I'm following your instruction to set the g++ flag (-D CMAKE_CXX_COMPILER=g++), the cmake command on the Mac OS is ignoring this:

CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

-- The C compiler identification is AppleClang 12.0.0.12000032
-- The CXX compiler identification is AppleClang 12.0.0.12000032
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Setting build type to 'Release' as none was specified.
-- Found ZLIB: /Library/Developer/CommandLineTools/SDKs/MacOSX11.1.sdk/usr/lib/libz.tbd (found version "1.2.11")
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/devonorourke/gitrepos/w2rap-contigger

Unfortunately, even after spending a bit of time trying to understand how to specify my machine to use gcc and not clang when executing a cmake command, I've only manage to fail spectacularly in trying to persuade the computer to not use clang.

This produces the same (clang) error as above, indicating to me that it's still compiling with clang, and not gcc:

cmake -DCMAKE_C_COMPILER=gcc -D CMAKE_CXX_COMPILER=g++

This also similarly failed:

cmake -D CMAKE_C_COMPILER=/usr/bin/gcc -D CMAKE_CXX_COMPILER=/usr/bin/g++ -DCMAKE_CXX_COMPILER=/usr/bin/g++  -DCMAKE_C_COMPILER=/usr/bin/gcc .

And this failed equally well:

CC=/usr/bin/gcc CXX=/usr/bin/g++ cmake -D CMAKE_C_COMPILER=/usr/bin/gcc -D CMAKE_CXX_COMPILER=/usr/bin/g++ -DCMAKE_CXX_COMPILER=/usr/bin/g++  -DCMAKE_C_COMPILER=/usr/bin/gcc .

I even tried creating a file to create aliases for these flags similar to this post, but to no avail.

An old post suggested that the clang compiler is not going to work, but a more recent post/commit suggested that gcc compilation was resolved for Mac OS. If you could point to any further details that illustrate how to install the software on a Mac OS I'd greatly appreciate it.

Thanks