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37 /* This file is completely threadsafe - keep it that way! */
49 #include "gmx_fatal.h"
54 #define block_bc(cr, d) gmx_bcast( sizeof(d), &(d), (cr))
55 /* Probably the test for (nr) > 0 in the next macro is only needed
56 * on BlueGene(/L), where IBM's MPI_Bcast will segfault after
57 * dereferencing a null pointer, even when no data is to be transferred. */
58 #define nblock_bc(cr, nr, d) { if ((nr) > 0) {gmx_bcast((nr)*sizeof((d)[0]), (d), (cr)); }}
59 #define snew_bc(cr, d, nr) { if (!MASTER(cr)) {snew((d), (nr)); }}
60 /* Dirty macro with bAlloc not as an argument */
61 #define nblock_abc(cr, nr, d) { if (bAlloc) {snew((d), (nr)); } nblock_bc(cr, (nr), (d)); }
63 static void bc_string(const t_commrec *cr, t_symtab *symtab, char ***s)
69 handle = lookup_symtab(symtab, *s);
74 *s = get_symtab_handle(symtab, handle);
78 static void bc_strings(const t_commrec *cr, t_symtab *symtab, int nr, char ****nm)
88 for (i = 0; (i < nr); i++)
90 handle[i] = lookup_symtab(symtab, NM[i]);
93 nblock_bc(cr, nr, handle);
99 for (i = 0; (i < nr); i++)
101 (*nm)[i] = get_symtab_handle(symtab, handle[i]);
107 static void bc_strings_resinfo(const t_commrec *cr, t_symtab *symtab,
108 int nr, t_resinfo *resinfo)
116 for (i = 0; (i < nr); i++)
118 handle[i] = lookup_symtab(symtab, resinfo[i].name);
121 nblock_bc(cr, nr, handle);
125 for (i = 0; (i < nr); i++)
127 resinfo[i].name = get_symtab_handle(symtab, handle[i]);
133 static void bc_symtab(const t_commrec *cr, t_symtab *symtab)
138 block_bc(cr, symtab->nr);
140 snew_bc(cr, symtab->symbuf, 1);
141 symbuf = symtab->symbuf;
142 symbuf->bufsize = nr;
143 snew_bc(cr, symbuf->buf, nr);
144 for (i = 0; i < nr; i++)
148 len = strlen(symbuf->buf[i]) + 1;
151 snew_bc(cr, symbuf->buf[i], len);
152 nblock_bc(cr, len, symbuf->buf[i]);
156 static void bc_block(const t_commrec *cr, t_block *block)
158 block_bc(cr, block->nr);
159 snew_bc(cr, block->index, block->nr+1);
160 nblock_bc(cr, block->nr+1, block->index);
163 static void bc_blocka(const t_commrec *cr, t_blocka *block)
165 block_bc(cr, block->nr);
166 snew_bc(cr, block->index, block->nr+1);
167 nblock_bc(cr, block->nr+1, block->index);
168 block_bc(cr, block->nra);
171 snew_bc(cr, block->a, block->nra);
172 nblock_bc(cr, block->nra, block->a);
176 static void bc_grps(const t_commrec *cr, t_grps grps[])
180 for (i = 0; (i < egcNR); i++)
182 block_bc(cr, grps[i].nr);
183 snew_bc(cr, grps[i].nm_ind, grps[i].nr);
184 nblock_bc(cr, grps[i].nr, grps[i].nm_ind);
188 static void bc_atoms(const t_commrec *cr, t_symtab *symtab, t_atoms *atoms)
192 block_bc(cr, atoms->nr);
193 snew_bc(cr, atoms->atom, atoms->nr);
194 nblock_bc(cr, atoms->nr, atoms->atom);
195 bc_strings(cr, symtab, atoms->nr, &atoms->atomname);
196 block_bc(cr, atoms->nres);
197 snew_bc(cr, atoms->resinfo, atoms->nres);
198 nblock_bc(cr, atoms->nres, atoms->resinfo);
199 bc_strings_resinfo(cr, symtab, atoms->nres, atoms->resinfo);
200 /* QMMM requires atomtypes to be known on all nodes as well */
201 bc_strings(cr, symtab, atoms->nr, &atoms->atomtype);
202 bc_strings(cr, symtab, atoms->nr, &atoms->atomtypeB);
205 static void bc_groups(const t_commrec *cr, t_symtab *symtab,
206 int natoms, gmx_groups_t *groups)
211 bc_grps(cr, groups->grps);
212 block_bc(cr, groups->ngrpname);
213 bc_strings(cr, symtab, groups->ngrpname, &groups->grpname);
214 for (g = 0; g < egcNR; g++)
218 if (groups->grpnr[g])
230 groups->grpnr[g] = NULL;
234 snew_bc(cr, groups->grpnr[g], n);
235 nblock_bc(cr, n, groups->grpnr[g]);
240 fprintf(debug, "after bc_groups\n");
244 void bcast_state(const t_commrec *cr, t_state *state)
254 /* Broadcasts the state sizes and flags from the master to all nodes
255 * in cr->mpi_comm_mygroup. The arrays are not broadcasted. */
256 block_bc(cr, state->natoms);
257 block_bc(cr, state->ngtc);
258 block_bc(cr, state->nnhpres);
259 block_bc(cr, state->nhchainlength);
260 block_bc(cr, state->flags);
261 if (state->lambda == NULL)
263 snew_bc(cr, state->lambda, efptNR)
268 /* We allocate dynamically in dd_partition_system. */
271 /* The code below is reachable only by TPI and NM, so it is not
272 tested by anything. */
274 nnht = (state->ngtc)*(state->nhchainlength);
275 nnhtp = (state->nnhpres)*(state->nhchainlength);
277 /* We still need to allocate the arrays in state for non-master
278 * ranks, which is done (implicitly via bAlloc) in the dirty,
279 * dirty nblock_abc macro. */
280 bAlloc = !MASTER(cr);
283 state->nalloc = state->natoms;
285 for (i = 0; i < estNR; i++)
287 if (state->flags & (1<<i))
291 case estLAMBDA: nblock_bc(cr, efptNR, state->lambda); break;
292 case estFEPSTATE: block_bc(cr, state->fep_state); break;
293 case estBOX: block_bc(cr, state->box); break;
294 case estBOX_REL: block_bc(cr, state->box_rel); break;
295 case estBOXV: block_bc(cr, state->boxv); break;
296 case estPRES_PREV: block_bc(cr, state->pres_prev); break;
297 case estSVIR_PREV: block_bc(cr, state->svir_prev); break;
298 case estFVIR_PREV: block_bc(cr, state->fvir_prev); break;
299 case estNH_XI: nblock_abc(cr, nnht, state->nosehoover_xi); break;
300 case estNH_VXI: nblock_abc(cr, nnht, state->nosehoover_vxi); break;
301 case estNHPRES_XI: nblock_abc(cr, nnhtp, state->nhpres_xi); break;
302 case estNHPRES_VXI: nblock_abc(cr, nnhtp, state->nhpres_vxi); break;
303 case estTC_INT: nblock_abc(cr, state->ngtc, state->therm_integral); break;
304 case estVETA: block_bc(cr, state->veta); break;
305 case estVOL0: block_bc(cr, state->vol0); break;
306 case estX: nblock_abc(cr, state->natoms, state->x); break;
307 case estV: nblock_abc(cr, state->natoms, state->v); break;
308 case estSDX: nblock_abc(cr, state->natoms, state->sd_X); break;
309 case estCGP: nblock_abc(cr, state->natoms, state->cg_p); break;
310 case estDISRE_INITF: block_bc(cr, state->hist.disre_initf); break;
311 case estDISRE_RM3TAV:
312 block_bc(cr, state->hist.ndisrepairs);
313 nblock_abc(cr, state->hist.ndisrepairs, state->hist.disre_rm3tav);
315 case estORIRE_INITF: block_bc(cr, state->hist.orire_initf); break;
317 block_bc(cr, state->hist.norire_Dtav);
318 nblock_abc(cr, state->hist.norire_Dtav, state->hist.orire_Dtav);
322 "Communication is not implemented for %s in bcast_state",
329 static void bc_ilists(const t_commrec *cr, t_ilist *ilist)
333 /* Here we only communicate the non-zero length ilists */
336 for (ftype = 0; ftype < F_NRE; ftype++)
338 if (ilist[ftype].nr > 0)
341 block_bc(cr, ilist[ftype].nr);
342 nblock_bc(cr, ilist[ftype].nr, ilist[ftype].iatoms);
350 for (ftype = 0; ftype < F_NRE; ftype++)
359 block_bc(cr, ilist[ftype].nr);
360 snew_bc(cr, ilist[ftype].iatoms, ilist[ftype].nr);
361 nblock_bc(cr, ilist[ftype].nr, ilist[ftype].iatoms);
369 fprintf(debug, "after bc_ilists\n");
373 static void bc_cmap(const t_commrec *cr, gmx_cmap_t *cmap_grid)
375 int i, j, nelem, ngrid;
377 block_bc(cr, cmap_grid->ngrid);
378 block_bc(cr, cmap_grid->grid_spacing);
380 ngrid = cmap_grid->ngrid;
381 nelem = cmap_grid->grid_spacing * cmap_grid->grid_spacing;
385 snew_bc(cr, cmap_grid->cmapdata, ngrid);
387 for (i = 0; i < ngrid; i++)
389 snew_bc(cr, cmap_grid->cmapdata[i].cmap, 4*nelem);
390 nblock_bc(cr, 4*nelem, cmap_grid->cmapdata[i].cmap);
395 static void bc_ffparams(const t_commrec *cr, gmx_ffparams_t *ffp)
399 block_bc(cr, ffp->ntypes);
400 block_bc(cr, ffp->atnr);
401 snew_bc(cr, ffp->functype, ffp->ntypes);
402 snew_bc(cr, ffp->iparams, ffp->ntypes);
403 nblock_bc(cr, ffp->ntypes, ffp->functype);
404 nblock_bc(cr, ffp->ntypes, ffp->iparams);
405 block_bc(cr, ffp->reppow);
406 block_bc(cr, ffp->fudgeQQ);
407 bc_cmap(cr, &ffp->cmap_grid);
410 static void bc_grpopts(const t_commrec *cr, t_grpopts *g)
414 block_bc(cr, g->ngtc);
415 block_bc(cr, g->ngacc);
416 block_bc(cr, g->ngfrz);
417 block_bc(cr, g->ngener);
418 snew_bc(cr, g->nrdf, g->ngtc);
419 snew_bc(cr, g->tau_t, g->ngtc);
420 snew_bc(cr, g->ref_t, g->ngtc);
421 snew_bc(cr, g->acc, g->ngacc);
422 snew_bc(cr, g->nFreeze, g->ngfrz);
423 snew_bc(cr, g->egp_flags, g->ngener*g->ngener);
425 nblock_bc(cr, g->ngtc, g->nrdf);
426 nblock_bc(cr, g->ngtc, g->tau_t);
427 nblock_bc(cr, g->ngtc, g->ref_t);
428 nblock_bc(cr, g->ngacc, g->acc);
429 nblock_bc(cr, g->ngfrz, g->nFreeze);
430 nblock_bc(cr, g->ngener*g->ngener, g->egp_flags);
431 snew_bc(cr, g->annealing, g->ngtc);
432 snew_bc(cr, g->anneal_npoints, g->ngtc);
433 snew_bc(cr, g->anneal_time, g->ngtc);
434 snew_bc(cr, g->anneal_temp, g->ngtc);
435 nblock_bc(cr, g->ngtc, g->annealing);
436 nblock_bc(cr, g->ngtc, g->anneal_npoints);
437 for (i = 0; (i < g->ngtc); i++)
439 n = g->anneal_npoints[i];
442 snew_bc(cr, g->anneal_time[i], n);
443 snew_bc(cr, g->anneal_temp[i], n);
444 nblock_bc(cr, n, g->anneal_time[i]);
445 nblock_bc(cr, n, g->anneal_temp[i]);
449 /* QMMM stuff, see inputrec */
450 block_bc(cr, g->ngQM);
451 snew_bc(cr, g->QMmethod, g->ngQM);
452 snew_bc(cr, g->QMbasis, g->ngQM);
453 snew_bc(cr, g->QMcharge, g->ngQM);
454 snew_bc(cr, g->QMmult, g->ngQM);
455 snew_bc(cr, g->bSH, g->ngQM);
456 snew_bc(cr, g->CASorbitals, g->ngQM);
457 snew_bc(cr, g->CASelectrons, g->ngQM);
458 snew_bc(cr, g->SAon, g->ngQM);
459 snew_bc(cr, g->SAoff, g->ngQM);
460 snew_bc(cr, g->SAsteps, g->ngQM);
464 nblock_bc(cr, g->ngQM, g->QMmethod);
465 nblock_bc(cr, g->ngQM, g->QMbasis);
466 nblock_bc(cr, g->ngQM, g->QMcharge);
467 nblock_bc(cr, g->ngQM, g->QMmult);
468 nblock_bc(cr, g->ngQM, g->bSH);
469 nblock_bc(cr, g->ngQM, g->CASorbitals);
470 nblock_bc(cr, g->ngQM, g->CASelectrons);
471 nblock_bc(cr, g->ngQM, g->SAon);
472 nblock_bc(cr, g->ngQM, g->SAoff);
473 nblock_bc(cr, g->ngQM, g->SAsteps);
474 /* end of QMMM stuff */
478 static void bc_cosines(const t_commrec *cr, t_cosines *cs)
481 snew_bc(cr, cs->a, cs->n);
482 snew_bc(cr, cs->phi, cs->n);
485 nblock_bc(cr, cs->n, cs->a);
486 nblock_bc(cr, cs->n, cs->phi);
490 static void bc_pull_group(const t_commrec *cr, t_pull_group *pgrp)
495 snew_bc(cr, pgrp->ind, pgrp->nat);
496 nblock_bc(cr, pgrp->nat, pgrp->ind);
498 if (pgrp->nweight > 0)
500 snew_bc(cr, pgrp->weight, pgrp->nweight);
501 nblock_bc(cr, pgrp->nweight, pgrp->weight);
505 static void bc_pull(const t_commrec *cr, t_pull *pull)
510 snew_bc(cr, pull->group, pull->ngroup);
511 for (g = 0; g < pull->ngroup; g++)
513 bc_pull_group(cr, &pull->group[g]);
515 snew_bc(cr, pull->coord, pull->ncoord);
516 nblock_bc(cr, pull->ncoord, pull->coord);
519 static void bc_rotgrp(const t_commrec *cr, t_rotgrp *rotg)
524 snew_bc(cr, rotg->ind, rotg->nat);
525 nblock_bc(cr, rotg->nat, rotg->ind);
526 snew_bc(cr, rotg->x_ref, rotg->nat);
527 nblock_bc(cr, rotg->nat, rotg->x_ref);
531 static void bc_rot(const t_commrec *cr, t_rot *rot)
536 snew_bc(cr, rot->grp, rot->ngrp);
537 for (g = 0; g < rot->ngrp; g++)
539 bc_rotgrp(cr, &rot->grp[g]);
543 static void bc_adress(const t_commrec *cr, t_adress *adress)
545 block_bc(cr, *adress);
546 if (adress->n_tf_grps > 0)
548 snew_bc(cr, adress->tf_table_index, adress->n_tf_grps);
549 nblock_bc(cr, adress->n_tf_grps, adress->tf_table_index);
551 if (adress->n_energy_grps > 0)
553 snew_bc(cr, adress->group_explicit, adress->n_energy_grps);
554 nblock_bc(cr, adress->n_energy_grps, adress->group_explicit);
557 static void bc_fepvals(const t_commrec *cr, t_lambda *fep)
559 gmx_bool bAlloc = TRUE;
562 block_bc(cr, fep->nstdhdl);
563 block_bc(cr, fep->init_lambda);
564 block_bc(cr, fep->init_fep_state);
565 block_bc(cr, fep->delta_lambda);
566 block_bc(cr, fep->bPrintEnergy);
567 block_bc(cr, fep->n_lambda);
568 if (fep->n_lambda > 0)
570 snew_bc(cr, fep->all_lambda, efptNR);
571 nblock_bc(cr, efptNR, fep->all_lambda);
572 for (i = 0; i < efptNR; i++)
574 snew_bc(cr, fep->all_lambda[i], fep->n_lambda);
575 nblock_bc(cr, fep->n_lambda, fep->all_lambda[i]);
578 block_bc(cr, fep->sc_alpha);
579 block_bc(cr, fep->sc_power);
580 block_bc(cr, fep->sc_r_power);
581 block_bc(cr, fep->sc_sigma);
582 block_bc(cr, fep->sc_sigma_min);
583 block_bc(cr, fep->bScCoul);
584 nblock_bc(cr, efptNR, &(fep->separate_dvdl[0]));
585 block_bc(cr, fep->dhdl_derivatives);
586 block_bc(cr, fep->dh_hist_size);
587 block_bc(cr, fep->dh_hist_spacing);
590 fprintf(debug, "after bc_fepvals\n");
594 static void bc_expandedvals(const t_commrec *cr, t_expanded *expand, int n_lambda)
596 gmx_bool bAlloc = TRUE;
599 block_bc(cr, expand->nstexpanded);
600 block_bc(cr, expand->elamstats);
601 block_bc(cr, expand->elmcmove);
602 block_bc(cr, expand->elmceq);
603 block_bc(cr, expand->equil_n_at_lam);
604 block_bc(cr, expand->equil_wl_delta);
605 block_bc(cr, expand->equil_ratio);
606 block_bc(cr, expand->equil_steps);
607 block_bc(cr, expand->equil_samples);
608 block_bc(cr, expand->lmc_seed);
609 block_bc(cr, expand->minvar);
610 block_bc(cr, expand->minvar_const);
611 block_bc(cr, expand->c_range);
612 block_bc(cr, expand->bSymmetrizedTMatrix);
613 block_bc(cr, expand->nstTij);
614 block_bc(cr, expand->lmc_repeats);
615 block_bc(cr, expand->lmc_forced_nstart);
616 block_bc(cr, expand->gibbsdeltalam);
617 block_bc(cr, expand->wl_scale);
618 block_bc(cr, expand->wl_ratio);
619 block_bc(cr, expand->init_wl_delta);
620 block_bc(cr, expand->bInit_weights);
621 snew_bc(cr, expand->init_lambda_weights, n_lambda);
622 nblock_bc(cr, n_lambda, expand->init_lambda_weights);
623 block_bc(cr, expand->mc_temp);
626 fprintf(debug, "after bc_expandedvals\n");
630 static void bc_simtempvals(const t_commrec *cr, t_simtemp *simtemp, int n_lambda)
632 gmx_bool bAlloc = TRUE;
635 block_bc(cr, simtemp->simtemp_low);
636 block_bc(cr, simtemp->simtemp_high);
637 block_bc(cr, simtemp->eSimTempScale);
638 snew_bc(cr, simtemp->temperatures, n_lambda);
639 nblock_bc(cr, n_lambda, simtemp->temperatures);
642 fprintf(debug, "after bc_simtempvals\n");
647 static void bc_swapions(const t_commrec *cr, t_swapcoords *swap)
654 /* Broadcast ion group atom indices */
655 snew_bc(cr, swap->ind, swap->nat);
656 nblock_bc(cr, swap->nat, swap->ind);
658 /* Broadcast split groups atom indices */
659 for (i = 0; i < 2; i++)
661 snew_bc(cr, swap->ind_split[i], swap->nat_split[i]);
662 nblock_bc(cr, swap->nat_split[i], swap->ind_split[i]);
665 /* Broadcast solvent group atom indices */
666 snew_bc(cr, swap->ind_sol, swap->nat_sol);
667 nblock_bc(cr, swap->nat_sol, swap->ind_sol);
671 static void bc_inputrec(const t_commrec *cr, t_inputrec *inputrec)
673 gmx_bool bAlloc = TRUE;
676 block_bc(cr, *inputrec);
678 bc_grpopts(cr, &(inputrec->opts));
680 /* even if efep is efepNO, we need to initialize to make sure that
681 * n_lambda is set to zero */
683 snew_bc(cr, inputrec->fepvals, 1);
684 if (inputrec->efep != efepNO || inputrec->bSimTemp)
686 bc_fepvals(cr, inputrec->fepvals);
688 /* need to initialize this as well because of data checked for in the logic */
689 snew_bc(cr, inputrec->expandedvals, 1);
690 if (inputrec->bExpanded)
692 bc_expandedvals(cr, inputrec->expandedvals, inputrec->fepvals->n_lambda);
694 snew_bc(cr, inputrec->simtempvals, 1);
695 if (inputrec->bSimTemp)
697 bc_simtempvals(cr, inputrec->simtempvals, inputrec->fepvals->n_lambda);
699 if (inputrec->ePull != epullNO)
701 snew_bc(cr, inputrec->pull, 1);
702 bc_pull(cr, inputrec->pull);
706 snew_bc(cr, inputrec->rot, 1);
707 bc_rot(cr, inputrec->rot);
709 for (i = 0; (i < DIM); i++)
711 bc_cosines(cr, &(inputrec->ex[i]));
712 bc_cosines(cr, &(inputrec->et[i]));
714 if (inputrec->eSwapCoords != eswapNO)
716 snew_bc(cr, inputrec->swap, 1);
717 bc_swapions(cr, inputrec->swap);
719 if (inputrec->bAdress)
721 snew_bc(cr, inputrec->adress, 1);
722 bc_adress(cr, inputrec->adress);
726 static void bc_moltype(const t_commrec *cr, t_symtab *symtab,
727 gmx_moltype_t *moltype)
729 bc_string(cr, symtab, &moltype->name);
730 bc_atoms(cr, symtab, &moltype->atoms);
733 fprintf(debug, "after bc_atoms\n");
736 bc_ilists(cr, moltype->ilist);
737 bc_block(cr, &moltype->cgs);
738 bc_blocka(cr, &moltype->excls);
741 static void bc_molblock(const t_commrec *cr, gmx_molblock_t *molb)
743 gmx_bool bAlloc = TRUE;
745 block_bc(cr, molb->type);
746 block_bc(cr, molb->nmol);
747 block_bc(cr, molb->natoms_mol);
748 block_bc(cr, molb->nposres_xA);
749 if (molb->nposres_xA > 0)
751 snew_bc(cr, molb->posres_xA, molb->nposres_xA);
752 nblock_bc(cr, molb->nposres_xA*DIM, molb->posres_xA[0]);
754 block_bc(cr, molb->nposres_xB);
755 if (molb->nposres_xB > 0)
757 snew_bc(cr, molb->posres_xB, molb->nposres_xB);
758 nblock_bc(cr, molb->nposres_xB*DIM, molb->posres_xB[0]);
762 fprintf(debug, "after bc_molblock\n");
766 static void bc_atomtypes(const t_commrec *cr, t_atomtypes *atomtypes)
770 block_bc(cr, atomtypes->nr);
774 snew_bc(cr, atomtypes->radius, nr);
775 snew_bc(cr, atomtypes->vol, nr);
776 snew_bc(cr, atomtypes->surftens, nr);
777 snew_bc(cr, atomtypes->gb_radius, nr);
778 snew_bc(cr, atomtypes->S_hct, nr);
780 nblock_bc(cr, nr, atomtypes->radius);
781 nblock_bc(cr, nr, atomtypes->vol);
782 nblock_bc(cr, nr, atomtypes->surftens);
783 nblock_bc(cr, nr, atomtypes->gb_radius);
784 nblock_bc(cr, nr, atomtypes->S_hct);
788 void bcast_ir_mtop(const t_commrec *cr, t_inputrec *inputrec, gmx_mtop_t *mtop)
793 fprintf(debug, "in bc_data\n");
795 bc_inputrec(cr, inputrec);
798 fprintf(debug, "after bc_inputrec\n");
800 bc_symtab(cr, &mtop->symtab);
803 fprintf(debug, "after bc_symtab\n");
805 bc_string(cr, &mtop->symtab, &mtop->name);
808 fprintf(debug, "after bc_name\n");
811 bc_ffparams(cr, &mtop->ffparams);
813 block_bc(cr, mtop->nmoltype);
814 snew_bc(cr, mtop->moltype, mtop->nmoltype);
815 for (i = 0; i < mtop->nmoltype; i++)
817 bc_moltype(cr, &mtop->symtab, &mtop->moltype[i]);
820 block_bc(cr, mtop->nmolblock);
821 snew_bc(cr, mtop->molblock, mtop->nmolblock);
822 for (i = 0; i < mtop->nmolblock; i++)
824 bc_molblock(cr, &mtop->molblock[i]);
827 block_bc(cr, mtop->natoms);
829 bc_atomtypes(cr, &mtop->atomtypes);
831 bc_block(cr, &mtop->mols);
832 bc_groups(cr, &mtop->symtab, mtop->natoms, &mtop->groups);