src/gromacs/mdlib/pme_pp.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.
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  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
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  28  * the papers on the package - you can find them in the top README file.
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  34  */
  35
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40
  41 #include <stdio.h>
  42 #include <string.h>
  43 #include <math.h>
  44 #include "typedefs.h"
  45 #include "smalloc.h"
  46 #include "gmx_fatal.h"
  47 #include "vec.h"
  48 #include "pme.h"
  49 #include "network.h"
  50 #include "domdec.h"
  51 #include "sighandler.h"
  52
  53 #ifdef GMX_LIB_MPI
  54 #include <mpi.h>
  55 #endif
  56 #ifdef GMX_THREAD_MPI
  57 #include "tmpi.h"
  58 #endif
  59
  60 #define PP_PME_CHARGE   (1<<0)
  61 #define PP_PME_CHARGEB  (1<<1)
  62 #define PP_PME_COORD    (1<<2)
  63 #define PP_PME_FEP      (1<<3)
  64 #define PP_PME_ENER_VIR (1<<4)
  65 #define PP_PME_FINISH   (1<<5)
  66
  67 #define PME_PP_SIGSTOP     (1<<0)
  68 #define PME_PP_SIGSTOPNSS     (1<<1)
  69
  70 typedef struct gmx_pme_pp {
  71 #ifdef GMX_MPI
  72   MPI_Comm mpi_comm_mysim;
  73 #endif
  74   int  nnode;        /* The number of PP node to communicate with  */
  75   int  *node;        /* The PP node ranks                          */
  76   int  node_peer;    /* The peer PP node rank                      */
  77   int  *nat;         /* The number of atom for each PP node        */
  78   int  flags_charge; /* The flags sent along with the last charges */
  79   real *chargeA;
  80   real *chargeB;
  81   rvec *x;
  82   rvec *f;
  83   int  nalloc;
  84 #ifdef GMX_MPI
  85   MPI_Request *req;
  86   MPI_Status  *stat;
  87 #endif
  88 } t_gmx_pme_pp;
  89
  90 typedef struct gmx_pme_comm_n_box {
  91   int    natoms;
  92   matrix box;
  93   int    maxshift_x;
  94   int    maxshift_y;
  95   real   lambda;
  96   int    flags;
  97   gmx_large_int_t step;
  98 } gmx_pme_comm_n_box_t;
  99
 100 typedef struct {
 101   matrix vir;
 102   real   energy;
 103   real   dvdlambda;
 104   float  cycles;
 105   gmx_stop_cond_t stop_cond;
 106 } gmx_pme_comm_vir_ene_t;
 107
 108
 109
 110
 111 gmx_pme_pp_t gmx_pme_pp_init(t_commrec *cr)
 112 {
 113   struct gmx_pme_pp *pme_pp;
 114   int rank;
 115
 116   snew(pme_pp,1);
 117
 118 #ifdef GMX_MPI
 119   pme_pp->mpi_comm_mysim = cr->mpi_comm_mysim;
 120   MPI_Comm_rank(cr->mpi_comm_mygroup,&rank);
 121   get_pme_ddnodes(cr,rank,&pme_pp->nnode,&pme_pp->node,&pme_pp->node_peer);
 122   snew(pme_pp->nat,pme_pp->nnode);
 123   snew(pme_pp->req,2*pme_pp->nnode);
 124   snew(pme_pp->stat,2*pme_pp->nnode);
 125   pme_pp->nalloc = 0;
 126   pme_pp->flags_charge = 0;
 127 #endif
 128
 129   return pme_pp;
 130 }
 131
 132 /* This should be faster with a real non-blocking MPI implementation */
 133 /* #define GMX_PME_DELAYED_WAIT */
 134
 135 static void gmx_pme_send_q_x_wait(gmx_domdec_t *dd)
 136 {
 137 #ifdef GMX_MPI
 138   if (dd->nreq_pme) {
 139     MPI_Waitall(dd->nreq_pme,dd->req_pme,MPI_STATUSES_IGNORE);
 140     dd->nreq_pme = 0;
 141   }
 142 #endif
 143 }
 144
 145 static void gmx_pme_send_q_x(t_commrec *cr, int flags,
 146                              real *chargeA, real *chargeB,
 147                              matrix box, rvec *x,
 148                              real lambda,
 149                              int maxshift_x, int maxshift_y,
 150                              gmx_large_int_t step)
 151 {
 152   gmx_domdec_t *dd;
 153   gmx_pme_comm_n_box_t *cnb;
 154   int  n;
 155
 156   dd = cr->dd;
 157   n = dd->nat_home;
 158
 159   if (debug)
 160     fprintf(debug,"PP node %d sending to PME node %d: %d%s%s\n",
 161             cr->sim_nodeid,dd->pme_nodeid,n,
 162             flags & PP_PME_CHARGE ? " charges" : "",
 163             flags & PP_PME_COORD  ? " coordinates" : "");
 164
 165 #ifdef GMX_PME_DELAYED_WAIT
 166   /* When can not use cnb until pending communication has finished */
 167   gmx_pme_send_x_q_wait(dd);
 168 #endif
 169
 170   if (dd->pme_receive_vir_ener) {
 171     /* Peer PP node: communicate all data */
 172     if (dd->cnb == NULL)
 173       snew(dd->cnb,1);
 174     cnb = dd->cnb;
 175
 176     cnb->flags      = flags;
 177     cnb->natoms     = n;
 178     cnb->maxshift_x = maxshift_x;
 179     cnb->maxshift_y = maxshift_y;
 180     cnb->lambda     = lambda;
 181     cnb->step       = step;
 182     if (flags & PP_PME_COORD)
 183       copy_mat(box,cnb->box);
 184 #ifdef GMX_MPI
 185     MPI_Isend(cnb,sizeof(*cnb),MPI_BYTE,
 186               dd->pme_nodeid,0,cr->mpi_comm_mysim,
 187               &dd->req_pme[dd->nreq_pme++]);
 188 #endif
 189   } else if (flags & PP_PME_CHARGE) {
 190 #ifdef GMX_MPI
 191     /* Communicate only the number of atoms */
 192     MPI_Isend(&n,sizeof(n),MPI_BYTE,
 193               dd->pme_nodeid,0,cr->mpi_comm_mysim,
 194               &dd->req_pme[dd->nreq_pme++]);
 195 #endif
 196   }
 197
 198 #ifdef GMX_MPI
 199   if (n > 0) {
 200     if (flags & PP_PME_CHARGE) {
 201       MPI_Isend(chargeA,n*sizeof(real),MPI_BYTE,
 202                 dd->pme_nodeid,1,cr->mpi_comm_mysim,
 203                 &dd->req_pme[dd->nreq_pme++]);
 204     }
 205     if (flags & PP_PME_CHARGEB) {
 206       MPI_Isend(chargeB,n*sizeof(real),MPI_BYTE,
 207                 dd->pme_nodeid,2,cr->mpi_comm_mysim,
 208                 &dd->req_pme[dd->nreq_pme++]);
 209     }
 210     if (flags & PP_PME_COORD) {
 211       MPI_Isend(x[0],n*sizeof(rvec),MPI_BYTE,
 212                 dd->pme_nodeid,3,cr->mpi_comm_mysim,
 213                 &dd->req_pme[dd->nreq_pme++]);
 214     }
 215   }
 216
 217 #ifndef GMX_PME_DELAYED_WAIT
 218   /* Wait for the data to arrive */
 219   /* We can skip this wait as we are sure x and q will not be modified
 220    * before the next call to gmx_pme_send_x_q or gmx_pme_receive_f.
 221    */
 222   gmx_pme_send_q_x_wait(dd);
 223 #endif
 224 #endif
 225 }
 226
 227 void gmx_pme_send_q(t_commrec *cr,
 228                     gmx_bool bFreeEnergy, real *chargeA, real *chargeB,
 229                     int maxshift_x, int maxshift_y)
 230 {
 231   int flags;
 232
 233   flags = PP_PME_CHARGE;
 234   if (bFreeEnergy)
 235     flags |= PP_PME_CHARGEB;
 236
 237   gmx_pme_send_q_x(cr,flags,
 238                    chargeA,chargeB,NULL,NULL,0,maxshift_x,maxshift_y,-1);
 239 }
 240
 241 void gmx_pme_send_x(t_commrec *cr, matrix box, rvec *x,
 242                     gmx_bool bFreeEnergy, real lambda,
 243                     gmx_bool bEnerVir,
 244                     gmx_large_int_t step)
 245 {
 246   int flags;
 247
 248   flags = PP_PME_COORD;
 249   if (bFreeEnergy)
 250     flags |= PP_PME_FEP;
 251   if (bEnerVir)
 252     flags |= PP_PME_ENER_VIR;
 253
 254   gmx_pme_send_q_x(cr,flags,NULL,NULL,box,x,lambda,0,0,step);
 255 }
 256
 257 void gmx_pme_finish(t_commrec *cr)
 258 {
 259   int flags;
 260
 261   flags = PP_PME_FINISH;
 262
 263   gmx_pme_send_q_x(cr,flags,NULL,NULL,NULL,NULL,0,0,0,-1);
 264 }
 265
 266 int gmx_pme_recv_q_x(struct gmx_pme_pp *pme_pp,
 267                      real **chargeA, real **chargeB,
 268                      matrix box, rvec **x,rvec **f,
 269                      int *maxshift_x, int *maxshift_y,
 270                      gmx_bool *bFreeEnergy,real *lambda,
 271                      gmx_bool *bEnerVir,
 272                      gmx_large_int_t *step)
 273 {
 274     gmx_pme_comm_n_box_t cnb;
 275     int  nat=0,q,messages,sender;
 276     real *charge_pp;
 277
 278     messages = 0;
 279
 280     /* avoid compiler warning about unused variable without MPI support */
 281     cnb.flags = 0;
 282 #ifdef GMX_MPI
 283     do {
 284         /* Receive the send count, box and time step from the peer PP node */
 285         MPI_Recv(&cnb,sizeof(cnb),MPI_BYTE,
 286                  pme_pp->node_peer,0,
 287                  pme_pp->mpi_comm_mysim,MPI_STATUS_IGNORE);
 288
 289         if (debug)
 290             fprintf(debug,"PME only node receiving:%s%s%s\n",
 291                     (cnb.flags & PP_PME_CHARGE) ? " charges" : "",
 292                         (cnb.flags & PP_PME_COORD ) ? " coordinates" : "",
 293                             (cnb.flags & PP_PME_FINISH) ? " finish" : "");
 294
 295         if (cnb.flags & PP_PME_CHARGE) {
 296             /* Receive the send counts from the other PP nodes */
 297             for(sender=0; sender<pme_pp->nnode; sender++) {
 298                 if (pme_pp->node[sender] == pme_pp->node_peer) {
 299                     pme_pp->nat[sender] = cnb.natoms;
 300                 } else {
 301                     MPI_Irecv(&(pme_pp->nat[sender]),sizeof(pme_pp->nat[0]),
 302                               MPI_BYTE,
 303                               pme_pp->node[sender],0,
 304                               pme_pp->mpi_comm_mysim,&pme_pp->req[messages++]);
 305                 }
 306             }
 307             MPI_Waitall(messages, pme_pp->req, pme_pp->stat);
 308             messages = 0;
 309
 310             nat = 0;
 311             for(sender=0; sender<pme_pp->nnode; sender++)
 312                 nat += pme_pp->nat[sender];
 313
 314             if (nat > pme_pp->nalloc) {
 315                 pme_pp->nalloc = over_alloc_dd(nat);
 316                 srenew(pme_pp->chargeA,pme_pp->nalloc);
 317                 if (cnb.flags & PP_PME_CHARGEB)
 318                     srenew(pme_pp->chargeB,pme_pp->nalloc);
 319                 srenew(pme_pp->x,pme_pp->nalloc);
 320                 srenew(pme_pp->f,pme_pp->nalloc);
 321             }
 322
 323             /* maxshift is sent when the charges are sent */
 324             *maxshift_x = cnb.maxshift_x;
 325             *maxshift_y = cnb.maxshift_y;
 326
 327             /* Receive the charges in place */
 328             for(q=0; q<((cnb.flags & PP_PME_CHARGEB) ? 2 : 1); q++) {
 329                 if (q == 0)
 330                     charge_pp = pme_pp->chargeA;
 331                 else
 332                     charge_pp = pme_pp->chargeB;
 333                 nat = 0;
 334                 for(sender=0; sender<pme_pp->nnode; sender++) {
 335                     if (pme_pp->nat[sender] > 0) {
 336                         MPI_Irecv(charge_pp+nat,
 337                                   pme_pp->nat[sender]*sizeof(real),
 338                                   MPI_BYTE,
 339                                   pme_pp->node[sender],1+q,
 340                                   pme_pp->mpi_comm_mysim,
 341                                   &pme_pp->req[messages++]);
 342                         nat += pme_pp->nat[sender];
 343                         if (debug)
 344                             fprintf(debug,"Received from PP node %d: %d "
 345                                 "charges\n",
 346                                     pme_pp->node[sender],pme_pp->nat[sender]);
 347                     }
 348                 }
 349             }
 350
 351             pme_pp->flags_charge = cnb.flags;
 352         }
 353
 354         if (cnb.flags & PP_PME_COORD) {
 355             if (!(pme_pp->flags_charge & PP_PME_CHARGE))
 356                 gmx_incons("PME-only node received coordinates before charges"
 357                     );
 358
 359             /* The box, FE flag and lambda are sent along with the coordinates
 360              *  */
 361             copy_mat(cnb.box,box);
 362             *bFreeEnergy = (cnb.flags & PP_PME_FEP);
 363             *lambda      = cnb.lambda;
 364             *bEnerVir    = (cnb.flags & PP_PME_ENER_VIR);
 365
 366             if (*bFreeEnergy && !(pme_pp->flags_charge & PP_PME_CHARGEB))
 367                 gmx_incons("PME-only node received free energy request, but "
 368                     "did not receive B-state charges");
 369
 370             /* Receive the coordinates in place */
 371             nat = 0;
 372             for(sender=0; sender<pme_pp->nnode; sender++) {
 373                 if (pme_pp->nat[sender] > 0) {
 374                     MPI_Irecv(pme_pp->x[nat],pme_pp->nat[sender]*sizeof(rvec),
 375                               MPI_BYTE,
 376                               pme_pp->node[sender],3,
 377                               pme_pp->mpi_comm_mysim,&pme_pp->req[messages++]);
 378                     nat += pme_pp->nat[sender];
 379                     if (debug)
 380                         fprintf(debug,"Received from PP node %d: %d "
 381                             "coordinates\n",
 382                                 pme_pp->node[sender],pme_pp->nat[sender]);
 383                 }
 384             }
 385         }
 386
 387         /* Wait for the coordinates and/or charges to arrive */
 388         MPI_Waitall(messages, pme_pp->req, pme_pp->stat);
 389         messages = 0;
 390     } while (!(cnb.flags & (PP_PME_COORD | PP_PME_FINISH)));
 391
 392     *step = cnb.step;
 393 #endif
 394
 395     *chargeA = pme_pp->chargeA;
 396     *chargeB = pme_pp->chargeB;
 397     *x       = pme_pp->x;
 398     *f       = pme_pp->f;
 399
 400
 401     return ((cnb.flags & PP_PME_FINISH) ? -1 : nat);
 402 }
 403
 404 static void receive_virial_energy(t_commrec *cr,
 405                                   matrix vir,real *energy,real *dvdlambda,
 406                                   float *pme_cycles)
 407 {
 408   gmx_pme_comm_vir_ene_t cve;
 409
 410   if (cr->dd->pme_receive_vir_ener) {
 411     if (debug)
 412       fprintf(debug,
 413               "PP node %d receiving from PME node %d: virial and energy\n",
 414               cr->sim_nodeid,cr->dd->pme_nodeid);
 415 #ifdef GMX_MPI
 416     MPI_Recv(&cve,sizeof(cve),MPI_BYTE,cr->dd->pme_nodeid,1,cr->mpi_comm_mysim,
 417              MPI_STATUS_IGNORE);
 418 #else
 419     memset(&cve,0,sizeof(cve));
 420 #endif
 421
 422     m_add(vir,cve.vir,vir);
 423     *energy = cve.energy;
 424     *dvdlambda += cve.dvdlambda;
 425     *pme_cycles = cve.cycles;
 426
 427     if ( cve.stop_cond != gmx_stop_cond_none )
 428     {
 429         gmx_set_stop_condition(cve.stop_cond);
 430     }
 431   } else {
 432     *energy = 0;
 433     *pme_cycles = 0;
 434   }
 435 }
 436
 437 void gmx_pme_receive_f(t_commrec *cr,
 438                        rvec f[], matrix vir,
 439                        real *energy, real *dvdlambda,
 440                        float *pme_cycles)
 441 {
 442   int natoms,i;
 443
 444 #ifdef GMX_PME_DELAYED_WAIT
 445   /* Wait for the x request to finish */
 446   gmx_pme_send_q_x_wait(cr->dd);
 447 #endif
 448
 449   natoms = cr->dd->nat_home;
 450
 451   if (natoms > cr->dd->pme_recv_f_alloc)
 452   {
 453       cr->dd->pme_recv_f_alloc = over_alloc_dd(natoms);
 454       srenew(cr->dd->pme_recv_f_buf, cr->dd->pme_recv_f_alloc);
 455   }
 456
 457 #ifdef GMX_MPI
 458   MPI_Recv(cr->dd->pme_recv_f_buf[0],
 459            natoms*sizeof(rvec),MPI_BYTE,
 460            cr->dd->pme_nodeid,0,cr->mpi_comm_mysim,
 461            MPI_STATUS_IGNORE);
 462 #endif
 463
 464   for(i=0; i<natoms; i++)
 465       rvec_inc(f[i],cr->dd->pme_recv_f_buf[i]);
 466
 467
 468   receive_virial_energy(cr,vir,energy,dvdlambda,pme_cycles);
 469 }
 470
 471 void gmx_pme_send_force_vir_ener(struct gmx_pme_pp *pme_pp,
 472                                  rvec *f, matrix vir,
 473                                  real energy, real dvdlambda,
 474                                  float cycles)
 475 {
 476   gmx_pme_comm_vir_ene_t cve;
 477   int messages,ind_start,ind_end,receiver;
 478
 479   cve.cycles = cycles;
 480
 481   /* Now the evaluated forces have to be transferred to the PP nodes */
 482   messages = 0;
 483   ind_end = 0;
 484   for (receiver=0; receiver<pme_pp->nnode; receiver++) {
 485     ind_start = ind_end;
 486     ind_end   = ind_start + pme_pp->nat[receiver];
 487 #ifdef GMX_MPI
 488     if (MPI_Isend(f[ind_start],(ind_end-ind_start)*sizeof(rvec),MPI_BYTE,
 489                   pme_pp->node[receiver],0,
 490                   pme_pp->mpi_comm_mysim,&pme_pp->req[messages++]) != 0)
 491       gmx_comm("MPI_Isend failed in do_pmeonly");
 492 #endif
 493     }
 494
 495   /* send virial and energy to our last PP node */
 496   copy_mat(vir,cve.vir);
 497   cve.energy    = energy;
 498   cve.dvdlambda = dvdlambda;
 499   /* check for the signals to send back to a PP node */
 500   cve.stop_cond = gmx_get_stop_condition();
 501
 502   cve.cycles = cycles;
 503
 504   if (debug)
 505     fprintf(debug,"PME node sending to PP node %d: virial and energy\n",
 506             pme_pp->node_peer);
 507 #ifdef GMX_MPI
 508   MPI_Isend(&cve,sizeof(cve),MPI_BYTE,
 509             pme_pp->node_peer,1,
 510             pme_pp->mpi_comm_mysim,&pme_pp->req[messages++]);
 511
 512   /* Wait for the forces to arrive */
 513   MPI_Waitall(messages, pme_pp->req, pme_pp->stat);
 514 #endif
 515 }