Ejemplo n.º 1
0
int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  int             i;
 
  /* Read one HMM from <hmmfile> */
  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");
  p7_hmmfile_Close(hfp);

  bg = p7_bg_Create(abc);

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    p7_bg_SetFilterByHMM(bg, hmm);
  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");

  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 2
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;

  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("Failed to read HMM");
  p7_hmmfile_Close(hfp);

  esl_stopwatch_Start(w);
  while (N--)
    { /*                cfg   rng   bg    gm    om  */
      p7_Calibrate(hmm, NULL, NULL, NULL, NULL, NULL);
    }
  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");

  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 3
0
int
main(int argc, char **argv)
{
    ESL_GETOPTS    *go      = p7_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_GMX         *gx1     = NULL;
    P7_GMX         *gx2     = NULL;
    int             L       = esl_opt_GetInteger(go, "-L");
    int             N       = esl_opt_GetInteger(go, "-N");
    ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
    float           null2[p7_MAXCODE];
    int             i;
    float           fsc, bsc;
    double          Mcs;

    if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != 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);
    gx1 = p7_gmx_Create(gm->M, L);
    gx2 = p7_gmx_Create(gm->M, L);

    esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
    p7_GForward (dsq, L, gm, gx1, &fsc);
    p7_GBackward(dsq, L, gm, gx2, &bsc);
    p7_GDecoding(gm, gx1, gx2, gx2);

    esl_stopwatch_Start(w);
    for (i = 0; i < N; i++)
        p7_GNull2_ByExpectation(gm, gx2, null2);
    esl_stopwatch_Stop(w);

    Mcs  = (double) N * (double) L * (double) gm->M * 1e-6 / w->user;
    esl_stopwatch_Display(stdout, w, "# CPU time: ");
    printf("# M    = %d\n", gm->M);
    printf("# %.1f Mc/s\n", Mcs);

    free(dsq);
    p7_gmx_Destroy(gx1);
    p7_gmx_Destroy(gx2);
    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;
}
Ejemplo n.º 4
0
int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 0, argc, argv, banner, usage);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  int             N       = esl_opt_GetInteger(go, "-N");
  float           origx   = 2.0;
  float           x       = origx;
  __m128          xv      = _mm_set1_ps(x);
  int             i;

  /* First, serial time. */
  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++) { x = logf(x); x = expf(x); }
  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# serial CPU time: ");
 
  /* Vector time */
  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++) { xv = esl_sse_logf(xv); xv = esl_sse_expf(xv); }
  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# vector CPU time: ");

  /* If you don't do something with x and xv, the compiler may optimize them away */
  printf("%g  => many scalar logf,expf cycles => %g\n", origx, x);
  printf("%g  => many vector logf,expf cycles => ", origx);
  esl_sse_dump_ps(stdout, xv); printf("\n");

  esl_stopwatch_Destroy(w);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 5
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS   *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  ESL_STOPWATCH *w       = esl_stopwatch_Create();
  char          *hmmfile = esl_opt_GetArg(go, 1);
  P7_HMMCACHE   *hcache  = NULL;
  char           errbuf[eslERRBUFSIZE];
  size_t         tot_mem;
  int            status;

  esl_stopwatch_Start(w);

  status = p7_hmmcache_Open(hmmfile, &hcache, errbuf);
  if      (status == eslENOTFOUND) p7_Fail("Failed to read %s\n  %s\n",           hmmfile, errbuf);
  else if (status == eslEFORMAT)   p7_Fail("Failed to parse %s\n  %s\n",          hmmfile, errbuf);
  else if (status == eslEINCOMPAT) p7_Fail("Mixed profile types in %s\n  %s\n",   hmmfile, errbuf);
  else if (status != eslOK)        p7_Fail("Failed to cache %s: error code %d\n", hmmfile, status);

  p7_hmmcache_SetNumericNames(hcache);
  tot_mem = p7_hmmcache_Sizeof(hcache);

  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("models     = %d\n",          hcache->n);
  printf("tot memory = %" PRIu64 "\n", (uint64_t) tot_mem);
  
  p7_hmmcache_Close(hcache);
  esl_getopts_Destroy(go);
  esl_stopwatch_Destroy(w);
  return 0;
}
Ejemplo n.º 6
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage);
  ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  int             N       = esl_opt_GetInteger(go, "-N");
  int             i;
  float          *A, *B, *C;

  p7_FLogsumInit();

  /* Create the problem: sample N values A,B on interval -1000,1000: about the range of H3 scores */
  A = malloc(sizeof(float) * N);
  B = malloc(sizeof(float) * N);
  C = malloc(sizeof(float) * N);
  for (i = 0; i < N; i++)
    {
      A[i] = esl_random(r) * 2000. - 1000.;
      B[i] = esl_random(r) * 2000. - 1000.;
    }
  
  /* Run */
  esl_stopwatch_Start(w);

  if (esl_opt_GetBoolean(go, "-n"))
    {
      for (i = 0; i < N; i++)
	C[i] = naive2(A[i], B[i]);
    }
  else if (esl_opt_GetBoolean(go, "-r"))
    {
      for (i = 0; i < N; i++)
	C[i] = naive1(A[i], B[i]);
    }
  else
    {
      for (i = 0; i < N; i++)
	C[i] = p7_FLogsum(A[i], B[i]);       
    }

  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");

  esl_stopwatch_Destroy(w);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 7
0
int 
main(void)
{
  ESL_STOPWATCH *w;
  
  w = esl_stopwatch_Create(); 

  esl_stopwatch_Start(w);
  sleep(5);
  esl_stopwatch_Stop(w);

  esl_stopwatch_Display(stdout, w, "CPU Time: ");
  esl_stopwatch_Destroy(w);
  return 0;
}
Ejemplo n.º 8
0
int
main(void)
{
  ESL_STOPWATCH *w = NULL;
  ESL_DMATRIX *Q  = NULL;
  ESL_DMATRIX *P  = NULL;
  double       t = 5.0;
  int          esl_iterations = 100;
  int          i;
#ifdef HAVE_LIBGSL
  gsl_matrix  *Qg = NULL;
  gsl_matrix  *Pg = NULL;
  int          gsl_iterations = 100;
#endif

  w = esl_stopwatch_Create();
  Q = esl_dmatrix_Create(20, 20);
  P = esl_dmatrix_Create(20, 20);
  esl_rmx_SetWAG(Q, NULL);

  esl_stopwatch_Start(w);
  for (i = 0; i < esl_iterations; i++)
    esl_dmx_Exp(Q, t, P);
  esl_stopwatch_Stop(w);
  printf("Easel takes:   %g sec\n", w->user / (double) esl_iterations);

#ifdef HAVE_LIBGSL
  if (esl_dmx_MorphGSL(Q, &Qg)             != eslOK) esl_fatal("morph to gsl_matrix failed");
  if ((Pg = gsl_matrix_alloc(20, 20))      == NULL)  esl_fatal("gsl alloc failed");
  gsl_matrix_scale(Qg, t);
  
  esl_stopwatch_Start(w);
  for (i = 0; i < gsl_iterations; i++)
    gsl_linalg_exponential_ss(Qg, Pg, GSL_PREC_DOUBLE);
  esl_stopwatch_Stop(w);
  printf("  GSL takes:   %g sec\n", w->user / (double) gsl_iterations);

  gsl_matrix_free(Qg);
  gsl_matrix_free(Pg);
#endif /*HAVE_LIBGSL*/

  esl_dmatrix_Destroy(Q);
  esl_dmatrix_Destroy(P);
  esl_stopwatch_Destroy(w);
  return 0;
}
Ejemplo n.º 9
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS   *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  ESL_STOPWATCH *w       = esl_stopwatch_Create();
  ESL_ALPHABET  *abc     = NULL;
  char          *hmmfile = esl_opt_GetArg(go, 1);
  P7_HMMFILE    *hfp     = NULL;
  P7_OPROFILE   *om      = NULL;
  int            nmodel  = 0;
  uint64_t       totM    = 0;
  int            status;
  char           errbuf[eslERRBUFSIZE];

  esl_stopwatch_Start(w);

  status = p7_hmmfile_OpenE(hmmfile, NULL, &hfp, errbuf);
  if      (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", hmmfile, errbuf);
  else if (status == eslEFORMAT)   p7_Fail("File format problem in trying to open HMM file %s.\n%s\n",                hmmfile, errbuf);
  else if (status != eslOK)        p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n",               status, hmmfile, errbuf);  

  while ((status = p7_oprofile_ReadMSV(hfp, &abc, &om)) == eslOK)
    {
      nmodel++;
      totM += om->M;

      p7_oprofile_Destroy(om);
    }
  if      (status == eslEFORMAT)   p7_Fail("bad file format in profile file %s",           hmmfile);
  else if (status == eslEINCOMPAT) p7_Fail("profile file %s contains different alphabets", hmmfile);
  else if (status != eslEOF)       p7_Fail("Unexpected error in reading profiles from %s", hmmfile);

  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# number of models: %d\n", nmodel);
  printf("# total M:          %" PRId64 "\n", totM);
  
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 10
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_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  int             i;

  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);

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    p7_oprofile_Convert(gm, om);
  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M = %d\n", gm->M);

  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_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 11
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS   *go      = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  ESL_STOPWATCH *w       = esl_stopwatch_Create();
  ESL_ALPHABET  *abc     = NULL;
  char          *msvfile = esl_opt_GetArg(go, 1);
  FILE          *msvfp   = NULL;
  P7_OPROFILE   *om      = NULL;
  int            nmodel  = 0;
  uint64_t       totM    = 0;
  int            status;

  esl_stopwatch_Start(w);

  if ((msvfp = fopen(msvfile, "r")) == NULL) p7_Fail("Failed to open MSV file %s for reading.\n", msvfile);

  while ((status = p7_oprofile_ReadMSV(msvfp, &abc, NULL, &om)) == eslOK)
    {
      nmodel++;
      totM += om->M;

      p7_oprofile_Destroy(om);
    }
  if      (status == eslEFORMAT)   p7_Fail("bad file format in profile file %s",           msvfile);
  else if (status == eslEINCOMPAT) p7_Fail("profile file %s contains different alphabets", msvfile);
  else if (status != eslEOF)       p7_Fail("Unexpected error in reading profiles from %s", msvfile);

  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# number of models: %d\n", nmodel);
  printf("# total M:          %" PRId64 "\n", totM);
  
  fclose(msvfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 12
0
int
main(int argc, char **argv)
{
  ESL_GETOPTS   *go        = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  ESL_STOPWATCH *w         = esl_stopwatch_Create();
  ESL_RECORDER  *rc        = NULL;
  char          *filename  = esl_opt_GetArg(go, 1);
  int            N         = esl_opt_GetInteger(go, "-N");
  FILE          *fp        = NULL;
  char          *buf       = NULL;
  int            balloc    = 0;
  int            status;
  
  if ((fp = fopen(filename, "r")) == NULL) esl_fatal("no such file %s\n", filename);
  rc = esl_recorder_Create(fp, N);
  esl_stopwatch_Start(w);
  while ((status = esl_recorder_Read(rc, &buf)) == eslOK);
  esl_recorder_Destroy(rc);
  fclose(fp);

  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "recorder time:    ");
  
  if ((fp = fopen(filename, "r")) == NULL) esl_fatal("no such file %s\n", filename);
  esl_stopwatch_Start(w);
  while ((status = esl_fgets(&buf, &balloc, fp)) == eslOK);
  free(buf);
  fclose(fp);

  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "esl_fgets() time: ");

  esl_stopwatch_Destroy(w);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 13
0
/* The LogGamma() function is rate-limiting in hmmbuild, because it is
 * used so heavily in mixture Dirichlet calculations.
 *    ./configure --with-gsl; [compile test driver]
 *    ./stats_utest -v
 * runs a comparison of time/precision against GSL.
 * SRE, Sat May 23 10:04:41 2009, on home Mac:
 *     LogGamma       = 1.29u  / N=1e8  =  13 nsec/call
 *     gsl_sf_lngamma = 1.43u  / N=1e8  =  14 nsec/call
 */
static void
utest_LogGamma(ESL_RANDOMNESS *r, int N, int be_verbose)
{
  char          *msg = "esl_stats_LogGamma() unit test failed";
  ESL_STOPWATCH *w   = esl_stopwatch_Create();
  double        *x   = malloc(sizeof(double) * N);
  double        *lg  = malloc(sizeof(double) * N);
  double        *lg2 = malloc(sizeof(double) * N);
  int            i;

  for (i = 0; i < N; i++) 
    x[i] = esl_random(r) * 100.;
  
  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++) 
    if (esl_stats_LogGamma(x[i], &(lg[i])) != eslOK) esl_fatal(msg);
  esl_stopwatch_Stop(w);

  if (be_verbose) esl_stopwatch_Display(stdout, w, "esl_stats_LogGamma() timing: ");

#ifdef HAVE_LIBGSL
  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++) lg2[i] = gsl_sf_lngamma(x[i]);
  esl_stopwatch_Stop(w);

  if (be_verbose) esl_stopwatch_Display(stdout, w, "gsl_sf_lngamma() timing:     ");
  
  for (i = 0; i < N; i++)
    if (esl_DCompare(lg[i], lg2[i], 1e-2) != eslOK) esl_fatal(msg);
#endif
  
  free(lg2);
  free(lg);
  free(x);
  esl_stopwatch_Destroy(w);
}
Ejemplo n.º 14
0
int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_ALPHABET   *abc     = esl_alphabet_Create(eslAMINO);
  P7_BG          *bg      = p7_bg_Create(abc);
  int             my_rank;
  int             nproc;
  char           *buf    = NULL;
  int             nbuf   = 0;
  int             subtotalM = 0;
  int             allM   = 0;
  int             stalling = esl_opt_GetBoolean(go, "--stall");

  MPI_Init(&argc, &argv);
  MPI_Comm_rank(MPI_COMM_WORLD, &my_rank);
  MPI_Comm_size(MPI_COMM_WORLD, &nproc);

  while (stalling); 

  /* Master MPI process: */
  if (my_rank == 0) 
    {
      ESL_STOPWATCH  *w       = esl_stopwatch_Create();
      P7_HMMFILE     *hfp     = NULL;
      P7_OPROFILE    *om      = NULL;
      P7_HMM         *hmm     = NULL;

      /* Read HMMs from a file. */
      if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);

      esl_stopwatch_Start(w);
      while (p7_oprofile_ReadMSV(hfp, &abc, &om)  == eslOK &&
	     p7_oprofile_ReadRest(hfp, om)       == eslOK)
	{
	  if (!esl_opt_GetBoolean(go, "-b"))
	    p7_oprofile_MPISend(om, 1, 0, MPI_COMM_WORLD, &buf, &nbuf); /* 1 = dest; 0 = tag */

	  p7_hmm_Destroy(hmm);
	  p7_oprofile_Destroy(om);
	}
      p7_oprofile_MPISend(NULL, 1, 0, MPI_COMM_WORLD, &buf, &nbuf); /* send the "no more HMMs" sign */
      MPI_Reduce(&subtotalM, &allM, 1, MPI_INT, MPI_SUM, 0, MPI_COMM_WORLD);

      printf("total: %d\n", allM);
      esl_stopwatch_Stop(w);
      esl_stopwatch_Display(stdout, w, "CPU Time: ");
      esl_stopwatch_Destroy(w);
    }
  /* Worker MPI process: */
  else 
    {
      P7_OPROFILE     *om_recd = NULL;      

      while (p7_oprofile_MPIRecv(0, 0, MPI_COMM_WORLD, &buf, &nbuf, &abc, &om_recd) == eslOK) 
	{
	  subtotalM += om_recd->M;
	  p7_oprofile_Destroy(om_recd);  
	}
      MPI_Reduce(&subtotalM, &allM, 1, MPI_INT, MPI_SUM, 0, MPI_COMM_WORLD);
    }

  free(buf);
  p7_bg_Destroy(bg);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  MPI_Finalize();
  exit(0);
}
Ejemplo n.º 15
0
int
main(int argc, char **argv)
{
  ESL_GETOPTS     *go	   = NULL;   
  ESL_STOPWATCH   *w       = esl_stopwatch_Create();
  struct cfg_s     cfg;

  p7_Init();

  /* Process command line options.  */
  go = esl_getopts_Create(options);
  if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK || 
      esl_opt_VerifyConfig(go)               != eslOK)
    {
      printf("Failed to parse command line: %s\n", go->errbuf);
      esl_usage(stdout, argv[0], usage);
      printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
      exit(1);
    }
  if (esl_opt_GetBoolean(go, "-h") == TRUE) 
    {
      p7_banner(stdout, argv[0], banner);
      esl_usage(stdout, argv[0], usage);
      puts("\nCommon options:");
      esl_opt_DisplayHelp(stdout, go, 1, 2, 80); /* 1=docgroup, 2 = indentation; 80=textwidth*/
      puts("\nChoice of score type :");
      esl_opt_DisplayHelp(stdout, go, 2, 2, 80); 
      puts("\nChoice of alignment mode :");
      esl_opt_DisplayHelp(stdout, go, 3, 2, 80); 
      puts("\nChoice of multi vs. unihit config :");
      esl_opt_DisplayHelp(stdout, go, 4, 2, 80); 
      puts("\nChoice of generic vs. vector DP implementation :");
      esl_opt_DisplayHelp(stdout, go, 5, 2, 80); 
      puts("\nOutput options (use only in serial mode, for single HMM input):");
      esl_opt_DisplayHelp(stdout, go, 6, 2, 80); 
      puts("\nControlling range of fitted tail masses :");
      esl_opt_DisplayHelp(stdout, go, 7, 2, 80);
      puts("\nRecalibrating E-values, and replacing HMM's existing parameters :");
      esl_opt_DisplayHelp(stdout, go, 8, 2, 80);
      puts("\nDebugging :");
      esl_opt_DisplayHelp(stdout, go, 9, 2, 80);
      puts("\nExperiments :");
      esl_opt_DisplayHelp(stdout, go, 10, 2, 80);
      exit(0);
    }
  if (esl_opt_ArgNumber(go) != 1) 
    {
      puts("Incorrect number of command line arguments.");
      esl_usage(stdout, argv[0], usage);
      puts("\nwhere general options are:");
      esl_opt_DisplayHelp(stdout, go, 1, 2, 80); /* 1=docgroup, 2 = indentation; 80=textwidth*/
      printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
      exit(1);
    }

  /* Validate combinations of score/config/implementation (4x3x2x2, score x mode x hit x DPimpl: 20 of 48 possible combos valid */
  if (esl_opt_GetBoolean(go, "--vector") && ! esl_opt_GetBoolean(go, "--local")) p7_Fail("SIMD vector implementations only work for local alignment.");    /* -16/48 */
  if (esl_opt_GetBoolean(go, "--msv")    && ! esl_opt_GetBoolean(go, "--local")) p7_Fail("MSV scoring is local by definition: use --local.");              /*  -4/48 */
  if (esl_opt_GetBoolean(go, "--vit")    && ! esl_opt_GetBoolean(go, "--local")) p7_Fail("no p7_GViterbiDual for new dual-mode profile implemented yet");  /*  -4/48 */

  /* Initialize configuration shared across all kinds of masters
   * and workers in this .c file.
   */
  cfg.hmmfile  = esl_opt_GetArg(go, 1);
  cfg.r        = esl_randomness_Create(esl_opt_GetInteger(go, "--seed"));
//  cfg.abc      = esl_alphabet_Create(eslAMINO);


  cfg.my_rank  = 0;		/* MPI init will change this soon, if --mpi was set */
  cfg.nproc    = 0;		/* MPI init will change this soon, if --mpi was set */
  cfg.do_mpi   = FALSE;		/* --mpi will change this soon (below) if necessary */
  cfg.do_stall = esl_opt_GetBoolean(go, "--stall");
  cfg.N        = esl_opt_GetInteger(go, "-N");
  cfg.L        = esl_opt_GetInteger(go, "-L");
  cfg.hfp      = NULL;
  cfg.ofp      = NULL;
  cfg.survfp   = NULL;
  cfg.efp      = NULL;
  cfg.ffp      = NULL;
  cfg.xfp      = NULL;
  cfg.alfp     = NULL;
  cfg.bg       = NULL;


  /* This is our stall point, if we need to wait until we get a
   * debugger attached to this process for debugging (especially
   * useful for MPI):
   */
  while (cfg.do_stall); 

  /* Start timing. */
  esl_stopwatch_Start(w);

  /* Main body:
   * Handed off to serial version or MPI masters and workers as appropriate.
   */
#ifdef HAVE_MPI
  if (esl_opt_GetBoolean(go, "--mpi")) 
    {
      /* Initialize MPI, figure out who we are, and whether we're running
       * this show (proc 0) or working in it (procs >0).
       */
      cfg.do_mpi = TRUE;
      MPI_Init(&argc, &argv);
      MPI_Comm_rank(MPI_COMM_WORLD, &(cfg.my_rank));
      MPI_Comm_size(MPI_COMM_WORLD, &(cfg.nproc));
      if (cfg.my_rank == 0 && cfg.nproc < 2) p7_Fail("Need at least 2 MPI processes to run --mpi mode.");

      if (cfg.my_rank > 0)   mpi_worker(go, &cfg);
      else                   mpi_master(go, &cfg);

      esl_stopwatch_Stop(w);
      esl_stopwatch_MPIReduce(w, 0, MPI_COMM_WORLD);
      MPI_Finalize();		/* both workers and masters reach this line */
    }
  else
#endif /*HAVE_MPI*/
    {		
      /* No MPI? Then we're just the serial master. */
      serial_master(go, &cfg);
      esl_stopwatch_Stop(w);
    }      

  /* Stop timing. */
  if (cfg.my_rank == 0) esl_stopwatch_Display(stdout, w, "# CPU time: ");

  /* Clean up and exit. */
  if (cfg.my_rank == 0) {
    if (cfg.hfp    != NULL)      p7_hmmfile_Close(cfg.hfp);
    if (esl_opt_IsOn(go, "-o"))  fclose(cfg.ofp); 
    if (cfg.survfp != NULL)      fclose(cfg.survfp);
    if (cfg.efp    != NULL)      fclose(cfg.efp);
    if (cfg.ffp    != NULL)      fclose(cfg.ffp);
    if (cfg.xfp    != NULL)      fclose(cfg.xfp);
    if (cfg.alfp   != NULL)      fclose(cfg.alfp);
  }
  p7_bg_Destroy(cfg.bg);
  esl_alphabet_Destroy(cfg.abc);
  esl_randomness_Destroy(cfg.r);
  esl_getopts_Destroy(go);
  esl_stopwatch_Destroy(w);
  return eslOK;
}
Ejemplo n.º 16
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;
}
Ejemplo n.º 17
0
int
main(int argc, char **argv)
{

  int i,j;

  ESL_GETOPTS     *go = NULL;	/* command line processing                 */
  ESL_STOPWATCH   *w  = esl_stopwatch_Create();

  int              status;
  ESL_MSA      *msa         = NULL;
  FILE         *ofp         = NULL;    /* output file (default is stdout) */
  ESL_ALPHABET *abc         = NULL;    /* digital alphabet */

  char         *alifile;  /* name of the alignment file we're building HMMs from  */
  ESLX_MSAFILE *afp         = NULL;            /* open alifile  */
  int           infmt       = eslMSAFILE_UNKNOWN;    /* autodetect alignment format by default. */
  int           outfmt      = eslMSAFILE_STOCKHOLM;


  char         *postmsafile;  /* optional file to resave annotated, modified MSAs to  */
  FILE         *postmsafp = NULL;  /* open <postmsafile>, or NULL */

  int           mask_range_cnt = 0;
  uint32_t      mask_starts[100]; // over-the-top allocation.
  uint32_t      mask_ends[100];

  char         *rangestr;
  char         *range;


  int     *map = NULL; /* map[i]=j,  means model position i comes from column j of the alignment; 1..alen */

  int    keep_mm;

  /* Set processor specific flags */
  impl_Init();
  alifile     = NULL;
  postmsafile = NULL;

  /* Parse the command line
   */
  process_commandline(argc, argv, &go, &alifile, &postmsafile);
  keep_mm = esl_opt_IsUsed(go, "--apendmask");

  /* Initialize what we can in the config structure (without knowing the alphabet yet).
   * Fields controlled by masters are set up in usual_master() or mpi_master()
   * Fields used by workers are set up in mpi_worker()
   */
  ofp         = NULL;
  infmt         = eslMSAFILE_UNKNOWN;
  afp         = NULL;
  abc         = NULL;

  if (esl_opt_IsOn(go, "--informat")) {
    infmt = eslx_msafile_EncodeFormat(esl_opt_GetString(go, "--informat"));
    if (infmt == eslMSAFILE_UNKNOWN) p7_Fail("%s is not a recognized input sequence file format\n", esl_opt_GetString(go, "--informat"));
  }

  /* Determine output alignment file format */
  outfmt = eslx_msafile_EncodeFormat(esl_opt_GetString(go, "--outformat"));
  if (outfmt == eslMSAFILE_UNKNOWN)    p7_Fail(argv[0], "%s is not a recognized output MSA file format\n", esl_opt_GetString(go, "--outformat"));



  /* Parse the ranges */

  if (esl_opt_IsUsed(go, "--alirange")) {
    esl_strdup(esl_opt_GetString(go, "--alirange"), -1, &rangestr) ;
  } else if (esl_opt_IsUsed(go, "--modelrange")) {
    esl_strdup(esl_opt_GetString(go, "--modelrange"), -1, &rangestr) ;
  } else if (esl_opt_IsUsed(go, "--model2ali")) {
    esl_strdup(esl_opt_GetString(go, "--model2ali"), -1, &rangestr) ;
  } else if (esl_opt_IsUsed(go, "--ali2model")) {
    esl_strdup(esl_opt_GetString(go, "--ali2model"), -1, &rangestr) ;
  } else {
    if (puts("Must specify mask range with --modelrange, --alirange, --model2ali, or --ali2model\n") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto ERROR;
  }

  while ( (status = esl_strtok(&rangestr, ",", &range) ) == eslOK) {
    status = esl_regexp_ParseCoordString(range, mask_starts + mask_range_cnt, mask_ends + mask_range_cnt );
    if (status == eslESYNTAX) esl_fatal("range flags take coords <from>..<to>; %s not recognized", range);
    if (status == eslFAIL)    esl_fatal("Failed to find <from> or <to> coord in %s", range);

    mask_range_cnt++;
  }


  /* Start timing. */
  esl_stopwatch_Start(w);


  /* Open files, set alphabet.
   *   afp       - open alignment file for input
   *   abc       - alphabet expected or guessed in ali file
   *   postmsafp - open MSA output file
   *   ofp       - optional open output file, or stdout
   */
  if      (esl_opt_GetBoolean(go, "--amino"))   abc = esl_alphabet_Create(eslAMINO);
  else if (esl_opt_GetBoolean(go, "--dna"))     abc = esl_alphabet_Create(eslDNA);
  else if (esl_opt_GetBoolean(go, "--rna"))     abc = esl_alphabet_Create(eslRNA);
  else                                          abc = NULL;
  
  status = eslx_msafile_Open(&abc, alifile, NULL, infmt, NULL, &afp);
  if (status != eslOK) eslx_msafile_OpenFailure(afp, status);

  if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) {
    postmsafp = fopen(postmsafile, "w");
    if (postmsafp == NULL) p7_Fail("Failed to MSA output file %s for writing", postmsafile);
  }

  if (esl_opt_IsUsed(go, "-o")) 
    {
      ofp = fopen(esl_opt_GetString(go, "-o"), "w");
      if (ofp == NULL) p7_Fail("Failed to open -o output file %s\n", esl_opt_GetString(go, "-o"));
    } 
  else ofp = stdout;


  /* Looks like the i/o is set up successfully...
   * Initial output to the user
   */
  output_header(go, ofp, alifile, postmsafile);                                  /* cheery output header                                */

  /* read the alignment */
  if ((status = eslx_msafile_Read(afp, &msa)) != eslOK)  eslx_msafile_ReadFailure(afp, status);


  if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) {
    /* add/modify mmline for the mask */
    if (msa->mm == NULL) {
      ESL_ALLOC(msa->mm, msa->alen);
      keep_mm = FALSE;
    }

    if (!keep_mm)
      for (i=0; i<msa->alen; i++) msa->mm[i] = '.';

  }

  // convert model coordinates to alignment coordinates, if necessary
  if (esl_opt_IsUsed(go, "--modelrange") || esl_opt_IsUsed(go, "--model2ali") || esl_opt_IsUsed(go, "--ali2model") ) {

    float symfrac = esl_opt_GetReal(go, "--symfrac");
    int do_hand  =  esl_opt_IsOn(go, "--hand");
    int L;

    //same as p7_builder relative_weights
    if      (esl_opt_IsOn(go, "--wnone")  )                  { esl_vec_DSet(msa->wgt, msa->nseq, 1.); }
    else if (esl_opt_IsOn(go, "--wgiven") )                  ;
    else if (esl_opt_IsOn(go, "--wpb")    )                  status = esl_msaweight_PB(msa);
    else if (esl_opt_IsOn(go, "--wgsc")   )                  status = esl_msaweight_GSC(msa);
    else if (esl_opt_IsOn(go, "--wblosum"))                  status = esl_msaweight_BLOSUM(msa, esl_opt_GetReal(go, "--wid"));

    if ((status =  esl_msa_MarkFragments(msa, esl_opt_GetReal(go, "--fragthresh")))           != eslOK) goto ERROR;

    //build a map of model mask coordinates to alignment coords
    ESL_ALLOC(map, sizeof(int)     * (msa->alen+1));
    L = p7_Alimask_MakeModel2AliMap(msa, do_hand, symfrac, map );


    if ( esl_opt_IsUsed(go, "--model2ali") ) {
      //print mapping
      printf ("model coordinates     alignment coordinates\n");
      for (i=0; i<mask_range_cnt; i++)
        printf ("%8d..%-8d -> %8d..%-8d\n", mask_starts[i], mask_ends[i], map[mask_starts[i]-1], map[mask_ends[i]-1]);
      /* If I wanted to, I could print all the map values independently:
        printf("\n\n-----------\n");
        printf("Map\n");
        printf("---\n");
        for (i=0; i<L; i++)
          printf("%d -> %d\n", i+1, map[i]);
      */
    } else if ( esl_opt_IsUsed(go, "--ali2model") ) {
      //print mapping  (requires scanning the inverted map
      int alistart = 0;
      int aliend = 0;
      printf ("alignment coordinates     model coordinates\n");
      for (i=0; i<mask_range_cnt; i++) {
        //find j for ali positions
        while (map[alistart] < mask_starts[i] )
          alistart++;
        aliend = alistart;
        while (map[aliend] < mask_ends[i] )
          aliend++;

        printf ("   %8d..%-8d -> %8d..%-8d\n", map[alistart], map[aliend], alistart+1, aliend+1);
      }
    } else {
      //convert the mask coords based on map
      for (i=0; i<mask_range_cnt; i++) {
          mask_starts[i] = map[mask_starts[i]-1]; //-1 because mmline is offset by one relative to the 1-base alignment
          mask_ends[i]   = map[mask_ends[i]-1];
      }
    }
  }

  if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) {
    //overwrite '.' with 'm' everywhere the range says to do it
    for (i=0; i<mask_range_cnt; i++)
      for (j=mask_starts[i]; j<=mask_ends[i]; j++)
        msa->mm[j-1] = 'm';

    if ((status = eslx_msafile_Write(postmsafp, msa, outfmt))  != eslOK) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
  }

  esl_stopwatch_Stop(w);

  if (esl_opt_IsOn(go, "-o"))  fclose(ofp);
  if (postmsafp) fclose(postmsafp);
  if (afp)   eslx_msafile_Close(afp);
  if (abc)   esl_alphabet_Destroy(abc);

  esl_getopts_Destroy(go);
  esl_stopwatch_Destroy(w);
  return 0;


  ERROR:
   return eslFAIL;
}
Ejemplo n.º 18
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_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         *ox1     = NULL;
  P7_OMX         *ox2     = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
  float           null2[p7_MAXCODE];
  int             i,j,d,pos;
  int             nsamples = 200;
  float           fsc, bsc;
  double          Mcs;

  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != 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);

  ox1 = p7_omx_Create(gm->M, L, L);
  ox2 = p7_omx_Create(gm->M, L, L);

  esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
  p7_Forward (dsq, L, om, ox1,      &fsc);

  if (esl_opt_GetBoolean(go, "-t"))
    {
      P7_TRACE *tr   = p7_trace_Create();
      float    *n2sc = malloc(sizeof(float) * (L+1));

      esl_stopwatch_Start(w);
      for (i = 0; i < N; i++)
	{ /* This is approximately what p7_domaindef.c::region_trace_ensemble() is doing: */
	  for (j = 0; j < nsamples; j++)
	    {
	      p7_StochasticTrace(r, dsq, L, om, ox1, tr);
	      p7_trace_Index(tr);
	      pos = 1; 
	      for (d = 0; d < tr->ndom; d++)
		{
		  p7_Null2_ByTrace(om, tr, tr->tfrom[d], tr->tto[d], ox2, null2);
		  for (; pos <= tr->sqfrom[d]; pos++) n2sc[pos] += 1.0;
		  for (; pos < tr->sqto[d];    pos++) n2sc[pos] += null2[dsq[pos]];
		}
	      for (; pos <= L; pos++)  n2sc[pos] += 1.0;
	      p7_trace_Reuse(tr);
	    }

	  for (pos = 1; pos <= L; pos++)
	    n2sc[pos] = logf(n2sc[pos] / nsamples);
	}
      esl_stopwatch_Stop(w);

      free(n2sc);
      p7_trace_Destroy(tr);
    }
  else
    {
      p7_Backward(dsq, L, om, ox1, ox2, &bsc);
      p7_Decoding(om, ox1, ox2, ox2);              

      esl_stopwatch_Start(w);
      for (i = 0; i < N; i++)
	p7_Null2_ByExpectation(om, ox2, null2);
      esl_stopwatch_Stop(w);
    }


  Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) w->user;
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M    = %d\n",   gm->M);
  printf("# %.1f Mc/s\n", Mcs);

  free(dsq);
  p7_omx_Destroy(ox1);
  p7_omx_Destroy(ox2);
  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;
}
Ejemplo n.º 19
0
int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go       = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage);
  ESL_STOPWATCH  *w        = esl_stopwatch_Create();
  ESL_RANDOMNESS *r        = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  int             N        = esl_opt_GetInteger(go, "-N");
  int             M        = esl_opt_GetInteger(go, "-M");
  P7_TOPHITS    **h        = NULL;
  P7_HIT         *hit      = NULL;
  double         *sortkeys = NULL;
  char            name[]   = "not_unique_name";
  char            acc[]    = "not_unique_acc";
  char            desc[]   = "Test description for the purposes of making the benchmark allocate space";
  int             i,j;
  int             status;

  /* prep work: generate our sort keys before starting to time anything    */
  ESL_ALLOC(h,        sizeof(P7_TOPHITS *) * M); /* allocate pointers for M lists */
  ESL_ALLOC(sortkeys, sizeof(double) * N * M);   
  for (i = 0; i < N*M; i++) sortkeys[i] = esl_random(r);

  esl_stopwatch_Start(w);

  /* generate M "random" lists and sort them */
  for (j = 0; j < M; j++)
  {
      h[j] = p7_tophits_Create(p7_TOPHITS_DEFAULT_INIT_ALLOC);
      for (i = 0; i < N; i++)
	{
	  p7_tophits_CreateNextHit(h[j], &hit);
	  esl_strdup(name, -1, &(hit->name));
	  esl_strdup(acc,  -1, &(hit->acc));
	  esl_strdup(desc, -1, &(hit->desc));
	  hit->sortkey    = sortkeys[j*N + i];
	  hit->score      = (float) sortkeys[j*N+i]; 
	  hit->pre_score  = 0.0;
	  hit->sum_score  = 0.0;
	  hit->lnP        = sortkeys[j*N+i];
	  hit->pre_lnP    = 0.0;
	  hit->sum_lnP    = 0.0;
	  hit->ndom       = N;
	  hit->noverlaps  = 0;
	  hit->nexpected  = 0;
	  hit->flags      = 0;
	  hit->nreported  = 0;
	  hit->nincluded  = 0;
	  hit->best_domain = 0;
	  hit->dcl         = NULL;
	}
      p7_tophits_SortBySortkey(h[j]);
  }
  /* then merge them into one big list in h[0] */
  for (j = 1; j < M; j++)
  {
      p7_tophits_Merge(h[0], h[j]);
      p7_tophits_Destroy(h[j]);
  }

  esl_stopwatch_Stop(w);

  p7_tophits_Destroy(h[0]);
  status = eslOK;
 ERROR:
  esl_getopts_Destroy(go);
  esl_stopwatch_Destroy(w);
  esl_randomness_Destroy(r);
  if (sortkeys != NULL) free(sortkeys);
  if (h != NULL) free(h);
  return status;
}
Ejemplo n.º 20
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_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_GMX         *gx1     = NULL;
  P7_GMX         *gx2     = NULL;
  P7_TRACE       *tr      = 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           fsc, bsc, accscore;
  double          Mcs;

  p7_FLogsumInit();

  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != 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_UNILOCAL);
  gx1 = p7_gmx_Create(gm->M, L);
  gx2 = p7_gmx_Create(gm->M, L);
  tr  = p7_trace_CreateWithPP();

  esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
  p7_GForward (dsq, L, gm, gx1, &fsc);
  p7_GBackward(dsq, L, gm, gx2, &bsc);
  p7_GDecoding(gm, gx1, gx2, gx2);                   /* <gx2> is now the posterior decoding matrix */

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    {
      p7_GOptimalAccuracy(gm, gx2, gx1, &accscore);	     /* <gx1> is now the OA matrix */

      if (! esl_opt_GetBoolean(go, "--notrace"))
	{
	  p7_GOATrace(gm, gx2, gx1, tr);
	  p7_trace_Reuse(tr);
	}
    }
  esl_stopwatch_Stop(w);
  Mcs        = (double) N * (double) L * (double) gm->M * 1e-6 / w->user;
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M    = %d\n", gm->M);
  printf("# %.1f Mc/s\n", Mcs);

  free(dsq);
  p7_trace_Destroy(tr);
  p7_gmx_Destroy(gx1);
  p7_gmx_Destroy(gx2);
  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;
}
Ejemplo n.º 21
0
static void 
scan_thread(void *arg)
{
  int               i;
  int               count;
  int               workeridx;
  WORKER_INFO      *info;
  ESL_THREADS      *obj;

  ESL_STOPWATCH    *w;

  P7_BG            *bg       = NULL;         /* null model                     */
  P7_PIPELINE      *pli      = NULL;         /* work pipeline                  */
  P7_TOPHITS       *th       = NULL;         /* top hit results                */

  obj = (ESL_THREADS *) arg;
  esl_threads_Started(obj, &workeridx);

  info = (WORKER_INFO *) esl_threads_GetData(obj, workeridx);

  w = esl_stopwatch_Create();
  esl_stopwatch_Start(w);

  /* Convert to an optimized model */
  bg = p7_bg_Create(info->abc);

  /* Create processing pipeline and hit list */
  th  = p7_tophits_Create(); 
  pli = p7_pipeline_Create(info->opts, 100, 100, FALSE, p7_SCAN_MODELS);

  p7_pli_NewSeq(pli, info->seq);

  /* loop until all sequences have been processed */
  count = 1;
  while (count > 0) {
    int           inx;
    int          blksz;
    P7_OPROFILE **om;

    /* grab the next block of sequences */
    if (pthread_mutex_lock(info->inx_mutex) != 0) p7_Fail("mutex lock failed");
    inx   = *info->inx;
    blksz = *info->blk_size;
    if (inx > *info->limit) {
      blksz /= 5;
      if (blksz < 1000) {
        *info->limit = info->om_cnt * 2;
      } else {
        *info->limit = inx + (info->om_cnt - inx) * 2 / 3; 
      }
    }
    *info->blk_size = blksz;
    *info->inx += blksz;
    if (pthread_mutex_unlock(info->inx_mutex) != 0) p7_Fail("mutex unlock failed");

    om    = info->om_list + inx;
    count = info->om_cnt - inx;
    if (count > blksz) count = blksz;

    /* Main loop: */
    for (i = 0; i < count; ++i, ++om) {
      p7_pli_NewModel(pli, *om, bg);
      p7_bg_SetLength(bg, info->seq->n);
      p7_oprofile_ReconfigLength(*om, info->seq->n);
	      
      p7_Pipeline(pli, *om, bg, info->seq, th);
      p7_pipeline_Reuse(pli);
    }
  }

  /* make available the pipeline objects to the main thread */
  info->th = th;
  info->pli = pli;

  /* clean up */
  p7_bg_Destroy(bg);

  esl_stopwatch_Stop(w);
  info->elapsed = w->elapsed;

  esl_stopwatch_Destroy(w);

  esl_threads_Finished(obj, workeridx);

  pthread_exit(NULL);
  return;
}
Ejemplo n.º 22
0
static void 
search_thread(void *arg)
{
  int               i;
  int               count;
  int               seed;
  int               status;
  int               workeridx;
  WORKER_INFO      *info;
  ESL_THREADS      *obj;
  ESL_SQ            dbsq;
  ESL_STOPWATCH    *w        = NULL;         /* timing stopwatch               */
  P7_BUILDER       *bld      = NULL;         /* HMM construction configuration */
  P7_BG            *bg       = NULL;         /* null model                     */
  P7_PIPELINE      *pli      = NULL;         /* work pipeline                  */
  P7_TOPHITS       *th       = NULL;         /* top hit results                */
  P7_PROFILE       *gm       = NULL;         /* generic model                  */
  P7_OPROFILE      *om       = NULL;         /* optimized query profile        */

  obj = (ESL_THREADS *) arg;
  esl_threads_Started(obj, &workeridx);

  info = (WORKER_INFO *) esl_threads_GetData(obj, workeridx);
  w    = esl_stopwatch_Create();
  bg   = p7_bg_Create(info->abc);
  esl_stopwatch_Start(w);

  /* set up the dummy description and accession fields */
  dbsq.desc = "";
  dbsq.acc  = "";

  /* process a query sequence or hmm */
  if (info->seq != NULL) {
    bld = p7_builder_Create(NULL, info->abc);
    if ((seed = esl_opt_GetInteger(info->opts, "--seed")) > 0) {
      esl_randomness_Init(bld->r, seed);
      bld->do_reseeding = TRUE;
    }
    bld->EmL = esl_opt_GetInteger(info->opts, "--EmL");
    bld->EmN = esl_opt_GetInteger(info->opts, "--EmN");
    bld->EvL = esl_opt_GetInteger(info->opts, "--EvL");
    bld->EvN = esl_opt_GetInteger(info->opts, "--EvN");
    bld->EfL = esl_opt_GetInteger(info->opts, "--EfL");
    bld->EfN = esl_opt_GetInteger(info->opts, "--EfN");
    bld->Eft = esl_opt_GetReal   (info->opts, "--Eft");

    if (esl_opt_IsOn(info->opts, "--mxfile")) status = p7_builder_SetScoreSystem (bld, esl_opt_GetString(info->opts, "--mxfile"), NULL, esl_opt_GetReal(info->opts, "--popen"), esl_opt_GetReal(info->opts, "--pextend"), bg);
    else                                      status = p7_builder_LoadScoreSystem(bld, esl_opt_GetString(info->opts, "--mx"),           esl_opt_GetReal(info->opts, "--popen"), esl_opt_GetReal(info->opts, "--pextend"), bg); 
    if (status != eslOK) {
      //client_error(info->sock, status, "hmmgpmd: failed to set single query sequence score system: %s", bld->errbuf);
      fprintf(stderr, "hmmpgmd: failed to set single query sequence score system: %s", bld->errbuf);
      pthread_exit(NULL);
      return;
    }
    p7_SingleBuilder(bld, info->seq, bg, NULL, NULL, NULL, &om); /* bypass HMM - only need model */
    p7_builder_Destroy(bld);
  } else {
    gm = p7_profile_Create (info->hmm->M, info->abc);
    om = p7_oprofile_Create(info->hmm->M, info->abc);
    p7_ProfileConfig(info->hmm, bg, gm, 100, p7_LOCAL);
    p7_oprofile_Convert(gm, om);
  }

  /* Create processing pipeline and hit list */
  th  = p7_tophits_Create(); 
  pli = p7_pipeline_Create(info->opts, om->M, 100, FALSE, p7_SEARCH_SEQS);
  p7_pli_NewModel(pli, om, bg);

  if (pli->Z_setby == p7_ZSETBY_NTARGETS) pli->Z = info->db_Z;

  /* loop until all sequences have been processed */
  count = 1;
  while (count > 0) {
    int          inx;
    int          blksz;
    HMMER_SEQ  **sq;

    /* grab the next block of sequences */
    if (pthread_mutex_lock(info->inx_mutex) != 0) p7_Fail("mutex lock failed");
    inx = *info->inx;
    blksz = *info->blk_size;
    if (inx > *info->limit) {
      blksz /= 5;
      if (blksz < 1000) {
        *info->limit = info->sq_cnt * 2;
      } else {
        *info->limit = inx + (info->sq_cnt - inx) * 2 / 3; 
      }
    }
    *info->blk_size = blksz;
    *info->inx += blksz;
    if (pthread_mutex_unlock(info->inx_mutex) != 0) p7_Fail("mutex unlock failed");

    sq = info->sq_list + inx;

    count = info->sq_cnt - inx;
    if (count > blksz) count = blksz;

    /* Main loop: */
    for (i = 0; i < count; ++i, ++sq) {
      if ( !(info->range_list) || hmmpgmd_IsWithinRanges ((*sq)->idx, info->range_list)) {
        dbsq.name  = (*sq)->name;
        dbsq.dsq   = (*sq)->dsq;
        dbsq.n     = (*sq)->n;
        dbsq.idx   = (*sq)->idx;
        if((*sq)->desc != NULL) dbsq.desc  = (*sq)->desc;

        p7_bg_SetLength(bg, dbsq.n);
        p7_oprofile_ReconfigLength(om, dbsq.n);

        p7_Pipeline(pli, om, bg, &dbsq, th);

        p7_pipeline_Reuse(pli);
      }
    }
  }

  /* make available the pipeline objects to the main thread */
  info->th = th;
  info->pli = pli;

  /* clean up */
  p7_bg_Destroy(bg);
  p7_oprofile_Destroy(om);

  if (gm != NULL)  p7_profile_Destroy(gm);

  esl_stopwatch_Stop(w);
  info->elapsed = w->elapsed;

  esl_stopwatch_Destroy(w);

  esl_threads_Finished(obj, workeridx);

  pthread_exit(NULL);
  return;
}
Ejemplo n.º 23
0
static void 
process_SearchCmd(HMMD_COMMAND *cmd, WORKER_ENV *env)
{ 
  int              i;
  int              cnt;
  int              limit;
  int              status;
  int              blk_size;
  WORKER_INFO     *info       = NULL;
  ESL_ALPHABET    *abc;
  ESL_STOPWATCH   *w;
  ESL_THREADS     *threadObj  = NULL;
  pthread_mutex_t  inx_mutex;
  int              current_index;
  QUEUE_DATA      *query      = NULL;
  time_t           date;
  char             timestamp[32];

  w = esl_stopwatch_Create();
  abc = esl_alphabet_Create(eslAMINO);

  if (pthread_mutex_init(&inx_mutex, NULL) != 0) p7_Fail("mutex init failed");
  ESL_ALLOC(info, sizeof(*info) * env->ncpus);

  /* Log the current time (at search start) */
  date = time(NULL);
  ctime_r(&date, timestamp);
  printf("\n%s", timestamp);	/* note that ctime_r() leaves \n on end of timestamp  */

  /* initialize thread data */
  query = process_QueryCmd(cmd, env);
  esl_stopwatch_Start(w);

  info->range_list = NULL;
  if (esl_opt_IsUsed(query->opts, "--seqdb_ranges")) {
    ESL_ALLOC(info->range_list, sizeof(RANGE_LIST));
    hmmpgmd_GetRanges(info->range_list, esl_opt_GetString(query->opts, "--seqdb_ranges"));
  }


  if (query->cmd_type == HMMD_CMD_SEARCH) threadObj = esl_threads_Create(&search_thread);
  else                                    threadObj = esl_threads_Create(&scan_thread);

  if (query->query_type == HMMD_SEQUENCE) {
    fprintf(stdout, "Search seq %s  [L=%ld]", query->seq->name, (long) query->seq->n);
  } else {
    fprintf(stdout, "Search hmm %s  [M=%d]", query->hmm->name, query->hmm->M);
  }
  fprintf(stdout, " vs %s DB %d [%d - %d]",
          (query->cmd_type == HMMD_CMD_SEARCH) ? "SEQ" : "HMM", 
          query->dbx, query->inx, query->inx + query->cnt - 1);

  if (info->range_list)
    fprintf(stdout, " in range(s) %s", esl_opt_GetString(query->opts, "--seqdb_ranges"));

  fprintf(stdout, "\n");

  /* Create processing pipeline and hit list */
  for (i = 0; i < env->ncpus; ++i) {
    info[i].abc   = query->abc;
    info[i].hmm   = query->hmm;
    info[i].seq   = query->seq;
    info[i].opts  = query->opts;

    info[i].range_list  = info[0].range_list;

    info[i].th    = NULL;
    info[i].pli   = NULL;

    info[i].inx_mutex = &inx_mutex;
    info[i].inx       = &current_index;/* this is confusing trickery - to share a single variable across all threads */
    info[i].blk_size  = &blk_size;     /* ditto */
    info[i].limit     = &limit;	       /* ditto. TODO: come back and clean this up. */

    if (query->cmd_type == HMMD_CMD_SEARCH) {
      HMMER_SEQ **list  = env->seq_db->db[query->dbx].list;
      info[i].sq_list   = &list[query->inx];
      info[i].sq_cnt    = query->cnt;
      info[i].db_Z      = env->seq_db->db[query->dbx].K;
      info[i].om_list   = NULL;
      info[i].om_cnt    = 0;
    } else {
      info[i].sq_list   = NULL;
      info[i].sq_cnt    = 0;
      info[i].db_Z      = 0;
      info[i].om_list   = &env->hmm_db->list[query->inx];
      info[i].om_cnt    = query->cnt;
    }

    esl_threads_AddThread(threadObj, &info[i]);
  }

  /* try block size of 5000.  we will need enough sequences for four
   * blocks per thread or better.
   */
  blk_size = 5000;
  cnt = query->cnt / env->ncpus / blk_size;
  limit = query->cnt * 2 / 3;
  if (cnt < 4) {
    /* try block size of 1000  */
    blk_size /= 5;
    cnt = query->cnt / env->ncpus / blk_size;
    if (cnt < 4) {
      /* still not enough.  just divide it up into one block per thread */
      blk_size = query->cnt / env->ncpus + 1;
      limit = query->cnt * 2;
    }
  }
  current_index = 0;

  esl_threads_WaitForStart(threadObj);
  esl_threads_WaitForFinish(threadObj);

  esl_stopwatch_Stop(w);
#if 1
  fprintf (stdout, "   Sequences  Residues                              Elapsed\n");
  for (i = 0; i < env->ncpus; ++i) {
    print_timings(i, info[i].elapsed, info[i].pli);
  }
#endif
  /* merge the results of the search results */
  for (i = 1; i < env->ncpus; ++i) {
    p7_tophits_Merge(info[0].th, info[i].th);
    p7_pipeline_Merge(info[0].pli, info[i].pli);
    p7_pipeline_Destroy(info[i].pli);
    p7_tophits_Destroy(info[i].th);
  }

  print_timings(99, w->elapsed, info[0].pli);
  send_results(env->fd, w, info);

  /* free the last of the pipeline data */
  p7_pipeline_Destroy(info->pli);
  p7_tophits_Destroy(info->th);

  free_QueueData(query);

  esl_threads_Destroy(threadObj);

  pthread_mutex_destroy(&inx_mutex);

  if (info->range_list) {
    if (info->range_list->starts)  free(info->range_list->starts);
    if (info->range_list->ends)    free(info->range_list->ends);
    free (info->range_list);
  }

  free(info);

  esl_stopwatch_Destroy(w);
  esl_alphabet_Destroy(abc);

  return;

 ERROR:
  LOG_FATAL_MSG("malloc", errno);
}
Ejemplo n.º 24
0
int
main(int argc, char **argv)
{
  ESL_GETOPTS     *go = NULL;	/* command line processing                 */
  ESL_STOPWATCH   *w  = esl_stopwatch_Create();
  struct cfg_s     cfg;

  /* Set processor specific flags */
  impl_Init();

  cfg.alifile     = NULL;
  cfg.hmmfile     = NULL;

  /* Parse the command line
   */
  process_commandline(argc, argv, &go, &cfg.hmmfile, &cfg.alifile);    

  /* Initialize what we can in the config structure (without knowing the alphabet yet) 
   */
  cfg.ofp         = NULL;	           /* opened in init_master_cfg() */
  cfg.fmt         = eslMSAFILE_UNKNOWN;     /* autodetect alignment format by default. */ 
  cfg.afp         = NULL;	           /* created in init_master_cfg() */
  cfg.abc         = NULL;	           /* created in init_master_cfg() in masters, or in mpi_worker() in workers */
  cfg.hmmfp       = NULL;	           /* opened in init_master_cfg() */
  cfg.postmsafile = esl_opt_GetString(go, "-O"); /* NULL by default */
  cfg.postmsafp   = NULL;                  /* opened in init_master_cfg() */

  cfg.nali       = 0;		           /* this counter is incremented in masters */
  cfg.nnamed     = 0;		           /* 0 or 1 if a single MSA; == nali if multiple MSAs */
  cfg.do_mpi     = FALSE;	           /* this gets reset below, if we init MPI */
  cfg.nproc      = 0;		           /* this gets reset below, if we init MPI */
  cfg.my_rank    = 0;		           /* this gets reset below, if we init MPI */
  cfg.do_stall   = esl_opt_GetBoolean(go, "--stall");
  cfg.hmmName    = esl_opt_GetString(go, "-n"); /* NULL by default */

  if (esl_opt_IsOn(go, "--informat")) {
    cfg.fmt = esl_msa_EncodeFormat(esl_opt_GetString(go, "--informat"));
    if (cfg.fmt == eslMSAFILE_UNKNOWN) p7_Fail("%s is not a recognized input sequence file format\n", esl_opt_GetString(go, "--informat"));
  }

  /* This is our stall point, if we need to wait until we get a
   * debugger attached to this process for debugging (especially
   * useful for MPI):
   */
  while (cfg.do_stall); 

  /* Start timing. */
  esl_stopwatch_Start(w);

  /* Figure out who we are, and send control there: 
   * we might be an MPI master, an MPI worker, or a serial program.
   */
#ifdef HAVE_MPI
  if (esl_opt_GetBoolean(go, "--mpi")) 
    {
      cfg.do_mpi     = TRUE;
      MPI_Init(&argc, &argv);
      MPI_Comm_rank(MPI_COMM_WORLD, &(cfg.my_rank));
      MPI_Comm_size(MPI_COMM_WORLD, &(cfg.nproc));

      if (cfg.my_rank > 0)  mpi_worker(go, &cfg);
      else 		    mpi_master(go, &cfg);

      esl_stopwatch_Stop(w);
      esl_stopwatch_MPIReduce(w, 0, MPI_COMM_WORLD);
      MPI_Finalize();
    }
  else
#endif /*HAVE_MPI*/
    {
      serial_master(go, &cfg);
      esl_stopwatch_Stop(w);
    }

  if (cfg.my_rank == 0) {
    fputc('\n', cfg.ofp);
    esl_stopwatch_Display(cfg.ofp, w, "# CPU time: ");
  }


  /* Clean up the shared cfg. 
   */
  if (cfg.my_rank == 0) {
    if (esl_opt_IsOn(go, "-o")) { fclose(cfg.ofp); }
    if (cfg.afp   != NULL) esl_msafile_Close(cfg.afp);
    if (cfg.abc   != NULL) esl_alphabet_Destroy(cfg.abc);
    if (cfg.hmmfp != NULL) fclose(cfg.hmmfp);
  }
  esl_getopts_Destroy(go);
  esl_stopwatch_Destroy(w);
  return 0;
}
Ejemplo n.º 25
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_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_GMX         *gx1     = NULL;
  P7_GMX         *gx2     = NULL;
  P7_OMX         *ox1     = NULL;
  P7_OMX         *ox2     = NULL;
  P7_TRACE       *tr      = 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           fsc, bsc, accscore;
  float           fsc_g, bsc_g, accscore_g;
  double          Mcs;

  p7_FLogsumInit();

  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != 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_FLogsumError(-0.4, -0.5) > 0.0001)
    p7_Fail("-x here requires p7_Logsum() recompiled in slow exact mode");

  ox1 = p7_omx_Create(gm->M, L, L);
  ox2 = p7_omx_Create(gm->M, L, L);
  tr  = p7_trace_CreateWithPP();

  esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
  p7_Forward (dsq, L, om, ox1,      &fsc);
  p7_Backward(dsq, L, om, ox1, ox2, &bsc);
  p7_Decoding(om, ox1, ox2, ox2);              

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    {
      p7_OptimalAccuracy(om, ox2, ox1, &accscore);

      if (! esl_opt_GetBoolean(go, "--notrace"))
	{
	  p7_OATrace(om, ox2, ox1, tr);
	  p7_trace_Reuse(tr);
	}
    }
  esl_stopwatch_Stop(w);

  Mcs        = (double) N * (double) L * (double) gm->M * 1e-6 / (double) w->user;
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M    = %d\n",   gm->M);
  printf("# %.1f Mc/s\n", Mcs);

  if (esl_opt_GetBoolean(go, "-c") || esl_opt_GetBoolean(go, "-x") )
    {
      gx1 = p7_gmx_Create(gm->M, L);
      gx2 = p7_gmx_Create(gm->M, L);
      
      p7_GForward (dsq, L, gm, gx1, &fsc_g);
      p7_GBackward(dsq, L, gm, gx2, &bsc_g);
      p7_GDecoding(gm, gx1, gx2, gx2);             
      p7_GOptimalAccuracy(gm, gx2, gx1, &accscore_g);

      printf("generic:  fwd=%8.4f  bck=%8.4f  acc=%8.4f\n", fsc_g, bsc_g, accscore_g);
      printf("VMX:      fwd=%8.4f  bck=%8.4f  acc=%8.4f\n", fsc,   bsc,   accscore);

      p7_gmx_Destroy(gx1);
      p7_gmx_Destroy(gx2);
    }

  free(dsq);
  p7_omx_Destroy(ox1);
  p7_omx_Destroy(ox2);
  p7_trace_Destroy(tr);
  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;
}
Ejemplo n.º 26
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_GMX         *gx      = NULL;
  P7_OMX         *fwd     = NULL;
  P7_TRACE       *tr      = 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           sc, fsc, vsc;
  float           bestsc  = -eslINFINITY;
  
  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_UNILOCAL);
  om = p7_oprofile_Create(gm->M, abc);   p7_oprofile_Convert(gm, om);

  fwd = p7_omx_Create(gm->M, L, L);
  gx  = p7_gmx_Create(gm->M, L);
  tr  = p7_trace_Create();
  esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);

  p7_GViterbi(dsq, L, gm, gx,  &vsc);
  p7_Forward (dsq, L, om, fwd, &fsc);

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    {
      p7_StochasticTrace(r, dsq, L, om, fwd, tr);
      p7_trace_Score(tr, dsq, gm, &sc);
      bestsc = ESL_MAX(bestsc, sc);
      p7_trace_Reuse(tr);
    }
  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");

  printf("forward sc   = %.4f nats\n", fsc);
  printf("viterbi sc   = %.4f nats\n", vsc);
  printf("max trace sc = %.4f nats\n", bestsc);

  free(dsq);
  p7_trace_Destroy(tr);
  p7_gmx_Destroy(gx);
  p7_omx_Destroy(fwd);
  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;
}
Ejemplo n.º 27
0
/* serial_master()
 * The serial version of hmmsearch.
 * For each query HMM in <hmmdb> search the database for hits.
 * 
 * A master can only return if it's successful. All errors are handled
 * immediately and fatally with p7_Fail().
 */
static int
serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
{
  FILE            *ofp      = stdout;	         /* output file for results (default stdout)        */
  FILE            *tblfp    = NULL;		 /* output stream for tabular per-seq (--tblout)    */
  FILE            *dfamtblfp    = NULL;            /* output stream for tabular Dfam format (--dfamtblout)    */
  FILE            *aliscoresfp  = NULL;            /* output stream for alignment scores (--aliscoresout)    */

//  P7_HMM          *hmm        = NULL;              /* one HMM query                                   */
//  P7_SCOREDATA    *scoredata  = NULL;

  int              seqfmt   = eslSQFILE_UNKNOWN; /* format of seqfile                               */
  ESL_SQFILE      *sqfp     = NULL;              /* open seqfile                                    */
  P7_HMMFILE      *hfp      = NULL;		 /* open HMM database file                          */
  ESL_ALPHABET    *abc      = NULL;              /* sequence alphabet                               */
  P7_OPROFILE     *om       = NULL;		 /* target profile                                  */
  ESL_STOPWATCH   *w        = NULL;              /* timing                                          */
  ESL_SQ          *qsq      = NULL;		 /* query sequence                                  */
  int              nquery   = 0;
  int              textw;
  int              status   = eslOK;
  int              hstatus  = eslOK;
  int              sstatus  = eslOK;
  int              i;

  int              ncpus    = 0;

  int              infocnt  = 0;
  WORKER_INFO     *info     = NULL;
#ifdef HMMER_THREADS
  P7_OM_BLOCK     *block    = NULL;
  ESL_THREADS     *threadObj= NULL;
  ESL_WORK_QUEUE  *queue    = NULL;
#endif
  char             errbuf[eslERRBUFSIZE];

  double window_beta = -1.0 ;
  int window_length  = -1;
  if (esl_opt_IsUsed(go, "--w_beta")) { if (  ( window_beta   = esl_opt_GetReal(go, "--w_beta") )  < 0 || window_beta > 1  ) esl_fatal("Invalid window-length beta value\n"); }
  if (esl_opt_IsUsed(go, "--w_length")) { if (( window_length = esl_opt_GetInteger(go, "--w_length")) < 4  ) esl_fatal("Invalid window length value\n"); }


  w = esl_stopwatch_Create();

  if (esl_opt_GetBoolean(go, "--notextw")) textw = 0;
  else                                     textw = esl_opt_GetInteger(go, "--textw");

  /* If caller declared an input format, decode it */
  if (esl_opt_IsOn(go, "--qformat")) {
    seqfmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--qformat"));
    if (seqfmt == eslSQFILE_UNKNOWN) p7_Fail("%s is not a recognized input sequence file format\n", esl_opt_GetString(go, "--qformat"));
  }

  /* validate options if running as a daemon */
//  if (esl_opt_IsOn(go, "--daemon")) {
    /* running as a daemon, the input format must be type daemon */
//    if (seqfmt != eslSQFILE_UNKNOWN && seqfmt != eslSQFILE_DAEMON)
//      esl_fatal("Input format %s not supported.  Must be daemon\n", esl_opt_GetString(go, "--qformat"));
//    seqfmt = eslSQFILE_DAEMON;

//    if (strcmp(cfg->seqfile, "-") != 0) esl_fatal("Query sequence file must be '-'\n");
//  }

  /* Open the target profile database to get the sequence alphabet */
  status = p7_hmmfile_OpenE(cfg->hmmfile, p7_HMMDBENV, &hfp, errbuf);
  if      (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", cfg->hmmfile, errbuf);
  else if (status == eslEFORMAT)   p7_Fail("File format problem, trying to open HMM file %s.\n%s\n",                  cfg->hmmfile, errbuf);
  else if (status != eslOK)        p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n",               status, cfg->hmmfile, errbuf);  
  if (! hfp->is_pressed)           p7_Fail("Failed to open binary auxfiles for %s: use hmmpress first\n",             hfp->fname);

  hstatus = p7_oprofile_ReadMSV(hfp, &abc, &om);
  if      (hstatus == eslEFORMAT)   p7_Fail("bad format, binary auxfiles, %s:\n%s",     cfg->hmmfile, hfp->errbuf);
  else if (hstatus == eslEINCOMPAT) p7_Fail("HMM file %s contains different alphabets", cfg->hmmfile);
  else if (hstatus != eslOK)        p7_Fail("Unexpected error in reading HMMs from %s", cfg->hmmfile); 

  p7_oprofile_Destroy(om);
  p7_hmmfile_Close(hfp);

  /* Open the query sequence database */
  status = esl_sqfile_OpenDigital(abc, cfg->seqfile, seqfmt, NULL, &sqfp);
  if      (status == eslENOTFOUND) p7_Fail("Failed to open sequence file %s for reading\n",      cfg->seqfile);
  else if (status == eslEFORMAT)   p7_Fail("Sequence file %s is empty or misformatted\n",        cfg->seqfile);
  else if (status == eslEINVAL)    p7_Fail("Can't autodetect format of a stdin or .gz seqfile");
  else if (status != eslOK)        p7_Fail("Unexpected error %d opening sequence file %s\n", status, cfg->seqfile);
  if (sqfp->format > 100) // breaking the law!  That range is reserved for msa, for aligned formats
    p7_Fail("%s contains a multiple sequence alignment; expect unaligned sequences, like FASTA\n",   cfg->seqfile);
  qsq = esl_sq_CreateDigital(abc);


  /* Open the results output files */
  if (esl_opt_IsOn(go, "-o"))          { if ((ofp      = fopen(esl_opt_GetString(go, "-o"),          "w")) == NULL)  esl_fatal("Failed to open output file %s for writing\n",                 esl_opt_GetString(go, "-o")); }
  if (esl_opt_IsOn(go, "--tblout"))    { if ((tblfp    = fopen(esl_opt_GetString(go, "--tblout"),    "w")) == NULL)  esl_fatal("Failed to open tabular per-seq output file %s for writing\n", esl_opt_GetString(go, "--tblfp")); }
  if (esl_opt_IsOn(go, "--dfamtblout"))    { if ((dfamtblfp    = fopen(esl_opt_GetString(go, "--dfamtblout"),"w"))    == NULL)  esl_fatal("Failed to open tabular dfam output file %s for writing\n", esl_opt_GetString(go, "--dfamtblout")); }
  if (esl_opt_IsOn(go, "--aliscoresout"))  { if ((aliscoresfp  = fopen(esl_opt_GetString(go, "--aliscoresout"),"w")) == NULL)  esl_fatal("Failed to open alignment scores output file %s for writing\n", esl_opt_GetString(go, "--aliscoresout")); }
 
  output_header(ofp, go, cfg->hmmfile, cfg->seqfile);

#ifdef HMMER_THREADS
  /* initialize thread data */
  if (esl_opt_IsOn(go, "--cpu")) ncpus = esl_opt_GetInteger(go, "--cpu");
  else                           esl_threads_CPUCount(&ncpus);

  if (ncpus > 0)
    {
      threadObj = esl_threads_Create(&pipeline_thread);
      queue = esl_workqueue_Create(ncpus * 2);
    }
#endif

  infocnt = (ncpus == 0) ? 1 : ncpus;
  ESL_ALLOC(info, sizeof(*info) * infocnt);

  for (i = 0; i < infocnt; ++i)
    {
      info[i].bg    = p7_bg_Create(abc);
#ifdef HMMER_THREADS
      info[i].queue = queue;
#endif
    }

#ifdef HMMER_THREADS
  for (i = 0; i < ncpus * 2; ++i)
    {
      block = p7_oprofile_CreateBlock(BLOCK_SIZE);
      if (block == NULL)    esl_fatal("Failed to allocate sequence block");

      status = esl_workqueue_Init(queue, block);
      if (status != eslOK)  esl_fatal("Failed to add block to work queue");
    }
#endif

  /* Outside loop: over each query sequence in <seqfile>. */
  while ((sstatus = esl_sqio_Read(sqfp, qsq)) == eslOK)
  {
      if (sstatus == eslEMEM)                 p7_Fail("Memory allocation error reading sequence file\n", status);
      if (sstatus == eslEINCONCEIVABLE)       p7_Fail("Unexpected error %d reading sequence file\n", status);
     // if (qsq->L > NHMMER_MAX_RESIDUE_COUNT)  p7_Fail("Input sequence %s in file %s exceeds maximum length of %d bases.\n",  qsq->name, cfg->seqfile, NHMMER_MAX_RESIDUE_COUNT);

      nquery++;
      esl_stopwatch_Start(w);	                          

      /* Open the target profile database */
      status = p7_hmmfile_OpenE(cfg->hmmfile, p7_HMMDBENV, &hfp, NULL);
      if (status != eslOK)        p7_Fail("Unexpected error %d in opening hmm file %s.\n",           status, cfg->hmmfile);  
  
#ifdef HMMER_THREADS
      /* if we are threaded, create a lock to prevent multiple readers */
      if (ncpus > 0)
      {
        status = p7_hmmfile_CreateLock(hfp);
        if (status != eslOK) p7_Fail("Unexpected error %d creating lock\n", status);
      }
#endif

      if (fprintf(ofp, "Query:       %s  [L=%ld]\n", qsq->name, (long) qsq->n) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
      if (qsq->acc[0]  != 0 && fprintf(ofp, "Accession:   %s\n", qsq->acc)     < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
      if (qsq->desc[0] != 0 && fprintf(ofp, "Description: %s\n", qsq->desc)    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");

      for (i = 0; i < infocnt; ++i)
      {
        /* Create processing pipeline and hit list */
        info[i].th  = p7_tophits_Create();
        info[i].pli = p7_pipeline_Create(go, 100, 100, TRUE, p7_SCAN_MODELS); /* M_hint = 100, L_hint = 100 are just dummies for now */
        info[i].pli->hfp = hfp;  /* for two-stage input, pipeline needs <hfp> */


        p7_pli_NewSeq(info[i].pli, qsq);
        info[i].qsq = qsq;

        if (  esl_opt_IsUsed(go, "--toponly") )
          info[i].pli->strand = p7_STRAND_TOPONLY;
        else if (  esl_opt_IsUsed(go, "--bottomonly") )
          info[i].pli->strand = p7_STRAND_BOTTOMONLY;
        else
          info[i].pli->strand = p7_STRAND_BOTH;


        #ifdef HMMER_THREADS
          if (ncpus > 0) esl_threads_AddThread(threadObj, &info[i]);
        #endif
      }

#ifdef HMMER_THREADS
      if (ncpus > 0)  hstatus = thread_loop(threadObj, queue, hfp);
      else	      hstatus = serial_loop(info, hfp);
#else
      hstatus = serial_loop(info, hfp);
#endif
      switch(hstatus)
      {
        case eslEFORMAT:   p7_Fail("bad file format in HMM file %s",             cfg->hmmfile);	  break;
        case eslEINCOMPAT: p7_Fail("HMM file %s contains different alphabets",   cfg->hmmfile);	  break;
        case eslEOF:
        case eslOK:   /* do nothing */
          break;
        default: 	   p7_Fail("Unexpected error in reading HMMs from %s",   cfg->hmmfile);
      }



      /* merge the results of the search results */
      for (i = 1; i < infocnt; ++i)
      {
        p7_tophits_Merge(info[0].th, info[i].th);
        p7_pipeline_Merge(info[0].pli, info[i].pli);

        p7_pipeline_Destroy(info[i].pli);
        p7_tophits_Destroy(info[i].th);
      }


      /* modify e-value to account for number of models */
      for (i = 0; i < info->th->N ; i++)
      {
        info->th->unsrt[i].lnP         += log((float)info->pli->nmodels);
        info->th->unsrt[i].dcl[0].lnP   = info->th->unsrt[i].lnP;
        info->th->unsrt[i].sortkey      = -1.0 * info->th->unsrt[i].lnP;
      }


      /* it's possible to have duplicates based on how viterbi ranges can overlap */
      p7_tophits_SortByModelnameAndAlipos(info->th);
      p7_tophits_RemoveDuplicates(info->th, info->pli->use_bit_cutoffs);

      /* Print results */
      p7_tophits_SortBySortkey(info->th);
      p7_tophits_Threshold(info->th, info->pli);

      //tally up total number of hits and target coverage
      info->pli->n_output = info->pli->pos_output = 0;
      for (i = 0; i < info->th->N; i++) {
          if ( (info->th->hit[i]->flags & p7_IS_REPORTED) || info->th->hit[i]->flags & p7_IS_INCLUDED) {
              info->pli->n_output++;
              info->pli->pos_output += abs(info->th->hit[i]->dcl[0].jali - info->th->hit[i]->dcl[0].iali) + 1;
          }
      }




      p7_tophits_Targets(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
      p7_tophits_Domains(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");

      if (tblfp)     p7_tophits_TabularTargets(tblfp,    qsq->name, qsq->acc, info->th, info->pli, (nquery == 1));
      if (dfamtblfp) p7_tophits_TabularXfam(dfamtblfp,   qsq->name, NULL, info->th, info->pli);
      if (aliscoresfp) p7_tophits_AliScores(aliscoresfp, qsq->name, info->th );


      esl_stopwatch_Stop(w);
      info->pli->nseqs = 1;
      p7_pli_Statistics(ofp, info->pli, w);
      if (fprintf(ofp, "//\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
      fflush(ofp);

      p7_hmmfile_Close(hfp);
      p7_pipeline_Destroy(info->pli);
      p7_tophits_Destroy(info->th);
      esl_sq_Reuse(qsq);
  }



  if      (sstatus == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n",
					    sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
  else if (sstatus != eslEOF)     esl_fatal("Unexpected error %d reading sequence file %s",
					    sstatus, sqfp->filename);

  /* Terminate outputs - any last words?
   */
  if (tblfp)    p7_tophits_TabularTail(tblfp,    "hmmscan", p7_SCAN_MODELS, cfg->seqfile, cfg->hmmfile, go);
  if (ofp)      { if (fprintf(ofp, "[ok]\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed"); }

  /* Cleanup - prepare for successful exit
   */
  for (i = 0; i < infocnt; ++i)
    p7_bg_Destroy(info[i].bg);

#ifdef HMMER_THREADS
  if (ncpus > 0)
    {
      esl_workqueue_Reset(queue);
      while (esl_workqueue_Remove(queue, (void **) &block) == eslOK)
        p7_oprofile_DestroyBlock(block);
      esl_workqueue_Destroy(queue);
      esl_threads_Destroy(threadObj);
    }
#endif

  free(info);

  esl_sq_Destroy(qsq);
  esl_stopwatch_Destroy(w);
  esl_alphabet_Destroy(abc);
  esl_sqfile_Close(sqfp);

  if (ofp != stdout) fclose(ofp);
  if (tblfp)         fclose(tblfp);
  if (dfamtblfp)     fclose(dfamtblfp);
  if (aliscoresfp)   fclose(aliscoresfp);

  return eslOK;

 ERROR:

 if (ofp != stdout) fclose(ofp);
 if (tblfp)         fclose(tblfp);
 if (dfamtblfp)     fclose(dfamtblfp);
 if (aliscoresfp)   fclose(aliscoresfp);

 return status;
}
Ejemplo n.º 28
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);
  int             N       = esl_opt_GetInteger(go, "-N");
  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_TRACE       *tr      = NULL;
  ESL_SQ         *sq      = NULL;
  P7_ALIDISPLAY  *ad      = NULL;
  int             i,z;

  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");
  p7_hmmfile_Close(hfp);
  

  bg = p7_bg_Create(abc);
  p7_bg_SetLength(bg, 0);
  gm = p7_profile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, 0, p7_UNIGLOCAL); /* that sets N,C,J to generate nothing */
  om = p7_oprofile_Create(gm->M, abc);
  p7_oprofile_Convert(gm, om);

  if (esl_opt_GetBoolean(go, "-p")) tr = p7_trace_CreateWithPP();
  else                              tr = p7_trace_Create();

  sq = esl_sq_CreateDigital(abc);

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    {
      p7_ProfileEmit(r, hmm, gm, bg, sq, tr);
      esl_sq_SetName(sq, "random");

      if (! esl_opt_GetBoolean(go, "-b")) 
	{
	  if (esl_opt_GetBoolean(go, "-p")) 
	    for (z = 0; z < tr->N; z++)
	      if (tr->i[z] > 0) tr->pp[z] = esl_random(r);

	  ad = p7_alidisplay_Create(tr, 0, om, sq);
	  p7_alidisplay_Print(stdout, ad, 40, 80, FALSE);
	  p7_alidisplay_Destroy(ad);
	}
      p7_trace_Reuse(tr);
      esl_sq_Reuse(sq);
    }
  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");

  esl_sq_Destroy(sq);
  p7_trace_Destroy(tr);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(r);
  esl_stopwatch_Destroy(w);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 29
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_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           sc;
  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_UNILOCAL);
  gx = p7_gmx_Create(gm->M, L);

  /* Baseline time. */
  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;

  /* Benchmark time. */
  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    {
      esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
      p7_GViterbi     (dsq, L, gm, gx, &sc);
    }
  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_gmx_Destroy(gx);
  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;
}
Ejemplo n.º 30
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_GMX         *gx      = NULL;
  P7_OMX         *fwd     = NULL;
  P7_OMX         *bck     = 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           fsc, bsc;
  float           fsc2, bsc2;
  double          base_time, bench_time, Mcs;

  p7_FLogsumInit();

  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_FLogsumError(-0.4, -0.5) > 0.0001)
    p7_Fail("-x here requires p7_Logsum() recompiled in slow exact mode");

  if (esl_opt_GetBoolean(go, "-P")) {
    fwd = p7_omx_Create(gm->M, 0, L);
    bck = p7_omx_Create(gm->M, 0, L);
  } else {
    fwd = p7_omx_Create(gm->M, L, L);
    bck = p7_omx_Create(gm->M, L, L);
  }
  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;

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    {
      esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
      if (esl_opt_GetBoolean(go, "-P")) {
	if (! esl_opt_GetBoolean(go, "-B"))  p7_ForwardParser (dsq, L, om,      fwd, &fsc);
	if (! esl_opt_GetBoolean(go, "-F"))  p7_BackwardParser(dsq, L, om, fwd, bck, &bsc);
      } else {
	if (! esl_opt_GetBoolean(go, "-B"))  p7_Forward (dsq, L, om,      fwd, &fsc);
	if (! esl_opt_GetBoolean(go, "-F"))  p7_Backward(dsq, L, om, fwd, bck, &bsc);
      }

      if (esl_opt_GetBoolean(go, "-c") || esl_opt_GetBoolean(go, "-x"))
	{
	  p7_GForward (dsq, L, gm, gx, &fsc2); 
	  p7_GBackward(dsq, L, gm, gx, &bsc2); 
	  printf("%.4f %.4f %.4f %.4f\n", fsc, bsc, fsc2, bsc2);  
	}
    }
  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(bck);
  p7_omx_Destroy(fwd);
  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;
}