src/gmxlib/network.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * GROningen Mixture of Alchemy and Childrens' Stories
  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <string.h>
  40 #include "gmx_fatal.h"
  41 #include "main.h"
  42 #include "smalloc.h"
  43 #include "network.h"
  44 #include "copyrite.h"
  45 #include "statutil.h"
  46 #include "ctype.h"
  47 #include "macros.h"
  48
  49 #ifdef GMX_LIB_MPI
  50 #include <mpi.h>
  51 #endif
  52
  53 #ifdef GMX_THREADS
  54 #include "tmpi.h"
  55 #endif
  56
  57 #include "mpelogging.h"
  58
  59 /* The source code in this file should be thread-safe.
  60       Please keep it that way. */
  61
  62 bool gmx_mpi_initialized(void)
  63 {
  64   int n;
  65 #ifndef GMX_MPI
  66   return 0;
  67 #else
  68   MPI_Initialized(&n);
  69
  70   return n;
  71 #endif
  72 }
  73
  74 int gmx_setup(int *argc,char **argv,int *nnodes)
  75 {
  76 #ifndef GMX_MPI
  77   gmx_call("gmx_setup");
  78   return 0;
  79 #else
  80   char   buf[256];
  81   int    resultlen;               /* actual length of node name      */
  82   int    i,flag;
  83   int  mpi_num_nodes;
  84   int  mpi_my_rank;
  85   char mpi_hostname[MPI_MAX_PROCESSOR_NAME];
  86
  87   /* Call the MPI routines */
  88 #ifdef GMX_LIB_MPI
  89 #ifdef GMX_FAHCORE
  90   (void) fah_MPI_Init(argc,&argv);
  91 #else
  92   (void) MPI_Init(argc,&argv);
  93 #endif
  94 #endif
  95   (void) MPI_Comm_size( MPI_COMM_WORLD, &mpi_num_nodes );
  96   (void) MPI_Comm_rank( MPI_COMM_WORLD, &mpi_my_rank );
  97   (void) MPI_Get_processor_name( mpi_hostname, &resultlen );
  98
  99
 100 #ifdef USE_MPE
 101   /* MPE logging routines. Get event IDs from MPE: */
 102   /* General events */
 103   ev_timestep1               = MPE_Log_get_event_number( );
 104   ev_timestep2               = MPE_Log_get_event_number( );
 105   ev_force_start             = MPE_Log_get_event_number( );
 106   ev_force_finish            = MPE_Log_get_event_number( );
 107   ev_do_fnbf_start           = MPE_Log_get_event_number( );
 108   ev_do_fnbf_finish          = MPE_Log_get_event_number( );
 109   ev_ns_start                = MPE_Log_get_event_number( );
 110   ev_ns_finish               = MPE_Log_get_event_number( );
 111   ev_calc_bonds_start        = MPE_Log_get_event_number( );
 112   ev_calc_bonds_finish       = MPE_Log_get_event_number( );
 113   ev_global_stat_start       = MPE_Log_get_event_number( );
 114   ev_global_stat_finish      = MPE_Log_get_event_number( );
 115   ev_virial_start            = MPE_Log_get_event_number( );
 116   ev_virial_finish           = MPE_Log_get_event_number( );
 117
 118   /* Shift related events */
 119   ev_shift_start             = MPE_Log_get_event_number( );
 120   ev_shift_finish            = MPE_Log_get_event_number( );
 121   ev_unshift_start           = MPE_Log_get_event_number( );
 122   ev_unshift_finish          = MPE_Log_get_event_number( );
 123   ev_mk_mshift_start         = MPE_Log_get_event_number( );
 124   ev_mk_mshift_finish        = MPE_Log_get_event_number( );
 125
 126   /* PME related events */
 127   ev_pme_start               = MPE_Log_get_event_number( );
 128   ev_pme_finish              = MPE_Log_get_event_number( );
 129   ev_spread_on_grid_start    = MPE_Log_get_event_number( );
 130   ev_spread_on_grid_finish   = MPE_Log_get_event_number( );
 131   ev_sum_qgrid_start         = MPE_Log_get_event_number( );
 132   ev_sum_qgrid_finish        = MPE_Log_get_event_number( );
 133   ev_gmxfft3d_start          = MPE_Log_get_event_number( );
 134   ev_gmxfft3d_finish         = MPE_Log_get_event_number( );
 135   ev_solve_pme_start         = MPE_Log_get_event_number( );
 136   ev_solve_pme_finish        = MPE_Log_get_event_number( );
 137   ev_gather_f_bsplines_start = MPE_Log_get_event_number( );
 138   ev_gather_f_bsplines_finish= MPE_Log_get_event_number( );
 139   ev_reduce_start            = MPE_Log_get_event_number( );
 140   ev_reduce_finish           = MPE_Log_get_event_number( );
 141   ev_rscatter_start          = MPE_Log_get_event_number( );
 142   ev_rscatter_finish         = MPE_Log_get_event_number( );
 143   ev_alltoall_start          = MPE_Log_get_event_number( );
 144   ev_alltoall_finish         = MPE_Log_get_event_number( );
 145   ev_pmeredist_start         = MPE_Log_get_event_number( );
 146   ev_pmeredist_finish        = MPE_Log_get_event_number( );
 147   ev_init_pme_start          = MPE_Log_get_event_number( );
 148   ev_init_pme_finish         = MPE_Log_get_event_number( );
 149   ev_send_coordinates_start  = MPE_Log_get_event_number( );
 150   ev_send_coordinates_finish = MPE_Log_get_event_number( );
 151   ev_update_fr_start         = MPE_Log_get_event_number( );
 152   ev_update_fr_finish        = MPE_Log_get_event_number( );
 153   ev_clear_rvecs_start       = MPE_Log_get_event_number( );
 154   ev_clear_rvecs_finish      = MPE_Log_get_event_number( );
 155   ev_update_start            = MPE_Log_get_event_number( );
 156   ev_update_finish           = MPE_Log_get_event_number( );
 157   ev_output_start            = MPE_Log_get_event_number( );
 158   ev_output_finish           = MPE_Log_get_event_number( );
 159   ev_sum_lrforces_start      = MPE_Log_get_event_number( );
 160   ev_sum_lrforces_finish     = MPE_Log_get_event_number( );
 161   ev_sort_start              = MPE_Log_get_event_number( );
 162   ev_sort_finish             = MPE_Log_get_event_number( );
 163   ev_sum_qgrid_start         = MPE_Log_get_event_number( );
 164   ev_sum_qgrid_finish        = MPE_Log_get_event_number( );
 165
 166   /* Essential dynamics related events */
 167   ev_edsam_start             = MPE_Log_get_event_number( );
 168   ev_edsam_finish            = MPE_Log_get_event_number( );
 169   ev_get_coords_start        = MPE_Log_get_event_number( );
 170   ev_get_coords_finish       = MPE_Log_get_event_number( );
 171   ev_ed_apply_cons_start     = MPE_Log_get_event_number( );
 172   ev_ed_apply_cons_finish    = MPE_Log_get_event_number( );
 173   ev_fit_to_reference_start  = MPE_Log_get_event_number( );
 174   ev_fit_to_reference_finish = MPE_Log_get_event_number( );
 175
 176   /* describe events: */
 177   if ( mpi_my_rank == 0 )
 178   {
 179     /* General events */
 180     MPE_Describe_state(ev_timestep1,               ev_timestep2,                "timestep START",  "magenta" );
 181     MPE_Describe_state(ev_force_start,             ev_force_finish,             "force",           "cornflower blue" );
 182     MPE_Describe_state(ev_do_fnbf_start,           ev_do_fnbf_finish,           "do_fnbf",         "navy" );
 183     MPE_Describe_state(ev_ns_start,                ev_ns_finish,                "neighbor search", "tomato" );
 184     MPE_Describe_state(ev_calc_bonds_start,        ev_calc_bonds_finish,        "bonded forces",   "slate blue" );
 185     MPE_Describe_state(ev_global_stat_start,       ev_global_stat_finish,       "global stat",     "firebrick3");
 186     MPE_Describe_state(ev_update_fr_start,         ev_update_fr_finish,         "update forcerec", "goldenrod");
 187     MPE_Describe_state(ev_clear_rvecs_start,       ev_clear_rvecs_finish,       "clear rvecs",     "bisque");
 188     MPE_Describe_state(ev_update_start,            ev_update_finish,            "update",          "cornsilk");
 189     MPE_Describe_state(ev_output_start,            ev_output_finish,            "output",          "black");
 190     MPE_Describe_state(ev_virial_start,            ev_virial_finish,            "calc_virial",     "thistle4");
 191
 192     /* PME related events */
 193     MPE_Describe_state(ev_pme_start,               ev_pme_finish,               "doing PME",       "grey" );
 194     MPE_Describe_state(ev_spread_on_grid_start,    ev_spread_on_grid_finish,    "spread",          "dark orange" );
 195     MPE_Describe_state(ev_sum_qgrid_start,         ev_sum_qgrid_finish,         "sum qgrid",       "slate blue");
 196     MPE_Describe_state(ev_gmxfft3d_start,          ev_gmxfft3d_finish,          "fft3d",           "snow2" );
 197     MPE_Describe_state(ev_solve_pme_start,         ev_solve_pme_finish,         "solve PME",       "indian red" );
 198     MPE_Describe_state(ev_gather_f_bsplines_start, ev_gather_f_bsplines_finish, "bsplines",        "light sea green" );
 199     MPE_Describe_state(ev_reduce_start,            ev_reduce_finish,            "reduce",          "cyan1" );
 200     MPE_Describe_state(ev_rscatter_start,          ev_rscatter_finish,          "rscatter",        "cyan3" );
 201     MPE_Describe_state(ev_alltoall_start,          ev_alltoall_finish,          "alltoall",        "LightCyan4" );
 202     MPE_Describe_state(ev_pmeredist_start,         ev_pmeredist_finish,         "pmeredist",       "thistle" );
 203     MPE_Describe_state(ev_init_pme_start,          ev_init_pme_finish,          "init PME",        "snow4");
 204     MPE_Describe_state(ev_send_coordinates_start,  ev_send_coordinates_finish,  "send_coordinates","blue");
 205     MPE_Describe_state(ev_sum_lrforces_start,      ev_sum_lrforces_finish,      "sum_LRforces",    "lime green");
 206     MPE_Describe_state(ev_sort_start,              ev_sort_finish,              "sort pme atoms",  "brown");
 207     MPE_Describe_state(ev_sum_qgrid_start,         ev_sum_qgrid_finish,         "sum charge grid", "medium orchid");
 208
 209     /* Shift related events */
 210     MPE_Describe_state(ev_shift_start,             ev_shift_finish,             "shift",           "orange");
 211     MPE_Describe_state(ev_unshift_start,           ev_unshift_finish,           "unshift",         "dark orange");
 212     MPE_Describe_state(ev_mk_mshift_start,         ev_mk_mshift_finish,         "mk_mshift",       "maroon");
 213
 214     /* Essential dynamics related events */
 215     MPE_Describe_state(ev_edsam_start,             ev_edsam_finish,             "EDSAM",           "deep sky blue");
 216     MPE_Describe_state(ev_get_coords_start,        ev_get_coords_finish,        "ED get coords",   "steel blue");
 217     MPE_Describe_state(ev_ed_apply_cons_start,     ev_ed_apply_cons_finish,     "ED apply constr", "forest green");
 218     MPE_Describe_state(ev_fit_to_reference_start,  ev_fit_to_reference_finish,  "ED fit to ref",   "lavender");
 219
 220   }
 221   MPE_Init_log();
 222 #endif
 223
 224 #ifdef GMX_LIB_MPI
 225   fprintf(stderr,"NNODES=%d, MYRANK=%d, HOSTNAME=%s\n",
 226           mpi_num_nodes,mpi_my_rank,mpi_hostname);
 227 #endif
 228
 229   *nnodes=mpi_num_nodes;
 230
 231   return mpi_my_rank;
 232 #endif
 233 }
 234
 235 int  gmx_node_num(void)
 236 {
 237 #ifndef GMX_MPI
 238   return 1;
 239 #else
 240   int i;
 241   (void) MPI_Comm_size(MPI_COMM_WORLD, &i);
 242   return i;
 243 #endif
 244 }
 245
 246 int gmx_node_rank(void)
 247 {
 248 #ifndef GMX_MPI
 249   return 0;
 250 #else
 251   int i;
 252   (void) MPI_Comm_rank(MPI_COMM_WORLD, &i);
 253   return i;
 254 #endif
 255 }
 256
 257 void gmx_setup_nodecomm(FILE *fplog,t_commrec *cr)
 258 {
 259   gmx_nodecomm_t *nc;
 260   int  n,rank,resultlen,hostnum,i,j,ng,ni;
 261 #ifdef GMX_MPI
 262   char mpi_hostname[MPI_MAX_PROCESSOR_NAME],num[MPI_MAX_PROCESSOR_NAME];
 263 #endif
 264
 265   /* Many MPI implementations do not optimize MPI_Allreduce
 266    * (and probably also other global communication calls)
 267    * for multi-core nodes connected by a network.
 268    * We can optimize such communication by using one MPI call
 269    * within each node and one between the nodes.
 270    * For MVAPICH2 and Intel MPI this reduces the time for
 271    * the global_stat communication by 25%
 272    * for 2x2-core 3 GHz Woodcrest connected by mixed DDR/SDR Infiniband.
 273    * B. Hess, November 2007
 274    */
 275
 276   nc = &cr->nc;
 277
 278   nc->bUse = FALSE;
 279 #ifndef GMX_THREADS
 280   if (getenv("GMX_NO_NODECOMM") == NULL) {
 281 #ifdef GMX_MPI
 282     MPI_Comm_size(cr->mpi_comm_mygroup,&n);
 283     MPI_Comm_rank(cr->mpi_comm_mygroup,&rank);
 284     MPI_Get_processor_name(mpi_hostname,&resultlen);
 285     /* This procedure can only differentiate nodes with host names
 286      * that end on unique numbers.
 287      */
 288     i = 0;
 289     j = 0;
 290     /* Only parse the host name up to the first dot */
 291     while(i < resultlen && mpi_hostname[i] != '.') {
 292       if (isdigit(mpi_hostname[i])) {
 293         num[j++] = mpi_hostname[i];
 294       }
 295       i++;
 296     }
 297     num[j] = '\0';
 298     if (j == 0) {
 299       hostnum = 0;
 300     } else {
 301       /* Use only the last 9 decimals, so we don't overflow an int */
 302       hostnum = strtol(num + max(0,j-9), NULL, 10);
 303     }
 304
 305     if (debug) {
 306       fprintf(debug,
 307               "In gmx_setup_nodecomm: splitting communicator of size %d\n",
 308               n);
 309       fprintf(debug,"In gmx_setup_nodecomm: hostname '%s', hostnum %d\n",
 310               mpi_hostname,hostnum);
 311     }
 312
 313     /* The intra-node communicator, split on node number */
 314     MPI_Comm_split(cr->mpi_comm_mygroup,hostnum,rank,&nc->comm_intra);
 315     MPI_Comm_rank(nc->comm_intra,&nc->rank_intra);
 316     if (debug) {
 317       fprintf(debug,"In gmx_setup_nodecomm: node rank %d rank_intra %d\n",
 318               rank,nc->rank_intra);
 319     }
 320     /* The inter-node communicator, split on rank_intra.
 321      * We actually only need the one for rank=0,
 322      * but it is easier to create them all.
 323      */
 324     MPI_Comm_split(cr->mpi_comm_mygroup,nc->rank_intra,rank,&nc->comm_inter);
 325     /* Check if this really created two step communication */
 326     MPI_Comm_size(nc->comm_inter,&ng);
 327     MPI_Comm_size(nc->comm_intra,&ni);
 328     if (debug) {
 329       fprintf(debug,"In gmx_setup_nodecomm: groups %d, my group size %d\n",
 330               ng,ni);
 331     }
 332     if ((ng > 1 && ng < n) || (ni > 1 && ni < n)) {
 333       nc->bUse = TRUE;
 334       if (fplog)
 335         fprintf(fplog,"Using two step summing over %d groups of on average %.1f processes\n\n",ng,(real)n/(real)ng);
 336       if (nc->rank_intra > 0)
 337         MPI_Comm_free(&nc->comm_inter);
 338     } else {
 339       /* One group or all processes in a separate group, use normal summing */
 340       MPI_Comm_free(&nc->comm_inter);
 341       MPI_Comm_free(&nc->comm_intra);
 342     }
 343 #endif
 344   }
 345 #endif
 346 }
 347
 348 void gmx_barrier(const t_commrec *cr)
 349 {
 350 #ifndef GMX_MPI
 351   gmx_call("gmx_barrier");
 352 #else
 353   MPI_Barrier(cr->mpi_comm_mygroup);
 354 #endif
 355 }
 356
 357 void gmx_abort(int noderank,int nnodes,int errorno)
 358 {
 359 #ifndef GMX_MPI
 360   gmx_call("gmx_abort");
 361 #else
 362 #ifdef GMX_THREADS
 363   fprintf(stderr,"Halting program %s\n",ShortProgram());
 364   thanx(stderr);
 365   exit(1);
 366 #else
 367   if (nnodes > 1)
 368   {
 369       fprintf(stderr,"Halting parallel program %s on CPU %d out of %d\n",
 370               ShortProgram(),noderank,nnodes);
 371   }
 372   else
 373   {
 374       fprintf(stderr,"Halting program %s\n",ShortProgram());
 375   }
 376
 377   thanx(stderr);
 378   MPI_Abort(MPI_COMM_WORLD,errorno);
 379   exit(1);
 380 #endif
 381 #endif
 382 }
 383
 384 void gmx_bcast(int nbytes,void *b,const t_commrec *cr)
 385 {
 386 #ifndef GMX_MPI
 387   gmx_call("gmx_bast");
 388 #else
 389   MPI_Bcast(b,nbytes,MPI_BYTE,MASTERRANK(cr),cr->mpi_comm_mygroup);
 390 #endif
 391 }
 392
 393 void gmx_bcast_sim(int nbytes,void *b,const t_commrec *cr)
 394 {
 395 #ifndef GMX_MPI
 396   gmx_call("gmx_bast");
 397 #else
 398   MPI_Bcast(b,nbytes,MPI_BYTE,MASTERRANK(cr),cr->mpi_comm_mysim);
 399 #endif
 400 }
 401
 402 void gmx_sumd(int nr,double r[],const t_commrec *cr)
 403 {
 404 #ifndef GMX_MPI
 405     gmx_call("gmx_sumd");
 406 #else
 407 #if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREADS)
 408     if (cr->nc.bUse) {
 409         if (cr->nc.rank_intra == 0)
 410         {
 411             /* Use two step summing. */
 412             MPI_Reduce(MPI_IN_PLACE,r,nr,MPI_DOUBLE,MPI_SUM,0,
 413                        cr->nc.comm_intra);
 414             /* Sum the roots of the internal (intra) buffers. */
 415             MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_DOUBLE,MPI_SUM,
 416                           cr->nc.comm_inter);
 417         }
 418         else
 419         {
 420             /* This is here because of the silly MPI specification
 421                 that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
 422             MPI_Reduce(r,NULL,nr,MPI_DOUBLE,MPI_SUM,0,cr->nc.comm_intra);
 423         }
 424         MPI_Bcast(r,nr,MPI_DOUBLE,0,cr->nc.comm_intra);
 425     }
 426     else
 427     {
 428         MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_DOUBLE,MPI_SUM,
 429                       cr->mpi_comm_mygroup);
 430     }
 431 #else
 432     int i;
 433
 434     if (nr > cr->mpb->dbuf_alloc) {
 435         cr->mpb->dbuf_alloc = nr;
 436         srenew(cr->mpb->dbuf,cr->mpb->dbuf_alloc);
 437     }
 438     if (cr->nc.bUse) {
 439         /* Use two step summing */
 440         MPI_Allreduce(r,cr->mpb->dbuf,nr,MPI_DOUBLE,MPI_SUM,cr->nc.comm_intra);
 441         if (cr->nc.rank_intra == 0) {
 442             /* Sum with the buffers reversed */
 443             MPI_Allreduce(cr->mpb->dbuf,r,nr,MPI_DOUBLE,MPI_SUM,
 444                           cr->nc.comm_inter);
 445         }
 446         MPI_Bcast(r,nr,MPI_DOUBLE,0,cr->nc.comm_intra);
 447     } else {
 448         MPI_Allreduce(r,cr->mpb->dbuf,nr,MPI_DOUBLE,MPI_SUM,
 449                       cr->mpi_comm_mygroup);
 450         for(i=0; i<nr; i++)
 451             r[i] = cr->mpb->dbuf[i];
 452     }
 453 #endif
 454 #endif
 455 }
 456
 457 void gmx_sumf(int nr,float r[],const t_commrec *cr)
 458 {
 459 #ifndef GMX_MPI
 460     gmx_call("gmx_sumf");
 461 #else
 462 #if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREADS)
 463     if (cr->nc.bUse) {
 464         /* Use two step summing.  */
 465         if (cr->nc.rank_intra == 0)
 466         {
 467             MPI_Reduce(MPI_IN_PLACE,r,nr,MPI_FLOAT,MPI_SUM,0,
 468                        cr->nc.comm_intra);
 469             /* Sum the roots of the internal (intra) buffers */
 470             MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_FLOAT,MPI_SUM,
 471                           cr->nc.comm_inter);
 472         }
 473         else
 474         {
 475             /* This is here because of the silly MPI specification
 476                 that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
 477             MPI_Reduce(r,NULL,nr,MPI_FLOAT,MPI_SUM,0,cr->nc.comm_intra);
 478         }
 479         MPI_Bcast(r,nr,MPI_FLOAT,0,cr->nc.comm_intra);
 480     }
 481     else
 482     {
 483         MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_FLOAT,MPI_SUM,cr->mpi_comm_mygroup);
 484     }
 485 #else
 486     int i;
 487
 488     if (nr > cr->mpb->fbuf_alloc) {
 489         cr->mpb->fbuf_alloc = nr;
 490         srenew(cr->mpb->fbuf,cr->mpb->fbuf_alloc);
 491     }
 492     if (cr->nc.bUse) {
 493         /* Use two step summing */
 494         MPI_Allreduce(r,cr->mpb->fbuf,nr,MPI_FLOAT,MPI_SUM,cr->nc.comm_intra);
 495         if (cr->nc.rank_intra == 0) {
 496             /* Sum with the buffers reversed */
 497             MPI_Allreduce(cr->mpb->fbuf,r,nr,MPI_FLOAT,MPI_SUM,
 498                           cr->nc.comm_inter);
 499         }
 500         MPI_Bcast(r,nr,MPI_FLOAT,0,cr->nc.comm_intra);
 501     } else {
 502         MPI_Allreduce(r,cr->mpb->fbuf,nr,MPI_FLOAT,MPI_SUM,
 503                       cr->mpi_comm_mygroup);
 504         for(i=0; i<nr; i++)
 505             r[i] = cr->mpb->fbuf[i];
 506     }
 507 #endif
 508 #endif
 509 }
 510
 511 void gmx_sumi(int nr,int r[],const t_commrec *cr)
 512 {
 513 #ifndef GMX_MPI
 514     gmx_call("gmx_sumi");
 515 #else
 516 #if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREADS)
 517     if (cr->nc.bUse) {
 518         /* Use two step summing */
 519         if (cr->nc.rank_intra == 0)
 520         {
 521             MPI_Reduce(MPI_IN_PLACE,r,nr,MPI_INT,MPI_SUM,0,cr->nc.comm_intra);
 522             /* Sum with the buffers reversed */
 523             MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_INT,MPI_SUM,cr->nc.comm_inter);
 524         }
 525         else
 526         {
 527             /* This is here because of the silly MPI specification
 528                 that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
 529             MPI_Reduce(r,NULL,nr,MPI_INT,MPI_SUM,0,cr->nc.comm_intra);
 530         }
 531         MPI_Bcast(r,nr,MPI_INT,0,cr->nc.comm_intra);
 532     }
 533     else
 534     {
 535         MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_INT,MPI_SUM,cr->mpi_comm_mygroup);
 536     }
 537 #else
 538     int i;
 539
 540     if (nr > cr->mpb->ibuf_alloc) {
 541         cr->mpb->ibuf_alloc = nr;
 542         srenew(cr->mpb->ibuf,cr->mpb->ibuf_alloc);
 543     }
 544     if (cr->nc.bUse) {
 545         /* Use two step summing */
 546         MPI_Allreduce(r,cr->mpb->ibuf,nr,MPI_INT,MPI_SUM,cr->nc.comm_intra);
 547         if (cr->nc.rank_intra == 0) {
 548             /* Sum with the buffers reversed */
 549             MPI_Allreduce(cr->mpb->ibuf,r,nr,MPI_INT,MPI_SUM,cr->nc.comm_inter);
 550         }
 551         MPI_Bcast(r,nr,MPI_INT,0,cr->nc.comm_intra);
 552     } else {
 553         MPI_Allreduce(r,cr->mpb->ibuf,nr,MPI_INT,MPI_SUM,cr->mpi_comm_mygroup);
 554         for(i=0; i<nr; i++)
 555             r[i] = cr->mpb->ibuf[i];
 556     }
 557 #endif
 558 #endif
 559 }
 560
 561 #ifdef GMX_MPI
 562 void gmx_sumd_comm(int nr,double r[],MPI_Comm mpi_comm)
 563 {
 564 #if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREADS)
 565     MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_DOUBLE,MPI_SUM,mpi_comm);
 566 #else
 567     /* this function is only used in code that is not performance critical,
 568        (during setup, when comm_rec is not the appropriate communication
 569        structure), so this isn't as bad as it looks. */
 570     double *buf;
 571     int i;
 572
 573     snew(buf, nr);
 574     MPI_Allreduce(r,buf,nr,MPI_DOUBLE,MPI_SUM,mpi_comm);
 575     for(i=0; i<nr; i++)
 576         r[i] = buf[i];
 577     sfree(buf);
 578 #endif
 579 }
 580 #endif
 581
 582 #ifdef GMX_MPI
 583 void gmx_sumf_comm(int nr,float r[],MPI_Comm mpi_comm)
 584 {
 585 #if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREADS)
 586     MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_FLOAT,MPI_SUM,mpi_comm);
 587 #else
 588     /* this function is only used in code that is not performance critical,
 589        (during setup, when comm_rec is not the appropriate communication
 590        structure), so this isn't as bad as it looks. */
 591     float *buf;
 592     int i;
 593
 594     snew(buf, nr);
 595     MPI_Allreduce(r,buf,nr,MPI_FLOAT,MPI_SUM,mpi_comm);
 596     for(i=0; i<nr; i++)
 597         r[i] = buf[i];
 598     sfree(buf);
 599 #endif
 600 }
 601 #endif
 602
 603 void gmx_sumd_sim(int nr,double r[],const gmx_multisim_t *ms)
 604 {
 605 #ifndef GMX_MPI
 606   gmx_call("gmx_sumd");
 607 #else
 608   gmx_sumd_comm(nr,r,ms->mpi_comm_masters);
 609 #endif
 610 }
 611
 612 void gmx_sumf_sim(int nr,float r[],const gmx_multisim_t *ms)
 613 {
 614 #ifndef GMX_MPI
 615   gmx_call("gmx_sumf");
 616 #else
 617   gmx_sumf_comm(nr,r,ms->mpi_comm_masters);
 618 #endif
 619 }
 620
 621 void gmx_sumi_sim(int nr,int r[], const gmx_multisim_t *ms)
 622 {
 623 #ifndef GMX_MPI
 624     gmx_call("gmx_sumd");
 625 #else
 626 #if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREADS)
 627     MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_INT,MPI_SUM,ms->mpi_comm_masters);
 628 #else
 629     /* this is thread-unsafe, but it will do for now: */
 630     int i;
 631
 632     if (nr > ms->mpb->ibuf_alloc) {
 633         ms->mpb->ibuf_alloc = nr;
 634         srenew(ms->mpb->ibuf,ms->mpb->ibuf_alloc);
 635     }
 636     MPI_Allreduce(r,ms->mpb->ibuf,nr,MPI_INT,MPI_SUM,ms->mpi_comm_masters);
 637     for(i=0; i<nr; i++)
 638         r[i] = ms->mpb->ibuf[i];
 639 #endif
 640 #endif
 641 }
 642
 643 void gmx_finalize(void)
 644 {
 645 #ifndef GMX_MPI
 646   gmx_call("gmx_finalize");
 647 #else
 648   int ret;
 649
 650   /* just as a check; we don't want to finalize twice */
 651   int finalized;
 652   MPI_Finalized(&finalized);
 653   if (finalized)
 654       return;
 655
 656   /* We sync the processes here to try to avoid problems
 657    * with buggy MPI implementations that could cause
 658    * unfinished processes to terminate.
 659    */
 660   MPI_Barrier(MPI_COMM_WORLD);
 661
 662   /*
 663   if (DOMAINDECOMP(cr)) {
 664     if (cr->npmenodes > 0 || cr->dd->bCartesian)
 665       MPI_Comm_free(&cr->mpi_comm_mygroup);
 666     if (cr->dd->bCartesian)
 667       MPI_Comm_free(&cr->mpi_comm_mysim);
 668   }
 669   */
 670
 671   /* Apparently certain mpich implementations cause problems
 672    * with MPI_Finalize. In that case comment out MPI_Finalize.
 673    */
 674   if (debug)
 675     fprintf(debug,"Will call MPI_Finalize now\n");
 676
 677   ret = MPI_Finalize();
 678   if (debug)
 679     fprintf(debug,"Return code from MPI_Finalize = %d\n",ret);
 680 #endif
 681 }
 682