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38 * \brief This file defines functions used by the domdec module
39 * in its initial setup phase.
41 * \author Berk Hess <hess@kth.se>
42 * \ingroup module_domdec
52 #include "gromacs/domdec/domdec.h"
53 #include "gromacs/domdec/domdec_struct.h"
54 #include "gromacs/ewald/pme.h"
55 #include "gromacs/gmxlib/network.h"
56 #include "gromacs/math/utilities.h"
57 #include "gromacs/math/vec.h"
58 #include "gromacs/mdlib/perf_est.h"
59 #include "gromacs/mdtypes/commrec.h"
60 #include "gromacs/mdtypes/inputrec.h"
61 #include "gromacs/mdtypes/md_enums.h"
62 #include "gromacs/pbcutil/pbc.h"
63 #include "gromacs/topology/topology.h"
64 #include "gromacs/utility/fatalerror.h"
65 #include "gromacs/utility/logger.h"
66 #include "gromacs/utility/stringutil.h"
68 #include "domdec_internal.h"
70 /*! \brief Margin for setting up the DD grid */
71 #define DD_GRID_MARGIN_PRES_SCALE 1.05
73 /*! \brief Factorize \p n.
75 * \param[in] n Value to factorize
76 * \param[out] fac Vector of factors (to be allocated in this function)
77 * \param[out] mfac Vector with the number of times each factor repeats in the factorization (to be allocated in this function)
79 static void factorize(int n,
80 std::vector<int> *fac,
81 std::vector<int> *mfac)
85 gmx_fatal(FARGS, "Can only factorize positive integers.");
88 /* Decompose n in factors */
96 if (fac->empty() || fac->back() != d)
111 /*! \brief Find largest divisor of \p n smaller than \p n*/
112 static int largest_divisor(int n)
114 std::vector<int> div;
115 std::vector<int> mdiv;
116 factorize(n, &div, &mdiv);
121 /*! \brief Compute largest common divisor of \p n1 and \b n2 */
122 static int lcd(int n1, int n2)
127 for (i = 2; (i <= n1 && i <= n2); i++)
129 if (n1 % i == 0 && n2 % i == 0)
138 /*! \brief Returns TRUE when there are enough PME ranks for the ratio */
139 static gmx_bool fits_pme_ratio(int nrank_tot, int nrank_pme, float ratio)
141 return (static_cast<double>(nrank_pme)/static_cast<double>(nrank_tot) > 0.95*ratio);
144 /*! \brief Returns TRUE when npme out of ntot ranks doing PME is expected to give reasonable performance */
145 static gmx_bool fits_pp_pme_perf(int ntot, int npme, float ratio)
147 std::vector<int> div;
148 std::vector<int> mdiv;
149 factorize(ntot - npme, &div, &mdiv);
151 int npp_root3 = gmx::roundToInt(std::cbrt(ntot - npme));
152 int npme_root2 = gmx::roundToInt(std::sqrt(static_cast<double>(npme)));
154 /* The check below gives a reasonable division:
155 * factor 5 allowed at 5 or more PP ranks,
156 * factor 7 allowed at 49 or more PP ranks.
158 if (div.back() > 3 + npp_root3)
163 /* Check if the number of PP and PME ranks have a reasonable sized
164 * denominator in common, such that we can use 2D PME decomposition
165 * when required (which requires nx_pp == nx_pme).
166 * The factor of 2 allows for a maximum ratio of 2^2=4
167 * between nx_pme and ny_pme.
169 if (lcd(ntot - npme, npme)*2 < npme_root2)
174 /* Does this division gives a reasonable PME load? */
175 return fits_pme_ratio(ntot, npme, ratio);
178 /*! \brief Make a guess for the number of PME ranks to use. */
179 static int guess_npme(const gmx::MDLogger &mdlog,
180 const gmx_mtop_t *mtop, const t_inputrec *ir,
187 ratio = pme_load_estimate(mtop, ir, box);
189 GMX_LOG(mdlog.info).appendTextFormatted(
190 "Guess for relative PME load: %.2f", ratio);
192 /* We assume the optimal rank ratio is close to the load ratio.
193 * The communication load is neglected,
194 * but (hopefully) this will balance out between PP and PME.
197 if (!fits_pme_ratio(nrank_tot, nrank_tot/2, ratio))
199 /* We would need more than nrank_tot/2 PME only nodes,
200 * which is not possible. Since the PME load is very high,
201 * we will not loose much performance when all ranks do PME.
207 /* First try to find npme as a factor of nrank_tot up to nrank_tot/3.
208 * We start with a minimum PME node fraction of 1/16
209 * and avoid ratios which lead to large prime factors in nnodes-npme.
211 npme = (nrank_tot + 15)/16;
212 while (npme <= nrank_tot/3)
214 if (nrank_tot % npme == 0)
216 /* Note that fits_perf might change the PME grid,
217 * in the current implementation it does not.
219 if (fits_pp_pme_perf(nrank_tot, npme, ratio))
226 if (npme > nrank_tot/3)
228 /* Try any possible number for npme */
230 while (npme <= nrank_tot/2)
232 /* Note that fits_perf may change the PME grid */
233 if (fits_pp_pme_perf(nrank_tot, npme, ratio))
240 if (npme > nrank_tot/2)
242 gmx_fatal(FARGS, "Could not find an appropriate number of separate PME ranks. i.e. >= %5f*#ranks (%d) and <= #ranks/2 (%d) and reasonable performance wise (grid_x=%d, grid_y=%d).\n"
243 "Use the -npme option of mdrun or change the number of ranks or the PME grid dimensions, see the manual for details.",
244 ratio, gmx::roundToInt(0.95*ratio*nrank_tot), nrank_tot/2, ir->nkx, ir->nky);
248 GMX_LOG(mdlog.info).appendTextFormatted(
249 "Will use %d particle-particle and %d PME only ranks\n"
250 "This is a guess, check the performance at the end of the log file",
251 nrank_tot - npme, npme);
257 /*! \brief Return \p n divided by \p f rounded up to the next integer. */
258 static int div_up(int n, int f)
260 return (n + f - 1)/f;
263 real comm_box_frac(const ivec dd_nc, real cutoff, const gmx_ddbox_t *ddbox)
269 for (i = 0; i < DIM; i++)
271 real bt = ddbox->box_size[i]*ddbox->skew_fac[i];
272 nw[i] = dd_nc[i]*cutoff/bt;
276 for (i = 0; i < DIM; i++)
281 for (j = i+1; j < DIM; j++)
285 comm_vol += nw[i]*nw[j]*M_PI/4;
286 for (k = j+1; k < DIM; k++)
290 comm_vol += nw[i]*nw[j]*nw[k]*M_PI/6;
301 /*! \brief Return whether the DD inhomogeneous in the z direction */
302 static gmx_bool inhomogeneous_z(const t_inputrec *ir)
304 return ((EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD) &&
305 ir->ePBC == epbcXYZ && ir->ewald_geometry == eewg3DC);
308 /*! \brief Estimate cost of PME FFT communication
310 * This only takes the communication into account and not imbalance
311 * in the calculation. But the imbalance in communication and calculation
312 * are similar and therefore these formulas also prefer load balance
313 * in the FFT and pme_solve calculation.
315 static float comm_pme_cost_vol(int npme, int a, int b, int c)
317 /* We use a float here, since an integer might overflow */
322 comm_vol *= div_up(a, npme);
323 comm_vol *= div_up(b, npme);
329 /*! \brief Estimate cost of communication for a possible domain decomposition. */
330 static float comm_cost_est(real limit, real cutoff,
331 const matrix box, const gmx_ddbox_t *ddbox,
332 int natoms, const t_inputrec *ir,
334 int npme_tot, ivec nc)
336 ivec npme = {1, 1, 1};
337 int i, j, nk, overlap;
339 float comm_vol, comm_vol_xf, comm_pme, cost_pbcdx;
340 /* This is the cost of a pbc_dx call relative to the cost
341 * of communicating the coordinate and force of an atom.
342 * This will be machine dependent.
343 * These factors are for x86 with SMP or Infiniband.
345 float pbcdx_rect_fac = 0.1;
346 float pbcdx_tric_fac = 0.2;
349 /* Check the DD algorithm restrictions */
350 if ((ir->ePBC == epbcXY && ir->nwall < 2 && nc[ZZ] > 1) ||
351 (ir->ePBC == epbcSCREW && (nc[XX] == 1 || nc[YY] > 1 || nc[ZZ] > 1)))
356 if (inhomogeneous_z(ir) && nc[ZZ] > 1)
361 assert(ddbox->npbcdim <= DIM);
363 /* Check if the triclinic requirements are met */
364 for (i = 0; i < DIM; i++)
366 for (j = i+1; j < ddbox->npbcdim; j++)
368 if (box[j][i] != 0 || ir->deform[j][i] != 0 ||
369 (ir->epc != epcNO && ir->compress[j][i] != 0))
371 if (nc[j] > 1 && nc[i] == 1)
379 for (i = 0; i < DIM; i++)
381 bt[i] = ddbox->box_size[i]*ddbox->skew_fac[i];
383 /* Without PBC and with 2 cells, there are no lower limits on the cell size */
384 if (!(i >= ddbox->npbcdim && nc[i] <= 2) && bt[i] < nc[i]*limit)
388 /* With PBC, check if the cut-off fits in nc[i]-1 cells */
389 if (i < ddbox->npbcdim && nc[i] > 1 && (nc[i] - 1)*bt[i] < nc[i]*cutoff)
397 /* The following choices should match those
398 * in init_domain_decomposition in domdec.c.
400 if (nc[XX] == 1 && nc[YY] > 1)
405 else if (nc[YY] == 1)
412 /* Will we use 1D or 2D PME decomposition? */
413 npme[XX] = (npme_tot % nc[XX] == 0) ? nc[XX] : npme_tot;
414 npme[YY] = npme_tot/npme[XX];
418 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
420 /* Check the PME grid restrictions.
421 * Currently these can only be invalid here with too few grid lines
422 * along the x dimension per rank doing PME.
424 int npme_x = (npme_tot > 1 ? npme[XX] : nc[XX]);
426 /* Currently we don't have the OpenMP thread count available here.
427 * But with threads we have only tighter restrictions and it's
428 * probably better anyhow to avoid settings where we need to reduce
429 * grid lines over multiple ranks, as the thread check will do.
431 bool useThreads = true;
432 bool errorsAreFatal = false;
433 if (!gmx_pme_check_restrictions(ir->pme_order, ir->nkx, ir->nky, ir->nkz,
434 npme_x, useThreads, errorsAreFatal))
440 /* When two dimensions are (nearly) equal, use more cells
441 * for the smallest index, so the decomposition does not
442 * depend sensitively on the rounding of the box elements.
444 for (i = 0; i < DIM; i++)
446 for (j = i+1; j < DIM; j++)
448 /* Check if the box size is nearly identical,
449 * in that case we prefer nx > ny and ny > nz.
451 if (std::fabs(bt[j] - bt[i]) < 0.01*bt[i] && nc[j] > nc[i])
453 /* The XX/YY check is a bit compact. If nc[YY]==npme[YY]
454 * this means the swapped nc has nc[XX]==npme[XX],
455 * and we can also swap X and Y for PME.
457 /* Check if dimension i and j are equivalent for PME.
458 * For x/y: if nc[YY]!=npme[YY], we can not swap x/y
459 * For y/z: we can not have PME decomposition in z
462 !((i == XX && j == YY && nc[YY] != npme[YY]) ||
463 (i == YY && j == ZZ && npme[YY] > 1)))
471 /* This function determines only half of the communication cost.
472 * All PP, PME and PP-PME communication is symmetric
473 * and the "back"-communication cost is identical to the forward cost.
476 comm_vol = comm_box_frac(nc, cutoff, ddbox);
479 for (i = 0; i < 2; i++)
481 /* Determine the largest volume for PME x/f redistribution */
482 if (nc[i] % npme[i] != 0)
486 comm_vol_xf = (npme[i] == 2 ? 1.0/3.0 : 0.5);
490 comm_vol_xf = 1.0 - lcd(nc[i], npme[i])/static_cast<double>(npme[i]);
492 comm_pme += 3*natoms*comm_vol_xf;
495 /* Grid overlap communication */
498 nk = (i == 0 ? ir->nkx : ir->nky);
499 overlap = (nk % npme[i] == 0 ? ir->pme_order-1 : ir->pme_order);
507 /* Old line comm_pme += npme[i]*overlap*ir->nkx*ir->nky*ir->nkz/nk; */
511 comm_pme += comm_pme_cost_vol(npme[YY], ir->nky, ir->nkz, ir->nkx);
512 comm_pme += comm_pme_cost_vol(npme[XX], ir->nkx, ir->nky, ir->nkz);
514 /* Add cost of pbc_dx for bondeds */
516 if ((nc[XX] == 1 || nc[YY] == 1) || (nc[ZZ] == 1 && ir->ePBC != epbcXY))
518 if ((ddbox->tric_dir[XX] && nc[XX] == 1) ||
519 (ddbox->tric_dir[YY] && nc[YY] == 1))
521 cost_pbcdx = pbcdxr*pbcdx_tric_fac;
525 cost_pbcdx = pbcdxr*pbcdx_rect_fac;
532 "nc %2d %2d %2d %2d %2d vol pp %6.4f pbcdx %6.4f pme %9.3e tot %9.3e\n",
533 nc[XX], nc[YY], nc[ZZ], npme[XX], npme[YY],
534 comm_vol, cost_pbcdx, comm_pme/(3*natoms),
535 comm_vol + cost_pbcdx + comm_pme/(3*natoms));
538 return 3*natoms*(comm_vol + cost_pbcdx) + comm_pme;
541 /*! \brief Assign penalty factors to possible domain decompositions, based on the estimated communication costs. */
542 static void assign_factors(real limit, real cutoff,
543 const matrix box, const gmx_ddbox_t *ddbox,
544 int natoms, const t_inputrec *ir,
545 float pbcdxr, int npme,
546 int ndiv, const int *div, const int *mdiv,
547 ivec ir_try, ivec opt)
554 ce = comm_cost_est(limit, cutoff, box, ddbox,
555 natoms, ir, pbcdxr, npme, ir_try);
556 if (ce >= 0 && (opt[XX] == 0 ||
557 ce < comm_cost_est(limit, cutoff, box, ddbox,
561 copy_ivec(ir_try, opt);
567 for (x = mdiv[0]; x >= 0; x--)
569 for (i = 0; i < x; i++)
571 ir_try[XX] *= div[0];
573 for (y = mdiv[0]-x; y >= 0; y--)
575 for (i = 0; i < y; i++)
577 ir_try[YY] *= div[0];
579 for (i = 0; i < mdiv[0]-x-y; i++)
581 ir_try[ZZ] *= div[0];
585 assign_factors(limit, cutoff, box, ddbox, natoms, ir, pbcdxr, npme,
586 ndiv-1, div+1, mdiv+1, ir_try, opt);
588 for (i = 0; i < mdiv[0]-x-y; i++)
590 ir_try[ZZ] /= div[0];
592 for (i = 0; i < y; i++)
594 ir_try[YY] /= div[0];
597 for (i = 0; i < x; i++)
599 ir_try[XX] /= div[0];
604 /*! \brief Determine the optimal distribution of DD cells for the simulation system and number of MPI ranks */
605 static real optimize_ncells(const gmx::MDLogger &mdlog,
606 int nnodes_tot, int npme_only,
607 gmx_bool bDynLoadBal, real dlb_scale,
608 const gmx_mtop_t *mtop,
609 const matrix box, const gmx_ddbox_t *ddbox,
610 const t_inputrec *ir,
611 const DDSystemInfo &systemInfo,
614 int npp, npme, d, nmax;
619 limit = systemInfo.cellsizeLimit;
621 npp = nnodes_tot - npme_only;
622 if (EEL_PME(ir->coulombtype))
624 npme = (npme_only > 0 ? npme_only : npp);
631 if (systemInfo.haveInterDomainBondeds)
633 /* If we can skip PBC for distance calculations in plain-C bondeds,
634 * we can save some time (e.g. 3D DD with pbc=xyz).
635 * Here we ignore SIMD bondeds as they always do (fast) PBC.
637 count_bonded_distances(mtop, ir, &pbcdxr, nullptr);
638 pbcdxr /= static_cast<double>(mtop->natoms);
642 /* Every molecule is a single charge group: no pbc required */
645 /* Add a margin for DLB and/or pressure scaling */
648 if (dlb_scale >= 1.0)
650 gmx_fatal(FARGS, "The value for option -dds should be smaller than 1");
652 GMX_LOG(mdlog.info).appendTextFormatted(
653 "Scaling the initial minimum size with 1/%g (option -dds) = %g",
654 dlb_scale, 1/dlb_scale);
657 else if (ir->epc != epcNO)
659 GMX_LOG(mdlog.info).appendTextFormatted(
660 "To account for pressure scaling, scaling the initial minimum size with %g",
661 DD_GRID_MARGIN_PRES_SCALE);
662 limit *= DD_GRID_MARGIN_PRES_SCALE;
665 GMX_LOG(mdlog.info).appendTextFormatted(
666 "Optimizing the DD grid for %d cells with a minimum initial size of %.3f nm",
669 if (inhomogeneous_z(ir))
671 GMX_LOG(mdlog.info).appendTextFormatted(
672 "Ewald_geometry=%s: assuming inhomogeneous particle distribution in z, will not decompose in z.",
673 eewg_names[ir->ewald_geometry]);
678 std::string maximumCells = "The maximum allowed number of cells is:";
679 for (d = 0; d < DIM; d++)
681 nmax = static_cast<int>(ddbox->box_size[d]*ddbox->skew_fac[d]/limit);
682 if (d >= ddbox->npbcdim && nmax < 2)
686 if (d == ZZ && inhomogeneous_z(ir))
690 maximumCells += gmx::formatString(" %c %d", 'X' + d, nmax);
692 GMX_LOG(mdlog.info).appendText(maximumCells);
697 fprintf(debug, "Average nr of pbc_dx calls per atom %.2f\n", pbcdxr);
700 /* Decompose npp in factors */
701 std::vector<int> div;
702 std::vector<int> mdiv;
703 factorize(npp, &div, &mdiv);
709 assign_factors(limit, systemInfo.cutoff, box, ddbox, mtop->natoms, ir, pbcdxr,
710 npme, div.size(), div.data(), mdiv.data(), itry, nc);
716 dd_choose_grid(const gmx::MDLogger &mdlog,
718 const t_inputrec *ir,
719 const gmx_mtop_t *mtop,
720 const matrix box, const gmx_ddbox_t *ddbox,
721 const int numPmeRanksRequested,
722 const gmx_bool bDynLoadBal, const real dlb_scale,
723 const DDSystemInfo &systemInfo)
729 int64_t nnodes_div = cr->nnodes;
730 if (EEL_PME(ir->coulombtype))
732 if (numPmeRanksRequested > 0)
734 if (numPmeRanksRequested >= cr->nnodes)
737 "Cannot have %d separate PME ranks with just %d total ranks",
738 numPmeRanksRequested, cr->nnodes);
741 /* If the user purposely selected the number of PME nodes,
742 * only check for large primes in the PP node count.
744 nnodes_div -= numPmeRanksRequested;
749 ddSetup.numPmeRanks = 0;
754 const int64_t ldiv = largest_divisor(nnodes_div);
755 /* Check if the largest divisor is more than nnodes^2/3 */
756 if (ldiv*ldiv*ldiv > nnodes_div*nnodes_div)
758 gmx_fatal(FARGS, "The number of ranks you selected (%" PRId64 ") contains a large prime factor %" PRId64 ". In most cases this will lead to bad performance. Choose a number with smaller prime factors or set the decomposition (option -dd) manually.",
763 if (EEL_PME(ir->coulombtype))
765 if (numPmeRanksRequested < 0)
767 /* Use PME nodes when the number of nodes is more than 16 */
768 if (cr->nnodes <= 18)
770 ddSetup.numPmeRanks = 0;
771 GMX_LOG(mdlog.info).appendTextFormatted(
772 "Using %d separate PME ranks, as there are too few total\n"
773 " ranks for efficient splitting",
778 ddSetup.numPmeRanks = guess_npme(mdlog, mtop, ir, box, cr->nnodes);
779 GMX_LOG(mdlog.info).appendTextFormatted(
780 "Using %d separate PME ranks, as guessed by mdrun", ddSetup.numPmeRanks);
785 /* We checked above that nPmeRanks is a valid number */
786 ddSetup.numPmeRanks = numPmeRanksRequested;
787 GMX_LOG(mdlog.info).appendTextFormatted(
788 "Using %d separate PME ranks", ddSetup.numPmeRanks);
789 // TODO: there was a ", per user request" note here, but it's not correct anymore,
790 // as with GPUs decision about nPmeRanks can be made in runner() as well.
791 // Consider a single spot for setting nPmeRanks.
795 ddSetup.cellsizeLimit =
796 optimize_ncells(mdlog, cr->nnodes, ddSetup.numPmeRanks,
797 bDynLoadBal, dlb_scale,
798 mtop, box, ddbox, ir,
803 /* Communicate the information set by the master to all nodes */
804 gmx_bcast(sizeof(ddSetup.numDomains), ddSetup.numDomains, cr);
805 if (EEL_PME(ir->coulombtype))
807 gmx_bcast(sizeof(ddSetup.numPmeRanks), &ddSetup.numPmeRanks, cr);
811 ddSetup.numPmeRanks = 0;