/* Function: p7_ViterbiMu()
* Synopsis: Determines the local Viterbi Gumbel mu parameter for a model.
* Incept: SRE, Tue May 19 10:26:19 2009 [Janelia]
*
* Purpose: Identical to p7_MSVMu(), above, except that it fits
* Viterbi scores instead of MSV scores.
*
* The difference between the two mus is small, but can be
* up to ~1 bit or so for large, low-info models [J4/126] so
* decided to calibrate the two mus separately [J5/8].
*
* Args: r : source of random numbers
* om : score profile (length config is changed upon return!)
* bg : null model (length config is changed upon return!)
* L : length of sequences to simulate
* N : number of sequences to simulate
* lambda : known Gumbel lambda parameter
* ret_vmu : RETURN: ML estimate of location param mu
*
* Returns: <eslOK> on success, and <ret_mu> contains the ML estimate
* of $\mu$.
*
* Throws: (no abnormal error conditions)
*/
int
p7_ViterbiMu(ESL_RANDOMNESS *r, P7_OPROFILE *om, P7_BG *bg, int L, int N, double lambda, double *ret_vmu)
{
P7_OMX *ox = p7_omx_Create(om->M, 0, 0); /* DP matrix: 1 row version */
ESL_DSQ *dsq = NULL;
double *xv = NULL;
int i;
float sc, nullsc;
#ifndef p7_IMPL_DUMMY
float maxsc = (32767.0 - om->base_w) / om->scale_w; /* if score overflows, use this [J4/139] */
#endif
int status;
if (ox == NULL) { status = eslEMEM; goto ERROR; }
ESL_ALLOC(xv, sizeof(double) * N);
ESL_ALLOC(dsq, sizeof(ESL_DSQ) * (L+2));
p7_oprofile_ReconfigLength(om, L);
p7_bg_SetLength(bg, L);
for (i = 0; i < N; i++)
{
if ((status = esl_rsq_xfIID(r, bg->f, om->abc->K, L, dsq)) != eslOK) goto ERROR;
if ((status = p7_bg_NullOne(bg, dsq, L, &nullsc)) != eslOK) goto ERROR;
status = p7_ViterbiFilter(dsq, L, om, ox, &sc);
#ifndef p7_IMPL_DUMMY
if (status == eslERANGE) { sc = maxsc; status = eslOK; }
#endif
if (status != eslOK) goto ERROR;
xv[i] = (sc - nullsc) / eslCONST_LOG2;
}
if ((status = esl_gumbel_FitCompleteLoc(xv, N, lambda, ret_vmu)) != eslOK) goto ERROR;
p7_omx_Destroy(ox);
free(xv);
free(dsq);
return eslOK;
ERROR:
*ret_vmu = 0.0;
if (ox != NULL) p7_omx_Destroy(ox);
if (xv != NULL) free(xv);
if (dsq != NULL) free(dsq);
return status;
}
/* ViterbiFilter() unit test
*
* We can check that scores are identical (within machine error) to
* scores of generic DP with scores rounded the same way. Do this for
* a random model of length <M>, for <N> test sequences of length <L>.
*
* We assume that we don't accidentally generate a high-scoring random
* sequence that overflows ViterbiFilter()'s limited range.
*
*/
static void
utest_viterbi_filter(ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N)
{
P7_HMM *hmm = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
P7_OMX *ox = p7_omx_Create(M, 0, 0);
P7_GMX *gx = p7_gmx_Create(M, L);
float sc1, sc2;
p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om);
p7_profile_SameAsVF(om, gm); /* round and scale the scores in <gm> the same as in <om> */
#if 0
p7_oprofile_Dump(stdout, om); // dumps the optimized profile
p7_omx_SetDumpMode(stdout, ox, TRUE); // makes the fast DP algorithms dump their matrices
#endif
while (N--)
{
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
p7_ViterbiFilter(dsq, L, om, ox, &sc1);
p7_GViterbi (dsq, L, gm, gx, &sc2);
#if 0
p7_gmx_Dump(stdout, gx); // dumps a generic DP matrix
#endif
sc2 /= om->scale_w;
sc2 -= 3.0;
if (fabs(sc1-sc2) > 0.001) esl_fatal("viterbi filter unit test failed: scores differ (%.2f, %.2f)", sc1, sc2);
}
free(dsq);
p7_hmm_Destroy(hmm);
p7_omx_Destroy(ox);
p7_gmx_Destroy(gx);
p7_profile_Destroy(gm);
p7_oprofile_Destroy(om);
}
int main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 2, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
char *seqfile = esl_opt_GetArg(go, 2);
ESL_STOPWATCH *w = esl_stopwatch_Create();
ESL_RANDOMNESS*r = esl_randomness_Create(esl_opt_GetInteger(go, "-s"));
ESL_ALPHABET*abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm1, *gm2;
int L = 2000; // esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
int MaxPart = esl_opt_GetInteger(go, "-M");
__m128 resdata[10];
float *sc1 = (float*) (resdata+0); // uses 1 __m128s
ESL_DSQ *dsq = NULL;
int i, j;
ESL_SQFILE *sqfp = NULL;
DATA_STREAM *dstream;
struct timeb tbstart, tbend;
int sumlengths = 0;
if (p7_hmmfile_Open(hmmfile, NULL, &hfp)!= eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
bg = p7_bg_Create(abc);
p7_bg_SetLength(bg, L);
gm1 = p7_profile_Create(hmm->M, abc);
gm2 = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm1, L, p7_UNILOCAL);
p7_ProfileConfig(hmm, bg, gm2, L, p7_UNILOCAL);
dstream = p7_ViterbiStream_Create(gm1);
p7_ViterbiStream_Setup(dstream, L+100, MaxPart); // use max L
dstream->L = L;
// No. of partitions computed without full parallelism ( == no. of threads active while some are idle)
int Niters_part = dstream->Npartitions % NTHREADS;
// No. of Model lines that could be computed but are wasted by idle threads waiting on the end
int Nwasted_threads = dstream->partition * ((NTHREADS-Niters_part) % NTHREADS);
// No. of lines in the last partition that go beyond M. It's wasted comp time by a single thread
int Nwasted_leftover= (dstream->partition - gm1->M % dstream->partition) % dstream->partition;
// Total number of wasted lines
int wastedcomp = Nwasted_threads + Nwasted_leftover;
// Total number of lines computed and waited for
int totalcomp = wastedcomp + gm1->M; // same as: roundtop(gm1->M, dstream->partition * NTHREADS);
printf("Viterbi Stream Word with %d Threads, model %s: Modelsize %d, #Segms: %d, SeqL: %d, Nseqs %d, Part %d, #Parts %d\n",
NTHREADS, hmmfile, gm1->M, (int) ceil(gm1->M/8.0), L, 8*N, dstream->partition, dstream->Npartitions);
printf("Total Comp Lines: %d | Wasted Comp Lines: %d\n", totalcomp, wastedcomp);
// for ViterbiFilter
P7_OPROFILE *om = p7_oprofile_Create(hmm->M, gm1->abc);
p7_oprofile_Convert(gm1, om);
P7_OMX *ox = p7_omx_Create(hmm->M, 0, 0);
dsq_cmp_t **seqsdb= calloc(8*N+64, sizeof(dsq_cmp_t*));
if(0)
{ ESL_SQ* sq = esl_sq_CreateDigital(abc);
if (esl_sqfile_OpenDigital(abc, seqfile, eslSQFILE_FASTA, NULL, &sqfp) != eslOK)
{ p7_Fail("Failed to open sequence file\n"); return -1; }
for (j = 0; j < 8*N; j++)
{
int res = esl_sqio_Read(sqfp, sq);
if (res != eslOK) { printf("ATENCAO: faltam sequencias\n"); break; }
int len = sq->n;
dsq = sq->dsq;
seqsdb[j] = malloc(sizeof(dsq_cmp_t));
seqsdb[j]->length = len;
seqsdb[j]->seq = malloc((len+4)*sizeof(ESL_DSQ));
memcpy(seqsdb[j]->seq, dsq, len+2);
sumlengths += len;
esl_sq_Reuse(sq);
}
ftime(&tbstart);
N = j/8;
printf("N = %d\n", N);
// Sort sequences by length
qsort(seqsdb, N*8, sizeof(dsq_cmp_t*), compare_seqs);
}
else if(0)
for (i = 0; i < N; i++)
{
for (j = 0; j < 8; j++)
{
int len = L - rand()%1000;
seqsdb[i*8+j] = malloc(sizeof(dsq_cmp_t));
seqsdb[i*8+j]->seq = malloc(len+4);
seqsdb[i*8+j]->length = len;
esl_rsq_xfIID(r, bg->f, abc->K, len, seqsdb[i*8+j]->seq);
sumlengths += len;
}
}
// double sumerrors = 0;
float* results = (float*) alloc_m128_aligned64(N*2+2);
ftime(&tbstart);
for (j = 0; j < N; j++)
for (i = 0; i < N; i++)
{
// if (i % 10000 == 0) printf("START %d\n", i);
p7_ViterbiStream(dstream, seqsdb+i*8, sc1);
// memcpy(results+i*8, sc1, 32);
}
ftime(&tbend);
double secs = TIMEDIFF(tbstart,tbend);
// printf("Qsort time: %6.3f | Viterbi time: %6.3f\n", TIMEDIFF(tbqsort,tbstart), secs);
w->elapsed = w->user = secs;
esl_stopwatch_Display(stdout, w, "# Opt CPU time: ");
printf("# %.0fM cells in %.1f Mc/s\n", (sumlengths * (double) gm1->M) / 1e6, (sumlengths * (double) gm1->M * 1e-6) / secs);
if(0) // compare results against base version
for (i = 0; i < 1000 && i < N; i++)
{
int maxll = 0; float sc2;
for (j = 0; j < 8; j++)
if (maxll < seqsdb[i*8+j]->length)
maxll = seqsdb[i*8+j]->length;
// for (j = 0; j < 8; j++) printf("%d ", seqsdb[i*8+j]->length); printf("\n");
// if (i % 10 == 0) printf("i %d\n", i);
p7_oprofile_ReconfigRestLength(om, maxll);
p7_ReconfigLength(gm2, maxll); // fazer Reconfig aqui para emular compl o VitStream
for (j = 0; j < 8; j++)
{
// p7_ReconfigLength(gm2, seqsdb[i*8+j]->length);
// p7_Viterbi_unilocal(seqsdb[i*8+j]->seq, seqsdb[i*8+j]->length, gm2, &sc3);
// p7_Viterbi_unilocal_word(seqsdb[i*8+j]->seq, seqsdb[i*8+j]->length, gm2, &sc2);
// p7_oprofile_ReconfigLength(om, seqsdb[i*8+j]->length);
p7_ViterbiFilter(seqsdb[i*8+j]->seq, seqsdb[i*8+j]->length, om, ox, &sc2);
//sumerrors += fabs(sc1[j]- sc2);
if (fabs(results[i*8+j] - sc2) > 0.00001)
{ printf("%3d-%d L %4d: VS %f d %f\t| Base SerI %f\n", i, j, seqsdb[i*8+j]->length,
results[i*8+j], fabs(results[i*8+j] - sc2), sc2);
getc(stdin);
}
}
}
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 2, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
char *seqfile = esl_opt_GetArg(go, 2);
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_OMX *ox = NULL;
P7_GMX *gx = NULL;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
int format = eslSQFILE_UNKNOWN;
float vfraw, nullsc, vfscore;
float graw, gscore;
double P, gP;
int status;
/* Read in one HMM */
if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
/* Read in one sequence */
sq = esl_sq_CreateDigital(abc);
status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("No such file.");
else if (status == eslEFORMAT) p7_Fail("Format unrecognized.");
else if (status == eslEINVAL) p7_Fail("Can't autodetect stdin or .gz.");
else if (status != eslOK) p7_Fail("Open failed, code %d.", status);
/* create default null model, then create and optimize profile */
bg = p7_bg_Create(abc);
p7_bg_SetLength(bg, sq->n);
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);
om = p7_oprofile_Create(gm->M, abc);
p7_oprofile_Convert(gm, om);
/* allocate DP matrices, both a generic and an optimized one */
ox = p7_omx_Create(gm->M, 0, sq->n);
gx = p7_gmx_Create(gm->M, sq->n);
/* Useful to place and compile in for debugging:
p7_oprofile_Dump(stdout, om); dumps the optimized profile
p7_omx_SetDumpMode(ox, TRUE); makes the fast DP algorithms dump their matrices
p7_gmx_Dump(stdout, gx); dumps a generic DP matrix
*/
while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
{
p7_oprofile_ReconfigLength(om, sq->n);
p7_ReconfigLength(gm, sq->n);
p7_bg_SetLength(bg, sq->n);
p7_omx_GrowTo(ox, om->M, 0, sq->n);
p7_gmx_GrowTo(gx, gm->M, sq->n);
p7_ViterbiFilter (sq->dsq, sq->n, om, ox, &vfraw);
p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc);
vfscore = (vfraw - nullsc) / eslCONST_LOG2;
P = esl_gumbel_surv(vfscore, om->evparam[p7_VMU], om->evparam[p7_VLAMBDA]);
p7_GViterbi (sq->dsq, sq->n, gm, gx, &graw);
gscore = (graw - nullsc) / eslCONST_LOG2;
gP = esl_gumbel_surv(gscore, gm->evparam[p7_VMU], gm->evparam[p7_VLAMBDA]);
if (esl_opt_GetBoolean(go, "-1"))
{
printf("%-30s\t%-20s\t%9.2g\t%7.2f\t%9.2g\t%7.2f\n", sq->name, hmm->name, P, vfscore, gP, gscore);
}
else if (esl_opt_GetBoolean(go, "-P"))
{ /* output suitable for direct use in profmark benchmark postprocessors: */
printf("%g\t%.2f\t%s\t%s\n", P, vfscore, sq->name, hmm->name);
}
else
{
printf("target sequence: %s\n", sq->name);
printf("vit filter raw score: %.2f nats\n", vfraw);
printf("null score: %.2f nats\n", nullsc);
printf("per-seq score: %.2f bits\n", vfscore);
printf("P-value: %g\n", P);
printf("GViterbi raw score: %.2f nats\n", graw);
printf("GViterbi seq score: %.2f bits\n", gscore);
printf("GViterbi P-value: %g\n", gP);
}
esl_sq_Reuse(sq);
}
/* cleanup */
esl_sq_Destroy(sq);
esl_sqfile_Close(sqfp);
p7_omx_Destroy(ox);
p7_gmx_Destroy(gx);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
p7_hmmfile_Close(hfp);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
ESL_STOPWATCH *w = esl_stopwatch_Create();
ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_OMX *ox = NULL;
P7_GMX *gx = NULL;
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
int i;
float sc1, sc2;
double base_time, bench_time, Mcs;
if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
bg = p7_bg_Create(abc);
p7_bg_SetLength(bg, L);
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
om = p7_oprofile_Create(gm->M, abc);
p7_oprofile_Convert(gm, om);
p7_oprofile_ReconfigLength(om, L);
if (esl_opt_GetBoolean(go, "-x")) p7_profile_SameAsVF(om, gm);
ox = p7_omx_Create(gm->M, 0, 0);
gx = p7_gmx_Create(gm->M, L);
/* Get a baseline time: how long it takes just to generate the sequences */
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
esl_stopwatch_Stop(w);
base_time = w->user;
/* Run the benchmark */
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
{
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
p7_ViterbiFilter(dsq, L, om, ox, &sc1);
if (esl_opt_GetBoolean(go, "-c"))
{
p7_GViterbi(dsq, L, gm, gx, &sc2);
printf("%.4f %.4f\n", sc1, sc2);
}
if (esl_opt_GetBoolean(go, "-x"))
{
p7_GViterbi(dsq, L, gm, gx, &sc2);
sc2 /= om->scale_w;
if (om->mode == p7_UNILOCAL) sc2 -= 2.0; /* that's ~ L \log \frac{L}{L+2}, for our NN,CC,JJ */
else if (om->mode == p7_LOCAL) sc2 -= 3.0; /* that's ~ L \log \frac{L}{L+3}, for our NN,CC,JJ */
printf("%.4f %.4f\n", sc1, sc2);
}
}
esl_stopwatch_Stop(w);
bench_time = w->user - base_time;
Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) bench_time;
esl_stopwatch_Display(stdout, w, "# CPU time: ");
printf("# M = %d\n", gm->M);
printf("# %.1f Mc/s\n", Mcs);
free(dsq);
p7_omx_Destroy(ox);
p7_gmx_Destroy(gx);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
p7_hmmfile_Close(hfp);
esl_alphabet_Destroy(abc);
esl_stopwatch_Destroy(w);
esl_randomness_Destroy(r);
esl_getopts_Destroy(go);
return 0;
}
int main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 2, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
char *seqfile = esl_opt_GetArg(go, 2);
ESL_STOPWATCH *w = esl_stopwatch_Create();
ESL_RANDOMNESS*r = esl_randomness_Create(esl_opt_GetInteger(go, "-s"));
ESL_ALPHABET*abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm1, *gm2;
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N") / SSE16_NVALS;
int MaxPart = esl_opt_GetInteger(go, "-M");
int NROUNDS = esl_opt_GetInteger(go, "-R");
int check = esl_opt_GetBoolean(go, "-c");
__m128 resdata[10];
int i, j;
float *sc1 = (float*) resdata;
ESL_SQFILE *sqfp = NULL;
DATA_COPS16 *dcops;
struct timeb tbstart, tbend;
int sumlengths = 0;
float* results = NULL;
srand(time(NULL));
if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
bg = p7_bg_Create(abc);
p7_bg_SetLength(bg, L);
gm1 = p7_profile_Create(hmm->M, abc);
gm2 = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm1, L, p7_UNILOCAL);
p7_ProfileConfig(hmm, bg, gm2, L, p7_UNILOCAL);
dcops = p7_ViterbiCOPSw_Create(gm1);
p7_ViterbiCOPSW_Setup(dcops, L+100, MaxPart); // use max L
dcops->L = L;
int dbsize = SSE16_NVALS*N;
SEQ **seqsdb= calloc(dbsize+1, sizeof(SEQ*));
int equallength = 1;
if (esl_sqfile_OpenDigital(abc, seqfile, eslSQFILE_FASTA, NULL, &sqfp) == eslOK)
{ // Use Sequence file
ESL_SQ* sq = esl_sq_CreateDigital(abc);
int maxseqs, len=0;
if (esl_opt_IsDefault(go, "-N")) // N not specified in cmdline
maxseqs = INT_MAX; // no limit
else
maxseqs = SSE16_NVALS*N; // use cmdline limit
for (j = 0; j < maxseqs && esl_sqio_Read(sqfp, sq) == eslOK; j++)
{
if (equallength && sq->n != len && j > 0)
equallength = 0;
len = sq->n;
if (j > dbsize)
{ seqsdb = realloc(seqsdb, 2*(dbsize+1)*sizeof(SEQ*));
dbsize *= 2;
}
ESL_DSQ* dsq = sq->dsq;
seqsdb[j] = malloc(sizeof(SEQ));
seqsdb[j]->length = len;
seqsdb[j]->seq = malloc((len+4)*sizeof(ESL_DSQ));
memcpy(seqsdb[j]->seq, dsq, len+2);
sumlengths += len;
esl_sq_Reuse(sq);
}
N = j/SSE16_NVALS;
}
else // Not found database. Generate random sequences
for (i = 0; i < N; i++)
for (j = 0; j < SSE16_NVALS; j++)
{
int len = L; // - rand()%1000;
seqsdb[i*SSE16_NVALS+j] = malloc(sizeof(SEQ));
seqsdb[i*SSE16_NVALS+j]->seq = malloc(len+4);
seqsdb[i*SSE16_NVALS+j]->length = len;
esl_rsq_xfIID(r, bg->f, abc->K, len, seqsdb[i*SSE16_NVALS+j]->seq);
sumlengths += len;
}
printf("Viterbi COPS Word with %d threads, model %s. ModelLen: %d, #Segms: %d, SeqL.: %d, #seqs: %d, Partition: %d, #parts: %d\n",
NTHREADS, hmmfile, gm1->M, (int) ceil(gm1->M/SSE16_NVALS), L, SSE16_NVALS*N*NROUNDS, dcops->partition, dcops->Npartitions);
/* // No. of partitions computed without full parallelism ( == no. of threads active while some are idle)
int Niters_part = dcops->Npartitions % NTHREADS;
// No. of Model lines that could be computed but are wasted by idle threads waiting on the end
int Nwasted_threads = dcops->partition * ((NTHREADS-Niters_part) % NTHREADS);
// No. of lines in the last partition that go beyond M. It's wasted comp time by a single thread
int Nwasted_leftover= (dcops->partition - gm1->M % dcops->partition) % dcops->partition;
// Total number of wasted lines
int wastedcomp = Nwasted_threads + Nwasted_leftover;
// Total number of lines computed and waited for
int totalcomp = wastedcomp + gm1->M; // same as: roundtop(gm1->M, dcops->partition * NTHREADS);
printf("Total Comp Lines: %d | Wasted Comp Lines: %d\n", totalcomp, wastedcomp);
*/
if (check) results = (float*) alloc_m128_aligned64((N+1)*2);
ftime(&tbstart);
if (!equallength)
{ // Sort sequences by length
qsort(seqsdb, N*SSE16_NVALS, sizeof(SEQ*), compare_seqs);
}
for (j = 0; j < NROUNDS; j++)
for (i = 0; i < N; i++)
{
// if (i % 1000 == 0) printf("Seq %d\n", i);
p7_ViterbiCOPSw_run(dcops, seqsdb+i*SSE16_NVALS, sc1);
if (check) memcpy(results+i*SSE16_NVALS, sc1, 32); // 32 bytes indeed! SSE16_NVALS floats
}
ftime(&tbend);
double secs = TIMEDIFF(tbstart,tbend);
w->elapsed = w->user = secs;
esl_stopwatch_Display(stdout, w, "# Opt CPU time: ");
double compmillioncells = NROUNDS * (double) sumlengths * (double) hmm->M * 1e-6;
printf("# %.0fM cells in %.1f Mc/s\n", compmillioncells, compmillioncells / secs);
if (check)
{ P7_OPROFILE *om = p7_oprofile_Create(hmm->M, gm1->abc);
p7_oprofile_Convert(gm1, om);
P7_OMX *ox = p7_omx_Create(hmm->M, 0, 0);
printf("Compare results against base version\n");
for (i = 0; i < N; i++)
{
int maxll = 0; float sc2;
for (j = 0; j < SSE16_NVALS; j++)
if (maxll < seqsdb[i*SSE16_NVALS+j]->length)
maxll = seqsdb[i*SSE16_NVALS+j]->length;
p7_oprofile_ReconfigRestLength(om, maxll);
// p7_ReconfigLength(gm2, maxll); // emulate the lock-step inter-sequence reconfigs
for (j = 0; j < SSE16_NVALS; j++)
{
// p7_ReconfigLength(gm2, seqsdb[i*SSE16_NVALS+j]->length);
// p7_Viterbi_unilocal(seqsdb[i*SSE16_NVALS+j]->seq, seqsdb[i*SSE16_NVALS+j]->length, gm2, &sc3);
// p7_Viterbi_unilocal_word(seqsdb[i*SSE16_NVALS+j]->seq, seqsdb[i*SSE16_NVALS+j]->length, gm2, &sc2);
// p7_oprofile_ReconfigLength(om, seqsdb[i*SSE16_NVALS+j]->length);
p7_ViterbiFilter(seqsdb[i*SSE16_NVALS+j]->seq, seqsdb[i*SSE16_NVALS+j]->length, om, ox, &sc2);
sc2 += 1.0; // -2.0nat optimization, Local to Unilocal mode
if (fabs(results[i*SSE16_NVALS+j] - sc2) > 0.0001)
{ printf("Seq %d Len %4d: %f - %f\tdiff: %f\n", i*SSE16_NVALS+j, seqsdb[i*SSE16_NVALS+j]->length,
results[i*SSE16_NVALS+j], sc2, fabs(results[i*SSE16_NVALS+j] - sc2));
}
}
}
}
return 0;
}
/* process_workunit()
*
* This is the routine that actually does the work.
*
* A work unit consists of one HMM, <hmm>.
* The result is the <scores> array, which contains an array of N scores;
* caller provides this memory.
* How those scores are generated is controlled by the application configuration in <cfg>.
*/
static int
process_workunit(ESL_GETOPTS *go, struct cfg_s *cfg, char *errbuf, P7_HMM *hmm, double *scores, int *alilens)
{
int L = esl_opt_GetInteger(go, "-L");
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_REFMX *rmx = NULL;
P7_CHECKPTMX *cx = NULL;
P7_FILTERMX *fx = NULL;
P7_TRACE *tr = NULL;
ESL_DSQ *dsq = NULL;
int i;
int scounts[p7T_NSTATETYPES]; /* state usage counts from a trace */
float sc;
float nullsc;
int status;
P7_HARDWARE *hw;
if ((hw = p7_hardware_Create ()) == NULL) p7_Fail("Couldn't get HW information data structure");
/* Optionally set a custom background, determined by model composition;
* an experimental hack.
*/
if (esl_opt_GetBoolean(go, "--bgcomp"))
{
float *p = NULL;
float KL;
p7_hmm_CompositionKLDist(hmm, cfg->bg, &KL, &p);
esl_vec_FCopy(p, cfg->abc->K, cfg->bg->f);
}
/* Create and configure our generic profile, as requested */
gm = p7_profile_Create(hmm->M, cfg->abc);
if (esl_opt_GetBoolean(go, "--multi"))
{
if (esl_opt_GetBoolean(go, "--dual")) { p7_profile_Config (gm, hmm, cfg->bg); }
else if (esl_opt_GetBoolean(go, "--local")) { p7_profile_ConfigLocal (gm, hmm, cfg->bg, L); }
else if (esl_opt_GetBoolean(go, "--glocal")) { p7_profile_ConfigGlocal(gm, hmm, cfg->bg, L); }
}
else if (esl_opt_GetBoolean(go, "--uni"))
{
if (esl_opt_GetBoolean(go, "--dual")) { p7_profile_ConfigCustom (gm, hmm, cfg->bg, L, 0.0, 0.5); }
else if (esl_opt_GetBoolean(go, "--local")) { p7_profile_ConfigUnilocal (gm, hmm, cfg->bg, L); }
else if (esl_opt_GetBoolean(go, "--glocal")) { p7_profile_ConfigUniglocal(gm, hmm, cfg->bg, L); }
}
p7_profile_SetLength(gm, L);
p7_bg_SetLength(cfg->bg, L);
if (esl_opt_GetBoolean(go, "--x-no-lengthmodel")) elide_length_model(gm, cfg->bg);
/* Allocate DP matrix for <gm>.
*/
rmx = p7_refmx_Create(gm->M, L);
/* Create and configure the vectorized profile, if needed;
* and allocate its DP matrix
*/
if (esl_opt_GetBoolean(go, "--vector"))
{
om = p7_oprofile_Create(gm->M, cfg->abc, om->simd);
p7_oprofile_Convert(gm, om);
cx = p7_checkptmx_Create(gm->M, L, ESL_MBYTES(32), om->simd);
fx = p7_filtermx_Create(gm->M, om->simd);
}
/* Remaining allocation */
ESL_ALLOC(dsq, sizeof(ESL_DSQ) * (L+2));
tr = p7_trace_Create();
/* Collect scores from N random sequences of length L */
for (i = 0; i < cfg->N; i++)
{
esl_rsq_xfIID(cfg->r, cfg->bg->f, cfg->abc->K, L, dsq);
sc = eslINFINITY;
/* Vectorized implementations of Viterbi, MSV may overflow.
* In this case, they'll leave sc=eslINFINITY.
* Then we fail over to the nonvector "generic" implementation.
* That's why this next block isn't an if/else.
*/
if (esl_opt_GetBoolean(go, "--vector"))
{
if (esl_opt_GetBoolean(go, "--vit")) p7_ViterbiFilter(dsq, L, om, fx, &sc);
else if (esl_opt_GetBoolean(go, "--fwd")) p7_ForwardFilter(dsq, L, om, cx, &sc);
else if (esl_opt_GetBoolean(go, "--msv")) p7_MSVFilter (dsq, L, om, fx, &sc);
}
/* If we tried a vector calculation above but it overflowed,
* or if we're to do --generic DP calculations, sc==eslINFINITY now;
* hence the if condition here:
*/
if (sc == eslINFINITY)
{
if (esl_opt_GetBoolean(go, "--fwd")) p7_ReferenceForward(dsq, L, gm, rmx, &sc); /* any mode: dual,local,glocal; gm's config takes care of this */
else if (esl_opt_GetBoolean(go, "--vit")) p7_ReferenceViterbi(dsq, L, gm, rmx, tr, &sc); /* local-only mode. cmdline opts processing has already assured that --local set */
else if (esl_opt_GetBoolean(go, "--msv")) p7_Die("We used to be able to do a generic MSV algorithm - but no longer");
}
/* Optional: get Viterbi alignment length too. */
if (esl_opt_GetBoolean(go, "-a")) /* -a only works with Viterbi; getopts has checked this already; <tr> must be valid */
{
p7_trace_GetStateUseCounts(tr, scounts);
/* there's various ways we could counts "alignment length".
* Here we'll use the total length of model used, in nodes: M+D states.
* score vs al would gives us relative entropy / model position.
*/
/* alilens[i] = scounts[p7T_D] + scounts[p7T_I]; SRE: temporarily testing this instead */
alilens[i] = scounts[p7T_ML] + scounts[p7T_DL] + scounts[p7T_IL] +
scounts[p7T_MG] + scounts[p7T_DG] + scounts[p7T_IG];
p7_trace_Reuse(tr);
}
p7_bg_NullOne(cfg->bg, dsq, L, &nullsc);
scores[i] = (sc - nullsc) / eslCONST_LOG2;
if (cx) p7_checkptmx_Reuse(cx);
if (fx) p7_filtermx_Reuse(fx);
p7_refmx_Reuse(rmx);
}
status = eslOK;
/* deliberate flowthru */
ERROR:
if (dsq != NULL) free(dsq);
p7_checkptmx_Destroy(cx);
p7_filtermx_Destroy(fx);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_refmx_Destroy(rmx);
p7_trace_Destroy(tr);
if (status == eslEMEM) sprintf(errbuf, "allocation failure");
return status;
}
void run_hmmer_pipeline(const char* seq) {
int index, i, status;
ESL_SQ* sq = esl_sq_CreateFrom(NULL, seq, NULL, NULL, NULL);
P7_OPROFILE *om = NULL;
P7_PROFILE *gm = NULL;
float usc, vfsc, fwdsc; /* filter scores */
float filtersc; /* HMM null filter score */
float nullsc; /* null model score */
float seqbias;
float seq_score; /* the corrected per-seq bit score */
double P;
WRAPPER_RESULT* result;
num_results = 0;
if(sq->n == 0) {
esl_sq_Destroy(sq);
return;
}
esl_sq_Digitize(abc, sq);
int n = 0;
float oasc;
for(index = 0;index < num_models;index++) {
om = models[index];
p7_omx_Reuse(oxf);
p7_omx_Reuse(oxb);
p7_omx_GrowTo(oxf, om->M, sq->n, sq->n);
p7_omx_GrowTo(oxb, om->M, sq->n, sq->n);
p7_oprofile_ReconfigLength(om, sq->n);
p7_bg_SetFilter(bg, om->M, om->compo);
p7_bg_SetLength(bg, sq->n);
//Calibrate null model
p7_bg_NullOne(bg, sq->dsq, sq->n, &nullsc);
//MSV Filter
p7_MSVFilter(sq->dsq, sq->n, om, oxf, &usc);
seq_score = (usc - nullsc) / eslCONST_LOG2;
P = esl_gumbel_surv(seq_score, om->evparam[p7_MMU], om->evparam[p7_MLAMBDA]);
if (P > f1) continue;
//Bias filter (model compo)
p7_bg_FilterScore(bg, sq->dsq, sq->n, &filtersc);
seq_score = (usc - filtersc) / eslCONST_LOG2;
P = esl_gumbel_surv(seq_score, om->evparam[p7_MMU], om->evparam[p7_MLAMBDA]);
if (P > f1) continue;
//Viterbi filter (Only do if P value from Bias is high)
if(P > f2) {
p7_ViterbiFilter(sq->dsq, sq->n, om, oxf, &vfsc);
seq_score = (vfsc - filtersc) / eslCONST_LOG2;
P = esl_gumbel_surv(seq_score, om->evparam[p7_VMU], om->evparam[p7_VLAMBDA]);
if (P > f2) continue;
}
//Get the real probability (forward)
p7_Forward(sq->dsq, sq->n, om, oxf, &fwdsc);
seq_score = (fwdsc - filtersc) / eslCONST_LOG2;
P = esl_exp_surv(seq_score, om->evparam[p7_FTAU], om->evparam[p7_FLAMBDA]);
if(hmmer_error) {
fprintf(stderr, "HMM: %s, seq: %s", om->name, seq);
hmmer_error = 0;
continue;
}
if (P > f3) continue;
//Real hit, go in to posterior decoding and alignment
p7_omx_Reuse(oxb);
p7_trace_Reuse(tr);
p7_Backward(sq->dsq, sq->n, om, oxf, oxb, NULL);
status = p7_Decoding(om, oxf, oxb, oxb);
if(status == eslOK) {
//And then trace the result
p7_OptimalAccuracy(om, oxb, oxf, &oasc);
p7_OATrace(om, oxb, oxf, tr);
} else if(status == eslERANGE) {
fprintf(stderr, "Decoding overflow on model %s\n", om->name);
gm = gmodels[index];
if(gxf == NULL) {
gxf = p7_gmx_Create(gm->M, sq->n);
gxb = p7_gmx_Create(gm->M, sq->n);
} else {
p7_gmx_GrowTo(gxf, gm->M, sq->n);
p7_gmx_GrowTo(gxb, gm->M, sq->n);
}
p7_ReconfigLength(gm, sq->n);
p7_GForward (sq->dsq, sq->n, gm, gxf, &fwdsc);
p7_GBackward(sq->dsq, sq->n, gm, gxb, NULL);
p7_GDecoding(gm, gxf, gxb, gxb);
p7_GOptimalAccuracy(gm, gxb, gxf, &oasc);
p7_GOATrace (gm, gxb, gxf, tr);
p7_gmx_Reuse(gxf);
p7_gmx_Reuse(gxb);
}
if(hmmer_error) {
fprintf(stderr, "HMM: %s, seq: %s", om->name, seq);
hmmer_error = 0;
continue;
}
result = wrapper_results[num_results];
reuse_result(result, tr->N + om->M, om->name); //We're way overallocating here, but it's hard to know at this point how much space we'll need for the alignment (plus leading and trailing gaps)
trace_into(tr, result, sq, abc, om->M);
result->bits = seq_score;
num_results++;
}
esl_sq_Destroy(sq);
}
