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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.h"
68 #include "gromacs/ewald/pme_gpu_program.h"
69 #include "gromacs/ewald/pme_only.h"
70 #include "gromacs/ewald/pme_pp_comm_gpu.h"
71 #include "gromacs/fileio/checkpoint.h"
72 #include "gromacs/fileio/gmxfio.h"
73 #include "gromacs/fileio/oenv.h"
74 #include "gromacs/fileio/tpxio.h"
75 #include "gromacs/gmxlib/network.h"
76 #include "gromacs/gmxlib/nrnb.h"
77 #include "gromacs/gpu_utils/device_stream_manager.h"
78 #include "gromacs/hardware/cpuinfo.h"
79 #include "gromacs/hardware/detecthardware.h"
80 #include "gromacs/hardware/device_management.h"
81 #include "gromacs/hardware/hardwaretopology.h"
82 #include "gromacs/hardware/printhardware.h"
83 #include "gromacs/imd/imd.h"
84 #include "gromacs/listed_forces/disre.h"
85 #include "gromacs/listed_forces/gpubonded.h"
86 #include "gromacs/listed_forces/listed_forces.h"
87 #include "gromacs/listed_forces/orires.h"
88 #include "gromacs/math/functions.h"
89 #include "gromacs/math/utilities.h"
90 #include "gromacs/math/vec.h"
91 #include "gromacs/mdlib/boxdeformation.h"
92 #include "gromacs/mdlib/broadcaststructs.h"
93 #include "gromacs/mdlib/calc_verletbuf.h"
94 #include "gromacs/mdlib/dispersioncorrection.h"
95 #include "gromacs/mdlib/enerdata_utils.h"
96 #include "gromacs/mdlib/force.h"
97 #include "gromacs/mdlib/forcerec.h"
98 #include "gromacs/mdlib/gmx_omp_nthreads.h"
99 #include "gromacs/mdlib/gpuforcereduction.h"
100 #include "gromacs/mdlib/makeconstraints.h"
101 #include "gromacs/mdlib/md_support.h"
102 #include "gromacs/mdlib/mdatoms.h"
103 #include "gromacs/mdlib/sighandler.h"
104 #include "gromacs/mdlib/stophandler.h"
105 #include "gromacs/mdlib/tgroup.h"
106 #include "gromacs/mdlib/updategroups.h"
107 #include "gromacs/mdlib/vsite.h"
108 #include "gromacs/mdrun/mdmodules.h"
109 #include "gromacs/mdrun/simulationcontext.h"
110 #include "gromacs/mdrun/simulationinput.h"
111 #include "gromacs/mdrun/simulationinputhandle.h"
112 #include "gromacs/mdrunutility/handlerestart.h"
113 #include "gromacs/mdrunutility/logging.h"
114 #include "gromacs/mdrunutility/multisim.h"
115 #include "gromacs/mdrunutility/printtime.h"
116 #include "gromacs/mdrunutility/threadaffinity.h"
117 #include "gromacs/mdtypes/checkpointdata.h"
118 #include "gromacs/mdtypes/commrec.h"
119 #include "gromacs/mdtypes/enerdata.h"
120 #include "gromacs/mdtypes/fcdata.h"
121 #include "gromacs/mdtypes/forcerec.h"
122 #include "gromacs/mdtypes/group.h"
123 #include "gromacs/mdtypes/inputrec.h"
124 #include "gromacs/mdtypes/interaction_const.h"
125 #include "gromacs/mdtypes/md_enums.h"
126 #include "gromacs/mdtypes/mdatom.h"
127 #include "gromacs/mdtypes/mdrunoptions.h"
128 #include "gromacs/mdtypes/observableshistory.h"
129 #include "gromacs/mdtypes/simulation_workload.h"
130 #include "gromacs/mdtypes/state.h"
131 #include "gromacs/mdtypes/state_propagator_data_gpu.h"
132 #include "gromacs/modularsimulator/modularsimulator.h"
133 #include "gromacs/nbnxm/gpu_data_mgmt.h"
134 #include "gromacs/nbnxm/nbnxm.h"
135 #include "gromacs/nbnxm/pairlist_tuning.h"
136 #include "gromacs/pbcutil/pbc.h"
137 #include "gromacs/pulling/output.h"
138 #include "gromacs/pulling/pull.h"
139 #include "gromacs/pulling/pull_rotation.h"
140 #include "gromacs/restraint/manager.h"
141 #include "gromacs/restraint/restraintmdmodule.h"
142 #include "gromacs/restraint/restraintpotential.h"
143 #include "gromacs/swap/swapcoords.h"
144 #include "gromacs/taskassignment/decidegpuusage.h"
145 #include "gromacs/taskassignment/decidesimulationworkload.h"
146 #include "gromacs/taskassignment/resourcedivision.h"
147 #include "gromacs/taskassignment/taskassignment.h"
148 #include "gromacs/taskassignment/usergpuids.h"
149 #include "gromacs/timing/gpu_timing.h"
150 #include "gromacs/timing/wallcycle.h"
151 #include "gromacs/timing/wallcyclereporting.h"
152 #include "gromacs/topology/mtop_util.h"
153 #include "gromacs/trajectory/trajectoryframe.h"
154 #include "gromacs/utility/basenetwork.h"
155 #include "gromacs/utility/cstringutil.h"
156 #include "gromacs/utility/exceptions.h"
157 #include "gromacs/utility/fatalerror.h"
158 #include "gromacs/utility/filestream.h"
159 #include "gromacs/utility/gmxassert.h"
160 #include "gromacs/utility/gmxmpi.h"
161 #include "gromacs/utility/keyvaluetree.h"
162 #include "gromacs/utility/logger.h"
163 #include "gromacs/utility/loggerbuilder.h"
164 #include "gromacs/utility/mdmodulenotification.h"
165 #include "gromacs/utility/physicalnodecommunicator.h"
166 #include "gromacs/utility/pleasecite.h"
167 #include "gromacs/utility/programcontext.h"
168 #include "gromacs/utility/smalloc.h"
169 #include "gromacs/utility/stringutil.h"
171 #include "isimulator.h"
172 #include "membedholder.h"
173 #include "replicaexchange.h"
174 #include "simulatorbuilder.h"
180 /*! \brief Manage any development feature flag variables encountered
182 * The use of dev features indicated by environment variables is
183 * logged in order to ensure that runs with such features enabled can
184 * be identified from their log and standard output. Any cross
185 * dependencies are also checked, and if unsatisfied, a fatal error
188 * Note that some development features overrides are applied already here:
189 * the GPU communication flags are set to false in non-tMPI and non-CUDA builds.
191 * \param[in] mdlog Logger object.
192 * \param[in] useGpuForNonbonded True if the nonbonded task is offloaded in this run.
193 * \param[in] pmeRunMode The PME run mode for this run
194 * \returns The object populated with development feature flags.
196 static DevelopmentFeatureFlags manageDevelopmentFeatures(const gmx::MDLogger& mdlog,
197 const bool useGpuForNonbonded,
198 const PmeRunMode pmeRunMode)
200 DevelopmentFeatureFlags devFlags;
202 // Some builds of GCC 5 give false positive warnings that these
203 // getenv results are ignored when clearly they are used.
204 #pragma GCC diagnostic push
205 #pragma GCC diagnostic ignored "-Wunused-result"
207 devFlags.enableGpuBufferOps =
208 GMX_GPU_CUDA && useGpuForNonbonded && (getenv("GMX_USE_GPU_BUFFER_OPS") != nullptr);
209 devFlags.enableGpuHaloExchange = GMX_GPU_CUDA && GMX_THREAD_MPI && getenv("GMX_GPU_DD_COMMS") != nullptr;
210 devFlags.forceGpuUpdateDefault = (getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") != nullptr) || GMX_FAHCORE;
211 devFlags.enableGpuPmePPComm =
212 GMX_GPU_CUDA && GMX_THREAD_MPI && getenv("GMX_GPU_PME_PP_COMMS") != nullptr;
214 #pragma GCC diagnostic pop
216 if (devFlags.enableGpuBufferOps)
218 GMX_LOG(mdlog.warning)
220 .appendTextFormatted(
221 "This run uses the 'GPU buffer ops' feature, enabled by the "
222 "GMX_USE_GPU_BUFFER_OPS environment variable.");
225 if (devFlags.forceGpuUpdateDefault)
227 GMX_LOG(mdlog.warning)
229 .appendTextFormatted(
230 "This run will default to '-update gpu' as requested by the "
231 "GMX_FORCE_UPDATE_DEFAULT_GPU environment variable. GPU update with domain "
232 "decomposition lacks substantial testing and should be used with caution.");
235 if (devFlags.enableGpuHaloExchange)
237 if (useGpuForNonbonded)
239 if (!devFlags.enableGpuBufferOps)
241 GMX_LOG(mdlog.warning)
243 .appendTextFormatted(
244 "Enabling GPU buffer operations required by GMX_GPU_DD_COMMS "
245 "(equivalent with GMX_USE_GPU_BUFFER_OPS=1).");
246 devFlags.enableGpuBufferOps = true;
248 GMX_LOG(mdlog.warning)
250 .appendTextFormatted(
251 "This run has requested the 'GPU halo exchange' feature, enabled by "
253 "GMX_GPU_DD_COMMS environment variable.");
257 GMX_LOG(mdlog.warning)
259 .appendTextFormatted(
260 "GMX_GPU_DD_COMMS environment variable detected, but the 'GPU "
261 "halo exchange' feature will not be enabled as nonbonded interactions "
262 "are not offloaded.");
263 devFlags.enableGpuHaloExchange = false;
267 if (devFlags.enableGpuPmePPComm)
269 if (pmeRunMode == PmeRunMode::GPU)
271 if (!devFlags.enableGpuBufferOps)
273 GMX_LOG(mdlog.warning)
275 .appendTextFormatted(
276 "Enabling GPU buffer operations required by GMX_GPU_PME_PP_COMMS "
277 "(equivalent with GMX_USE_GPU_BUFFER_OPS=1).");
278 devFlags.enableGpuBufferOps = true;
280 GMX_LOG(mdlog.warning)
282 .appendTextFormatted(
283 "This run uses the 'GPU PME-PP communications' feature, enabled "
284 "by the GMX_GPU_PME_PP_COMMS environment variable.");
288 std::string clarification;
289 if (pmeRunMode == PmeRunMode::Mixed)
292 "PME FFT and gather are not offloaded to the GPU (PME is running in mixed "
297 clarification = "PME is not offloaded to the GPU.";
299 GMX_LOG(mdlog.warning)
302 "GMX_GPU_PME_PP_COMMS environment variable detected, but the "
303 "'GPU PME-PP communications' feature was not enabled as "
305 devFlags.enableGpuPmePPComm = false;
312 /*! \brief Barrier for safe simultaneous thread access to mdrunner data
314 * Used to ensure that the master thread does not modify mdrunner during copy
315 * on the spawned threads. */
316 static void threadMpiMdrunnerAccessBarrier()
319 MPI_Barrier(MPI_COMM_WORLD);
323 Mdrunner Mdrunner::cloneOnSpawnedThread() const
325 auto newRunner = Mdrunner(std::make_unique<MDModules>());
327 // All runners in the same process share a restraint manager resource because it is
328 // part of the interface to the client code, which is associated only with the
329 // original thread. Handles to the same resources can be obtained by copy.
331 newRunner.restraintManager_ = std::make_unique<RestraintManager>(*restraintManager_);
334 // Copy members of master runner.
335 // \todo Replace with builder when Simulation context and/or runner phases are better defined.
336 // Ref https://gitlab.com/gromacs/gromacs/-/issues/2587 and https://gitlab.com/gromacs/gromacs/-/issues/2375
337 newRunner.hw_opt = hw_opt;
338 newRunner.filenames = filenames;
340 newRunner.hwinfo_ = hwinfo_;
341 newRunner.oenv = oenv;
342 newRunner.mdrunOptions = mdrunOptions;
343 newRunner.domdecOptions = domdecOptions;
344 newRunner.nbpu_opt = nbpu_opt;
345 newRunner.pme_opt = pme_opt;
346 newRunner.pme_fft_opt = pme_fft_opt;
347 newRunner.bonded_opt = bonded_opt;
348 newRunner.update_opt = update_opt;
349 newRunner.nstlist_cmdline = nstlist_cmdline;
350 newRunner.replExParams = replExParams;
351 newRunner.pforce = pforce;
352 // Give the spawned thread the newly created valid communicator
353 // for the simulation.
354 newRunner.libraryWorldCommunicator = MPI_COMM_WORLD;
355 newRunner.simulationCommunicator = MPI_COMM_WORLD;
357 newRunner.startingBehavior = startingBehavior;
358 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>(*stopHandlerBuilder_);
359 newRunner.inputHolder_ = inputHolder_;
361 threadMpiMdrunnerAccessBarrier();
366 /*! \brief The callback used for running on spawned threads.
368 * Obtains the pointer to the master mdrunner object from the one
369 * argument permitted to the thread-launch API call, copies it to make
370 * a new runner for this thread, reinitializes necessary data, and
371 * proceeds to the simulation. */
372 static void mdrunner_start_fn(const void* arg)
376 auto masterMdrunner = reinterpret_cast<const gmx::Mdrunner*>(arg);
377 /* copy the arg list to make sure that it's thread-local. This
378 doesn't copy pointed-to items, of course; fnm, cr and fplog
379 are reset in the call below, all others should be const. */
380 gmx::Mdrunner mdrunner = masterMdrunner->cloneOnSpawnedThread();
383 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
387 void Mdrunner::spawnThreads(int numThreadsToLaunch)
390 /* now spawn new threads that start mdrunner_start_fn(), while
391 the main thread returns. Thread affinity is handled later. */
392 if (tMPI_Init_fn(TRUE, numThreadsToLaunch, TMPI_AFFINITY_NONE, mdrunner_start_fn, static_cast<const void*>(this))
395 GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
398 // Give the master thread the newly created valid communicator for
400 libraryWorldCommunicator = MPI_COMM_WORLD;
401 simulationCommunicator = MPI_COMM_WORLD;
402 threadMpiMdrunnerAccessBarrier();
404 GMX_UNUSED_VALUE(numThreadsToLaunch);
405 GMX_UNUSED_VALUE(mdrunner_start_fn);
411 /*! \brief Initialize variables for Verlet scheme simulation */
412 static void prepare_verlet_scheme(FILE* fplog,
416 const gmx_mtop_t& mtop,
418 bool makeGpuPairList,
419 const gmx::CpuInfo& cpuinfo)
421 // We checked the cut-offs in grompp, but double-check here.
422 // We have PME+LJcutoff kernels for rcoulomb>rvdw.
423 if (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == VanDerWaalsType::Cut)
425 GMX_RELEASE_ASSERT(ir->rcoulomb >= ir->rvdw,
426 "With Verlet lists and PME we should have rcoulomb>=rvdw");
430 GMX_RELEASE_ASSERT(ir->rcoulomb == ir->rvdw,
431 "With Verlet lists and no PME rcoulomb and rvdw should be identical");
433 /* For NVE simulations, we will retain the initial list buffer */
434 if (EI_DYNAMICS(ir->eI) && ir->verletbuf_tol > 0
435 && !(EI_MD(ir->eI) && ir->etc == TemperatureCoupling::No))
437 /* Update the Verlet buffer size for the current run setup */
439 /* Here we assume SIMD-enabled kernels are being used. But as currently
440 * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
441 * and 4x2 gives a larger buffer than 4x4, this is ok.
443 ListSetupType listType =
444 (makeGpuPairList ? ListSetupType::Gpu : ListSetupType::CpuSimdWhenSupported);
445 VerletbufListSetup listSetup = verletbufGetSafeListSetup(listType);
447 const real rlist_new =
448 calcVerletBufferSize(mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
450 if (rlist_new != ir->rlist)
452 if (fplog != nullptr)
455 "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
458 listSetup.cluster_size_i,
459 listSetup.cluster_size_j);
461 ir->rlist = rlist_new;
465 if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
468 "Can not set nstlist without %s",
469 !EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
472 if (EI_DYNAMICS(ir->eI))
474 /* Set or try nstlist values */
475 increaseNstlist(fplog, cr, ir, nstlist_cmdline, &mtop, box, makeGpuPairList, cpuinfo);
479 /*! \brief Override the nslist value in inputrec
481 * with value passed on the command line (if any)
483 static void override_nsteps_cmdline(const gmx::MDLogger& mdlog, int64_t nsteps_cmdline, t_inputrec* ir)
487 /* override with anything else than the default -2 */
488 if (nsteps_cmdline > -2)
490 char sbuf_steps[STEPSTRSIZE];
491 char sbuf_msg[STRLEN];
493 ir->nsteps = nsteps_cmdline;
494 if (EI_DYNAMICS(ir->eI) && nsteps_cmdline != -1)
497 "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
498 gmx_step_str(nsteps_cmdline, sbuf_steps),
499 fabs(nsteps_cmdline * ir->delta_t));
504 "Overriding nsteps with value passed on the command line: %s steps",
505 gmx_step_str(nsteps_cmdline, sbuf_steps));
508 GMX_LOG(mdlog.warning).asParagraph().appendText(sbuf_msg);
510 else if (nsteps_cmdline < -2)
512 gmx_fatal(FARGS, "Invalid nsteps value passed on the command line: %" PRId64, nsteps_cmdline);
514 /* Do nothing if nsteps_cmdline == -2 */
520 /*! \brief Return whether GPU acceleration of nonbondeds is supported with the given settings.
522 * If not, and if a warning may be issued, logs a warning about
523 * falling back to CPU code. With thread-MPI, only the first
524 * call to this function should have \c issueWarning true. */
525 static bool gpuAccelerationOfNonbondedIsUseful(const MDLogger& mdlog, const t_inputrec& ir, bool issueWarning)
527 bool gpuIsUseful = true;
530 if (ir.opts.ngener - ir.nwall > 1)
532 /* The GPU code does not support more than one energy group.
533 * If the user requested GPUs explicitly, a fatal error is given later.
537 "Multiple energy groups is not implemented for GPUs, falling back to the CPU. "
538 "For better performance, run on the GPU without energy groups and then do "
539 "gmx mdrun -rerun option on the trajectory with an energy group .tpr file.";
545 warning = "TPI is not implemented for GPUs.";
548 if (!gpuIsUseful && issueWarning)
550 GMX_LOG(mdlog.warning).asParagraph().appendText(warning);
556 //! Initializes the logger for mdrun.
557 static gmx::LoggerOwner buildLogger(FILE* fplog, const bool isSimulationMasterRank)
559 gmx::LoggerBuilder builder;
560 if (fplog != nullptr)
562 builder.addTargetFile(gmx::MDLogger::LogLevel::Info, fplog);
564 if (isSimulationMasterRank)
566 builder.addTargetStream(gmx::MDLogger::LogLevel::Warning, &gmx::TextOutputFile::standardError());
568 return builder.build();
571 //! Make a TaskTarget from an mdrun argument string.
572 static TaskTarget findTaskTarget(const char* optionString)
574 TaskTarget returnValue = TaskTarget::Auto;
576 if (strncmp(optionString, "auto", 3) == 0)
578 returnValue = TaskTarget::Auto;
580 else if (strncmp(optionString, "cpu", 3) == 0)
582 returnValue = TaskTarget::Cpu;
584 else if (strncmp(optionString, "gpu", 3) == 0)
586 returnValue = TaskTarget::Gpu;
590 GMX_ASSERT(false, "Option string should have been checked for sanity already");
596 //! Finish run, aggregate data to print performance info.
597 static void finish_run(FILE* fplog,
598 const gmx::MDLogger& mdlog,
600 const t_inputrec& inputrec,
602 gmx_wallcycle_t wcycle,
603 gmx_walltime_accounting_t walltime_accounting,
604 nonbonded_verlet_t* nbv,
605 const gmx_pme_t* pme,
609 double nbfs = 0, mflop = 0;
610 double elapsed_time, elapsed_time_over_all_ranks, elapsed_time_over_all_threads,
611 elapsed_time_over_all_threads_over_all_ranks;
612 /* Control whether it is valid to print a report. Only the
613 simulation master may print, but it should not do so if the run
614 terminated e.g. before a scheduled reset step. This is
615 complicated by the fact that PME ranks are unaware of the
616 reason why they were sent a pmerecvqxFINISH. To avoid
617 communication deadlocks, we always do the communication for the
618 report, even if we've decided not to write the report, because
619 how long it takes to finish the run is not important when we've
620 decided not to report on the simulation performance.
622 Further, we only report performance for dynamical integrators,
623 because those are the only ones for which we plan to
624 consider doing any optimizations. */
625 bool printReport = EI_DYNAMICS(inputrec.eI) && SIMMASTER(cr);
627 if (printReport && !walltime_accounting_get_valid_finish(walltime_accounting))
629 GMX_LOG(mdlog.warning)
631 .appendText("Simulation ended prematurely, no performance report will be written.");
636 std::unique_ptr<t_nrnb> nrnbTotalStorage;
639 nrnbTotalStorage = std::make_unique<t_nrnb>();
640 nrnb_tot = nrnbTotalStorage.get();
642 MPI_Allreduce(nrnb->n, nrnb_tot->n, eNRNB, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
650 elapsed_time = walltime_accounting_get_time_since_reset(walltime_accounting);
651 elapsed_time_over_all_threads =
652 walltime_accounting_get_time_since_reset_over_all_threads(walltime_accounting);
656 /* reduce elapsed_time over all MPI ranks in the current simulation */
657 MPI_Allreduce(&elapsed_time, &elapsed_time_over_all_ranks, 1, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
658 elapsed_time_over_all_ranks /= cr->nnodes;
659 /* Reduce elapsed_time_over_all_threads over all MPI ranks in the
660 * current simulation. */
661 MPI_Allreduce(&elapsed_time_over_all_threads,
662 &elapsed_time_over_all_threads_over_all_ranks,
671 elapsed_time_over_all_ranks = elapsed_time;
672 elapsed_time_over_all_threads_over_all_ranks = elapsed_time_over_all_threads;
677 print_flop(fplog, nrnb_tot, &nbfs, &mflop);
680 if (thisRankHasDuty(cr, DUTY_PP) && DOMAINDECOMP(cr))
682 print_dd_statistics(cr, inputrec, fplog);
685 /* TODO Move the responsibility for any scaling by thread counts
686 * to the code that handled the thread region, so that there's a
687 * mechanism to keep cycle counting working during the transition
688 * to task parallelism. */
689 int nthreads_pp = gmx_omp_nthreads_get(emntNonbonded);
690 int nthreads_pme = gmx_omp_nthreads_get(emntPME);
691 wallcycle_scale_by_num_threads(
692 wcycle, thisRankHasDuty(cr, DUTY_PME) && !thisRankHasDuty(cr, DUTY_PP), nthreads_pp, nthreads_pme);
693 auto cycle_sum(wallcycle_sum(cr, wcycle));
697 auto nbnxn_gpu_timings =
698 (nbv != nullptr && nbv->useGpu()) ? Nbnxm::gpu_get_timings(nbv->gpu_nbv) : nullptr;
699 gmx_wallclock_gpu_pme_t pme_gpu_timings = {};
701 if (pme_gpu_task_enabled(pme))
703 pme_gpu_get_timings(pme, &pme_gpu_timings);
705 wallcycle_print(fplog,
711 elapsed_time_over_all_ranks,
717 if (EI_DYNAMICS(inputrec.eI))
719 delta_t = inputrec.delta_t;
725 elapsed_time_over_all_threads_over_all_ranks,
726 elapsed_time_over_all_ranks,
727 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
735 elapsed_time_over_all_threads_over_all_ranks,
736 elapsed_time_over_all_ranks,
737 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
745 int Mdrunner::mdrunner()
748 std::unique_ptr<t_forcerec> fr;
749 real ewaldcoeff_q = 0;
750 real ewaldcoeff_lj = 0;
751 int nChargePerturbed = -1, nTypePerturbed = 0;
752 gmx_wallcycle_t wcycle;
753 gmx_walltime_accounting_t walltime_accounting = nullptr;
754 MembedHolder membedHolder(filenames.size(), filenames.data());
756 /* CAUTION: threads may be started later on in this function, so
757 cr doesn't reflect the final parallel state right now */
760 /* TODO: inputrec should tell us whether we use an algorithm, not a file option */
761 const bool doEssentialDynamics = opt2bSet("-ei", filenames.size(), filenames.data());
762 const bool doRerun = mdrunOptions.rerun;
764 // Handle task-assignment related user options.
765 EmulateGpuNonbonded emulateGpuNonbonded =
766 (getenv("GMX_EMULATE_GPU") != nullptr ? EmulateGpuNonbonded::Yes : EmulateGpuNonbonded::No);
768 std::vector<int> userGpuTaskAssignment;
771 userGpuTaskAssignment = parseUserTaskAssignmentString(hw_opt.userGpuTaskAssignment);
773 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
774 auto nonbondedTarget = findTaskTarget(nbpu_opt);
775 auto pmeTarget = findTaskTarget(pme_opt);
776 auto pmeFftTarget = findTaskTarget(pme_fft_opt);
777 auto bondedTarget = findTaskTarget(bonded_opt);
778 auto updateTarget = findTaskTarget(update_opt);
780 FILE* fplog = nullptr;
781 // If we are appending, we don't write log output because we need
782 // to check that the old log file matches what the checkpoint file
783 // expects. Otherwise, we should start to write log output now if
784 // there is a file ready for it.
785 if (logFileHandle != nullptr && startingBehavior != StartingBehavior::RestartWithAppending)
787 fplog = gmx_fio_getfp(logFileHandle);
789 const bool isSimulationMasterRank = findIsSimulationMasterRank(ms, simulationCommunicator);
790 gmx::LoggerOwner logOwner(buildLogger(fplog, isSimulationMasterRank));
791 gmx::MDLogger mdlog(logOwner.logger());
793 gmx_print_detected_hardware(fplog, isSimulationMasterRank && isMasterSim(ms), mdlog, hwinfo_);
795 std::vector<int> availableDevices =
796 makeListOfAvailableDevices(hwinfo_->deviceInfoList, hw_opt.devicesSelectedByUser);
797 const int numAvailableDevices = gmx::ssize(availableDevices);
799 // Print citation requests after all software/hardware printing
800 pleaseCiteGromacs(fplog);
802 // Note: legacy program logic relies on checking whether these pointers are assigned.
803 // Objects may or may not be allocated later.
804 std::unique_ptr<t_inputrec> inputrec;
805 std::unique_ptr<t_state> globalState;
807 auto partialDeserializedTpr = std::make_unique<PartialDeserializedTprFile>();
809 if (isSimulationMasterRank)
811 // Allocate objects to be initialized by later function calls.
812 /* Only the master rank has the global state */
813 globalState = std::make_unique<t_state>();
814 inputrec = std::make_unique<t_inputrec>();
816 /* Read (nearly) all data required for the simulation
817 * and keep the partly serialized tpr contents to send to other ranks later
819 applyGlobalSimulationState(
820 *inputHolder_.get(), partialDeserializedTpr.get(), globalState.get(), inputrec.get(), &mtop);
823 /* Check and update the hardware options for internal consistency */
824 checkAndUpdateHardwareOptions(
825 mdlog, &hw_opt, isSimulationMasterRank, domdecOptions.numPmeRanks, inputrec.get());
827 if (GMX_THREAD_MPI && isSimulationMasterRank)
829 bool useGpuForNonbonded = false;
830 bool useGpuForPme = false;
833 GMX_RELEASE_ASSERT(inputrec != nullptr, "Keep the compiler happy");
835 // If the user specified the number of ranks, then we must
836 // respect that, but in default mode, we need to allow for
837 // the number of GPUs to choose the number of ranks.
838 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
839 useGpuForNonbonded = decideWhetherToUseGpusForNonbondedWithThreadMpi(
841 numAvailableDevices > 0,
842 userGpuTaskAssignment,
844 canUseGpuForNonbonded,
845 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, GMX_THREAD_MPI),
846 hw_opt.nthreads_tmpi);
847 useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi(useGpuForNonbonded,
850 userGpuTaskAssignment,
853 hw_opt.nthreads_tmpi,
854 domdecOptions.numPmeRanks);
856 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
858 /* Determine how many thread-MPI ranks to start.
860 * TODO Over-writing the user-supplied value here does
861 * prevent any possible subsequent checks from working
863 hw_opt.nthreads_tmpi = get_nthreads_mpi(hwinfo_,
871 membedHolder.doMembed());
873 // Now start the threads for thread MPI.
874 spawnThreads(hw_opt.nthreads_tmpi);
875 // The spawned threads enter mdrunner() and execution of
876 // master and spawned threads joins at the end of this block.
879 GMX_RELEASE_ASSERT(ms || simulationCommunicator != MPI_COMM_NULL,
880 "Must have valid communicator unless running a multi-simulation");
881 CommrecHandle crHandle = init_commrec(simulationCommunicator);
882 t_commrec* cr = crHandle.get();
883 GMX_RELEASE_ASSERT(cr != nullptr, "Must have valid commrec");
885 PhysicalNodeCommunicator physicalNodeComm(libraryWorldCommunicator, gmx_physicalnode_id_hash());
887 // If we detected the topology on this system, double-check that it makes sense
888 if (hwinfo_->hardwareTopology->isThisSystem())
890 hardwareTopologyDoubleCheckDetection(mdlog, *hwinfo_->hardwareTopology);
895 /* now broadcast everything to the non-master nodes/threads: */
896 if (!isSimulationMasterRank)
898 // Until now, only the master rank has a non-null pointer.
899 // On non-master ranks, allocate the object that will receive data in the following call.
900 inputrec = std::make_unique<t_inputrec>();
902 init_parallel(cr->mpiDefaultCommunicator,
906 partialDeserializedTpr.get());
908 GMX_RELEASE_ASSERT(inputrec != nullptr, "All ranks should have a valid inputrec now");
909 partialDeserializedTpr.reset(nullptr);
912 !inputrec->useConstantAcceleration,
913 "Linear acceleration has been removed in GROMACS 2022, and was broken for many years "
914 "before that. Use GROMACS 4.5 or earlier if you need this feature.");
916 // Now the number of ranks is known to all ranks, and each knows
917 // the inputrec read by the master rank. The ranks can now all run
918 // the task-deciding functions and will agree on the result
919 // without needing to communicate.
920 const bool useDomainDecomposition =
921 (PAR(cr) && !(EI_TPI(inputrec->eI) || inputrec->eI == IntegrationAlgorithm::NM));
923 // Note that these variables describe only their own node.
925 // Note that when bonded interactions run on a GPU they always run
926 // alongside a nonbonded task, so do not influence task assignment
927 // even though they affect the force calculation workload.
928 bool useGpuForNonbonded = false;
929 bool useGpuForPme = false;
930 bool useGpuForBonded = false;
931 bool useGpuForUpdate = false;
932 bool gpusWereDetected = hwinfo_->ngpu_compatible_tot > 0;
935 // It's possible that there are different numbers of GPUs on
936 // different nodes, which is the user's responsibility to
937 // handle. If unsuitable, we will notice that during task
939 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
940 useGpuForNonbonded = decideWhetherToUseGpusForNonbonded(
942 userGpuTaskAssignment,
944 canUseGpuForNonbonded,
945 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, !GMX_THREAD_MPI),
947 useGpuForPme = decideWhetherToUseGpusForPme(useGpuForNonbonded,
949 userGpuTaskAssignment,
952 cr->sizeOfDefaultCommunicator,
953 domdecOptions.numPmeRanks,
955 useGpuForBonded = decideWhetherToUseGpusForBonded(
956 useGpuForNonbonded, useGpuForPme, bondedTarget, *inputrec, mtop, domdecOptions.numPmeRanks, gpusWereDetected);
958 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
960 const PmeRunMode pmeRunMode = determinePmeRunMode(useGpuForPme, pmeFftTarget, *inputrec);
962 // Initialize development feature flags that enabled by environment variable
963 // and report those features that are enabled.
964 const DevelopmentFeatureFlags devFlags =
965 manageDevelopmentFeatures(mdlog, useGpuForNonbonded, pmeRunMode);
967 const bool useModularSimulator = checkUseModularSimulator(false,
975 membedHolder.doMembed());
978 // TODO: hide restraint implementation details from Mdrunner.
979 // There is nothing unique about restraints at this point as far as the
980 // Mdrunner is concerned. The Mdrunner should just be getting a sequence of
981 // factory functions from the SimulationContext on which to call mdModules_->add().
982 // TODO: capture all restraints into a single RestraintModule, passed to the runner builder.
983 for (auto&& restraint : restraintManager_->getRestraints())
985 auto module = RestraintMDModule::create(restraint, restraint->sites());
986 mdModules_->add(std::move(module));
989 // TODO: Error handling
990 mdModules_->assignOptionsToModules(*inputrec->params, nullptr);
991 // now that the MdModules know their options, they know which callbacks to sign up to
992 mdModules_->subscribeToSimulationSetupNotifications();
993 const auto& mdModulesNotifier = mdModules_->notifier().simulationSetupNotifications_;
995 if (inputrec->internalParameters != nullptr)
997 mdModulesNotifier.notify(*inputrec->internalParameters);
1000 if (fplog != nullptr)
1002 pr_inputrec(fplog, 0, "Input Parameters", inputrec.get(), FALSE);
1003 fprintf(fplog, "\n");
1008 /* In rerun, set velocities to zero if present */
1009 if (doRerun && ((globalState->flags & enumValueToBitMask(StateEntry::V)) != 0))
1011 // rerun does not use velocities
1015 "Rerun trajectory contains velocities. Rerun does only evaluate "
1016 "potential energy and forces. The velocities will be ignored.");
1017 for (int i = 0; i < globalState->natoms; i++)
1019 clear_rvec(globalState->v[i]);
1021 globalState->flags &= ~enumValueToBitMask(StateEntry::V);
1024 /* now make sure the state is initialized and propagated */
1025 set_state_entries(globalState.get(), inputrec.get(), useModularSimulator);
1028 /* NM and TPI parallelize over force/energy calculations, not atoms,
1029 * so we need to initialize and broadcast the global state.
1031 if (inputrec->eI == IntegrationAlgorithm::NM || inputrec->eI == IntegrationAlgorithm::TPI)
1035 globalState = std::make_unique<t_state>();
1037 broadcastStateWithoutDynamics(
1038 cr->mpiDefaultCommunicator, DOMAINDECOMP(cr), PAR(cr), globalState.get());
1041 /* A parallel command line option consistency check that we can
1042 only do after any threads have started. */
1044 && (domdecOptions.numCells[XX] > 1 || domdecOptions.numCells[YY] > 1
1045 || domdecOptions.numCells[ZZ] > 1 || domdecOptions.numPmeRanks > 0))
1048 "The -dd or -npme option request a parallel simulation, "
1050 "but %s was compiled without threads or MPI enabled",
1051 output_env_get_program_display_name(oenv));
1052 #elif GMX_THREAD_MPI
1053 "but the number of MPI-threads (option -ntmpi) is not set or is 1");
1055 "but %s was not started through mpirun/mpiexec or only one rank was requested "
1056 "through mpirun/mpiexec",
1057 output_env_get_program_display_name(oenv));
1061 if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || IntegrationAlgorithm::NM == inputrec->eI))
1064 "The .mdp file specified an energy mininization or normal mode algorithm, and "
1065 "these are not compatible with mdrun -rerun");
1068 /* Object for collecting reasons for not using PME-only ranks */
1069 SeparatePmeRanksPermitted separatePmeRanksPermitted;
1071 /* Permit MDModules to notify whether they want to use PME-only ranks */
1072 mdModulesNotifier.notify(&separatePmeRanksPermitted);
1074 /* If simulation is not using PME then disable PME-only ranks */
1075 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
1077 separatePmeRanksPermitted.disablePmeRanks(
1078 "PME-only ranks are requested, but the system does not use PME "
1079 "for electrostatics or LJ");
1082 /* With NB GPUs we don't automatically use PME-only CPU ranks. PME ranks can
1083 * improve performance with many threads per GPU, since our OpenMP
1084 * scaling is bad, but it's difficult to automate the setup.
1086 if (useGpuForNonbonded && domdecOptions.numPmeRanks < 0)
1088 separatePmeRanksPermitted.disablePmeRanks(
1089 "PME-only CPU ranks are not automatically used when "
1090 "non-bonded interactions are computed on GPUs");
1093 /* If GPU is used for PME then only 1 PME rank is permitted */
1094 if (useGpuForPme && (domdecOptions.numPmeRanks < 0 || domdecOptions.numPmeRanks > 1))
1096 separatePmeRanksPermitted.disablePmeRanks(
1097 "PME GPU decomposition is not supported. Only one separate PME-only GPU rank "
1101 /* Disable PME-only ranks if some parts of the code requested so and it's up to GROMACS to decide */
1102 if (!separatePmeRanksPermitted.permitSeparatePmeRanks() && domdecOptions.numPmeRanks < 0)
1104 domdecOptions.numPmeRanks = 0;
1107 .appendText("Simulation will not use PME-only ranks because: "
1108 + separatePmeRanksPermitted.reasonsWhyDisabled());
1111 /* If some parts of the code could not use PME-only ranks and
1112 * user explicitly used mdrun -npme option then throw an error */
1113 if (!separatePmeRanksPermitted.permitSeparatePmeRanks() && domdecOptions.numPmeRanks > 0)
1115 gmx_fatal_collective(FARGS,
1116 cr->mpiDefaultCommunicator,
1118 "Requested -npme %d option is not viable because: %s",
1119 domdecOptions.numPmeRanks,
1120 separatePmeRanksPermitted.reasonsWhyDisabled().c_str());
1123 /* NMR restraints must be initialized before load_checkpoint,
1124 * since with time averaging the history is added to t_state.
1125 * For proper consistency check we therefore need to extend
1127 * So the PME-only nodes (if present) will also initialize
1128 * the distance restraints.
1131 /* This needs to be called before read_checkpoint to extend the state */
1132 t_disresdata* disresdata;
1133 snew(disresdata, 1);
1137 DisResRunMode::MDRun,
1138 MASTER(cr) ? DDRole::Master : DDRole::Agent,
1139 PAR(cr) ? NumRanks::Multiple : NumRanks::Single,
1144 replExParams.exchangeInterval > 0);
1146 t_oriresdata* oriresdata;
1147 snew(oriresdata, 1);
1148 init_orires(fplog, mtop, inputrec.get(), cr, ms, globalState.get(), oriresdata);
1150 auto deform = prepareBoxDeformation(globalState != nullptr ? globalState->box : box,
1151 MASTER(cr) ? DDRole::Master : DDRole::Agent,
1152 PAR(cr) ? NumRanks::Multiple : NumRanks::Single,
1153 cr->mpi_comm_mygroup,
1157 /* We have to remember the generation's first step before reading checkpoint.
1158 This way, we can report to the F@H core both the generation's first step
1159 and the restored first step, thus making it able to distinguish between
1160 an interruption/resume and start of the n-th generation simulation.
1161 Having this information, the F@H core can correctly calculate and report
1164 int gen_first_step = 0;
1167 gen_first_step = inputrec->init_step;
1171 ObservablesHistory observablesHistory = {};
1173 auto modularSimulatorCheckpointData = std::make_unique<ReadCheckpointDataHolder>();
1174 if (startingBehavior != StartingBehavior::NewSimulation)
1176 /* Check if checkpoint file exists before doing continuation.
1177 * This way we can use identical input options for the first and subsequent runs...
1179 if (mdrunOptions.numStepsCommandline > -2)
1181 /* Temporarily set the number of steps to unlimited to avoid
1182 * triggering the nsteps check in load_checkpoint().
1183 * This hack will go away soon when the -nsteps option is removed.
1185 inputrec->nsteps = -1;
1188 // Finish applying initial simulation state information from external sources on all ranks.
1189 // Reconcile checkpoint file data with Mdrunner state established up to this point.
1190 applyLocalState(*inputHolder_.get(),
1193 domdecOptions.numCells,
1196 &observablesHistory,
1197 mdrunOptions.reproducible,
1198 mdModules_->notifier(),
1199 modularSimulatorCheckpointData.get(),
1200 useModularSimulator);
1201 // TODO: (#3652) Synchronize filesystem state, SimulationInput contents, and program
1203 // on all code paths.
1204 // Write checkpoint or provide hook to update SimulationInput.
1205 // If there was a checkpoint file, SimulationInput contains more information
1206 // than if there wasn't. At this point, we have synchronized the in-memory
1207 // state with the filesystem state only for restarted simulations. We should
1208 // be calling applyLocalState unconditionally and expect that the completeness
1209 // of SimulationInput is not dependent on its creation method.
1211 if (startingBehavior == StartingBehavior::RestartWithAppending && logFileHandle)
1213 // Now we can start normal logging to the truncated log file.
1214 fplog = gmx_fio_getfp(logFileHandle);
1215 prepareLogAppending(fplog);
1216 logOwner = buildLogger(fplog, MASTER(cr));
1217 mdlog = logOwner.logger();
1224 fcRegisterSteps(inputrec->nsteps + inputrec->init_step, gen_first_step);
1228 if (mdrunOptions.numStepsCommandline > -2)
1233 "The -nsteps functionality is deprecated, and may be removed in a future "
1235 "Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp "
1238 /* override nsteps with value set on the commandline */
1239 override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec.get());
1241 if (isSimulationMasterRank)
1243 copy_mat(globalState->box, box);
1248 gmx_bcast(sizeof(box), box, cr->mpiDefaultCommunicator);
1251 if (inputrec->cutoff_scheme != CutoffScheme::Verlet)
1254 "This group-scheme .tpr file can no longer be run by mdrun. Please update to the "
1255 "Verlet scheme, or use an earlier version of GROMACS if necessary.");
1257 /* Update rlist and nstlist. */
1258 /* Note: prepare_verlet_scheme is calling increaseNstlist(...), which (while attempting to
1259 * increase rlist) tries to check if the newly chosen value fits with the DD scheme. As this is
1260 * run before any DD scheme is set up, this check is never executed. See #3334 for more details.
1262 prepare_verlet_scheme(fplog,
1268 useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes),
1271 // This builder is necessary while we have multi-part construction
1272 // of DD. Before DD is constructed, we use the existence of
1273 // the builder object to indicate that further construction of DD
1275 std::unique_ptr<DomainDecompositionBuilder> ddBuilder;
1276 if (useDomainDecomposition)
1278 ddBuilder = std::make_unique<DomainDecompositionBuilder>(
1286 positionsFromStatePointer(globalState.get()));
1290 /* PME, if used, is done on all nodes with 1D decomposition */
1291 cr->nnodes = cr->sizeOfDefaultCommunicator;
1292 cr->sim_nodeid = cr->rankInDefaultCommunicator;
1293 cr->nodeid = cr->rankInDefaultCommunicator;
1295 cr->duty = (DUTY_PP | DUTY_PME);
1297 if (inputrec->pbcType == PbcType::Screw)
1299 gmx_fatal(FARGS, "pbc=screw is only implemented with domain decomposition");
1303 // Produce the task assignment for this rank - done after DD is constructed
1304 GpuTaskAssignments gpuTaskAssignments = GpuTaskAssignmentsBuilder::build(
1306 userGpuTaskAssignment,
1308 simulationCommunicator,
1316 thisRankHasDuty(cr, DUTY_PP),
1317 // TODO cr->duty & DUTY_PME should imply that a PME
1318 // algorithm is active, but currently does not.
1319 EEL_PME(inputrec->coulombtype) && thisRankHasDuty(cr, DUTY_PME));
1321 // Get the device handles for the modules, nullptr when no task is assigned.
1323 DeviceInformation* deviceInfo = gpuTaskAssignments.initDevice(&deviceId);
1325 // timing enabling - TODO put this in gpu_utils (even though generally this is just option handling?)
1326 bool useTiming = true;
1330 /* WARNING: CUDA timings are incorrect with multiple streams.
1331 * This is the main reason why they are disabled by default.
1333 // TODO: Consider turning on by default when we can detect nr of streams.
1334 useTiming = (getenv("GMX_ENABLE_GPU_TIMING") != nullptr);
1336 else if (GMX_GPU_OPENCL)
1338 useTiming = (getenv("GMX_DISABLE_GPU_TIMING") == nullptr);
1341 // TODO Currently this is always built, yet DD partition code
1342 // checks if it is built before using it. Probably it should
1343 // become an MDModule that is made only when another module
1344 // requires it (e.g. pull, CompEl, density fitting), so that we
1345 // don't update the local atom sets unilaterally every step.
1346 LocalAtomSetManager atomSets;
1349 // TODO Pass the GPU streams to ddBuilder to use in buffer
1350 // transfers (e.g. halo exchange)
1351 cr->dd = ddBuilder->build(&atomSets);
1352 // The builder's job is done, so destruct it
1353 ddBuilder.reset(nullptr);
1354 // Note that local state still does not exist yet.
1357 // The GPU update is decided here because we need to know whether the constraints or
1358 // SETTLEs can span accross the domain borders (i.e. whether or not update groups are
1359 // defined). This is only known after DD is initialized, hence decision on using GPU
1360 // update is done so late.
1363 const bool useUpdateGroups = cr->dd ? ddUsesUpdateGroups(*cr->dd) : false;
1364 const bool haveFrozenAtoms = inputrecFrozenAtoms(inputrec.get());
1366 useGpuForUpdate = decideWhetherToUseGpuForUpdate(useDomainDecomposition,
1369 domdecOptions.numPmeRanks > 0,
1375 doEssentialDynamics,
1376 gmx_mtop_ftype_count(mtop, F_ORIRES) > 0,
1377 replExParams.exchangeInterval > 0,
1383 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1385 const bool printHostName = (cr->nnodes > 1);
1386 gpuTaskAssignments.reportGpuUsage(mdlog, printHostName, useGpuForBonded, pmeRunMode, useGpuForUpdate);
1388 const bool disableNonbondedCalculation = (getenv("GMX_NO_NONBONDED") != nullptr);
1389 if (disableNonbondedCalculation)
1391 /* turn off non-bonded calculations */
1392 GMX_LOG(mdlog.warning)
1395 "Found environment variable GMX_NO_NONBONDED.\n"
1396 "Disabling nonbonded calculations.");
1399 MdrunScheduleWorkload runScheduleWork;
1401 bool useGpuDirectHalo = decideWhetherToUseGpuForHalo(devFlags,
1402 havePPDomainDecomposition(cr),
1404 useModularSimulator,
1406 EI_ENERGY_MINIMIZATION(inputrec->eI));
1408 // Also populates the simulation constant workload description.
1409 runScheduleWork.simulationWork = createSimulationWorkload(*inputrec,
1410 disableNonbondedCalculation,
1418 std::unique_ptr<DeviceStreamManager> deviceStreamManager = nullptr;
1420 if (deviceInfo != nullptr)
1422 if (DOMAINDECOMP(cr) && thisRankHasDuty(cr, DUTY_PP))
1424 dd_setup_dlb_resource_sharing(cr, deviceId);
1426 deviceStreamManager = std::make_unique<DeviceStreamManager>(
1427 *deviceInfo, havePPDomainDecomposition(cr), runScheduleWork.simulationWork, useTiming);
1430 // If the user chose a task assignment, give them some hints
1431 // where appropriate.
1432 if (!userGpuTaskAssignment.empty())
1434 gpuTaskAssignments.logPerformanceHints(mdlog, numAvailableDevices);
1439 /* After possible communicator splitting in make_dd_communicators.
1440 * we can set up the intra/inter node communication.
1442 gmx_setup_nodecomm(fplog, cr);
1448 GMX_LOG(mdlog.warning)
1450 .appendTextFormatted(
1451 "This is simulation %d out of %d running as a composite GROMACS\n"
1452 "multi-simulation job. Setup for this simulation:\n",
1453 ms->simulationIndex_,
1454 ms->numSimulations_);
1456 GMX_LOG(mdlog.warning)
1457 .appendTextFormatted("Using %d MPI %s\n",
1460 cr->nnodes == 1 ? "thread" : "threads"
1462 cr->nnodes == 1 ? "process" : "processes"
1468 // If mdrun -pin auto honors any affinity setting that already
1469 // exists. If so, it is nice to provide feedback about whether
1470 // that existing affinity setting was from OpenMP or something
1471 // else, so we run this code both before and after we initialize
1472 // the OpenMP support.
1473 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo_->nthreads_hw_avail, FALSE);
1474 /* Check and update the number of OpenMP threads requested */
1475 checkAndUpdateRequestedNumOpenmpThreads(
1476 &hw_opt, *hwinfo_, cr, ms, physicalNodeComm.size_, pmeRunMode, mtop, *inputrec);
1478 gmx_omp_nthreads_init(mdlog,
1480 hwinfo_->nthreads_hw_avail,
1481 physicalNodeComm.size_,
1482 hw_opt.nthreads_omp,
1483 hw_opt.nthreads_omp_pme,
1484 !thisRankHasDuty(cr, DUTY_PP));
1486 const bool bEnableFPE = gmxShouldEnableFPExceptions();
1487 // FIXME - reconcile with gmx_feenableexcept() call from CommandLineModuleManager::run()
1490 gmx_feenableexcept();
1493 /* Now that we know the setup is consistent, check for efficiency */
1494 check_resource_division_efficiency(
1495 hwinfo_, gpuTaskAssignments.thisRankHasAnyGpuTask(), mdrunOptions.ntompOptionIsSet, cr, mdlog);
1497 /* getting number of PP/PME threads on this MPI / tMPI rank.
1498 PME: env variable should be read only on one node to make sure it is
1499 identical everywhere;
1501 const int numThreadsOnThisRank = thisRankHasDuty(cr, DUTY_PP) ? gmx_omp_nthreads_get(emntNonbonded)
1502 : gmx_omp_nthreads_get(emntPME);
1503 checkHardwareOversubscription(
1504 numThreadsOnThisRank, cr->nodeid, *hwinfo_->hardwareTopology, physicalNodeComm, mdlog);
1506 // Enable Peer access between GPUs where available
1507 // Only for DD, only master PP rank needs to perform setup, and only if thread MPI plus
1508 // any of the GPU communication features are active.
1509 if (DOMAINDECOMP(cr) && MASTER(cr) && thisRankHasDuty(cr, DUTY_PP) && GMX_THREAD_MPI
1510 && (runScheduleWork.simulationWork.useGpuHaloExchange
1511 || runScheduleWork.simulationWork.useGpuPmePpCommunication))
1513 setupGpuDevicePeerAccess(gpuTaskAssignments.deviceIdsAssigned(), mdlog);
1516 if (hw_opt.threadAffinity != ThreadAffinity::Off)
1518 /* Before setting affinity, check whether the affinity has changed
1519 * - which indicates that probably the OpenMP library has changed it
1520 * since we first checked).
1522 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo_->nthreads_hw_avail, TRUE);
1524 int numThreadsOnThisNode, intraNodeThreadOffset;
1525 analyzeThreadsOnThisNode(
1526 physicalNodeComm, numThreadsOnThisRank, &numThreadsOnThisNode, &intraNodeThreadOffset);
1528 /* Set the CPU affinity */
1529 gmx_set_thread_affinity(mdlog,
1532 *hwinfo_->hardwareTopology,
1533 numThreadsOnThisRank,
1534 numThreadsOnThisNode,
1535 intraNodeThreadOffset,
1539 if (mdrunOptions.timingOptions.resetStep > -1)
1544 "The -resetstep functionality is deprecated, and may be removed in a "
1547 wcycle = wallcycle_init(fplog, mdrunOptions.timingOptions.resetStep, cr);
1551 /* Master synchronizes its value of reset_counters with all nodes
1552 * including PME only nodes */
1553 int64_t reset_counters = wcycle_get_reset_counters(wcycle);
1554 gmx_bcast(sizeof(reset_counters), &reset_counters, cr->mpi_comm_mysim);
1555 wcycle_set_reset_counters(wcycle, reset_counters);
1558 // Membrane embedding must be initialized before we call init_forcerec()
1559 membedHolder.initializeMembed(fplog,
1566 &mdrunOptions.checkpointOptions.period);
1568 const bool thisRankHasPmeGpuTask = gpuTaskAssignments.thisRankHasPmeGpuTask();
1569 std::unique_ptr<MDAtoms> mdAtoms;
1570 std::unique_ptr<VirtualSitesHandler> vsite;
1571 std::unique_ptr<GpuBonded> gpuBonded;
1574 if (thisRankHasDuty(cr, DUTY_PP))
1576 mdModulesNotifier.notify(*cr);
1577 mdModulesNotifier.notify(&atomSets);
1578 mdModulesNotifier.notify(mtop);
1579 mdModulesNotifier.notify(inputrec->pbcType);
1580 mdModulesNotifier.notify(SimulationTimeStep{ inputrec->delta_t });
1581 /* Initiate forcerecord */
1582 fr = std::make_unique<t_forcerec>();
1583 fr->forceProviders = mdModules_->initForceProviders();
1584 init_forcerec(fplog,
1591 opt2fn("-table", filenames.size(), filenames.data()),
1592 opt2fn("-tablep", filenames.size(), filenames.data()),
1593 opt2fns("-tableb", filenames.size(), filenames.data()),
1595 // Dirty hack, for fixing disres and orires should be made mdmodules
1596 fr->fcdata->disres = disresdata;
1597 fr->fcdata->orires = oriresdata;
1599 // Save a handle to device stream manager to use elsewhere in the code
1600 // TODO: Forcerec is not a correct place to store it.
1601 fr->deviceStreamManager = deviceStreamManager.get();
1603 if (runScheduleWork.simulationWork.useGpuPmePpCommunication && !thisRankHasDuty(cr, DUTY_PME))
1606 deviceStreamManager != nullptr,
1607 "GPU device stream manager should be valid in order to use PME-PP direct "
1610 deviceStreamManager->streamIsValid(DeviceStreamType::PmePpTransfer),
1611 "GPU PP-PME stream should be valid in order to use GPU PME-PP direct "
1613 fr->pmePpCommGpu = std::make_unique<gmx::PmePpCommGpu>(
1616 deviceStreamManager->context(),
1617 deviceStreamManager->stream(DeviceStreamType::PmePpTransfer));
1620 fr->nbv = Nbnxm::init_nb_verlet(mdlog,
1625 runScheduleWork.simulationWork.useGpuNonbonded,
1626 deviceStreamManager.get(),
1630 // TODO: Move the logic below to a GPU bonded builder
1631 if (runScheduleWork.simulationWork.useGpuBonded)
1633 GMX_RELEASE_ASSERT(deviceStreamManager != nullptr,
1634 "GPU device stream manager should be valid in order to use GPU "
1635 "version of bonded forces.");
1636 gpuBonded = std::make_unique<GpuBonded>(
1638 fr->ic->epsfac * fr->fudgeQQ,
1639 deviceStreamManager->context(),
1640 deviceStreamManager->bondedStream(havePPDomainDecomposition(cr)),
1642 fr->gpuBonded = gpuBonded.get();
1645 /* Initialize the mdAtoms structure.
1646 * mdAtoms is not filled with atom data,
1647 * as this can not be done now with domain decomposition.
1649 mdAtoms = makeMDAtoms(fplog, mtop, *inputrec, thisRankHasPmeGpuTask);
1650 if (globalState && thisRankHasPmeGpuTask)
1652 // The pinning of coordinates in the global state object works, because we only use
1653 // PME on GPU without DD or on a separate PME rank, and because the local state pointer
1654 // points to the global state object without DD.
1655 // FIXME: MD and EM separately set up the local state - this should happen in the same
1656 // function, which should also perform the pinning.
1657 changePinningPolicy(&globalState->x, pme_get_pinning_policy());
1660 /* Initialize the virtual site communication */
1661 vsite = makeVirtualSitesHandler(mtop, cr, fr->pbcType);
1663 calc_shifts(box, fr->shift_vec);
1665 /* With periodic molecules the charge groups should be whole at start up
1666 * and the virtual sites should not be far from their proper positions.
1668 if (!inputrec->bContinuation && MASTER(cr)
1669 && !(inputrec->pbcType != PbcType::No && inputrec->bPeriodicMols))
1671 /* Make molecules whole at start of run */
1672 if (fr->pbcType != PbcType::No)
1674 do_pbc_first_mtop(fplog, inputrec->pbcType, box, &mtop, globalState->x.rvec_array());
1678 /* Correct initial vsite positions are required
1679 * for the initial distribution in the domain decomposition
1680 * and for the initial shell prediction.
1682 constructVirtualSitesGlobal(mtop, globalState->x);
1686 if (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
1688 ewaldcoeff_q = fr->ic->ewaldcoeff_q;
1689 ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
1694 /* This is a PME only node */
1696 GMX_ASSERT(globalState == nullptr,
1697 "We don't need the state on a PME only rank and expect it to be unitialized");
1699 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
1700 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
1703 gmx_pme_t* sepPmeData = nullptr;
1704 // This reference hides the fact that PME data is owned by runner on PME-only ranks and by forcerec on other ranks
1705 GMX_ASSERT(thisRankHasDuty(cr, DUTY_PP) == (fr != nullptr),
1706 "Double-checking that only PME-only ranks have no forcerec");
1707 gmx_pme_t*& pmedata = fr ? fr->pmedata : sepPmeData;
1709 // TODO should live in ewald module once its testing is improved
1711 // Later, this program could contain kernels that might be later
1712 // re-used as auto-tuning progresses, or subsequent simulations
1714 PmeGpuProgramStorage pmeGpuProgram;
1715 if (thisRankHasPmeGpuTask)
1718 (deviceStreamManager != nullptr),
1719 "GPU device stream manager should be initialized in order to use GPU for PME.");
1720 GMX_RELEASE_ASSERT((deviceInfo != nullptr),
1721 "GPU device should be initialized in order to use GPU for PME.");
1722 pmeGpuProgram = buildPmeGpuProgram(deviceStreamManager->context());
1725 /* Initiate PME if necessary,
1726 * either on all nodes or on dedicated PME nodes only. */
1727 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
1729 if (mdAtoms && mdAtoms->mdatoms())
1731 nChargePerturbed = mdAtoms->mdatoms()->nChargePerturbed;
1732 if (EVDW_PME(inputrec->vdwtype))
1734 nTypePerturbed = mdAtoms->mdatoms()->nTypePerturbed;
1737 if (cr->npmenodes > 0)
1739 /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
1740 gmx_bcast(sizeof(nChargePerturbed), &nChargePerturbed, cr->mpi_comm_mysim);
1741 gmx_bcast(sizeof(nTypePerturbed), &nTypePerturbed, cr->mpi_comm_mysim);
1744 if (thisRankHasDuty(cr, DUTY_PME))
1748 // TODO: This should be in the builder.
1749 GMX_RELEASE_ASSERT(!runScheduleWork.simulationWork.useGpuPme
1750 || (deviceStreamManager != nullptr),
1751 "Device stream manager should be valid in order to use GPU "
1754 !runScheduleWork.simulationWork.useGpuPme
1755 || deviceStreamManager->streamIsValid(DeviceStreamType::Pme),
1756 "GPU PME stream should be valid in order to use GPU version of PME.");
1758 const DeviceContext* deviceContext = runScheduleWork.simulationWork.useGpuPme
1759 ? &deviceStreamManager->context()
1761 const DeviceStream* pmeStream =
1762 runScheduleWork.simulationWork.useGpuPme
1763 ? &deviceStreamManager->stream(DeviceStreamType::Pme)
1766 pmedata = gmx_pme_init(cr,
1767 getNumPmeDomains(cr->dd),
1769 nChargePerturbed != 0,
1770 nTypePerturbed != 0,
1771 mdrunOptions.reproducible,
1774 gmx_omp_nthreads_get(emntPME),
1779 pmeGpuProgram.get(),
1782 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1787 if (EI_DYNAMICS(inputrec->eI))
1789 /* Turn on signal handling on all nodes */
1791 * (A user signal from the PME nodes (if any)
1792 * is communicated to the PP nodes.
1794 signal_handler_install();
1797 pull_t* pull_work = nullptr;
1798 if (thisRankHasDuty(cr, DUTY_PP))
1800 /* Assumes uniform use of the number of OpenMP threads */
1801 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
1803 if (inputrec->bPull)
1805 /* Initialize pull code */
1806 pull_work = init_pull(fplog,
1807 inputrec->pull.get(),
1812 inputrec->fepvals->init_lambda);
1813 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
1815 initPullHistory(pull_work, &observablesHistory);
1817 if (EI_DYNAMICS(inputrec->eI) && MASTER(cr))
1819 init_pull_output_files(pull_work, filenames.size(), filenames.data(), oenv, startingBehavior);
1823 std::unique_ptr<EnforcedRotation> enforcedRotation;
1826 /* Initialize enforced rotation code */
1827 enforcedRotation = init_rot(fplog,
1840 t_swap* swap = nullptr;
1841 if (inputrec->eSwapCoords != SwapType::No)
1843 /* Initialize ion swapping code */
1844 swap = init_swapcoords(fplog,
1846 opt2fn_master("-swap", filenames.size(), filenames.data(), cr),
1849 &observablesHistory,
1857 /* Let makeConstraints know whether we have essential dynamics constraints. */
1858 auto constr = makeConstraints(
1859 mtop, *inputrec, pull_work, doEssentialDynamics, fplog, cr, ms, &nrnb, wcycle, fr->bMolPBC);
1861 /* Energy terms and groups */
1862 gmx_enerdata_t enerd(mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
1863 inputrec->fepvals->n_lambda);
1865 // cos acceleration is only supported by md, but older tpr
1866 // files might still combine it with other integrators
1867 GMX_RELEASE_ASSERT(inputrec->cos_accel == 0.0 || inputrec->eI == IntegrationAlgorithm::MD,
1868 "cos_acceleration is only supported by integrator=md");
1870 /* Kinetic energy data */
1871 gmx_ekindata_t ekind;
1872 init_ekindata(fplog, &(inputrec->opts), &ekind, inputrec->cos_accel);
1874 /* Set up interactive MD (IMD) */
1875 auto imdSession = makeImdSession(inputrec.get(),
1882 MASTER(cr) ? globalState->x.rvec_array() : nullptr,
1886 mdrunOptions.imdOptions,
1889 if (DOMAINDECOMP(cr))
1891 GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
1892 /* This call is not included in init_domain_decomposition mainly
1893 * because fr->cginfo_mb is set later.
1895 dd_init_bondeds(fplog,
1900 domdecOptions.checkBondedInteractions ? DDBondedChecking::All
1901 : DDBondedChecking::ExcludeZeroLimit,
1905 if (runScheduleWork.simulationWork.useGpuBufferOps)
1907 fr->gpuForceReduction[gmx::AtomLocality::Local] = std::make_unique<gmx::GpuForceReduction>(
1908 deviceStreamManager->context(),
1909 deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedLocal),
1911 fr->gpuForceReduction[gmx::AtomLocality::NonLocal] = std::make_unique<gmx::GpuForceReduction>(
1912 deviceStreamManager->context(),
1913 deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedNonLocal),
1917 std::unique_ptr<gmx::StatePropagatorDataGpu> stateGpu;
1918 if (gpusWereDetected
1919 && ((runScheduleWork.simulationWork.useGpuPme && thisRankHasDuty(cr, DUTY_PME))
1920 || runScheduleWork.simulationWork.useGpuBufferOps))
1922 GpuApiCallBehavior transferKind =
1923 (inputrec->eI == IntegrationAlgorithm::MD && !doRerun && !useModularSimulator)
1924 ? GpuApiCallBehavior::Async
1925 : GpuApiCallBehavior::Sync;
1926 GMX_RELEASE_ASSERT(deviceStreamManager != nullptr,
1927 "GPU device stream manager should be initialized to use GPU.");
1928 stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(
1929 *deviceStreamManager, transferKind, pme_gpu_get_block_size(fr->pmedata), wcycle);
1930 fr->stateGpu = stateGpu.get();
1933 GMX_ASSERT(stopHandlerBuilder_, "Runner must provide StopHandlerBuilder to simulator.");
1934 SimulatorBuilder simulatorBuilder;
1936 simulatorBuilder.add(SimulatorStateData(globalState.get(), &observablesHistory, &enerd, &ekind));
1937 simulatorBuilder.add(std::move(membedHolder));
1938 simulatorBuilder.add(std::move(stopHandlerBuilder_));
1939 simulatorBuilder.add(SimulatorConfig(mdrunOptions, startingBehavior, &runScheduleWork));
1942 simulatorBuilder.add(SimulatorEnv(fplog, cr, ms, mdlog, oenv));
1943 simulatorBuilder.add(Profiling(&nrnb, walltime_accounting, wcycle));
1944 simulatorBuilder.add(ConstraintsParam(
1945 constr.get(), enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr, vsite.get()));
1946 // TODO: Separate `fr` to a separate add, and make the `build` handle the coupling sensibly.
1947 simulatorBuilder.add(LegacyInput(
1948 static_cast<int>(filenames.size()), filenames.data(), inputrec.get(), fr.get()));
1949 simulatorBuilder.add(ReplicaExchangeParameters(replExParams));
1950 simulatorBuilder.add(InteractiveMD(imdSession.get()));
1951 simulatorBuilder.add(SimulatorModules(mdModules_->outputProvider(), mdModules_->notifier()));
1952 simulatorBuilder.add(CenterOfMassPulling(pull_work));
1953 // Todo move to an MDModule
1954 simulatorBuilder.add(IonSwapping(swap));
1955 simulatorBuilder.add(TopologyData(mtop, mdAtoms.get()));
1956 simulatorBuilder.add(BoxDeformationHandle(deform.get()));
1957 simulatorBuilder.add(std::move(modularSimulatorCheckpointData));
1959 // build and run simulator object based on user-input
1960 auto simulator = simulatorBuilder.build(useModularSimulator);
1963 if (fr->pmePpCommGpu)
1965 // destroy object since it is no longer required. (This needs to be done while the GPU context still exists.)
1966 fr->pmePpCommGpu.reset();
1969 if (inputrec->bPull)
1971 finish_pull(pull_work);
1973 finish_swapcoords(swap);
1977 GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
1979 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
1980 gmx_pmeonly(pmedata,
1984 walltime_accounting,
1987 deviceStreamManager.get());
1990 wallcycle_stop(wcycle, ewcRUN);
1992 /* Finish up, write some stuff
1993 * if rerunMD, don't write last frame again
2001 walltime_accounting,
2002 fr ? fr->nbv.get() : nullptr,
2004 EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
2006 // clean up cycle counter
2007 wallcycle_destroy(wcycle);
2009 deviceStreamManager.reset(nullptr);
2013 gmx_pme_destroy(pmedata);
2017 // FIXME: this is only here to manually unpin mdAtoms->chargeA_ and state->x,
2018 // before we destroy the GPU context(s)
2019 // Pinned buffers are associated with contexts in CUDA.
2020 // As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
2021 mdAtoms.reset(nullptr);
2022 globalState.reset(nullptr);
2023 mdModules_.reset(nullptr); // destruct force providers here as they might also use the GPU
2024 gpuBonded.reset(nullptr);
2025 fr.reset(nullptr); // destruct forcerec before gpu
2026 // TODO convert to C++ so we can get rid of these frees
2030 if (!hwinfo_->deviceInfoList.empty())
2032 /* stop the GPU profiler (only CUDA) */
2036 /* With tMPI we need to wait for all ranks to finish deallocation before
2037 * destroying the CUDA context as some tMPI ranks may be sharing
2040 * This is not a concern in OpenCL where we use one context per rank.
2042 * Note: it is safe to not call the barrier on the ranks which do not use GPU,
2043 * but it is easier and more futureproof to call it on the whole node.
2045 * Note that this function needs to be called even if GPUs are not used
2046 * in this run because the PME ranks have no knowledge of whether GPUs
2047 * are used or not, but all ranks need to enter the barrier below.
2048 * \todo Remove this physical node barrier after making sure
2049 * that it's not needed anymore (with a shared GPU run).
2053 physicalNodeComm.barrier();
2055 releaseDevice(deviceInfo);
2057 /* Does what it says */
2058 print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
2059 walltime_accounting_destroy(walltime_accounting);
2061 // Ensure log file content is written
2064 gmx_fio_flush(logFileHandle);
2067 /* Reset FPEs (important for unit tests) by disabling them. Assumes no
2068 * exceptions were enabled before function was called. */
2071 gmx_fedisableexcept();
2074 auto rc = static_cast<int>(gmx_get_stop_condition());
2077 /* we need to join all threads. The sub-threads join when they
2078 exit this function, but the master thread needs to be told to
2088 Mdrunner::~Mdrunner()
2090 // Clean up of the Manager.
2091 // This will end up getting called on every thread-MPI rank, which is unnecessary,
2092 // but okay as long as threads synchronize some time before adding or accessing
2093 // a new set of restraints.
2094 if (restraintManager_)
2096 restraintManager_->clear();
2097 GMX_ASSERT(restraintManager_->countRestraints() == 0,
2098 "restraints added during runner life time should be cleared at runner "
2103 void Mdrunner::addPotential(std::shared_ptr<gmx::IRestraintPotential> puller, const std::string& name)
2105 GMX_ASSERT(restraintManager_, "Mdrunner must have a restraint manager.");
2106 // Not sure if this should be logged through the md logger or something else,
2107 // but it is helpful to have some sort of INFO level message sent somewhere.
2108 // std::cout << "Registering restraint named " << name << std::endl;
2110 // When multiple restraints are used, it may be wasteful to register them separately.
2111 // Maybe instead register an entire Restraint Manager as a force provider.
2112 restraintManager_->addToSpec(std::move(puller), name);
2115 Mdrunner::Mdrunner(std::unique_ptr<MDModules> mdModules) : mdModules_(std::move(mdModules)) {}
2117 Mdrunner::Mdrunner(Mdrunner&&) noexcept = default;
2119 //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265 in CentOS 7
2120 Mdrunner& Mdrunner::operator=(Mdrunner&& /*handle*/) noexcept(BUGFREE_NOEXCEPT_STRING) = default;
2122 class Mdrunner::BuilderImplementation
2125 BuilderImplementation() = delete;
2126 BuilderImplementation(std::unique_ptr<MDModules> mdModules, compat::not_null<SimulationContext*> context);
2127 ~BuilderImplementation();
2129 BuilderImplementation& setExtraMdrunOptions(const MdrunOptions& options,
2130 real forceWarningThreshold,
2131 StartingBehavior startingBehavior);
2133 void addHardwareDetectionResult(const gmx_hw_info_t* hwinfo);
2135 void addDomdec(const DomdecOptions& options);
2137 void addInput(SimulationInputHandle inputHolder);
2139 void addVerletList(int nstlist);
2141 void addReplicaExchange(const ReplicaExchangeParameters& params);
2143 void addNonBonded(const char* nbpu_opt);
2145 void addPME(const char* pme_opt_, const char* pme_fft_opt_);
2147 void addBondedTaskAssignment(const char* bonded_opt);
2149 void addUpdateTaskAssignment(const char* update_opt);
2151 void addHardwareOptions(const gmx_hw_opt_t& hardwareOptions);
2153 void addFilenames(ArrayRef<const t_filenm> filenames);
2155 void addOutputEnvironment(gmx_output_env_t* outputEnvironment);
2157 void addLogFile(t_fileio* logFileHandle);
2159 void addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
2164 // Default parameters copied from runner.h
2165 // \todo Clarify source(s) of default parameters.
2167 const char* nbpu_opt_ = nullptr;
2168 const char* pme_opt_ = nullptr;
2169 const char* pme_fft_opt_ = nullptr;
2170 const char* bonded_opt_ = nullptr;
2171 const char* update_opt_ = nullptr;
2173 MdrunOptions mdrunOptions_;
2175 DomdecOptions domdecOptions_;
2177 ReplicaExchangeParameters replicaExchangeParameters_;
2179 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
2182 //! World communicator, used for hardware detection and task assignment
2183 MPI_Comm libraryWorldCommunicator_ = MPI_COMM_NULL;
2185 //! Multisim communicator handle.
2186 gmx_multisim_t* multiSimulation_;
2188 //! mdrun communicator
2189 MPI_Comm simulationCommunicator_ = MPI_COMM_NULL;
2191 //! Print a warning if any force is larger than this (in kJ/mol nm).
2192 real forceWarningThreshold_ = -1;
2194 //! Whether the simulation will start afresh, or restart with/without appending.
2195 StartingBehavior startingBehavior_ = StartingBehavior::NewSimulation;
2197 //! The modules that comprise the functionality of mdrun.
2198 std::unique_ptr<MDModules> mdModules_;
2200 //! Detected hardware.
2201 const gmx_hw_info_t* hwinfo_ = nullptr;
2203 //! \brief Parallelism information.
2204 gmx_hw_opt_t hardwareOptions_;
2206 //! filename options for simulation.
2207 ArrayRef<const t_filenm> filenames_;
2209 /*! \brief Handle to output environment.
2211 * \todo gmx_output_env_t needs lifetime management.
2213 gmx_output_env_t* outputEnvironment_ = nullptr;
2215 /*! \brief Non-owning handle to MD log file.
2217 * \todo Context should own output facilities for client.
2218 * \todo Improve log file handle management.
2220 * Code managing the FILE* relies on the ability to set it to
2221 * nullptr to check whether the filehandle is valid.
2223 t_fileio* logFileHandle_ = nullptr;
2226 * \brief Builder for simulation stop signal handler.
2228 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_ = nullptr;
2231 * \brief Sources for initial simulation state.
2233 * See issue #3652 for near-term refinements to the SimulationInput interface.
2235 * See issue #3379 for broader discussion on API aspects of simulation inputs and outputs.
2237 SimulationInputHandle inputHolder_;
2240 Mdrunner::BuilderImplementation::BuilderImplementation(std::unique_ptr<MDModules> mdModules,
2241 compat::not_null<SimulationContext*> context) :
2242 mdModules_(std::move(mdModules))
2244 libraryWorldCommunicator_ = context->libraryWorldCommunicator_;
2245 simulationCommunicator_ = context->simulationCommunicator_;
2246 multiSimulation_ = context->multiSimulation_.get();
2249 Mdrunner::BuilderImplementation::~BuilderImplementation() = default;
2251 Mdrunner::BuilderImplementation&
2252 Mdrunner::BuilderImplementation::setExtraMdrunOptions(const MdrunOptions& options,
2253 const real forceWarningThreshold,
2254 const StartingBehavior startingBehavior)
2256 mdrunOptions_ = options;
2257 forceWarningThreshold_ = forceWarningThreshold;
2258 startingBehavior_ = startingBehavior;
2262 void Mdrunner::BuilderImplementation::addDomdec(const DomdecOptions& options)
2264 domdecOptions_ = options;
2267 void Mdrunner::BuilderImplementation::addVerletList(int nstlist)
2272 void Mdrunner::BuilderImplementation::addReplicaExchange(const ReplicaExchangeParameters& params)
2274 replicaExchangeParameters_ = params;
2277 Mdrunner Mdrunner::BuilderImplementation::build()
2279 auto newRunner = Mdrunner(std::move(mdModules_));
2281 newRunner.mdrunOptions = mdrunOptions_;
2282 newRunner.pforce = forceWarningThreshold_;
2283 newRunner.startingBehavior = startingBehavior_;
2284 newRunner.domdecOptions = domdecOptions_;
2286 // \todo determine an invariant to check or confirm that all gmx_hw_opt_t objects are valid
2287 newRunner.hw_opt = hardwareOptions_;
2289 // No invariant to check. This parameter exists to optionally override other behavior.
2290 newRunner.nstlist_cmdline = nstlist_;
2292 newRunner.replExParams = replicaExchangeParameters_;
2294 newRunner.filenames = filenames_;
2296 newRunner.libraryWorldCommunicator = libraryWorldCommunicator_;
2298 newRunner.simulationCommunicator = simulationCommunicator_;
2300 // nullptr is a valid value for the multisim handle
2301 newRunner.ms = multiSimulation_;
2305 newRunner.hwinfo_ = hwinfo_;
2309 GMX_THROW(gmx::APIError(
2310 "MdrunnerBuilder::addHardwareDetectionResult() is required before build()"));
2315 newRunner.inputHolder_ = std::move(inputHolder_);
2319 GMX_THROW(gmx::APIError("MdrunnerBuilder::addInput() is required before build()."));
2322 // \todo Clarify ownership and lifetime management for gmx_output_env_t
2323 // \todo Update sanity checking when output environment has clearly specified invariants.
2324 // Initialization and default values for oenv are not well specified in the current version.
2325 if (outputEnvironment_)
2327 newRunner.oenv = outputEnvironment_;
2331 GMX_THROW(gmx::APIError(
2332 "MdrunnerBuilder::addOutputEnvironment() is required before build()"));
2335 newRunner.logFileHandle = logFileHandle_;
2339 newRunner.nbpu_opt = nbpu_opt_;
2343 GMX_THROW(gmx::APIError("MdrunnerBuilder::addNonBonded() is required before build()"));
2346 if (pme_opt_ && pme_fft_opt_)
2348 newRunner.pme_opt = pme_opt_;
2349 newRunner.pme_fft_opt = pme_fft_opt_;
2353 GMX_THROW(gmx::APIError("MdrunnerBuilder::addElectrostatics() is required before build()"));
2358 newRunner.bonded_opt = bonded_opt_;
2362 GMX_THROW(gmx::APIError(
2363 "MdrunnerBuilder::addBondedTaskAssignment() is required before build()"));
2368 newRunner.update_opt = update_opt_;
2372 GMX_THROW(gmx::APIError(
2373 "MdrunnerBuilder::addUpdateTaskAssignment() is required before build() "));
2377 newRunner.restraintManager_ = std::make_unique<gmx::RestraintManager>();
2379 if (stopHandlerBuilder_)
2381 newRunner.stopHandlerBuilder_ = std::move(stopHandlerBuilder_);
2385 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>();
2391 void Mdrunner::BuilderImplementation::addHardwareDetectionResult(const gmx_hw_info_t* hwinfo)
2396 void Mdrunner::BuilderImplementation::addNonBonded(const char* nbpu_opt)
2398 nbpu_opt_ = nbpu_opt;
2401 void Mdrunner::BuilderImplementation::addPME(const char* pme_opt, const char* pme_fft_opt)
2404 pme_fft_opt_ = pme_fft_opt;
2407 void Mdrunner::BuilderImplementation::addBondedTaskAssignment(const char* bonded_opt)
2409 bonded_opt_ = bonded_opt;
2412 void Mdrunner::BuilderImplementation::addUpdateTaskAssignment(const char* update_opt)
2414 update_opt_ = update_opt;
2417 void Mdrunner::BuilderImplementation::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2419 hardwareOptions_ = hardwareOptions;
2422 void Mdrunner::BuilderImplementation::addFilenames(ArrayRef<const t_filenm> filenames)
2424 filenames_ = filenames;
2427 void Mdrunner::BuilderImplementation::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2429 outputEnvironment_ = outputEnvironment;
2432 void Mdrunner::BuilderImplementation::addLogFile(t_fileio* logFileHandle)
2434 logFileHandle_ = logFileHandle;
2437 void Mdrunner::BuilderImplementation::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2439 stopHandlerBuilder_ = std::move(builder);
2442 void Mdrunner::BuilderImplementation::addInput(SimulationInputHandle inputHolder)
2444 inputHolder_ = std::move(inputHolder);
2447 MdrunnerBuilder::MdrunnerBuilder(std::unique_ptr<MDModules> mdModules,
2448 compat::not_null<SimulationContext*> context) :
2449 impl_{ std::make_unique<Mdrunner::BuilderImplementation>(std::move(mdModules), context) }
2453 MdrunnerBuilder::~MdrunnerBuilder() = default;
2455 MdrunnerBuilder& MdrunnerBuilder::addHardwareDetectionResult(const gmx_hw_info_t* hwinfo)
2457 impl_->addHardwareDetectionResult(hwinfo);
2461 MdrunnerBuilder& MdrunnerBuilder::addSimulationMethod(const MdrunOptions& options,
2462 real forceWarningThreshold,
2463 const StartingBehavior startingBehavior)
2465 impl_->setExtraMdrunOptions(options, forceWarningThreshold, startingBehavior);
2469 MdrunnerBuilder& MdrunnerBuilder::addDomainDecomposition(const DomdecOptions& options)
2471 impl_->addDomdec(options);
2475 MdrunnerBuilder& MdrunnerBuilder::addNeighborList(int nstlist)
2477 impl_->addVerletList(nstlist);
2481 MdrunnerBuilder& MdrunnerBuilder::addReplicaExchange(const ReplicaExchangeParameters& params)
2483 impl_->addReplicaExchange(params);
2487 MdrunnerBuilder& MdrunnerBuilder::addNonBonded(const char* nbpu_opt)
2489 impl_->addNonBonded(nbpu_opt);
2493 MdrunnerBuilder& MdrunnerBuilder::addElectrostatics(const char* pme_opt, const char* pme_fft_opt)
2495 // The builder method may become more general in the future, but in this version,
2496 // parameters for PME electrostatics are both required and the only parameters
2498 if (pme_opt && pme_fft_opt)
2500 impl_->addPME(pme_opt, pme_fft_opt);
2505 gmx::InvalidInputError("addElectrostatics() arguments must be non-null pointers."));
2510 MdrunnerBuilder& MdrunnerBuilder::addBondedTaskAssignment(const char* bonded_opt)
2512 impl_->addBondedTaskAssignment(bonded_opt);
2516 MdrunnerBuilder& MdrunnerBuilder::addUpdateTaskAssignment(const char* update_opt)
2518 impl_->addUpdateTaskAssignment(update_opt);
2522 Mdrunner MdrunnerBuilder::build()
2524 return impl_->build();
2527 MdrunnerBuilder& MdrunnerBuilder::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2529 impl_->addHardwareOptions(hardwareOptions);
2533 MdrunnerBuilder& MdrunnerBuilder::addFilenames(ArrayRef<const t_filenm> filenames)
2535 impl_->addFilenames(filenames);
2539 MdrunnerBuilder& MdrunnerBuilder::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2541 impl_->addOutputEnvironment(outputEnvironment);
2545 MdrunnerBuilder& MdrunnerBuilder::addLogFile(t_fileio* logFileHandle)
2547 impl_->addLogFile(logFileHandle);
2551 MdrunnerBuilder& MdrunnerBuilder::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2553 impl_->addStopHandlerBuilder(std::move(builder));
2557 MdrunnerBuilder& MdrunnerBuilder::addInput(SimulationInputHandle input)
2559 impl_->addInput(std::move(input));
2563 MdrunnerBuilder::MdrunnerBuilder(MdrunnerBuilder&&) noexcept = default;
2565 MdrunnerBuilder& MdrunnerBuilder::operator=(MdrunnerBuilder&&) noexcept = default;