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39 * \brief Implements the MD runner routine calling all integrators.
41 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
42 * \ingroup module_mdrun
59 #include "gromacs/commandline/filenm.h"
60 #include "gromacs/domdec/builder.h"
61 #include "gromacs/domdec/domdec.h"
62 #include "gromacs/domdec/domdec_struct.h"
63 #include "gromacs/domdec/gpuhaloexchange.h"
64 #include "gromacs/domdec/localatomsetmanager.h"
65 #include "gromacs/domdec/partition.h"
66 #include "gromacs/ewald/ewald_utils.h"
67 #include "gromacs/ewald/pme_gpu_program.h"
68 #include "gromacs/ewald/pme_only.h"
69 #include "gromacs/ewald/pme_pp_comm_gpu.h"
70 #include "gromacs/fileio/checkpoint.h"
71 #include "gromacs/fileio/gmxfio.h"
72 #include "gromacs/fileio/oenv.h"
73 #include "gromacs/fileio/tpxio.h"
74 #include "gromacs/gmxlib/network.h"
75 #include "gromacs/gmxlib/nrnb.h"
76 #include "gromacs/gpu_utils/device_context.h"
77 #include "gromacs/gpu_utils/gpu_utils.h"
78 #include "gromacs/hardware/cpuinfo.h"
79 #include "gromacs/hardware/detecthardware.h"
80 #include "gromacs/hardware/printhardware.h"
81 #include "gromacs/imd/imd.h"
82 #include "gromacs/listed_forces/disre.h"
83 #include "gromacs/listed_forces/gpubonded.h"
84 #include "gromacs/listed_forces/orires.h"
85 #include "gromacs/math/functions.h"
86 #include "gromacs/math/utilities.h"
87 #include "gromacs/math/vec.h"
88 #include "gromacs/mdlib/boxdeformation.h"
89 #include "gromacs/mdlib/broadcaststructs.h"
90 #include "gromacs/mdlib/calc_verletbuf.h"
91 #include "gromacs/mdlib/dispersioncorrection.h"
92 #include "gromacs/mdlib/enerdata_utils.h"
93 #include "gromacs/mdlib/force.h"
94 #include "gromacs/mdlib/forcerec.h"
95 #include "gromacs/mdlib/gmx_omp_nthreads.h"
96 #include "gromacs/mdlib/makeconstraints.h"
97 #include "gromacs/mdlib/md_support.h"
98 #include "gromacs/mdlib/mdatoms.h"
99 #include "gromacs/mdlib/membed.h"
100 #include "gromacs/mdlib/sighandler.h"
101 #include "gromacs/mdlib/stophandler.h"
102 #include "gromacs/mdlib/tgroup.h"
103 #include "gromacs/mdlib/updategroups.h"
104 #include "gromacs/mdlib/vsite.h"
105 #include "gromacs/mdrun/mdmodules.h"
106 #include "gromacs/mdrun/simulationcontext.h"
107 #include "gromacs/mdrunutility/handlerestart.h"
108 #include "gromacs/mdrunutility/logging.h"
109 #include "gromacs/mdrunutility/multisim.h"
110 #include "gromacs/mdrunutility/printtime.h"
111 #include "gromacs/mdrunutility/threadaffinity.h"
112 #include "gromacs/mdtypes/commrec.h"
113 #include "gromacs/mdtypes/enerdata.h"
114 #include "gromacs/mdtypes/fcdata.h"
115 #include "gromacs/mdtypes/forcerec.h"
116 #include "gromacs/mdtypes/group.h"
117 #include "gromacs/mdtypes/inputrec.h"
118 #include "gromacs/mdtypes/interaction_const.h"
119 #include "gromacs/mdtypes/md_enums.h"
120 #include "gromacs/mdtypes/mdatom.h"
121 #include "gromacs/mdtypes/mdrunoptions.h"
122 #include "gromacs/mdtypes/observableshistory.h"
123 #include "gromacs/mdtypes/simulation_workload.h"
124 #include "gromacs/mdtypes/state.h"
125 #include "gromacs/mdtypes/state_propagator_data_gpu.h"
126 #include "gromacs/nbnxm/gpu_data_mgmt.h"
127 #include "gromacs/nbnxm/nbnxm.h"
128 #include "gromacs/nbnxm/pairlist_tuning.h"
129 #include "gromacs/pbcutil/pbc.h"
130 #include "gromacs/pulling/output.h"
131 #include "gromacs/pulling/pull.h"
132 #include "gromacs/pulling/pull_rotation.h"
133 #include "gromacs/restraint/manager.h"
134 #include "gromacs/restraint/restraintmdmodule.h"
135 #include "gromacs/restraint/restraintpotential.h"
136 #include "gromacs/swap/swapcoords.h"
137 #include "gromacs/taskassignment/decidegpuusage.h"
138 #include "gromacs/taskassignment/decidesimulationworkload.h"
139 #include "gromacs/taskassignment/resourcedivision.h"
140 #include "gromacs/taskassignment/taskassignment.h"
141 #include "gromacs/taskassignment/usergpuids.h"
142 #include "gromacs/timing/gpu_timing.h"
143 #include "gromacs/timing/wallcycle.h"
144 #include "gromacs/timing/wallcyclereporting.h"
145 #include "gromacs/topology/mtop_util.h"
146 #include "gromacs/trajectory/trajectoryframe.h"
147 #include "gromacs/utility/basenetwork.h"
148 #include "gromacs/utility/cstringutil.h"
149 #include "gromacs/utility/exceptions.h"
150 #include "gromacs/utility/fatalerror.h"
151 #include "gromacs/utility/filestream.h"
152 #include "gromacs/utility/gmxassert.h"
153 #include "gromacs/utility/gmxmpi.h"
154 #include "gromacs/utility/keyvaluetree.h"
155 #include "gromacs/utility/logger.h"
156 #include "gromacs/utility/loggerbuilder.h"
157 #include "gromacs/utility/mdmodulenotification.h"
158 #include "gromacs/utility/physicalnodecommunicator.h"
159 #include "gromacs/utility/pleasecite.h"
160 #include "gromacs/utility/programcontext.h"
161 #include "gromacs/utility/smalloc.h"
162 #include "gromacs/utility/stringutil.h"
164 #include "isimulator.h"
165 #include "replicaexchange.h"
166 #include "simulatorbuilder.h"
169 # include "corewrap.h"
176 /*! \brief Manage any development feature flag variables encountered
178 * The use of dev features indicated by environment variables is
179 * logged in order to ensure that runs with such features enabled can
180 * be identified from their log and standard output. Any cross
181 * dependencies are also checked, and if unsatisfied, a fatal error
184 * Note that some development features overrides are applied already here:
185 * the GPU communication flags are set to false in non-tMPI and non-CUDA builds.
187 * \param[in] mdlog Logger object.
188 * \param[in] useGpuForNonbonded True if the nonbonded task is offloaded in this run.
189 * \param[in] pmeRunMode The PME run mode for this run
190 * \returns The object populated with development feature flags.
192 static DevelopmentFeatureFlags manageDevelopmentFeatures(const gmx::MDLogger& mdlog,
193 const bool useGpuForNonbonded,
194 const PmeRunMode pmeRunMode)
196 DevelopmentFeatureFlags devFlags;
198 // Some builds of GCC 5 give false positive warnings that these
199 // getenv results are ignored when clearly they are used.
200 #pragma GCC diagnostic push
201 #pragma GCC diagnostic ignored "-Wunused-result"
202 devFlags.enableGpuBufferOps = (getenv("GMX_USE_GPU_BUFFER_OPS") != nullptr)
203 && (GMX_GPU == GMX_GPU_CUDA) && useGpuForNonbonded;
204 devFlags.forceGpuUpdateDefault = (getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") != nullptr);
205 devFlags.enableGpuHaloExchange =
206 (getenv("GMX_GPU_DD_COMMS") != nullptr && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA));
207 devFlags.enableGpuPmePPComm =
208 (getenv("GMX_GPU_PME_PP_COMMS") != nullptr && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA));
209 #pragma GCC diagnostic pop
211 if (devFlags.enableGpuBufferOps)
213 GMX_LOG(mdlog.warning)
215 .appendTextFormatted(
216 "This run uses the 'GPU buffer ops' feature, enabled by the "
217 "GMX_USE_GPU_BUFFER_OPS environment variable.");
220 if (devFlags.forceGpuUpdateDefault)
222 GMX_LOG(mdlog.warning)
224 .appendTextFormatted(
225 "This run will default to '-update gpu' as requested by the "
226 "GMX_FORCE_UPDATE_DEFAULT_GPU environment variable. GPU update with domain "
227 "decomposition lacks substantial testing and should be used with caution.");
230 if (devFlags.enableGpuHaloExchange)
232 if (useGpuForNonbonded)
234 if (!devFlags.enableGpuBufferOps)
236 GMX_LOG(mdlog.warning)
238 .appendTextFormatted(
239 "Enabling GPU buffer operations required by GMX_GPU_DD_COMMS "
240 "(equivalent with GMX_USE_GPU_BUFFER_OPS=1).");
241 devFlags.enableGpuBufferOps = true;
243 GMX_LOG(mdlog.warning)
245 .appendTextFormatted(
246 "This run has requested the 'GPU halo exchange' feature, enabled by "
248 "GMX_GPU_DD_COMMS environment variable.");
252 GMX_LOG(mdlog.warning)
254 .appendTextFormatted(
255 "GMX_GPU_DD_COMMS environment variable detected, but the 'GPU "
256 "halo exchange' feature will not be enabled as nonbonded interactions "
257 "are not offloaded.");
258 devFlags.enableGpuHaloExchange = false;
262 if (devFlags.enableGpuPmePPComm)
264 if (pmeRunMode == PmeRunMode::GPU)
266 GMX_LOG(mdlog.warning)
268 .appendTextFormatted(
269 "This run uses the 'GPU PME-PP communications' feature, enabled "
270 "by the GMX_GPU_PME_PP_COMMS environment variable.");
274 std::string clarification;
275 if (pmeRunMode == PmeRunMode::Mixed)
278 "PME FFT and gather are not offloaded to the GPU (PME is running in mixed "
283 clarification = "PME is not offloaded to the GPU.";
285 GMX_LOG(mdlog.warning)
288 "GMX_GPU_PME_PP_COMMS environment variable detected, but the "
289 "'GPU PME-PP communications' feature was not enabled as "
291 devFlags.enableGpuPmePPComm = false;
298 /*! \brief Barrier for safe simultaneous thread access to mdrunner data
300 * Used to ensure that the master thread does not modify mdrunner during copy
301 * on the spawned threads. */
302 static void threadMpiMdrunnerAccessBarrier()
305 MPI_Barrier(MPI_COMM_WORLD);
309 Mdrunner Mdrunner::cloneOnSpawnedThread() const
311 auto newRunner = Mdrunner(std::make_unique<MDModules>());
313 // All runners in the same process share a restraint manager resource because it is
314 // part of the interface to the client code, which is associated only with the
315 // original thread. Handles to the same resources can be obtained by copy.
317 newRunner.restraintManager_ = std::make_unique<RestraintManager>(*restraintManager_);
320 // Copy members of master runner.
321 // \todo Replace with builder when Simulation context and/or runner phases are better defined.
322 // Ref https://redmine.gromacs.org/issues/2587 and https://redmine.gromacs.org/issues/2375
323 newRunner.hw_opt = hw_opt;
324 newRunner.filenames = filenames;
326 newRunner.oenv = oenv;
327 newRunner.mdrunOptions = mdrunOptions;
328 newRunner.domdecOptions = domdecOptions;
329 newRunner.nbpu_opt = nbpu_opt;
330 newRunner.pme_opt = pme_opt;
331 newRunner.pme_fft_opt = pme_fft_opt;
332 newRunner.bonded_opt = bonded_opt;
333 newRunner.update_opt = update_opt;
334 newRunner.nstlist_cmdline = nstlist_cmdline;
335 newRunner.replExParams = replExParams;
336 newRunner.pforce = pforce;
337 // Give the spawned thread the newly created valid communicator
338 // for the simulation.
339 newRunner.communicator = MPI_COMM_WORLD;
341 newRunner.startingBehavior = startingBehavior;
342 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>(*stopHandlerBuilder_);
344 threadMpiMdrunnerAccessBarrier();
349 /*! \brief The callback used for running on spawned threads.
351 * Obtains the pointer to the master mdrunner object from the one
352 * argument permitted to the thread-launch API call, copies it to make
353 * a new runner for this thread, reinitializes necessary data, and
354 * proceeds to the simulation. */
355 static void mdrunner_start_fn(const void* arg)
359 auto masterMdrunner = reinterpret_cast<const gmx::Mdrunner*>(arg);
360 /* copy the arg list to make sure that it's thread-local. This
361 doesn't copy pointed-to items, of course; fnm, cr and fplog
362 are reset in the call below, all others should be const. */
363 gmx::Mdrunner mdrunner = masterMdrunner->cloneOnSpawnedThread();
366 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
370 void Mdrunner::spawnThreads(int numThreadsToLaunch)
373 /* now spawn new threads that start mdrunner_start_fn(), while
374 the main thread returns. Thread affinity is handled later. */
375 if (tMPI_Init_fn(TRUE, numThreadsToLaunch, TMPI_AFFINITY_NONE, mdrunner_start_fn,
376 static_cast<const void*>(this))
379 GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
382 // Give the master thread the newly created valid communicator for
384 communicator = MPI_COMM_WORLD;
385 threadMpiMdrunnerAccessBarrier();
387 GMX_UNUSED_VALUE(numThreadsToLaunch);
388 GMX_UNUSED_VALUE(mdrunner_start_fn);
394 /*! \brief Initialize variables for Verlet scheme simulation */
395 static void prepare_verlet_scheme(FILE* fplog,
399 const gmx_mtop_t* mtop,
401 bool makeGpuPairList,
402 const gmx::CpuInfo& cpuinfo)
404 // We checked the cut-offs in grompp, but double-check here.
405 // We have PME+LJcutoff kernels for rcoulomb>rvdw.
406 if (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == eelCUT)
408 GMX_RELEASE_ASSERT(ir->rcoulomb >= ir->rvdw,
409 "With Verlet lists and PME we should have rcoulomb>=rvdw");
413 GMX_RELEASE_ASSERT(ir->rcoulomb == ir->rvdw,
414 "With Verlet lists and no PME rcoulomb and rvdw should be identical");
416 /* For NVE simulations, we will retain the initial list buffer */
417 if (EI_DYNAMICS(ir->eI) && ir->verletbuf_tol > 0 && !(EI_MD(ir->eI) && ir->etc == etcNO))
419 /* Update the Verlet buffer size for the current run setup */
421 /* Here we assume SIMD-enabled kernels are being used. But as currently
422 * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
423 * and 4x2 gives a larger buffer than 4x4, this is ok.
425 ListSetupType listType =
426 (makeGpuPairList ? ListSetupType::Gpu : ListSetupType::CpuSimdWhenSupported);
427 VerletbufListSetup listSetup = verletbufGetSafeListSetup(listType);
429 const real rlist_new =
430 calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
432 if (rlist_new != ir->rlist)
434 if (fplog != nullptr)
437 "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
438 ir->rlist, rlist_new, listSetup.cluster_size_i, listSetup.cluster_size_j);
440 ir->rlist = rlist_new;
444 if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
446 gmx_fatal(FARGS, "Can not set nstlist without %s",
447 !EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
450 if (EI_DYNAMICS(ir->eI))
452 /* Set or try nstlist values */
453 increaseNstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, makeGpuPairList, cpuinfo);
457 /*! \brief Override the nslist value in inputrec
459 * with value passed on the command line (if any)
461 static void override_nsteps_cmdline(const gmx::MDLogger& mdlog, int64_t nsteps_cmdline, t_inputrec* ir)
465 /* override with anything else than the default -2 */
466 if (nsteps_cmdline > -2)
468 char sbuf_steps[STEPSTRSIZE];
469 char sbuf_msg[STRLEN];
471 ir->nsteps = nsteps_cmdline;
472 if (EI_DYNAMICS(ir->eI) && nsteps_cmdline != -1)
475 "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
476 gmx_step_str(nsteps_cmdline, sbuf_steps), fabs(nsteps_cmdline * ir->delta_t));
480 sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps",
481 gmx_step_str(nsteps_cmdline, sbuf_steps));
484 GMX_LOG(mdlog.warning).asParagraph().appendText(sbuf_msg);
486 else if (nsteps_cmdline < -2)
488 gmx_fatal(FARGS, "Invalid nsteps value passed on the command line: %" PRId64, nsteps_cmdline);
490 /* Do nothing if nsteps_cmdline == -2 */
496 /*! \brief Return whether GPU acceleration of nonbondeds is supported with the given settings.
498 * If not, and if a warning may be issued, logs a warning about
499 * falling back to CPU code. With thread-MPI, only the first
500 * call to this function should have \c issueWarning true. */
501 static bool gpuAccelerationOfNonbondedIsUseful(const MDLogger& mdlog, const t_inputrec& ir, bool issueWarning)
503 bool gpuIsUseful = true;
506 if (ir.opts.ngener - ir.nwall > 1)
508 /* The GPU code does not support more than one energy group.
509 * If the user requested GPUs explicitly, a fatal error is given later.
513 "Multiple energy groups is not implemented for GPUs, falling back to the CPU. "
514 "For better performance, run on the GPU without energy groups and then do "
515 "gmx mdrun -rerun option on the trajectory with an energy group .tpr file.";
521 warning = "TPI is not implemented for GPUs.";
524 if (!gpuIsUseful && issueWarning)
526 GMX_LOG(mdlog.warning).asParagraph().appendText(warning);
532 //! Initializes the logger for mdrun.
533 static gmx::LoggerOwner buildLogger(FILE* fplog, const bool isSimulationMasterRank)
535 gmx::LoggerBuilder builder;
536 if (fplog != nullptr)
538 builder.addTargetFile(gmx::MDLogger::LogLevel::Info, fplog);
540 if (isSimulationMasterRank)
542 builder.addTargetStream(gmx::MDLogger::LogLevel::Warning, &gmx::TextOutputFile::standardError());
544 return builder.build();
547 //! Make a TaskTarget from an mdrun argument string.
548 static TaskTarget findTaskTarget(const char* optionString)
550 TaskTarget returnValue = TaskTarget::Auto;
552 if (strncmp(optionString, "auto", 3) == 0)
554 returnValue = TaskTarget::Auto;
556 else if (strncmp(optionString, "cpu", 3) == 0)
558 returnValue = TaskTarget::Cpu;
560 else if (strncmp(optionString, "gpu", 3) == 0)
562 returnValue = TaskTarget::Gpu;
566 GMX_ASSERT(false, "Option string should have been checked for sanity already");
572 //! Finish run, aggregate data to print performance info.
573 static void finish_run(FILE* fplog,
574 const gmx::MDLogger& mdlog,
576 const t_inputrec* inputrec,
578 gmx_wallcycle_t wcycle,
579 gmx_walltime_accounting_t walltime_accounting,
580 nonbonded_verlet_t* nbv,
581 const gmx_pme_t* pme,
585 double nbfs = 0, mflop = 0;
586 double elapsed_time, elapsed_time_over_all_ranks, elapsed_time_over_all_threads,
587 elapsed_time_over_all_threads_over_all_ranks;
588 /* Control whether it is valid to print a report. Only the
589 simulation master may print, but it should not do so if the run
590 terminated e.g. before a scheduled reset step. This is
591 complicated by the fact that PME ranks are unaware of the
592 reason why they were sent a pmerecvqxFINISH. To avoid
593 communication deadlocks, we always do the communication for the
594 report, even if we've decided not to write the report, because
595 how long it takes to finish the run is not important when we've
596 decided not to report on the simulation performance.
598 Further, we only report performance for dynamical integrators,
599 because those are the only ones for which we plan to
600 consider doing any optimizations. */
601 bool printReport = EI_DYNAMICS(inputrec->eI) && SIMMASTER(cr);
603 if (printReport && !walltime_accounting_get_valid_finish(walltime_accounting))
605 GMX_LOG(mdlog.warning)
607 .appendText("Simulation ended prematurely, no performance report will be written.");
612 std::unique_ptr<t_nrnb> nrnbTotalStorage;
615 nrnbTotalStorage = std::make_unique<t_nrnb>();
616 nrnb_tot = nrnbTotalStorage.get();
618 MPI_Allreduce(nrnb->n, nrnb_tot->n, eNRNB, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
626 elapsed_time = walltime_accounting_get_time_since_reset(walltime_accounting);
627 elapsed_time_over_all_threads =
628 walltime_accounting_get_time_since_reset_over_all_threads(walltime_accounting);
632 /* reduce elapsed_time over all MPI ranks in the current simulation */
633 MPI_Allreduce(&elapsed_time, &elapsed_time_over_all_ranks, 1, MPI_DOUBLE, MPI_SUM,
635 elapsed_time_over_all_ranks /= cr->nnodes;
636 /* Reduce elapsed_time_over_all_threads over all MPI ranks in the
637 * current simulation. */
638 MPI_Allreduce(&elapsed_time_over_all_threads, &elapsed_time_over_all_threads_over_all_ranks,
639 1, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
644 elapsed_time_over_all_ranks = elapsed_time;
645 elapsed_time_over_all_threads_over_all_ranks = elapsed_time_over_all_threads;
650 print_flop(fplog, nrnb_tot, &nbfs, &mflop);
653 if (thisRankHasDuty(cr, DUTY_PP) && DOMAINDECOMP(cr))
655 print_dd_statistics(cr, inputrec, fplog);
658 /* TODO Move the responsibility for any scaling by thread counts
659 * to the code that handled the thread region, so that there's a
660 * mechanism to keep cycle counting working during the transition
661 * to task parallelism. */
662 int nthreads_pp = gmx_omp_nthreads_get(emntNonbonded);
663 int nthreads_pme = gmx_omp_nthreads_get(emntPME);
664 wallcycle_scale_by_num_threads(wcycle, thisRankHasDuty(cr, DUTY_PME) && !thisRankHasDuty(cr, DUTY_PP),
665 nthreads_pp, nthreads_pme);
666 auto cycle_sum(wallcycle_sum(cr, wcycle));
670 auto nbnxn_gpu_timings =
671 (nbv != nullptr && nbv->useGpu()) ? Nbnxm::gpu_get_timings(nbv->gpu_nbv) : nullptr;
672 gmx_wallclock_gpu_pme_t pme_gpu_timings = {};
674 if (pme_gpu_task_enabled(pme))
676 pme_gpu_get_timings(pme, &pme_gpu_timings);
678 wallcycle_print(fplog, mdlog, cr->nnodes, cr->npmenodes, nthreads_pp, nthreads_pme,
679 elapsed_time_over_all_ranks, wcycle, cycle_sum, nbnxn_gpu_timings,
682 if (EI_DYNAMICS(inputrec->eI))
684 delta_t = inputrec->delta_t;
689 print_perf(fplog, elapsed_time_over_all_threads_over_all_ranks, elapsed_time_over_all_ranks,
690 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
691 delta_t, nbfs, mflop);
695 print_perf(stderr, elapsed_time_over_all_threads_over_all_ranks, elapsed_time_over_all_ranks,
696 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
697 delta_t, nbfs, mflop);
702 int Mdrunner::mdrunner()
705 t_forcerec* fr = nullptr;
706 t_fcdata* fcd = nullptr;
707 real ewaldcoeff_q = 0;
708 real ewaldcoeff_lj = 0;
709 int nChargePerturbed = -1, nTypePerturbed = 0;
710 gmx_wallcycle_t wcycle;
711 gmx_walltime_accounting_t walltime_accounting = nullptr;
712 gmx_membed_t* membed = nullptr;
713 gmx_hw_info_t* hwinfo = nullptr;
715 /* CAUTION: threads may be started later on in this function, so
716 cr doesn't reflect the final parallel state right now */
719 /* TODO: inputrec should tell us whether we use an algorithm, not a file option */
720 const bool doEssentialDynamics = opt2bSet("-ei", filenames.size(), filenames.data());
721 const bool doMembed = opt2bSet("-membed", filenames.size(), filenames.data());
722 const bool doRerun = mdrunOptions.rerun;
724 // Handle task-assignment related user options.
725 EmulateGpuNonbonded emulateGpuNonbonded =
726 (getenv("GMX_EMULATE_GPU") != nullptr ? EmulateGpuNonbonded::Yes : EmulateGpuNonbonded::No);
728 std::vector<int> userGpuTaskAssignment;
731 userGpuTaskAssignment = parseUserTaskAssignmentString(hw_opt.userGpuTaskAssignment);
733 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
734 auto nonbondedTarget = findTaskTarget(nbpu_opt);
735 auto pmeTarget = findTaskTarget(pme_opt);
736 auto pmeFftTarget = findTaskTarget(pme_fft_opt);
737 auto bondedTarget = findTaskTarget(bonded_opt);
738 auto updateTarget = findTaskTarget(update_opt);
740 FILE* fplog = nullptr;
741 // If we are appending, we don't write log output because we need
742 // to check that the old log file matches what the checkpoint file
743 // expects. Otherwise, we should start to write log output now if
744 // there is a file ready for it.
745 if (logFileHandle != nullptr && startingBehavior != StartingBehavior::RestartWithAppending)
747 fplog = gmx_fio_getfp(logFileHandle);
749 const bool isSimulationMasterRank = findIsSimulationMasterRank(ms, communicator);
750 gmx::LoggerOwner logOwner(buildLogger(fplog, isSimulationMasterRank));
751 gmx::MDLogger mdlog(logOwner.logger());
753 // TODO The thread-MPI master rank makes a working
754 // PhysicalNodeCommunicator here, but it gets rebuilt by all ranks
755 // after the threads have been launched. This works because no use
756 // is made of that communicator until after the execution paths
757 // have rejoined. But it is likely that we can improve the way
758 // this is expressed, e.g. by expressly running detection only the
759 // master rank for thread-MPI, rather than relying on the mutex
760 // and reference count.
761 PhysicalNodeCommunicator physicalNodeComm(communicator, gmx_physicalnode_id_hash());
762 hwinfo = gmx_detect_hardware(mdlog, physicalNodeComm);
764 gmx_print_detected_hardware(fplog, isSimulationMasterRank && isMasterSim(ms), mdlog, hwinfo);
766 std::vector<int> gpuIdsToUse = makeGpuIdsToUse(hwinfo->gpu_info, hw_opt.gpuIdsAvailable);
768 // Print citation requests after all software/hardware printing
769 pleaseCiteGromacs(fplog);
771 // TODO Replace this by unique_ptr once t_inputrec is C++
772 t_inputrec inputrecInstance;
773 t_inputrec* inputrec = nullptr;
774 std::unique_ptr<t_state> globalState;
776 auto partialDeserializedTpr = std::make_unique<PartialDeserializedTprFile>();
778 if (isSimulationMasterRank)
780 /* Only the master rank has the global state */
781 globalState = std::make_unique<t_state>();
783 /* Read (nearly) all data required for the simulation
784 * and keep the partly serialized tpr contents to send to other ranks later
786 *partialDeserializedTpr = read_tpx_state(ftp2fn(efTPR, filenames.size(), filenames.data()),
787 &inputrecInstance, globalState.get(), &mtop);
788 inputrec = &inputrecInstance;
791 /* Check and update the hardware options for internal consistency */
792 checkAndUpdateHardwareOptions(mdlog, &hw_opt, isSimulationMasterRank, domdecOptions.numPmeRanks,
795 if (GMX_THREAD_MPI && isSimulationMasterRank)
797 bool useGpuForNonbonded = false;
798 bool useGpuForPme = false;
801 GMX_RELEASE_ASSERT(inputrec != nullptr, "Keep the compiler happy");
803 // If the user specified the number of ranks, then we must
804 // respect that, but in default mode, we need to allow for
805 // the number of GPUs to choose the number of ranks.
806 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
807 useGpuForNonbonded = decideWhetherToUseGpusForNonbondedWithThreadMpi(
808 nonbondedTarget, gpuIdsToUse, userGpuTaskAssignment, emulateGpuNonbonded,
809 canUseGpuForNonbonded,
810 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, GMX_THREAD_MPI),
811 hw_opt.nthreads_tmpi);
812 useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi(
813 useGpuForNonbonded, pmeTarget, gpuIdsToUse, userGpuTaskAssignment, *hwinfo,
814 *inputrec, mtop, hw_opt.nthreads_tmpi, domdecOptions.numPmeRanks);
816 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
818 /* Determine how many thread-MPI ranks to start.
820 * TODO Over-writing the user-supplied value here does
821 * prevent any possible subsequent checks from working
823 hw_opt.nthreads_tmpi = get_nthreads_mpi(hwinfo, &hw_opt, gpuIdsToUse, useGpuForNonbonded,
824 useGpuForPme, inputrec, &mtop, mdlog, doMembed);
826 // Now start the threads for thread MPI.
827 spawnThreads(hw_opt.nthreads_tmpi);
828 // The spawned threads enter mdrunner() and execution of
829 // master and spawned threads joins at the end of this block.
830 physicalNodeComm = PhysicalNodeCommunicator(communicator, gmx_physicalnode_id_hash());
833 GMX_RELEASE_ASSERT(communicator == MPI_COMM_WORLD, "Must have valid world communicator");
834 CommrecHandle crHandle = init_commrec(communicator, ms);
835 t_commrec* cr = crHandle.get();
836 GMX_RELEASE_ASSERT(cr != nullptr, "Must have valid commrec");
840 /* now broadcast everything to the non-master nodes/threads: */
841 if (!isSimulationMasterRank)
843 inputrec = &inputrecInstance;
845 init_parallel(cr, inputrec, &mtop, partialDeserializedTpr.get());
847 GMX_RELEASE_ASSERT(inputrec != nullptr, "All ranks should have a valid inputrec now");
848 partialDeserializedTpr.reset(nullptr);
850 // Now the number of ranks is known to all ranks, and each knows
851 // the inputrec read by the master rank. The ranks can now all run
852 // the task-deciding functions and will agree on the result
853 // without needing to communicate.
854 const bool useDomainDecomposition = (PAR(cr) && !(EI_TPI(inputrec->eI) || inputrec->eI == eiNM));
856 // Note that these variables describe only their own node.
858 // Note that when bonded interactions run on a GPU they always run
859 // alongside a nonbonded task, so do not influence task assignment
860 // even though they affect the force calculation workload.
861 bool useGpuForNonbonded = false;
862 bool useGpuForPme = false;
863 bool useGpuForBonded = false;
864 bool useGpuForUpdate = false;
865 bool gpusWereDetected = hwinfo->ngpu_compatible_tot > 0;
868 // It's possible that there are different numbers of GPUs on
869 // different nodes, which is the user's responsibility to
870 // handle. If unsuitable, we will notice that during task
872 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
873 useGpuForNonbonded = decideWhetherToUseGpusForNonbonded(
874 nonbondedTarget, userGpuTaskAssignment, emulateGpuNonbonded, canUseGpuForNonbonded,
875 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, !GMX_THREAD_MPI), gpusWereDetected);
876 useGpuForPme = decideWhetherToUseGpusForPme(
877 useGpuForNonbonded, pmeTarget, userGpuTaskAssignment, *hwinfo, *inputrec, mtop,
878 cr->nnodes, domdecOptions.numPmeRanks, gpusWereDetected);
879 auto canUseGpuForBonded = buildSupportsGpuBondeds(nullptr)
880 && inputSupportsGpuBondeds(*inputrec, mtop, nullptr);
881 useGpuForBonded = decideWhetherToUseGpusForBonded(
882 useGpuForNonbonded, useGpuForPme, bondedTarget, canUseGpuForBonded,
883 EVDW_PME(inputrec->vdwtype), EEL_PME_EWALD(inputrec->coulombtype),
884 domdecOptions.numPmeRanks, gpusWereDetected);
886 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
888 const PmeRunMode pmeRunMode = determinePmeRunMode(useGpuForPme, pmeFftTarget, *inputrec);
890 // Initialize development feature flags that enabled by environment variable
891 // and report those features that are enabled.
892 const DevelopmentFeatureFlags devFlags =
893 manageDevelopmentFeatures(mdlog, useGpuForNonbonded, pmeRunMode);
895 const bool useModularSimulator = checkUseModularSimulator(
896 false, inputrec, doRerun, mtop, ms, replExParams, nullptr, doEssentialDynamics, doMembed);
899 // TODO: hide restraint implementation details from Mdrunner.
900 // There is nothing unique about restraints at this point as far as the
901 // Mdrunner is concerned. The Mdrunner should just be getting a sequence of
902 // factory functions from the SimulationContext on which to call mdModules_->add().
903 // TODO: capture all restraints into a single RestraintModule, passed to the runner builder.
904 for (auto&& restraint : restraintManager_->getRestraints())
906 auto module = RestraintMDModule::create(restraint, restraint->sites());
907 mdModules_->add(std::move(module));
910 // TODO: Error handling
911 mdModules_->assignOptionsToModules(*inputrec->params, nullptr);
912 // now that the MdModules know their options, they know which callbacks to sign up to
913 mdModules_->subscribeToSimulationSetupNotifications();
914 const auto& mdModulesNotifier = mdModules_->notifier().simulationSetupNotifications_;
916 if (inputrec->internalParameters != nullptr)
918 mdModulesNotifier.notify(*inputrec->internalParameters);
921 if (fplog != nullptr)
923 pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
924 fprintf(fplog, "\n");
929 /* In rerun, set velocities to zero if present */
930 if (doRerun && ((globalState->flags & (1 << estV)) != 0))
932 // rerun does not use velocities
936 "Rerun trajectory contains velocities. Rerun does only evaluate "
937 "potential energy and forces. The velocities will be ignored.");
938 for (int i = 0; i < globalState->natoms; i++)
940 clear_rvec(globalState->v[i]);
942 globalState->flags &= ~(1 << estV);
945 /* now make sure the state is initialized and propagated */
946 set_state_entries(globalState.get(), inputrec, useModularSimulator);
949 /* NM and TPI parallelize over force/energy calculations, not atoms,
950 * so we need to initialize and broadcast the global state.
952 if (inputrec->eI == eiNM || inputrec->eI == eiTPI)
956 globalState = std::make_unique<t_state>();
958 broadcastStateWithoutDynamics(cr, globalState.get());
961 /* A parallel command line option consistency check that we can
962 only do after any threads have started. */
964 && (domdecOptions.numCells[XX] > 1 || domdecOptions.numCells[YY] > 1
965 || domdecOptions.numCells[ZZ] > 1 || domdecOptions.numPmeRanks > 0))
968 "The -dd or -npme option request a parallel simulation, "
970 "but %s was compiled without threads or MPI enabled",
971 output_env_get_program_display_name(oenv));
973 "but the number of MPI-threads (option -ntmpi) is not set or is 1");
975 "but %s was not started through mpirun/mpiexec or only one rank was requested "
976 "through mpirun/mpiexec",
977 output_env_get_program_display_name(oenv));
981 if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
984 "The .mdp file specified an energy mininization or normal mode algorithm, and "
985 "these are not compatible with mdrun -rerun");
988 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
990 if (domdecOptions.numPmeRanks > 0)
992 gmx_fatal_collective(FARGS, cr->mpi_comm_mysim, MASTER(cr),
993 "PME-only ranks are requested, but the system does not use PME "
994 "for electrostatics or LJ");
997 domdecOptions.numPmeRanks = 0;
1000 if (useGpuForNonbonded && domdecOptions.numPmeRanks < 0)
1002 /* With NB GPUs we don't automatically use PME-only CPU ranks. PME ranks can
1003 * improve performance with many threads per GPU, since our OpenMP
1004 * scaling is bad, but it's difficult to automate the setup.
1006 domdecOptions.numPmeRanks = 0;
1010 if (domdecOptions.numPmeRanks < 0)
1012 domdecOptions.numPmeRanks = 0;
1013 // TODO possibly print a note that one can opt-in for a separate PME GPU rank?
1017 GMX_RELEASE_ASSERT(domdecOptions.numPmeRanks <= 1,
1018 "PME GPU decomposition is not supported");
1025 fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
1029 /* NMR restraints must be initialized before load_checkpoint,
1030 * since with time averaging the history is added to t_state.
1031 * For proper consistency check we therefore need to extend
1033 * So the PME-only nodes (if present) will also initialize
1034 * the distance restraints.
1038 /* This needs to be called before read_checkpoint to extend the state */
1039 init_disres(fplog, &mtop, inputrec, cr, ms, fcd, globalState.get(), replExParams.exchangeInterval > 0);
1041 init_orires(fplog, &mtop, inputrec, cr, ms, globalState.get(), &(fcd->orires));
1043 auto deform = prepareBoxDeformation(globalState->box, cr, *inputrec);
1045 ObservablesHistory observablesHistory = {};
1047 if (startingBehavior != StartingBehavior::NewSimulation)
1049 /* Check if checkpoint file exists before doing continuation.
1050 * This way we can use identical input options for the first and subsequent runs...
1052 if (mdrunOptions.numStepsCommandline > -2)
1054 /* Temporarily set the number of steps to unlimited to avoid
1055 * triggering the nsteps check in load_checkpoint().
1056 * This hack will go away soon when the -nsteps option is removed.
1058 inputrec->nsteps = -1;
1061 load_checkpoint(opt2fn_master("-cpi", filenames.size(), filenames.data(), cr),
1062 logFileHandle, cr, domdecOptions.numCells, inputrec, globalState.get(),
1063 &observablesHistory, mdrunOptions.reproducible, mdModules_->notifier());
1065 if (startingBehavior == StartingBehavior::RestartWithAppending && logFileHandle)
1067 // Now we can start normal logging to the truncated log file.
1068 fplog = gmx_fio_getfp(logFileHandle);
1069 prepareLogAppending(fplog);
1070 logOwner = buildLogger(fplog, MASTER(cr));
1071 mdlog = logOwner.logger();
1075 if (mdrunOptions.numStepsCommandline > -2)
1080 "The -nsteps functionality is deprecated, and may be removed in a future "
1082 "Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp "
1085 /* override nsteps with value set on the commandline */
1086 override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec);
1090 copy_mat(globalState->box, box);
1095 gmx_bcast(sizeof(box), box, cr);
1098 if (inputrec->cutoff_scheme != ecutsVERLET)
1101 "This group-scheme .tpr file can no longer be run by mdrun. Please update to the "
1102 "Verlet scheme, or use an earlier version of GROMACS if necessary.");
1104 /* Update rlist and nstlist. */
1105 prepare_verlet_scheme(fplog, cr, inputrec, nstlist_cmdline, &mtop, box,
1106 useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes),
1109 const bool prefer1DAnd1PulseDD = (devFlags.enableGpuHaloExchange && useGpuForNonbonded);
1110 // This builder is necessary while we have multi-part construction
1111 // of DD. Before DD is constructed, we use the existence of
1112 // the builder object to indicate that further construction of DD
1114 std::unique_ptr<DomainDecompositionBuilder> ddBuilder;
1115 if (useDomainDecomposition)
1117 ddBuilder = std::make_unique<DomainDecompositionBuilder>(
1118 mdlog, cr, domdecOptions, mdrunOptions, prefer1DAnd1PulseDD, mtop, *inputrec, box,
1119 positionsFromStatePointer(globalState.get()));
1123 /* PME, if used, is done on all nodes with 1D decomposition */
1125 cr->duty = (DUTY_PP | DUTY_PME);
1127 if (inputrec->pbcType == PbcType::Screw)
1129 gmx_fatal(FARGS, "pbc=screw is only implemented with domain decomposition");
1133 // Produce the task assignment for this rank.
1134 GpuTaskAssignmentsBuilder gpuTaskAssignmentsBuilder;
1135 GpuTaskAssignments gpuTaskAssignments = gpuTaskAssignmentsBuilder.build(
1136 gpuIdsToUse, userGpuTaskAssignment, *hwinfo, communicator, physicalNodeComm,
1137 nonbondedTarget, pmeTarget, bondedTarget, updateTarget, useGpuForNonbonded,
1138 useGpuForPme, thisRankHasDuty(cr, DUTY_PP),
1139 // TODO cr->duty & DUTY_PME should imply that a PME
1140 // algorithm is active, but currently does not.
1141 EEL_PME(inputrec->coulombtype) && thisRankHasDuty(cr, DUTY_PME));
1143 // Get the device handles for the modules, nullptr when no task is assigned.
1145 DeviceInformation* deviceInfo = gpuTaskAssignments.initDevice(&deviceId);
1146 std::unique_ptr<DeviceContext> deviceContext = nullptr;
1147 if (deviceInfo != nullptr)
1149 if (DOMAINDECOMP(cr) && thisRankHasDuty(cr, DUTY_PP))
1151 dd_setup_dlb_resource_sharing(cr, deviceId);
1153 deviceContext = std::make_unique<DeviceContext>(*deviceInfo);
1156 // TODO Initialize GPU streams here.
1158 // TODO Currently this is always built, yet DD partition code
1159 // checks if it is built before using it. Probably it should
1160 // become an MDModule that is made only when another module
1161 // requires it (e.g. pull, CompEl, density fitting), so that we
1162 // don't update the local atom sets unilaterally every step.
1163 LocalAtomSetManager atomSets;
1166 // TODO Pass the GPU streams to ddBuilder to use in buffer
1167 // transfers (e.g. halo exchange)
1168 cr->dd = ddBuilder->build(&atomSets);
1169 // The builder's job is done, so destruct it
1170 ddBuilder.reset(nullptr);
1171 // Note that local state still does not exist yet.
1174 // The GPU update is decided here because we need to know whether the constraints or
1175 // SETTLEs can span accross the domain borders (i.e. whether or not update groups are
1176 // defined). This is only known after DD is initialized, hence decision on using GPU
1177 // update is done so late.
1180 const bool useUpdateGroups = cr->dd ? ddUsesUpdateGroups(*cr->dd) : false;
1182 useGpuForUpdate = decideWhetherToUseGpuForUpdate(
1183 useDomainDecomposition, useUpdateGroups, pmeRunMode, domdecOptions.numPmeRanks > 0,
1184 useGpuForNonbonded, updateTarget, gpusWereDetected, *inputrec, mtop,
1185 doEssentialDynamics, gmx_mtop_ftype_count(mtop, F_ORIRES) > 0,
1186 replExParams.exchangeInterval > 0, doRerun, devFlags, mdlog);
1188 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1190 const bool printHostName = (cr->nnodes > 1);
1191 gpuTaskAssignments.reportGpuUsage(mdlog, printHostName, useGpuForBonded, pmeRunMode, useGpuForUpdate);
1193 // If the user chose a task assignment, give them some hints
1194 // where appropriate.
1195 if (!userGpuTaskAssignment.empty())
1197 gpuTaskAssignments.logPerformanceHints(mdlog, ssize(gpuIdsToUse));
1202 /* After possible communicator splitting in make_dd_communicators.
1203 * we can set up the intra/inter node communication.
1205 gmx_setup_nodecomm(fplog, cr);
1211 GMX_LOG(mdlog.warning)
1213 .appendTextFormatted(
1214 "This is simulation %d out of %d running as a composite GROMACS\n"
1215 "multi-simulation job. Setup for this simulation:\n",
1218 GMX_LOG(mdlog.warning)
1219 .appendTextFormatted("Using %d MPI %s\n", cr->nnodes,
1221 cr->nnodes == 1 ? "thread" : "threads"
1223 cr->nnodes == 1 ? "process" : "processes"
1229 // If mdrun -pin auto honors any affinity setting that already
1230 // exists. If so, it is nice to provide feedback about whether
1231 // that existing affinity setting was from OpenMP or something
1232 // else, so we run this code both before and after we initialize
1233 // the OpenMP support.
1234 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo->nthreads_hw_avail, FALSE);
1235 /* Check and update the number of OpenMP threads requested */
1236 checkAndUpdateRequestedNumOpenmpThreads(&hw_opt, *hwinfo, cr, ms, physicalNodeComm.size_,
1237 pmeRunMode, mtop, *inputrec);
1239 gmx_omp_nthreads_init(mdlog, cr, hwinfo->nthreads_hw_avail, physicalNodeComm.size_,
1240 hw_opt.nthreads_omp, hw_opt.nthreads_omp_pme, !thisRankHasDuty(cr, DUTY_PP));
1242 // Enable FP exception detection, but not in
1243 // Release mode and not for compilers with known buggy FP
1244 // exception support (clang with any optimization) or suspected
1245 // buggy FP exception support (gcc 7.* with optimization).
1246 #if !defined NDEBUG \
1247 && !((defined __clang__ || (defined(__GNUC__) && !defined(__ICC) && __GNUC__ == 7)) \
1248 && defined __OPTIMIZE__)
1249 const bool bEnableFPE = true;
1251 const bool bEnableFPE = false;
1253 // FIXME - reconcile with gmx_feenableexcept() call from CommandLineModuleManager::run()
1256 gmx_feenableexcept();
1259 /* Now that we know the setup is consistent, check for efficiency */
1260 check_resource_division_efficiency(hwinfo, gpuTaskAssignments.thisRankHasAnyGpuTask(),
1261 mdrunOptions.ntompOptionIsSet, cr, mdlog);
1263 /* getting number of PP/PME threads on this MPI / tMPI rank.
1264 PME: env variable should be read only on one node to make sure it is
1265 identical everywhere;
1267 const int numThreadsOnThisRank = thisRankHasDuty(cr, DUTY_PP) ? gmx_omp_nthreads_get(emntNonbonded)
1268 : gmx_omp_nthreads_get(emntPME);
1269 checkHardwareOversubscription(numThreadsOnThisRank, cr->nodeid, *hwinfo->hardwareTopology,
1270 physicalNodeComm, mdlog);
1272 // Enable Peer access between GPUs where available
1273 // Only for DD, only master PP rank needs to perform setup, and only if thread MPI plus
1274 // any of the GPU communication features are active.
1275 if (DOMAINDECOMP(cr) && MASTER(cr) && thisRankHasDuty(cr, DUTY_PP) && GMX_THREAD_MPI
1276 && (devFlags.enableGpuHaloExchange || devFlags.enableGpuPmePPComm))
1278 setupGpuDevicePeerAccess(gpuIdsToUse, mdlog);
1281 if (hw_opt.threadAffinity != ThreadAffinity::Off)
1283 /* Before setting affinity, check whether the affinity has changed
1284 * - which indicates that probably the OpenMP library has changed it
1285 * since we first checked).
1287 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo->nthreads_hw_avail, TRUE);
1289 int numThreadsOnThisNode, intraNodeThreadOffset;
1290 analyzeThreadsOnThisNode(physicalNodeComm, numThreadsOnThisRank, &numThreadsOnThisNode,
1291 &intraNodeThreadOffset);
1293 /* Set the CPU affinity */
1294 gmx_set_thread_affinity(mdlog, cr, &hw_opt, *hwinfo->hardwareTopology, numThreadsOnThisRank,
1295 numThreadsOnThisNode, intraNodeThreadOffset, nullptr);
1298 if (mdrunOptions.timingOptions.resetStep > -1)
1303 "The -resetstep functionality is deprecated, and may be removed in a "
1306 wcycle = wallcycle_init(fplog, mdrunOptions.timingOptions.resetStep, cr);
1310 /* Master synchronizes its value of reset_counters with all nodes
1311 * including PME only nodes */
1312 int64_t reset_counters = wcycle_get_reset_counters(wcycle);
1313 gmx_bcast_sim(sizeof(reset_counters), &reset_counters, cr);
1314 wcycle_set_reset_counters(wcycle, reset_counters);
1317 // Membrane embedding must be initialized before we call init_forcerec()
1322 fprintf(stderr, "Initializing membed");
1324 /* Note that membed cannot work in parallel because mtop is
1325 * changed here. Fix this if we ever want to make it run with
1326 * multiple ranks. */
1327 membed = init_membed(fplog, filenames.size(), filenames.data(), &mtop, inputrec,
1328 globalState.get(), cr, &mdrunOptions.checkpointOptions.period);
1331 const bool thisRankHasPmeGpuTask = gpuTaskAssignments.thisRankHasPmeGpuTask();
1332 std::unique_ptr<MDAtoms> mdAtoms;
1333 std::unique_ptr<gmx_vsite_t> vsite;
1334 std::unique_ptr<GpuBonded> gpuBonded;
1337 if (thisRankHasDuty(cr, DUTY_PP))
1339 mdModulesNotifier.notify(*cr);
1340 mdModulesNotifier.notify(&atomSets);
1341 mdModulesNotifier.notify(inputrec->pbcType);
1342 mdModulesNotifier.notify(SimulationTimeStep{ inputrec->delta_t });
1343 /* Initiate forcerecord */
1344 fr = new t_forcerec;
1345 fr->forceProviders = mdModules_->initForceProviders();
1346 init_forcerec(fplog, mdlog, fr, fcd, inputrec, &mtop, cr, box,
1347 opt2fn("-table", filenames.size(), filenames.data()),
1348 opt2fn("-tablep", filenames.size(), filenames.data()),
1349 opt2fns("-tableb", filenames.size(), filenames.data()), pforce);
1351 fr->deviceContext = deviceContext.get();
1353 if (devFlags.enableGpuPmePPComm && !thisRankHasDuty(cr, DUTY_PME))
1356 deviceContext != nullptr,
1357 "Device context can not be nullptr when PME-PP direct communications object.");
1358 fr->pmePpCommGpu = std::make_unique<gmx::PmePpCommGpu>(
1359 cr->mpi_comm_mysim, cr->dd->pme_nodeid, *deviceContext);
1362 fr->nbv = Nbnxm::init_nb_verlet(mdlog, inputrec, fr, cr, *hwinfo, deviceInfo,
1363 fr->deviceContext, &mtop, box, wcycle);
1364 if (useGpuForBonded)
1366 auto stream = havePPDomainDecomposition(cr)
1367 ? Nbnxm::gpu_get_command_stream(
1368 fr->nbv->gpu_nbv, gmx::InteractionLocality::NonLocal)
1369 : Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv,
1370 gmx::InteractionLocality::Local);
1372 fr->deviceContext != nullptr,
1373 "Device context can not be nullptr when computing bonded interactions on GPU.");
1374 GMX_RELEASE_ASSERT(stream != nullptr,
1375 "Can'r run GPU version of bonded forces in nullptr stream.");
1376 gpuBonded = std::make_unique<GpuBonded>(mtop.ffparams, *fr->deviceContext, *stream, wcycle);
1377 fr->gpuBonded = gpuBonded.get();
1380 /* Initialize the mdAtoms structure.
1381 * mdAtoms is not filled with atom data,
1382 * as this can not be done now with domain decomposition.
1384 mdAtoms = makeMDAtoms(fplog, mtop, *inputrec, thisRankHasPmeGpuTask);
1385 if (globalState && thisRankHasPmeGpuTask)
1387 // The pinning of coordinates in the global state object works, because we only use
1388 // PME on GPU without DD or on a separate PME rank, and because the local state pointer
1389 // points to the global state object without DD.
1390 // FIXME: MD and EM separately set up the local state - this should happen in the same
1391 // function, which should also perform the pinning.
1392 changePinningPolicy(&globalState->x, pme_get_pinning_policy());
1395 /* Initialize the virtual site communication */
1396 vsite = initVsite(mtop, cr);
1398 calc_shifts(box, fr->shift_vec);
1400 /* With periodic molecules the charge groups should be whole at start up
1401 * and the virtual sites should not be far from their proper positions.
1403 if (!inputrec->bContinuation && MASTER(cr)
1404 && !(inputrec->pbcType != PbcType::No && inputrec->bPeriodicMols))
1406 /* Make molecules whole at start of run */
1407 if (fr->pbcType != PbcType::No)
1409 do_pbc_first_mtop(fplog, inputrec->pbcType, box, &mtop, globalState->x.rvec_array());
1413 /* Correct initial vsite positions are required
1414 * for the initial distribution in the domain decomposition
1415 * and for the initial shell prediction.
1417 constructVsitesGlobal(mtop, globalState->x);
1421 if (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
1423 ewaldcoeff_q = fr->ic->ewaldcoeff_q;
1424 ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
1429 /* This is a PME only node */
1431 GMX_ASSERT(globalState == nullptr,
1432 "We don't need the state on a PME only rank and expect it to be unitialized");
1434 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
1435 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
1438 gmx_pme_t* sepPmeData = nullptr;
1439 // This reference hides the fact that PME data is owned by runner on PME-only ranks and by forcerec on other ranks
1440 GMX_ASSERT(thisRankHasDuty(cr, DUTY_PP) == (fr != nullptr),
1441 "Double-checking that only PME-only ranks have no forcerec");
1442 gmx_pme_t*& pmedata = fr ? fr->pmedata : sepPmeData;
1444 // TODO should live in ewald module once its testing is improved
1446 // Later, this program could contain kernels that might be later
1447 // re-used as auto-tuning progresses, or subsequent simulations
1449 PmeGpuProgramStorage pmeGpuProgram;
1450 if (thisRankHasPmeGpuTask)
1453 deviceContext != nullptr,
1454 "Device context can not be nullptr when building PME GPU program object.");
1455 pmeGpuProgram = buildPmeGpuProgram(*deviceContext);
1458 /* Initiate PME if necessary,
1459 * either on all nodes or on dedicated PME nodes only. */
1460 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
1462 if (mdAtoms && mdAtoms->mdatoms())
1464 nChargePerturbed = mdAtoms->mdatoms()->nChargePerturbed;
1465 if (EVDW_PME(inputrec->vdwtype))
1467 nTypePerturbed = mdAtoms->mdatoms()->nTypePerturbed;
1470 if (cr->npmenodes > 0)
1472 /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
1473 gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
1474 gmx_bcast_sim(sizeof(nTypePerturbed), &nTypePerturbed, cr);
1477 if (thisRankHasDuty(cr, DUTY_PME))
1481 pmedata = gmx_pme_init(cr, getNumPmeDomains(cr->dd), inputrec, nChargePerturbed != 0,
1482 nTypePerturbed != 0, mdrunOptions.reproducible, ewaldcoeff_q,
1483 ewaldcoeff_lj, gmx_omp_nthreads_get(emntPME), pmeRunMode,
1484 nullptr, deviceInfo, pmeGpuProgram.get(), mdlog);
1486 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1491 if (EI_DYNAMICS(inputrec->eI))
1493 /* Turn on signal handling on all nodes */
1495 * (A user signal from the PME nodes (if any)
1496 * is communicated to the PP nodes.
1498 signal_handler_install();
1501 pull_t* pull_work = nullptr;
1502 if (thisRankHasDuty(cr, DUTY_PP))
1504 /* Assumes uniform use of the number of OpenMP threads */
1505 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
1507 if (inputrec->bPull)
1509 /* Initialize pull code */
1510 pull_work = init_pull(fplog, inputrec->pull, inputrec, &mtop, cr, &atomSets,
1511 inputrec->fepvals->init_lambda);
1512 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
1514 initPullHistory(pull_work, &observablesHistory);
1516 if (EI_DYNAMICS(inputrec->eI) && MASTER(cr))
1518 init_pull_output_files(pull_work, filenames.size(), filenames.data(), oenv, startingBehavior);
1522 std::unique_ptr<EnforcedRotation> enforcedRotation;
1525 /* Initialize enforced rotation code */
1527 init_rot(fplog, inputrec, filenames.size(), filenames.data(), cr, &atomSets,
1528 globalState.get(), &mtop, oenv, mdrunOptions, startingBehavior);
1531 t_swap* swap = nullptr;
1532 if (inputrec->eSwapCoords != eswapNO)
1534 /* Initialize ion swapping code */
1535 swap = init_swapcoords(fplog, inputrec,
1536 opt2fn_master("-swap", filenames.size(), filenames.data(), cr),
1537 &mtop, globalState.get(), &observablesHistory, cr, &atomSets,
1538 oenv, mdrunOptions, startingBehavior);
1541 /* Let makeConstraints know whether we have essential dynamics constraints. */
1542 auto constr = makeConstraints(mtop, *inputrec, pull_work, doEssentialDynamics, fplog,
1543 *mdAtoms->mdatoms(), cr, ms, &nrnb, wcycle, fr->bMolPBC);
1545 /* Energy terms and groups */
1546 gmx_enerdata_t enerd(mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
1547 inputrec->fepvals->n_lambda);
1549 /* Kinetic energy data */
1550 gmx_ekindata_t ekind;
1551 init_ekindata(fplog, &mtop, &(inputrec->opts), &ekind, inputrec->cos_accel);
1553 /* Set up interactive MD (IMD) */
1555 makeImdSession(inputrec, cr, wcycle, &enerd, ms, &mtop, mdlog,
1556 MASTER(cr) ? globalState->x.rvec_array() : nullptr, filenames.size(),
1557 filenames.data(), oenv, mdrunOptions.imdOptions, startingBehavior);
1559 if (DOMAINDECOMP(cr))
1561 GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
1562 /* This call is not included in init_domain_decomposition mainly
1563 * because fr->cginfo_mb is set later.
1565 dd_init_bondeds(fplog, cr->dd, mtop, vsite.get(), inputrec,
1566 domdecOptions.checkBondedInteractions, fr->cginfo_mb);
1569 // TODO This is not the right place to manage the lifetime of
1570 // this data structure, but currently it's the easiest way to
1572 MdrunScheduleWorkload runScheduleWork;
1573 // Also populates the simulation constant workload description.
1574 runScheduleWork.simulationWork =
1575 createSimulationWorkload(*inputrec, useGpuForNonbonded, pmeRunMode, useGpuForBonded,
1576 useGpuForUpdate, devFlags.enableGpuBufferOps,
1577 devFlags.enableGpuHaloExchange, devFlags.enableGpuPmePPComm);
1579 std::unique_ptr<gmx::StatePropagatorDataGpu> stateGpu;
1580 if (gpusWereDetected
1581 && ((useGpuForPme && thisRankHasDuty(cr, DUTY_PME))
1582 || runScheduleWork.simulationWork.useGpuBufferOps))
1584 const DeviceStream* pmeStream = pme_gpu_get_device_stream(fr->pmedata);
1585 const DeviceStream* localStream =
1586 fr->nbv->gpu_nbv != nullptr
1587 ? Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::Local)
1589 const DeviceStream* nonLocalStream =
1590 fr->nbv->gpu_nbv != nullptr
1591 ? Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::NonLocal)
1593 GpuApiCallBehavior transferKind = (inputrec->eI == eiMD && !doRerun && !useModularSimulator)
1594 ? GpuApiCallBehavior::Async
1595 : GpuApiCallBehavior::Sync;
1597 deviceContext != nullptr,
1598 "Device context can not be nullptr when building GPU propagator data object.");
1599 stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(
1600 pmeStream, localStream, nonLocalStream, *deviceContext, transferKind,
1601 pme_gpu_get_block_size(fr->pmedata), wcycle);
1602 fr->stateGpu = stateGpu.get();
1605 GMX_ASSERT(stopHandlerBuilder_, "Runner must provide StopHandlerBuilder to simulator.");
1606 SimulatorBuilder simulatorBuilder;
1608 // build and run simulator object based on user-input
1609 auto simulator = simulatorBuilder.build(
1610 useModularSimulator, fplog, cr, ms, mdlog, static_cast<int>(filenames.size()),
1611 filenames.data(), oenv, mdrunOptions, startingBehavior, vsite.get(), constr.get(),
1612 enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr, deform.get(),
1613 mdModules_->outputProvider(), mdModules_->notifier(), inputrec, imdSession.get(),
1614 pull_work, swap, &mtop, fcd, globalState.get(), &observablesHistory, mdAtoms.get(),
1615 &nrnb, wcycle, fr, &enerd, &ekind, &runScheduleWork, replExParams, membed,
1616 walltime_accounting, std::move(stopHandlerBuilder_), doRerun);
1619 if (fr->pmePpCommGpu)
1621 // destroy object since it is no longer required. (This needs to be done while the GPU context still exists.)
1622 fr->pmePpCommGpu.reset();
1625 if (inputrec->bPull)
1627 finish_pull(pull_work);
1629 finish_swapcoords(swap);
1633 GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
1635 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
1636 gmx_pmeonly(pmedata, cr, &nrnb, wcycle, walltime_accounting, inputrec, pmeRunMode,
1637 deviceContext.get());
1640 wallcycle_stop(wcycle, ewcRUN);
1642 /* Finish up, write some stuff
1643 * if rerunMD, don't write last frame again
1645 finish_run(fplog, mdlog, cr, inputrec, &nrnb, wcycle, walltime_accounting,
1646 fr ? fr->nbv.get() : nullptr, pmedata, EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
1648 // clean up cycle counter
1649 wallcycle_destroy(wcycle);
1654 gmx_pme_destroy(pmedata);
1658 // FIXME: this is only here to manually unpin mdAtoms->chargeA_ and state->x,
1659 // before we destroy the GPU context(s) in free_gpu().
1660 // Pinned buffers are associated with contexts in CUDA.
1661 // As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
1662 mdAtoms.reset(nullptr);
1663 globalState.reset(nullptr);
1664 mdModules_.reset(nullptr); // destruct force providers here as they might also use the GPU
1665 gpuBonded.reset(nullptr);
1666 /* Free pinned buffers in *fr */
1670 if (hwinfo->gpu_info.n_dev > 0)
1672 /* stop the GPU profiler (only CUDA) */
1676 /* With tMPI we need to wait for all ranks to finish deallocation before
1677 * destroying the CUDA context in free_gpu() as some tMPI ranks may be sharing
1680 * This is not a concern in OpenCL where we use one context per rank which
1681 * is freed in nbnxn_gpu_free().
1683 * Note: it is safe to not call the barrier on the ranks which do not use GPU,
1684 * but it is easier and more futureproof to call it on the whole node.
1686 * Note that this function needs to be called even if GPUs are not used
1687 * in this run because the PME ranks have no knowledge of whether GPUs
1688 * are used or not, but all ranks need to enter the barrier below.
1689 * \todo Remove this physical node barrier after making sure
1690 * that it's not needed anymore (with a shared GPU run).
1694 physicalNodeComm.barrier();
1697 free_gpu(deviceInfo);
1698 deviceContext.reset(nullptr);
1703 free_membed(membed);
1706 /* Does what it says */
1707 print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
1708 walltime_accounting_destroy(walltime_accounting);
1710 // Ensure log file content is written
1713 gmx_fio_flush(logFileHandle);
1716 /* Reset FPEs (important for unit tests) by disabling them. Assumes no
1717 * exceptions were enabled before function was called. */
1720 gmx_fedisableexcept();
1723 auto rc = static_cast<int>(gmx_get_stop_condition());
1726 /* we need to join all threads. The sub-threads join when they
1727 exit this function, but the master thread needs to be told to
1729 if (PAR(cr) && MASTER(cr))
1737 Mdrunner::~Mdrunner()
1739 // Clean up of the Manager.
1740 // This will end up getting called on every thread-MPI rank, which is unnecessary,
1741 // but okay as long as threads synchronize some time before adding or accessing
1742 // a new set of restraints.
1743 if (restraintManager_)
1745 restraintManager_->clear();
1746 GMX_ASSERT(restraintManager_->countRestraints() == 0,
1747 "restraints added during runner life time should be cleared at runner "
1752 void Mdrunner::addPotential(std::shared_ptr<gmx::IRestraintPotential> puller, const std::string& name)
1754 GMX_ASSERT(restraintManager_, "Mdrunner must have a restraint manager.");
1755 // Not sure if this should be logged through the md logger or something else,
1756 // but it is helpful to have some sort of INFO level message sent somewhere.
1757 // std::cout << "Registering restraint named " << name << std::endl;
1759 // When multiple restraints are used, it may be wasteful to register them separately.
1760 // Maybe instead register an entire Restraint Manager as a force provider.
1761 restraintManager_->addToSpec(std::move(puller), name);
1764 Mdrunner::Mdrunner(std::unique_ptr<MDModules> mdModules) : mdModules_(std::move(mdModules)) {}
1766 Mdrunner::Mdrunner(Mdrunner&&) noexcept = default;
1768 //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265
1769 Mdrunner& Mdrunner::operator=(Mdrunner&& /*handle*/) noexcept(BUGFREE_NOEXCEPT_STRING) = default;
1771 class Mdrunner::BuilderImplementation
1774 BuilderImplementation() = delete;
1775 BuilderImplementation(std::unique_ptr<MDModules> mdModules, compat::not_null<SimulationContext*> context);
1776 ~BuilderImplementation();
1778 BuilderImplementation& setExtraMdrunOptions(const MdrunOptions& options,
1779 real forceWarningThreshold,
1780 StartingBehavior startingBehavior);
1782 void addDomdec(const DomdecOptions& options);
1784 void addVerletList(int nstlist);
1786 void addReplicaExchange(const ReplicaExchangeParameters& params);
1788 void addNonBonded(const char* nbpu_opt);
1790 void addPME(const char* pme_opt_, const char* pme_fft_opt_);
1792 void addBondedTaskAssignment(const char* bonded_opt);
1794 void addUpdateTaskAssignment(const char* update_opt);
1796 void addHardwareOptions(const gmx_hw_opt_t& hardwareOptions);
1798 void addFilenames(ArrayRef<const t_filenm> filenames);
1800 void addOutputEnvironment(gmx_output_env_t* outputEnvironment);
1802 void addLogFile(t_fileio* logFileHandle);
1804 void addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
1809 // Default parameters copied from runner.h
1810 // \todo Clarify source(s) of default parameters.
1812 const char* nbpu_opt_ = nullptr;
1813 const char* pme_opt_ = nullptr;
1814 const char* pme_fft_opt_ = nullptr;
1815 const char* bonded_opt_ = nullptr;
1816 const char* update_opt_ = nullptr;
1818 MdrunOptions mdrunOptions_;
1820 DomdecOptions domdecOptions_;
1822 ReplicaExchangeParameters replicaExchangeParameters_;
1824 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
1827 //! Multisim communicator handle.
1828 gmx_multisim_t* multiSimulation_;
1830 //! mdrun communicator
1831 MPI_Comm communicator_ = MPI_COMM_NULL;
1833 //! Print a warning if any force is larger than this (in kJ/mol nm).
1834 real forceWarningThreshold_ = -1;
1836 //! Whether the simulation will start afresh, or restart with/without appending.
1837 StartingBehavior startingBehavior_ = StartingBehavior::NewSimulation;
1839 //! The modules that comprise the functionality of mdrun.
1840 std::unique_ptr<MDModules> mdModules_;
1842 //! \brief Parallelism information.
1843 gmx_hw_opt_t hardwareOptions_;
1845 //! filename options for simulation.
1846 ArrayRef<const t_filenm> filenames_;
1848 /*! \brief Handle to output environment.
1850 * \todo gmx_output_env_t needs lifetime management.
1852 gmx_output_env_t* outputEnvironment_ = nullptr;
1854 /*! \brief Non-owning handle to MD log file.
1856 * \todo Context should own output facilities for client.
1857 * \todo Improve log file handle management.
1859 * Code managing the FILE* relies on the ability to set it to
1860 * nullptr to check whether the filehandle is valid.
1862 t_fileio* logFileHandle_ = nullptr;
1865 * \brief Builder for simulation stop signal handler.
1867 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_ = nullptr;
1870 Mdrunner::BuilderImplementation::BuilderImplementation(std::unique_ptr<MDModules> mdModules,
1871 compat::not_null<SimulationContext*> context) :
1872 mdModules_(std::move(mdModules))
1874 communicator_ = context->communicator_;
1875 multiSimulation_ = context->multiSimulation_.get();
1878 Mdrunner::BuilderImplementation::~BuilderImplementation() = default;
1880 Mdrunner::BuilderImplementation&
1881 Mdrunner::BuilderImplementation::setExtraMdrunOptions(const MdrunOptions& options,
1882 const real forceWarningThreshold,
1883 const StartingBehavior startingBehavior)
1885 mdrunOptions_ = options;
1886 forceWarningThreshold_ = forceWarningThreshold;
1887 startingBehavior_ = startingBehavior;
1891 void Mdrunner::BuilderImplementation::addDomdec(const DomdecOptions& options)
1893 domdecOptions_ = options;
1896 void Mdrunner::BuilderImplementation::addVerletList(int nstlist)
1901 void Mdrunner::BuilderImplementation::addReplicaExchange(const ReplicaExchangeParameters& params)
1903 replicaExchangeParameters_ = params;
1906 Mdrunner Mdrunner::BuilderImplementation::build()
1908 auto newRunner = Mdrunner(std::move(mdModules_));
1910 newRunner.mdrunOptions = mdrunOptions_;
1911 newRunner.pforce = forceWarningThreshold_;
1912 newRunner.startingBehavior = startingBehavior_;
1913 newRunner.domdecOptions = domdecOptions_;
1915 // \todo determine an invariant to check or confirm that all gmx_hw_opt_t objects are valid
1916 newRunner.hw_opt = hardwareOptions_;
1918 // No invariant to check. This parameter exists to optionally override other behavior.
1919 newRunner.nstlist_cmdline = nstlist_;
1921 newRunner.replExParams = replicaExchangeParameters_;
1923 newRunner.filenames = filenames_;
1925 newRunner.communicator = communicator_;
1927 // nullptr is a valid value for the multisim handle
1928 newRunner.ms = multiSimulation_;
1930 // \todo Clarify ownership and lifetime management for gmx_output_env_t
1931 // \todo Update sanity checking when output environment has clearly specified invariants.
1932 // Initialization and default values for oenv are not well specified in the current version.
1933 if (outputEnvironment_)
1935 newRunner.oenv = outputEnvironment_;
1939 GMX_THROW(gmx::APIError(
1940 "MdrunnerBuilder::addOutputEnvironment() is required before build()"));
1943 newRunner.logFileHandle = logFileHandle_;
1947 newRunner.nbpu_opt = nbpu_opt_;
1951 GMX_THROW(gmx::APIError("MdrunnerBuilder::addNonBonded() is required before build()"));
1954 if (pme_opt_ && pme_fft_opt_)
1956 newRunner.pme_opt = pme_opt_;
1957 newRunner.pme_fft_opt = pme_fft_opt_;
1961 GMX_THROW(gmx::APIError("MdrunnerBuilder::addElectrostatics() is required before build()"));
1966 newRunner.bonded_opt = bonded_opt_;
1970 GMX_THROW(gmx::APIError(
1971 "MdrunnerBuilder::addBondedTaskAssignment() is required before build()"));
1976 newRunner.update_opt = update_opt_;
1980 GMX_THROW(gmx::APIError(
1981 "MdrunnerBuilder::addUpdateTaskAssignment() is required before build() "));
1985 newRunner.restraintManager_ = std::make_unique<gmx::RestraintManager>();
1987 if (stopHandlerBuilder_)
1989 newRunner.stopHandlerBuilder_ = std::move(stopHandlerBuilder_);
1993 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>();
1999 void Mdrunner::BuilderImplementation::addNonBonded(const char* nbpu_opt)
2001 nbpu_opt_ = nbpu_opt;
2004 void Mdrunner::BuilderImplementation::addPME(const char* pme_opt, const char* pme_fft_opt)
2007 pme_fft_opt_ = pme_fft_opt;
2010 void Mdrunner::BuilderImplementation::addBondedTaskAssignment(const char* bonded_opt)
2012 bonded_opt_ = bonded_opt;
2015 void Mdrunner::BuilderImplementation::addUpdateTaskAssignment(const char* update_opt)
2017 update_opt_ = update_opt;
2020 void Mdrunner::BuilderImplementation::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2022 hardwareOptions_ = hardwareOptions;
2025 void Mdrunner::BuilderImplementation::addFilenames(ArrayRef<const t_filenm> filenames)
2027 filenames_ = filenames;
2030 void Mdrunner::BuilderImplementation::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2032 outputEnvironment_ = outputEnvironment;
2035 void Mdrunner::BuilderImplementation::addLogFile(t_fileio* logFileHandle)
2037 logFileHandle_ = logFileHandle;
2040 void Mdrunner::BuilderImplementation::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2042 stopHandlerBuilder_ = std::move(builder);
2045 MdrunnerBuilder::MdrunnerBuilder(std::unique_ptr<MDModules> mdModules,
2046 compat::not_null<SimulationContext*> context) :
2047 impl_{ std::make_unique<Mdrunner::BuilderImplementation>(std::move(mdModules), context) }
2051 MdrunnerBuilder::~MdrunnerBuilder() = default;
2053 MdrunnerBuilder& MdrunnerBuilder::addSimulationMethod(const MdrunOptions& options,
2054 real forceWarningThreshold,
2055 const StartingBehavior startingBehavior)
2057 impl_->setExtraMdrunOptions(options, forceWarningThreshold, startingBehavior);
2061 MdrunnerBuilder& MdrunnerBuilder::addDomainDecomposition(const DomdecOptions& options)
2063 impl_->addDomdec(options);
2067 MdrunnerBuilder& MdrunnerBuilder::addNeighborList(int nstlist)
2069 impl_->addVerletList(nstlist);
2073 MdrunnerBuilder& MdrunnerBuilder::addReplicaExchange(const ReplicaExchangeParameters& params)
2075 impl_->addReplicaExchange(params);
2079 MdrunnerBuilder& MdrunnerBuilder::addNonBonded(const char* nbpu_opt)
2081 impl_->addNonBonded(nbpu_opt);
2085 MdrunnerBuilder& MdrunnerBuilder::addElectrostatics(const char* pme_opt, const char* pme_fft_opt)
2087 // The builder method may become more general in the future, but in this version,
2088 // parameters for PME electrostatics are both required and the only parameters
2090 if (pme_opt && pme_fft_opt)
2092 impl_->addPME(pme_opt, pme_fft_opt);
2097 gmx::InvalidInputError("addElectrostatics() arguments must be non-null pointers."));
2102 MdrunnerBuilder& MdrunnerBuilder::addBondedTaskAssignment(const char* bonded_opt)
2104 impl_->addBondedTaskAssignment(bonded_opt);
2108 MdrunnerBuilder& MdrunnerBuilder::addUpdateTaskAssignment(const char* update_opt)
2110 impl_->addUpdateTaskAssignment(update_opt);
2114 Mdrunner MdrunnerBuilder::build()
2116 return impl_->build();
2119 MdrunnerBuilder& MdrunnerBuilder::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2121 impl_->addHardwareOptions(hardwareOptions);
2125 MdrunnerBuilder& MdrunnerBuilder::addFilenames(ArrayRef<const t_filenm> filenames)
2127 impl_->addFilenames(filenames);
2131 MdrunnerBuilder& MdrunnerBuilder::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2133 impl_->addOutputEnvironment(outputEnvironment);
2137 MdrunnerBuilder& MdrunnerBuilder::addLogFile(t_fileio* logFileHandle)
2139 impl_->addLogFile(logFileHandle);
2143 MdrunnerBuilder& MdrunnerBuilder::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2145 impl_->addStopHandlerBuilder(std::move(builder));
2149 MdrunnerBuilder::MdrunnerBuilder(MdrunnerBuilder&&) noexcept = default;
2151 MdrunnerBuilder& MdrunnerBuilder::operator=(MdrunnerBuilder&&) noexcept = default;