src/gromacs/modularsimulator/modularsimulator.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2019,2020, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
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   8  *
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  11  * as published by the Free Software Foundation; either version 2.1
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  35 /*! \internal \file
  36  * \brief Defines the modular simulator
  37  *
  38  * \author Pascal Merz <pascal.merz@me.com>
  39  * \ingroup module_modularsimulator
  40  */
  41
  42 #include "gmxpre.h"
  43
  44 #include "modularsimulator.h"
  45
  46 #include "gromacs/commandline/filenm.h"
  47 #include "gromacs/domdec/domdec.h"
  48 #include "gromacs/ewald/pme.h"
  49 #include "gromacs/ewald/pme_load_balancing.h"
  50 #include "gromacs/ewald/pme_pp.h"
  51 #include "gromacs/gmxlib/network.h"
  52 #include "gromacs/gmxlib/nrnb.h"
  53 #include "gromacs/math/vec.h"
  54 #include "gromacs/mdlib/checkpointhandler.h"
  55 #include "gromacs/mdlib/constr.h"
  56 #include "gromacs/mdlib/coupling.h"
  57 #include "gromacs/mdlib/energyoutput.h"
  58 #include "gromacs/mdlib/forcerec.h"
  59 #include "gromacs/mdlib/mdatoms.h"
  60 #include "gromacs/mdlib/resethandler.h"
  61 #include "gromacs/mdlib/stat.h"
  62 #include "gromacs/mdlib/update.h"
  63 #include "gromacs/mdrun/replicaexchange.h"
  64 #include "gromacs/mdrun/shellfc.h"
  65 #include "gromacs/mdrunutility/handlerestart.h"
  66 #include "gromacs/mdrunutility/printtime.h"
  67 #include "gromacs/mdtypes/commrec.h"
  68 #include "gromacs/mdtypes/fcdata.h"
  69 #include "gromacs/mdtypes/forcerec.h"
  70 #include "gromacs/mdtypes/inputrec.h"
  71 #include "gromacs/mdtypes/mdatom.h"
  72 #include "gromacs/mdtypes/mdrunoptions.h"
  73 #include "gromacs/mdtypes/observableshistory.h"
  74 #include "gromacs/mdtypes/state.h"
  75 #include "gromacs/nbnxm/nbnxm.h"
  76 #include "gromacs/timing/walltime_accounting.h"
  77 #include "gromacs/topology/mtop_util.h"
  78 #include "gromacs/topology/topology.h"
  79 #include "gromacs/utility/cstringutil.h"
  80 #include "gromacs/utility/fatalerror.h"
  81
  82 #include "compositesimulatorelement.h"
  83 #include "computeglobalselement.h"
  84 #include "constraintelement.h"
  85 #include "energyelement.h"
  86 #include "forceelement.h"
  87 #include "freeenergyperturbationelement.h"
  88 #include "parrinellorahmanbarostat.h"
  89 #include "propagator.h"
  90 #include "signallers.h"
  91 #include "statepropagatordata.h"
  92 #include "trajectoryelement.h"
  93 #include "vrescalethermostat.h"
  94
  95 namespace gmx
  96 {
  97 void ModularSimulator::run()
  98 {
  99     GMX_LOG(mdlog.info).asParagraph().appendText("Using the modular simulator.");
 100     constructElementsAndSignallers();
 101     simulatorSetup();
 102     for (auto& signaller : signallerList_)
 103     {
 104         signaller->setup();
 105     }
 106     if (domDecHelper_)
 107     {
 108         domDecHelper_->setup();
 109     }
 110
 111     for (auto& element : elementsOwnershipList_)
 112     {
 113         element->elementSetup();
 114     }
 115     if (pmeLoadBalanceHelper_)
 116     {
 117         // State must have been initialized so pmeLoadBalanceHelper_ gets a valid box
 118         pmeLoadBalanceHelper_->setup();
 119     }
 120
 121     while (step_ <= signalHelper_->lastStep_)
 122     {
 123         populateTaskQueue();
 124
 125         while (!taskQueue_.empty())
 126         {
 127             auto task = std::move(taskQueue_.front());
 128             taskQueue_.pop();
 129             // run function
 130             (*task)();
 131         }
 132     }
 133
 134     for (auto& element : elementsOwnershipList_)
 135     {
 136         element->elementTeardown();
 137     }
 138     if (pmeLoadBalanceHelper_)
 139     {
 140         pmeLoadBalanceHelper_->teardown();
 141     }
 142     simulatorTeardown();
 143 }
 144
 145 void ModularSimulator::simulatorSetup()
 146 {
 147     if (!mdrunOptions.writeConfout)
 148     {
 149         // This is on by default, and the main known use case for
 150         // turning it off is for convenience in benchmarking, which is
 151         // something that should not show up in the general user
 152         // interface.
 153         GMX_LOG(mdlog.info)
 154                 .asParagraph()
 155                 .appendText(
 156                         "The -noconfout functionality is deprecated, and "
 157                         "may be removed in a future version.");
 158     }
 159
 160     if (MASTER(cr))
 161     {
 162         char        sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
 163         std::string timeString;
 164         fprintf(stderr, "starting mdrun '%s'\n", *(top_global->name));
 165         if (inputrec->nsteps >= 0)
 166         {
 167             timeString = formatString("%8.1f", static_cast<double>(inputrec->init_step + inputrec->nsteps)
 168                                                        * inputrec->delta_t);
 169         }
 170         else
 171         {
 172             timeString = "infinite";
 173         }
 174         if (inputrec->init_step > 0)
 175         {
 176             fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
 177                     gmx_step_str(inputrec->init_step + inputrec->nsteps, sbuf), timeString.c_str(),
 178                     gmx_step_str(inputrec->init_step, sbuf2), inputrec->init_step * inputrec->delta_t);
 179         }
 180         else
 181         {
 182             fprintf(stderr, "%s steps, %s ps.\n", gmx_step_str(inputrec->nsteps, sbuf),
 183                     timeString.c_str());
 184         }
 185         fprintf(fplog, "\n");
 186     }
 187
 188     walltime_accounting_start_time(walltime_accounting);
 189     wallcycle_start(wcycle, ewcRUN);
 190     print_start(fplog, cr, walltime_accounting, "mdrun");
 191
 192     step_ = inputrec->init_step;
 193 }
 194
 195 void ModularSimulator::preStep(Step step, Time gmx_unused time, bool isNeighborSearchingStep)
 196 {
 197     if (stopHandler_->stoppingAfterCurrentStep(isNeighborSearchingStep) && step != signalHelper_->lastStep_)
 198     {
 199         /*
 200          * Stop handler wants to stop after the current step, which was
 201          * not known when building the current task queue. This happens
 202          * e.g. when a stop is signalled by OS. We therefore want to purge
 203          * the task queue now, and re-schedule this step as last step.
 204          */
 205         // clear task queue
 206         std::queue<SimulatorRunFunctionPtr>().swap(taskQueue_);
 207         // rewind step
 208         step_ = step;
 209         return;
 210     }
 211
 212     resetHandler_->setSignal(walltime_accounting);
 213     // This is a hack to avoid having to rewrite StopHandler to be a NeighborSearchSignaller
 214     // and accept the step as input. Eventually, we want to do that, but currently this would
 215     // require introducing NeighborSearchSignaller in the legacy do_md or a lot of code
 216     // duplication.
 217     stophandlerIsNSStep_    = isNeighborSearchingStep;
 218     stophandlerCurrentStep_ = step;
 219     stopHandler_->setSignal();
 220
 221     wallcycle_start(wcycle, ewcSTEP);
 222 }
 223
 224 void ModularSimulator::postStep(Step step, Time gmx_unused time)
 225 {
 226     // Output stuff
 227     if (MASTER(cr))
 228     {
 229         if (do_per_step(step, inputrec->nstlog))
 230         {
 231             if (fflush(fplog) != 0)
 232             {
 233                 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 234             }
 235         }
 236     }
 237     const bool do_verbose = mdrunOptions.verbose
 238                             && (step % mdrunOptions.verboseStepPrintInterval == 0
 239                                 || step == inputrec->init_step || step == signalHelper_->lastStep_);
 240     // Print the remaining wall clock time for the run
 241     if (MASTER(cr) && (do_verbose || gmx_got_usr_signal())
 242         && !(pmeLoadBalanceHelper_ && pmeLoadBalanceHelper_->pmePrinting()))
 243     {
 244         print_time(stderr, walltime_accounting, step, inputrec, cr);
 245     }
 246
 247     double cycles = wallcycle_stop(wcycle, ewcSTEP);
 248     if (DOMAINDECOMP(cr) && wcycle)
 249     {
 250         dd_cycles_add(cr->dd, static_cast<float>(cycles), ddCyclStep);
 251     }
 252
 253     resetHandler_->resetCounters(
 254             step, step - inputrec->init_step, mdlog, fplog, cr, fr->nbv.get(), nrnb, fr->pmedata,
 255             pmeLoadBalanceHelper_ ? pmeLoadBalanceHelper_->loadBalancingObject() : nullptr, wcycle,
 256             walltime_accounting);
 257 }
 258
 259 void ModularSimulator::simulatorTeardown()
 260 {
 261
 262     // Stop measuring walltime
 263     walltime_accounting_end_time(walltime_accounting);
 264
 265     if (!thisRankHasDuty(cr, DUTY_PME))
 266     {
 267         /* Tell the PME only node to finish */
 268         gmx_pme_send_finish(cr);
 269     }
 270
 271     walltime_accounting_set_nsteps_done(walltime_accounting, step_ - inputrec->init_step);
 272 }
 273
 274 void ModularSimulator::populateTaskQueue()
 275 {
 276     auto registerRunFunction = std::make_unique<RegisterRunFunction>(
 277             [this](SimulatorRunFunctionPtr ptr) { taskQueue_.push(std::move(ptr)); });
 278
 279     Time startTime = inputrec->init_t;
 280     Time timeStep  = inputrec->delta_t;
 281     Time time      = startTime + step_ * timeStep;
 282
 283     // Run an initial call to the signallers
 284     for (auto& signaller : signallerList_)
 285     {
 286         signaller->signal(step_, time);
 287     }
 288
 289     if (checkpointHelper_)
 290     {
 291         checkpointHelper_->run(step_, time);
 292     }
 293
 294     if (pmeLoadBalanceHelper_)
 295     {
 296         pmeLoadBalanceHelper_->run(step_, time);
 297     }
 298     if (domDecHelper_)
 299     {
 300         domDecHelper_->run(step_, time);
 301     }
 302
 303     do
 304     {
 305         // local variables for lambda capturing
 306         const int  step     = step_;
 307         const bool isNSStep = step == signalHelper_->nextNSStep_;
 308
 309         // register pre-step
 310         (*registerRunFunction)(std::make_unique<SimulatorRunFunction>(
 311                 [this, step, time, isNSStep]() { preStep(step, time, isNSStep); }));
 312         // register elements for step
 313         for (auto& element : elementCallList_)
 314         {
 315             element->scheduleTask(step_, time, registerRunFunction);
 316         }
 317         // register post-step
 318         (*registerRunFunction)(
 319                 std::make_unique<SimulatorRunFunction>([this, step, time]() { postStep(step, time); }));
 320
 321         // prepare next step
 322         step_++;
 323         time = startTime + step_ * timeStep;
 324         for (auto& signaller : signallerList_)
 325         {
 326             signaller->signal(step_, time);
 327         }
 328     } while (step_ != signalHelper_->nextNSStep_ && step_ <= signalHelper_->lastStep_);
 329 }
 330
 331 void ModularSimulator::constructElementsAndSignallers()
 332 {
 333     /* When restarting from a checkpoint, it can be appropriate to
 334      * initialize ekind from quantities in the checkpoint. Otherwise,
 335      * compute_globals must initialize ekind before the simulation
 336      * starts/restarts. However, only the master rank knows what was
 337      * found in the checkpoint file, so we have to communicate in
 338      * order to coordinate the restart.
 339      *
 340      * TODO (modular) This should become obsolete when checkpoint reading
 341      *      happens within the modular simulator framework: The energy
 342      *      element should read its data from the checkpoint file pointer,
 343      *      and signal to the compute globals element if it needs anything
 344      *      reduced.
 345      *
 346      * TODO (legacy) Consider removing this communication if/when checkpoint
 347      *      reading directly follows .tpr reading, because all ranks can
 348      *      agree on hasReadEkinState at that time.
 349      */
 350     bool hasReadEkinState = MASTER(cr) ? state_global->ekinstate.hasReadEkinState : false;
 351     if (PAR(cr))
 352     {
 353         gmx_bcast(sizeof(hasReadEkinState), &hasReadEkinState, cr->mpi_comm_mygroup);
 354     }
 355     if (hasReadEkinState)
 356     {
 357         restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
 358     }
 359
 360     /*
 361      * Build data structures
 362      */
 363     topologyHolder_ =
 364             std::make_unique<TopologyHolder>(*top_global, cr, inputrec, fr, mdAtoms, constr, vsite);
 365
 366     std::unique_ptr<FreeEnergyPerturbationElement> freeEnergyPerturbationElement    = nullptr;
 367     FreeEnergyPerturbationElement*                 freeEnergyPerturbationElementPtr = nullptr;
 368     if (inputrec->efep != efepNO)
 369     {
 370         freeEnergyPerturbationElement =
 371                 std::make_unique<FreeEnergyPerturbationElement>(fplog, inputrec, mdAtoms);
 372         freeEnergyPerturbationElementPtr = freeEnergyPerturbationElement.get();
 373     }
 374
 375     auto statePropagatorData = std::make_unique<StatePropagatorData>(
 376             top_global->natoms, fplog, cr, state_global, inputrec->nstxout, inputrec->nstvout,
 377             inputrec->nstfout, inputrec->nstxout_compressed, fr->nbv->useGpu(),
 378             freeEnergyPerturbationElementPtr, topologyHolder_.get(), fr->bMolPBC,
 379             mdrunOptions.writeConfout, opt2fn("-c", nfile, fnm), inputrec, mdAtoms->mdatoms());
 380     auto statePropagatorDataPtr = compat::make_not_null(statePropagatorData.get());
 381
 382     auto energyElement = std::make_unique<EnergyElement>(
 383             statePropagatorDataPtr, freeEnergyPerturbationElementPtr, top_global, inputrec, mdAtoms,
 384             enerd, ekind, constr, fplog, fcd, mdModulesNotifier, MASTER(cr), observablesHistory,
 385             startingBehavior);
 386     auto energyElementPtr = compat::make_not_null(energyElement.get());
 387
 388     /*
 389      * Build stop handler
 390      */
 391     const bool simulationsShareState = false;
 392     stopHandler_                     = stopHandlerBuilder->getStopHandlerMD(
 393             compat::not_null<SimulationSignal*>(&signals_[eglsSTOPCOND]), simulationsShareState,
 394             MASTER(cr), inputrec->nstlist, mdrunOptions.reproducible, nstglobalcomm_,
 395             mdrunOptions.maximumHoursToRun, inputrec->nstlist == 0, fplog, stophandlerCurrentStep_,
 396             stophandlerIsNSStep_, walltime_accounting);
 397
 398     /*
 399      * Create simulator builders
 400      */
 401     SignallerBuilder<NeighborSearchSignaller> neighborSearchSignallerBuilder;
 402     SignallerBuilder<LastStepSignaller>       lastStepSignallerBuilder;
 403     SignallerBuilder<LoggingSignaller>        loggingSignallerBuilder;
 404     SignallerBuilder<EnergySignaller>         energySignallerBuilder;
 405     SignallerBuilder<TrajectorySignaller>     trajectorySignallerBuilder;
 406     TrajectoryElementBuilder                  trajectoryElementBuilder;
 407
 408     /*
 409      * Register data structures to signallers
 410      */
 411     trajectoryElementBuilder.registerWriterClient(statePropagatorDataPtr);
 412     trajectorySignallerBuilder.registerSignallerClient(statePropagatorDataPtr);
 413     lastStepSignallerBuilder.registerSignallerClient(statePropagatorDataPtr);
 414
 415     trajectoryElementBuilder.registerWriterClient(energyElementPtr);
 416     trajectorySignallerBuilder.registerSignallerClient(energyElementPtr);
 417     energySignallerBuilder.registerSignallerClient(energyElementPtr);
 418
 419     // Register the simulator itself to the neighbor search / last step signaller
 420     neighborSearchSignallerBuilder.registerSignallerClient(compat::make_not_null(signalHelper_.get()));
 421     lastStepSignallerBuilder.registerSignallerClient(compat::make_not_null(signalHelper_.get()));
 422
 423     /*
 424      * Build integrator - this takes care of force calculation, propagation,
 425      * constraining, and of the place the statePropagatorData and the energy element
 426      * have a full timestep state.
 427      */
 428     // TODO: Make a CheckpointHelperBuilder
 429     std::vector<ICheckpointHelperClient*> checkpointClients = { statePropagatorDataPtr, energyElementPtr,
 430                                                                 freeEnergyPerturbationElementPtr };
 431     CheckBondedInteractionsCallbackPtr checkBondedInteractionsCallback = nullptr;
 432     auto integrator = buildIntegrator(&neighborSearchSignallerBuilder, &energySignallerBuilder,
 433                                       &loggingSignallerBuilder, &trajectorySignallerBuilder,
 434                                       &checkpointClients, &checkBondedInteractionsCallback,
 435                                       statePropagatorDataPtr, energyElementPtr,
 436                                       freeEnergyPerturbationElementPtr, hasReadEkinState);
 437
 438     /*
 439      * Build infrastructure elements
 440      */
 441
 442     if (PmeLoadBalanceHelper::doPmeLoadBalancing(mdrunOptions, inputrec, fr))
 443     {
 444         pmeLoadBalanceHelper_ = std::make_unique<PmeLoadBalanceHelper>(
 445                 mdrunOptions.verbose, statePropagatorDataPtr, fplog, cr, mdlog, inputrec, wcycle, fr);
 446         neighborSearchSignallerBuilder.registerSignallerClient(
 447                 compat::make_not_null(pmeLoadBalanceHelper_.get()));
 448     }
 449
 450     if (DOMAINDECOMP(cr))
 451     {
 452         GMX_ASSERT(checkBondedInteractionsCallback,
 453                    "Domain decomposition needs a callback for check the number of bonded "
 454                    "interactions.");
 455         domDecHelper_ = std::make_unique<DomDecHelper>(
 456                 mdrunOptions.verbose, mdrunOptions.verboseStepPrintInterval, statePropagatorDataPtr,
 457                 topologyHolder_.get(), std::move(checkBondedInteractionsCallback), nstglobalcomm_, fplog,
 458                 cr, mdlog, constr, inputrec, mdAtoms, nrnb, wcycle, fr, vsite, imdSession, pull_work);
 459         neighborSearchSignallerBuilder.registerSignallerClient(compat::make_not_null(domDecHelper_.get()));
 460     }
 461
 462     const bool simulationsShareResetCounters = false;
 463     resetHandler_                            = std::make_unique<ResetHandler>(
 464             compat::make_not_null<SimulationSignal*>(&signals_[eglsRESETCOUNTERS]),
 465             simulationsShareResetCounters, inputrec->nsteps, MASTER(cr),
 466             mdrunOptions.timingOptions.resetHalfway, mdrunOptions.maximumHoursToRun, mdlog, wcycle,
 467             walltime_accounting);
 468
 469     /*
 470      * Build signaller list
 471      *
 472      * Note that as signallers depend on each others, the order of calling the signallers
 473      * matters. It is the responsibility of this builder to ensure that the order is
 474      * maintained.
 475      */
 476     auto energySignaller = energySignallerBuilder.build(
 477             inputrec->nstcalcenergy, inputrec->fepvals->nstdhdl, inputrec->nstpcouple);
 478     trajectorySignallerBuilder.registerSignallerClient(compat::make_not_null(energySignaller.get()));
 479     loggingSignallerBuilder.registerSignallerClient(compat::make_not_null(energySignaller.get()));
 480     auto trajectoryElement = trajectoryElementBuilder.build(
 481             fplog, nfile, fnm, mdrunOptions, cr, outputProvider, mdModulesNotifier, inputrec,
 482             top_global, oenv, wcycle, startingBehavior, simulationsShareState);
 483     loggingSignallerBuilder.registerSignallerClient(compat::make_not_null(trajectoryElement.get()));
 484     trajectorySignallerBuilder.registerSignallerClient(compat::make_not_null(trajectoryElement.get()));
 485     auto trajectorySignaller = trajectorySignallerBuilder.build(
 486             inputrec->nstxout, inputrec->nstvout, inputrec->nstfout, inputrec->nstxout_compressed,
 487             trajectoryElement->tngBoxOut(), trajectoryElement->tngLambdaOut(),
 488             trajectoryElement->tngBoxOutCompressed(), trajectoryElement->tngLambdaOutCompressed(),
 489             inputrec->nstenergy);
 490
 491     // Add checkpoint helper here since we need a pointer to the trajectory element and
 492     // need to register it with the lastStepSignallerBuilder
 493     auto checkpointHandler = std::make_unique<CheckpointHandler>(
 494             compat::make_not_null<SimulationSignal*>(&signals_[eglsCHKPT]), simulationsShareState,
 495             inputrec->nstlist == 0, MASTER(cr), mdrunOptions.writeConfout,
 496             mdrunOptions.checkpointOptions.period);
 497     checkpointHelper_ = std::make_unique<CheckpointHelper>(
 498             std::move(checkpointClients), std::move(checkpointHandler), inputrec->init_step,
 499             trajectoryElement.get(), top_global->natoms, fplog, cr, observablesHistory,
 500             walltime_accounting, state_global, mdrunOptions.writeConfout);
 501     lastStepSignallerBuilder.registerSignallerClient(compat::make_not_null(checkpointHelper_.get()));
 502
 503     lastStepSignallerBuilder.registerSignallerClient(compat::make_not_null(trajectorySignaller.get()));
 504     auto loggingSignaller =
 505             loggingSignallerBuilder.build(inputrec->nstlog, inputrec->init_step, inputrec->init_t);
 506     lastStepSignallerBuilder.registerSignallerClient(compat::make_not_null(loggingSignaller.get()));
 507     auto lastStepSignaller =
 508             lastStepSignallerBuilder.build(inputrec->nsteps, inputrec->init_step, stopHandler_.get());
 509     neighborSearchSignallerBuilder.registerSignallerClient(compat::make_not_null(lastStepSignaller.get()));
 510     auto neighborSearchSignaller = neighborSearchSignallerBuilder.build(
 511             inputrec->nstlist, inputrec->init_step, inputrec->init_t);
 512
 513     signallerList_.emplace_back(std::move(neighborSearchSignaller));
 514     signallerList_.emplace_back(std::move(lastStepSignaller));
 515     signallerList_.emplace_back(std::move(loggingSignaller));
 516     signallerList_.emplace_back(std::move(trajectorySignaller));
 517     signallerList_.emplace_back(std::move(energySignaller));
 518
 519     /*
 520      * Build the element list
 521      *
 522      * This is the actual sequence of (non-infrastructure) elements to be run.
 523      * For NVE, the trajectory element is used outside of the integrator
 524      * (composite) element, as well as the checkpoint helper. The checkpoint
 525      * helper should be on top of the loop, and is only part of the simulator
 526      * call list to be able to react to the last step being signalled.
 527      */
 528     addToCallList(checkpointHelper_, elementCallList_);
 529     if (freeEnergyPerturbationElement)
 530     {
 531         addToCallListAndMove(std::move(freeEnergyPerturbationElement), elementCallList_,
 532                              elementsOwnershipList_);
 533     }
 534     addToCallListAndMove(std::move(integrator), elementCallList_, elementsOwnershipList_);
 535     addToCallListAndMove(std::move(trajectoryElement), elementCallList_, elementsOwnershipList_);
 536     // for vv, we need to setup statePropagatorData after the compute
 537     // globals so that we reset the right velocities
 538     // TODO: Avoid this by getting rid of the need of resetting velocities in vv
 539     elementsOwnershipList_.emplace_back(std::move(statePropagatorData));
 540     elementsOwnershipList_.emplace_back(std::move(energyElement));
 541 }
 542
 543 std::unique_ptr<ISimulatorElement>
 544 ModularSimulator::buildForces(SignallerBuilder<NeighborSearchSignaller>* neighborSearchSignallerBuilder,
 545                               SignallerBuilder<EnergySignaller>*         energySignallerBuilder,
 546                               StatePropagatorData*                       statePropagatorDataPtr,
 547                               EnergyElement*                             energyElementPtr,
 548                               FreeEnergyPerturbationElement* freeEnergyPerturbationElement)
 549 {
 550     const bool isVerbose    = mdrunOptions.verbose;
 551     const bool isDynamicBox = inputrecDynamicBox(inputrec);
 552
 553     auto forceElement = std::make_unique<ForceElement>(
 554             statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElement, isVerbose,
 555             isDynamicBox, fplog, cr, inputrec, mdAtoms, nrnb, fr, fcd, wcycle, runScheduleWork, vsite,
 556             imdSession, pull_work, constr, &topologyHolder_->globalTopology(), enforcedRotation);
 557     topologyHolder_->registerClient(forceElement.get());
 558     neighborSearchSignallerBuilder->registerSignallerClient(compat::make_not_null(forceElement.get()));
 559     energySignallerBuilder->registerSignallerClient(compat::make_not_null(forceElement.get()));
 560
 561     // std::move *should* not be needed with c++-14, but clang-3.6 still requires it
 562     return std::move(forceElement);
 563 }
 564
 565 std::unique_ptr<ISimulatorElement> ModularSimulator::buildIntegrator(
 566         SignallerBuilder<NeighborSearchSignaller>* neighborSearchSignallerBuilder,
 567         SignallerBuilder<EnergySignaller>*         energySignallerBuilder,
 568         SignallerBuilder<LoggingSignaller>*        loggingSignallerBuilder,
 569         SignallerBuilder<TrajectorySignaller>*     trajectorySignallerBuilder,
 570         std::vector<ICheckpointHelperClient*>*     checkpointClients,
 571         CheckBondedInteractionsCallbackPtr*        checkBondedInteractionsCallback,
 572         compat::not_null<StatePropagatorData*>     statePropagatorDataPtr,
 573         compat::not_null<EnergyElement*>           energyElementPtr,
 574         FreeEnergyPerturbationElement*             freeEnergyPerturbationElementPtr,
 575         bool                                       hasReadEkinState)
 576 {
 577     auto forceElement =
 578             buildForces(neighborSearchSignallerBuilder, energySignallerBuilder,
 579                         statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr);
 580
 581     // list of elements owned by the simulator composite object
 582     std::vector<std::unique_ptr<ISimulatorElement>> elementsOwnershipList;
 583     // call list of the simulator composite object
 584     std::vector<compat::not_null<ISimulatorElement*>> elementCallList;
 585
 586     std::function<void()> needToCheckNumberOfBondedInteractions;
 587     if (inputrec->eI == eiMD)
 588     {
 589         auto computeGlobalsElement =
 590                 std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>>(
 591                         statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
 592                         &signals_, nstglobalcomm_, fplog, mdlog, cr, inputrec, mdAtoms, nrnb,
 593                         wcycle, fr, &topologyHolder_->globalTopology(), constr, hasReadEkinState);
 594         topologyHolder_->registerClient(computeGlobalsElement.get());
 595         energySignallerBuilder->registerSignallerClient(compat::make_not_null(computeGlobalsElement.get()));
 596         trajectorySignallerBuilder->registerSignallerClient(
 597                 compat::make_not_null(computeGlobalsElement.get()));
 598
 599         *checkBondedInteractionsCallback =
 600                 computeGlobalsElement->getCheckNumberOfBondedInteractionsCallback();
 601
 602         auto propagator = std::make_unique<Propagator<IntegrationStep::LeapFrog>>(
 603                 inputrec->delta_t, statePropagatorDataPtr, mdAtoms, wcycle);
 604
 605         addToCallListAndMove(std::move(forceElement), elementCallList, elementsOwnershipList);
 606         addToCallList(statePropagatorDataPtr, elementCallList); // we have a full microstate at time t here!
 607         if (inputrec->etc == etcVRESCALE)
 608         {
 609             // TODO: With increased complexity of the propagator, this will need further development,
 610             //       e.g. using propagators templated for velocity propagation policies and a builder
 611             propagator->setNumVelocityScalingVariables(inputrec->opts.ngtc);
 612             auto thermostat = std::make_unique<VRescaleThermostat>(
 613                     inputrec->nsttcouple, -1, false, inputrec->ld_seed, inputrec->opts.ngtc,
 614                     inputrec->delta_t * inputrec->nsttcouple, inputrec->opts.ref_t, inputrec->opts.tau_t,
 615                     inputrec->opts.nrdf, energyElementPtr, propagator->viewOnVelocityScaling(),
 616                     propagator->velocityScalingCallback(), state_global, cr, inputrec->bContinuation);
 617             checkpointClients->emplace_back(thermostat.get());
 618             energyElementPtr->setVRescaleThermostat(thermostat.get());
 619             addToCallListAndMove(std::move(thermostat), elementCallList, elementsOwnershipList);
 620         }
 621
 622         std::unique_ptr<ParrinelloRahmanBarostat> prBarostat = nullptr;
 623         if (inputrec->epc == epcPARRINELLORAHMAN)
 624         {
 625             // Building the PR barostat here since it needs access to the propagator
 626             // and we want to be able to move the propagator object
 627             prBarostat = std::make_unique<ParrinelloRahmanBarostat>(
 628                     inputrec->nstpcouple, -1, inputrec->delta_t * inputrec->nstpcouple,
 629                     inputrec->init_step, propagator->viewOnPRScalingMatrix(),
 630                     propagator->prScalingCallback(), statePropagatorDataPtr, energyElementPtr,
 631                     fplog, inputrec, mdAtoms, state_global, cr, inputrec->bContinuation);
 632             energyElementPtr->setParrinelloRahamnBarostat(prBarostat.get());
 633             checkpointClients->emplace_back(prBarostat.get());
 634         }
 635         addToCallListAndMove(std::move(propagator), elementCallList, elementsOwnershipList);
 636         if (constr)
 637         {
 638             auto constraintElement = std::make_unique<ConstraintsElement<ConstraintVariable::Positions>>(
 639                     constr, statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
 640                     MASTER(cr), fplog, inputrec, mdAtoms->mdatoms());
 641             auto constraintElementPtr = compat::make_not_null(constraintElement.get());
 642             energySignallerBuilder->registerSignallerClient(constraintElementPtr);
 643             trajectorySignallerBuilder->registerSignallerClient(constraintElementPtr);
 644             loggingSignallerBuilder->registerSignallerClient(constraintElementPtr);
 645
 646             addToCallListAndMove(std::move(constraintElement), elementCallList, elementsOwnershipList);
 647         }
 648
 649         addToCallListAndMove(std::move(computeGlobalsElement), elementCallList, elementsOwnershipList);
 650         addToCallList(energyElementPtr, elementCallList); // we have the energies at time t here!
 651         if (prBarostat)
 652         {
 653             addToCallListAndMove(std::move(prBarostat), elementCallList, elementsOwnershipList);
 654         }
 655     }
 656     else if (inputrec->eI == eiVV)
 657     {
 658         auto computeGlobalsElement =
 659                 std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>(
 660                         statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
 661                         &signals_, nstglobalcomm_, fplog, mdlog, cr, inputrec, mdAtoms, nrnb,
 662                         wcycle, fr, &topologyHolder_->globalTopology(), constr, hasReadEkinState);
 663         topologyHolder_->registerClient(computeGlobalsElement.get());
 664         energySignallerBuilder->registerSignallerClient(compat::make_not_null(computeGlobalsElement.get()));
 665         trajectorySignallerBuilder->registerSignallerClient(
 666                 compat::make_not_null(computeGlobalsElement.get()));
 667
 668         *checkBondedInteractionsCallback =
 669                 computeGlobalsElement->getCheckNumberOfBondedInteractionsCallback();
 670
 671         auto propagatorVelocities = std::make_unique<Propagator<IntegrationStep::VelocitiesOnly>>(
 672                 inputrec->delta_t * 0.5, statePropagatorDataPtr, mdAtoms, wcycle);
 673         auto propagatorVelocitiesAndPositions =
 674                 std::make_unique<Propagator<IntegrationStep::VelocityVerletPositionsAndVelocities>>(
 675                         inputrec->delta_t, statePropagatorDataPtr, mdAtoms, wcycle);
 676
 677         addToCallListAndMove(std::move(forceElement), elementCallList, elementsOwnershipList);
 678
 679         std::unique_ptr<ParrinelloRahmanBarostat> prBarostat = nullptr;
 680         if (inputrec->epc == epcPARRINELLORAHMAN)
 681         {
 682             // Building the PR barostat here since it needs access to the propagator
 683             // and we want to be able to move the propagator object
 684             prBarostat = std::make_unique<ParrinelloRahmanBarostat>(
 685                     inputrec->nstpcouple, -1, inputrec->delta_t * inputrec->nstpcouple,
 686                     inputrec->init_step, propagatorVelocities->viewOnPRScalingMatrix(),
 687                     propagatorVelocities->prScalingCallback(), statePropagatorDataPtr, energyElementPtr,
 688                     fplog, inputrec, mdAtoms, state_global, cr, inputrec->bContinuation);
 689             energyElementPtr->setParrinelloRahamnBarostat(prBarostat.get());
 690             checkpointClients->emplace_back(prBarostat.get());
 691         }
 692         addToCallListAndMove(std::move(propagatorVelocities), elementCallList, elementsOwnershipList);
 693         if (constr)
 694         {
 695             auto constraintElement = std::make_unique<ConstraintsElement<ConstraintVariable::Velocities>>(
 696                     constr, statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
 697                     MASTER(cr), fplog, inputrec, mdAtoms->mdatoms());
 698             energySignallerBuilder->registerSignallerClient(compat::make_not_null(constraintElement.get()));
 699             trajectorySignallerBuilder->registerSignallerClient(
 700                     compat::make_not_null(constraintElement.get()));
 701             loggingSignallerBuilder->registerSignallerClient(
 702                     compat::make_not_null(constraintElement.get()));
 703
 704             addToCallListAndMove(std::move(constraintElement), elementCallList, elementsOwnershipList);
 705         }
 706         addToCallList(compat::make_not_null(computeGlobalsElement.get()), elementCallList);
 707         addToCallList(statePropagatorDataPtr, elementCallList); // we have a full microstate at time t here!
 708         if (inputrec->etc == etcVRESCALE)
 709         {
 710             // TODO: With increased complexity of the propagator, this will need further development,
 711             //       e.g. using propagators templated for velocity propagation policies and a builder
 712             propagatorVelocitiesAndPositions->setNumVelocityScalingVariables(inputrec->opts.ngtc);
 713             auto thermostat = std::make_unique<VRescaleThermostat>(
 714                     inputrec->nsttcouple, 0, true, inputrec->ld_seed, inputrec->opts.ngtc,
 715                     inputrec->delta_t * inputrec->nsttcouple, inputrec->opts.ref_t,
 716                     inputrec->opts.tau_t, inputrec->opts.nrdf, energyElementPtr,
 717                     propagatorVelocitiesAndPositions->viewOnVelocityScaling(),
 718                     propagatorVelocitiesAndPositions->velocityScalingCallback(), state_global, cr,
 719                     inputrec->bContinuation);
 720             checkpointClients->emplace_back(thermostat.get());
 721             energyElementPtr->setVRescaleThermostat(thermostat.get());
 722             addToCallListAndMove(std::move(thermostat), elementCallList, elementsOwnershipList);
 723         }
 724         addToCallListAndMove(std::move(propagatorVelocitiesAndPositions), elementCallList,
 725                              elementsOwnershipList);
 726         if (constr)
 727         {
 728             auto constraintElement = std::make_unique<ConstraintsElement<ConstraintVariable::Positions>>(
 729                     constr, statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
 730                     MASTER(cr), fplog, inputrec, mdAtoms->mdatoms());
 731             energySignallerBuilder->registerSignallerClient(compat::make_not_null(constraintElement.get()));
 732             trajectorySignallerBuilder->registerSignallerClient(
 733                     compat::make_not_null(constraintElement.get()));
 734             loggingSignallerBuilder->registerSignallerClient(
 735                     compat::make_not_null(constraintElement.get()));
 736
 737             addToCallListAndMove(std::move(constraintElement), elementCallList, elementsOwnershipList);
 738         }
 739         addToCallListAndMove(std::move(computeGlobalsElement), elementCallList, elementsOwnershipList);
 740         addToCallList(energyElementPtr, elementCallList); // we have the energies at time t here!
 741         if (prBarostat)
 742         {
 743             addToCallListAndMove(std::move(prBarostat), elementCallList, elementsOwnershipList);
 744         }
 745     }
 746     else
 747     {
 748         gmx_fatal(FARGS, "Integrator not implemented for the modular simulator.");
 749     }
 750
 751     auto integrator = std::make_unique<CompositeSimulatorElement>(std::move(elementCallList),
 752                                                                   std::move(elementsOwnershipList));
 753     // std::move *should* not be needed with c++-14, but clang-3.6 still requires it
 754     return std::move(integrator);
 755 }
 756
 757 bool ModularSimulator::isInputCompatible(bool                             exitOnFailure,
 758                                          const t_inputrec*                inputrec,
 759                                          bool                             doRerun,
 760                                          const gmx_mtop_t&                globalTopology,
 761                                          const gmx_multisim_t*            ms,
 762                                          const ReplicaExchangeParameters& replExParams,
 763                                          const t_fcdata*                  fcd,
 764                                          bool                             doEssentialDynamics,
 765                                          bool                             doMembed)
 766 {
 767     auto conditionalAssert = [exitOnFailure](bool condition, const char* message) {
 768         if (exitOnFailure)
 769         {
 770             GMX_RELEASE_ASSERT(condition, message);
 771         }
 772         return condition;
 773     };
 774
 775     bool isInputCompatible = true;
 776
 777     // GMX_USE_MODULAR_SIMULATOR allows to use modular simulator also for non-standard uses,
 778     // such as the leap-frog integrator
 779     const auto modularSimulatorExplicitlyTurnedOn = (getenv("GMX_USE_MODULAR_SIMULATOR") != nullptr);
 780     // GMX_USE_MODULAR_SIMULATOR allows to use disable modular simulator for all uses,
 781     // including the velocity-verlet integrator used by default
 782     const auto modularSimulatorExplicitlyTurnedOff = (getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
 783
 784     GMX_RELEASE_ASSERT(
 785             !(modularSimulatorExplicitlyTurnedOn && modularSimulatorExplicitlyTurnedOff),
 786             "Cannot have both GMX_USE_MODULAR_SIMULATOR=ON and GMX_DISABLE_MODULAR_SIMULATOR=ON. "
 787             "Unset one of the two environment variables to explicitly chose which simulator to "
 788             "use, "
 789             "or unset both to recover default behavior.");
 790
 791     GMX_RELEASE_ASSERT(
 792             !(modularSimulatorExplicitlyTurnedOff && inputrec->eI == eiVV
 793               && inputrec->epc == epcPARRINELLORAHMAN),
 794             "Cannot use a Parrinello-Rahman barostat with md-vv and "
 795             "GMX_DISABLE_MODULAR_SIMULATOR=ON, "
 796             "as the Parrinello-Rahman barostat is not implemented in the legacy simulator. Unset "
 797             "GMX_DISABLE_MODULAR_SIMULATOR or use a different pressure control algorithm.");
 798
 799     isInputCompatible =
 800             isInputCompatible
 801             && conditionalAssert(
 802                        inputrec->eI == eiMD || inputrec->eI == eiVV,
 803                        "Only integrators md and md-vv are supported by the modular simulator.");
 804     isInputCompatible = isInputCompatible
 805                         && conditionalAssert(inputrec->eI != eiMD || modularSimulatorExplicitlyTurnedOn,
 806                                              "Set GMX_USE_MODULAR_SIMULATOR=ON to use the modular "
 807                                              "simulator with integrator md.");
 808     isInputCompatible =
 809             isInputCompatible
 810             && conditionalAssert(!doRerun, "Rerun is not supported by the modular simulator.");
 811     isInputCompatible =
 812             isInputCompatible
 813             && conditionalAssert(
 814                        inputrec->etc == etcNO || inputrec->etc == etcVRESCALE,
 815                        "Only v-rescale thermostat is supported by the modular simulator.");
 816     isInputCompatible =
 817             isInputCompatible
 818             && conditionalAssert(
 819                        inputrec->epc == epcNO || inputrec->epc == epcPARRINELLORAHMAN,
 820                        "Only Parrinello-Rahman barostat is supported by the modular simulator.");
 821     isInputCompatible =
 822             isInputCompatible
 823             && conditionalAssert(
 824                        !(inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec)
 825                          || inputrecNvtTrotter(inputrec)),
 826                        "Legacy Trotter decomposition is not supported by the modular simulator.");
 827     isInputCompatible = isInputCompatible
 828                         && conditionalAssert(inputrec->efep == efepNO || inputrec->efep == efepYES
 829                                                      || inputrec->efep == efepSLOWGROWTH,
 830                                              "Expanded ensemble free energy calculation is not "
 831                                              "supported by the modular simulator.");
 832     isInputCompatible = isInputCompatible
 833                         && conditionalAssert(!inputrec->bPull,
 834                                              "Pulling is not supported by the modular simulator.");
 835     isInputCompatible =
 836             isInputCompatible
 837             && conditionalAssert(inputrec->opts.ngacc == 1 && inputrec->opts.acc[0][XX] == 0.0
 838                                          && inputrec->opts.acc[0][YY] == 0.0
 839                                          && inputrec->opts.acc[0][ZZ] == 0.0 && inputrec->cos_accel == 0.0,
 840                                  "Acceleration is not supported by the modular simulator.");
 841     isInputCompatible =
 842             isInputCompatible
 843             && conditionalAssert(inputrec->opts.ngfrz == 1 && inputrec->opts.nFreeze[0][XX] == 0
 844                                          && inputrec->opts.nFreeze[0][YY] == 0
 845                                          && inputrec->opts.nFreeze[0][ZZ] == 0,
 846                                  "Freeze groups are not supported by the modular simulator.");
 847     isInputCompatible =
 848             isInputCompatible
 849             && conditionalAssert(
 850                        inputrec->deform[XX][XX] == 0.0 && inputrec->deform[XX][YY] == 0.0
 851                                && inputrec->deform[XX][ZZ] == 0.0 && inputrec->deform[YY][XX] == 0.0
 852                                && inputrec->deform[YY][YY] == 0.0 && inputrec->deform[YY][ZZ] == 0.0
 853                                && inputrec->deform[ZZ][XX] == 0.0 && inputrec->deform[ZZ][YY] == 0.0
 854                                && inputrec->deform[ZZ][ZZ] == 0.0,
 855                        "Deformation is not supported by the modular simulator.");
 856     isInputCompatible =
 857             isInputCompatible
 858             && conditionalAssert(gmx_mtop_interaction_count(globalTopology, IF_VSITE) == 0,
 859                                  "Virtual sites are not supported by the modular simulator.");
 860     isInputCompatible = isInputCompatible
 861                         && conditionalAssert(!inputrec->bDoAwh,
 862                                              "AWH is not supported by the modular simulator.");
 863     isInputCompatible =
 864             isInputCompatible
 865             && conditionalAssert(gmx_mtop_ftype_count(globalTopology, F_DISRES) == 0,
 866                                  "Distance restraints are not supported by the modular simulator.");
 867     isInputCompatible =
 868             isInputCompatible
 869             && conditionalAssert(
 870                        gmx_mtop_ftype_count(globalTopology, F_ORIRES) == 0,
 871                        "Orientation restraints are not supported by the modular simulator.");
 872     isInputCompatible =
 873             isInputCompatible
 874             && conditionalAssert(ms == nullptr,
 875                                  "Multi-sim are not supported by the modular simulator.");
 876     isInputCompatible =
 877             isInputCompatible
 878             && conditionalAssert(replExParams.exchangeInterval == 0,
 879                                  "Replica exchange is not supported by the modular simulator.");
 880
 881     int numEnsembleRestraintSystems;
 882     if (fcd)
 883     {
 884         numEnsembleRestraintSystems = fcd->disres.nsystems;
 885     }
 886     else
 887     {
 888         auto distantRestraintEnsembleEnvVar = getenv("GMX_DISRE_ENSEMBLE_SIZE");
 889         numEnsembleRestraintSystems =
 890                 (ms != nullptr && distantRestraintEnsembleEnvVar != nullptr)
 891                         ? static_cast<int>(strtol(distantRestraintEnsembleEnvVar, nullptr, 10))
 892                         : 0;
 893     }
 894     isInputCompatible =
 895             isInputCompatible
 896             && conditionalAssert(numEnsembleRestraintSystems <= 1,
 897                                  "Ensemble restraints are not supported by the modular simulator.");
 898     isInputCompatible =
 899             isInputCompatible
 900             && conditionalAssert(!doSimulatedAnnealing(inputrec),
 901                                  "Simulated annealing is not supported by the modular simulator.");
 902     isInputCompatible =
 903             isInputCompatible
 904             && conditionalAssert(!inputrec->bSimTemp,
 905                                  "Simulated tempering is not supported by the modular simulator.");
 906     isInputCompatible = isInputCompatible
 907                         && conditionalAssert(!inputrec->bExpanded,
 908                                              "Expanded ensemble simulations are not supported by "
 909                                              "the modular simulator.");
 910     isInputCompatible =
 911             isInputCompatible
 912             && conditionalAssert(!doEssentialDynamics,
 913                                  "Essential dynamics is not supported by the modular simulator.");
 914     isInputCompatible = isInputCompatible
 915                         && conditionalAssert(inputrec->eSwapCoords == eswapNO,
 916                                              "Ion / water position swapping is not supported by "
 917                                              "the modular simulator.");
 918     isInputCompatible =
 919             isInputCompatible
 920             && conditionalAssert(!inputrec->bIMD,
 921                                  "Interactive MD is not supported by the modular simulator.");
 922     isInputCompatible =
 923             isInputCompatible
 924             && conditionalAssert(!doMembed,
 925                                  "Membrane embedding is not supported by the modular simulator.");
 926     // TODO: Change this to the boolean passed when we merge the user interface change for the GPU update.
 927     isInputCompatible =
 928             isInputCompatible
 929             && conditionalAssert(
 930                        getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") == nullptr,
 931                        "Integration on the GPU is not supported by the modular simulator.");
 932     // Modular simulator is centered around NS updates
 933     // TODO: think how to handle nstlist == 0
 934     isInputCompatible = isInputCompatible
 935                         && conditionalAssert(inputrec->nstlist != 0,
 936                                              "Simulations without neighbor list update are not "
 937                                              "supported by the modular simulator.");
 938     isInputCompatible = isInputCompatible
 939                         && conditionalAssert(!GMX_FAHCORE,
 940                                              "GMX_FAHCORE not supported by the modular simulator.");
 941
 942     return isInputCompatible;
 943 }
 944
 945 void ModularSimulator::checkInputForDisabledFunctionality()
 946 {
 947     isInputCompatible(true, inputrec, doRerun, *top_global, ms, replExParams, fcd,
 948                       opt2bSet("-ei", nfile, fnm), membed != nullptr);
 949     if (observablesHistory->edsamHistory)
 950     {
 951         gmx_fatal(FARGS,
 952                   "The checkpoint is from a run with essential dynamics sampling, "
 953                   "but the current run did not specify the -ei option. "
 954                   "Either specify the -ei option to mdrun, or do not use this checkpoint file.");
 955     }
 956 }
 957
 958 SignallerCallbackPtr ModularSimulator::SignalHelper::registerLastStepCallback()
 959 {
 960     return std::make_unique<SignallerCallback>(
 961             [this](Step step, Time gmx_unused time) { this->lastStep_ = step; });
 962 }
 963
 964 SignallerCallbackPtr ModularSimulator::SignalHelper::registerNSCallback()
 965 {
 966     return std::make_unique<SignallerCallback>(
 967             [this](Step step, Time gmx_unused time) { this->nextNSStep_ = step; });
 968 }
 969 } // namespace gmx