src/gromacs/mdrun/mimic.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2018,2019, by the GROMACS development team, led by
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  35
  36 /*! \internal \file
  37  *
  38  * \brief Declares the loop for MiMiC QM/MM
  39  *
  40  * \author Viacheslav Bolnykh <v.bolnykh@hpc-leap.eu>
  41  * \ingroup module_mdrun
  42  */
  43 #include "gmxpre.h"
  44
  45 #include <cinttypes>
  46 #include <cmath>
  47 #include <cstdio>
  48 #include <cstdlib>
  49
  50 #include <algorithm>
  51 #include <memory>
  52
  53 #include "gromacs/awh/awh.h"
  54 #include "gromacs/commandline/filenm.h"
  55 #include "gromacs/domdec/collect.h"
  56 #include "gromacs/domdec/dlbtiming.h"
  57 #include "gromacs/domdec/domdec.h"
  58 #include "gromacs/domdec/domdec_network.h"
  59 #include "gromacs/domdec/domdec_struct.h"
  60 #include "gromacs/domdec/mdsetup.h"
  61 #include "gromacs/domdec/partition.h"
  62 #include "gromacs/essentialdynamics/edsam.h"
  63 #include "gromacs/ewald/pme.h"
  64 #include "gromacs/ewald/pme_load_balancing.h"
  65 #include "gromacs/fileio/trxio.h"
  66 #include "gromacs/gmxlib/network.h"
  67 #include "gromacs/gmxlib/nrnb.h"
  68 #include "gromacs/gpu_utils/gpu_utils.h"
  69 #include "gromacs/listed_forces/manage_threading.h"
  70 #include "gromacs/math/functions.h"
  71 #include "gromacs/math/utilities.h"
  72 #include "gromacs/math/vec.h"
  73 #include "gromacs/math/vectypes.h"
  74 #include "gromacs/mdlib/checkpointhandler.h"
  75 #include "gromacs/mdlib/compute_io.h"
  76 #include "gromacs/mdlib/constr.h"
  77 #include "gromacs/mdlib/ebin.h"
  78 #include "gromacs/mdlib/enerdata_utils.h"
  79 #include "gromacs/mdlib/energyoutput.h"
  80 #include "gromacs/mdlib/expanded.h"
  81 #include "gromacs/mdlib/force.h"
  82 #include "gromacs/mdlib/force_flags.h"
  83 #include "gromacs/mdlib/forcerec.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/enerdata.h"
 106 #include "gromacs/mdtypes/energyhistory.h"
 107 #include "gromacs/mdtypes/fcdata.h"
 108 #include "gromacs/mdtypes/forcerec.h"
 109 #include "gromacs/mdtypes/group.h"
 110 #include "gromacs/mdtypes/inputrec.h"
 111 #include "gromacs/mdtypes/interaction_const.h"
 112 #include "gromacs/mdtypes/md_enums.h"
 113 #include "gromacs/mdtypes/mdatom.h"
 114 #include "gromacs/mdtypes/mdrunoptions.h"
 115 #include "gromacs/mdtypes/observableshistory.h"
 116 #include "gromacs/mdtypes/state.h"
 117 #include "gromacs/mimic/communicator.h"
 118 #include "gromacs/mimic/utilities.h"
 119 #include "gromacs/pbcutil/mshift.h"
 120 #include "gromacs/pbcutil/pbc.h"
 121 #include "gromacs/pulling/pull.h"
 122 #include "gromacs/timing/wallcycle.h"
 123 #include "gromacs/timing/walltime_accounting.h"
 124 #include "gromacs/topology/atoms.h"
 125 #include "gromacs/topology/idef.h"
 126 #include "gromacs/topology/mtop_util.h"
 127 #include "gromacs/topology/topology.h"
 128 #include "gromacs/trajectory/trajectoryframe.h"
 129 #include "gromacs/utility/basedefinitions.h"
 130 #include "gromacs/utility/cstringutil.h"
 131 #include "gromacs/utility/fatalerror.h"
 132 #include "gromacs/utility/logger.h"
 133 #include "gromacs/utility/real.h"
 134 #include "gromacs/utility/smalloc.h"
 135
 136 #include "legacysimulator.h"
 137 #include "replicaexchange.h"
 138 #include "shellfc.h"
 139
 140 using gmx::SimulationSignaller;
 141
 142 void gmx::LegacySimulator::do_mimic()
 143 {
 144     t_inputrec                  *ir   = inputrec;
 145     int64_t                      step, step_rel;
 146     double                       t, lam0[efptNR];
 147     bool                         isLastStep               = false;
 148     bool                         doFreeEnergyPerturbation = false;
 149     unsigned int                 force_flags;
 150     tensor                       force_vir, shake_vir, total_vir, pres;
 151     rvec                         mu_tot;
 152     gmx_localtop_t               top;
 153     PaddedHostVector<gmx::RVec>  f {};
 154     gmx_global_stat_t            gstat;
 155     t_graph                     *graph = nullptr;
 156     gmx_shellfc_t               *shellfc;
 157
 158     double                       cycles;
 159
 160     /* Domain decomposition could incorrectly miss a bonded
 161        interaction, but checking for that requires a global
 162        communication stage, which does not otherwise happen in DD
 163        code. So we do that alongside the first global energy reduction
 164        after a new DD is made. These variables handle whether the
 165        check happens, and the result it returns. */
 166     bool              shouldCheckNumberOfBondedInteractions = false;
 167     int               totalNumberOfBondedInteractions       = -1;
 168
 169     SimulationSignals signals;
 170     // Most global communnication stages don't propagate mdrun
 171     // signals, and will use this object to achieve that.
 172     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 173
 174     if (ir->bExpanded)
 175     {
 176         gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
 177     }
 178     if (ir->bSimTemp)
 179     {
 180         gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
 181     }
 182     if (ir->bDoAwh)
 183     {
 184         gmx_fatal(FARGS, "AWH not supported by MiMiC.");
 185     }
 186     if (replExParams.exchangeInterval > 0)
 187     {
 188         gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
 189     }
 190     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 191     {
 192         gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
 193     }
 194     if (ir->bIMD)
 195     {
 196         gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
 197     }
 198     if (isMultiSim(ms))
 199     {
 200         gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
 201     }
 202     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
 203                     [](int i){return i != eannNO; }))
 204     {
 205         gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
 206     }
 207
 208     /* Settings for rerun */
 209     ir->nstlist       = 1;
 210     ir->nstcalcenergy = 1;
 211     int        nstglobalcomm = 1;
 212     const bool bNS           = true;
 213
 214     // Communicator to interact with MiMiC
 215     MimicCommunicator mimicCommunicator {};
 216     if (MASTER(cr))
 217     {
 218         mimicCommunicator.init();
 219         mimicCommunicator.sendInitData(top_global, state_global->x);
 220         ir->nsteps = mimicCommunicator.getStepNumber();
 221     }
 222
 223     ir->nstxout_compressed                   = 0;
 224     SimulationGroups *groups                        = &top_global->groups;
 225     top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 226
 227     initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
 228
 229     gmx_mdoutf        *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, mdModulesNotifier, ir, top_global, oenv, wcycle,
 230                                           StartingBehavior::NewSimulation);
 231     gmx::EnergyOutput  energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work, mdoutf_get_fp_dhdl(outf), true, mdModulesNotifier);
 232
 233     gstat = global_stat_init(ir);
 234
 235     /* Check for polarizable models and flexible constraints */
 236     shellfc = init_shell_flexcon(fplog,
 237                                  top_global, constr ? constr->numFlexibleConstraints() : 0,
 238                                  ir->nstcalcenergy, DOMAINDECOMP(cr));
 239
 240     {
 241         double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
 242         if ((io > 2000) && MASTER(cr))
 243         {
 244             fprintf(stderr,
 245                     "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
 246                     io);
 247         }
 248     }
 249
 250     // Local state only becomes valid now.
 251     std::unique_ptr<t_state> stateInstance;
 252     t_state *                state;
 253
 254     if (DOMAINDECOMP(cr))
 255     {
 256         dd_init_local_top(*top_global, &top);
 257
 258         stateInstance = std::make_unique<t_state>();
 259         state         = stateInstance.get();
 260         dd_init_local_state(cr->dd, state_global, state);
 261
 262         /* Distribute the charge groups over the nodes from the master node */
 263         dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1,
 264                             state_global, *top_global, ir, imdSession,
 265                             pull_work,
 266                             state, &f, mdAtoms, &top, fr,
 267                             vsite, constr,
 268                             nrnb, nullptr, FALSE);
 269         shouldCheckNumberOfBondedInteractions = true;
 270         gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr);
 271     }
 272     else
 273     {
 274         state_change_natoms(state_global, state_global->natoms);
 275         /* We need to allocate one element extra, since we might use
 276          * (unaligned) 4-wide SIMD loads to access rvec entries.
 277          */
 278         f.resizeWithPadding(state_global->natoms);
 279         /* Copy the pointer to the global state */
 280         state = state_global;
 281
 282         mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr,
 283                                   &graph, mdAtoms, constr, vsite, shellfc);
 284     }
 285
 286     auto mdatoms = mdAtoms->mdatoms();
 287
 288     // NOTE: The global state is no longer used at this point.
 289     // But state_global is still used as temporary storage space for writing
 290     // the global state to file and potentially for replica exchange.
 291     // (Global topology should persist.)
 292
 293     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 294
 295     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 296     {
 297         doFreeEnergyPerturbation = true;
 298     }
 299
 300     {
 301         int    cglo_flags = (CGLO_GSTAT |
 302                              (shouldCheckNumberOfBondedInteractions ?
 303                               CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 304         bool   bSumEkinhOld = false;
 305         t_vcm *vcm          = nullptr;
 306         compute_globals(gstat, cr, ir, fr, ekind,
 307                         state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
 308                         mdatoms, nrnb, vcm,
 309                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
 310                         constr, &nullSignaller, state->box,
 311                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 312     }
 313     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 314                                     top_global, &top, state->x.rvec_array(), state->box,
 315                                     &shouldCheckNumberOfBondedInteractions);
 316
 317     if (MASTER(cr))
 318     {
 319         fprintf(stderr, "starting MiMiC MD run '%s'\n\n",
 320                 *(top_global->name));
 321         if (mdrunOptions.verbose)
 322         {
 323             fprintf(stderr, "Calculated time to finish depends on nsteps from "
 324                     "run input file,\nwhich may not correspond to the time "
 325                     "needed to process input trajectory.\n\n");
 326         }
 327         fprintf(fplog, "\n");
 328     }
 329
 330     walltime_accounting_start_time(walltime_accounting);
 331     wallcycle_start(wcycle, ewcRUN);
 332     print_start(fplog, cr, walltime_accounting, "mdrun");
 333
 334     /***********************************************************
 335      *
 336      *             Loop over MD steps
 337      *
 338      ************************************************************/
 339
 340     if (constr)
 341     {
 342         GMX_LOG(mdlog.info).asParagraph().
 343             appendText("Simulations has constraints. Constraints will "
 344                        "be handled by CPMD.");
 345     }
 346
 347     GMX_LOG(mdlog.info).asParagraph().
 348         appendText("MiMiC does not report kinetic energy, total energy, temperature, virial and pressure.");
 349
 350     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 351                 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
 352                 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
 353                 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
 354
 355     // we don't do counter resetting in rerun - finish will always be valid
 356     walltime_accounting_set_valid_finish(walltime_accounting);
 357
 358     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 359
 360     step     = ir->init_step;
 361     step_rel = 0;
 362
 363     /* and stop now if we should */
 364     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 365     while (!isLastStep)
 366     {
 367         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 368         wallcycle_start(wcycle, ewcSTEP);
 369
 370         t = step;
 371
 372         if (MASTER(cr))
 373         {
 374             mimicCommunicator.getCoords(&state_global->x, state_global->natoms);
 375         }
 376
 377         if (ir->efep != efepNO)
 378         {
 379             setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
 380         }
 381
 382         if (MASTER(cr))
 383         {
 384             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 385             if (constructVsites && DOMAINDECOMP(cr))
 386             {
 387                 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
 388                           "use a single rank");
 389             }
 390         }
 391
 392         if (DOMAINDECOMP(cr))
 393         {
 394             /* Repartition the domain decomposition */
 395             const bool bMasterState = true;
 396             dd_partition_system(fplog, mdlog, step, cr,
 397                                 bMasterState, nstglobalcomm,
 398                                 state_global, *top_global, ir, imdSession,
 399                                 pull_work,
 400                                 state, &f, mdAtoms, &top, fr,
 401                                 vsite, constr,
 402                                 nrnb, wcycle,
 403                                 mdrunOptions.verbose);
 404             shouldCheckNumberOfBondedInteractions = true;
 405         }
 406
 407         if (MASTER(cr))
 408         {
 409             energyOutput.printHeader(fplog, step, t); /* can we improve the information printed here? */
 410         }
 411
 412         if (ir->efep != efepNO)
 413         {
 414             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 415         }
 416
 417         force_flags = (GMX_FORCE_STATECHANGED |
 418                        GMX_FORCE_DYNAMICBOX |
 419                        GMX_FORCE_ALLFORCES |
 420                        GMX_FORCE_VIRIAL |  // TODO: Get rid of this once #2649 is solved
 421                        GMX_FORCE_ENERGY |
 422                        (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 423
 424         if (shellfc)
 425         {
 426             /* Now is the time to relax the shells */
 427             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
 428                                 enforcedRotation, step,
 429                                 ir, imdSession, pull_work, bNS, force_flags, &top,
 430                                 constr, enerd, fcd,
 431                                 state->natoms,
 432                                 state->x.arrayRefWithPadding(),
 433                                 state->v.arrayRefWithPadding(),
 434                                 state->box,
 435                                 state->lambda,
 436                                 &state->hist,
 437                                 f.arrayRefWithPadding(), force_vir, mdatoms,
 438                                 nrnb, wcycle, graph,
 439                                 shellfc, fr, mdScheduleWork, t, mu_tot,
 440                                 vsite,
 441                                 ddBalanceRegionHandler);
 442         }
 443         else
 444         {
 445             /* The coordinates (x) are shifted (to get whole molecules)
 446              * in do_force.
 447              * This is parallellized as well, and does communication too.
 448              * Check comments in sim_util.c
 449              */
 450             Awh       *awh = nullptr;
 451             gmx_edsam *ed  = nullptr;
 452             do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession,
 453                      pull_work,
 454                      step, nrnb, wcycle, &top,
 455                      state->box, state->x.arrayRefWithPadding(), &state->hist,
 456                      f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
 457                      state->lambda, graph,
 458                      fr, mdScheduleWork, vsite, mu_tot, t, ed,
 459                      GMX_FORCE_NS | force_flags,
 460                      ddBalanceRegionHandler);
 461         }
 462
 463         /* Now we have the energies and forces corresponding to the
 464          * coordinates at time t.
 465          */
 466         {
 467             const bool isCheckpointingStep = false;
 468             const bool doRerun             = false;
 469             const bool bSumEkinhOld        = false;
 470             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
 471                                      ir, state, state_global, observablesHistory,
 472                                      top_global, fr,
 473                                      outf, energyOutput, ekind, f,
 474                                      isCheckpointingStep, doRerun, isLastStep,
 475                                      mdrunOptions.writeConfout,
 476                                      bSumEkinhOld);
 477         }
 478
 479         stopHandler->setSignal();
 480
 481         if (graph)
 482         {
 483             /* Need to unshift here */
 484             unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 485         }
 486
 487         if (vsite != nullptr)
 488         {
 489             wallcycle_start(wcycle, ewcVSITECONSTR);
 490             if (graph != nullptr)
 491             {
 492                 shift_self(graph, state->box, as_rvec_array(state->x.data()));
 493             }
 494             construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
 495                              top.idef.iparams, top.idef.il,
 496                              fr->ePBC, fr->bMolPBC, cr, state->box);
 497
 498             if (graph != nullptr)
 499             {
 500                 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 501             }
 502             wallcycle_stop(wcycle, ewcVSITECONSTR);
 503         }
 504
 505         {
 506             const bool          doInterSimSignal = false;
 507             const bool          doIntraSimSignal = true;
 508             bool                bSumEkinhOld     = false;
 509             t_vcm              *vcm              = nullptr;
 510             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 511
 512             compute_globals(gstat, cr, ir, fr, ekind,
 513                             state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
 514                             mdatoms, nrnb, vcm,
 515                             wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
 516                             constr, &signaller,
 517                             state->box,
 518                             &totalNumberOfBondedInteractions, &bSumEkinhOld,
 519                             CGLO_GSTAT | CGLO_ENERGY
 520                             | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
 521                             );
 522             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 523                                             top_global, &top, state->x.rvec_array(), state->box,
 524                                             &shouldCheckNumberOfBondedInteractions);
 525         }
 526
 527         {
 528             gmx::HostVector<gmx::RVec>     fglobal(top_global->natoms);
 529             gmx::ArrayRef<gmx::RVec>       ftemp;
 530             gmx::ArrayRef<const gmx::RVec> flocal = gmx::makeArrayRef(f);
 531             if (DOMAINDECOMP(cr))
 532             {
 533                 ftemp = gmx::makeArrayRef(fglobal);
 534                 dd_collect_vec(cr->dd, state, flocal, ftemp);
 535             }
 536             else
 537             {
 538                 ftemp = gmx::makeArrayRef(f);
 539             }
 540
 541             if (MASTER(cr))
 542             {
 543                 mimicCommunicator.sendEnergies(enerd->term[F_EPOT]);
 544                 mimicCommunicator.sendForces(ftemp, state_global->natoms);
 545             }
 546         }
 547
 548
 549
 550         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 551            the virial that should probably be addressed eventually. state->veta has better properies,
 552            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 553            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 554
 555         if (ir->efep != efepNO)
 556         {
 557             /* Sum up the foreign energy and dhdl terms for md and sd.
 558                Currently done every step so that dhdl is correct in the .edr */
 559             sum_dhdl(enerd, state->lambda, *ir->fepvals);
 560         }
 561
 562         /* Output stuff */
 563         if (MASTER(cr))
 564         {
 565             const bool bCalcEnerStep = true;
 566             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep,
 567                                              t, mdatoms->tmass, enerd, state,
 568                                              ir->fepvals, ir->expandedvals, state->box,
 569                                              shake_vir, force_vir, total_vir, pres,
 570                                              ekind, mu_tot, constr);
 571
 572             const bool do_ene = true;
 573             const bool do_log = true;
 574             Awh       *awh    = nullptr;
 575             const bool do_dr  = ir->nstdisreout != 0;
 576             const bool do_or  = ir->nstorireout != 0;
 577
 578             energyOutput.printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 579             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
 580                                                do_log ? fplog : nullptr,
 581                                                step, t,
 582                                                fcd, awh);
 583
 584             if (do_per_step(step, ir->nstlog))
 585             {
 586                 if (fflush(fplog) != 0)
 587                 {
 588                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 589                 }
 590             }
 591         }
 592
 593         /* Print the remaining wall clock time for the run */
 594         if (isMasterSimMasterRank(ms, MASTER(cr)) &&
 595             (mdrunOptions.verbose || gmx_got_usr_signal()))
 596         {
 597             if (shellfc)
 598             {
 599                 fprintf(stderr, "\n");
 600             }
 601             print_time(stderr, walltime_accounting, step, ir, cr);
 602         }
 603
 604         cycles = wallcycle_stop(wcycle, ewcSTEP);
 605         if (DOMAINDECOMP(cr) && wcycle)
 606         {
 607             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 608         }
 609
 610         /* increase the MD step number */
 611         step++;
 612         step_rel++;
 613     }
 614     /* End of main MD loop */
 615
 616     /* Closing TNG files can include compressing data. Therefore it is good to do that
 617      * before stopping the time measurements. */
 618     mdoutf_tng_close(outf);
 619
 620     /* Stop measuring walltime */
 621     walltime_accounting_end_time(walltime_accounting);
 622
 623     if (MASTER(cr))
 624     {
 625         mimicCommunicator.finalize();
 626     }
 627
 628     if (!thisRankHasDuty(cr, DUTY_PME))
 629     {
 630         /* Tell the PME only node to finish */
 631         gmx_pme_send_finish(cr);
 632     }
 633
 634     done_mdoutf(outf);
 635
 636     done_shellfc(fplog, shellfc, step_rel);
 637
 638     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 639 }