/* Function: p7_omx_FDeconvert()
* Synopsis: Convert an optimized DP matrix to generic one.
* Incept: SRE, Tue Aug 19 17:58:13 2008 [Janelia]
*
* Purpose: Convert the 32-bit float values in optimized DP matrix
* <ox> to a generic one <gx>. Caller provides <gx> with sufficient
* space to hold the <ox->M> by <ox->L> matrix.
*
* This function is used to gain access to the
* somewhat more powerful debugging and display
* tools available for generic DP matrices.
*/
int
p7_omx_FDeconvert(P7_OMX *ox, P7_GMX *gx)
{
int Q = p7O_NQF(ox->M);
int i, q, r, k;
union { __m128 v; float p[4]; } u;
float **dp = gx->dp;
float *xmx = gx->xmx;
for (i = 0; i <= ox->L; i++)
{
MMX(i,0) = DMX(i,0) = IMX(i,0) = -eslINFINITY;
for (q = 0; q < Q; q++)
{
u.v = MMO(ox->dpf[i],q); for (r = 0; r < 4; r++) { k = (Q*r)+q+1; if (k <= ox->M) MMX(i, (Q*r)+q+1) = u.p[r]; }
u.v = DMO(ox->dpf[i],q); for (r = 0; r < 4; r++) { k = (Q*r)+q+1; if (k <= ox->M) DMX(i, (Q*r)+q+1) = u.p[r]; }
u.v = IMO(ox->dpf[i],q); for (r = 0; r < 4; r++) { k = (Q*r)+q+1; if (k <= ox->M) IMX(i, (Q*r)+q+1) = u.p[r]; }
}
XMX(i,p7G_E) = ox->xmx[i*p7X_NXCELLS+p7X_E];
XMX(i,p7G_N) = ox->xmx[i*p7X_NXCELLS+p7X_N];
XMX(i,p7G_J) = ox->xmx[i*p7X_NXCELLS+p7X_J];
XMX(i,p7G_B) = ox->xmx[i*p7X_NXCELLS+p7X_B];
XMX(i,p7G_C) = ox->xmx[i*p7X_NXCELLS+p7X_C];
}
gx->L = ox->L;
gx->M = ox->M;
return eslOK;
}
/* Function: p7_OptimalAccuracy()
* Synopsis: DP fill of an optimal accuracy alignment calculation.
* Incept: SRE, Mon Aug 18 11:04:48 2008 [Janelia]
*
* Purpose: Calculates the fill step of the optimal accuracy decoding
* algorithm \citep{Kall05}.
*
* Caller provides the posterior decoding matrix <pp>,
* which was calculated by Forward/Backward on a target sequence
* of length <pp->L> using the query model <om>.
*
* Caller also provides a DP matrix <ox>, allocated for a full
* <om->M> by <L> comparison. The routine fills this in
* with OA scores.
*
* Args: gm - query profile
* pp - posterior decoding matrix created by <p7_GPosteriorDecoding()>
* gx - RESULT: caller provided DP matrix for <gm->M> by <L>
* ret_e - RETURN: expected number of correctly decoded positions
*
* Returns: <eslOK> on success, and <*ret_e> contains the final OA
* score, which is the expected number of correctly decoded
* positions in the target sequence (up to <L>).
*
* Throws: (no abnormal error conditions)
*/
int
p7_OptimalAccuracy(const P7_OPROFILE *om, const P7_OMX *pp, P7_OMX *ox, float *ret_e)
{
vector float mpv, dpv, ipv; /* previous row values */
vector float sv; /* temp storage of 1 curr row value in progress */
vector float xEv; /* E state: keeps max for Mk->E as we go */
vector float xBv; /* B state: splatted vector of B[i-1] for B->Mk calculations */
vector float dcv;
float *xmx = ox->xmx;
vector float *dpc = ox->dpf[0]; /* current row, for use in {MDI}MO(dpp,q) access macro */
vector float *dpp; /* previous row, for use in {MDI}MO(dpp,q) access macro */
vector float *ppp; /* quads in the <pp> posterior probability matrix */
vector float *tp; /* quads in the <om->tfv> transition scores */
vector float zerov;
vector float infv;
int M = om->M;
int Q = p7O_NQF(M);
int q;
int j;
int i;
float t1, t2;
zerov = (vector float) vec_splat_u32(0);
infv = esl_vmx_set_float(-eslINFINITY);
ox->M = om->M;
ox->L = pp->L;
for (q = 0; q < Q; q++) MMO(dpc, q) = IMO(dpc,q) = DMO(dpc,q) = infv;
XMXo(0, p7X_E) = -eslINFINITY;
XMXo(0, p7X_N) = 0.;
XMXo(0, p7X_J) = -eslINFINITY;
XMXo(0, p7X_B) = 0.;
XMXo(0, p7X_C) = -eslINFINITY;
for (i = 1; i <= pp->L; i++)
{
dpp = dpc; /* previous DP row in OA matrix */
dpc = ox->dpf[i]; /* current DP row in OA matrix */
ppp = pp->dpf[i]; /* current row in the posterior probabilities per position */
tp = om->tfv; /* transition probabilities */
dcv = infv;
xEv = infv;
xBv = esl_vmx_set_float(XMXo(i-1, p7X_B));
mpv = vec_sld(infv, MMO(dpp,Q-1), 12); /* Right shifts by 4 bytes. 4,8,12,x becomes x,4,8,12. */
dpv = vec_sld(infv, DMO(dpp,Q-1), 12);
ipv = vec_sld(infv, IMO(dpp,Q-1), 12);
for (q = 0; q < Q; q++)
{
sv = vec_and(vec_cmpgt(*tp, zerov), xBv); tp++;
sv = vec_max(sv, vec_and(vec_cmpgt(*tp, zerov), mpv)); tp++;
sv = vec_max(sv, vec_and(vec_cmpgt(*tp, zerov), ipv)); tp++;
sv = vec_max(sv, vec_and(vec_cmpgt(*tp, zerov), dpv)); tp++;
sv = vec_add(sv, *ppp); ppp += 2;
xEv = vec_max(xEv, sv);
mpv = MMO(dpp,q);
dpv = DMO(dpp,q);
ipv = IMO(dpp,q);
MMO(dpc,q) = sv;
DMO(dpc,q) = dcv;
dcv = vec_and(vec_cmpgt(*tp, zerov), sv); tp++;
sv = vec_and(vec_cmpgt(*tp, zerov), mpv); tp++;
sv = vec_max(sv, vec_and(vec_cmpgt(*tp, zerov), ipv)); tp++;
IMO(dpc,q) = vec_add(sv, *ppp); ppp++;
}
/* dcv has carried through from end of q loop above; store it
* in first pass, we add M->D and D->D path into DMX
*/
dcv = vec_sld(infv, dcv, 12);
tp = om->tfv + 7*Q; /* set tp to start of the DD's */
for (q = 0; q < Q; q++)
{
DMO(dpc, q) = vec_max(dcv, DMO(dpc, q));
dcv = vec_and(vec_cmpgt(*tp, zerov), DMO(dpc,q)); tp++;
}
/* fully serialized D->D; can optimize later */
for (j = 1; j < 4; j++)
{
dcv = vec_sld(infv, dcv, 12);
tp = om->tfv + 7*Q;
for (q = 0; q < Q; q++)
{
DMO(dpc, q) = vec_max(dcv, DMO(dpc, q));
dcv = vec_and(vec_cmpgt(*tp, zerov), dcv); tp++;
}
}
/* D->E paths */
for (q = 0; q < Q; q++) xEv = vec_max(xEv, DMO(dpc,q));
/* Specials */
XMXo(i,p7X_E) = esl_vmx_hmax_float(xEv);
t1 = ( (om->xf[p7O_J][p7O_LOOP] == 0.0) ? 0.0 : ox->xmx[(i-1)*p7X_NXCELLS+p7X_J] + pp->xmx[i*p7X_NXCELLS+p7X_J]);
t2 = ( (om->xf[p7O_E][p7O_LOOP] == 0.0) ? 0.0 : ox->xmx[ i *p7X_NXCELLS+p7X_E]);
ox->xmx[i*p7X_NXCELLS+p7X_J] = ESL_MAX(t1, t2);
t1 = ( (om->xf[p7O_C][p7O_LOOP] == 0.0) ? 0.0 : ox->xmx[(i-1)*p7X_NXCELLS+p7X_C] + pp->xmx[i*p7X_NXCELLS+p7X_C]);
t2 = ( (om->xf[p7O_E][p7O_MOVE] == 0.0) ? 0.0 : ox->xmx[ i *p7X_NXCELLS+p7X_E]);
ox->xmx[i*p7X_NXCELLS+p7X_C] = ESL_MAX(t1, t2);
ox->xmx[i*p7X_NXCELLS+p7X_N] = ((om->xf[p7O_N][p7O_LOOP] == 0.0) ? 0.0 : ox->xmx[(i-1)*p7X_NXCELLS+p7X_N] + pp->xmx[i*p7X_NXCELLS+p7X_N]);
t1 = ( (om->xf[p7O_N][p7O_MOVE] == 0.0) ? 0.0 : ox->xmx[i*p7X_NXCELLS+p7X_N]);
t2 = ( (om->xf[p7O_J][p7O_MOVE] == 0.0) ? 0.0 : ox->xmx[i*p7X_NXCELLS+p7X_J]);
ox->xmx[i*p7X_NXCELLS+p7X_B] = ESL_MAX(t1, t2);
}
*ret_e = ox->xmx[pp->L*p7X_NXCELLS+p7X_C];
return eslOK;
}
static int
backward_engine(int do_full, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *fwd, P7_OMX *bck, float *opt_sc)
{
register __m128 mpv, ipv, dpv; /* previous row values */
register __m128 mcv, dcv; /* current row values */
register __m128 tmmv, timv, tdmv; /* tmp vars for accessing rotated transition scores */
register __m128 xBv; /* collects B->Mk components of B(i) */
register __m128 xEv; /* splatted E(i) */
__m128 zerov; /* splatted 0.0's in a vector */
float xN, xE, xB, xC, xJ; /* special states' scores */
int i; /* counter over sequence positions 0,1..L */
int q; /* counter over quads 0..Q-1 */
int Q = p7O_NQF(om->M); /* segment length: # of vectors */
int j; /* DD segment iteration counter (4 = full serialization) */
__m128 *dpc; /* current DP row */
__m128 *dpp; /* next ("previous") DP row */
__m128 *rp; /* will point into om->rfv[x] for residue x[i+1] */
__m128 *tp; /* will point into (and step thru) om->tfv transition scores */
/* initialize the L row. */
bck->M = om->M;
bck->L = L;
bck->has_own_scales = FALSE; /* backwards scale factors are *usually* given by <fwd> */
dpc = bck->dpf[L * do_full];
xJ = 0.0;
xB = 0.0;
xN = 0.0;
xC = om->xf[p7O_C][p7O_MOVE]; /* C<-T */
xE = xC * om->xf[p7O_E][p7O_MOVE]; /* E<-C, no tail */
xEv = _mm_set1_ps(xE);
zerov = _mm_setzero_ps();
dcv = zerov; /* solely to silence a compiler warning */
for (q = 0; q < Q; q++) MMO(dpc,q) = DMO(dpc,q) = xEv;
for (q = 0; q < Q; q++) IMO(dpc,q) = zerov;
/* init row L's DD paths, 1) first segment includes xE, from DMO(q) */
tp = om->tfv + 8*Q - 1; /* <*tp> now the [4 8 12 x] TDD quad */
dpv = _mm_move_ss(DMO(dpc,Q-1), zerov); /* start leftshift: [1 5 9 13] -> [x 5 9 13] */
dpv = _mm_shuffle_ps(dpv, dpv, _MM_SHUFFLE(0,3,2,1)); /* finish leftshift:[x 5 9 13] -> [5 9 13 x] */
for (q = Q-1; q >= 0; q--)
{
dcv = _mm_mul_ps(dpv, *tp); tp--;
DMO(dpc,q) = _mm_add_ps(DMO(dpc,q), dcv);
dpv = DMO(dpc,q);
}
/* 2) three more passes, only extending DD component (dcv only; no xE contrib from DMO(q)) */
for (j = 1; j < 4; j++)
{
tp = om->tfv + 8*Q - 1; /* <*tp> now the [4 8 12 x] TDD quad */
dcv = _mm_move_ss(dcv, zerov); /* start leftshift: [1 5 9 13] -> [x 5 9 13] */
dcv = _mm_shuffle_ps(dcv, dcv, _MM_SHUFFLE(0,3,2,1)); /* finish leftshift:[x 5 9 13] -> [5 9 13 x] */
for (q = Q-1; q >= 0; q--)
{
dcv = _mm_mul_ps(dcv, *tp); tp--;
DMO(dpc,q) = _mm_add_ps(DMO(dpc,q), dcv);
}
}
/* now MD init */
tp = om->tfv + 7*Q - 3; /* <*tp> now the [4 8 12 x] Mk->Dk+1 quad */
dcv = _mm_move_ss(DMO(dpc,0), zerov); /* start leftshift: [1 5 9 13] -> [x 5 9 13] */
dcv = _mm_shuffle_ps(dcv, dcv, _MM_SHUFFLE(0,3,2,1)); /* finish leftshift:[x 5 9 13] -> [5 9 13 x] */
for (q = Q-1; q >= 0; q--)
{
MMO(dpc,q) = _mm_add_ps(MMO(dpc,q), _mm_mul_ps(dcv, *tp)); tp -= 7;
dcv = DMO(dpc,q);
}
/* Sparse rescaling: same scale factors as fwd matrix */
if (fwd->xmx[L*p7X_NXCELLS+p7X_SCALE] > 1.0)
{
xE = xE / fwd->xmx[L*p7X_NXCELLS+p7X_SCALE];
xN = xN / fwd->xmx[L*p7X_NXCELLS+p7X_SCALE];
xC = xC / fwd->xmx[L*p7X_NXCELLS+p7X_SCALE];
xJ = xJ / fwd->xmx[L*p7X_NXCELLS+p7X_SCALE];
xB = xB / fwd->xmx[L*p7X_NXCELLS+p7X_SCALE];
xEv = _mm_set1_ps(1.0 / fwd->xmx[L*p7X_NXCELLS+p7X_SCALE]);
for (q = 0; q < Q; q++) {
MMO(dpc,q) = _mm_mul_ps(MMO(dpc,q), xEv);
DMO(dpc,q) = _mm_mul_ps(DMO(dpc,q), xEv);
IMO(dpc,q) = _mm_mul_ps(IMO(dpc,q), xEv);
}
}
bck->xmx[L*p7X_NXCELLS+p7X_SCALE] = fwd->xmx[L*p7X_NXCELLS+p7X_SCALE];
bck->totscale = log(bck->xmx[L*p7X_NXCELLS+p7X_SCALE]);
/* Stores */
bck->xmx[L*p7X_NXCELLS+p7X_E] = xE;
bck->xmx[L*p7X_NXCELLS+p7X_N] = xN;
bck->xmx[L*p7X_NXCELLS+p7X_J] = xJ;
bck->xmx[L*p7X_NXCELLS+p7X_B] = xB;
bck->xmx[L*p7X_NXCELLS+p7X_C] = xC;
#if p7_DEBUGGING
if (bck->debugging) p7_omx_DumpFBRow(bck, TRUE, L, 9, 4, xE, xN, xJ, xB, xC); /* logify=TRUE, <rowi>=L, width=9, precision=4*/
#endif
/* main recursion */
for (i = L-1; i >= 1; i--) /* backwards stride */
{
/* phase 1. B(i) collected. Old row destroyed, new row contains
* complete I(i,k), partial {MD}(i,k) w/ no {MD}->{DE} paths yet.
*/
dpc = bck->dpf[i * do_full];
dpp = bck->dpf[(i+1) * do_full];
rp = om->rfv[dsq[i+1]] + Q-1; /* <*rp> is now the [4 8 12 x] match emission quad */
tp = om->tfv + 7*Q - 1; /* <*tp> is now the [4 8 12 x] TII transition quad */
/* leftshift the first transition quads */
tmmv = _mm_move_ss(om->tfv[1], zerov); tmmv = _mm_shuffle_ps(tmmv, tmmv, _MM_SHUFFLE(0,3,2,1));
timv = _mm_move_ss(om->tfv[2], zerov); timv = _mm_shuffle_ps(timv, timv, _MM_SHUFFLE(0,3,2,1));
tdmv = _mm_move_ss(om->tfv[3], zerov); tdmv = _mm_shuffle_ps(tdmv, tdmv, _MM_SHUFFLE(0,3,2,1));
mpv = _mm_mul_ps(MMO(dpp,0), om->rfv[dsq[i+1]][0]); /* precalc M(i+1,k+1) * e(M_k+1, x_{i+1}) */
mpv = _mm_move_ss(mpv, zerov);
mpv = _mm_shuffle_ps(mpv, mpv, _MM_SHUFFLE(0,3,2,1));
xBv = zerov;
for (q = Q-1; q >= 0; q--) /* backwards stride */
{
ipv = IMO(dpp,q); /* assumes emission odds ratio of 1.0; i+1's IMO(q) now free */
IMO(dpc,q) = _mm_add_ps(_mm_mul_ps(ipv, *tp), _mm_mul_ps(mpv, timv)); tp--;
DMO(dpc,q) = _mm_mul_ps(mpv, tdmv);
mcv = _mm_add_ps(_mm_mul_ps(ipv, *tp), _mm_mul_ps(mpv, tmmv)); tp-= 2;
mpv = _mm_mul_ps(MMO(dpp,q), *rp); rp--; /* obtain mpv for next q. i+1's MMO(q) is freed */
MMO(dpc,q) = mcv;
tdmv = *tp; tp--;
timv = *tp; tp--;
tmmv = *tp; tp--;
xBv = _mm_add_ps(xBv, _mm_mul_ps(mpv, *tp)); tp--;
}
/* phase 2: now that we have accumulated the B->Mk transitions in xBv, we can do the specials */
/* this incantation is a horiz sum of xBv elements: (_mm_hadd_ps() would require SSE3) */
xBv = _mm_add_ps(xBv, _mm_shuffle_ps(xBv, xBv, _MM_SHUFFLE(0, 3, 2, 1)));
xBv = _mm_add_ps(xBv, _mm_shuffle_ps(xBv, xBv, _MM_SHUFFLE(1, 0, 3, 2)));
_mm_store_ss(&xB, xBv);
xC = xC * om->xf[p7O_C][p7O_LOOP];
xJ = (xB * om->xf[p7O_J][p7O_MOVE]) + (xJ * om->xf[p7O_J][p7O_LOOP]); /* must come after xB */
xN = (xB * om->xf[p7O_N][p7O_MOVE]) + (xN * om->xf[p7O_N][p7O_LOOP]); /* must come after xB */
xE = (xC * om->xf[p7O_E][p7O_MOVE]) + (xJ * om->xf[p7O_E][p7O_LOOP]); /* must come after xJ, xC */
xEv = _mm_set1_ps(xE); /* splat */
/* phase 3: {MD}->E paths and one step of the D->D paths */
tp = om->tfv + 8*Q - 1; /* <*tp> now the [4 8 12 x] TDD quad */
dpv = _mm_add_ps(DMO(dpc,0), xEv);
dpv = _mm_move_ss(dpv, zerov);
dpv = _mm_shuffle_ps(dpv, dpv, _MM_SHUFFLE(0,3,2,1));
for (q = Q-1; q >= 0; q--)
{
dcv = _mm_mul_ps(dpv, *tp); tp--;
DMO(dpc,q) = _mm_add_ps(DMO(dpc,q), _mm_add_ps(dcv, xEv));
dpv = DMO(dpc,q);
MMO(dpc,q) = _mm_add_ps(MMO(dpc,q), xEv);
}
/* phase 4: finish extending the DD paths */
/* fully serialized for now */
for (j = 1; j < 4; j++) /* three passes: we've already done 1 segment, we need 4 total */
{
dcv = _mm_move_ss(dcv, zerov);
dcv = _mm_shuffle_ps(dcv, dcv, _MM_SHUFFLE(0,3,2,1));
tp = om->tfv + 8*Q - 1; /* <*tp> now the [4 8 12 x] TDD quad */
for (q = Q-1; q >= 0; q--)
{
dcv = _mm_mul_ps(dcv, *tp); tp--;
DMO(dpc,q) = _mm_add_ps(DMO(dpc,q), dcv);
}
}
/* phase 5: add M->D paths */
dcv = _mm_move_ss(DMO(dpc,0), zerov);
dcv = _mm_shuffle_ps(dcv, dcv, _MM_SHUFFLE(0,3,2,1));
tp = om->tfv + 7*Q - 3; /* <*tp> is now the [4 8 12 x] Mk->Dk+1 quad */
for (q = Q-1; q >= 0; q--)
{
MMO(dpc,q) = _mm_add_ps(MMO(dpc,q), _mm_mul_ps(dcv, *tp)); tp -= 7;
dcv = DMO(dpc,q);
}
/* Sparse rescaling */
/* In rare cases [J3/119] scale factors from <fwd> are
* insufficient and backwards will overflow. In this case, we
* switch on the fly to using our own scale factors, different
* from those in <fwd>. This will complicate subsequent
* posterior decoding routines.
*/
if (xB > 1.0e16) bck->has_own_scales = TRUE;
if (bck->has_own_scales) bck->xmx[i*p7X_NXCELLS+p7X_SCALE] = (xB > 1.0e4) ? xB : 1.0;
else bck->xmx[i*p7X_NXCELLS+p7X_SCALE] = fwd->xmx[i*p7X_NXCELLS+p7X_SCALE];
if (bck->xmx[i*p7X_NXCELLS+p7X_SCALE] > 1.0)
{
xE /= bck->xmx[i*p7X_NXCELLS+p7X_SCALE];
xN /= bck->xmx[i*p7X_NXCELLS+p7X_SCALE];
xJ /= bck->xmx[i*p7X_NXCELLS+p7X_SCALE];
xB /= bck->xmx[i*p7X_NXCELLS+p7X_SCALE];
xC /= bck->xmx[i*p7X_NXCELLS+p7X_SCALE];
xBv = _mm_set1_ps(1.0 / bck->xmx[i*p7X_NXCELLS+p7X_SCALE]);
for (q = 0; q < Q; q++) {
MMO(dpc,q) = _mm_mul_ps(MMO(dpc,q), xBv);
DMO(dpc,q) = _mm_mul_ps(DMO(dpc,q), xBv);
IMO(dpc,q) = _mm_mul_ps(IMO(dpc,q), xBv);
}
bck->totscale += log(bck->xmx[i*p7X_NXCELLS+p7X_SCALE]);
}
/* Stores are separate only for pedagogical reasons: easy to
* turn this into a more memory efficient version just by
* deleting the stores.
*/
bck->xmx[i*p7X_NXCELLS+p7X_E] = xE;
bck->xmx[i*p7X_NXCELLS+p7X_N] = xN;
bck->xmx[i*p7X_NXCELLS+p7X_J] = xJ;
bck->xmx[i*p7X_NXCELLS+p7X_B] = xB;
bck->xmx[i*p7X_NXCELLS+p7X_C] = xC;
#if p7_DEBUGGING
if (bck->debugging) p7_omx_DumpFBRow(bck, TRUE, i, 9, 4, xE, xN, xJ, xB, xC); /* logify=TRUE, <rowi>=i, width=9, precision=4*/
#endif
} /* thus ends the loop over sequence positions i */
/* Termination at i=0, where we can only reach N,B states. */
dpp = bck->dpf[1 * do_full];
tp = om->tfv; /* <*tp> is now the [1 5 9 13] TBMk transition quad */
rp = om->rfv[dsq[1]]; /* <*rp> is now the [1 5 9 13] match emission quad */
xBv = zerov;
for (q = 0; q < Q; q++)
{
mpv = _mm_mul_ps(MMO(dpp,q), *rp); rp++;
mpv = _mm_mul_ps(mpv, *tp); tp += 7;
xBv = _mm_add_ps(xBv, mpv);
}
/* horizontal sum of xBv */
xBv = _mm_add_ps(xBv, _mm_shuffle_ps(xBv, xBv, _MM_SHUFFLE(0, 3, 2, 1)));
xBv = _mm_add_ps(xBv, _mm_shuffle_ps(xBv, xBv, _MM_SHUFFLE(1, 0, 3, 2)));
_mm_store_ss(&xB, xBv);
xN = (xB * om->xf[p7O_N][p7O_MOVE]) + (xN * om->xf[p7O_N][p7O_LOOP]);
bck->xmx[p7X_B] = xB;
bck->xmx[p7X_C] = 0.0;
bck->xmx[p7X_J] = 0.0;
bck->xmx[p7X_N] = xN;
bck->xmx[p7X_E] = 0.0;
bck->xmx[p7X_SCALE] = 1.0;
#if p7_DEBUGGING
dpc = bck->dpf[0];
for (q = 0; q < Q; q++) /* Not strictly necessary, but if someone's looking at DP matrices, this is nice to do: */
MMO(dpc,q) = DMO(dpc,q) = IMO(dpc,q) = zerov;
if (bck->debugging) p7_omx_DumpFBRow(bck, TRUE, 0, 9, 4, bck->xmx[p7X_E], bck->xmx[p7X_N], bck->xmx[p7X_J], bck->xmx[p7X_B], bck->xmx[p7X_C]); /* logify=TRUE, <rowi>=0, width=9, precision=4*/
#endif
if (isnan(xN)) ESL_EXCEPTION(eslERANGE, "backward score is NaN");
else if (L>0 && xN == 0.0) ESL_EXCEPTION(eslERANGE, "backward score underflow (is 0.0)"); /* if L==0, xN *should* be 0.0 [J5/118]*/
else if (isinf(xN) == 1) ESL_EXCEPTION(eslERANGE, "backward score overflow (is infinity)");
if (opt_sc != NULL) *opt_sc = bck->totscale + log(xN);
return eslOK;
}
static int
forward_engine(int do_full, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7_OMX *ox, float *opt_sc)
{
register __m128 mpv, dpv, ipv; /* previous row values */
register __m128 sv; /* temp storage of 1 curr row value in progress */
register __m128 dcv; /* delayed storage of D(i,q+1) */
register __m128 xEv; /* E state: keeps max for Mk->E as we go */
register __m128 xBv; /* B state: splatted vector of B[i-1] for B->Mk calculations */
__m128 zerov; /* splatted 0.0's in a vector */
float xN, xE, xB, xC, xJ; /* special states' scores */
int i; /* counter over sequence positions 1..L */
int q; /* counter over quads 0..nq-1 */
int j; /* counter over DD iterations (4 is full serialization) */
int Q = p7O_NQF(om->M); /* segment length: # of vectors */
__m128 *dpc = ox->dpf[0]; /* current row, for use in {MDI}MO(dpp,q) access macro */
__m128 *dpp; /* previous row, for use in {MDI}MO(dpp,q) access macro */
__m128 *rp; /* will point at om->rfv[x] for residue x[i] */
__m128 *tp; /* will point into (and step thru) om->tfv */
/* Initialization. */
ox->M = om->M;
ox->L = L;
ox->has_own_scales = TRUE; /* all forward matrices control their own scalefactors */
zerov = _mm_setzero_ps();
for (q = 0; q < Q; q++)
MMO(dpc,q) = IMO(dpc,q) = DMO(dpc,q) = zerov;
xE = ox->xmx[p7X_E] = 0.;
xN = ox->xmx[p7X_N] = 1.;
xJ = ox->xmx[p7X_J] = 0.;
xB = ox->xmx[p7X_B] = om->xf[p7O_N][p7O_MOVE];
xC = ox->xmx[p7X_C] = 0.;
ox->xmx[p7X_SCALE] = 1.0;
ox->totscale = 0.0;
#if p7_DEBUGGING
if (ox->debugging) p7_omx_DumpFBRow(ox, TRUE, 0, 9, 5, xE, xN, xJ, xB, xC); /* logify=TRUE, <rowi>=0, width=8, precision=5*/
#endif
for (i = 1; i <= L; i++)
{
dpp = dpc;
dpc = ox->dpf[do_full * i]; /* avoid conditional, use do_full as kronecker delta */
rp = om->rfv[dsq[i]];
tp = om->tfv;
dcv = _mm_setzero_ps();
xEv = _mm_setzero_ps();
xBv = _mm_set1_ps(xB);
/* Right shifts by 4 bytes. 4,8,12,x becomes x,4,8,12. Shift zeros on. */
mpv = esl_sse_rightshift_ps(MMO(dpp,Q-1), zerov);
dpv = esl_sse_rightshift_ps(DMO(dpp,Q-1), zerov);
ipv = esl_sse_rightshift_ps(IMO(dpp,Q-1), zerov);
for (q = 0; q < Q; q++)
{
/* Calculate new MMO(i,q); don't store it yet, hold it in sv. */
sv = _mm_mul_ps(xBv, *tp); tp++;
sv = _mm_add_ps(sv, _mm_mul_ps(mpv, *tp)); tp++;
sv = _mm_add_ps(sv, _mm_mul_ps(ipv, *tp)); tp++;
sv = _mm_add_ps(sv, _mm_mul_ps(dpv, *tp)); tp++;
sv = _mm_mul_ps(sv, *rp); rp++;
xEv = _mm_add_ps(xEv, sv);
/* Load {MDI}(i-1,q) into mpv, dpv, ipv;
* {MDI}MX(q) is then the current, not the prev row
*/
mpv = MMO(dpp,q);
dpv = DMO(dpp,q);
ipv = IMO(dpp,q);
/* Do the delayed stores of {MD}(i,q) now that memory is usable */
MMO(dpc,q) = sv;
DMO(dpc,q) = dcv;
/* Calculate the next D(i,q+1) partially: M->D only;
* delay storage, holding it in dcv
*/
dcv = _mm_mul_ps(sv, *tp); tp++;
/* Calculate and store I(i,q); assumes odds ratio for emission is 1.0 */
sv = _mm_mul_ps(mpv, *tp); tp++;
IMO(dpc,q) = _mm_add_ps(sv, _mm_mul_ps(ipv, *tp)); tp++;
}
/* Now the DD paths. We would rather not serialize them but
* in an accurate Forward calculation, we have few options.
*/
/* dcv has carried through from end of q loop above; store it
* in first pass, we add M->D and D->D path into DMX
*/
/* We're almost certainly're obligated to do at least one complete
* DD path to be sure:
*/
dcv = esl_sse_rightshift_ps(dcv, zerov);
DMO(dpc,0) = zerov;
tp = om->tfv + 7*Q; /* set tp to start of the DD's */
for (q = 0; q < Q; q++)
{
DMO(dpc,q) = _mm_add_ps(dcv, DMO(dpc,q));
dcv = _mm_mul_ps(DMO(dpc,q), *tp); tp++; /* extend DMO(q), so we include M->D and D->D paths */
}
/* now. on small models, it seems best (empirically) to just go
* ahead and serialize. on large models, we can do a bit better,
* by testing for when dcv (DD path) accrued to DMO(q) is below
* machine epsilon for all q, in which case we know DMO(q) are all
* at their final values. The tradeoff point is (empirically) somewhere around M=100,
* at least on my desktop. We don't worry about the conditional here;
* it's outside any inner loops.
*/
if (om->M < 100)
{ /* Fully serialized version */
for (j = 1; j < 4; j++)
{
dcv = esl_sse_rightshift_ps(dcv, zerov);
tp = om->tfv + 7*Q; /* set tp to start of the DD's */
for (q = 0; q < Q; q++)
{ /* note, extend dcv, not DMO(q); only adding DD paths now */
DMO(dpc,q) = _mm_add_ps(dcv, DMO(dpc,q));
dcv = _mm_mul_ps(dcv, *tp); tp++;
}
}
}
else
{ /* Slightly parallelized version, but which incurs some overhead */
for (j = 1; j < 4; j++)
{
register __m128 cv; /* keeps track of whether any DD's change DMO(q) */
dcv = esl_sse_rightshift_ps(dcv, zerov);
tp = om->tfv + 7*Q; /* set tp to start of the DD's */
cv = zerov;
for (q = 0; q < Q; q++)
{ /* using cmpgt below tests if DD changed any DMO(q) *without* conditional branch */
sv = _mm_add_ps(dcv, DMO(dpc,q));
cv = _mm_or_ps(cv, _mm_cmpgt_ps(sv, DMO(dpc,q)));
DMO(dpc,q) = sv; /* store new DMO(q) */
dcv = _mm_mul_ps(dcv, *tp); tp++; /* note, extend dcv, not DMO(q) */
}
if (! _mm_movemask_ps(cv)) break; /* DD's didn't change any DMO(q)? Then done, break out. */
}
}
/* Add D's to xEv */
for (q = 0; q < Q; q++) xEv = _mm_add_ps(DMO(dpc,q), xEv);
/* Finally the "special" states, which start from Mk->E (->C, ->J->B) */
/* The following incantation is a horizontal sum of xEv's elements */
/* These must follow DD calculations, because D's contribute to E in Forward
* (as opposed to Viterbi)
*/
xEv = _mm_add_ps(xEv, _mm_shuffle_ps(xEv, xEv, _MM_SHUFFLE(0, 3, 2, 1)));
xEv = _mm_add_ps(xEv, _mm_shuffle_ps(xEv, xEv, _MM_SHUFFLE(1, 0, 3, 2)));
_mm_store_ss(&xE, xEv);
xN = xN * om->xf[p7O_N][p7O_LOOP];
xC = (xC * om->xf[p7O_C][p7O_LOOP]) + (xE * om->xf[p7O_E][p7O_MOVE]);
xJ = (xJ * om->xf[p7O_J][p7O_LOOP]) + (xE * om->xf[p7O_E][p7O_LOOP]);
xB = (xJ * om->xf[p7O_J][p7O_MOVE]) + (xN * om->xf[p7O_N][p7O_MOVE]);
/* and now xB will carry over into next i, and xC carries over after i=L */
/* Sparse rescaling. xE above threshold? trigger a rescaling event. */
if (xE > 1.0e4) /* that's a little less than e^10, ~10% of our dynamic range */
{
xN = xN / xE;
xC = xC / xE;
xJ = xJ / xE;
xB = xB / xE;
xEv = _mm_set1_ps(1.0 / xE);
for (q = 0; q < Q; q++)
{
MMO(dpc,q) = _mm_mul_ps(MMO(dpc,q), xEv);
DMO(dpc,q) = _mm_mul_ps(DMO(dpc,q), xEv);
IMO(dpc,q) = _mm_mul_ps(IMO(dpc,q), xEv);
}
ox->xmx[i*p7X_NXCELLS+p7X_SCALE] = xE;
ox->totscale += log(xE);
xE = 1.0;
}
else ox->xmx[i*p7X_NXCELLS+p7X_SCALE] = 1.0;
/* Storage of the specials. We could've stored these already
* but using xE, etc. variables makes it easy to convert this
* code to O(M) memory versions just by deleting storage steps.
*/
ox->xmx[i*p7X_NXCELLS+p7X_E] = xE;
ox->xmx[i*p7X_NXCELLS+p7X_N] = xN;
ox->xmx[i*p7X_NXCELLS+p7X_J] = xJ;
ox->xmx[i*p7X_NXCELLS+p7X_B] = xB;
ox->xmx[i*p7X_NXCELLS+p7X_C] = xC;
#if p7_DEBUGGING
if (ox->debugging) p7_omx_DumpFBRow(ox, TRUE, i, 9, 5, xE, xN, xJ, xB, xC); /* logify=TRUE, <rowi>=i, width=8, precision=5*/
#endif
} /* end loop over sequence residues 1..L */
/* finally C->T, and flip total score back to log space (nats) */
/* On overflow, xC is inf or nan (nan arises because inf*0 = nan). */
/* On an underflow (which shouldn't happen), we counterintuitively return infinity:
* the effect of this is to force the caller to rescore us with full range.
*/
if (isnan(xC)) ESL_EXCEPTION(eslERANGE, "forward score is NaN");
else if (L>0 && xC == 0.0) ESL_EXCEPTION(eslERANGE, "forward score underflow (is 0.0)"); /* if L==0, xC *should* be 0.0; J5/118 */
else if (isinf(xC) == 1) ESL_EXCEPTION(eslERANGE, "forward score overflow (is infinity)");
if (opt_sc != NULL) *opt_sc = ox->totscale + log(xC * om->xf[p7O_C][p7O_MOVE]);
return eslOK;
}