src/gmxlib/main.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
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   3  *
   4  *                This source code is part of
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   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.2.0
  11  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  12  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  13  * Copyright (c) 2001-2004, The GROMACS development team,
  14  * check out http://www.gromacs.org for more information.
  15
  16  * This program is free software; you can redistribute it and/or
  17  * modify it under the terms of the GNU General Public License
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  19  * of the License, or (at your option) any later version.
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  35  */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39 #include "gmx_header_config.h"
  40
  41 #include <stdio.h>
  42 #include <stdlib.h>
  43 #include <string.h>
  44 #include <limits.h>
  45 #include <time.h>
  46
  47 #ifdef HAVE_SYS_TIME_H
  48 #include <sys/time.h>
  49 #endif
  50
  51 #ifdef HAVE_DIRECT_H
  52 /* windows-specific include for _chdir() */
  53 #include <direct.h>
  54 #endif
  55
  56
  57 #include "smalloc.h"
  58 #include "gmx_fatal.h"
  59 #include "network.h"
  60 #include "main.h"
  61 #include "macros.h"
  62 #include "futil.h"
  63 #include "filenm.h"
  64 #include "gmxfio.h"
  65 #include "string2.h"
  66
  67 #ifdef GMX_THREAD_MPI
  68 #include "thread_mpi.h"
  69 #endif
  70
  71 /* The source code in this file should be thread-safe.
  72          Please keep it that way. */
  73
  74
  75 #ifdef HAVE_UNISTD_H
  76 #include <unistd.h>
  77 #endif
  78
  79 #ifdef GMX_NATIVE_WINDOWS
  80 #include <process.h>
  81 #endif
  82
  83
  84 /* Portable version of ctime_r implemented in src/gmxlib/string2.c, but we do not want it declared in public installed headers */
  85 char *
  86 gmx_ctime_r(const time_t *clock,char *buf, int n);
  87
  88
  89 #define BUFSIZE 1024
  90
  91
  92 static void par_fn(char *base,int ftp,const t_commrec *cr,
  93                    gmx_bool bAppendSimId,gmx_bool bAppendNodeId,
  94                    char buf[],int bufsize)
  95 {
  96   int n;
  97
  98   if((size_t)bufsize<(strlen(base)+10))
  99      gmx_mem("Character buffer too small!");
 100
 101   /* Copy to buf, and strip extension */
 102   strcpy(buf,base);
 103   buf[strlen(base) - strlen(ftp2ext(fn2ftp(base))) - 1] = '\0';
 104
 105   if (bAppendSimId) {
 106     sprintf(buf+strlen(buf),"%d",cr->ms->sim);
 107   }
 108   if (bAppendNodeId) {
 109     strcat(buf,"_node");
 110     sprintf(buf+strlen(buf),"%d",cr->nodeid);
 111   }
 112   strcat(buf,".");
 113
 114   /* Add extension again */
 115   strcat(buf,(ftp == efTPX) ? "tpr" : (ftp == efEDR) ? "edr" : ftp2ext(ftp));
 116   if (debug)
 117   {
 118       fprintf(debug, "node %d par_fn '%s'\n",cr->nodeid,buf);
 119       if (fn2ftp(buf) == efLOG)
 120       {
 121           fprintf(debug,"log\n");
 122       }
 123   }
 124 }
 125
 126 void check_multi_int(FILE *log,const gmx_multisim_t *ms,int val,
 127                      const char *name)
 128 {
 129   int  *ibuf,p;
 130   gmx_bool bCompatible;
 131
 132   if (NULL != log)
 133       fprintf(log,"Multi-checking %s ... ",name);
 134
 135   if (ms == NULL)
 136     gmx_fatal(FARGS,
 137               "check_multi_int called with a NULL communication pointer");
 138
 139   snew(ibuf,ms->nsim);
 140   ibuf[ms->sim] = val;
 141   gmx_sumi_sim(ms->nsim,ibuf,ms);
 142
 143   bCompatible = TRUE;
 144   for(p=1; p<ms->nsim; p++)
 145     bCompatible = bCompatible && (ibuf[p-1] == ibuf[p]);
 146
 147   if (bCompatible)
 148   {
 149       if (NULL != log)
 150           fprintf(log,"OK\n");
 151   }
 152   else
 153   {
 154       if (NULL != log)
 155       {
 156           fprintf(log,"\n%s is not equal for all subsystems\n",name);
 157           for(p=0; p<ms->nsim; p++)
 158               fprintf(log,"  subsystem %d: %d\n",p,ibuf[p]);
 159       }
 160       gmx_fatal(FARGS,"The %d subsystems are not compatible\n",ms->nsim);
 161   }
 162
 163   sfree(ibuf);
 164 }
 165
 166 void check_multi_large_int(FILE *log,const gmx_multisim_t *ms,
 167                            gmx_large_int_t val, const char *name)
 168 {
 169   gmx_large_int_t  *ibuf;
 170   int p;
 171   gmx_bool bCompatible;
 172
 173   if (NULL != log)
 174       fprintf(log,"Multi-checking %s ... ",name);
 175
 176   if (ms == NULL)
 177     gmx_fatal(FARGS,
 178               "check_multi_int called with a NULL communication pointer");
 179
 180   snew(ibuf,ms->nsim);
 181   ibuf[ms->sim] = val;
 182   gmx_sumli_sim(ms->nsim,ibuf,ms);
 183
 184   bCompatible = TRUE;
 185   for(p=1; p<ms->nsim; p++)
 186     bCompatible = bCompatible && (ibuf[p-1] == ibuf[p]);
 187
 188   if (bCompatible)
 189   {
 190       if (NULL != log)
 191           fprintf(log,"OK\n");
 192   }
 193   else
 194   {
 195       if (NULL != log)
 196       {
 197           fprintf(log,"\n%s is not equal for all subsystems\n",name);
 198           for(p=0; p<ms->nsim; p++)
 199           {
 200               char strbuf[255];
 201               /* first make the format string */
 202               snprintf(strbuf, 255, "  subsystem %%d: %s\n",
 203                        gmx_large_int_pfmt);
 204               fprintf(log,strbuf,p,ibuf[p]);
 205           }
 206       }
 207       gmx_fatal(FARGS,"The %d subsystems are not compatible\n",ms->nsim);
 208   }
 209
 210   sfree(ibuf);
 211 }
 212
 213
 214 char *gmx_gethostname(char *name, size_t len)
 215 {
 216     if (len < 8)
 217     {
 218         gmx_incons("gmx_gethostname called with len<8");
 219     }
 220 #ifdef HAVE_UNISTD_H
 221     if (gethostname(name, len-1) != 0)
 222     {
 223         strncpy(name, "unknown",8);
 224     }
 225 #else
 226     strncpy(name, "unknown",8);
 227 #endif
 228
 229     return name;
 230 }
 231
 232
 233 void gmx_log_open(const char *lognm,const t_commrec *cr,gmx_bool bMasterOnly,
 234                   gmx_bool bAppendFiles, FILE** fplog)
 235 {
 236     int  len,testlen,pid;
 237     char buf[256],host[256];
 238     time_t t;
 239     char timebuf[STRLEN];
 240     FILE *fp=*fplog;
 241     char *tmpnm;
 242
 243     debug_gmx();
 244
 245     /* Communicate the filename for logfile */
 246     if (cr->nnodes > 1 && !bMasterOnly
 247 #ifdef GMX_THREAD_MPI
 248         /* With thread MPI the non-master log files are opened later
 249          * when the files names are already known on all nodes.
 250          */
 251         && FALSE
 252 #endif
 253         )
 254     {
 255         if (MASTER(cr))
 256         {
 257             len = strlen(lognm) + 1;
 258         }
 259         gmx_bcast(sizeof(len),&len,cr);
 260         if (!MASTER(cr))
 261         {
 262             snew(tmpnm,len+8);
 263         }
 264         else
 265         {
 266             tmpnm=gmx_strdup(lognm);
 267         }
 268         gmx_bcast(len*sizeof(*tmpnm),tmpnm,cr);
 269     }
 270     else
 271     {
 272         tmpnm=gmx_strdup(lognm);
 273     }
 274
 275     debug_gmx();
 276
 277     if (!bMasterOnly && !MASTER(cr))
 278     {
 279         /* Since log always ends with '.log' let's use this info */
 280         par_fn(tmpnm,efLOG,cr,FALSE,!bMasterOnly,buf,255);
 281         fp = gmx_fio_fopen(buf, bAppendFiles ? "a+" : "w+" );
 282     }
 283     else if (!bAppendFiles)
 284     {
 285         fp = gmx_fio_fopen(tmpnm, bAppendFiles ? "a+" : "w+" );
 286     }
 287
 288     sfree(tmpnm);
 289
 290     gmx_fatal_set_log_file(fp);
 291
 292     /* Get some machine parameters */
 293     gmx_gethostname(host,256);
 294
 295     time(&t);
 296
 297 #ifndef NO_GETPID
 298 #   ifdef GMX_NATIVE_WINDOWS
 299     pid = _getpid();
 300 #   else
 301     pid = getpid();
 302 #   endif
 303 #else
 304         pid = 0;
 305 #endif
 306
 307     if (bAppendFiles)
 308     {
 309         fprintf(fp,
 310                 "\n"
 311                 "\n"
 312                 "-----------------------------------------------------------\n"
 313                 "Restarting from checkpoint, appending to previous log file.\n"
 314                 "\n"
 315             );
 316     }
 317
 318     gmx_ctime_r(&t,timebuf,STRLEN);
 319
 320     fprintf(fp,
 321             "Log file opened on %s"
 322             "Host: %s  pid: %d  nodeid: %d  nnodes:  %d\n",
 323             timebuf,host,pid,cr->nodeid,cr->nnodes);
 324     fprintf(fp,
 325             "Built %s by %s\n"
 326             "Build os/architecture: %s\n"
 327             "Build CPU Vendor: %s  Brand: %s\n"
 328             "Build CPU Family: %d  Model: %d  Stepping: %d\n"
 329             "Build CPU Features: %s\n"
 330             "Compiler: %s\n"
 331             "CFLAGS: %s\n\n",
 332             BUILD_TIME,BUILD_USER,BUILD_HOST,
 333             BUILD_CPU_VENDOR,BUILD_CPU_BRAND,
 334             BUILD_CPU_FAMILY,BUILD_CPU_MODEL,BUILD_CPU_STEPPING,
 335             BUILD_CPU_FEATURES,BUILD_COMPILER,BUILD_CFLAGS);
 336
 337     fflush(fp);
 338     debug_gmx();
 339
 340     *fplog = fp;
 341 }
 342
 343 void gmx_log_close(FILE *fp)
 344 {
 345   if (fp) {
 346     gmx_fatal_set_log_file(NULL);
 347     gmx_fio_fclose(fp);
 348   }
 349 }
 350
 351 static void comm_args(const t_commrec *cr,int *argc,char ***argv)
 352 {
 353   int i,len;
 354
 355   if (PAR(cr))
 356     gmx_bcast(sizeof(*argc),argc,cr);
 357
 358   if (!MASTER(cr))
 359     snew(*argv,*argc+1);
 360   fprintf(stderr,"NODEID=%d argc=%d\n",cr->nodeid,*argc);
 361   for(i=0; (i<*argc); i++) {
 362     if (MASTER(cr))
 363       len = strlen((*argv)[i])+1;
 364     gmx_bcast(sizeof(len),&len,cr);
 365     if (!MASTER(cr))
 366       snew((*argv)[i],len);
 367     /*gmx_bcast(len*sizeof((*argv)[i][0]),(*argv)[i],cr);*/
 368     gmx_bcast(len*sizeof(char),(*argv)[i],cr);
 369   }
 370   debug_gmx();
 371 }
 372
 373 void init_multisystem(t_commrec *cr,int nsim, char **multidirs,
 374                       int nfile, const t_filenm fnm[],gmx_bool bParFn)
 375 {
 376     gmx_multisim_t *ms;
 377     int  nnodes,nnodpersim,sim,i,ftp;
 378     char buf[256];
 379 #ifdef GMX_MPI
 380     MPI_Group mpi_group_world;
 381 #endif
 382     int *rank;
 383
 384 #ifndef GMX_MPI
 385     if (nsim > 1)
 386     {
 387         gmx_fatal(FARGS,"This binary is compiled without MPI support, can not do multiple simulations.");
 388     }
 389 #endif
 390
 391     nnodes  = cr->nnodes;
 392     if (nnodes % nsim != 0)
 393     {
 394         gmx_fatal(FARGS,"The number of nodes (%d) is not a multiple of the number of simulations (%d)",nnodes,nsim);
 395     }
 396
 397     nnodpersim = nnodes/nsim;
 398     sim = cr->nodeid/nnodpersim;
 399
 400     if (debug)
 401     {
 402         fprintf(debug,"We have %d simulations, %d nodes per simulation, local simulation is %d\n",nsim,nnodpersim,sim);
 403     }
 404
 405     snew(ms,1);
 406     cr->ms = ms;
 407     ms->nsim = nsim;
 408     ms->sim  = sim;
 409 #ifdef GMX_MPI
 410     /* Create a communicator for the master nodes */
 411     snew(rank,ms->nsim);
 412     for(i=0; i<ms->nsim; i++)
 413     {
 414         rank[i] = i*nnodpersim;
 415     }
 416     MPI_Comm_group(MPI_COMM_WORLD,&mpi_group_world);
 417     MPI_Group_incl(mpi_group_world,nsim,rank,&ms->mpi_group_masters);
 418     sfree(rank);
 419     MPI_Comm_create(MPI_COMM_WORLD,ms->mpi_group_masters,
 420                     &ms->mpi_comm_masters);
 421
 422 #if !defined(GMX_THREAD_MPI) && !defined(MPI_IN_PLACE_EXISTS)
 423     /* initialize the MPI_IN_PLACE replacement buffers */
 424     snew(ms->mpb, 1);
 425     ms->mpb->ibuf=NULL;
 426     ms->mpb->libuf=NULL;
 427     ms->mpb->fbuf=NULL;
 428     ms->mpb->dbuf=NULL;
 429     ms->mpb->ibuf_alloc=0;
 430     ms->mpb->libuf_alloc=0;
 431     ms->mpb->fbuf_alloc=0;
 432     ms->mpb->dbuf_alloc=0;
 433 #endif
 434
 435 #endif
 436
 437     /* Reduce the intra-simulation communication */
 438     cr->sim_nodeid = cr->nodeid % nnodpersim;
 439     cr->nnodes = nnodpersim;
 440 #ifdef GMX_MPI
 441     MPI_Comm_split(MPI_COMM_WORLD,sim,cr->sim_nodeid,&cr->mpi_comm_mysim);
 442     cr->mpi_comm_mygroup = cr->mpi_comm_mysim;
 443     cr->nodeid = cr->sim_nodeid;
 444 #endif
 445
 446     if (debug)
 447     {
 448         fprintf(debug,"This is simulation %d",cr->ms->sim);
 449         if (PAR(cr))
 450         {
 451             fprintf(debug,", local number of nodes %d, local nodeid %d",
 452                     cr->nnodes,cr->sim_nodeid);
 453         }
 454         fprintf(debug,"\n\n");
 455     }
 456
 457     if (multidirs)
 458     {
 459         int ret;
 460         if (debug)
 461         {
 462             fprintf(debug,"Changing to directory %s\n",multidirs[cr->ms->sim]);
 463         }
 464         if (chdir(multidirs[cr->ms->sim]) != 0)
 465         {
 466             gmx_fatal(FARGS, "Couldn't change directory to %s: %s",
 467                       multidirs[cr->ms->sim],
 468                       strerror(errno));
 469         }
 470     }
 471     else if (bParFn)
 472     {
 473         /* Patch output and tpx, cpt and rerun input file names */
 474         for(i=0; (i<nfile); i++)
 475         {
 476             /* Because of possible multiple extensions per type we must look
 477              * at the actual file name
 478              */
 479             if (is_output(&fnm[i]) ||
 480                 fnm[i].ftp == efTPX || fnm[i].ftp == efCPT ||
 481                 strcmp(fnm[i].opt,"-rerun") == 0)
 482             {
 483                 ftp = fn2ftp(fnm[i].fns[0]);
 484                 par_fn(fnm[i].fns[0],ftp,cr,TRUE,FALSE,buf,255);
 485                 sfree(fnm[i].fns[0]);
 486                 fnm[i].fns[0] = gmx_strdup(buf);
 487             }
 488         }
 489     }
 490 }
 491
 492 t_commrec *init_par(int *argc,char ***argv_ptr)
 493 {
 494     t_commrec *cr;
 495     char      **argv;
 496     int       i;
 497     gmx_bool      pe=FALSE;
 498
 499     snew(cr,1);
 500
 501     argv = argv_ptr ? *argv_ptr : NULL;
 502
 503 #if defined GMX_MPI && !defined GMX_THREAD_MPI
 504     cr->sim_nodeid = gmx_setup(argc,argv,&cr->nnodes);
 505
 506     if (!PAR(cr) && (cr->sim_nodeid != 0))
 507     {
 508         gmx_comm("(!PAR(cr) && (cr->sim_nodeid != 0))");
 509     }
 510
 511     cr->mpi_comm_mysim   = MPI_COMM_WORLD;
 512     cr->mpi_comm_mygroup = cr->mpi_comm_mysim;
 513 #else
 514     /* These should never be accessed */
 515     cr->mpi_comm_mysim   = NULL;
 516     cr->mpi_comm_mygroup = NULL;
 517     cr->nnodes           = 1;
 518     cr->sim_nodeid       = 0;
 519 #endif
 520
 521     cr->nodeid = cr->sim_nodeid;
 522
 523     cr->duty = (DUTY_PP | DUTY_PME);
 524
 525     /* Communicate arguments if parallel */
 526 #ifndef GMX_THREAD_MPI
 527     if (PAR(cr))
 528     {
 529         comm_args(cr,argc,argv_ptr);
 530     }
 531 #endif /* GMX_THREAD_MPI */
 532
 533 #ifdef GMX_MPI
 534 #if !defined(GMX_THREAD_MPI) && !defined(MPI_IN_PLACE_EXISTS)
 535   /* initialize the MPI_IN_PLACE replacement buffers */
 536   snew(cr->mpb, 1);
 537   cr->mpb->ibuf=NULL;
 538   cr->mpb->libuf=NULL;
 539   cr->mpb->fbuf=NULL;
 540   cr->mpb->dbuf=NULL;
 541   cr->mpb->ibuf_alloc=0;
 542   cr->mpb->libuf_alloc=0;
 543   cr->mpb->fbuf_alloc=0;
 544   cr->mpb->dbuf_alloc=0;
 545 #endif
 546 #endif
 547
 548     return cr;
 549 }
 550
 551 t_commrec *init_par_threads(const t_commrec *cro)
 552 {
 553 #ifdef GMX_THREAD_MPI
 554     int initialized;
 555     t_commrec *cr;
 556
 557     /* make a thread-specific commrec */
 558     snew(cr,1);
 559     /* now copy the whole thing, so settings like the number of PME nodes
 560        get propagated. */
 561     *cr=*cro;
 562
 563     /* and we start setting our own thread-specific values for things */
 564     MPI_Initialized(&initialized);
 565     if (!initialized)
 566     {
 567         gmx_comm("Initializing threads without comm");
 568     }
 569     /* once threads will be used together with MPI, we'll
 570        fill the cr structure with distinct data here. This might even work: */
 571     cr->sim_nodeid = gmx_setup(0,NULL, &cr->nnodes);
 572
 573     cr->mpi_comm_mysim = MPI_COMM_WORLD;
 574     cr->mpi_comm_mygroup = cr->mpi_comm_mysim;
 575     cr->nodeid = cr->sim_nodeid;
 576     cr->duty = (DUTY_PP | DUTY_PME);
 577
 578     return cr;
 579 #else
 580     return NULL;
 581 #endif
 582 }