[Bio-bwa-help] BWA compile on ppc64

[Skalar M. <ska...@gm...>]

Hi

I'm trying to compile bwa 0.7.9a on out HPC running linux with ppc64 cpu.
These are my results after typing make

$ make
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD
-DUSE_MALLOC_WRAPPERS  ksw.c -o ksw.o
ksw.c:29:23: error: emmintrin.h: No such file or directory
ksw.c:49: error: expected specifier-qualifier-list before ‘__m128i’
ksw.c: In function ‘ksw_qinit’:
ksw.c:72: error: ‘kswq_t’ has no member named ‘qp’
ksw.c:72: error: ‘__m128i’ undeclared (first use in this function)
ksw.c:72: error: (Each undeclared identifier is reported only once
ksw.c:72: error: for each function it appears in.)
ksw.c:72: error: expected expression before ‘)’ token
ksw.c:73: error: ‘kswq_t’ has no member named ‘H0’
ksw.c:73: error: ‘kswq_t’ has no member named ‘qp’
ksw.c:74: error: ‘kswq_t’ has no member named ‘H1’
ksw.c:74: error: ‘kswq_t’ has no member named ‘H0’
ksw.c:75: error: ‘kswq_t’ has no member named ‘E’
ksw.c:75: error: ‘kswq_t’ has no member named ‘H1’
ksw.c:76: error: ‘kswq_t’ has no member named ‘Hmax’
ksw.c:76: error: ‘kswq_t’ has no member named ‘E’
ksw.c:90: error: ‘kswq_t’ has no member named ‘qp’
ksw.c:99: error: ‘kswq_t’ has no member named ‘qp’
ksw.c: In function ‘ksw_u8’:
ksw.c:115: error: ‘__m128i’ undeclared (first use in this function)
ksw.c:115: error: expected ‘;’ before ‘zero’
ksw.c:131: error: ‘zero’ undeclared (first use in this function)
ksw.c:131: warning: implicit declaration of function ‘_mm_set1_epi32’
ksw.c:132: error: ‘oe_del’ undeclared (first use in this function)
ksw.c:132: warning: implicit declaration of function ‘_mm_set1_epi8’
ksw.c:133: error: ‘e_del’ undeclared (first use in this function)
ksw.c:134: error: ‘oe_ins’ undeclared (first use in this function)
ksw.c:135: error: ‘e_ins’ undeclared (first use in this function)
ksw.c:136: error: ‘shift’ undeclared (first use in this function)
ksw.c:137: error: ‘H0’ undeclared (first use in this function)
ksw.c:137: error: ‘kswq_t’ has no member named ‘H0’
ksw.c:137: error: ‘H1’ undeclared (first use in this function)
ksw.c:137: error: ‘kswq_t’ has no member named ‘H1’
ksw.c:137: error: ‘E’ undeclared (first use in this function)
ksw.c:137: error: ‘kswq_t’ has no member named ‘E’
ksw.c:137: error: ‘Hmax’ undeclared (first use in this function)
ksw.c:137: error: ‘kswq_t’ has no member named ‘Hmax’
ksw.c:140: warning: implicit declaration of function ‘_mm_store_si128’
ksw.c:147: error: expected ‘;’ before ‘e’
ksw.c:148: error: ‘h’ undeclared (first use in this function)
ksw.c:148: warning: implicit declaration of function ‘_mm_load_si128’
ksw.c:149: warning: implicit declaration of function ‘_mm_slli_si128’
ksw.c:157: warning: implicit declaration of function ‘_mm_adds_epu8’
ksw.c:157: error: ‘S’ undeclared (first use in this function)
ksw.c:158: warning: implicit declaration of function ‘_mm_subs_epu8’
ksw.c:159: error: ‘e’ undeclared (first use in this function)
ksw.c:160: warning: implicit declaration of function ‘_mm_max_epu8’
ksw.c:161: error: ‘f’ undeclared (first use in this function)
ksw.c:162: error: ‘max’ undeclared (first use in this function)
ksw.c:166: error: ‘t’ undeclared (first use in this function)
ksw.c:185: warning: implicit declaration of function ‘_mm_movemask_epi8’
ksw.c:185: warning: implicit declaration of function ‘_mm_cmpeq_epi8’
ksw.c:191: warning: implicit declaration of function ‘_mm_srli_si128’
ksw.c:191: warning: implicit declaration of function ‘_mm_extract_epi16’
ksw.c: In function ‘ksw_i16’:
ksw.c:236: error: ‘__m128i’ undeclared (first use in this function)
ksw.c:236: error: expected ‘;’ before ‘zero’
ksw.c:251: error: ‘zero’ undeclared (first use in this function)
ksw.c:252: error: ‘oe_del’ undeclared (first use in this function)
ksw.c:252: warning: implicit declaration of function ‘_mm_set1_epi16’
ksw.c:253: error: ‘e_del’ undeclared (first use in this function)
ksw.c:254: error: ‘oe_ins’ undeclared (first use in this function)
ksw.c:255: error: ‘e_ins’ undeclared (first use in this function)
ksw.c:256: error: ‘H0’ undeclared (first use in this function)
ksw.c:256: error: ‘kswq_t’ has no member named ‘H0’
ksw.c:256: error: ‘H1’ undeclared (first use in this function)
ksw.c:256: error: ‘kswq_t’ has no member named ‘H1’
ksw.c:256: error: ‘E’ undeclared (first use in this function)
ksw.c:256: error: ‘kswq_t’ has no member named ‘E’
ksw.c:256: error: ‘Hmax’ undeclared (first use in this function)
ksw.c:256: error: ‘kswq_t’ has no member named ‘Hmax’
ksw.c:266: error: expected ‘;’ before ‘e’
ksw.c:267: error: ‘h’ undeclared (first use in this function)
ksw.c:270: warning: implicit declaration of function ‘_mm_adds_epi16’
ksw.c:270: error: ‘S’ undeclared (first use in this function)
ksw.c:271: error: ‘e’ undeclared (first use in this function)
ksw.c:272: warning: implicit declaration of function ‘_mm_max_epi16’
ksw.c:273: error: ‘f’ undeclared (first use in this function)
ksw.c:274: error: ‘max’ undeclared (first use in this function)
ksw.c:276: warning: implicit declaration of function ‘_mm_subs_epu16’
ksw.c:277: error: ‘t’ undeclared (first use in this function)
ksw.c:293: warning: implicit declaration of function ‘_mm_cmpgt_epi16’
make: *** [ksw.o] Error 1

As far a i understand, gcc on powerpc doesn't have emmintrin.h which is
needed, but emmintrin.h requires sse2 which is not supported on ppc64.
Google search revealed that there are some older versions of bwa (around
0.6) which are compiled for ppc but i need new version as dependency for
Trans-Abyss and some other programs.

Can somebody point me in the right direction?

------------------------
With Regards
Erik Bircak