src/gromacs/gmxlib/main.cpp

   1 /*
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  37 #include "config.h"
  38
  39 #include <stdio.h>
  40 #include <stdlib.h>
  41 #include <string.h>
  42 #include <limits.h>
  43 #include <time.h>
  44
  45 #ifdef HAVE_SYS_TIME_H
  46 #include <sys/time.h>
  47 #endif
  48 #ifdef HAVE_UNISTD_H
  49 #include <unistd.h>
  50 #endif
  51 #ifdef GMX_NATIVE_WINDOWS
  52 #include <process.h>
  53 #endif
  54
  55 #include "types/commrec.h"
  56 #include "network.h"
  57 #include "main.h"
  58 #include "macros.h"
  59 #include "gromacs/utility/futil.h"
  60 #include "gromacs/fileio/filenm.h"
  61 #include "gromacs/fileio/gmxfio.h"
  62 #include "copyrite.h"
  63
  64 #include "gromacs/utility/basenetwork.h"
  65 #include "gromacs/utility/cstringutil.h"
  66 #include "gromacs/utility/exceptions.h"
  67 #include "gromacs/utility/fatalerror.h"
  68 #include "gromacs/utility/gmxmpi.h"
  69 #include "gromacs/utility/programcontext.h"
  70 #include "gromacs/utility/smalloc.h"
  71
  72 /* The source code in this file should be thread-safe.
  73          Please keep it that way. */
  74
  75 #define BUFSIZE 1024
  76
  77 static void par_fn(char *base, int ftp, const t_commrec *cr,
  78                    gmx_bool bAppendSimId, gmx_bool bAppendNodeId,
  79                    char buf[], int bufsize)
  80 {
  81     if ((size_t)bufsize < (strlen(base)+10))
  82     {
  83         gmx_mem("Character buffer too small!");
  84     }
  85
  86     /* Copy to buf, and strip extension */
  87     strcpy(buf, base);
  88     buf[strlen(base) - strlen(ftp2ext(fn2ftp(base))) - 1] = '\0';
  89
  90     if (bAppendSimId)
  91     {
  92         sprintf(buf+strlen(buf), "%d", cr->ms->sim);
  93     }
  94     if (bAppendNodeId)
  95     {
  96         strcat(buf, "_rank");
  97         sprintf(buf+strlen(buf), "%d", cr->nodeid);
  98     }
  99     strcat(buf, ".");
 100
 101     /* Add extension again */
 102     strcat(buf, (ftp == efTPX) ? "tpr" : (ftp == efEDR) ? "edr" : ftp2ext(ftp));
 103     if (debug)
 104     {
 105         fprintf(debug, "rank %d par_fn '%s'\n", cr->nodeid, buf);
 106         if (fn2ftp(buf) == efLOG)
 107         {
 108             fprintf(debug, "log\n");
 109         }
 110     }
 111 }
 112
 113 void check_multi_int(FILE *log, const gmx_multisim_t *ms, int val,
 114                      const char *name,
 115                      gmx_bool bQuiet)
 116 {
 117     int     *ibuf, p;
 118     gmx_bool bCompatible;
 119
 120     if (NULL != log && !bQuiet)
 121     {
 122         fprintf(log, "Multi-checking %s ... ", name);
 123     }
 124
 125     if (ms == NULL)
 126     {
 127         gmx_fatal(FARGS,
 128                   "check_multi_int called with a NULL communication pointer");
 129     }
 130
 131     snew(ibuf, ms->nsim);
 132     ibuf[ms->sim] = val;
 133     gmx_sumi_sim(ms->nsim, ibuf, ms);
 134
 135     bCompatible = TRUE;
 136     for (p = 1; p < ms->nsim; p++)
 137     {
 138         bCompatible = bCompatible && (ibuf[p-1] == ibuf[p]);
 139     }
 140
 141     if (bCompatible)
 142     {
 143         if (NULL != log && !bQuiet)
 144         {
 145             fprintf(log, "OK\n");
 146         }
 147     }
 148     else
 149     {
 150         if (NULL != log)
 151         {
 152             fprintf(log, "\n%s is not equal for all subsystems\n", name);
 153             for (p = 0; p < ms->nsim; p++)
 154             {
 155                 fprintf(log, "  subsystem %d: %d\n", p, ibuf[p]);
 156             }
 157         }
 158         gmx_fatal(FARGS, "The %d subsystems are not compatible\n", ms->nsim);
 159     }
 160
 161     sfree(ibuf);
 162 }
 163
 164 void check_multi_int64(FILE *log, const gmx_multisim_t *ms,
 165                        gmx_int64_t val, const char *name,
 166                        gmx_bool bQuiet)
 167 {
 168     gmx_int64_t      *ibuf;
 169     int               p;
 170     gmx_bool          bCompatible;
 171
 172     if (NULL != log && !bQuiet)
 173     {
 174         fprintf(log, "Multi-checking %s ... ", name);
 175     }
 176
 177     if (ms == NULL)
 178     {
 179         gmx_fatal(FARGS,
 180                   "check_multi_int called with a NULL communication pointer");
 181     }
 182
 183     snew(ibuf, ms->nsim);
 184     ibuf[ms->sim] = val;
 185     gmx_sumli_sim(ms->nsim, ibuf, ms);
 186
 187     bCompatible = TRUE;
 188     for (p = 1; p < ms->nsim; p++)
 189     {
 190         bCompatible = bCompatible && (ibuf[p-1] == ibuf[p]);
 191     }
 192
 193     if (bCompatible)
 194     {
 195         if (NULL != log && !bQuiet)
 196         {
 197             fprintf(log, "OK\n");
 198         }
 199     }
 200     else
 201     {
 202         if (NULL != log)
 203         {
 204             fprintf(log, "\n%s is not equal for all subsystems\n", name);
 205             for (p = 0; p < ms->nsim; p++)
 206             {
 207                 char strbuf[255];
 208                 /* first make the format string */
 209                 snprintf(strbuf, 255, "  subsystem %%d: %s\n",
 210                          "%" GMX_PRId64);
 211                 fprintf(log, strbuf, p, ibuf[p]);
 212             }
 213         }
 214         gmx_fatal(FARGS, "The %d subsystems are not compatible\n", ms->nsim);
 215     }
 216
 217     sfree(ibuf);
 218 }
 219
 220
 221 void gmx_log_open(const char *lognm, const t_commrec *cr, gmx_bool bMasterOnly,
 222                   gmx_bool bAppendFiles, FILE** fplog)
 223 {
 224     int    len, pid;
 225     char   buf[256], host[256];
 226     time_t t;
 227     char   timebuf[STRLEN];
 228     FILE  *fp = *fplog;
 229     char  *tmpnm;
 230
 231     debug_gmx();
 232
 233     /* Communicate the filename for logfile */
 234     if (cr->nnodes > 1 && !bMasterOnly
 235 #ifdef GMX_THREAD_MPI
 236         /* With thread MPI the non-master log files are opened later
 237          * when the files names are already known on all nodes.
 238          */
 239         && FALSE
 240 #endif
 241         )
 242     {
 243         if (MASTER(cr))
 244         {
 245             len = strlen(lognm) + 1;
 246         }
 247         gmx_bcast(sizeof(len), &len, cr);
 248         if (!MASTER(cr))
 249         {
 250             snew(tmpnm, len+8);
 251         }
 252         else
 253         {
 254             tmpnm = gmx_strdup(lognm);
 255         }
 256         gmx_bcast(len*sizeof(*tmpnm), tmpnm, cr);
 257     }
 258     else
 259     {
 260         tmpnm = gmx_strdup(lognm);
 261     }
 262
 263     debug_gmx();
 264
 265     if (!bMasterOnly && !MASTER(cr))
 266     {
 267         /* Since log always ends with '.log' let's use this info */
 268         par_fn(tmpnm, efLOG, cr, FALSE, !bMasterOnly, buf, 255);
 269         fp = gmx_fio_fopen(buf, bAppendFiles ? "a+" : "w+" );
 270     }
 271     else if (!bAppendFiles)
 272     {
 273         fp = gmx_fio_fopen(tmpnm, bAppendFiles ? "a+" : "w+" );
 274     }
 275
 276     sfree(tmpnm);
 277
 278     gmx_fatal_set_log_file(fp);
 279
 280     /* Get some machine parameters */
 281     gmx_gethostname(host, 256);
 282
 283     time(&t);
 284
 285 #ifndef NO_GETPID
 286 #   ifdef GMX_NATIVE_WINDOWS
 287     pid = _getpid();
 288 #   else
 289     pid = getpid();
 290 #   endif
 291 #else
 292     pid = 0;
 293 #endif
 294
 295     if (bAppendFiles)
 296     {
 297         fprintf(fp,
 298                 "\n"
 299                 "\n"
 300                 "-----------------------------------------------------------\n"
 301                 "Restarting from checkpoint, appending to previous log file.\n"
 302                 "\n"
 303                 );
 304     }
 305
 306     gmx_ctime_r(&t, timebuf, STRLEN);
 307
 308     fprintf(fp,
 309             "Log file opened on %s"
 310             "Host: %s  pid: %d  rank ID: %d  number of ranks:  %d\n",
 311             timebuf, host, pid, cr->nodeid, cr->nnodes);
 312     try
 313     {
 314         gmx::BinaryInformationSettings settings;
 315         settings.extendedInfo(true);
 316         settings.copyright(!bAppendFiles);
 317         gmx::printBinaryInformation(fp, gmx::getProgramContext(), settings);
 318     }
 319     GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
 320     fprintf(fp, "\n\n");
 321
 322     fflush(fp);
 323     debug_gmx();
 324
 325     *fplog = fp;
 326 }
 327
 328 void gmx_log_close(FILE *fp)
 329 {
 330     if (fp)
 331     {
 332         gmx_fatal_set_log_file(NULL);
 333         gmx_fio_fclose(fp);
 334     }
 335 }
 336
 337 void init_multisystem(t_commrec *cr, int nsim, char **multidirs,
 338                       int nfile, const t_filenm fnm[], gmx_bool bParFn)
 339 {
 340     gmx_multisim_t *ms;
 341     int             nnodes, nnodpersim, sim, i, ftp;
 342     char            buf[256];
 343 #ifdef GMX_MPI
 344     MPI_Group       mpi_group_world;
 345     int            *rank;
 346 #endif
 347
 348 #ifndef GMX_MPI
 349     if (nsim > 1)
 350     {
 351         gmx_fatal(FARGS, "This binary is compiled without MPI support, can not do multiple simulations.");
 352     }
 353 #endif
 354
 355     nnodes  = cr->nnodes;
 356     if (nnodes % nsim != 0)
 357     {
 358         gmx_fatal(FARGS, "The number of ranks (%d) is not a multiple of the number of simulations (%d)", nnodes, nsim);
 359     }
 360
 361     nnodpersim = nnodes/nsim;
 362     sim        = cr->nodeid/nnodpersim;
 363
 364     if (debug)
 365     {
 366         fprintf(debug, "We have %d simulations, %d ranks per simulation, local simulation is %d\n", nsim, nnodpersim, sim);
 367     }
 368
 369     snew(ms, 1);
 370     cr->ms   = ms;
 371     ms->nsim = nsim;
 372     ms->sim  = sim;
 373 #ifdef GMX_MPI
 374     /* Create a communicator for the master nodes */
 375     snew(rank, ms->nsim);
 376     for (i = 0; i < ms->nsim; i++)
 377     {
 378         rank[i] = i*nnodpersim;
 379     }
 380     MPI_Comm_group(MPI_COMM_WORLD, &mpi_group_world);
 381     MPI_Group_incl(mpi_group_world, nsim, rank, &ms->mpi_group_masters);
 382     sfree(rank);
 383     MPI_Comm_create(MPI_COMM_WORLD, ms->mpi_group_masters,
 384                     &ms->mpi_comm_masters);
 385
 386 #if !defined(MPI_IN_PLACE_EXISTS)
 387     /* initialize the MPI_IN_PLACE replacement buffers */
 388     snew(ms->mpb, 1);
 389     ms->mpb->ibuf        = NULL;
 390     ms->mpb->libuf       = NULL;
 391     ms->mpb->fbuf        = NULL;
 392     ms->mpb->dbuf        = NULL;
 393     ms->mpb->ibuf_alloc  = 0;
 394     ms->mpb->libuf_alloc = 0;
 395     ms->mpb->fbuf_alloc  = 0;
 396     ms->mpb->dbuf_alloc  = 0;
 397 #endif
 398
 399 #endif
 400
 401     /* Reduce the intra-simulation communication */
 402     cr->sim_nodeid = cr->nodeid % nnodpersim;
 403     cr->nnodes     = nnodpersim;
 404 #ifdef GMX_MPI
 405     MPI_Comm_split(MPI_COMM_WORLD, sim, cr->sim_nodeid, &cr->mpi_comm_mysim);
 406     cr->mpi_comm_mygroup = cr->mpi_comm_mysim;
 407     cr->nodeid           = cr->sim_nodeid;
 408 #endif
 409
 410     if (debug)
 411     {
 412         fprintf(debug, "This is simulation %d", cr->ms->sim);
 413         if (PAR(cr))
 414         {
 415             fprintf(debug, ", local number of ranks %d, local rank ID %d",
 416                     cr->nnodes, cr->sim_nodeid);
 417         }
 418         fprintf(debug, "\n\n");
 419     }
 420
 421     if (multidirs)
 422     {
 423         if (debug)
 424         {
 425             fprintf(debug, "Changing to directory %s\n", multidirs[cr->ms->sim]);
 426         }
 427         gmx_chdir(multidirs[cr->ms->sim]);
 428     }
 429     else if (bParFn)
 430     {
 431         /* Patch output and tpx, cpt and rerun input file names */
 432         for (i = 0; (i < nfile); i++)
 433         {
 434             /* Because of possible multiple extensions per type we must look
 435              * at the actual file name
 436              */
 437             if (is_output(&fnm[i]) ||
 438                 fnm[i].ftp == efTPX || fnm[i].ftp == efCPT ||
 439                 strcmp(fnm[i].opt, "-rerun") == 0)
 440             {
 441                 ftp = fn2ftp(fnm[i].fns[0]);
 442                 par_fn(fnm[i].fns[0], ftp, cr, TRUE, FALSE, buf, 255);
 443                 sfree(fnm[i].fns[0]);
 444                 fnm[i].fns[0] = gmx_strdup(buf);
 445             }
 446         }
 447     }
 448 }