Fails compile on POWER8: SSE2 intrinsics -> VSX/AltiVec

[jlost]

bwa fails to compile on IBM POWER8 platforms due to dependency on SSE2 intrinsics.

Make output:

[u0017592@sys-81783 bwa]$ make
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  ksw.c -o ksw.o
ksw.c:29:23: fatal error: emmintrin.h: No such file or directory
 #include <emmintrin.h>
                       ^
compilation terminated.
make: *** [ksw.o] Error 1

Make after removing ##include <emmintrin.h>:

[u0017592@sys-81783 bwa]$ make
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  ksw.c -o ksw.o
ksw.c:48:2: error: unknown type name ‘__m128i’
  __m128i *qp, *H0, *H1, *E, *Hmax;
  ^
ksw.c: In function ‘ksw_qinit’:
ksw.c:71:11: error: ‘__m128i’ undeclared (first use in this function)
  q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // align memory
           ^
ksw.c:71:11: note: each undeclared identifier is reported only once for each function it appears in
ksw.c:71:19: error: expected expression before ‘)’ token
  q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // align memory
                   ^
ksw.c: In function ‘ksw_u8’:
ksw.c:114:2: error: unknown type name ‘__m128i’
  __m128i zero, oe_del, e_del, oe_ins, e_ins, shift, *H0, *H1, *E, *Hmax;
  ^
ksw.c:130:2: warning: implicit declaration of function ‘_mm_set1_epi32’ [-Wimplicit-function-declaration]
  zero = _mm_set1_epi32(0);
  ^
ksw.c:131:2: warning: implicit declaration of function ‘_mm_set1_epi8’ [-Wimplicit-function-declaration]
  oe_del = _mm_set1_epi8(_o_del + _e_del);
  ^
ksw.c:139:3: warning: implicit declaration of function ‘_mm_store_si128’ [-Wimplicit-function-declaration]
   _mm_store_si128(E + i, zero);
   ^
ksw.c:146:3: error: unknown type name ‘__m128i’
   __m128i e, h, t, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
   ^
ksw.c:147:3: warning: implicit declaration of function ‘_mm_load_si128’ [-Wimplicit-function-declaration]
   h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
   ^
ksw.c:148:3: warning: implicit declaration of function ‘_mm_slli_si128’ [-Wimplicit-function-declaration]
   h = _mm_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> because x64 is little-endian
   ^
ksw.c:156:4: warning: implicit declaration of function ‘_mm_adds_epu8’ [-Wimplicit-function-declaration]
    h = _mm_adds_epu8(h, _mm_load_si128(S + j));
    ^
ksw.c:157:4: warning: implicit declaration of function ‘_mm_subs_epu8’ [-Wimplicit-function-declaration]
    h = _mm_subs_epu8(h, shift); // h=H'(i-1,j-1)+S(i,j)
    ^
ksw.c:159:4: warning: implicit declaration of function ‘_mm_max_epu8’ [-Wimplicit-function-declaration]
    h = _mm_max_epu8(h, e);
    ^
ksw.c:184:5: warning: implicit declaration of function ‘_mm_movemask_epi8’ [-Wimplicit-function-declaration]
     cmp = _mm_movemask_epi8(_mm_cmpeq_epi8(_mm_subs_epu8(f, h), zero));
     ^
ksw.c:184:5: warning: implicit declaration of function ‘_mm_cmpeq_epi8’ [-Wimplicit-function-declaration]
ksw.c:190:3: warning: implicit declaration of function ‘_mm_srli_si128’ [-Wimplicit-function-declaration]
   __max_16(imax, max); // imax is the maximum number in max
   ^
ksw.c:190:3: warning: implicit declaration of function ‘_mm_extract_epi16’ [-Wimplicit-function-declaration]
ksw.c: In function ‘ksw_i16’:
ksw.c:235:2: error: unknown type name ‘__m128i’
  __m128i zero, oe_del, e_del, oe_ins, e_ins, *H0, *H1, *E, *Hmax;
  ^
ksw.c:251:2: warning: implicit declaration of function ‘_mm_set1_epi16’ [-Wimplicit-function-declaration]
  oe_del = _mm_set1_epi16(_o_del + _e_del);
  ^
ksw.c:265:3: error: unknown type name ‘__m128i’
   __m128i e, t, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
   ^
ksw.c:269:4: warning: implicit declaration of function ‘_mm_adds_epi16’ [-Wimplicit-function-declaration]
    h = _mm_adds_epi16(h, *S++);
    ^
ksw.c:271:4: warning: implicit declaration of function ‘_mm_max_epi16’ [-Wimplicit-function-declaration]
    h = _mm_max_epi16(h, e);
    ^
ksw.c:275:4: warning: implicit declaration of function ‘_mm_subs_epu16’ [-Wimplicit-function-declaration]
    e = _mm_subs_epu16(e, e_del);
    ^
ksw.c:292:5: warning: implicit declaration of function ‘_mm_cmpgt_epi16’ [-Wimplicit-function-declaration]
     if(UNLIKELY(!_mm_movemask_epi8(_mm_cmpgt_epi16(f, h)))) goto end_loop8;
     ^
make: *** [ksw.o] Error 1

To support the POWER8 platform, this code will have to be changed to optionally use VSX/AltiVec.

More information: https://bitbucket.org/umarcts/ppc64le-wiki/wiki/vsx.md

[IvantheDugtrio]

See #71

[junaruga]

Here is a PR to build bwa on ppc64le with simde. #283

[jlost]

It looks like #359 fixed this. Closing.