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Adding comments to pairhmm-template-kernel

This commit is contained in:
mghodrat 2014-02-06 20:13:06 -08:00
parent b729fc0136
commit 7815c30df8
1 changed files with 40 additions and 28 deletions
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68
public/c++/VectorPairHMM/pairhmm-template-kernel.cc
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@ -79,6 +79,12 @@ inline void CONCAT(CONCAT(computeDistVec,SIMD_ENGINE), PRECISION) (BITMASK_VEC&
bitMaskVec.shift_left_1bit() ;
}
/*
* This function:
* 1- Intializes probability values p_MM, p_XX, P_YY, p_MX, p_GAPM and pack them into vectors (SSE or AVX)
* 2- Precompute parts of "distm" which only depeneds on a row number and pack it into vector
*/
template<class NUMBER> void CONCAT(CONCAT(initializeVectors,SIMD_ENGINE), PRECISION)(int ROWS, int COLS, NUMBER* shiftOutM, NUMBER *shiftOutX, NUMBER *shiftOutY, Context<NUMBER> ctx, testcase *tc, SIMD_TYPE *p_MM, SIMD_TYPE *p_GAPM, SIMD_TYPE *p_MX, SIMD_TYPE *p_XX, SIMD_TYPE *p_MY, SIMD_TYPE *p_YY, SIMD_TYPE *distm1D)
{
NUMBER zero = ctx._(0.0);
@ -126,6 +132,11 @@ template<class NUMBER> void CONCAT(CONCAT(initializeVectors,SIMD_ENGINE), PRECIS
}
}
/*
* This function handles pre-stripe computation:
* 1- Retrieve probaility vectors from memory
* 2- Initialize M, X, Y vectors with all 0's (for the first stripe) and shifting the last row from previous stripe for the rest
*/
template<class NUMBER> inline void CONCAT(CONCAT(stripeINITIALIZATION,SIMD_ENGINE), PRECISION)(
int stripeIdx, Context<NUMBER> ctx, testcase *tc, SIMD_TYPE &pGAPM, SIMD_TYPE &pMM, SIMD_TYPE &pMX, SIMD_TYPE &pXX, SIMD_TYPE &pMY, SIMD_TYPE &pYY,
@ -170,34 +181,9 @@ template<class NUMBER> inline void CONCAT(CONCAT(stripeINITIALIZATION,SIMD_ENGIN
M_t_1_y = M_t_1;
}
inline SIMD_TYPE CONCAT(CONCAT(computeDISTM,SIMD_ENGINE), PRECISION)(int d, int COLS, testcase * tc, HAP_TYPE &hap, SIMD_TYPE rs, UNION_TYPE rsN, SIMD_TYPE N_packed256,
SIMD_TYPE distm, SIMD_TYPE _1_distm)
{
UNION_TYPE hapN, rshap;
SIMD_TYPE cond;
IF_32 shiftInHap;
int *hap_ptr = tc->ihap;
shiftInHap.i = (d<COLS) ? hap_ptr[d-1] : hap_ptr[COLS-1];
/* shift hap */
SHIFT_HAP(hap, shiftInHap);
SIMD_TYPE hapF = VEC_CVT_128_256(hap);
rshap.d = VEC_CMP_EQ(rs, hapF);
hapN.d = VEC_CMP_EQ(N_packed256, hapF);
/* OR rsN, rshap, hapN */
cond = VEC_OR(rsN.d, rshap.d);
cond = VEC_OR(cond, hapN.d);
/* distm1D = (cond) ? 1-distm1D : distm1D; */
SIMD_TYPE distmSel = VEC_BLENDV(distm, _1_distm, cond);
return distmSel;
}
/*
* This function is the main compute kernel to compute M, X and Y
*/
inline void CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(UNION_TYPE &M_t, UNION_TYPE &X_t, UNION_TYPE &Y_t, UNION_TYPE &M_t_y,
UNION_TYPE M_t_2, UNION_TYPE X_t_2, UNION_TYPE Y_t_2, UNION_TYPE M_t_1, UNION_TYPE X_t_1, UNION_TYPE M_t_1_y, UNION_TYPE Y_t_1,
@ -205,6 +191,7 @@ inline void CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(UNION_TYPE &M_t, U
{
/* Compute M_t <= distm * (p_MM*M_t_2 + p_GAPM*X_t_2 + p_GAPM*Y_t_2) */
M_t.d = VEC_MUL(VEC_ADD(VEC_ADD(VEC_MUL(M_t_2.d, pMM), VEC_MUL(X_t_2.d, pGAPM)), VEC_MUL(Y_t_2.d, pGAPM)), distmSel);
//M_t.d = VEC_MUL( VEC_ADD(VEC_MUL(M_t_2.d, pMM), VEC_MUL(VEC_ADD(X_t_2.d, Y_t_2.d), pGAPM)), distmSel);
M_t_y = M_t;
@ -215,17 +202,39 @@ inline void CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(UNION_TYPE &M_t, U
Y_t.d = VEC_ADD(VEC_MUL(M_t_1_y.d, pMY) , VEC_MUL(Y_t_1.d, pYY));
}
/*
* This is the main compute function. It operates on the matrix in s stripe manner.
* The stripe height is determined by the SIMD engine type.
* Stripe height: "AVX float": 8, "AVX double": 4, "SSE float": 4, "SSE double": 2
* For each stripe the operations are anti-diagonal based.
* Each anti-diagonal (M_t, Y_t, X_t) depends on the two previous anti-diagonals (M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, Y_t_1).
* Each stripe (except the fist one) depends on the last row of the previous stripe.
* The last stripe computation handles the addition of the last row of M and X, that's the reason for loop spliting.
*/
template<class NUMBER> NUMBER CONCAT(CONCAT(compute_full_prob_,SIMD_ENGINE), PRECISION) (testcase *tc, NUMBER *before_last_log = NULL)
{
int ROWS = tc->rslen + 1;
int COLS = tc->haplen + 1;
int MAVX_COUNT = (ROWS+AVX_LENGTH-1)/AVX_LENGTH;
/* Probaility arrays */
SIMD_TYPE p_MM [MAVX_COUNT], p_GAPM [MAVX_COUNT], p_MX [MAVX_COUNT];
SIMD_TYPE p_XX [MAVX_COUNT], p_MY [MAVX_COUNT], p_YY [MAVX_COUNT];
/* For distm precomputation */
SIMD_TYPE distm1D[MAVX_COUNT];
/* Carries the values from each stripe to the next stripe */
NUMBER shiftOutM[ROWS+COLS+AVX_LENGTH], shiftOutX[ROWS+COLS+AVX_LENGTH], shiftOutY[ROWS+COLS+AVX_LENGTH];
/* The vector to keep the anti-diagonals of M, X, Y*/
/* Current: M_t, X_t, Y_t */
/* Previous: M_t_1, X_t_1, Y_t_1 */
/* Previous to previous: M_t_2, X_t_2, Y_t_2 */
UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y;
/* Probality vectors */
SIMD_TYPE pGAPM, pMM, pMX, pXX, pMY, pYY;
struct timeval start, end;
@ -247,11 +256,14 @@ template<class NUMBER> NUMBER CONCAT(CONCAT(compute_full_prob_,SIMD_ENGINE), PRE
const int maskBitCnt = MAIN_TYPE_SIZE ;
const int numMaskVecs = (COLS+ROWS+maskBitCnt-1)/maskBitCnt ; // ceil function
/* Mask precomputation for distm*/
MASK_TYPE maskArr[numMaskVecs][NUM_DISTINCT_CHARS] ;
CONCAT(CONCAT(precompute_masks_,SIMD_ENGINE), PRECISION)(*tc, COLS, numMaskVecs, maskArr) ;
char rsArr[AVX_LENGTH] ;
MASK_TYPE lastMaskShiftOut[AVX_LENGTH] ;
/* Precompute initialization for probabilities and shift vector*/
CONCAT(CONCAT(initializeVectors,SIMD_ENGINE), PRECISION)<NUMBER>(ROWS, COLS, shiftOutM, shiftOutX, shiftOutY,
ctx, tc, p_MM, p_GAPM, p_MX, p_XX, p_MY, p_YY, distm1D);