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search16s.cc
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/*
SWIPE
Smith-Waterman database searches with Inter-sequence Parallel Execution
Copyright (C) 2008-2014 Torbjorn Rognes, University of Oslo,
Oslo University Hospital and Sencel Bioinformatics AS
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
Contact: Torbjorn Rognes <[email protected]>,
Department of Informatics, University of Oslo,
PO Box 1080 Blindern, NO-0316 Oslo, Norway
*/
#include "swipe.h"
//#define DEBUG
#define CHANNELS 8
#define CDEPTH 1
void dprofile_dump16s(WORD * dprofile)
{
const char * s = sym_ncbi_aa;
printf("dprofile_word:\n");
for(int i=0; i<32; i++)
{
printf("%c: ",s[i]);
for(int k=0; k<CDEPTH; k++)
{
printf("[");
for(int j=0; j<CHANNELS; j++)
printf("%2d", (short) dprofile[CHANNELS*CDEPTH*i + CHANNELS*k + j]);
printf("]");
}
printf("\n");
}
exit(1);
}
// Register usage
// rdi: hep
// rsi: qp
// rdx: Qm
// rcx: Rm
// r8: ql
// r9: Sm/Mm
// rax: x, temp
// r10: ql2
// r11: qi
// xmm0: H0
// xmm1: H1
// xmm2: H2
// xmm3: H3
// xmm4: F0
// xmm5: F1
// xmm6: F2
// xmm7: F3
// xmm8: N0
// xmm9: N1
// xmm10: N2
// xmm11: N3
// xmm12: E
// xmm13: S
// xmm14: Q
// xmm15: R
#define INITIALIZE \
" movq %0, %%rax \n" \
" movdqa (%%rax), %%xmm13 \n" \
" movdqa (%3), %%xmm14 \n" \
" movdqa (%4), %%xmm15 \n" \
" movq %6, %%rax \n" \
" movdqa (%%rax), %%xmm0 \n" \
" movdqa %%xmm0, %%xmm4 \n" \
" shlq $3, %5 \n" \
" movq %5, %%r10 \n" \
" andq $-16, %%r10 \n" \
" xorq %%r11, %%r11 \n"
#define ONESTEP(H, N, F, V) \
" paddsw " V "(%%rax), " H " \n" \
" pmaxsw " F ", " H " \n" \
" pmaxsw %%xmm12, " H " \n" \
" pmaxsw " H ", %%xmm13 \n" \
" psubsw %%xmm15, " F " \n" \
" psubsw %%xmm15, %%xmm12 \n" \
" movdqa " H ", " N " \n" \
" psubsw %%xmm14, " H " \n" \
" pmaxsw " H ", %%xmm12 \n" \
" pmaxsw " H ", " F " \n"
inline void donormal16s(volatile __m128i * Sm, /* r9 */
__m128i * hep, /* rdi */
__m128i ** qp, /* rsi */
__m128i * Qm, /* rdx */
__m128i * Rm, /* rcx */
long ql, /* r8 */
__m128i * Zm)
{
__asm__
__volatile__
(
"## donormal16s \n"
INITIALIZE
" jmp 2f \n"
"1: movq 0(%2,%%r11,1), %%rax \n" // load x from qp[qi]
" movdqa 0(%1,%%r11,4), %%xmm8 \n" // load N0
" movdqa 16(%1,%%r11,4), %%xmm12 \n" // load E
ONESTEP("%%xmm0", "0(%1,%%r11,4)", "%%xmm4", "0" )
" movq 8(%2,%%r11,1), %%rax \n" // load x from qp[qi+1]
" movdqa %%xmm12, 16(%1,%%r11,4) \n" // save E
" movdqa 32(%1,%%r11,4), %%xmm0 \n" // load H0
" movdqa 48(%1,%%r11,4), %%xmm12 \n" // load E
ONESTEP("%%xmm8", "32(%1,%%r11,4)", "%%xmm4", "0" )
" movdqa %%xmm12, 48(%1,%%r11,4) \n" // save E
" addq $16, %%r11 \n" // qi++
"2: cmpq %%r11, %%r10 \n" // qi = ql4 ?
" jne 1b \n" // loop
" cmpq %%r11, %5 \n"
" je 3f \n"
" movq 0(%2,%%r11,1), %%rax \n" // load x from qp[qi]
" movdqa 16(%1,%%r11,4), %%xmm12 \n" // load E
ONESTEP("%%xmm0", "0(%1,%%r11,4)", "%%xmm4", "0" )
" movdqa %%xmm12, 16(%1,%%r11,4) \n" // save E
"3: movq %0, %%rax \n" // save S
" movdqa %%xmm13, (%%rax) \n"
" shrq $3, %5 "
:
: "m"(Sm), "r"(hep),"r"(qp),
"r"(Qm), "r"(Rm), "r"(ql), "m"(Zm)
: "xmm0", "xmm4", "xmm8",
"xmm12", "xmm13", "xmm14", "xmm15",
"rax", "r10", "r11", "cc",
"memory"
);
}
/* not used: 1 2 3 5 6 7 9 10 11 */
/* used 0 (H0) 4 (F0) 8 (N0) 12 (E) 13 (S) 14 (Q) 15 (R) */
inline void domasked16s(volatile __m128i * Sm,
__m128i * hep,
__m128i ** qp,
__m128i * Qm,
__m128i * Rm,
long ql,
__m128i * Zm,
__m128i * Mm)
{
__asm__
__volatile__
(
"## domasked16 \n"
INITIALIZE
" paddsw (%7), %%xmm13 \n" // add M
" paddsw (%7), %%xmm13 \n" // add M
" jmp 2f \n"
"1: movq 0(%2,%%r11,1), %%rax \n" // load x from qp[qi]
" movdqa 0(%1,%%r11,4), %%xmm8 \n" // load N0
" paddsw (%7), %%xmm8 \n" // add M
" paddsw (%7), %%xmm8 \n" // add M
" movdqa 16(%1,%%r11,4), %%xmm12 \n" // load E
" paddsw (%7), %%xmm12 \n" // add M
" paddsw (%7), %%xmm12 \n" // add M
ONESTEP("%%xmm0", "0(%1,%%r11,4)", "%%xmm4", "0" )
" movdqa %%xmm12, 16(%1,%%r11,4) \n" // save E
" movq 8(%2,%%r11,1), %%rax \n" // load x from qp[qi+1]
" movdqa 32(%1,%%r11,4), %%xmm0 \n" // load H0
" paddsw (%7), %%xmm0 \n" // add M
" paddsw (%7), %%xmm0 \n" // add M
" movdqa 48(%1,%%r11,4), %%xmm12 \n" // load E
" paddsw (%7), %%xmm12 \n" // add M
" paddsw (%7), %%xmm12 \n" // add M
ONESTEP("%%xmm8", "32(%1,%%r11,4)", "%%xmm4", "0" )
" movdqa %%xmm12, 48(%1,%%r11,4) \n" // save E
" addq $16, %%r11 \n" // qi++
"2: cmpq %%r11, %%r10 \n" // qi = ql4 ?
" jne 1b \n" // loop
" cmpq %%r11, %5 \n"
" je 3f \n"
" movq 0(%2,%%r11,1), %%rax \n" // load x from qp[qi]
" movdqa 16(%1,%%r11,4), %%xmm12 \n" // load E
" paddsw (%7), %%xmm12 \n" // add M
" paddsw (%7), %%xmm12 \n" // add M
ONESTEP("%%xmm0", "0(%1,%%r11,4)", "%%xmm4", "0" )
" movdqa %%xmm12, 16(%1,%%r11,4) \n" // save E
"3: movq %0, %%rax \n" // save S
" movdqa %%xmm13, (%%rax) \n"
" shrq $3, %5 "
:
: "m"(Sm), "r"(hep),"r"(qp), "r"(Qm), "r"(Rm), "r"(ql), "m"(Zm),
"r"(Mm)
: "xmm0", "xmm4", "xmm8",
"xmm12", "xmm13", "xmm14", "xmm15",
"rax", "r10", "r11", "cc",
"memory"
);
}
inline void dprofile_fill16s(WORD * dprofile_word,
WORD * score_matrix_word,
BYTE * dseq)
{
__m128i xmm0, xmm1, xmm2, xmm3, xmm4, xmm5, xmm6, xmm7;
__m128i xmm8, xmm9, xmm10, xmm11, xmm12, xmm13, xmm14, xmm15;
__m128i xmm16, xmm17, xmm18, xmm19, xmm20, xmm21, xmm22, xmm23;
__m128i xmm24, xmm25, xmm26, xmm27, xmm28, xmm29, xmm30, xmm31;
for (int j=0; j<CDEPTH; j++)
{
int d[CHANNELS];
for(int z=0; z<CHANNELS; z++)
d[z] = dseq[j*CHANNELS+z] << 5;
// for(int i=0; i<24; i += 8)
for(int i=0; i<32; i += 8)
{
xmm0 = _mm_load_si128((__m128i*)(score_matrix_word + d[0] + i));
xmm1 = _mm_load_si128((__m128i*)(score_matrix_word + d[1] + i));
xmm2 = _mm_load_si128((__m128i*)(score_matrix_word + d[2] + i));
xmm3 = _mm_load_si128((__m128i*)(score_matrix_word + d[3] + i));
xmm4 = _mm_load_si128((__m128i*)(score_matrix_word + d[4] + i));
xmm5 = _mm_load_si128((__m128i*)(score_matrix_word + d[5] + i));
xmm6 = _mm_load_si128((__m128i*)(score_matrix_word + d[6] + i));
xmm7 = _mm_load_si128((__m128i*)(score_matrix_word + d[7] + i));
xmm8 = _mm_unpacklo_epi16(xmm0, xmm1);
xmm9 = _mm_unpackhi_epi16(xmm0, xmm1);
xmm10 = _mm_unpacklo_epi16(xmm2, xmm3);
xmm11 = _mm_unpackhi_epi16(xmm2, xmm3);
xmm12 = _mm_unpacklo_epi16(xmm4, xmm5);
xmm13 = _mm_unpackhi_epi16(xmm4, xmm5);
xmm14 = _mm_unpacklo_epi16(xmm6, xmm7);
xmm15 = _mm_unpackhi_epi16(xmm6, xmm7);
xmm16 = _mm_unpacklo_epi32(xmm8, xmm10);
xmm17 = _mm_unpackhi_epi32(xmm8, xmm10);
xmm18 = _mm_unpacklo_epi32(xmm12, xmm14);
xmm19 = _mm_unpackhi_epi32(xmm12, xmm14);
xmm20 = _mm_unpacklo_epi32(xmm9, xmm11);
xmm21 = _mm_unpackhi_epi32(xmm9, xmm11);
xmm22 = _mm_unpacklo_epi32(xmm13, xmm15);
xmm23 = _mm_unpackhi_epi32(xmm13, xmm15);
xmm24 = _mm_unpacklo_epi64(xmm16, xmm18);
xmm25 = _mm_unpackhi_epi64(xmm16, xmm18);
xmm26 = _mm_unpacklo_epi64(xmm17, xmm19);
xmm27 = _mm_unpackhi_epi64(xmm17, xmm19);
xmm28 = _mm_unpacklo_epi64(xmm20, xmm22);
xmm29 = _mm_unpackhi_epi64(xmm20, xmm22);
xmm30 = _mm_unpacklo_epi64(xmm21, xmm23);
xmm31 = _mm_unpackhi_epi64(xmm21, xmm23);
_mm_store_si128((__m128i*)(dprofile_word + CDEPTH*CHANNELS*(i+0) + CHANNELS*j), xmm24);
_mm_store_si128((__m128i*)(dprofile_word + CDEPTH*CHANNELS*(i+1) + CHANNELS*j), xmm25);
_mm_store_si128((__m128i*)(dprofile_word + CDEPTH*CHANNELS*(i+2) + CHANNELS*j), xmm26);
_mm_store_si128((__m128i*)(dprofile_word + CDEPTH*CHANNELS*(i+3) + CHANNELS*j), xmm27);
_mm_store_si128((__m128i*)(dprofile_word + CDEPTH*CHANNELS*(i+4) + CHANNELS*j), xmm28);
_mm_store_si128((__m128i*)(dprofile_word + CDEPTH*CHANNELS*(i+5) + CHANNELS*j), xmm29);
_mm_store_si128((__m128i*)(dprofile_word + CDEPTH*CHANNELS*(i+6) + CHANNELS*j), xmm30);
_mm_store_si128((__m128i*)(dprofile_word + CDEPTH*CHANNELS*(i+7) + CHANNELS*j), xmm31);
}
}
// dprofile_dump16s(dprofile_word);
}
void search16s(WORD * * q_start,
WORD gap_open_penalty,
WORD gap_extend_penalty,
WORD * score_matrix,
WORD * dprofile,
WORD * hearray,
struct db_thread_s * * dbta,
long sequences,
long * seqnos,
long * scores,
long * bestpos,
long * bestq,
int qlen)
{
volatile __m128i S;
__m128i SL, Q, R, T, M, Z, T0;
__m128i *hep, **qp;
BYTE * d_begin[CHANNELS];
BYTE * d_pos[CHANNELS];
BYTE * d_end[CHANNELS];
BYTE * d_best[CHANNELS];
long q_best[CHANNELS];
__m128i dseqalloc[CDEPTH];
BYTE * dseq = (BYTE *) & dseqalloc;
BYTE zero;
long seq_id[CHANNELS];
long next_id = 0;
unsigned done;
Z = _mm_set_epi16(0x8000, 0x8000, 0x8000, 0x8000, 0x8000, 0x8000, 0x8000, 0x8000);
T0 = _mm_set_epi16(0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x8000);
Q = _mm_set_epi16(gap_open_penalty, gap_open_penalty,
gap_open_penalty, gap_open_penalty,
gap_open_penalty, gap_open_penalty,
gap_open_penalty, gap_open_penalty);
R = _mm_set_epi16(gap_extend_penalty, gap_extend_penalty,
gap_extend_penalty, gap_extend_penalty,
gap_extend_penalty, gap_extend_penalty,
gap_extend_penalty, gap_extend_penalty);
zero = 0;
done = 0;
S = Z;
SL = Z;
hep = (__m128i*) hearray;
qp = (__m128i**) q_start;
for(int a=0; a < qlen; a++)
{
hep[2*a] = Z;
hep[2*a+1] = Z;
}
for (int c=0; c<CHANNELS; c++)
{
d_begin[c] = &zero;
d_pos[c] = d_begin[c];
d_end[c] = d_begin[c];
d_best[c] = d_begin[c];
q_best[c] = -1;
seq_id[c] = -1;
}
int easy = 0;
while(1)
{
if (easy)
{
for(int c=0; c<CHANNELS; c++)
{
for(int j=0; j<CDEPTH; j++)
{
if (d_pos[c] < d_end[c])
dseq[CHANNELS*j+c] = *(d_pos[c]++);
else
dseq[CHANNELS*j+c] = 0;
}
if ((d_pos[c] == d_end[c]) && (seq_id[c] > -1))
easy = 0;
}
dprofile_fill16s(dprofile, score_matrix, dseq);
donormal16s(&S, hep, qp, &Q, &R, qlen, &Z);
/* save column address if new highscore */
int mask = _mm_movemask_epi8(_mm_cmpgt_epi16((__m128i)S, SL));
if (mask)
{
for(int c=0; c<CHANNELS; c++)
if (mask & (3 << 2*c))
d_best[c] = d_pos[c] - 1;
for(long i = qlen-1; i >= 0; i--)
{
int m2 = mask & _mm_movemask_epi8(_mm_cmpeq_epi16(hep[2*i], (__m128i)S));
if (m2)
for(int c=0; c<CHANNELS; c++)
if (m2 & (3 << 2*c))
q_best[c] = i;
}
}
#ifdef DEBUG
printf("E mask=%04x\n", mask);
printf("SL=");
vector_print_word((WORD*)&SL);
printf("\nS =");
vector_print_word((WORD*)&S);
printf("\nBe:");
for (int c=0; c<CHANNELS; c++)
printf(" %4ld", d_best[c]-d_begin[c]);
printf("\n");
#endif
SL = (__m128i)S;
}
else
{
easy = 1;
M = _mm_setzero_si128();
T = T0;
for (int c=0; c<CHANNELS; c++)
{
if (d_pos[c] < d_end[c])
{
for(int j=0; j<CDEPTH; j++)
{
if (d_pos[c] < d_end[c])
dseq[CHANNELS*j+c] = *(d_pos[c]++);
else
dseq[CHANNELS*j+c] = 0;
}
if (d_pos[c] == d_end[c])
easy = 0;
}
else
{
M = _mm_xor_si128(M, T);
long cand_id = seq_id[c];
if (cand_id >= 0)
{
long score = ((WORD*)&S)[c] ^ 0x8000;
scores[cand_id] = score;
bestpos[cand_id] = d_best[c] - d_begin[c];
bestq[cand_id] = q_best[c];
done++;
}
if (next_id < sequences)
{
seq_id[c] = next_id;
long seqnosf = seqnos[next_id];
char* address;
long length, ntlen;
long strand = (seqnosf >> 2) & 1;
long frame = seqnosf & 3;
long seqno = seqnosf >> 3;
db_mapsequences(dbta[c], seqno, seqno);
db_getsequence(dbta[c], seqno, strand, frame,
& address, & length, & ntlen, c);
d_begin[c] = (unsigned char*) address;
d_pos[c] = d_begin[c];
d_best[c] = d_begin[c];
d_end[c] = (unsigned char*) address + length - 1;
q_best[c] = -1;
next_id++;
for(int j=0; j<CDEPTH; j++)
{
if (d_pos[c] < d_end[c])
dseq[CHANNELS*j+c] = *(d_pos[c]++);
else
dseq[CHANNELS*j+c] = 0;
}
if (d_pos[c] == d_end[c])
easy = 0;
}
else
{
seq_id[c] = -1;
d_pos[c] = &zero;
d_end[c] = d_pos[c];
for (int j=0; j<CDEPTH; j++)
dseq[CHANNELS*j+c] = 0;
}
}
T = _mm_slli_si128(T, 2);
}
if (done == sequences)
break;
dprofile_fill16s(dprofile, score_matrix, dseq);
domasked16s(&S, hep, qp, &Q, &R, qlen, &Z, &M);
/* save column address if new highscore */
SL = _mm_adds_epi16(SL, M);
SL = _mm_adds_epi16(SL, M);
int mask = _mm_movemask_epi8(_mm_cmpgt_epi16((__m128i)S, SL));
if (mask)
{
for(int c=0; c<CHANNELS; c++)
if (mask & (3 << 2*c))
d_best[c] = d_pos[c] - 1;
for(long i = qlen-1; i >= 0; i--)
{
int m2 = mask & _mm_movemask_epi8(_mm_cmpeq_epi16(hep[2*i], (__m128i)S));
if (m2)
for(int c=0; c<CHANNELS; c++)
if (m2 & (3 << 2*c))
q_best[c] = i;
}
}
#ifdef DEBUG
printf("H mask=%04x\n", mask);
printf("SL=");
vector_print_word((WORD*)&SL);
printf("\nS =");
vector_print_word((WORD*)&S);
printf("\nBe:");
for (int c=0; c<CHANNELS; c++)
printf(" %4ld", d_best[c]-d_begin[c]);
printf("\n");
#endif
SL = (__m128i)S;
}
}
}