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37 * \brief Implements the loop for simulation reruns
39 * \author Pascal Merz <pascal.merz@colorado.edu>
40 * \ingroup module_mdrun
52 #include "gromacs/applied_forces/awh/awh.h"
53 #include "gromacs/commandline/filenm.h"
54 #include "gromacs/domdec/collect.h"
55 #include "gromacs/domdec/dlbtiming.h"
56 #include "gromacs/domdec/domdec.h"
57 #include "gromacs/domdec/domdec_network.h"
58 #include "gromacs/domdec/domdec_struct.h"
59 #include "gromacs/domdec/mdsetup.h"
60 #include "gromacs/domdec/partition.h"
61 #include "gromacs/essentialdynamics/edsam.h"
62 #include "gromacs/ewald/pme_load_balancing.h"
63 #include "gromacs/ewald/pme_pp.h"
64 #include "gromacs/fileio/trxio.h"
65 #include "gromacs/gmxlib/network.h"
66 #include "gromacs/gmxlib/nrnb.h"
67 #include "gromacs/gpu_utils/gpu_utils.h"
68 #include "gromacs/listed_forces/listed_forces.h"
69 #include "gromacs/math/functions.h"
70 #include "gromacs/math/utilities.h"
71 #include "gromacs/math/vec.h"
72 #include "gromacs/math/vectypes.h"
73 #include "gromacs/mdlib/checkpointhandler.h"
74 #include "gromacs/mdlib/compute_io.h"
75 #include "gromacs/mdlib/constr.h"
76 #include "gromacs/mdlib/ebin.h"
77 #include "gromacs/mdlib/enerdata_utils.h"
78 #include "gromacs/mdlib/energyoutput.h"
79 #include "gromacs/mdlib/expanded.h"
80 #include "gromacs/mdlib/force.h"
81 #include "gromacs/mdlib/force_flags.h"
82 #include "gromacs/mdlib/forcerec.h"
83 #include "gromacs/mdlib/freeenergyparameters.h"
84 #include "gromacs/mdlib/md_support.h"
85 #include "gromacs/mdlib/mdatoms.h"
86 #include "gromacs/mdlib/mdoutf.h"
87 #include "gromacs/mdlib/membed.h"
88 #include "gromacs/mdlib/resethandler.h"
89 #include "gromacs/mdlib/sighandler.h"
90 #include "gromacs/mdlib/simulationsignal.h"
91 #include "gromacs/mdlib/stat.h"
92 #include "gromacs/mdlib/stophandler.h"
93 #include "gromacs/mdlib/tgroup.h"
94 #include "gromacs/mdlib/trajectory_writing.h"
95 #include "gromacs/mdlib/update.h"
96 #include "gromacs/mdlib/vcm.h"
97 #include "gromacs/mdlib/vsite.h"
98 #include "gromacs/mdrunutility/handlerestart.h"
99 #include "gromacs/mdrunutility/multisim.h"
100 #include "gromacs/mdrunutility/printtime.h"
101 #include "gromacs/mdtypes/awh_history.h"
102 #include "gromacs/mdtypes/awh_params.h"
103 #include "gromacs/mdtypes/commrec.h"
104 #include "gromacs/mdtypes/df_history.h"
105 #include "gromacs/mdtypes/energyhistory.h"
106 #include "gromacs/mdtypes/forcebuffers.h"
107 #include "gromacs/mdtypes/forcerec.h"
108 #include "gromacs/mdtypes/group.h"
109 #include "gromacs/mdtypes/inputrec.h"
110 #include "gromacs/mdtypes/interaction_const.h"
111 #include "gromacs/mdtypes/md_enums.h"
112 #include "gromacs/mdtypes/mdatom.h"
113 #include "gromacs/mdtypes/mdrunoptions.h"
114 #include "gromacs/mdtypes/observableshistory.h"
115 #include "gromacs/mdtypes/simulation_workload.h"
116 #include "gromacs/mdtypes/state.h"
117 #include "gromacs/mimic/utilities.h"
118 #include "gromacs/pbcutil/pbc.h"
119 #include "gromacs/pulling/pull.h"
120 #include "gromacs/swap/swapcoords.h"
121 #include "gromacs/timing/wallcycle.h"
122 #include "gromacs/timing/walltime_accounting.h"
123 #include "gromacs/topology/atoms.h"
124 #include "gromacs/topology/idef.h"
125 #include "gromacs/topology/mtop_util.h"
126 #include "gromacs/topology/topology.h"
127 #include "gromacs/trajectory/trajectoryframe.h"
128 #include "gromacs/utility/basedefinitions.h"
129 #include "gromacs/utility/cstringutil.h"
130 #include "gromacs/utility/fatalerror.h"
131 #include "gromacs/utility/logger.h"
132 #include "gromacs/utility/real.h"
134 #include "legacysimulator.h"
135 #include "replicaexchange.h"
138 using gmx::SimulationSignaller;
139 using gmx::VirtualSitesHandler;
141 /*! \brief Copy the state from \p rerunFrame to \p globalState and, if requested, construct vsites
143 * \param[in] rerunFrame The trajectory frame to compute energy/forces for
144 * \param[in,out] globalState The global state container
145 * \param[in] constructVsites When true, vsite coordinates are constructed
146 * \param[in] vsite Vsite setup, can be nullptr when \p constructVsites = false
148 static void prepareRerunState(const t_trxframe& rerunFrame,
149 t_state* globalState,
150 bool constructVsites,
151 const VirtualSitesHandler* vsite)
153 auto x = makeArrayRef(globalState->x);
154 auto rerunX = arrayRefFromArray(reinterpret_cast<gmx::RVec*>(rerunFrame.x), globalState->natoms);
155 std::copy(rerunX.begin(), rerunX.end(), x.begin());
156 copy_mat(rerunFrame.box, globalState->box);
160 GMX_ASSERT(vsite, "Need valid vsite for constructing vsites");
162 vsite->construct(globalState->x, globalState->v, globalState->box, gmx::VSiteOperation::PositionsAndVelocities);
166 void gmx::LegacySimulator::do_rerun()
168 // TODO Historically, the EM and MD "integrators" used different
169 // names for the t_inputrec *parameter, but these must have the
170 // same name, now that it's a member of a struct. We use this ir
171 // alias to avoid a large ripple of nearly useless changes.
172 // t_inputrec is being replaced by IMdpOptionsProvider, so this
173 // will go away eventually.
174 const t_inputrec* ir = inputrec;
175 int64_t step, step_rel;
177 bool isLastStep = false;
178 bool doFreeEnergyPerturbation = false;
179 unsigned int force_flags;
180 tensor force_vir, shake_vir, total_vir, pres;
181 t_trxstatus* status = nullptr;
184 gmx_localtop_t top(top_global->ffparams);
186 gmx_global_stat_t gstat;
187 gmx_shellfc_t* shellfc;
191 /* Domain decomposition could incorrectly miss a bonded
192 interaction, but checking for that requires a global
193 communication stage, which does not otherwise happen in DD
194 code. So we do that alongside the first global energy reduction
195 after a new DD is made. These variables handle whether the
196 check happens, and the result it returns. */
197 bool shouldCheckNumberOfBondedInteractions = false;
198 int totalNumberOfBondedInteractions = -1;
200 SimulationSignals signals;
201 // Most global communnication stages don't propagate mdrun
202 // signals, and will use this object to achieve that.
203 SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
208 "Note that it is planned that the command gmx mdrun -rerun will "
209 "be available in a different form in a future version of GROMACS, "
210 "e.g. gmx rerun -f.");
212 if (ir->efep != FreeEnergyPerturbationType::No
213 && (mdAtoms->mdatoms()->nMassPerturbed > 0 || (constr && constr->havePerturbedConstraints())))
216 "Perturbed masses or constraints are not supported by rerun. "
217 "Either make a .tpr without mass and constraint perturbation, "
218 "or use GROMACS 2018.4, 2018.5 or later 2018 version.");
222 gmx_fatal(FARGS, "Expanded ensemble not supported by rerun.");
226 gmx_fatal(FARGS, "Simulated tempering not supported by rerun.");
230 gmx_fatal(FARGS, "AWH not supported by rerun.");
232 if (replExParams.exchangeInterval > 0)
234 gmx_fatal(FARGS, "Replica exchange not supported by rerun.");
236 if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
238 gmx_fatal(FARGS, "Essential dynamics not supported by rerun.");
242 gmx_fatal(FARGS, "Interactive MD not supported by rerun.");
246 gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
248 if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](SimulatedAnnealing i) {
249 return i != SimulatedAnnealing::No;
252 gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
255 /* Rerun can't work if an output file name is the same as the input file name.
256 * If this is the case, the user will get an error telling them what the issue is.
258 if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0
259 || strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
262 "When using mdrun -rerun, the name of the input trajectory file "
263 "%s cannot be identical to the name of an output file (whether "
264 "given explicitly with -o or -x, or by default)",
265 opt2fn("-rerun", nfile, fnm));
268 /* Settings for rerun */
270 // TODO: Avoid changing inputrec (#3854)
271 auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
272 nonConstInputrec->nstlist = 1;
273 nonConstInputrec->nstcalcenergy = 1;
274 nonConstInputrec->nstxout_compressed = 0;
276 int nstglobalcomm = 1;
277 const bool bNS = true;
279 const SimulationGroups* groups = &top_global->groups;
280 if (ir->eI == IntegrationAlgorithm::Mimic)
282 auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(top_global);
283 nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(*top_global);
285 int* fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
286 gmx::ArrayRef<real> lambda = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
287 initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
288 const bool simulationsShareState = false;
289 gmx_mdoutf* outf = init_mdoutf(fplog,
300 StartingBehavior::NewSimulation,
301 simulationsShareState,
303 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
307 mdoutf_get_fp_dhdl(outf),
309 StartingBehavior::NewSimulation,
310 simulationsShareState,
313 gstat = global_stat_init(ir);
315 /* Check for polarizable models and flexible constraints */
316 shellfc = init_shell_flexcon(fplog,
318 constr ? constr->numFlexibleConstraints() : 0,
321 runScheduleWork->simulationWork.useGpuPme);
324 double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
325 if ((io > 2000) && MASTER(cr))
327 fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
331 // Local state only becomes valid now.
332 std::unique_ptr<t_state> stateInstance;
335 if (DOMAINDECOMP(cr))
337 stateInstance = std::make_unique<t_state>();
338 state = stateInstance.get();
339 dd_init_local_state(*cr->dd, state_global, state);
341 /* Distribute the charge groups over the nodes from the master node */
342 dd_partition_system(fplog,
363 shouldCheckNumberOfBondedInteractions = true;
367 state_change_natoms(state_global, state_global->natoms);
368 /* Copy the pointer to the global state */
369 state = state_global;
371 mdAlgorithmsSetupAtomData(cr, *ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
374 auto mdatoms = mdAtoms->mdatoms();
376 // NOTE: The global state is no longer used at this point.
377 // But state_global is still used as temporary storage space for writing
378 // the global state to file and potentially for replica exchange.
379 // (Global topology should persist.)
381 update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
383 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
385 doFreeEnergyPerturbation = true;
391 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
392 bool bSumEkinhOld = false;
393 t_vcm* vcm = nullptr;
394 compute_globals(gstat,
399 makeConstArrayRef(state->x),
400 makeConstArrayRef(state->v),
411 gmx::ArrayRef<real>{},
414 &totalNumberOfBondedInteractions,
418 checkNumberOfBondedInteractions(mdlog,
420 totalNumberOfBondedInteractions,
423 makeConstArrayRef(state->x),
425 &shouldCheckNumberOfBondedInteractions);
430 "starting md rerun '%s', reading coordinates from"
431 " input trajectory '%s'\n\n",
433 opt2fn("-rerun", nfile, fnm));
434 if (mdrunOptions.verbose)
437 "Calculated time to finish depends on nsteps from "
438 "run input file,\nwhich may not correspond to the time "
439 "needed to process input trajectory.\n\n");
441 fprintf(fplog, "\n");
444 walltime_accounting_start_time(walltime_accounting);
445 wallcycle_start(wcycle, ewcRUN);
446 print_start(fplog, cr, walltime_accounting, "mdrun");
448 /***********************************************************
452 ************************************************************/
458 .appendText("Simulations has constraints. Rerun does not recalculate constraints.");
464 isLastStep = !read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
465 if (rerun_fr.natoms != top_global->natoms)
468 "Number of atoms in trajectory (%d) does not match the "
469 "run input file (%d)\n",
474 if (ir->pbcType != PbcType::No)
479 "Rerun trajectory frame step %" PRId64
481 "does not contain a box, while pbc is used",
485 if (max_cutoff2(ir->pbcType, rerun_fr.box) < gmx::square(fr->rlist))
488 "Rerun trajectory frame step %" PRId64
490 "has too small box dimensions",
500 "Rerun does not report kinetic energy, total energy, temperature, virial and "
505 rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
508 if (ir->pbcType != PbcType::No)
510 /* Set the shift vectors.
511 * Necessary here when have a static box different from the tpr box.
513 calc_shifts(rerun_fr.box, fr->shift_vec);
516 step = ir->init_step;
519 auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
520 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
524 mdrunOptions.reproducible,
526 mdrunOptions.maximumHoursToRun,
531 walltime_accounting);
533 // we don't do counter resetting in rerun - finish will always be valid
534 walltime_accounting_set_valid_finish(walltime_accounting);
536 const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
538 /* and stop now if we should */
539 isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
542 wallcycle_start(wcycle, ewcSTEP);
546 step = rerun_fr.step;
547 step_rel = step - ir->init_step;
558 if (ir->efep != FreeEnergyPerturbationType::No && MASTER(cr))
560 if (rerun_fr.bLambda)
562 ir->fepvals->init_lambda = rerun_fr.lambda;
566 if (rerun_fr.bFepState)
568 state->fep_state = rerun_fr.fep_state;
572 state_global->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
577 const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
578 if (constructVsites && DOMAINDECOMP(cr))
581 "Vsite recalculation with -rerun is not implemented with domain "
583 "use a single rank");
585 prepareRerunState(rerun_fr, state_global, constructVsites, vsite);
588 isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
590 if (DOMAINDECOMP(cr))
592 /* Repartition the domain decomposition */
593 const bool bMasterState = true;
594 dd_partition_system(fplog,
614 mdrunOptions.verbose);
615 shouldCheckNumberOfBondedInteractions = true;
620 EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
623 if (ir->efep != FreeEnergyPerturbationType::No)
625 update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
628 force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
629 | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 and #3400 are solved
630 GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
634 /* Now is the time to relax the shells */
635 relax_shell_flexcon(fplog,
638 mdrunOptions.verbose,
650 state->x.arrayRefWithPadding(),
651 state->v.arrayRefWithPadding(),
666 ddBalanceRegionHandler);
670 /* The coordinates (x) are shifted (to get whole molecules)
672 * This is parallellized as well, and does communication too.
673 * Check comments in sim_util.c
676 gmx_edsam* ed = nullptr;
690 state->x.arrayRefWithPadding(),
703 GMX_FORCE_NS | force_flags,
704 ddBalanceRegionHandler);
707 /* Now we have the energies and forces corresponding to the
708 * coordinates at time t.
711 const bool isCheckpointingStep = false;
712 const bool doRerun = true;
713 const bool bSumEkinhOld = false;
714 do_md_trajectory_writing(fplog,
734 mdrunOptions.writeConfout,
738 stopHandler->setSignal();
741 const bool doInterSimSignal = false;
742 const bool doIntraSimSignal = true;
743 bool bSumEkinhOld = false;
744 t_vcm* vcm = nullptr;
745 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
747 compute_globals(gstat,
752 makeConstArrayRef(state->x),
753 makeConstArrayRef(state->v),
764 constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
767 &totalNumberOfBondedInteractions,
769 CGLO_GSTAT | CGLO_ENERGY
770 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
772 checkNumberOfBondedInteractions(mdlog,
774 totalNumberOfBondedInteractions,
777 makeConstArrayRef(state->x),
779 &shouldCheckNumberOfBondedInteractions);
782 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
783 the virial that should probably be addressed eventually. state->veta has better properies,
784 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
785 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
790 const bool bCalcEnerStep = true;
791 energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
797 ir->expandedvals.get(),
799 PTCouplingArrays({ state->boxv,
800 state->nosehoover_xi,
801 state->nosehoover_vxi,
803 state->nhpres_vxi }),
813 const bool do_ene = true;
814 const bool do_log = true;
816 const bool do_dr = ir->nstdisreout != 0;
817 const bool do_or = ir->nstorireout != 0;
819 EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
820 energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
824 do_log ? fplog : nullptr,
830 if (do_per_step(step, ir->nstlog))
832 if (fflush(fplog) != 0)
834 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
839 /* Print the remaining wall clock time for the run */
840 if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
844 fprintf(stderr, "\n");
846 print_time(stderr, walltime_accounting, step, ir, cr);
849 /* Ion/water position swapping.
850 * Not done in last step since trajectory writing happens before this call
851 * in the MD loop and exchanges would be lost anyway. */
852 if ((ir->eSwapCoords != SwapType::No) && (step > 0) && !isLastStep
853 && do_per_step(step, ir->swap->nstswap))
855 const bool doRerun = true;
864 MASTER(cr) && mdrunOptions.verbose,
870 /* read next frame from input trajectory */
871 isLastStep = !read_next_frame(oenv, status, &rerun_fr);
876 rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
879 cycles = wallcycle_stop(wcycle, ewcSTEP);
880 if (DOMAINDECOMP(cr) && wcycle)
882 dd_cycles_add(cr->dd, cycles, ddCyclStep);
887 /* increase the MD step number */
892 /* End of main MD loop */
894 /* Closing TNG files can include compressing data. Therefore it is good to do that
895 * before stopping the time measurements. */
896 mdoutf_tng_close(outf);
898 /* Stop measuring walltime */
899 walltime_accounting_end_time(walltime_accounting);
906 if (!thisRankHasDuty(cr, DUTY_PME))
908 /* Tell the PME only node to finish */
909 gmx_pme_send_finish(cr);
914 done_shellfc(fplog, shellfc, step_rel);
916 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);