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;
}
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;
}
