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Filter out SSE usage for non-x86_64. #1147

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Filter out SSE usage for non-x86_64. #1147

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7 changes: 6 additions & 1 deletion src/Rmain.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,12 @@
///#ifdef _WIN32 // Windows
#if defined(_WIN32) && !defined(__MINGW32__) // Windows and not MINGW
#define cpuid(info, x) __cpuidex(info, x, 0)
#else // GCC Intrinsics
#elif defined(__ppc64__) || defined(__PPC64__) || defined(__s390x__) || defined(__aarch64__)
void cpuid(int32_t out[4], int32_t x) {
// Just disable it as anything better is unimplemented.
out[0] = 0;
}
#else // GCC Intrinsics on x86_64
#include <cpuid.h>
void cpuid(int info[4], int InfoType){
__cpuid_count(InfoType, 0, info[0], info[1], info[2], info[3]);
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19 changes: 19 additions & 0 deletions src/kmers.cpp
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
#include <stdlib.h>
#include "dada.h"
#if ! (defined(__ppc64__) || defined(__PPC64__) || defined(__s390x__) || defined(__aarch64__))
#include "emmintrin.h"
#endif
// #if _WIN32
// #include <intrin.h>
// #endif
Expand All @@ -26,6 +28,15 @@ double kmer_dist(uint16_t *kv1, int len1, uint16_t *kv2, int len2, int k) {
return (1. - dot);
}

// These should never be called, but the symbols will have to exist
#if (defined(__ppc64__) || defined(__PPC64__) || defined(__s390x__) || defined(__aarch64__))
double kmer_dist_SSEi(uint16_t *kv1, int len1, uint16_t *kv2, int len2, int k) {
return 0.0;
}
double kmer_dist_SSEi_8(uint8_t *kv1, int len1, uint8_t *kv2, int len2, int k) {
return 0.0;
}
#else
// Computes kmer distance with SSE2 intrinsics.
double kmer_dist_SSEi(uint16_t *kv1, int len1, uint16_t *kv2, int len2, int k) {
size_t n_kmer = 1 << (2*k); // 4^k kmers
Expand Down Expand Up @@ -87,6 +98,8 @@ double kmer_dist_SSEi_8(uint8_t *kv1, int len1, uint8_t *kv2, int len2, int k) {
dot = ((double) dotsum)/((len1 < len2 ? len1 : len2) - k + 1.);
return (1. - dot);
}
#endif


// Computes "kmer distance" with SSE2 intrinsics, based on ordered kmers (e.g. gapless align)
// If different lengths, returns -1 (invalid)
Expand All @@ -106,6 +119,11 @@ double kord_dist(uint16_t *kord1, int len1, uint16_t *kord2, int len2, int k) {
return (1. - dot);
}

#if (defined(__ppc64__) || defined(__PPC64__) || defined(__s390x__) || defined(__aarch64__))
double kord_dist_SSEi(uint16_t *kord1, int len1, uint16_t *kord2, int len2, int k) {
return 0.0;
}
#else
// Computes "kmer distance" with SSE2 intrinsics, based on ordered kmers (e.g. gapless align)
// If different lengths, returns -1 (invalid)
double kord_dist_SSEi(uint16_t *kord1, int len1, uint16_t *kord2, int len2, int k) {
Expand Down Expand Up @@ -138,6 +156,7 @@ double kord_dist_SSEi(uint16_t *kord1, int len1, uint16_t *kord2, int len2, int
dot = ((double) dotsum)/((len1 < len2 ? len1 : len2) - k + 1.);
return (1. - dot);
}
#endif

void assign_kmer8(uint8_t *kvec8, const char *seq, int k) { // Assumes a clean seq (just 1s,2s,3s,4s)
int i, j, nti;
Expand Down