GMAP GSNAP installation

Question

[vincenz]

I'm trying to install GMAP GSNAP on my mac following all the README.txt instructions. ./configure works fine but "make" runs for some time but eventually gives me this error message.

sarray-read.c:2407:13: error: always_inline function '_pext_u32' requires target feature 'bmi2', but would be inlined into function
      'fill_positions_filtered_first' that is compiled without support for 'bmi2'
        selector = _pext_u32(univ_selector,mask);

1 error generated.
make[2]: *** [gsnap_avx2-sarray-read.o] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1

Can anybody give me a hint what these errors mean. Thank you,

[GenoMax]

Have you installed/updated to the latest Xcode and command line tools for OS X?

[vincenz]

I think I have the latest Xcode: Version 7.3.1 (7D1014)

Answer 1

[WouterDeCoster]

Are you perhaps using an outdated compiler? You can check the version using

gcc --version

[GenoMax]

@vincenz is compiling on OS X. One never knows what errors would show up.

[WouterDeCoster]

oh right, missed the mac part

[vincenz]

Here is what I get for gcc version.

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/c++/4.2.1
Apple LLVM version 7.3.0 (clang-703.0.31)
Target: x86_64-apple-darwin15.5.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Does that look out of date to you?

[GenoMax]

That looks like the latest Xcode.

Googling around for that error seems to indicate that this may not be a simple fix. Perhaps a C++/Clang programmer would suggest a workaround.

In a pinch you could look at this site and try the workarounds suggested: https://github.com/juliangehring/GMAP-GSNAP

[WouterDeCoster]

From what I heard the author is very responsive in email, so contacting him might be worth trying.

[vincenz]

Excellent suggestion. Thomas Wu was very responsive and identified the problem as having to do with "compilation errors on AVX2-capable machines" In any case all is peachy if you download the latest gmap-2016-06-03.

[WouterDeCoster]

Glad that your problem is solved, good luck with the analysis.

[WouterDeCoster]

Current gcc is 6.1, but I guess that's not easy to upgrade... GMAP GSNAP works fine here, compiled using GCC 4.4.7