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Split the inner loop to avoid the overhead incurred when -fPIC flag is enabled.

This commit is contained in:
mozdal 2014-01-21 11:47:30 -08:00
parent 0170d4f3d5
commit 1b1c0c8e76
2 changed files with 47 additions and 35 deletions
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80
PairHMM_JNI/pairhmm-template-kernel.cc
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@ -345,33 +345,38 @@ template<class NUMBER> NUMBER GEN_INTRINSIC(GEN_INTRINSIC(compute_full_prob_,SIM
BITMASK_VEC bitMaskVec ; BITMASK_VEC bitMaskVec ;
for (int d=1;d<COLS+AVX_LENGTH;d++) for (int begin_d=1;begin_d<COLS+AVX_LENGTH;begin_d+=MAIN_TYPE_SIZE)
{ {
int numMaskBitsToProcess = std::min(MAIN_TYPE_SIZE, COLS+AVX_LENGTH-begin_d) ;
#ifdef MUSTAFA #ifdef MUSTAFA
if (d % MAIN_TYPE_SIZE == 1) GEN_INTRINSIC(GEN_INTRINSIC(update_masks_for_cols_,SIMD_TYPE), PRECISION)((begin_d-1)/MAIN_TYPE_SIZE, bitMaskVec, maskArr, rsArr, lastMaskShiftOut, maskBitCnt) ;
GEN_INTRINSIC(GEN_INTRINSIC(update_masks_for_cols_,SIMD_TYPE), PRECISION)((d-1)/MAIN_TYPE_SIZE, bitMaskVec, maskArr, rsArr, lastMaskShiftOut, maskBitCnt) ;
GEN_INTRINSIC(GEN_INTRINSIC(computeDistVec,SIMD_TYPE), PRECISION) (bitMaskVec, distm, _1_distm, distmChosen) ;
#else
distmChosen = GEN_INTRINSIC(GEN_INTRINSIC(computeDISTM,SIMD_TYPE), PRECISION)(d, COLS, tc, hap, rs.d, rsN, N_packed256, distm, _1_distm);
#endif #endif
int ShiftIdx = d+AVX_LENGTH;
GEN_INTRINSIC(GEN_INTRINSIC(computeMXY,SIMD_TYPE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, // if (d % MAIN_TYPE_SIZE == 1)
for (int mbi=0; mbi < numMaskBitsToProcess; ++mbi) {
#ifdef MUSTAFA
GEN_INTRINSIC(GEN_INTRINSIC(computeDistVec,SIMD_TYPE), PRECISION) (bitMaskVec, distm, _1_distm, distmChosen) ;
#else
distmChosen = GEN_INTRINSIC(GEN_INTRINSIC(computeDISTM,SIMD_TYPE), PRECISION)(begin_d+mbi, COLS, tc, hap, rs.d, rsN, N_packed256, distm, _1_distm);
#endif
int ShiftIdx = begin_d + mbi + AVX_LENGTH;
GEN_INTRINSIC(GEN_INTRINSIC(computeMXY,SIMD_TYPE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1,
pMM, pGAPM, pMX, pXX, pMY, pYY, distmChosen); pMM, pGAPM, pMX, pXX, pMY, pYY, distmChosen);
GEN_INTRINSIC(GEN_INTRINSIC(_vector_shift, SIMD_TYPE), PRECISION)(M_t, shiftOutM[ShiftIdx], shiftOutM[d]); GEN_INTRINSIC(GEN_INTRINSIC(_vector_shift, SIMD_TYPE), PRECISION)(M_t, shiftOutM[ShiftIdx], shiftOutM[begin_d+mbi]);
GEN_INTRINSIC(GEN_INTRINSIC(_vector_shift, SIMD_TYPE), PRECISION)(X_t, shiftOutX[ShiftIdx], shiftOutX[begin_d+mbi]);
GEN_INTRINSIC(GEN_INTRINSIC(_vector_shift, SIMD_TYPE), PRECISION)(X_t, shiftOutX[ShiftIdx], shiftOutX[d]); GEN_INTRINSIC(GEN_INTRINSIC(_vector_shift, SIMD_TYPE), PRECISION)(Y_t_1, shiftOutY[ShiftIdx], shiftOutY[begin_d+mbi]);
GEN_INTRINSIC(GEN_INTRINSIC(_vector_shift, SIMD_TYPE), PRECISION)(Y_t_1, shiftOutY[ShiftIdx], shiftOutY[d]);
M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t;
Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y;
M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t;
Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y;
}
} }
} }
int i = strip_cnt-1; int i = strip_cnt-1;
{ {
//STRIP_INITIALIZATION //STRIP_INITIALIZATION
@ -389,32 +394,39 @@ template<class NUMBER> NUMBER GEN_INTRINSIC(GEN_INTRINSIC(compute_full_prob_,SIM
// Since there are no shift intrinsics in AVX, keep the masks in 2 SSE vectors // Since there are no shift intrinsics in AVX, keep the masks in 2 SSE vectors
BITMASK_VEC bitMaskVec ; BITMASK_VEC bitMaskVec ;
for (int d=1;d<COLS+remainingRows-1;d++) for (int begin_d=1;begin_d<COLS+remainingRows-1;begin_d+=MAIN_TYPE_SIZE)
{ {
int numMaskBitsToProcess = std::min(MAIN_TYPE_SIZE, COLS+remainingRows-1-begin_d) ;
#ifdef MUSTAFA #ifdef MUSTAFA
if (d % MAIN_TYPE_SIZE == 1) GEN_INTRINSIC(GEN_INTRINSIC(update_masks_for_cols_, SIMD_TYPE),PRECISION)((begin_d-1)/MAIN_TYPE_SIZE, bitMaskVec, maskArr, rsArr, lastMaskShiftOut, maskBitCnt) ;
GEN_INTRINSIC(GEN_INTRINSIC(update_masks_for_cols_, SIMD_TYPE),PRECISION)((d-1)/MAIN_TYPE_SIZE, bitMaskVec, maskArr, rsArr, lastMaskShiftOut, maskBitCnt) ;
GEN_INTRINSIC(GEN_INTRINSIC(computeDistVec, SIMD_TYPE), PRECISION) (bitMaskVec, distm, _1_distm, distmChosen) ;
#else
distmChosen = GEN_INTRINSIC(GEN_INTRINSIC(computeDISTM,SIMD_TYPE), PRECISION)(d, COLS, tc, hap, rs.d, rsN, N_packed256, distm, _1_distm);
#endif #endif
int ShiftIdx = d+AVX_LENGTH;
GEN_INTRINSIC(GEN_INTRINSIC(computeMXY, SIMD_TYPE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, for (int mbi=0; mbi < numMaskBitsToProcess; ++mbi) {
pMM, pGAPM, pMX, pXX, pMY, pYY, distmChosen);
sumM = VEC_ADD(sumM, M_t.d); #ifdef MUSTAFA
GEN_INTRINSIC(GEN_INTRINSIC(_vector_shift_last, SIMD_TYPE), PRECISION)(M_t, shiftOutM[ShiftIdx]); GEN_INTRINSIC(GEN_INTRINSIC(computeDistVec, SIMD_TYPE), PRECISION) (bitMaskVec, distm, _1_distm, distmChosen) ;
#else
distmChosen = GEN_INTRINSIC(GEN_INTRINSIC(computeDISTM,SIMD_TYPE), PRECISION)(begin_d+mbi, COLS, tc, hap, rs.d, rsN, N_packed256, distm, _1_distm);
#endif
int ShiftIdx = begin_d + mbi +AVX_LENGTH;
sumX = VEC_ADD(sumX, X_t.d); GEN_INTRINSIC(GEN_INTRINSIC(computeMXY, SIMD_TYPE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1,
GEN_INTRINSIC(GEN_INTRINSIC(_vector_shift_last, SIMD_TYPE), PRECISION)(X_t, shiftOutX[ShiftIdx]); pMM, pGAPM, pMX, pXX, pMY, pYY, distmChosen);
GEN_INTRINSIC(GEN_INTRINSIC(_vector_shift_last, SIMD_TYPE), PRECISION)(Y_t_1, shiftOutY[ShiftIdx]); sumM = VEC_ADD(sumM, M_t.d);
GEN_INTRINSIC(GEN_INTRINSIC(_vector_shift_last, SIMD_TYPE), PRECISION)(M_t, shiftOutM[ShiftIdx]);
M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; sumX = VEC_ADD(sumX, X_t.d);
Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; GEN_INTRINSIC(GEN_INTRINSIC(_vector_shift_last, SIMD_TYPE), PRECISION)(X_t, shiftOutX[ShiftIdx]);
} GEN_INTRINSIC(GEN_INTRINSIC(_vector_shift_last, SIMD_TYPE), PRECISION)(Y_t_1, shiftOutY[ShiftIdx]);
M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t;
Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y;
}
}
UNION_TYPE sumMX; UNION_TYPE sumMX;
sumMX.d = VEC_ADD(sumM, sumX); sumMX.d = VEC_ADD(sumM, sumX);
result_avx2 = sumMX.f[remainingRows-1]; result_avx2 = sumMX.f[remainingRows-1];

2
PairHMM_JNI/utils.cc
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@ -35,7 +35,7 @@ bool is_sse42_supported()
void initialize_function_pointers() void initialize_function_pointers()
{ {
if(0 && is_avx_supported()) if(is_avx_supported())
{ {
cout << "Using AVX accelerated implementation of PairHMM\n"; cout << "Using AVX accelerated implementation of PairHMM\n";
g_compute_full_prob_float = compute_full_prob_avxs<float>; g_compute_full_prob_float = compute_full_prob_avxs<float>;