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37 * \brief This file defines functions for mdrun to call to make a new
38 * domain decomposition, and check it.
40 * \author Berk Hess <hess@kth.se>
41 * \ingroup module_domdec
46 #include "gromacs/utility/arrayref.h"
47 #include "partition.h"
56 #include "gromacs/domdec/collect.h"
57 #include "gromacs/domdec/dlb.h"
58 #include "gromacs/domdec/dlbtiming.h"
59 #include "gromacs/domdec/domdec.h"
60 #include "gromacs/domdec/domdec_network.h"
61 #include "gromacs/domdec/ga2la.h"
62 #include "gromacs/domdec/localatomsetmanager.h"
63 #include "gromacs/domdec/mdsetup.h"
64 #include "gromacs/domdec/nsgrid.h"
65 #include "gromacs/ewald/pme_pp.h"
66 #include "gromacs/gmxlib/network.h"
67 #include "gromacs/gmxlib/nrnb.h"
68 #include "gromacs/imd/imd.h"
69 #include "gromacs/math/functions.h"
70 #include "gromacs/math/vec.h"
71 #include "gromacs/mdlib/forcerec.h"
72 #include "gromacs/mdlib/gmx_omp_nthreads.h"
73 #include "gromacs/mdlib/mdatoms.h"
74 #include "gromacs/mdlib/vsite.h"
75 #include "gromacs/mdtypes/commrec.h"
76 #include "gromacs/mdtypes/forcerec.h"
77 #include "gromacs/mdtypes/inputrec.h"
78 #include "gromacs/mdtypes/md_enums.h"
79 #include "gromacs/mdtypes/mdatom.h"
80 #include "gromacs/mdtypes/nblist.h"
81 #include "gromacs/mdtypes/state.h"
82 #include "gromacs/nbnxm/nbnxm.h"
83 #include "gromacs/pulling/pull.h"
84 #include "gromacs/timing/wallcycle.h"
85 #include "gromacs/topology/mtop_util.h"
86 #include "gromacs/topology/topology.h"
87 #include "gromacs/utility/cstringutil.h"
88 #include "gromacs/utility/fatalerror.h"
89 #include "gromacs/utility/logger.h"
90 #include "gromacs/utility/real.h"
91 #include "gromacs/utility/smalloc.h"
92 #include "gromacs/utility/strconvert.h"
93 #include "gromacs/utility/stringstream.h"
94 #include "gromacs/utility/stringutil.h"
95 #include "gromacs/utility/textwriter.h"
98 #include "cellsizes.h"
99 #include "distribute.h"
100 #include "domdec_constraints.h"
101 #include "domdec_internal.h"
102 #include "domdec_vsite.h"
104 #include "redistribute.h"
107 /*! \brief Turn on DLB when the load imbalance causes this amount of total loss.
109 * There is a bit of overhead with DLB and it's difficult to achieve
110 * a load imbalance of less than 2% with DLB.
112 #define DD_PERF_LOSS_DLB_ON 0.02
114 //! Warn about imbalance due to PP or PP/PME load imbalance at this loss.
115 #define DD_PERF_LOSS_WARN 0.05
118 //! Debug helper printing a DD zone
119 static void print_ddzone(FILE* fp, int d, int i, int j, gmx_ddzone_t* zone)
122 "zone d0 %d d1 %d d2 %d min0 %6.3f max1 %6.3f mch0 %6.3f mch1 %6.3f p1_0 %6.3f p1_1 "
135 /*! \brief Using the home grid size as input in cell_ns_x0 and cell_ns_x1
136 * takes the extremes over all home and remote zones in the halo
137 * and returns the results in cell_ns_x0 and cell_ns_x1.
138 * Note: only used with the group cut-off scheme.
140 static void dd_move_cellx(gmx_domdec_t* dd, const gmx_ddbox_t* ddbox, rvec cell_ns_x0, rvec cell_ns_x1)
142 constexpr int c_ddZoneCommMaxNumZones = 5;
143 gmx_ddzone_t buf_s[c_ddZoneCommMaxNumZones];
144 gmx_ddzone_t buf_r[c_ddZoneCommMaxNumZones];
145 gmx_ddzone_t buf_e[c_ddZoneCommMaxNumZones];
146 gmx_domdec_comm_t* comm = dd->comm;
150 for (int d = 1; d < dd->ndim; d++)
152 int dim = dd->dim[d];
153 gmx_ddzone_t& zp = (d == 1) ? comm->zone_d1[0] : comm->zone_d2[0][0];
155 /* Copy the base sizes of the home zone */
156 zp.min0 = cell_ns_x0[dim];
157 zp.max1 = cell_ns_x1[dim];
158 zp.min1 = cell_ns_x1[dim];
159 zp.mch0 = cell_ns_x0[dim];
160 zp.mch1 = cell_ns_x1[dim];
161 zp.p1_0 = cell_ns_x0[dim];
162 zp.p1_1 = cell_ns_x1[dim];
166 gmx::ArrayRef<DDCellsizesWithDlb> cellsizes = comm->cellsizesWithDlb;
168 /* Loop backward over the dimensions and aggregate the extremes
171 for (int d = dd->ndim - 2; d >= 0; d--)
173 const int dim = dd->dim[d];
174 const bool applyPbc = (dim < ddbox->npbcdim);
176 /* Use an rvec to store two reals */
177 extr_s[d][0] = cellsizes[d + 1].fracLower;
178 extr_s[d][1] = cellsizes[d + 1].fracUpper;
179 extr_s[d][2] = cellsizes[d + 1].fracUpper;
182 GMX_ASSERT(pos < c_ddZoneCommMaxNumZones, "The buffers should be sufficiently large");
183 /* Store the extremes in the backward sending buffer,
184 * so they get updated separately from the forward communication.
186 for (int d1 = d; d1 < dd->ndim - 1; d1++)
188 gmx_ddzone_t& buf = buf_s[pos];
190 /* We invert the order to be able to use the same loop for buf_e */
191 buf.min0 = extr_s[d1][1];
192 buf.max1 = extr_s[d1][0];
193 buf.min1 = extr_s[d1][2];
196 /* Store the cell corner of the dimension we communicate along */
197 buf.p1_0 = comm->cell_x0[dim];
203 buf_s[pos] = (dd->ndim == 2) ? comm->zone_d1[0] : comm->zone_d2[0][0];
206 if (dd->ndim == 3 && d == 0)
208 buf_s[pos] = comm->zone_d2[0][1];
210 buf_s[pos] = comm->zone_d1[0];
214 /* We only need to communicate the extremes
215 * in the forward direction
217 int numPulses = comm->cd[d].numPulses();
221 /* Take the minimum to avoid double communication */
222 numPulsesMin = std::min(numPulses, dd->numCells[dim] - 1 - numPulses);
226 /* Without PBC we should really not communicate over
227 * the boundaries, but implementing that complicates
228 * the communication setup and therefore we simply
229 * do all communication, but ignore some data.
231 numPulsesMin = numPulses;
233 for (int pulse = 0; pulse < numPulsesMin; pulse++)
235 /* Communicate the extremes forward */
236 bool receiveValidData = (applyPbc || dd->ci[dim] > 0);
238 int numElements = dd->ndim - d - 1;
239 ddSendrecv(dd, d, dddirForward, extr_s + d, numElements, extr_r + d, numElements);
241 if (receiveValidData)
243 for (int d1 = d; d1 < dd->ndim - 1; d1++)
245 extr_s[d1][0] = std::max(extr_s[d1][0], extr_r[d1][0]);
246 extr_s[d1][1] = std::min(extr_s[d1][1], extr_r[d1][1]);
247 extr_s[d1][2] = std::min(extr_s[d1][2], extr_r[d1][2]);
252 const int numElementsInBuffer = pos;
253 for (int pulse = 0; pulse < numPulses; pulse++)
255 /* Communicate all the zone information backward */
256 bool receiveValidData = (applyPbc || dd->ci[dim] < dd->numCells[dim] - 1);
259 sizeof(gmx_ddzone_t) == c_ddzoneNumReals * sizeof(real),
260 "Here we expect gmx_ddzone_t to consist of c_ddzoneNumReals reals (only)");
262 int numReals = numElementsInBuffer * c_ddzoneNumReals;
266 gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
267 gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
272 for (int d1 = d + 1; d1 < dd->ndim; d1++)
274 /* Determine the decrease of maximum required
275 * communication height along d1 due to the distance along d,
276 * this avoids a lot of useless atom communication.
278 real dist_d = comm->cell_x1[dim] - buf_r[0].p1_0;
281 if (ddbox->tric_dir[dim])
283 /* c is the off-diagonal coupling between the cell planes
284 * along directions d and d1.
286 c = ddbox->v[dim][dd->dim[d1]][dim];
292 real det = (1 + c * c) * gmx::square(comm->systemInfo.cutoff) - dist_d * dist_d;
295 dh[d1] = comm->systemInfo.cutoff - (c * dist_d + std::sqrt(det)) / (1 + c * c);
299 /* A negative value signals out of range */
305 /* Accumulate the extremes over all pulses */
306 for (int i = 0; i < numElementsInBuffer; i++)
314 if (receiveValidData)
316 buf_e[i].min0 = std::min(buf_e[i].min0, buf_r[i].min0);
317 buf_e[i].max1 = std::max(buf_e[i].max1, buf_r[i].max1);
318 buf_e[i].min1 = std::min(buf_e[i].min1, buf_r[i].min1);
322 if (dd->ndim == 3 && d == 0 && i == numElementsInBuffer - 1)
330 if (receiveValidData && dh[d1] >= 0)
332 buf_e[i].mch0 = std::max(buf_e[i].mch0, buf_r[i].mch0 - dh[d1]);
333 buf_e[i].mch1 = std::max(buf_e[i].mch1, buf_r[i].mch1 - dh[d1]);
336 /* Copy the received buffer to the send buffer,
337 * to pass the data through with the next pulse.
341 if (((applyPbc || dd->ci[dim] + numPulses < dd->numCells[dim]) && pulse == numPulses - 1)
342 || (!applyPbc && dd->ci[dim] + 1 + pulse == dd->numCells[dim] - 1))
344 /* Store the extremes */
347 for (int d1 = d; d1 < dd->ndim - 1; d1++)
349 extr_s[d1][1] = std::min(extr_s[d1][1], buf_e[pos].min0);
350 extr_s[d1][0] = std::max(extr_s[d1][0], buf_e[pos].max1);
351 extr_s[d1][2] = std::min(extr_s[d1][2], buf_e[pos].min1);
355 if (d == 1 || (d == 0 && dd->ndim == 3))
357 for (int i = d; i < 2; i++)
359 comm->zone_d2[1 - d][i] = buf_e[pos];
365 comm->zone_d1[1] = buf_e[pos];
371 if (d == 1 || (d == 0 && dd->ndim == 3))
373 for (int i = d; i < 2; i++)
375 comm->zone_d2[1 - d][i].dataSet = 0;
380 comm->zone_d1[1].dataSet = 0;
388 int dim = dd->dim[1];
389 for (int i = 0; i < 2; i++)
391 if (comm->zone_d1[i].dataSet != 0)
395 print_ddzone(debug, 1, i, 0, &comm->zone_d1[i]);
397 cell_ns_x0[dim] = std::min(cell_ns_x0[dim], comm->zone_d1[i].min0);
398 cell_ns_x1[dim] = std::max(cell_ns_x1[dim], comm->zone_d1[i].max1);
404 int dim = dd->dim[2];
405 for (int i = 0; i < 2; i++)
407 for (int j = 0; j < 2; j++)
409 if (comm->zone_d2[i][j].dataSet != 0)
413 print_ddzone(debug, 2, i, j, &comm->zone_d2[i][j]);
415 cell_ns_x0[dim] = std::min(cell_ns_x0[dim], comm->zone_d2[i][j].min0);
416 cell_ns_x1[dim] = std::max(cell_ns_x1[dim], comm->zone_d2[i][j].max1);
421 for (int d = 1; d < dd->ndim; d++)
423 cellsizes[d].fracLowerMax = extr_s[d - 1][0];
424 cellsizes[d].fracUpperMin = extr_s[d - 1][1];
428 "Cell fraction d %d, max0 %f, min1 %f\n",
430 cellsizes[d].fracLowerMax,
431 cellsizes[d].fracUpperMin);
436 //! Sets the charge-group zones to be equal to the home zone.
437 static void set_zones_ncg_home(gmx_domdec_t* dd)
439 gmx_domdec_zones_t* zones;
442 zones = &dd->comm->zones;
444 zones->cg_range[0] = 0;
445 for (i = 1; i < zones->n + 1; i++)
447 zones->cg_range[i] = dd->ncg_home;
449 /* zone_ncg1[0] should always be equal to ncg_home */
450 dd->comm->zone_ncg1[0] = dd->ncg_home;
453 //! Restore atom groups for the charge groups.
454 static void restoreAtomGroups(gmx_domdec_t* dd, const t_state* state)
456 gmx::ArrayRef<const int> atomGroupsState = state->cg_gl;
458 std::vector<int>& globalAtomGroupIndices = dd->globalAtomGroupIndices;
460 globalAtomGroupIndices.resize(atomGroupsState.size());
462 /* Copy back the global charge group indices from state
463 * and rebuild the local charge group to atom index.
465 for (gmx::index i = 0; i < atomGroupsState.ssize(); i++)
467 globalAtomGroupIndices[i] = atomGroupsState[i];
470 dd->ncg_home = atomGroupsState.size();
471 dd->comm->atomRanges.setEnd(DDAtomRanges::Type::Home, atomGroupsState.ssize());
473 set_zones_ncg_home(dd);
476 //! Sets the cginfo structures.
477 static void dd_set_cginfo(gmx::ArrayRef<const int> index_gl, int cg0, int cg1, t_forcerec* fr)
481 gmx::ArrayRef<cginfo_mb_t> cginfo_mb = fr->cginfo_mb;
482 gmx::ArrayRef<int> cginfo = fr->cginfo;
484 for (int cg = cg0; cg < cg1; cg++)
486 cginfo[cg] = ddcginfo(cginfo_mb, index_gl[cg]);
491 //! Makes the mappings between global and local atom indices during DD repartioning.
492 static void make_dd_indices(gmx_domdec_t* dd, const int atomStart)
494 const int numZones = dd->comm->zones.n;
495 gmx::ArrayRef<const int> zone2cg = dd->comm->zones.cg_range;
496 gmx::ArrayRef<const int> zone_ncg1 = dd->comm->zone_ncg1;
497 gmx::ArrayRef<const int> globalAtomGroupIndices = dd->globalAtomGroupIndices;
499 std::vector<int>& globalAtomIndices = dd->globalAtomIndices;
500 gmx_ga2la_t& ga2la = *dd->ga2la;
502 if (zone2cg[1] != dd->ncg_home)
504 gmx_incons("dd->ncg_zone is not up to date");
507 /* Make the local to global and global to local atom index */
509 globalAtomIndices.resize(a);
510 for (int zone = 0; zone < numZones; zone++)
521 int cg1 = zone2cg[zone + 1];
522 int cg1_p1 = cg0 + zone_ncg1[zone];
524 for (int cg = cg0; cg < cg1; cg++)
529 /* Signal that this cg is from more than one pulse away */
532 int cg_gl = globalAtomGroupIndices[cg];
533 globalAtomIndices.push_back(cg_gl);
534 ga2la.insert(cg_gl, { a, zone1 });
540 //! Checks whether global and local atom indices are consistent.
541 static void check_index_consistency(const gmx_domdec_t* dd, int natoms_sys, const char* where)
545 const int numAtomsInZones = dd->comm->atomRanges.end(DDAtomRanges::Type::Zones);
547 if (dd->comm->ddSettings.DD_debug > 1)
549 std::vector<int> have(natoms_sys);
550 for (int a = 0; a < numAtomsInZones; a++)
552 int globalAtomIndex = dd->globalAtomIndices[a];
553 if (have[globalAtomIndex] > 0)
556 "DD rank %d: global atom %d occurs twice: index %d and %d\n",
559 have[globalAtomIndex],
564 have[globalAtomIndex] = a + 1;
569 std::vector<int> have(numAtomsInZones);
572 for (int i = 0; i < natoms_sys; i++)
574 if (const auto* entry = dd->ga2la->find(i))
576 const int a = entry->la;
577 if (a >= numAtomsInZones)
580 "DD rank %d: global atom %d marked as local atom %d, which is larger than "
591 if (dd->globalAtomIndices[a] != i)
594 "DD rank %d: global atom %d marked as local atom %d, which has global "
599 dd->globalAtomIndices[a] + 1);
606 if (ngl != numAtomsInZones)
608 fprintf(stderr, "DD rank %d, %s: %d global atom indices, %d local atoms\n", dd->rank, where, ngl, numAtomsInZones);
610 for (int a = 0; a < numAtomsInZones; a++)
615 "DD rank %d, %s: local atom %d, global %d has no global index\n",
619 dd->globalAtomIndices[a] + 1);
625 gmx_fatal(FARGS, "DD rank %d, %s: %d atom(group) index inconsistencies", dd->rank, where, nerr);
629 //! Clear all DD global state indices
630 static void clearDDStateIndices(gmx_domdec_t* dd, const bool keepLocalAtomIndices)
632 gmx_ga2la_t& ga2la = *dd->ga2la;
634 if (!keepLocalAtomIndices)
636 /* Clear the whole list without the overhead of searching */
641 const int numAtomsInZones = dd->comm->atomRanges.end(DDAtomRanges::Type::Zones);
642 for (int i = 0; i < numAtomsInZones; i++)
644 ga2la.erase(dd->globalAtomIndices[i]);
648 dd_clear_local_vsite_indices(dd);
652 dd_clear_local_constraint_indices(dd);
656 //! Return the duration of force calculations on this rank.
657 static float dd_force_load(gmx_domdec_comm_t* comm)
661 if (comm->ddSettings.eFlop)
664 if (comm->ddSettings.eFlop > 1)
666 load *= 1.0 + (comm->ddSettings.eFlop - 1) * (0.1 * rand() / RAND_MAX - 0.05);
671 load = comm->cycl[ddCyclF];
672 if (comm->cycl_n[ddCyclF] > 1)
674 /* Subtract the maximum of the last n cycle counts
675 * to get rid of possible high counts due to other sources,
676 * for instance system activity, that would otherwise
677 * affect the dynamic load balancing.
679 load -= comm->cycl_max[ddCyclF];
683 if (comm->cycl_n[ddCyclWaitGPU] && comm->nrank_gpu_shared > 1)
685 float gpu_wait, gpu_wait_sum;
687 gpu_wait = comm->cycl[ddCyclWaitGPU];
688 if (comm->cycl_n[ddCyclF] > 1)
690 /* We should remove the WaitGPU time of the same MD step
691 * as the one with the maximum F time, since the F time
692 * and the wait time are not independent.
693 * Furthermore, the step for the max F time should be chosen
694 * the same on all ranks that share the same GPU.
695 * But to keep the code simple, we remove the average instead.
696 * The main reason for artificially long times at some steps
697 * is spurious CPU activity or MPI time, so we don't expect
698 * that changes in the GPU wait time matter a lot here.
700 gpu_wait *= (comm->cycl_n[ddCyclF] - 1) / static_cast<float>(comm->cycl_n[ddCyclF]);
702 /* Sum the wait times over the ranks that share the same GPU */
703 MPI_Allreduce(&gpu_wait, &gpu_wait_sum, 1, MPI_FLOAT, MPI_SUM, comm->mpi_comm_gpu_shared);
704 /* Replace the wait time by the average over the ranks */
705 load += -gpu_wait + gpu_wait_sum / comm->nrank_gpu_shared;
713 //! Runs cell size checks and communicates the boundaries.
714 static void comm_dd_ns_cell_sizes(gmx_domdec_t* dd, gmx_ddbox_t* ddbox, rvec cell_ns_x0, rvec cell_ns_x1, int64_t step)
716 gmx_domdec_comm_t* comm;
721 for (dim_ind = 0; dim_ind < dd->ndim; dim_ind++)
723 dim = dd->dim[dim_ind];
725 /* Without PBC we don't have restrictions on the outer cells */
726 if (!(dim >= ddbox->npbcdim && (dd->ci[dim] == 0 || dd->ci[dim] == dd->numCells[dim] - 1))
728 && (comm->cell_x1[dim] - comm->cell_x0[dim]) * ddbox->skew_fac[dim] < comm->cellsize_min[dim])
732 "step %s: The %c-size (%f) times the triclinic skew factor (%f) is smaller "
733 "than the smallest allowed cell size (%f) for domain decomposition grid cell "
735 gmx_step_str(step, buf),
737 comm->cell_x1[dim] - comm->cell_x0[dim],
738 ddbox->skew_fac[dim],
739 dd->comm->cellsize_min[dim],
746 if ((isDlbOn(dd->comm) && dd->ndim > 1) || ddbox->nboundeddim < DIM)
748 /* Communicate the boundaries and update cell_ns_x0/1 */
749 dd_move_cellx(dd, ddbox, cell_ns_x0, cell_ns_x1);
750 if (isDlbOn(dd->comm) && dd->ndim > 1)
752 gmx::check_grid_jump(step, dd, dd->comm->systemInfo.cutoff, ddbox, TRUE);
757 //! Compute and communicate to determine the load distribution across PP ranks.
758 static void get_load_distribution(gmx_domdec_t* dd, gmx_wallcycle* wcycle)
760 gmx_domdec_comm_t* comm;
762 float cell_frac = 0, sbuf[DD_NLOAD_MAX];
767 fprintf(debug, "get_load_distribution start\n");
770 wallcycle_start(wcycle, WallCycleCounter::DDCommLoad);
774 bSepPME = (dd->pme_nodeid >= 0);
776 if (dd->ndim == 0 && bSepPME)
778 /* Without decomposition, but with PME nodes, we need the load */
779 comm->load[0].mdf = comm->cycl[ddCyclPPduringPME];
780 comm->load[0].pme = comm->cycl[ddCyclPME];
783 // Either we have DLB off, or we have it on and the array is large enough
784 GMX_ASSERT(!isDlbOn(dd->comm) || static_cast<int>(dd->comm->cellsizesWithDlb.size()) == dd->ndim,
785 "DLB cell sizes data not set up properly ");
786 for (int d = dd->ndim - 1; d >= 0; d--)
788 const int dim = dd->dim[d];
789 /* Check if we participate in the communication in this dimension */
790 if (d == dd->ndim - 1 || (dd->ci[dd->dim[d + 1]] == 0 && dd->ci[dd->dim[dd->ndim - 1]] == 0))
792 load = &comm->load[d];
793 if (isDlbOn(dd->comm))
795 cell_frac = comm->cellsizesWithDlb[d].fracUpper - comm->cellsizesWithDlb[d].fracLower;
798 if (d == dd->ndim - 1)
800 sbuf[pos++] = dd_force_load(comm);
801 sbuf[pos++] = sbuf[0];
802 if (isDlbOn(dd->comm))
804 sbuf[pos++] = sbuf[0];
805 sbuf[pos++] = cell_frac;
808 sbuf[pos++] = comm->cellsizesWithDlb[d].fracLowerMax;
809 sbuf[pos++] = comm->cellsizesWithDlb[d].fracUpperMin;
814 sbuf[pos++] = comm->cycl[ddCyclPPduringPME];
815 sbuf[pos++] = comm->cycl[ddCyclPME];
820 sbuf[pos++] = comm->load[d + 1].sum;
821 sbuf[pos++] = comm->load[d + 1].max;
822 if (isDlbOn(dd->comm))
824 sbuf[pos++] = comm->load[d + 1].sum_m;
825 sbuf[pos++] = comm->load[d + 1].cvol_min * cell_frac;
826 sbuf[pos++] = comm->load[d + 1].flags;
829 sbuf[pos++] = comm->cellsizesWithDlb[d].fracLowerMax;
830 sbuf[pos++] = comm->cellsizesWithDlb[d].fracUpperMin;
835 sbuf[pos++] = comm->load[d + 1].mdf;
836 sbuf[pos++] = comm->load[d + 1].pme;
840 /* Communicate a row in DD direction d.
841 * The communicators are setup such that the root always has rank 0.
845 load->nload * sizeof(float),
848 load->nload * sizeof(float),
851 comm->mpi_comm_load[d]);
853 if (dd->ci[dim] == dd->master_ci[dim])
855 /* We are the master along this row, process this row */
856 RowMaster* rowMaster = nullptr;
860 rowMaster = comm->cellsizesWithDlb[d].rowMaster.get();
870 for (int i = 0; i < dd->numCells[dim]; i++)
872 load->sum += load->load[pos++];
873 load->max = std::max(load->max, load->load[pos]);
875 if (isDlbOn(dd->comm))
877 if (rowMaster->dlbIsLimited)
879 /* This direction could not be load balanced properly,
880 * therefore we need to use the maximum iso the average load.
882 load->sum_m = std::max(load->sum_m, load->load[pos]);
886 load->sum_m += load->load[pos];
889 load->cvol_min = std::min(load->cvol_min, load->load[pos]);
891 if (d < dd->ndim - 1)
893 load->flags = gmx::roundToInt(load->load[pos++]);
897 rowMaster->bounds[i].cellFracLowerMax = load->load[pos++];
898 rowMaster->bounds[i].cellFracUpperMin = load->load[pos++];
903 load->mdf = std::max(load->mdf, load->load[pos]);
905 load->pme = std::max(load->pme, load->load[pos]);
909 if (isDlbOn(comm) && rowMaster->dlbIsLimited)
911 load->sum_m *= dd->numCells[dim];
912 load->flags |= (1 << d);
920 comm->nload += dd_load_count(comm);
921 comm->load_step += comm->cycl[ddCyclStep];
922 comm->load_sum += comm->load[0].sum;
923 comm->load_max += comm->load[0].max;
926 for (int d = 0; d < dd->ndim; d++)
928 if (comm->load[0].flags & (1 << d))
936 comm->load_mdf += comm->load[0].mdf;
937 comm->load_pme += comm->load[0].pme;
941 wallcycle_stop(wcycle, WallCycleCounter::DDCommLoad);
945 fprintf(debug, "get_load_distribution finished\n");
949 /*! \brief Return the relative performance loss on the total run time
950 * due to the force calculation load imbalance. */
951 static float dd_force_load_fraction(gmx_domdec_t* dd)
953 if (dd->comm->nload > 0 && dd->comm->load_step > 0)
955 return dd->comm->load_sum / (dd->comm->load_step * dd->nnodes);
963 /*! \brief Return the relative performance loss on the total run time
964 * due to the force calculation load imbalance. */
965 static float dd_force_imb_perf_loss(gmx_domdec_t* dd)
967 if (dd->comm->nload > 0 && dd->comm->load_step > 0)
969 return (dd->comm->load_max * dd->nnodes - dd->comm->load_sum) / (dd->comm->load_step * dd->nnodes);
977 //! Print load-balance report e.g. at the end of a run.
978 static void print_dd_load_av(FILE* fplog, gmx_domdec_t* dd)
980 gmx_domdec_comm_t* comm = dd->comm;
982 /* Only the master rank prints loads and only if we measured loads */
983 if (!DDMASTER(dd) || comm->nload == 0)
989 int numPpRanks = dd->nnodes;
990 int numPmeRanks = (comm->ddRankSetup.usePmeOnlyRanks ? comm->ddRankSetup.numRanksDoingPme : 0);
991 int numRanks = numPpRanks + numPmeRanks;
992 float lossFraction = 0;
994 /* Print the average load imbalance and performance loss */
995 if (dd->nnodes > 1 && comm->load_sum > 0)
997 float imbalance = comm->load_max * numPpRanks / comm->load_sum - 1;
998 lossFraction = dd_force_imb_perf_loss(dd);
1000 std::string msg = "\nDynamic load balancing report:\n";
1001 std::string dlbStateStr;
1003 switch (dd->comm->dlbState)
1005 case DlbState::offUser:
1006 dlbStateStr = "DLB was off during the run per user request.";
1008 case DlbState::offForever:
1009 /* Currectly this can happen due to performance loss observed, cell size
1010 * limitations or incompatibility with other settings observed during
1011 * determineInitialDlbState(). */
1012 dlbStateStr = "DLB got disabled because it was unsuitable to use.";
1014 case DlbState::offCanTurnOn:
1015 dlbStateStr = "DLB was off during the run due to low measured imbalance.";
1017 case DlbState::offTemporarilyLocked:
1019 "DLB was locked at the end of the run due to unfinished PP-PME "
1022 case DlbState::onCanTurnOff:
1023 dlbStateStr = "DLB was turned on during the run due to measured imbalance.";
1025 case DlbState::onUser:
1026 dlbStateStr = "DLB was permanently on during the run per user request.";
1028 default: GMX_ASSERT(false, "Undocumented DLB state");
1031 msg += " " + dlbStateStr + "\n";
1032 msg += gmx::formatString(" Average load imbalance: %.1f%%.\n", imbalance * 100);
1033 msg += gmx::formatString(
1034 " The balanceable part of the MD step is %d%%, load imbalance is computed from "
1036 gmx::roundToInt(dd_force_load_fraction(dd) * 100));
1037 msg += gmx::formatString(
1038 " Part of the total run time spent waiting due to load imbalance: %.1f%%.\n",
1039 lossFraction * 100);
1040 fprintf(fplog, "%s", msg.c_str());
1041 fprintf(stderr, "\n%s", msg.c_str());
1044 /* Print during what percentage of steps the load balancing was limited */
1045 bool dlbWasLimited = false;
1048 sprintf(buf, " Steps where the load balancing was limited by -rdd, -rcon and/or -dds:");
1049 for (int d = 0; d < dd->ndim; d++)
1051 int limitPercentage = (200 * comm->load_lim[d] + 1) / (2 * comm->nload);
1052 sprintf(buf + strlen(buf), " %c %d %%", dim2char(dd->dim[d]), limitPercentage);
1053 if (limitPercentage >= 50)
1055 dlbWasLimited = true;
1058 sprintf(buf + strlen(buf), "\n");
1059 fprintf(fplog, "%s", buf);
1060 fprintf(stderr, "%s", buf);
1063 /* Print the performance loss due to separate PME - PP rank imbalance */
1064 float lossFractionPme = 0;
1065 if (numPmeRanks > 0 && comm->load_mdf > 0 && comm->load_step > 0)
1067 float pmeForceRatio = comm->load_pme / comm->load_mdf;
1068 lossFractionPme = (comm->load_pme - comm->load_mdf) / comm->load_step;
1069 if (lossFractionPme <= 0)
1071 lossFractionPme *= numPmeRanks / static_cast<float>(numRanks);
1075 lossFractionPme *= numPpRanks / static_cast<float>(numRanks);
1077 sprintf(buf, " Average PME mesh/force load: %5.3f\n", pmeForceRatio);
1078 fprintf(fplog, "%s", buf);
1079 fprintf(stderr, "%s", buf);
1081 " Part of the total run time spent waiting due to PP/PME imbalance: %.1f %%\n",
1082 std::fabs(lossFractionPme) * 100);
1083 fprintf(fplog, "%s", buf);
1084 fprintf(stderr, "%s", buf);
1086 fprintf(fplog, "\n");
1087 fprintf(stderr, "\n");
1089 if ((lossFraction >= DD_PERF_LOSS_WARN) && (dd->comm->dlbState != DlbState::offTemporarilyLocked))
1091 std::string message = gmx::formatString(
1092 "NOTE: %.1f %% of the available CPU time was lost due to load imbalance\n"
1093 " in the domain decomposition.\n",
1094 lossFraction * 100);
1096 bool hadSuggestion = false;
1097 if (dd->comm->dlbState == DlbState::offUser)
1099 message += " You might want to allow dynamic load balancing (option -dlb auto.)\n";
1100 hadSuggestion = true;
1102 else if (dd->comm->dlbState == DlbState::offCanTurnOn)
1105 " Dynamic load balancing was automatically disabled, but it might be "
1106 "beneficial to manually tuning it on (option -dlb on.)\n";
1107 hadSuggestion = true;
1109 else if (dlbWasLimited)
1112 " You might want to decrease the cell size limit (options -rdd, -rcon "
1114 hadSuggestion = true;
1116 message += gmx::formatString(
1117 " You can %sconsider manually changing the decomposition (option -dd);\n"
1118 " e.g. by using fewer domains along the box dimension in which there is\n"
1119 " considerable inhomogeneity in the simulated system.",
1120 hadSuggestion ? "also " : "");
1122 fprintf(fplog, "%s\n", message.c_str());
1123 fprintf(stderr, "%s\n", message.c_str());
1125 if (numPmeRanks > 0 && std::fabs(lossFractionPme) >= DD_PERF_LOSS_WARN)
1128 "NOTE: %.1f %% performance was lost because the PME ranks\n"
1129 " had %s work to do than the PP ranks.\n"
1130 " You might want to %s the number of PME ranks\n"
1131 " or %s the cut-off and the grid spacing.\n",
1132 std::fabs(lossFractionPme * 100),
1133 (lossFractionPme < 0) ? "less" : "more",
1134 (lossFractionPme < 0) ? "decrease" : "increase",
1135 (lossFractionPme < 0) ? "decrease" : "increase");
1136 fprintf(fplog, "%s\n", buf);
1137 fprintf(stderr, "%s\n", buf);
1141 //! Return the minimum communication volume.
1142 static float dd_vol_min(gmx_domdec_t* dd)
1144 return dd->comm->load[0].cvol_min * dd->nnodes;
1147 //! Return the DD load flags.
1148 static int dd_load_flags(gmx_domdec_t* dd)
1150 return dd->comm->load[0].flags;
1153 //! Return the reported load imbalance in force calculations.
1154 static float dd_f_imbal(gmx_domdec_t* dd)
1156 if (dd->comm->load[0].sum > 0)
1158 return dd->comm->load[0].max * dd->nnodes / dd->comm->load[0].sum - 1.0F;
1162 /* Something is wrong in the cycle counting, report no load imbalance */
1167 //! Returns DD load balance report.
1168 static std::string dd_print_load(gmx_domdec_t* dd, int64_t step)
1170 gmx::StringOutputStream stream;
1171 gmx::TextWriter log(&stream);
1173 int flags = dd_load_flags(dd);
1176 log.writeString("DD load balancing is limited by minimum cell size in dimension");
1177 for (int d = 0; d < dd->ndim; d++)
1179 if (flags & (1 << d))
1181 log.writeStringFormatted(" %c", dim2char(dd->dim[d]));
1184 log.ensureLineBreak();
1186 log.writeString("DD step " + gmx::toString(step));
1187 if (isDlbOn(dd->comm))
1189 log.writeStringFormatted(" vol min/aver %5.3f%c", dd_vol_min(dd), flags ? '!' : ' ');
1193 log.writeStringFormatted(" load imb.: force %4.1f%%", dd_f_imbal(dd) * 100);
1195 if (dd->comm->cycl_n[ddCyclPME])
1197 log.writeStringFormatted(" pme mesh/force %5.3f", dd_pme_f_ratio(dd));
1199 log.ensureLineBreak();
1200 return stream.toString();
1203 //! Prints DD load balance report in mdrun verbose mode.
1204 static void dd_print_load_verbose(gmx_domdec_t* dd)
1206 if (isDlbOn(dd->comm))
1208 fprintf(stderr, "vol %4.2f%c ", dd_vol_min(dd), dd_load_flags(dd) ? '!' : ' ');
1212 fprintf(stderr, "imb F %2d%% ", gmx::roundToInt(dd_f_imbal(dd) * 100));
1214 if (dd->comm->cycl_n[ddCyclPME])
1216 fprintf(stderr, "pme/F %4.2f ", dd_pme_f_ratio(dd));
1220 //! Turns on dynamic load balancing if possible and needed.
1221 static void turn_on_dlb(const gmx::MDLogger& mdlog, gmx_domdec_t* dd, int64_t step)
1223 gmx_domdec_comm_t* comm = dd->comm;
1225 real cellsize_min = comm->cellsize_min[dd->dim[0]];
1226 for (int d = 1; d < dd->ndim; d++)
1228 cellsize_min = std::min(cellsize_min, comm->cellsize_min[dd->dim[d]]);
1231 /* Turn off DLB if we're too close to the cell size limit. */
1232 if (cellsize_min < comm->cellsize_limit * 1.05)
1235 .appendTextFormatted(
1236 "step %s Measured %.1f %% performance loss due to load imbalance, "
1237 "but the minimum cell size is smaller than 1.05 times the cell size limit. "
1238 "Will no longer try dynamic load balancing.",
1239 gmx::toString(step).c_str(),
1240 dd_force_imb_perf_loss(dd) * 100);
1242 comm->dlbState = DlbState::offForever;
1247 .appendTextFormatted(
1248 "step %s Turning on dynamic load balancing, because the performance loss due "
1249 "to load imbalance is %.1f %%.",
1250 gmx::toString(step).c_str(),
1251 dd_force_imb_perf_loss(dd) * 100);
1252 comm->dlbState = DlbState::onCanTurnOff;
1254 /* Store the non-DLB performance, so we can check if DLB actually
1255 * improves performance.
1257 GMX_RELEASE_ASSERT(comm->cycl_n[ddCyclStep] > 0,
1258 "When we turned on DLB, we should have measured cycles");
1259 comm->cyclesPerStepBeforeDLB = comm->cycl[ddCyclStep] / comm->cycl_n[ddCyclStep];
1263 /* We can set the required cell size info here,
1264 * so we do not need to communicate this.
1265 * The grid is completely uniform.
1267 for (int d = 0; d < dd->ndim; d++)
1269 RowMaster* rowMaster = comm->cellsizesWithDlb[d].rowMaster.get();
1273 comm->load[d].sum_m = comm->load[d].sum;
1275 int nc = dd->numCells[dd->dim[d]];
1276 for (int i = 0; i < nc; i++)
1278 rowMaster->cellFrac[i] = i / static_cast<real>(nc);
1281 rowMaster->bounds[i].cellFracLowerMax = i / static_cast<real>(nc);
1282 rowMaster->bounds[i].cellFracUpperMin = (i + 1) / static_cast<real>(nc);
1285 rowMaster->cellFrac[nc] = 1.0;
1290 //! Turns off dynamic load balancing (but leave it able to turn back on).
1291 static void turn_off_dlb(const gmx::MDLogger& mdlog, gmx_domdec_t* dd, int64_t step)
1295 "step " + gmx::toString(step)
1296 + " Turning off dynamic load balancing, because it is degrading performance.");
1297 dd->comm->dlbState = DlbState::offCanTurnOn;
1298 dd->comm->haveTurnedOffDlb = true;
1299 dd->comm->ddPartioningCountFirstDlbOff = dd->ddp_count;
1302 //! Turns off dynamic load balancing permanently.
1303 static void turn_off_dlb_forever(const gmx::MDLogger& mdlog, gmx_domdec_t* dd, int64_t step)
1305 GMX_RELEASE_ASSERT(dd->comm->dlbState == DlbState::offCanTurnOn,
1306 "Can only turn off DLB forever when it was in the can-turn-on state");
1309 "step " + gmx::toString(step)
1310 + " Will no longer try dynamic load balancing, as it degraded performance.");
1311 dd->comm->dlbState = DlbState::offForever;
1314 void set_dd_dlb_max_cutoff(t_commrec* cr, real cutoff)
1316 gmx_domdec_comm_t* comm;
1318 comm = cr->dd->comm;
1320 /* Turn on the DLB limiting (might have been on already) */
1321 comm->bPMELoadBalDLBLimits = TRUE;
1323 /* Change the cut-off limit */
1324 comm->PMELoadBal_max_cutoff = cutoff;
1329 "PME load balancing set a limit to the DLB staggering such that a %f cut-off will "
1330 "continue to fit\n",
1331 comm->PMELoadBal_max_cutoff);
1335 //! Merge atom buffers.
1336 static void merge_cg_buffers(int ncell,
1337 gmx_domdec_comm_dim_t* cd,
1340 gmx::ArrayRef<int> index_gl,
1342 gmx::ArrayRef<gmx::RVec> x,
1343 gmx::ArrayRef<const gmx::RVec> recv_vr,
1344 gmx::ArrayRef<cginfo_mb_t> cginfo_mb,
1345 gmx::ArrayRef<int> cginfo)
1347 gmx_domdec_ind_t *ind, *ind_p;
1348 int p, cell, c, cg, cg0, cg1, cg_gl;
1351 ind = &cd->ind[pulse];
1353 /* First correct the already stored data */
1354 shift = ind->nrecv[ncell];
1355 for (cell = ncell - 1; cell >= 0; cell--)
1357 shift -= ind->nrecv[cell];
1360 /* Move the cg's present from previous grid pulses */
1361 cg0 = ncg_cell[ncell + cell];
1362 cg1 = ncg_cell[ncell + cell + 1];
1363 for (cg = cg1 - 1; cg >= cg0; cg--)
1365 index_gl[cg + shift] = index_gl[cg];
1366 x[cg + shift] = x[cg];
1367 cginfo[cg + shift] = cginfo[cg];
1369 /* Correct the already stored send indices for the shift */
1370 for (p = 1; p <= pulse; p++)
1372 ind_p = &cd->ind[p];
1374 for (c = 0; c < cell; c++)
1376 cg0 += ind_p->nsend[c];
1378 cg1 = cg0 + ind_p->nsend[cell];
1379 for (cg = cg0; cg < cg1; cg++)
1381 ind_p->index[cg] += shift;
1387 /* Merge in the communicated buffers */
1390 for (cell = 0; cell < ncell; cell++)
1392 cg1 = ncg_cell[ncell + cell + 1] + shift;
1393 for (cg = 0; cg < ind->nrecv[cell]; cg++)
1395 /* Copy this atom from the buffer */
1396 index_gl[cg1] = recv_i[cg0];
1397 x[cg1] = recv_vr[cg0];
1398 /* Copy information */
1399 cg_gl = index_gl[cg1];
1400 cginfo[cg1] = ddcginfo(cginfo_mb, cg_gl);
1404 shift += ind->nrecv[cell];
1405 ncg_cell[ncell + cell + 1] = cg1;
1409 //! Makes a range partitioning for the atom groups wthin a cell
1410 static void make_cell2at_index(gmx_domdec_comm_dim_t* cd, int nzone, int atomGroupStart)
1412 /* Store the atom block boundaries for easy copying of communication buffers
1414 int g = atomGroupStart;
1415 for (int zone = 0; zone < nzone; zone++)
1417 for (gmx_domdec_ind_t& ind : cd->ind)
1419 ind.cell2at0[zone] = g;
1420 g += ind.nrecv[zone];
1421 ind.cell2at1[zone] = g;
1426 //! Returns whether a link is missing.
1427 static gmx_bool missing_link(const t_blocka& link, const int globalAtomIndex, const gmx_ga2la_t& ga2la)
1429 for (int i = link.index[globalAtomIndex]; i < link.index[globalAtomIndex + 1]; i++)
1431 if (!ga2la.findHome(link.a[i]))
1440 //! Domain corners for communication, a maximum of 4 i-zones see a j domain
1443 //! The corners for the non-bonded communication.
1445 //! Corner for rounding.
1447 //! Corners for rounding.
1449 //! Corners for bounded communication.
1451 //! Corner for rounding for bonded communication.
1455 //! Determine the corners of the domain(s) we are communicating with.
1456 static void set_dd_corners(const gmx_domdec_t* dd, int dim0, int dim1, int dim2, gmx_bool bDistMB, dd_corners_t* c)
1458 const gmx_domdec_comm_t* comm;
1459 const gmx_domdec_zones_t* zones;
1463 zones = &comm->zones;
1465 /* Keep the compiler happy */
1469 /* The first dimension is equal for all cells */
1470 c->c[0][0] = comm->cell_x0[dim0];
1473 c->bc[0] = c->c[0][0];
1478 /* This cell row is only seen from the first row */
1479 c->c[1][0] = comm->cell_x0[dim1];
1480 /* All rows can see this row */
1481 c->c[1][1] = comm->cell_x0[dim1];
1482 if (isDlbOn(dd->comm))
1484 c->c[1][1] = std::max(comm->cell_x0[dim1], comm->zone_d1[1].mch0);
1487 /* For the multi-body distance we need the maximum */
1488 c->bc[1] = std::max(comm->cell_x0[dim1], comm->zone_d1[1].p1_0);
1491 /* Set the upper-right corner for rounding */
1492 c->cr0 = comm->cell_x1[dim0];
1497 for (int j = 0; j < 4; j++)
1499 c->c[2][j] = comm->cell_x0[dim2];
1501 if (isDlbOn(dd->comm))
1503 /* Use the maximum of the i-cells that see a j-cell */
1504 for (const auto& iZone : zones->iZones)
1506 const int iZoneIndex = iZone.iZoneIndex;
1507 for (int jZone : iZone.jZoneRange)
1511 c->c[2][jZone - 4] = std::max(
1513 comm->zone_d2[zones->shift[iZoneIndex][dim0]][zones->shift[iZoneIndex][dim1]]
1520 /* For the multi-body distance we need the maximum */
1521 c->bc[2] = comm->cell_x0[dim2];
1522 for (int i = 0; i < 2; i++)
1524 for (int j = 0; j < 2; j++)
1526 c->bc[2] = std::max(c->bc[2], comm->zone_d2[i][j].p1_0);
1532 /* Set the upper-right corner for rounding */
1533 /* Cell (0,0,0) and cell (1,0,0) can see cell 4 (0,1,1)
1534 * Only cell (0,0,0) can see cell 7 (1,1,1)
1536 c->cr1[0] = comm->cell_x1[dim1];
1537 c->cr1[3] = comm->cell_x1[dim1];
1538 if (isDlbOn(dd->comm))
1540 c->cr1[0] = std::max(comm->cell_x1[dim1], comm->zone_d1[1].mch1);
1543 /* For the multi-body distance we need the maximum */
1544 c->bcr1 = std::max(comm->cell_x1[dim1], comm->zone_d1[1].p1_1);
1551 /*! \brief Add the atom groups and coordinates we need to send in this
1552 * pulse from this zone to \p localAtomGroups and \p work. */
1553 static void get_zone_pulse_groups(gmx_domdec_t* dd,
1558 gmx::ArrayRef<const int> globalAtomGroupIndices,
1567 bool distanceIsTriclinic,
1574 const dd_corners_t* c,
1575 const rvec sf2_round,
1576 gmx_bool bDistBonded,
1580 gmx::ArrayRef<const gmx::RVec> coordinates,
1581 gmx::ArrayRef<const int> cginfo,
1582 std::vector<int>* localAtomGroups,
1583 dd_comm_setup_work_t* work)
1585 gmx_domdec_comm_t* comm;
1587 gmx_bool bDistMB_pulse;
1589 real r2, rb2, r, tric_sh;
1596 bScrew = (dd->unitCellInfo.haveScrewPBC && dim == XX);
1598 bDistMB_pulse = (bDistMB && bDistBonded);
1600 /* Unpack the work data */
1601 std::vector<int>& ibuf = work->atomGroupBuffer;
1602 std::vector<gmx::RVec>& vbuf = work->positionBuffer;
1606 for (cg = cg0; cg < cg1; cg++)
1610 if (!distanceIsTriclinic)
1612 /* Rectangular direction, easy */
1613 r = coordinates[cg][dim] - c->c[dim_ind][zone];
1620 r = coordinates[cg][dim] - c->bc[dim_ind];
1626 /* Rounding gives at most a 16% reduction
1627 * in communicated atoms
1629 if (dim_ind >= 1 && (zonei == 1 || zonei == 2))
1631 r = coordinates[cg][dim0] - c->cr0;
1632 /* This is the first dimension, so always r >= 0 */
1639 if (dim_ind == 2 && (zonei == 2 || zonei == 3))
1641 r = coordinates[cg][dim1] - c->cr1[zone];
1648 r = coordinates[cg][dim1] - c->bcr1;
1658 /* Triclinic direction, more complicated */
1661 /* Rounding, conservative as the skew_fac multiplication
1662 * will slightly underestimate the distance.
1664 if (dim_ind >= 1 && (zonei == 1 || zonei == 2))
1666 rn[dim0] = coordinates[cg][dim0] - c->cr0;
1667 for (i = dim0 + 1; i < DIM; i++)
1669 rn[dim0] -= coordinates[cg][i] * v_0[i][dim0];
1671 r2 = rn[dim0] * rn[dim0] * sf2_round[dim0];
1674 rb[dim0] = rn[dim0];
1677 /* Take care that the cell planes along dim0 might not
1678 * be orthogonal to those along dim1 and dim2.
1680 for (i = 1; i <= dim_ind; i++)
1683 if (normal[dim0][dimd] > 0)
1685 rn[dimd] -= rn[dim0] * normal[dim0][dimd];
1688 rb[dimd] -= rb[dim0] * normal[dim0][dimd];
1693 if (dim_ind == 2 && (zonei == 2 || zonei == 3))
1695 GMX_ASSERT(dim1 >= 0 && dim1 < DIM, "Must have a valid dimension index");
1696 rn[dim1] += coordinates[cg][dim1] - c->cr1[zone];
1698 for (i = dim1 + 1; i < DIM; i++)
1700 tric_sh -= coordinates[cg][i] * v_1[i][dim1];
1702 rn[dim1] += tric_sh;
1705 r2 += rn[dim1] * rn[dim1] * sf2_round[dim1];
1706 /* Take care of coupling of the distances
1707 * to the planes along dim0 and dim1 through dim2.
1709 r2 -= rn[dim0] * rn[dim1] * skew_fac_01;
1710 /* Take care that the cell planes along dim1
1711 * might not be orthogonal to that along dim2.
1713 if (normal[dim1][dim2] > 0)
1715 rn[dim2] -= rn[dim1] * normal[dim1][dim2];
1720 rb[dim1] += coordinates[cg][dim1] - c->bcr1 + tric_sh;
1723 rb2 += rb[dim1] * rb[dim1] * sf2_round[dim1];
1724 /* Take care of coupling of the distances
1725 * to the planes along dim0 and dim1 through dim2.
1727 rb2 -= rb[dim0] * rb[dim1] * skew_fac_01;
1728 /* Take care that the cell planes along dim1
1729 * might not be orthogonal to that along dim2.
1731 if (normal[dim1][dim2] > 0)
1733 rb[dim2] -= rb[dim1] * normal[dim1][dim2];
1738 /* The distance along the communication direction */
1739 rn[dim] += coordinates[cg][dim] - c->c[dim_ind][zone];
1741 for (i = dim + 1; i < DIM; i++)
1743 tric_sh -= coordinates[cg][i] * v_d[i][dim];
1748 r2 += rn[dim] * rn[dim] * skew_fac2_d;
1749 /* Take care of coupling of the distances
1750 * to the planes along dim0 and dim1 through dim2.
1752 if (dim_ind == 1 && zonei == 1)
1754 r2 -= rn[dim0] * rn[dim] * skew_fac_01;
1760 GMX_ASSERT(dim >= 0 && dim < DIM, "Must have a valid dimension index");
1761 rb[dim] += coordinates[cg][dim] - c->bc[dim_ind] + tric_sh;
1764 rb2 += rb[dim] * rb[dim] * skew_fac2_d;
1765 /* Take care of coupling of the distances
1766 * to the planes along dim0 and dim1 through dim2.
1768 if (dim_ind == 1 && zonei == 1)
1770 rb2 -= rb[dim0] * rb[dim] * skew_fac_01;
1777 || (bDistBonded && ((bDistMB && rb2 < r_bcomm2) || (bDist2B && r2 < r_bcomm2))
1779 || (GET_CGINFO_BOND_INTER(cginfo[cg])
1780 && missing_link(*comm->bondedLinks, globalAtomGroupIndices[cg], *dd->ga2la)))))
1782 /* Store the local and global atom group indices and position */
1783 localAtomGroups->push_back(cg);
1784 ibuf.push_back(globalAtomGroupIndices[cg]);
1788 if (dd->ci[dim] == 0)
1790 /* Correct coordinates for pbc */
1791 rvec_add(coordinates[cg], box[dim], posPbc);
1794 posPbc[YY] = box[YY][YY] - posPbc[YY];
1795 posPbc[ZZ] = box[ZZ][ZZ] - posPbc[ZZ];
1800 copy_rvec(coordinates[cg], posPbc);
1802 vbuf.emplace_back(posPbc[XX], posPbc[YY], posPbc[ZZ]);
1809 work->nsend_zone = nsend_z;
1813 static void clearCommSetupData(dd_comm_setup_work_t* work)
1815 work->localAtomGroupBuffer.clear();
1816 work->atomGroupBuffer.clear();
1817 work->positionBuffer.clear();
1819 work->nsend_zone = 0;
1822 //! Prepare DD communication.
1823 static void setup_dd_communication(gmx_domdec_t* dd, matrix box, gmx_ddbox_t* ddbox, t_forcerec* fr, t_state* state)
1825 int dim_ind, dim, dim0, dim1, dim2, dimd, nat_tot;
1826 int nzone, nzone_send, zone, zonei, cg0, cg1;
1828 int * zone_cg_range, pos_cg;
1829 gmx_domdec_comm_t* comm;
1830 gmx_domdec_zones_t* zones;
1831 gmx_domdec_comm_dim_t* cd;
1832 gmx_bool bBondComm, bDist2B, bDistMB, bDistBonded;
1833 dd_corners_t corners;
1834 rvec * normal, *v_d, *v_0 = nullptr, *v_1 = nullptr;
1835 real skew_fac2_d, skew_fac_01;
1840 fprintf(debug, "Setting up DD communication\n");
1845 if (comm->dth.empty())
1847 /* Initialize the thread data.
1848 * This can not be done in init_domain_decomposition,
1849 * as the numbers of threads is determined later.
1851 int numThreads = gmx_omp_nthreads_get(ModuleMultiThread::Domdec);
1852 comm->dth.resize(numThreads);
1855 bBondComm = comm->systemInfo.filterBondedCommunication;
1857 /* Do we need to determine extra distances for multi-body bondeds? */
1858 bDistMB = (comm->systemInfo.haveInterDomainMultiBodyBondeds && isDlbOn(dd->comm) && dd->ndim > 1);
1860 /* Do we need to determine extra distances for only two-body bondeds? */
1861 bDist2B = (bBondComm && !bDistMB);
1863 const real r_comm2 =
1864 gmx::square(domainToDomainIntoAtomToDomainCutoff(comm->systemInfo, comm->systemInfo.cutoff));
1865 const real r_bcomm2 =
1866 gmx::square(domainToDomainIntoAtomToDomainCutoff(comm->systemInfo, comm->cutoff_mbody));
1870 fprintf(debug, "bBondComm %s, r_bc %f\n", gmx::boolToString(bBondComm), std::sqrt(r_bcomm2));
1873 zones = &comm->zones;
1876 dim1 = (dd->ndim >= 2 ? dd->dim[1] : -1);
1877 dim2 = (dd->ndim >= 3 ? dd->dim[2] : -1);
1879 set_dd_corners(dd, dim0, dim1, dim2, bDistMB, &corners);
1881 /* Triclinic stuff */
1882 normal = ddbox->normal;
1886 v_0 = ddbox->v[dim0];
1887 if (ddbox->tric_dir[dim0] && ddbox->tric_dir[dim1])
1889 /* Determine the coupling coefficient for the distances
1890 * to the cell planes along dim0 and dim1 through dim2.
1891 * This is required for correct rounding.
1893 skew_fac_01 = ddbox->v[dim0][dim1 + 1][dim0] * ddbox->v[dim1][dim1 + 1][dim1];
1896 fprintf(debug, "\nskew_fac_01 %f\n", skew_fac_01);
1902 v_1 = ddbox->v[dim1];
1905 zone_cg_range = zones->cg_range.data();
1906 gmx::ArrayRef<cginfo_mb_t> cginfo_mb = fr->cginfo_mb;
1908 zone_cg_range[0] = 0;
1909 zone_cg_range[1] = dd->ncg_home;
1910 comm->zone_ncg1[0] = dd->ncg_home;
1911 pos_cg = dd->ncg_home;
1913 nat_tot = comm->atomRanges.numHomeAtoms();
1915 for (dim_ind = 0; dim_ind < dd->ndim; dim_ind++)
1917 dim = dd->dim[dim_ind];
1918 cd = &comm->cd[dim_ind];
1920 /* Check if we need to compute triclinic distances along this dim */
1921 bool distanceIsTriclinic = false;
1922 for (int i = 0; i <= dim_ind; i++)
1924 if (ddbox->tric_dir[dd->dim[i]])
1926 distanceIsTriclinic = true;
1930 if (dim >= ddbox->npbcdim && dd->ci[dim] == 0)
1932 /* No pbc in this dimension, the first node should not comm. */
1940 v_d = ddbox->v[dim];
1941 skew_fac2_d = gmx::square(ddbox->skew_fac[dim]);
1943 cd->receiveInPlace = true;
1944 for (int p = 0; p < cd->numPulses(); p++)
1946 /* Only atoms communicated in the first pulse are used
1947 * for multi-body bonded interactions or for bBondComm.
1949 bDistBonded = ((bDistMB || bDist2B) && p == 0);
1951 gmx_domdec_ind_t* ind = &cd->ind[p];
1953 /* Thread 0 writes in the global index array */
1955 clearCommSetupData(&comm->dth[0]);
1957 for (zone = 0; zone < nzone_send; zone++)
1959 if (dim_ind > 0 && distanceIsTriclinic)
1961 /* Determine slightly more optimized skew_fac's
1963 * This reduces the number of communicated atoms
1964 * by about 10% for 3D DD of rhombic dodecahedra.
1966 for (dimd = 0; dimd < dim; dimd++)
1968 sf2_round[dimd] = 1;
1969 if (ddbox->tric_dir[dimd])
1971 for (int i = dd->dim[dimd] + 1; i < DIM; i++)
1973 /* If we are shifted in dimension i
1974 * and the cell plane is tilted forward
1975 * in dimension i, skip this coupling.
1977 if (!(zones->shift[nzone + zone][i] && ddbox->v[dimd][i][dimd] >= 0))
1979 sf2_round[dimd] += gmx::square(ddbox->v[dimd][i][dimd]);
1982 sf2_round[dimd] = 1 / sf2_round[dimd];
1987 zonei = zone_perm[dim_ind][zone];
1990 /* Here we permutate the zones to obtain a convenient order
1991 * for neighbor searching
1993 cg0 = zone_cg_range[zonei];
1994 cg1 = zone_cg_range[zonei + 1];
1998 /* Look only at the cg's received in the previous grid pulse
2000 cg1 = zone_cg_range[nzone + zone + 1];
2001 cg0 = cg1 - cd->ind[p - 1].nrecv[zone];
2004 const int numThreads = gmx::ssize(comm->dth);
2005 #pragma omp parallel for num_threads(numThreads) schedule(static)
2006 for (int th = 0; th < numThreads; th++)
2010 dd_comm_setup_work_t& work = comm->dth[th];
2012 /* Retain data accumulated into buffers of thread 0 */
2015 clearCommSetupData(&work);
2018 int cg0_th = cg0 + ((cg1 - cg0) * th) / numThreads;
2019 int cg1_th = cg0 + ((cg1 - cg0) * (th + 1)) / numThreads;
2021 /* Get the atom groups and coordinates for this pulse in this zone */
2022 get_zone_pulse_groups(dd,
2027 dd->globalAtomGroupIndices,
2036 distanceIsTriclinic,
2051 th == 0 ? &ind->index : &work.localAtomGroupBuffer,
2054 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
2057 std::vector<int>& atomGroups = comm->dth[0].atomGroupBuffer;
2058 std::vector<gmx::RVec>& positions = comm->dth[0].positionBuffer;
2059 ind->nsend[zone] = comm->dth[0].nsend_zone;
2060 /* Append data of threads>=1 to the communication buffers */
2061 for (int th = 1; th < numThreads; th++)
2063 const dd_comm_setup_work_t& dth = comm->dth[th];
2065 ind->index.insert(ind->index.end(),
2066 dth.localAtomGroupBuffer.begin(),
2067 dth.localAtomGroupBuffer.end());
2069 atomGroups.end(), dth.atomGroupBuffer.begin(), dth.atomGroupBuffer.end());
2071 positions.end(), dth.positionBuffer.begin(), dth.positionBuffer.end());
2072 comm->dth[0].nat += dth.nat;
2073 ind->nsend[zone] += dth.nsend_zone;
2076 /* Clear the counts in case we do not have pbc */
2077 for (zone = nzone_send; zone < nzone; zone++)
2079 ind->nsend[zone] = 0;
2081 ind->nsend[nzone] = ind->index.size();
2082 ind->nsend[nzone + 1] = comm->dth[0].nat;
2083 /* Communicate the number of cg's and atoms to receive */
2084 ddSendrecv(dd, dim_ind, dddirBackward, ind->nsend, nzone + 2, ind->nrecv, nzone + 2);
2088 /* We can receive in place if only the last zone is not empty */
2089 for (zone = 0; zone < nzone - 1; zone++)
2091 if (ind->nrecv[zone] > 0)
2093 cd->receiveInPlace = false;
2098 int receiveBufferSize = 0;
2099 if (!cd->receiveInPlace)
2101 receiveBufferSize = ind->nrecv[nzone];
2103 /* These buffer are actually only needed with in-place */
2104 DDBufferAccess<int> globalAtomGroupBuffer(comm->intBuffer, receiveBufferSize);
2105 DDBufferAccess<gmx::RVec> rvecBuffer(comm->rvecBuffer, receiveBufferSize);
2107 dd_comm_setup_work_t& work = comm->dth[0];
2109 /* Make space for the global cg indices */
2110 int numAtomGroupsNew = pos_cg + ind->nrecv[nzone];
2111 dd->globalAtomGroupIndices.resize(numAtomGroupsNew);
2112 /* Communicate the global cg indices */
2113 gmx::ArrayRef<int> integerBufferRef;
2114 if (cd->receiveInPlace)
2116 integerBufferRef = gmx::arrayRefFromArray(
2117 dd->globalAtomGroupIndices.data() + pos_cg, ind->nrecv[nzone]);
2121 integerBufferRef = globalAtomGroupBuffer.buffer;
2123 ddSendrecv<int>(dd, dim_ind, dddirBackward, work.atomGroupBuffer, integerBufferRef);
2125 /* Make space for cginfo */
2126 dd_resize_atominfo_and_state(fr, state, pos_cg + ind->nrecv[nzone]);
2128 /* Communicate the coordinates */
2129 gmx::ArrayRef<gmx::RVec> rvecBufferRef;
2130 if (cd->receiveInPlace)
2132 rvecBufferRef = gmx::makeArrayRef(state->x).subArray(pos_cg, ind->nrecv[nzone]);
2136 rvecBufferRef = rvecBuffer.buffer;
2138 ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward, work.positionBuffer, rvecBufferRef);
2140 /* Make the charge group index */
2141 if (cd->receiveInPlace)
2143 zone = (p == 0 ? 0 : nzone - 1);
2144 while (zone < nzone)
2146 for (int i = 0; i < ind->nrecv[zone]; i++)
2148 int globalAtomIndex = dd->globalAtomGroupIndices[pos_cg];
2149 fr->cginfo[pos_cg] = ddcginfo(cginfo_mb, globalAtomIndex);
2154 comm->zone_ncg1[nzone + zone] = ind->nrecv[zone];
2157 zone_cg_range[nzone + zone] = pos_cg;
2162 /* This part of the code is never executed with bBondComm. */
2163 merge_cg_buffers(nzone,
2167 dd->globalAtomGroupIndices,
2168 integerBufferRef.data(),
2173 pos_cg += ind->nrecv[nzone];
2175 nat_tot += ind->nrecv[nzone + 1];
2177 if (!cd->receiveInPlace)
2179 /* Store the atom block for easy copying of communication buffers */
2180 make_cell2at_index(cd, nzone, zone_cg_range[nzone]);
2185 comm->atomRanges.setEnd(DDAtomRanges::Type::Zones, nat_tot);
2189 /* We don't need to update cginfo, since that was alrady done above.
2190 * So we pass NULL for the forcerec.
2192 dd_set_cginfo(dd->globalAtomGroupIndices, dd->ncg_home, dd->globalAtomGroupIndices.size(), nullptr);
2197 fprintf(debug, "Finished setting up DD communication, zones:");
2198 for (c = 0; c < zones->n; c++)
2200 fprintf(debug, " %d", zones->cg_range[c + 1] - zones->cg_range[c]);
2202 fprintf(debug, "\n");
2206 //! Set boundaries for the charge group range.
2207 static void set_cg_boundaries(gmx_domdec_zones_t* zones)
2209 for (auto& iZone : zones->iZones)
2211 iZone.iAtomRange = gmx::Range<int>(0, zones->cg_range[iZone.iZoneIndex + 1]);
2212 iZone.jAtomRange = gmx::Range<int>(zones->cg_range[iZone.jZoneRange.begin()],
2213 zones->cg_range[iZone.jZoneRange.end()]);
2217 /*! \brief Set zone dimensions for zones \p zone_start to \p zone_end-1
2219 * Also sets the atom density for the home zone when \p zone_start=0.
2220 * For this \p numMovedChargeGroupsInHomeZone needs to be passed to tell
2221 * how many charge groups will move but are still part of the current range.
2222 * \todo When converting domdec to use proper classes, all these variables
2223 * should be private and a method should return the correct count
2224 * depending on an internal state.
2226 * \param[in,out] dd The domain decomposition struct
2227 * \param[in] box The box
2228 * \param[in] ddbox The domain decomposition box struct
2229 * \param[in] zone_start The start of the zone range to set sizes for
2230 * \param[in] zone_end The end of the zone range to set sizes for
2231 * \param[in] numMovedChargeGroupsInHomeZone The number of charge groups in the home zone that should moved but are still present in dd->comm->zones.cg_range
2233 static void set_zones_size(gmx_domdec_t* dd,
2235 const gmx_ddbox_t* ddbox,
2238 int numMovedChargeGroupsInHomeZone)
2240 gmx_domdec_comm_t* comm;
2241 gmx_domdec_zones_t* zones;
2250 zones = &comm->zones;
2252 /* Do we need to determine extra distances for multi-body bondeds? */
2253 bDistMB = (comm->systemInfo.haveInterDomainMultiBodyBondeds && isDlbOn(dd->comm) && dd->ndim > 1);
2255 for (z = zone_start; z < zone_end; z++)
2257 /* Copy cell limits to zone limits.
2258 * Valid for non-DD dims and non-shifted dims.
2260 copy_rvec(comm->cell_x0, zones->size[z].x0);
2261 copy_rvec(comm->cell_x1, zones->size[z].x1);
2264 for (d = 0; d < dd->ndim; d++)
2268 for (z = 0; z < zones->n; z++)
2270 /* With a staggered grid we have different sizes
2271 * for non-shifted dimensions.
2273 if (isDlbOn(dd->comm) && zones->shift[z][dim] == 0)
2277 zones->size[z].x0[dim] = comm->zone_d1[zones->shift[z][dd->dim[d - 1]]].min0;
2278 zones->size[z].x1[dim] = comm->zone_d1[zones->shift[z][dd->dim[d - 1]]].max1;
2282 zones->size[z].x0[dim] =
2283 comm->zone_d2[zones->shift[z][dd->dim[d - 2]]][zones->shift[z][dd->dim[d - 1]]]
2285 zones->size[z].x1[dim] =
2286 comm->zone_d2[zones->shift[z][dd->dim[d - 2]]][zones->shift[z][dd->dim[d - 1]]]
2292 rcs = comm->systemInfo.cutoff;
2293 rcmbs = comm->cutoff_mbody;
2294 if (ddbox->tric_dir[dim])
2296 rcs /= ddbox->skew_fac[dim];
2297 rcmbs /= ddbox->skew_fac[dim];
2300 /* Set the lower limit for the shifted zone dimensions */
2301 for (z = zone_start; z < zone_end; z++)
2303 if (zones->shift[z][dim] > 0)
2306 if (!isDlbOn(dd->comm) || d == 0)
2308 zones->size[z].x0[dim] = comm->cell_x1[dim];
2309 zones->size[z].x1[dim] = comm->cell_x1[dim] + rcs;
2313 /* Here we take the lower limit of the zone from
2314 * the lowest domain of the zone below.
2318 zones->size[z].x0[dim] = comm->zone_d1[zones->shift[z][dd->dim[d - 1]]].min1;
2324 zones->size[z].x0[dim] = zones->size[zone_perm[2][z - 4]].x0[dim];
2328 zones->size[z].x0[dim] =
2329 comm->zone_d2[zones->shift[z][dd->dim[d - 2]]][zones->shift[z][dd->dim[d - 1]]]
2333 /* A temporary limit, is updated below */
2334 zones->size[z].x1[dim] = zones->size[z].x0[dim];
2338 for (size_t zi = 0; zi < zones->iZones.size(); zi++)
2340 if (zones->shift[zi][dim] == 0)
2342 /* This takes the whole zone into account.
2343 * With multiple pulses this will lead
2344 * to a larger zone then strictly necessary.
2346 zones->size[z].x1[dim] = std::max(zones->size[z].x1[dim],
2347 zones->size[zi].x1[dim] + rcmbs);
2355 /* Loop over the i-zones to set the upper limit of each
2358 for (const auto& iZone : zones->iZones)
2360 const int zi = iZone.iZoneIndex;
2361 if (zones->shift[zi][dim] == 0)
2363 /* We should only use zones up to zone_end */
2364 const auto& jZoneRangeFull = iZone.jZoneRange;
2365 if (zone_end <= *jZoneRangeFull.begin())
2369 const gmx::Range<int> jZoneRange(*jZoneRangeFull.begin(),
2370 std::min(*jZoneRangeFull.end(), zone_end));
2371 for (int jZone : jZoneRange)
2373 if (zones->shift[jZone][dim] > 0)
2375 zones->size[jZone].x1[dim] =
2376 std::max(zones->size[jZone].x1[dim], zones->size[zi].x1[dim] + rcs);
2383 for (z = zone_start; z < zone_end; z++)
2385 /* Initialization only required to keep the compiler happy */
2386 rvec corner_min = { 0, 0, 0 }, corner_max = { 0, 0, 0 }, corner;
2389 /* To determine the bounding box for a zone we need to find
2390 * the extreme corners of 4, 2 or 1 corners.
2392 nc = 1 << (ddbox->nboundeddim - 1);
2394 for (c = 0; c < nc; c++)
2396 /* Set up a zone corner at x=0, ignoring trilinic couplings */
2400 corner[YY] = zones->size[z].x0[YY];
2404 corner[YY] = zones->size[z].x1[YY];
2408 corner[ZZ] = zones->size[z].x0[ZZ];
2412 corner[ZZ] = zones->size[z].x1[ZZ];
2414 if (dd->ndim == 1 && dd->dim[0] < ZZ && ZZ < dd->unitCellInfo.npbcdim
2415 && box[ZZ][1 - dd->dim[0]] != 0)
2417 /* With 1D domain decomposition the cg's are not in
2418 * the triclinic box, but triclinic x-y and rectangular y/x-z.
2419 * Shift the corner of the z-vector back to along the box
2420 * vector of dimension d, so it will later end up at 0 along d.
2421 * This can affect the location of this corner along dd->dim[0]
2422 * through the matrix operation below if box[d][dd->dim[0]]!=0.
2424 int d = 1 - dd->dim[0];
2426 corner[d] -= corner[ZZ] * box[ZZ][d] / box[ZZ][ZZ];
2428 /* Apply the triclinic couplings */
2429 for (i = YY; i < ddbox->npbcdim && i < DIM; i++)
2431 for (j = XX; j < i; j++)
2433 corner[j] += corner[i] * box[i][j] / box[i][i];
2438 copy_rvec(corner, corner_min);
2439 copy_rvec(corner, corner_max);
2443 for (i = 0; i < DIM; i++)
2445 corner_min[i] = std::min(corner_min[i], corner[i]);
2446 corner_max[i] = std::max(corner_max[i], corner[i]);
2450 /* Copy the extreme cornes without offset along x */
2451 for (i = 0; i < DIM; i++)
2453 zones->size[z].bb_x0[i] = corner_min[i];
2454 zones->size[z].bb_x1[i] = corner_max[i];
2456 /* Add the offset along x */
2457 zones->size[z].bb_x0[XX] += zones->size[z].x0[XX];
2458 zones->size[z].bb_x1[XX] += zones->size[z].x1[XX];
2461 if (zone_start == 0)
2464 for (dim = 0; dim < DIM; dim++)
2466 vol *= zones->size[0].x1[dim] - zones->size[0].x0[dim];
2469 (zones->cg_range[1] - zones->cg_range[0] - numMovedChargeGroupsInHomeZone) / vol;
2474 for (z = zone_start; z < zone_end; z++)
2477 "zone %d %6.3f - %6.3f %6.3f - %6.3f %6.3f - %6.3f\n",
2479 zones->size[z].x0[XX],
2480 zones->size[z].x1[XX],
2481 zones->size[z].x0[YY],
2482 zones->size[z].x1[YY],
2483 zones->size[z].x0[ZZ],
2484 zones->size[z].x1[ZZ]);
2486 "zone %d bb %6.3f - %6.3f %6.3f - %6.3f %6.3f - %6.3f\n",
2488 zones->size[z].bb_x0[XX],
2489 zones->size[z].bb_x1[XX],
2490 zones->size[z].bb_x0[YY],
2491 zones->size[z].bb_x1[YY],
2492 zones->size[z].bb_x0[ZZ],
2493 zones->size[z].bb_x1[ZZ]);
2498 /*! \brief Order data in \p dataToSort according to \p sort
2500 * Note: both buffers should have at least \p sort.size() elements.
2502 template<typename T>
2503 static void orderVector(gmx::ArrayRef<const gmx_cgsort_t> sort,
2504 gmx::ArrayRef<T> dataToSort,
2505 gmx::ArrayRef<T> sortBuffer)
2507 GMX_ASSERT(dataToSort.size() >= sort.size(), "The vector needs to be sufficiently large");
2508 GMX_ASSERT(sortBuffer.size() >= sort.size(),
2509 "The sorting buffer needs to be sufficiently large");
2511 /* Order the data into the temporary buffer */
2513 for (const gmx_cgsort_t& entry : sort)
2515 sortBuffer[i++] = dataToSort[entry.ind];
2518 /* Copy back to the original array */
2519 std::copy(sortBuffer.begin(), sortBuffer.begin() + sort.size(), dataToSort.begin());
2522 /*! \brief Order data in \p dataToSort according to \p sort
2524 * Note: \p vectorToSort should have at least \p sort.size() elements,
2525 * \p workVector is resized when it is too small.
2527 template<typename T>
2528 static void orderVector(gmx::ArrayRef<const gmx_cgsort_t> sort,
2529 gmx::ArrayRef<T> vectorToSort,
2530 std::vector<T>* workVector)
2532 if (gmx::index(workVector->size()) < sort.ssize())
2534 workVector->resize(sort.size());
2536 orderVector<T>(sort, vectorToSort, *workVector);
2539 //! Returns the sorting order for atoms based on the nbnxn grid order in sort
2540 static void dd_sort_order_nbnxn(const t_forcerec* fr, std::vector<gmx_cgsort_t>* sort)
2542 gmx::ArrayRef<const int> atomOrder = fr->nbv->getLocalAtomOrder();
2544 /* Using push_back() instead of this resize results in much slower code */
2545 sort->resize(atomOrder.size());
2546 gmx::ArrayRef<gmx_cgsort_t> buffer = *sort;
2547 size_t numSorted = 0;
2548 for (int i : atomOrder)
2552 /* The values of nsc and ind_gl are not used in this case */
2553 buffer[numSorted++].ind = i;
2556 sort->resize(numSorted);
2559 //! Returns the sorting state for DD.
2560 static void dd_sort_state(gmx_domdec_t* dd, t_forcerec* fr, t_state* state)
2562 gmx_domdec_sort_t* sort = dd->comm->sort.get();
2564 dd_sort_order_nbnxn(fr, &sort->sorted);
2566 /* We alloc with the old size, since cgindex is still old */
2567 DDBufferAccess<gmx::RVec> rvecBuffer(dd->comm->rvecBuffer, dd->ncg_home);
2569 /* Set the new home atom/charge group count */
2570 dd->ncg_home = sort->sorted.size();
2573 fprintf(debug, "Set the new home atom count to %d\n", dd->ncg_home);
2576 /* Reorder the state */
2577 gmx::ArrayRef<const gmx_cgsort_t> cgsort = sort->sorted;
2578 GMX_RELEASE_ASSERT(cgsort.ssize() == dd->ncg_home, "We should sort all the home atom groups");
2580 if (state->flags & enumValueToBitMask(StateEntry::X))
2582 orderVector(cgsort, makeArrayRef(state->x), rvecBuffer.buffer);
2584 if (state->flags & enumValueToBitMask(StateEntry::V))
2586 orderVector(cgsort, makeArrayRef(state->v), rvecBuffer.buffer);
2588 if (state->flags & enumValueToBitMask(StateEntry::Cgp))
2590 orderVector(cgsort, makeArrayRef(state->cg_p), rvecBuffer.buffer);
2593 /* Reorder the global cg index */
2594 orderVector<int>(cgsort, dd->globalAtomGroupIndices, &sort->intBuffer);
2595 /* Reorder the cginfo */
2596 orderVector<int>(cgsort, fr->cginfo, &sort->intBuffer);
2597 /* Set the home atom number */
2598 dd->comm->atomRanges.setEnd(DDAtomRanges::Type::Home, dd->ncg_home);
2600 /* The atoms are now exactly in grid order, update the grid order */
2601 fr->nbv->setLocalAtomOrder();
2604 //! Accumulates load statistics.
2605 static void add_dd_statistics(gmx_domdec_t* dd)
2607 gmx_domdec_comm_t* comm = dd->comm;
2609 for (int i = 0; i < static_cast<int>(DDAtomRanges::Type::Number); i++)
2611 auto range = static_cast<DDAtomRanges::Type>(i);
2612 comm->sum_nat[i] += comm->atomRanges.end(range) - comm->atomRanges.start(range);
2617 void reset_dd_statistics_counters(gmx_domdec_t* dd)
2619 gmx_domdec_comm_t* comm = dd->comm;
2621 /* Reset all the statistics and counters for total run counting */
2622 for (int i = 0; i < static_cast<int>(DDAtomRanges::Type::Number); i++)
2624 comm->sum_nat[i] = 0;
2628 comm->load_step = 0;
2631 clear_ivec(comm->load_lim);
2639 bool check_grid_jump(int64_t step, const gmx_domdec_t* dd, real cutoff, const gmx_ddbox_t* ddbox, bool bFatal)
2641 gmx_domdec_comm_t* comm = dd->comm;
2642 bool invalid = false;
2644 for (int d = 1; d < dd->ndim; d++)
2646 const DDCellsizesWithDlb& cellsizes = comm->cellsizesWithDlb[d];
2647 const int dim = dd->dim[d];
2648 const real limit = grid_jump_limit(comm, cutoff, d);
2649 real bfac = ddbox->box_size[dim];
2650 if (ddbox->tric_dir[dim])
2652 bfac *= ddbox->skew_fac[dim];
2654 if ((cellsizes.fracUpper - cellsizes.fracLowerMax) * bfac < limit
2655 || (cellsizes.fracLower - cellsizes.fracUpperMin) * bfac > -limit)
2663 /* This error should never be triggered under normal
2664 * circumstances, but you never know ...
2667 "step %s: The domain decomposition grid has shifted too much in the "
2668 "%c-direction around cell %d %d %d. This should not have happened. "
2669 "Running with fewer ranks might avoid this issue.",
2670 gmx_step_str(step, buf),
2682 void print_dd_statistics(const t_commrec* cr, const t_inputrec& inputrec, FILE* fplog)
2684 gmx_domdec_comm_t* comm = cr->dd->comm;
2686 const int numRanges = static_cast<int>(DDAtomRanges::Type::Number);
2687 gmx_sumd(numRanges, comm->sum_nat, cr);
2689 if (fplog == nullptr)
2694 fprintf(fplog, "\n D O M A I N D E C O M P O S I T I O N S T A T I S T I C S\n\n");
2696 for (int i = static_cast<int>(DDAtomRanges::Type::Zones); i < numRanges; i++)
2698 auto range = static_cast<DDAtomRanges::Type>(i);
2699 double av = comm->sum_nat[i] / comm->ndecomp;
2702 case DDAtomRanges::Type::Zones:
2703 fprintf(fplog, " av. #atoms communicated per step for force: %d x %.1f\n", 2, av);
2705 case DDAtomRanges::Type::Vsites:
2706 if (cr->dd->vsite_comm)
2709 " av. #atoms communicated per step for vsites: %d x %.1f\n",
2710 (EEL_PME(inputrec.coulombtype)
2711 || inputrec.coulombtype == CoulombInteractionType::Ewald)
2717 case DDAtomRanges::Type::Constraints:
2718 if (cr->dd->constraint_comm)
2721 " av. #atoms communicated per step for LINCS: %d x %.1f\n",
2722 1 + inputrec.nLincsIter,
2726 default: gmx_incons(" Unknown type for DD statistics");
2729 fprintf(fplog, "\n");
2731 if (comm->ddSettings.recordLoad && EI_DYNAMICS(inputrec.eI))
2733 print_dd_load_av(fplog, cr->dd);
2737 //!\brief TODO Remove fplog when group scheme and charge groups are gone
2738 void dd_partition_system(FILE* fplog,
2739 const gmx::MDLogger& mdlog,
2741 const t_commrec* cr,
2744 t_state* state_global,
2745 const gmx_mtop_t& top_global,
2746 const t_inputrec& inputrec,
2747 gmx::ImdSession* imdSession,
2749 t_state* state_local,
2750 gmx::ForceBuffers* f,
2751 gmx::MDAtoms* mdAtoms,
2752 gmx_localtop_t* top_local,
2754 gmx::VirtualSitesHandler* vsite,
2755 gmx::Constraints* constr,
2757 gmx_wallcycle* wcycle,
2760 gmx_ddbox_t ddbox = { 0 };
2764 wallcycle_start(wcycle, WallCycleCounter::Domdec);
2766 gmx_domdec_t* dd = cr->dd;
2767 gmx_domdec_comm_t* comm = dd->comm;
2769 // TODO if the update code becomes accessible here, use
2770 // upd->deform for this logic.
2771 bool bBoxChanged = (bMasterState || inputrecDeform(&inputrec));
2772 if (inputrec.epc != PressureCoupling::No)
2774 /* With nstpcouple > 1 pressure coupling happens.
2775 * one step after calculating the pressure.
2776 * Box scaling happens at the end of the MD step,
2777 * after the DD partitioning.
2778 * We therefore have to do DLB in the first partitioning
2779 * after an MD step where P-coupling occurred.
2780 * We need to determine the last step in which p-coupling occurred.
2781 * MRS -- need to validate this for vv?
2783 int n = inputrec.nstpcouple;
2784 int64_t step_pcoupl;
2787 step_pcoupl = step - 1;
2791 step_pcoupl = ((step - 1) / n) * n + 1;
2793 if (step_pcoupl >= comm->partition_step)
2799 bool bNStGlobalComm = (step % nstglobalcomm == 0);
2807 /* Should we do dynamic load balacing this step?
2808 * Since it requires (possibly expensive) global communication,
2809 * we might want to do DLB less frequently.
2811 if (bBoxChanged || inputrec.epc != PressureCoupling::No)
2813 bDoDLB = bBoxChanged;
2817 bDoDLB = bNStGlobalComm;
2821 /* Check if we have recorded loads on the nodes */
2822 if (comm->ddSettings.recordLoad && dd_load_count(comm) > 0)
2824 bool bCheckWhetherToTurnDlbOn = dd_dlb_get_should_check_whether_to_turn_dlb_on(dd);
2826 /* Print load every nstlog, first and last step to the log file */
2827 bool bLogLoad = ((inputrec.nstlog > 0 && step % inputrec.nstlog == 0) || comm->n_load_collect == 0
2828 || (inputrec.nsteps >= 0
2829 && (step + inputrec.nstlist > inputrec.init_step + inputrec.nsteps)));
2831 /* Avoid extra communication due to verbose screen output
2832 * when nstglobalcomm is set.
2834 if (bDoDLB || bLogLoad || bCheckWhetherToTurnDlbOn
2835 || (bVerbose && (inputrec.nstlist == 0 || nstglobalcomm <= inputrec.nstlist)))
2837 get_load_distribution(dd, wcycle);
2842 GMX_LOG(mdlog.info).asParagraph().appendText(dd_print_load(dd, step - 1));
2846 dd_print_load_verbose(dd);
2849 comm->n_load_collect++;
2855 /* Add the measured cycles to the running average */
2856 const float averageFactor = 0.1F;
2857 comm->cyclesPerStepDlbExpAverage =
2858 (1 - averageFactor) * comm->cyclesPerStepDlbExpAverage
2859 + averageFactor * comm->cycl[ddCyclStep] / comm->cycl_n[ddCyclStep];
2861 if (comm->dlbState == DlbState::onCanTurnOff
2862 && dd->comm->n_load_have % c_checkTurnDlbOffInterval == c_checkTurnDlbOffInterval - 1)
2867 /* If the running averaged cycles with DLB are more
2868 * than before we turned on DLB, turn off DLB.
2869 * We will again run and check the cycles without DLB
2870 * and we can then decide if to turn off DLB forever.
2872 turnOffDlb = (comm->cyclesPerStepDlbExpAverage > comm->cyclesPerStepBeforeDLB);
2874 dd_bcast(dd, sizeof(turnOffDlb), &turnOffDlb);
2877 /* To turn off DLB, we need to redistribute the atoms */
2878 dd_collect_state(dd, state_local, state_global);
2879 bMasterState = true;
2880 turn_off_dlb(mdlog, dd, step);
2884 else if (bCheckWhetherToTurnDlbOn)
2886 bool turnOffDlbForever = false;
2887 bool turnOnDlb = false;
2889 /* Since the timings are node dependent, the master decides */
2892 /* If we recently turned off DLB, we want to check if
2893 * performance is better without DLB. We want to do this
2894 * ASAP to minimize the chance that external factors
2895 * slowed down the DLB step are gone here and we
2896 * incorrectly conclude that DLB was causing the slowdown.
2897 * So we measure one nstlist block, no running average.
2899 if (comm->haveTurnedOffDlb
2900 && comm->cycl[ddCyclStep] / comm->cycl_n[ddCyclStep] < comm->cyclesPerStepDlbExpAverage)
2902 /* After turning off DLB we ran nstlist steps in fewer
2903 * cycles than with DLB. This likely means that DLB
2904 * in not benefical, but this could be due to a one
2905 * time unlucky fluctuation, so we require two such
2906 * observations in close succession to turn off DLB
2909 if (comm->dlbSlowerPartitioningCount > 0
2910 && dd->ddp_count < comm->dlbSlowerPartitioningCount + 10 * c_checkTurnDlbOnInterval)
2912 turnOffDlbForever = true;
2914 comm->haveTurnedOffDlb = false;
2915 /* Register when we last measured DLB slowdown */
2916 comm->dlbSlowerPartitioningCount = dd->ddp_count;
2920 /* Here we check if the max PME rank load is more than 0.98
2921 * the max PP force load. If so, PP DLB will not help,
2922 * since we are (almost) limited by PME. Furthermore,
2923 * DLB will cause a significant extra x/f redistribution
2924 * cost on the PME ranks, which will then surely result
2925 * in lower total performance.
2927 if (comm->ddRankSetup.usePmeOnlyRanks && dd_pme_f_ratio(dd) > 1 - DD_PERF_LOSS_DLB_ON)
2933 turnOnDlb = (dd_force_imb_perf_loss(dd) >= DD_PERF_LOSS_DLB_ON);
2939 bool turnOffDlbForever;
2941 } bools{ turnOffDlbForever, turnOnDlb };
2942 dd_bcast(dd, sizeof(bools), &bools);
2943 if (bools.turnOffDlbForever)
2945 turn_off_dlb_forever(mdlog, dd, step);
2947 else if (bools.turnOnDlb)
2949 turn_on_dlb(mdlog, dd, step);
2954 comm->n_load_have++;
2957 bool bRedist = false;
2960 /* Clear the old state */
2961 clearDDStateIndices(dd, false);
2964 auto xGlobal = positionsFromStatePointer(state_global);
2966 set_ddbox(*dd, true, DDMASTER(dd) ? state_global->box : nullptr, true, xGlobal, &ddbox);
2968 distributeState(mdlog, dd, top_global, state_global, ddbox, state_local);
2970 /* Ensure that we have space for the new distribution */
2971 dd_resize_atominfo_and_state(fr, state_local, dd->ncg_home);
2973 inc_nrnb(nrnb, eNR_CGCM, comm->atomRanges.numHomeAtoms());
2975 dd_set_cginfo(dd->globalAtomGroupIndices, 0, dd->ncg_home, fr);
2977 else if (state_local->ddp_count != dd->ddp_count)
2979 if (state_local->ddp_count > dd->ddp_count)
2982 "Internal inconsistency state_local->ddp_count (%d) > dd->ddp_count (%" PRId64
2984 state_local->ddp_count,
2988 if (state_local->ddp_count_cg_gl != state_local->ddp_count)
2991 "Internal inconsistency state_local->ddp_count_cg_gl (%d) != "
2992 "state_local->ddp_count (%d)",
2993 state_local->ddp_count_cg_gl,
2994 state_local->ddp_count);
2997 /* Clear the old state */
2998 clearDDStateIndices(dd, false);
3000 /* Restore the atom group indices from state_local */
3001 restoreAtomGroups(dd, state_local);
3002 make_dd_indices(dd, 0);
3003 ncgindex_set = dd->ncg_home;
3005 inc_nrnb(nrnb, eNR_CGCM, comm->atomRanges.numHomeAtoms());
3007 dd_set_cginfo(dd->globalAtomGroupIndices, 0, dd->ncg_home, fr);
3009 set_ddbox(*dd, bMasterState, state_local->box, true, state_local->x, &ddbox);
3011 bRedist = isDlbOn(comm);
3015 /* We have the full state, only redistribute the cgs */
3017 /* Clear the non-home indices */
3018 clearDDStateIndices(dd, true);
3021 /* To avoid global communication, we do not recompute the extent
3022 * of the system for dims without pbc. Therefore we need to copy
3023 * the previously computed values when we do not communicate.
3025 if (!bNStGlobalComm)
3027 copy_rvec(comm->box0, ddbox.box0);
3028 copy_rvec(comm->box_size, ddbox.box_size);
3030 set_ddbox(*dd, bMasterState, state_local->box, bNStGlobalComm, state_local->x, &ddbox);
3035 /* Copy needed for dim's without pbc when avoiding communication */
3036 copy_rvec(ddbox.box0, comm->box0);
3037 copy_rvec(ddbox.box_size, comm->box_size);
3039 set_dd_cell_sizes(dd, &ddbox, dd->unitCellInfo.ddBoxIsDynamic, bMasterState, bDoDLB, step, wcycle);
3041 if (comm->ddSettings.nstDDDumpGrid > 0 && step % comm->ddSettings.nstDDDumpGrid == 0)
3043 write_dd_grid_pdb("dd_grid", step, dd, state_local->box, &ddbox);
3046 if (comm->systemInfo.useUpdateGroups)
3048 comm->updateGroupsCog->addCogs(
3049 gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), state_local->x);
3052 /* Check if we should sort the charge groups */
3053 const bool bSortCG = (bMasterState || bRedist);
3055 /* When repartitioning we mark atom groups that will move to neighboring
3056 * DD cells, but we do not move them right away for performance reasons.
3057 * Thus we need to keep track of how many charge groups will move for
3058 * obtaining correct local charge group / atom counts.
3063 wallcycle_sub_start(wcycle, WallCycleSubCounter::DDRedist);
3065 ncgindex_set = dd->ncg_home;
3066 dd_redistribute_cg(fplog, step, dd, ddbox.tric_dir, state_local, fr, nrnb, &ncg_moved);
3068 GMX_RELEASE_ASSERT(bSortCG, "Sorting is required after redistribution");
3070 if (comm->systemInfo.useUpdateGroups)
3072 comm->updateGroupsCog->addCogs(
3073 gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
3077 wallcycle_sub_stop(wcycle, WallCycleSubCounter::DDRedist);
3080 RVec cell_ns_x0, cell_ns_x1;
3081 get_nsgrid_boundaries(ddbox.nboundeddim,
3088 as_rvec_array(state_local->x.data()),
3094 comm_dd_ns_cell_sizes(dd, &ddbox, cell_ns_x0, cell_ns_x1, step);
3099 wallcycle_sub_start(wcycle, WallCycleSubCounter::DDGrid);
3101 /* Sort the state on charge group position.
3102 * This enables exact restarts from this step.
3103 * It also improves performance by about 15% with larger numbers
3104 * of atoms per node.
3107 /* Fill the ns grid with the home cell,
3108 * so we can sort with the indices.
3110 set_zones_ncg_home(dd);
3112 set_zones_size(dd, state_local->box, &ddbox, 0, 1, ncg_moved);
3114 nbnxn_put_on_grid(fr->nbv.get(),
3117 comm->zones.size[0].bb_x0,
3118 comm->zones.size[0].bb_x1,
3119 comm->updateGroupsCog.get(),
3120 { 0, dd->ncg_home },
3121 comm->zones.dens_zone0,
3125 bRedist ? comm->movedBuffer.data() : nullptr);
3129 fprintf(debug, "Step %s, sorting the %d home charge groups\n", gmx_step_str(step, sbuf), dd->ncg_home);
3131 dd_sort_state(dd, fr, state_local);
3133 /* After sorting and compacting we set the correct size */
3134 state_change_natoms(state_local, comm->atomRanges.numHomeAtoms());
3136 /* Rebuild all the indices */
3140 wallcycle_sub_stop(wcycle, WallCycleSubCounter::DDGrid);
3144 /* With the group scheme the sorting array is part of the DD state,
3145 * but it just got out of sync, so mark as invalid by emptying it.
3147 if (inputrec.cutoff_scheme == CutoffScheme::Group)
3149 comm->sort->sorted.clear();
3153 if (comm->systemInfo.useUpdateGroups)
3155 /* The update groups cog's are invalid after sorting
3156 * and need to be cleared before the next partitioning anyhow.
3158 comm->updateGroupsCog->clear();
3161 wallcycle_sub_start(wcycle, WallCycleSubCounter::DDSetupComm);
3163 /* Set the induces for the home atoms */
3164 set_zones_ncg_home(dd);
3165 make_dd_indices(dd, ncgindex_set);
3167 /* Setup up the communication and communicate the coordinates */
3168 setup_dd_communication(dd, state_local->box, &ddbox, fr, state_local);
3170 /* Set the indices for the halo atoms */
3171 make_dd_indices(dd, dd->ncg_home);
3173 /* Set the charge group boundaries for neighbor searching */
3174 set_cg_boundaries(&comm->zones);
3176 /* When bSortCG=true, we have already set the size for zone 0 */
3177 set_zones_size(dd, state_local->box, &ddbox, bSortCG ? 1 : 0, comm->zones.n, 0);
3179 wallcycle_sub_stop(wcycle, WallCycleSubCounter::DDSetupComm);
3182 write_dd_pdb("dd_home",step,"dump",top_global,cr,
3183 -1,state_local->x.rvec_array(),state_local->box);
3186 wallcycle_sub_start(wcycle, WallCycleSubCounter::DDMakeTop);
3188 /* Extract a local topology from the global topology */
3190 for (int i = 0; i < dd->ndim; i++)
3192 numPulses[dd->dim[i]] = comm->cd[i].numPulses();
3194 dd_make_local_top(dd,
3196 dd->unitCellInfo.npbcdim,
3205 wallcycle_sub_stop(wcycle, WallCycleSubCounter::DDMakeTop);
3207 wallcycle_sub_start(wcycle, WallCycleSubCounter::DDMakeConstr);
3209 /* Set up the special atom communication */
3210 int n = comm->atomRanges.end(DDAtomRanges::Type::Zones);
3211 for (int i = static_cast<int>(DDAtomRanges::Type::Zones) + 1;
3212 i < static_cast<int>(DDAtomRanges::Type::Number);
3215 auto range = static_cast<DDAtomRanges::Type>(i);
3218 case DDAtomRanges::Type::Vsites:
3219 if (vsite && vsite->numInterUpdategroupVirtualSites())
3221 n = dd_make_local_vsites(dd, n, top_local->idef.il);
3224 case DDAtomRanges::Type::Constraints:
3225 if (dd->comm->systemInfo.haveSplitConstraints || dd->comm->systemInfo.haveSplitSettles)
3227 /* Only for inter-cg constraints we need special code */
3228 n = dd_make_local_constraints(dd,
3233 inputrec.nProjOrder,
3234 top_local->idef.il);
3237 default: gmx_incons("Unknown special atom type setup");
3239 comm->atomRanges.setEnd(range, n);
3242 wallcycle_sub_stop(wcycle, WallCycleSubCounter::DDMakeConstr);
3244 wallcycle_sub_start(wcycle, WallCycleSubCounter::DDTopOther);
3246 /* Make space for the extra coordinates for virtual site
3247 * or constraint communication.
3249 state_local->natoms = comm->atomRanges.numAtomsTotal();
3251 state_change_natoms(state_local, state_local->natoms);
3254 if (vsite && vsite->numInterUpdategroupVirtualSites())
3256 nat_f_novirsum = comm->atomRanges.end(DDAtomRanges::Type::Vsites);
3260 if (EEL_FULL(inputrec.coulombtype) && dd->haveExclusions)
3262 nat_f_novirsum = comm->atomRanges.end(DDAtomRanges::Type::Zones);
3266 nat_f_novirsum = comm->atomRanges.numHomeAtoms();
3270 /* Set the number of atoms required for the force calculation.
3271 * Forces need to be constrained when doing energy
3272 * minimization. For simple simulations we could avoid some
3273 * allocation, zeroing and copying, but this is probably not worth
3274 * the complications and checking.
3276 forcerec_set_ranges(fr,
3277 comm->atomRanges.end(DDAtomRanges::Type::Zones),
3278 comm->atomRanges.end(DDAtomRanges::Type::Constraints),
3281 /* Update atom data for mdatoms and several algorithms */
3282 mdAlgorithmsSetupAtomData(cr, inputrec, top_global, top_local, fr, f, mdAtoms, constr, vsite, nullptr);
3284 auto* mdatoms = mdAtoms->mdatoms();
3285 if (!thisRankHasDuty(cr, DUTY_PME))
3287 /* Send the charges and/or c6/sigmas to our PME only node */
3288 gmx_pme_send_parameters(cr,
3290 mdatoms->nChargePerturbed != 0,
3291 mdatoms->nTypePerturbed != 0,
3292 gmx::arrayRefFromArray(mdatoms->chargeA, mdatoms->nr),
3293 mdatoms->chargeB ? gmx::arrayRefFromArray(mdatoms->chargeB, mdatoms->nr)
3294 : gmx::ArrayRef<real>{},
3295 gmx::arrayRefFromArray(mdatoms->sqrt_c6A, mdatoms->nr),
3296 mdatoms->sqrt_c6B ? gmx::arrayRefFromArray(mdatoms->sqrt_c6B, mdatoms->nr)
3297 : gmx::ArrayRef<real>{},
3298 gmx::arrayRefFromArray(mdatoms->sigmaA, mdatoms->nr),
3299 mdatoms->sigmaB ? gmx::arrayRefFromArray(mdatoms->sigmaB, mdatoms->nr)
3300 : gmx::ArrayRef<real>{},
3301 dd_pme_maxshift_x(*dd),
3302 dd_pme_maxshift_y(*dd));
3305 if (dd->atomSets != nullptr)
3307 /* Update the local atom sets */
3308 dd->atomSets->setIndicesInDomainDecomposition(*(dd->ga2la));
3311 // The pull group construction can need the atom sets updated above
3314 /* Update the local pull groups */
3315 dd_make_local_pull_groups(cr, pull_work);
3318 /* Update the local atoms to be communicated via the IMD protocol if bIMD is true. */
3319 imdSession->dd_make_local_IMD_atoms(dd);
3321 add_dd_statistics(dd);
3323 /* Make sure we only count the cycles for this DD partitioning */
3324 clear_dd_cycle_counts(dd);
3326 /* Because the order of the atoms might have changed since
3327 * the last vsite construction, we need to communicate the constructing
3328 * atom coordinates again (for spreading the forces this MD step).
3330 dd_move_x_vsites(*dd, state_local->box, state_local->x.rvec_array());
3332 wallcycle_sub_stop(wcycle, WallCycleSubCounter::DDTopOther);
3334 if (comm->ddSettings.nstDDDump > 0 && step % comm->ddSettings.nstDDDump == 0)
3336 dd_move_x(dd, state_local->box, state_local->x, nullptr);
3337 write_dd_pdb("dd_dump",
3343 state_local->x.rvec_array(),
3347 /* Store the partitioning step */
3348 comm->partition_step = step;
3350 /* Increase the DD partitioning counter */
3352 /* The state currently matches this DD partitioning count, store it */
3353 state_local->ddp_count = dd->ddp_count;
3356 /* The DD master node knows the complete cg distribution,
3357 * store the count so we can possibly skip the cg info communication.
3359 comm->master_cg_ddp_count = (bSortCG ? 0 : dd->ddp_count);
3362 if (comm->ddSettings.DD_debug > 0)
3364 /* Set the env var GMX_DD_DEBUG if you suspect corrupted indices */
3365 check_index_consistency(dd, top_global.natoms, "after partitioning");
3368 wallcycle_stop(wcycle, WallCycleCounter::Domdec);