Make Issue

[vincentye2]

Hi there,

When trying to install and build gem3 I get this error when using 'make' :

make --directory=resources release
make[1]: Entering directory `/hpf/projects/dirkslab/People/Vincent/gem3-mapper/resources'
make[1]: Leaving directory `/hpf/projects/dirkslab/People/Vincent/gem3-mapper/resources'
make --directory=src release
make[1]: Entering directory `/hpf/projects/dirkslab/People/Vincent/gem3-mapper/src'
make --directory=align release
make[2]: Entering directory `/hpf/projects/dirkslab/People/Vincent/gem3-mapper/src/align'
make --directory=pattern release
make[3]: Entering directory `/hpf/projects/dirkslab/People/Vincent/gem3-mapper/src/align/pattern'
gcc -Ofast -march=skylake-avx512 -flto -std=c99 -Wall -DNDEBUG  -I../../../include -c pattern.c -o ../../../build/pattern.o
pattern.c:1:0: error: bad value (skylake-avx512) for -march= switch
 /*
 ^
make[3]: *** [../../../build/pattern.o] Error 1
make[3]: Leaving directory `/hpf/projects/dirkslab/People/Vincent/gem3-mapper/src/align/pattern'
make[2]: *** [pattern] Error 2
make[2]: Leaving directory `/hpf/projects/dirkslab/People/Vincent/gem3-mapper/src/align'
make[1]: *** [align] Error 2
make[1]: Leaving directory `/hpf/projects/dirkslab/People/Vincent/gem3-mapper/src'
make: *** [release] Error 2

I'm not sure what the issue is but would greatly appreciate any help. Thanks!

[smarco]

Hi,

Seems weird at first. I never configured the build-make to use ´skylake-avx512´. It is supposed to be native. Have you changed something on your end?

In any case, this is the compiler complaining that it doesn't support ´skylake-avx512´ (that particular gcc version).

Let me know.

[vincentye2]

No I was just doing a standard install. Even tried to redownload the git a few times but same issue. Eventually I went into Makefile.mk.ini and changed line 152 from: FLAGS_OPT=-Ofast -march=skylake-avx512 $(OPT_LTO)

To: FLAGS_OPT=-Ofast -march=native $(OPT_LTO)

and that seemed to work

[smarco]

Good!

In any case, which compiler/version are you using?

[vincentye2]

I'm running on the institutional HPC. Default is gcc 4.8.5. I saw there was another issue listed earlier and I had tried loading gcc 4.9.1 but the issue persisted

[smarco]

Ok, skylake is not a supported arch in GCC 4.9.1 (see here).

native should do fine.