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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_setup(const t_commrec *cr, t_state *state)
246 block_bc(cr, state->natoms);
247 block_bc(cr, state->ngtc);
248 block_bc(cr, state->nnhpres);
249 block_bc(cr, state->nhchainlength);
250 block_bc(cr, state->nrng);
251 block_bc(cr, state->nrngi);
252 block_bc(cr, state->flags);
253 if (state->lambda == NULL)
255 snew_bc(cr, state->lambda, efptNR)
259 void bcast_state(const t_commrec *cr, t_state *state, gmx_bool bAlloc)
263 bcast_state_setup(cr, state);
265 nnht = (state->ngtc)*(state->nhchainlength);
266 nnhtp = (state->nnhpres)*(state->nhchainlength);
274 state->nalloc = state->natoms;
276 for (i = 0; i < estNR; i++)
278 if (state->flags & (1<<i))
282 case estLAMBDA: nblock_bc(cr, efptNR, state->lambda); break;
283 case estFEPSTATE: block_bc(cr, state->fep_state); break;
284 case estBOX: block_bc(cr, state->box); break;
285 case estBOX_REL: block_bc(cr, state->box_rel); break;
286 case estBOXV: block_bc(cr, state->boxv); break;
287 case estPRES_PREV: block_bc(cr, state->pres_prev); break;
288 case estSVIR_PREV: block_bc(cr, state->svir_prev); break;
289 case estFVIR_PREV: block_bc(cr, state->fvir_prev); break;
290 case estNH_XI: nblock_abc(cr, nnht, state->nosehoover_xi); break;
291 case estNH_VXI: nblock_abc(cr, nnht, state->nosehoover_vxi); break;
292 case estNHPRES_XI: nblock_abc(cr, nnhtp, state->nhpres_xi); break;
293 case estNHPRES_VXI: nblock_abc(cr, nnhtp, state->nhpres_vxi); break;
294 case estTC_INT: nblock_abc(cr, state->ngtc, state->therm_integral); break;
295 case estVETA: block_bc(cr, state->veta); break;
296 case estVOL0: block_bc(cr, state->vol0); break;
297 case estX: nblock_abc(cr, state->natoms, state->x); break;
298 case estV: nblock_abc(cr, state->natoms, state->v); break;
299 case estSDX: nblock_abc(cr, state->natoms, state->sd_X); break;
300 case estCGP: nblock_abc(cr, state->natoms, state->cg_p); break;
301 case estLD_RNG: if (state->nrngi == 1)
303 nblock_abc(cr, state->nrng, state->ld_rng);
306 case estLD_RNGI: if (state->nrngi == 1)
308 nblock_abc(cr, state->nrngi, state->ld_rngi);
311 case estDISRE_INITF: block_bc(cr, state->hist.disre_initf); break;
312 case estDISRE_RM3TAV:
313 block_bc(cr, state->hist.ndisrepairs);
314 nblock_abc(cr, state->hist.ndisrepairs, state->hist.disre_rm3tav);
316 case estORIRE_INITF: block_bc(cr, state->hist.orire_initf); break;
318 block_bc(cr, state->hist.norire_Dtav);
319 nblock_abc(cr, state->hist.norire_Dtav, state->hist.orire_Dtav);
323 "Communication is not implemented for %s in bcast_state",
330 static void bc_ilists(const t_commrec *cr, t_ilist *ilist)
334 /* Here we only communicate the non-zero length ilists */
337 for (ftype = 0; ftype < F_NRE; ftype++)
339 if (ilist[ftype].nr > 0)
342 block_bc(cr, ilist[ftype].nr);
343 nblock_bc(cr, ilist[ftype].nr, ilist[ftype].iatoms);
351 for (ftype = 0; ftype < F_NRE; ftype++)
360 block_bc(cr, ilist[ftype].nr);
361 snew_bc(cr, ilist[ftype].iatoms, ilist[ftype].nr);
362 nblock_bc(cr, ilist[ftype].nr, ilist[ftype].iatoms);
370 fprintf(debug, "after bc_ilists\n");
374 static void bc_cmap(const t_commrec *cr, gmx_cmap_t *cmap_grid)
376 int i, j, nelem, ngrid;
378 block_bc(cr, cmap_grid->ngrid);
379 block_bc(cr, cmap_grid->grid_spacing);
381 ngrid = cmap_grid->ngrid;
382 nelem = cmap_grid->grid_spacing * cmap_grid->grid_spacing;
386 snew_bc(cr, cmap_grid->cmapdata, ngrid);
388 for (i = 0; i < ngrid; i++)
390 snew_bc(cr, cmap_grid->cmapdata[i].cmap, 4*nelem);
391 nblock_bc(cr, 4*nelem, cmap_grid->cmapdata[i].cmap);
396 static void bc_ffparams(const t_commrec *cr, gmx_ffparams_t *ffp)
400 block_bc(cr, ffp->ntypes);
401 block_bc(cr, ffp->atnr);
402 snew_bc(cr, ffp->functype, ffp->ntypes);
403 snew_bc(cr, ffp->iparams, ffp->ntypes);
404 nblock_bc(cr, ffp->ntypes, ffp->functype);
405 nblock_bc(cr, ffp->ntypes, ffp->iparams);
406 block_bc(cr, ffp->reppow);
407 block_bc(cr, ffp->fudgeQQ);
408 bc_cmap(cr, &ffp->cmap_grid);
411 static void bc_grpopts(const t_commrec *cr, t_grpopts *g)
415 block_bc(cr, g->ngtc);
416 block_bc(cr, g->ngacc);
417 block_bc(cr, g->ngfrz);
418 block_bc(cr, g->ngener);
419 snew_bc(cr, g->nrdf, g->ngtc);
420 snew_bc(cr, g->tau_t, g->ngtc);
421 snew_bc(cr, g->ref_t, g->ngtc);
422 snew_bc(cr, g->acc, g->ngacc);
423 snew_bc(cr, g->nFreeze, g->ngfrz);
424 snew_bc(cr, g->egp_flags, g->ngener*g->ngener);
426 nblock_bc(cr, g->ngtc, g->nrdf);
427 nblock_bc(cr, g->ngtc, g->tau_t);
428 nblock_bc(cr, g->ngtc, g->ref_t);
429 nblock_bc(cr, g->ngacc, g->acc);
430 nblock_bc(cr, g->ngfrz, g->nFreeze);
431 nblock_bc(cr, g->ngener*g->ngener, g->egp_flags);
432 snew_bc(cr, g->annealing, g->ngtc);
433 snew_bc(cr, g->anneal_npoints, g->ngtc);
434 snew_bc(cr, g->anneal_time, g->ngtc);
435 snew_bc(cr, g->anneal_temp, g->ngtc);
436 nblock_bc(cr, g->ngtc, g->annealing);
437 nblock_bc(cr, g->ngtc, g->anneal_npoints);
438 for (i = 0; (i < g->ngtc); i++)
440 n = g->anneal_npoints[i];
443 snew_bc(cr, g->anneal_time[i], n);
444 snew_bc(cr, g->anneal_temp[i], n);
445 nblock_bc(cr, n, g->anneal_time[i]);
446 nblock_bc(cr, n, g->anneal_temp[i]);
450 /* QMMM stuff, see inputrec */
451 block_bc(cr, g->ngQM);
452 snew_bc(cr, g->QMmethod, g->ngQM);
453 snew_bc(cr, g->QMbasis, g->ngQM);
454 snew_bc(cr, g->QMcharge, g->ngQM);
455 snew_bc(cr, g->QMmult, g->ngQM);
456 snew_bc(cr, g->bSH, g->ngQM);
457 snew_bc(cr, g->CASorbitals, g->ngQM);
458 snew_bc(cr, g->CASelectrons, g->ngQM);
459 snew_bc(cr, g->SAon, g->ngQM);
460 snew_bc(cr, g->SAoff, g->ngQM);
461 snew_bc(cr, g->SAsteps, g->ngQM);
465 nblock_bc(cr, g->ngQM, g->QMmethod);
466 nblock_bc(cr, g->ngQM, g->QMbasis);
467 nblock_bc(cr, g->ngQM, g->QMcharge);
468 nblock_bc(cr, g->ngQM, g->QMmult);
469 nblock_bc(cr, g->ngQM, g->bSH);
470 nblock_bc(cr, g->ngQM, g->CASorbitals);
471 nblock_bc(cr, g->ngQM, g->CASelectrons);
472 nblock_bc(cr, g->ngQM, g->SAon);
473 nblock_bc(cr, g->ngQM, g->SAoff);
474 nblock_bc(cr, g->ngQM, g->SAsteps);
475 /* end of QMMM stuff */
479 static void bc_cosines(const t_commrec *cr, t_cosines *cs)
482 snew_bc(cr, cs->a, cs->n);
483 snew_bc(cr, cs->phi, cs->n);
486 nblock_bc(cr, cs->n, cs->a);
487 nblock_bc(cr, cs->n, cs->phi);
491 static void bc_pull_group(const t_commrec *cr, t_pull_group *pgrp)
496 snew_bc(cr, pgrp->ind, pgrp->nat);
497 nblock_bc(cr, pgrp->nat, pgrp->ind);
499 if (pgrp->nweight > 0)
501 snew_bc(cr, pgrp->weight, pgrp->nweight);
502 nblock_bc(cr, pgrp->nweight, pgrp->weight);
506 static void bc_pull(const t_commrec *cr, t_pull *pull)
511 snew_bc(cr, pull->group, pull->ngroup);
512 for (g = 0; g < pull->ngroup; g++)
514 bc_pull_group(cr, &pull->group[g]);
516 snew_bc(cr, pull->coord, pull->ncoord);
517 nblock_bc(cr, pull->ncoord, pull->coord);
520 static void bc_rotgrp(const t_commrec *cr, t_rotgrp *rotg)
525 snew_bc(cr, rotg->ind, rotg->nat);
526 nblock_bc(cr, rotg->nat, rotg->ind);
527 snew_bc(cr, rotg->x_ref, rotg->nat);
528 nblock_bc(cr, rotg->nat, rotg->x_ref);
532 static void bc_rot(const t_commrec *cr, t_rot *rot)
537 snew_bc(cr, rot->grp, rot->ngrp);
538 for (g = 0; g < rot->ngrp; g++)
540 bc_rotgrp(cr, &rot->grp[g]);
544 static void bc_adress(const t_commrec *cr, t_adress *adress)
546 block_bc(cr, *adress);
547 if (adress->n_tf_grps > 0)
549 snew_bc(cr, adress->tf_table_index, adress->n_tf_grps);
550 nblock_bc(cr, adress->n_tf_grps, adress->tf_table_index);
552 if (adress->n_energy_grps > 0)
554 snew_bc(cr, adress->group_explicit, adress->n_energy_grps);
555 nblock_bc(cr, adress->n_energy_grps, adress->group_explicit);
558 static void bc_fepvals(const t_commrec *cr, t_lambda *fep)
560 gmx_bool bAlloc = TRUE;
563 block_bc(cr, fep->nstdhdl);
564 block_bc(cr, fep->init_lambda);
565 block_bc(cr, fep->init_fep_state);
566 block_bc(cr, fep->delta_lambda);
567 block_bc(cr, fep->bPrintEnergy);
568 block_bc(cr, fep->n_lambda);
569 if (fep->n_lambda > 0)
571 snew_bc(cr, fep->all_lambda, efptNR);
572 nblock_bc(cr, efptNR, fep->all_lambda);
573 for (i = 0; i < efptNR; i++)
575 snew_bc(cr, fep->all_lambda[i], fep->n_lambda);
576 nblock_bc(cr, fep->n_lambda, fep->all_lambda[i]);
579 block_bc(cr, fep->sc_alpha);
580 block_bc(cr, fep->sc_power);
581 block_bc(cr, fep->sc_r_power);
582 block_bc(cr, fep->sc_sigma);
583 block_bc(cr, fep->sc_sigma_min);
584 block_bc(cr, fep->bScCoul);
585 nblock_bc(cr, efptNR, &(fep->separate_dvdl[0]));
586 block_bc(cr, fep->dhdl_derivatives);
587 block_bc(cr, fep->dh_hist_size);
588 block_bc(cr, fep->dh_hist_spacing);
591 fprintf(debug, "after bc_fepvals\n");
595 static void bc_expandedvals(const t_commrec *cr, t_expanded *expand, int n_lambda)
597 gmx_bool bAlloc = TRUE;
600 block_bc(cr, expand->nstexpanded);
601 block_bc(cr, expand->elamstats);
602 block_bc(cr, expand->elmcmove);
603 block_bc(cr, expand->elmceq);
604 block_bc(cr, expand->equil_n_at_lam);
605 block_bc(cr, expand->equil_wl_delta);
606 block_bc(cr, expand->equil_ratio);
607 block_bc(cr, expand->equil_steps);
608 block_bc(cr, expand->equil_samples);
609 block_bc(cr, expand->lmc_seed);
610 block_bc(cr, expand->minvar);
611 block_bc(cr, expand->minvar_const);
612 block_bc(cr, expand->c_range);
613 block_bc(cr, expand->bSymmetrizedTMatrix);
614 block_bc(cr, expand->nstTij);
615 block_bc(cr, expand->lmc_repeats);
616 block_bc(cr, expand->lmc_forced_nstart);
617 block_bc(cr, expand->gibbsdeltalam);
618 block_bc(cr, expand->wl_scale);
619 block_bc(cr, expand->wl_ratio);
620 block_bc(cr, expand->init_wl_delta);
621 block_bc(cr, expand->bInit_weights);
622 snew_bc(cr, expand->init_lambda_weights, n_lambda);
623 nblock_bc(cr, n_lambda, expand->init_lambda_weights);
624 block_bc(cr, expand->mc_temp);
627 fprintf(debug, "after bc_expandedvals\n");
631 static void bc_simtempvals(const t_commrec *cr, t_simtemp *simtemp, int n_lambda)
633 gmx_bool bAlloc = TRUE;
636 block_bc(cr, simtemp->simtemp_low);
637 block_bc(cr, simtemp->simtemp_high);
638 block_bc(cr, simtemp->eSimTempScale);
639 snew_bc(cr, simtemp->temperatures, n_lambda);
640 nblock_bc(cr, n_lambda, simtemp->temperatures);
643 fprintf(debug, "after bc_simtempvals\n");
647 static void bc_inputrec(const t_commrec *cr, t_inputrec *inputrec)
649 gmx_bool bAlloc = TRUE;
652 block_bc(cr, *inputrec);
654 bc_grpopts(cr, &(inputrec->opts));
656 /* even if efep is efepNO, we need to initialize to make sure that
657 * n_lambda is set to zero */
659 snew_bc(cr, inputrec->fepvals, 1);
660 if (inputrec->efep != efepNO || inputrec->bSimTemp)
662 bc_fepvals(cr, inputrec->fepvals);
664 /* need to initialize this as well because of data checked for in the logic */
665 snew_bc(cr, inputrec->expandedvals, 1);
666 if (inputrec->bExpanded)
668 bc_expandedvals(cr, inputrec->expandedvals, inputrec->fepvals->n_lambda);
670 snew_bc(cr, inputrec->simtempvals, 1);
671 if (inputrec->bSimTemp)
673 bc_simtempvals(cr, inputrec->simtempvals, inputrec->fepvals->n_lambda);
675 if (inputrec->ePull != epullNO)
677 snew_bc(cr, inputrec->pull, 1);
678 bc_pull(cr, inputrec->pull);
682 snew_bc(cr, inputrec->rot, 1);
683 bc_rot(cr, inputrec->rot);
685 for (i = 0; (i < DIM); i++)
687 bc_cosines(cr, &(inputrec->ex[i]));
688 bc_cosines(cr, &(inputrec->et[i]));
690 if (inputrec->bAdress)
692 snew_bc(cr, inputrec->adress, 1);
693 bc_adress(cr, inputrec->adress);
697 static void bc_moltype(const t_commrec *cr, t_symtab *symtab,
698 gmx_moltype_t *moltype)
700 bc_string(cr, symtab, &moltype->name);
701 bc_atoms(cr, symtab, &moltype->atoms);
704 fprintf(debug, "after bc_atoms\n");
707 bc_ilists(cr, moltype->ilist);
708 bc_block(cr, &moltype->cgs);
709 bc_blocka(cr, &moltype->excls);
712 static void bc_molblock(const t_commrec *cr, gmx_molblock_t *molb)
714 gmx_bool bAlloc = TRUE;
716 block_bc(cr, molb->type);
717 block_bc(cr, molb->nmol);
718 block_bc(cr, molb->natoms_mol);
719 block_bc(cr, molb->nposres_xA);
720 if (molb->nposres_xA > 0)
722 snew_bc(cr, molb->posres_xA, molb->nposres_xA);
723 nblock_bc(cr, molb->nposres_xA*DIM, molb->posres_xA[0]);
725 block_bc(cr, molb->nposres_xB);
726 if (molb->nposres_xB > 0)
728 snew_bc(cr, molb->posres_xB, molb->nposres_xB);
729 nblock_bc(cr, molb->nposres_xB*DIM, molb->posres_xB[0]);
733 fprintf(debug, "after bc_molblock\n");
737 static void bc_atomtypes(const t_commrec *cr, t_atomtypes *atomtypes)
741 block_bc(cr, atomtypes->nr);
745 snew_bc(cr, atomtypes->radius, nr);
746 snew_bc(cr, atomtypes->vol, nr);
747 snew_bc(cr, atomtypes->surftens, nr);
748 snew_bc(cr, atomtypes->gb_radius, nr);
749 snew_bc(cr, atomtypes->S_hct, nr);
751 nblock_bc(cr, nr, atomtypes->radius);
752 nblock_bc(cr, nr, atomtypes->vol);
753 nblock_bc(cr, nr, atomtypes->surftens);
754 nblock_bc(cr, nr, atomtypes->gb_radius);
755 nblock_bc(cr, nr, atomtypes->S_hct);
759 void bcast_ir_mtop(const t_commrec *cr, t_inputrec *inputrec, gmx_mtop_t *mtop)
764 fprintf(debug, "in bc_data\n");
766 bc_inputrec(cr, inputrec);
769 fprintf(debug, "after bc_inputrec\n");
771 bc_symtab(cr, &mtop->symtab);
774 fprintf(debug, "after bc_symtab\n");
776 bc_string(cr, &mtop->symtab, &mtop->name);
779 fprintf(debug, "after bc_name\n");
782 bc_ffparams(cr, &mtop->ffparams);
784 block_bc(cr, mtop->nmoltype);
785 snew_bc(cr, mtop->moltype, mtop->nmoltype);
786 for (i = 0; i < mtop->nmoltype; i++)
788 bc_moltype(cr, &mtop->symtab, &mtop->moltype[i]);
791 block_bc(cr, mtop->nmolblock);
792 snew_bc(cr, mtop->molblock, mtop->nmolblock);
793 for (i = 0; i < mtop->nmolblock; i++)
795 bc_molblock(cr, &mtop->molblock[i]);
798 block_bc(cr, mtop->natoms);
800 bc_atomtypes(cr, &mtop->atomtypes);
802 bc_block(cr, &mtop->mols);
803 bc_groups(cr, &mtop->symtab, mtop->natoms, &mtop->groups);