Issues with install

[wbender1]

I have tried two methods of installing hyphy but cannot get the program to open or run. I have used conda to install hyphy, but when I try and open an interactive session it gives an error. I have also tried to build from the source but I believe the compiler is failing to build properly.

Command line attempt to run via conda install
wbender@wills-urmc-mbp hyphy-2.5.49 % hyphy -i
zsh: illegal hardware instruction hyphy -i

Command line attempt to build from source
wbender@wills-urmc-mbp hyphy-2.5.49 % cmake .
Set default compiler flags to -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)
/Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/usr/lib/libcurl.tbd
-- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS)
-- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS)
-- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND)
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/wbender/hyphy-2.5.49
(base) wbender@wills-urmc-mbp hyphy-2.5.49 % make MP
[ 4%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o
/Users/wbender/hyphy-2.5.49/src/core/likefunc.cpp:250:13: error: no member named 'SetThreadCount' in '_LikelihoodFunction'
lf->SetThreadCount(MIN(nt, hy_global::system_CPU_count));
~~ ^
1 error generated.
make[3]: *** [CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o] Error 1
make[2]: *** [CMakeFiles/hyphy.dir/all] Error 2
make[1]: *** [CMakeFiles/MP.dir/rule] Error 2
make: *** [MP] Error 2

[stevenweaver]

Dear @wbender1 ,

Can you please pull down the latest version from GitHub (2.5.50) and try compiling again? I've found that if OpenMP isn't installed on a user's system, then SetThreadCount is not defined. I've defined a dummy function so that hyphy will run under such circumstances (as it did before 2.5.48).

Best,
Steven

[wbender1]

I tried to compile version 2.5.50 but it is still unable to find OpenMP. I appreciate you looking into this for me!

wbender@wills-urmc-mbp hyphy % cmake .
-- The C compiler identification is AppleClang 14.0.0.14000029
-- The CXX compiler identification is AppleClang 14.0.0.14000029
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - 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: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test HAVE_AVX_EXTENSIONS
-- Performing Test HAVE_AVX_EXTENSIONS - Failed
-- Performing Test HAVE_SSE4_EXTENSIONS
-- Performing Test HAVE_SSE4_EXTENSIONS - Failed
-- Performing Test HAVE_NEON_EXTENSIONS
-- Performing Test HAVE_NEON_EXTENSIONS - Success
Set default compiler flags to -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)
-- Found CURL: /Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/usr/lib/libcurl.tbd (found version "7.85.0")
/Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/usr/lib/libcurl.tbd
-- Found ZLIB: /Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/usr/lib/libz.tbd (found suitable version "1.2.11", minimum required is "1.2.9")
-- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS)
-- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS)
-- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND)
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/wbender/hyphy

[stevenweaver]

Dear @wbender1,

Yes but it will still compile.

If you want OpenMP support, try the following.

On M1 or M2 Mac, follow the instructions here to install libomp.
microsoft/LightGBM#4229 (comment)

On an Intel-based Mac, simply

brew install libomp

Best,
Steven

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