Compile error - unsupported option '-fopenmp'

edawson / rkmh

Classify sequencing reads using MinHash.

MIT License

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Compile error - unsupported option '-fopenmp' #12

Open george-githinji opened 5 years ago

george-githinji commented 5 years ago

I ran into the following error on Macos

cd mkmh && /Applications/Xcode.app/Contents/Developer/usr/bin/make
g++ -O3 -std=c++11 -fopenmp -mtune=native -ggdb -c HASHTCounter.cpp -Lmurmur3 -L. -I. -Imurmur3
clang: error: unsupported option '-fopenmp'
make[1]: *** [HASHTCounter.o] Error 1
make: *** [mkmh/libmkmh.a] Error 2

edawson commented 5 years ago

Hi @george-githinji ,

Clang doesn't support openmp in MacOS by default, and rkmh uses it extensively for threading. IF you install gcc (either with MacPorts or HomeBrew) then run make, it should work. You'll also need xcode installed. Sorry it is such a pain on Mac OS! I'm hoping to make it easier by putting things in homebrew or conda over the next few months.

george-githinji commented 5 years ago

Thanks for the response! I will compile it with gcc. It compile on our linux hpc but I ran on to a different issue