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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_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/gpu_utils.h"
77 #include "gromacs/hardware/cpuinfo.h"
78 #include "gromacs/hardware/detecthardware.h"
79 #include "gromacs/hardware/printhardware.h"
80 #include "gromacs/imd/imd.h"
81 #include "gromacs/listed_forces/disre.h"
82 #include "gromacs/listed_forces/gpubonded.h"
83 #include "gromacs/listed_forces/orires.h"
84 #include "gromacs/math/functions.h"
85 #include "gromacs/math/utilities.h"
86 #include "gromacs/math/vec.h"
87 #include "gromacs/mdlib/boxdeformation.h"
88 #include "gromacs/mdlib/broadcaststructs.h"
89 #include "gromacs/mdlib/calc_verletbuf.h"
90 #include "gromacs/mdlib/dispersioncorrection.h"
91 #include "gromacs/mdlib/enerdata_utils.h"
92 #include "gromacs/mdlib/force.h"
93 #include "gromacs/mdlib/forcerec.h"
94 #include "gromacs/mdlib/gmx_omp_nthreads.h"
95 #include "gromacs/mdlib/makeconstraints.h"
96 #include "gromacs/mdlib/md_support.h"
97 #include "gromacs/mdlib/mdatoms.h"
98 #include "gromacs/mdlib/membed.h"
99 #include "gromacs/mdlib/qmmm.h"
100 #include "gromacs/mdlib/sighandler.h"
101 #include "gromacs/mdlib/stophandler.h"
102 #include "gromacs/mdlib/updategroups.h"
103 #include "gromacs/mdrun/mdmodules.h"
104 #include "gromacs/mdrun/simulationcontext.h"
105 #include "gromacs/mdrunutility/handlerestart.h"
106 #include "gromacs/mdrunutility/logging.h"
107 #include "gromacs/mdrunutility/multisim.h"
108 #include "gromacs/mdrunutility/printtime.h"
109 #include "gromacs/mdrunutility/threadaffinity.h"
110 #include "gromacs/mdtypes/commrec.h"
111 #include "gromacs/mdtypes/enerdata.h"
112 #include "gromacs/mdtypes/fcdata.h"
113 #include "gromacs/mdtypes/group.h"
114 #include "gromacs/mdtypes/inputrec.h"
115 #include "gromacs/mdtypes/md_enums.h"
116 #include "gromacs/mdtypes/mdrunoptions.h"
117 #include "gromacs/mdtypes/observableshistory.h"
118 #include "gromacs/mdtypes/simulation_workload.h"
119 #include "gromacs/mdtypes/state.h"
120 #include "gromacs/mdtypes/state_propagator_data_gpu.h"
121 #include "gromacs/nbnxm/gpu_data_mgmt.h"
122 #include "gromacs/nbnxm/nbnxm.h"
123 #include "gromacs/nbnxm/pairlist_tuning.h"
124 #include "gromacs/pbcutil/pbc.h"
125 #include "gromacs/pulling/output.h"
126 #include "gromacs/pulling/pull.h"
127 #include "gromacs/pulling/pull_rotation.h"
128 #include "gromacs/restraint/manager.h"
129 #include "gromacs/restraint/restraintmdmodule.h"
130 #include "gromacs/restraint/restraintpotential.h"
131 #include "gromacs/swap/swapcoords.h"
132 #include "gromacs/taskassignment/decidegpuusage.h"
133 #include "gromacs/taskassignment/decidesimulationworkload.h"
134 #include "gromacs/taskassignment/resourcedivision.h"
135 #include "gromacs/taskassignment/taskassignment.h"
136 #include "gromacs/taskassignment/usergpuids.h"
137 #include "gromacs/timing/gpu_timing.h"
138 #include "gromacs/timing/wallcycle.h"
139 #include "gromacs/timing/wallcyclereporting.h"
140 #include "gromacs/topology/mtop_util.h"
141 #include "gromacs/trajectory/trajectoryframe.h"
142 #include "gromacs/utility/basenetwork.h"
143 #include "gromacs/utility/cstringutil.h"
144 #include "gromacs/utility/exceptions.h"
145 #include "gromacs/utility/fatalerror.h"
146 #include "gromacs/utility/filestream.h"
147 #include "gromacs/utility/gmxassert.h"
148 #include "gromacs/utility/gmxmpi.h"
149 #include "gromacs/utility/keyvaluetree.h"
150 #include "gromacs/utility/logger.h"
151 #include "gromacs/utility/loggerbuilder.h"
152 #include "gromacs/utility/mdmodulenotification.h"
153 #include "gromacs/utility/physicalnodecommunicator.h"
154 #include "gromacs/utility/pleasecite.h"
155 #include "gromacs/utility/programcontext.h"
156 #include "gromacs/utility/smalloc.h"
157 #include "gromacs/utility/stringutil.h"
159 #include "isimulator.h"
160 #include "replicaexchange.h"
161 #include "simulatorbuilder.h"
164 # include "corewrap.h"
170 /*! \brief Structure that holds boolean flags corresponding to the development
171 * features present enabled through environment variables.
174 struct DevelopmentFeatureFlags
176 //! True if the Buffer ops development feature is enabled
177 // TODO: when the trigger of the buffer ops offload is fully automated this should go away
178 bool enableGpuBufferOps = false;
179 //! If true, forces 'mdrun -update auto' default to 'gpu'
180 bool forceGpuUpdateDefault = false;
181 //! True if the GPU halo exchange development feature is enabled
182 bool enableGpuHaloExchange = false;
183 //! True if the PME PP direct communication GPU development feature is enabled
184 bool enableGpuPmePPComm = false;
187 /*! \brief Manage any development feature flag variables encountered
189 * The use of dev features indicated by environment variables is
190 * logged in order to ensure that runs with such features enabled can
191 * be identified from their log and standard output. Any cross
192 * dependencies are also checked, and if unsatisfied, a fatal error
195 * Note that some development features overrides are applied already here:
196 * the GPU communication flags are set to false in non-tMPI and non-CUDA builds.
198 * \param[in] mdlog Logger object.
199 * \param[in] useGpuForNonbonded True if the nonbonded task is offloaded in this run.
200 * \param[in] pmeRunMode The PME run mode for this run
201 * \returns The object populated with development feature flags.
203 static DevelopmentFeatureFlags manageDevelopmentFeatures(const gmx::MDLogger& mdlog,
204 const bool useGpuForNonbonded,
205 const PmeRunMode pmeRunMode)
207 DevelopmentFeatureFlags devFlags;
209 // Some builds of GCC 5 give false positive warnings that these
210 // getenv results are ignored when clearly they are used.
211 #pragma GCC diagnostic push
212 #pragma GCC diagnostic ignored "-Wunused-result"
213 devFlags.enableGpuBufferOps = (getenv("GMX_USE_GPU_BUFFER_OPS") != nullptr)
214 && (GMX_GPU == GMX_GPU_CUDA) && useGpuForNonbonded;
215 devFlags.forceGpuUpdateDefault = (getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") != nullptr);
216 devFlags.enableGpuHaloExchange =
217 (getenv("GMX_GPU_DD_COMMS") != nullptr && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA));
218 devFlags.enableGpuPmePPComm =
219 (getenv("GMX_GPU_PME_PP_COMMS") != nullptr && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA));
220 #pragma GCC diagnostic pop
222 if (devFlags.enableGpuBufferOps)
224 GMX_LOG(mdlog.warning)
226 .appendTextFormatted(
227 "This run uses the 'GPU buffer ops' feature, enabled by the "
228 "GMX_USE_GPU_BUFFER_OPS environment variable.");
231 if (devFlags.forceGpuUpdateDefault)
233 GMX_LOG(mdlog.warning)
235 .appendTextFormatted(
236 "This run will default to '-update gpu' as requested by the "
237 "GMX_FORCE_UPDATE_DEFAULT_GPU environment variable. GPU update with domain "
238 "decomposition lacks substantial testing and should be used with caution.");
241 if (devFlags.enableGpuHaloExchange)
243 if (useGpuForNonbonded)
245 if (!devFlags.enableGpuBufferOps)
247 GMX_LOG(mdlog.warning)
249 .appendTextFormatted(
250 "Enabling GPU buffer operations required by GMX_GPU_DD_COMMS "
251 "(equivalent with GMX_USE_GPU_BUFFER_OPS=1).");
252 devFlags.enableGpuBufferOps = true;
254 GMX_LOG(mdlog.warning)
256 .appendTextFormatted(
257 "This run uses the 'GPU halo exchange' feature, enabled by the "
258 "GMX_GPU_DD_COMMS environment variable.");
262 GMX_LOG(mdlog.warning)
264 .appendTextFormatted(
265 "GMX_GPU_DD_COMMS environment variable detected, but the 'GPU "
266 "halo exchange' feature will not be enabled as nonbonded interactions "
267 "are not offloaded.");
268 devFlags.enableGpuHaloExchange = false;
272 if (devFlags.enableGpuPmePPComm)
274 if (pmeRunMode == PmeRunMode::GPU)
276 GMX_LOG(mdlog.warning)
278 .appendTextFormatted(
279 "This run uses the 'GPU PME-PP communications' feature, enabled "
280 "by the GMX_GPU_PME_PP_COMMS environment variable.");
284 std::string clarification;
285 if (pmeRunMode == PmeRunMode::Mixed)
288 "PME FFT and gather are not offloaded to the GPU (PME is running in mixed "
293 clarification = "PME is not offloaded to the GPU.";
295 GMX_LOG(mdlog.warning)
298 "GMX_GPU_PME_PP_COMMS environment variable detected, but the "
299 "'GPU PME-PP communications' feature was not enabled as "
301 devFlags.enableGpuPmePPComm = false;
308 /*! \brief Barrier for safe simultaneous thread access to mdrunner data
310 * Used to ensure that the master thread does not modify mdrunner during copy
311 * on the spawned threads. */
312 static void threadMpiMdrunnerAccessBarrier()
315 MPI_Barrier(MPI_COMM_WORLD);
319 Mdrunner Mdrunner::cloneOnSpawnedThread() const
321 auto newRunner = Mdrunner(std::make_unique<MDModules>());
323 // All runners in the same process share a restraint manager resource because it is
324 // part of the interface to the client code, which is associated only with the
325 // original thread. Handles to the same resources can be obtained by copy.
327 newRunner.restraintManager_ = std::make_unique<RestraintManager>(*restraintManager_);
330 // Copy members of master runner.
331 // \todo Replace with builder when Simulation context and/or runner phases are better defined.
332 // Ref https://redmine.gromacs.org/issues/2587 and https://redmine.gromacs.org/issues/2375
333 newRunner.hw_opt = hw_opt;
334 newRunner.filenames = filenames;
336 newRunner.oenv = oenv;
337 newRunner.mdrunOptions = mdrunOptions;
338 newRunner.domdecOptions = domdecOptions;
339 newRunner.nbpu_opt = nbpu_opt;
340 newRunner.pme_opt = pme_opt;
341 newRunner.pme_fft_opt = pme_fft_opt;
342 newRunner.bonded_opt = bonded_opt;
343 newRunner.update_opt = update_opt;
344 newRunner.nstlist_cmdline = nstlist_cmdline;
345 newRunner.replExParams = replExParams;
346 newRunner.pforce = pforce;
347 // Give the spawned thread the newly created valid communicator
348 // for the simulation.
349 newRunner.communicator = MPI_COMM_WORLD;
351 newRunner.startingBehavior = startingBehavior;
352 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>(*stopHandlerBuilder_);
354 threadMpiMdrunnerAccessBarrier();
359 /*! \brief The callback used for running on spawned threads.
361 * Obtains the pointer to the master mdrunner object from the one
362 * argument permitted to the thread-launch API call, copies it to make
363 * a new runner for this thread, reinitializes necessary data, and
364 * proceeds to the simulation. */
365 static void mdrunner_start_fn(const void* arg)
369 auto masterMdrunner = reinterpret_cast<const gmx::Mdrunner*>(arg);
370 /* copy the arg list to make sure that it's thread-local. This
371 doesn't copy pointed-to items, of course; fnm, cr and fplog
372 are reset in the call below, all others should be const. */
373 gmx::Mdrunner mdrunner = masterMdrunner->cloneOnSpawnedThread();
376 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
380 void Mdrunner::spawnThreads(int numThreadsToLaunch)
383 /* now spawn new threads that start mdrunner_start_fn(), while
384 the main thread returns. Thread affinity is handled later. */
385 if (tMPI_Init_fn(TRUE, numThreadsToLaunch, TMPI_AFFINITY_NONE, mdrunner_start_fn,
386 static_cast<const void*>(this))
389 GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
392 // Give the master thread the newly created valid communicator for
394 communicator = MPI_COMM_WORLD;
395 threadMpiMdrunnerAccessBarrier();
397 GMX_UNUSED_VALUE(numThreadsToLaunch);
398 GMX_UNUSED_VALUE(mdrunner_start_fn);
404 /*! \brief Initialize variables for Verlet scheme simulation */
405 static void prepare_verlet_scheme(FILE* fplog,
409 const gmx_mtop_t* mtop,
411 bool makeGpuPairList,
412 const gmx::CpuInfo& cpuinfo)
414 /* For NVE simulations, we will retain the initial list buffer */
415 if (EI_DYNAMICS(ir->eI) && ir->verletbuf_tol > 0 && !(EI_MD(ir->eI) && ir->etc == etcNO))
417 /* Update the Verlet buffer size for the current run setup */
419 /* Here we assume SIMD-enabled kernels are being used. But as currently
420 * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
421 * and 4x2 gives a larger buffer than 4x4, this is ok.
423 ListSetupType listType =
424 (makeGpuPairList ? ListSetupType::Gpu : ListSetupType::CpuSimdWhenSupported);
425 VerletbufListSetup listSetup = verletbufGetSafeListSetup(listType);
427 const real rlist_new =
428 calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
430 if (rlist_new != ir->rlist)
432 if (fplog != nullptr)
435 "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
436 ir->rlist, rlist_new, listSetup.cluster_size_i, listSetup.cluster_size_j);
438 ir->rlist = rlist_new;
442 if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
444 gmx_fatal(FARGS, "Can not set nstlist without %s",
445 !EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
448 if (EI_DYNAMICS(ir->eI))
450 /* Set or try nstlist values */
451 increaseNstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, makeGpuPairList, cpuinfo);
455 /*! \brief Override the nslist value in inputrec
457 * with value passed on the command line (if any)
459 static void override_nsteps_cmdline(const gmx::MDLogger& mdlog, int64_t nsteps_cmdline, t_inputrec* ir)
463 /* override with anything else than the default -2 */
464 if (nsteps_cmdline > -2)
466 char sbuf_steps[STEPSTRSIZE];
467 char sbuf_msg[STRLEN];
469 ir->nsteps = nsteps_cmdline;
470 if (EI_DYNAMICS(ir->eI) && nsteps_cmdline != -1)
473 "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
474 gmx_step_str(nsteps_cmdline, sbuf_steps), fabs(nsteps_cmdline * ir->delta_t));
478 sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps",
479 gmx_step_str(nsteps_cmdline, sbuf_steps));
482 GMX_LOG(mdlog.warning).asParagraph().appendText(sbuf_msg);
484 else if (nsteps_cmdline < -2)
486 gmx_fatal(FARGS, "Invalid nsteps value passed on the command line: %" PRId64, nsteps_cmdline);
488 /* Do nothing if nsteps_cmdline == -2 */
494 /*! \brief Return whether GPU acceleration of nonbondeds is supported with the given settings.
496 * If not, and if a warning may be issued, logs a warning about
497 * falling back to CPU code. With thread-MPI, only the first
498 * call to this function should have \c issueWarning true. */
499 static bool gpuAccelerationOfNonbondedIsUseful(const MDLogger& mdlog, const t_inputrec& ir, bool issueWarning)
501 bool gpuIsUseful = true;
504 if (ir.opts.ngener - ir.nwall > 1)
506 /* The GPU code does not support more than one energy group.
507 * If the user requested GPUs explicitly, a fatal error is given later.
511 "Multiple energy groups is not implemented for GPUs, falling back to the CPU. "
512 "For better performance, run on the GPU without energy groups and then do "
513 "gmx mdrun -rerun option on the trajectory with an energy group .tpr file.";
519 warning = "TPI is not implemented for GPUs.";
522 if (!gpuIsUseful && issueWarning)
524 GMX_LOG(mdlog.warning).asParagraph().appendText(warning);
530 //! Initializes the logger for mdrun.
531 static gmx::LoggerOwner buildLogger(FILE* fplog, const bool isSimulationMasterRank)
533 gmx::LoggerBuilder builder;
534 if (fplog != nullptr)
536 builder.addTargetFile(gmx::MDLogger::LogLevel::Info, fplog);
538 if (isSimulationMasterRank)
540 builder.addTargetStream(gmx::MDLogger::LogLevel::Warning, &gmx::TextOutputFile::standardError());
542 return builder.build();
545 //! Make a TaskTarget from an mdrun argument string.
546 static TaskTarget findTaskTarget(const char* optionString)
548 TaskTarget returnValue = TaskTarget::Auto;
550 if (strncmp(optionString, "auto", 3) == 0)
552 returnValue = TaskTarget::Auto;
554 else if (strncmp(optionString, "cpu", 3) == 0)
556 returnValue = TaskTarget::Cpu;
558 else if (strncmp(optionString, "gpu", 3) == 0)
560 returnValue = TaskTarget::Gpu;
564 GMX_ASSERT(false, "Option string should have been checked for sanity already");
570 //! Finish run, aggregate data to print performance info.
571 static void finish_run(FILE* fplog,
572 const gmx::MDLogger& mdlog,
574 const t_inputrec* inputrec,
576 gmx_wallcycle_t wcycle,
577 gmx_walltime_accounting_t walltime_accounting,
578 nonbonded_verlet_t* nbv,
579 const gmx_pme_t* pme,
583 double nbfs = 0, mflop = 0;
584 double elapsed_time, elapsed_time_over_all_ranks, elapsed_time_over_all_threads,
585 elapsed_time_over_all_threads_over_all_ranks;
586 /* Control whether it is valid to print a report. Only the
587 simulation master may print, but it should not do so if the run
588 terminated e.g. before a scheduled reset step. This is
589 complicated by the fact that PME ranks are unaware of the
590 reason why they were sent a pmerecvqxFINISH. To avoid
591 communication deadlocks, we always do the communication for the
592 report, even if we've decided not to write the report, because
593 how long it takes to finish the run is not important when we've
594 decided not to report on the simulation performance.
596 Further, we only report performance for dynamical integrators,
597 because those are the only ones for which we plan to
598 consider doing any optimizations. */
599 bool printReport = EI_DYNAMICS(inputrec->eI) && SIMMASTER(cr);
601 if (printReport && !walltime_accounting_get_valid_finish(walltime_accounting))
603 GMX_LOG(mdlog.warning)
605 .appendText("Simulation ended prematurely, no performance report will be written.");
610 std::unique_ptr<t_nrnb> nrnbTotalStorage;
613 nrnbTotalStorage = std::make_unique<t_nrnb>();
614 nrnb_tot = nrnbTotalStorage.get();
616 MPI_Allreduce(nrnb->n, nrnb_tot->n, eNRNB, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
624 elapsed_time = walltime_accounting_get_time_since_reset(walltime_accounting);
625 elapsed_time_over_all_threads =
626 walltime_accounting_get_time_since_reset_over_all_threads(walltime_accounting);
630 /* reduce elapsed_time over all MPI ranks in the current simulation */
631 MPI_Allreduce(&elapsed_time, &elapsed_time_over_all_ranks, 1, MPI_DOUBLE, MPI_SUM,
633 elapsed_time_over_all_ranks /= cr->nnodes;
634 /* Reduce elapsed_time_over_all_threads over all MPI ranks in the
635 * current simulation. */
636 MPI_Allreduce(&elapsed_time_over_all_threads, &elapsed_time_over_all_threads_over_all_ranks,
637 1, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
642 elapsed_time_over_all_ranks = elapsed_time;
643 elapsed_time_over_all_threads_over_all_ranks = elapsed_time_over_all_threads;
648 print_flop(fplog, nrnb_tot, &nbfs, &mflop);
651 if (thisRankHasDuty(cr, DUTY_PP) && DOMAINDECOMP(cr))
653 print_dd_statistics(cr, inputrec, fplog);
656 /* TODO Move the responsibility for any scaling by thread counts
657 * to the code that handled the thread region, so that there's a
658 * mechanism to keep cycle counting working during the transition
659 * to task parallelism. */
660 int nthreads_pp = gmx_omp_nthreads_get(emntNonbonded);
661 int nthreads_pme = gmx_omp_nthreads_get(emntPME);
662 wallcycle_scale_by_num_threads(wcycle, thisRankHasDuty(cr, DUTY_PME) && !thisRankHasDuty(cr, DUTY_PP),
663 nthreads_pp, nthreads_pme);
664 auto cycle_sum(wallcycle_sum(cr, wcycle));
668 auto nbnxn_gpu_timings =
669 (nbv != nullptr && nbv->useGpu()) ? Nbnxm::gpu_get_timings(nbv->gpu_nbv) : nullptr;
670 gmx_wallclock_gpu_pme_t pme_gpu_timings = {};
672 if (pme_gpu_task_enabled(pme))
674 pme_gpu_get_timings(pme, &pme_gpu_timings);
676 wallcycle_print(fplog, mdlog, cr->nnodes, cr->npmenodes, nthreads_pp, nthreads_pme,
677 elapsed_time_over_all_ranks, wcycle, cycle_sum, nbnxn_gpu_timings,
680 if (EI_DYNAMICS(inputrec->eI))
682 delta_t = inputrec->delta_t;
687 print_perf(fplog, elapsed_time_over_all_threads_over_all_ranks, elapsed_time_over_all_ranks,
688 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
689 delta_t, nbfs, mflop);
693 print_perf(stderr, elapsed_time_over_all_threads_over_all_ranks, elapsed_time_over_all_ranks,
694 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
695 delta_t, nbfs, mflop);
700 int Mdrunner::mdrunner()
703 t_forcerec* fr = nullptr;
704 t_fcdata* fcd = nullptr;
705 real ewaldcoeff_q = 0;
706 real ewaldcoeff_lj = 0;
707 int nChargePerturbed = -1, nTypePerturbed = 0;
708 gmx_wallcycle_t wcycle;
709 gmx_walltime_accounting_t walltime_accounting = nullptr;
710 gmx_membed_t* membed = nullptr;
711 gmx_hw_info_t* hwinfo = nullptr;
713 /* CAUTION: threads may be started later on in this function, so
714 cr doesn't reflect the final parallel state right now */
717 /* TODO: inputrec should tell us whether we use an algorithm, not a file option */
718 const bool doEssentialDynamics = opt2bSet("-ei", filenames.size(), filenames.data());
719 const bool doMembed = opt2bSet("-membed", filenames.size(), filenames.data());
720 const bool doRerun = mdrunOptions.rerun;
722 // Handle task-assignment related user options.
723 EmulateGpuNonbonded emulateGpuNonbonded =
724 (getenv("GMX_EMULATE_GPU") != nullptr ? EmulateGpuNonbonded::Yes : EmulateGpuNonbonded::No);
726 std::vector<int> userGpuTaskAssignment;
729 userGpuTaskAssignment = parseUserTaskAssignmentString(hw_opt.userGpuTaskAssignment);
731 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
732 auto nonbondedTarget = findTaskTarget(nbpu_opt);
733 auto pmeTarget = findTaskTarget(pme_opt);
734 auto pmeFftTarget = findTaskTarget(pme_fft_opt);
735 auto bondedTarget = findTaskTarget(bonded_opt);
736 auto updateTarget = findTaskTarget(update_opt);
738 FILE* fplog = nullptr;
739 // If we are appending, we don't write log output because we need
740 // to check that the old log file matches what the checkpoint file
741 // expects. Otherwise, we should start to write log output now if
742 // there is a file ready for it.
743 if (logFileHandle != nullptr && startingBehavior != StartingBehavior::RestartWithAppending)
745 fplog = gmx_fio_getfp(logFileHandle);
747 const bool isSimulationMasterRank = findIsSimulationMasterRank(ms, communicator);
748 gmx::LoggerOwner logOwner(buildLogger(fplog, isSimulationMasterRank));
749 gmx::MDLogger mdlog(logOwner.logger());
751 // TODO The thread-MPI master rank makes a working
752 // PhysicalNodeCommunicator here, but it gets rebuilt by all ranks
753 // after the threads have been launched. This works because no use
754 // is made of that communicator until after the execution paths
755 // have rejoined. But it is likely that we can improve the way
756 // this is expressed, e.g. by expressly running detection only the
757 // master rank for thread-MPI, rather than relying on the mutex
758 // and reference count.
759 PhysicalNodeCommunicator physicalNodeComm(communicator, gmx_physicalnode_id_hash());
760 hwinfo = gmx_detect_hardware(mdlog, physicalNodeComm);
762 gmx_print_detected_hardware(fplog, isSimulationMasterRank && isMasterSim(ms), mdlog, hwinfo);
764 std::vector<int> gpuIdsToUse = makeGpuIdsToUse(hwinfo->gpu_info, hw_opt.gpuIdsAvailable);
766 // Print citation requests after all software/hardware printing
767 pleaseCiteGromacs(fplog);
769 // TODO Replace this by unique_ptr once t_inputrec is C++
770 t_inputrec inputrecInstance;
771 t_inputrec* inputrec = nullptr;
772 std::unique_ptr<t_state> globalState;
774 auto partialDeserializedTpr = std::make_unique<PartialDeserializedTprFile>();
776 if (isSimulationMasterRank)
778 /* Only the master rank has the global state */
779 globalState = std::make_unique<t_state>();
781 /* Read (nearly) all data required for the simulation
782 * and keep the partly serialized tpr contents to send to other ranks later
784 *partialDeserializedTpr = read_tpx_state(ftp2fn(efTPR, filenames.size(), filenames.data()),
785 &inputrecInstance, globalState.get(), &mtop);
786 inputrec = &inputrecInstance;
789 /* Check and update the hardware options for internal consistency */
790 checkAndUpdateHardwareOptions(mdlog, &hw_opt, isSimulationMasterRank, domdecOptions.numPmeRanks,
793 if (GMX_THREAD_MPI && isSimulationMasterRank)
795 bool useGpuForNonbonded = false;
796 bool useGpuForPme = false;
799 GMX_RELEASE_ASSERT(inputrec != nullptr, "Keep the compiler happy");
801 // If the user specified the number of ranks, then we must
802 // respect that, but in default mode, we need to allow for
803 // the number of GPUs to choose the number of ranks.
804 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
805 useGpuForNonbonded = decideWhetherToUseGpusForNonbondedWithThreadMpi(
806 nonbondedTarget, gpuIdsToUse, userGpuTaskAssignment, emulateGpuNonbonded,
807 canUseGpuForNonbonded,
808 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, GMX_THREAD_MPI),
809 hw_opt.nthreads_tmpi);
810 useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi(
811 useGpuForNonbonded, pmeTarget, gpuIdsToUse, userGpuTaskAssignment, *hwinfo,
812 *inputrec, mtop, hw_opt.nthreads_tmpi, domdecOptions.numPmeRanks);
814 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
816 /* Determine how many thread-MPI ranks to start.
818 * TODO Over-writing the user-supplied value here does
819 * prevent any possible subsequent checks from working
821 hw_opt.nthreads_tmpi = get_nthreads_mpi(hwinfo, &hw_opt, gpuIdsToUse, useGpuForNonbonded,
822 useGpuForPme, inputrec, &mtop, mdlog, doMembed);
824 // Now start the threads for thread MPI.
825 spawnThreads(hw_opt.nthreads_tmpi);
826 // The spawned threads enter mdrunner() and execution of
827 // master and spawned threads joins at the end of this block.
828 physicalNodeComm = PhysicalNodeCommunicator(communicator, gmx_physicalnode_id_hash());
831 GMX_RELEASE_ASSERT(communicator == MPI_COMM_WORLD, "Must have valid world communicator");
832 CommrecHandle crHandle = init_commrec(communicator, ms);
833 t_commrec* cr = crHandle.get();
834 GMX_RELEASE_ASSERT(cr != nullptr, "Must have valid commrec");
838 /* now broadcast everything to the non-master nodes/threads: */
839 if (!isSimulationMasterRank)
841 inputrec = &inputrecInstance;
843 init_parallel(cr, inputrec, &mtop, partialDeserializedTpr.get());
845 GMX_RELEASE_ASSERT(inputrec != nullptr, "All ranks should have a valid inputrec now");
846 partialDeserializedTpr.reset(nullptr);
848 // Now the number of ranks is known to all ranks, and each knows
849 // the inputrec read by the master rank. The ranks can now all run
850 // the task-deciding functions and will agree on the result
851 // without needing to communicate.
853 // TODO Should we do the communication in debug mode to support
854 // having an assertion?
855 const bool useDomainDecomposition = (PAR(cr) && !(EI_TPI(inputrec->eI) || inputrec->eI == eiNM));
857 // Note that these variables describe only their own node.
859 // Note that when bonded interactions run on a GPU they always run
860 // alongside a nonbonded task, so do not influence task assignment
861 // even though they affect the force calculation workload.
862 bool useGpuForNonbonded = false;
863 bool useGpuForPme = false;
864 bool useGpuForBonded = false;
865 bool useGpuForUpdate = false;
866 bool gpusWereDetected = hwinfo->ngpu_compatible_tot > 0;
869 // It's possible that there are different numbers of GPUs on
870 // different nodes, which is the user's responsibility to
871 // handle. If unsuitable, we will notice that during task
873 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
874 useGpuForNonbonded = decideWhetherToUseGpusForNonbonded(
875 nonbondedTarget, userGpuTaskAssignment, emulateGpuNonbonded, canUseGpuForNonbonded,
876 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, !GMX_THREAD_MPI), gpusWereDetected);
877 useGpuForPme = decideWhetherToUseGpusForPme(
878 useGpuForNonbonded, pmeTarget, userGpuTaskAssignment, *hwinfo, *inputrec, mtop,
879 cr->nnodes, domdecOptions.numPmeRanks, gpusWereDetected);
880 auto canUseGpuForBonded = buildSupportsGpuBondeds(nullptr)
881 && inputSupportsGpuBondeds(*inputrec, mtop, nullptr);
882 useGpuForBonded = decideWhetherToUseGpusForBonded(
883 useGpuForNonbonded, useGpuForPme, bondedTarget, canUseGpuForBonded,
884 EVDW_PME(inputrec->vdwtype), EEL_PME_EWALD(inputrec->coulombtype),
885 domdecOptions.numPmeRanks, gpusWereDetected);
887 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
889 const PmeRunMode pmeRunMode = determinePmeRunMode(useGpuForPme, pmeFftTarget, *inputrec);
891 // Initialize development feature flags that enabled by environment variable
892 // and report those features that are enabled.
893 const DevelopmentFeatureFlags devFlags =
894 manageDevelopmentFeatures(mdlog, useGpuForNonbonded, pmeRunMode);
897 // TODO: hide restraint implementation details from Mdrunner.
898 // There is nothing unique about restraints at this point as far as the
899 // Mdrunner is concerned. The Mdrunner should just be getting a sequence of
900 // factory functions from the SimulationContext on which to call mdModules_->add().
901 // TODO: capture all restraints into a single RestraintModule, passed to the runner builder.
902 for (auto&& restraint : restraintManager_->getRestraints())
904 auto module = RestraintMDModule::create(restraint, restraint->sites());
905 mdModules_->add(std::move(module));
908 // TODO: Error handling
909 mdModules_->assignOptionsToModules(*inputrec->params, nullptr);
910 const auto& mdModulesNotifier = mdModules_->notifier().notifier_;
912 if (inputrec->internalParameters != nullptr)
914 mdModulesNotifier.notify(*inputrec->internalParameters);
917 if (fplog != nullptr)
919 pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
920 fprintf(fplog, "\n");
925 /* In rerun, set velocities to zero if present */
926 if (doRerun && ((globalState->flags & (1 << estV)) != 0))
928 // rerun does not use velocities
932 "Rerun trajectory contains velocities. Rerun does only evaluate "
933 "potential energy and forces. The velocities will be ignored.");
934 for (int i = 0; i < globalState->natoms; i++)
936 clear_rvec(globalState->v[i]);
938 globalState->flags &= ~(1 << estV);
941 /* now make sure the state is initialized and propagated */
942 set_state_entries(globalState.get(), inputrec);
945 /* NM and TPI parallelize over force/energy calculations, not atoms,
946 * so we need to initialize and broadcast the global state.
948 if (inputrec->eI == eiNM || inputrec->eI == eiTPI)
952 globalState = std::make_unique<t_state>();
954 broadcastStateWithoutDynamics(cr, globalState.get());
957 /* A parallel command line option consistency check that we can
958 only do after any threads have started. */
960 && (domdecOptions.numCells[XX] > 1 || domdecOptions.numCells[YY] > 1
961 || domdecOptions.numCells[ZZ] > 1 || domdecOptions.numPmeRanks > 0))
964 "The -dd or -npme option request a parallel simulation, "
966 "but %s was compiled without threads or MPI enabled",
967 output_env_get_program_display_name(oenv));
969 "but the number of MPI-threads (option -ntmpi) is not set or is 1");
971 "but %s was not started through mpirun/mpiexec or only one rank was requested "
972 "through mpirun/mpiexec",
973 output_env_get_program_display_name(oenv));
977 if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
980 "The .mdp file specified an energy mininization or normal mode algorithm, and "
981 "these are not compatible with mdrun -rerun");
984 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
986 if (domdecOptions.numPmeRanks > 0)
988 gmx_fatal_collective(FARGS, cr->mpi_comm_mysim, MASTER(cr),
989 "PME-only ranks are requested, but the system does not use PME "
990 "for electrostatics or LJ");
993 domdecOptions.numPmeRanks = 0;
996 if (useGpuForNonbonded && domdecOptions.numPmeRanks < 0)
998 /* With NB GPUs we don't automatically use PME-only CPU ranks. PME ranks can
999 * improve performance with many threads per GPU, since our OpenMP
1000 * scaling is bad, but it's difficult to automate the setup.
1002 domdecOptions.numPmeRanks = 0;
1006 if (domdecOptions.numPmeRanks < 0)
1008 domdecOptions.numPmeRanks = 0;
1009 // TODO possibly print a note that one can opt-in for a separate PME GPU rank?
1013 GMX_RELEASE_ASSERT(domdecOptions.numPmeRanks <= 1,
1014 "PME GPU decomposition is not supported");
1021 fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
1025 /* NMR restraints must be initialized before load_checkpoint,
1026 * since with time averaging the history is added to t_state.
1027 * For proper consistency check we therefore need to extend
1029 * So the PME-only nodes (if present) will also initialize
1030 * the distance restraints.
1034 /* This needs to be called before read_checkpoint to extend the state */
1035 init_disres(fplog, &mtop, inputrec, cr, ms, fcd, globalState.get(), replExParams.exchangeInterval > 0);
1037 init_orires(fplog, &mtop, inputrec, cr, ms, globalState.get(), &(fcd->orires));
1039 auto deform = prepareBoxDeformation(globalState->box, cr, *inputrec);
1041 ObservablesHistory observablesHistory = {};
1043 if (startingBehavior != StartingBehavior::NewSimulation)
1045 /* Check if checkpoint file exists before doing continuation.
1046 * This way we can use identical input options for the first and subsequent runs...
1048 if (mdrunOptions.numStepsCommandline > -2)
1050 /* Temporarily set the number of steps to unlimited to avoid
1051 * triggering the nsteps check in load_checkpoint().
1052 * This hack will go away soon when the -nsteps option is removed.
1054 inputrec->nsteps = -1;
1057 load_checkpoint(opt2fn_master("-cpi", filenames.size(), filenames.data(), cr),
1058 logFileHandle, cr, domdecOptions.numCells, inputrec, globalState.get(),
1059 &observablesHistory, mdrunOptions.reproducible, mdModules_->notifier());
1061 if (startingBehavior == StartingBehavior::RestartWithAppending && logFileHandle)
1063 // Now we can start normal logging to the truncated log file.
1064 fplog = gmx_fio_getfp(logFileHandle);
1065 prepareLogAppending(fplog);
1066 logOwner = buildLogger(fplog, MASTER(cr));
1067 mdlog = logOwner.logger();
1071 if (mdrunOptions.numStepsCommandline > -2)
1076 "The -nsteps functionality is deprecated, and may be removed in a future "
1078 "Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp "
1081 /* override nsteps with value set on the commandline */
1082 override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec);
1086 copy_mat(globalState->box, box);
1091 gmx_bcast(sizeof(box), box, cr);
1094 if (inputrec->cutoff_scheme != ecutsVERLET)
1097 "This group-scheme .tpr file can no longer be run by mdrun. Please update to the "
1098 "Verlet scheme, or use an earlier version of GROMACS if necessary.");
1100 /* Update rlist and nstlist. */
1101 prepare_verlet_scheme(fplog, cr, inputrec, nstlist_cmdline, &mtop, box,
1102 useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes),
1105 const bool prefer1DAnd1PulseDD = (devFlags.enableGpuHaloExchange && useGpuForNonbonded);
1106 // This builder is necessary while we have multi-part construction
1107 // of DD. Before DD is constructed, we use the existence of
1108 // the builder object to indicate that further construction of DD
1110 std::unique_ptr<DomainDecompositionBuilder> ddBuilder;
1111 if (useDomainDecomposition)
1113 ddBuilder = std::make_unique<DomainDecompositionBuilder>(
1114 mdlog, cr, domdecOptions, mdrunOptions, prefer1DAnd1PulseDD, mtop, *inputrec, box,
1115 positionsFromStatePointer(globalState.get()));
1119 /* PME, if used, is done on all nodes with 1D decomposition */
1121 cr->duty = (DUTY_PP | DUTY_PME);
1123 if (inputrec->ePBC == epbcSCREW)
1125 gmx_fatal(FARGS, "pbc=screw is only implemented with domain decomposition");
1129 // Produce the task assignment for this rank.
1130 GpuTaskAssignmentsBuilder gpuTaskAssignmentsBuilder;
1131 GpuTaskAssignments gpuTaskAssignments = gpuTaskAssignmentsBuilder.build(
1132 gpuIdsToUse, userGpuTaskAssignment, *hwinfo, communicator, physicalNodeComm,
1133 nonbondedTarget, pmeTarget, bondedTarget, updateTarget, useGpuForNonbonded,
1134 useGpuForPme, thisRankHasDuty(cr, DUTY_PP),
1135 // TODO cr->duty & DUTY_PME should imply that a PME
1136 // algorithm is active, but currently does not.
1137 EEL_PME(inputrec->coulombtype) && thisRankHasDuty(cr, DUTY_PME));
1139 // Get the device handles for the modules, nullptr when no task is assigned.
1140 gmx_device_info_t* nonbondedDeviceInfo = gpuTaskAssignments.initNonbondedDevice(cr);
1141 gmx_device_info_t* pmeDeviceInfo = gpuTaskAssignments.initPmeDevice();
1143 // TODO Initialize GPU streams here.
1145 // TODO Currently this is always built, yet DD partition code
1146 // checks if it is built before using it. Probably it should
1147 // become an MDModule that is made only when another module
1148 // requires it (e.g. pull, CompEl, density fitting), so that we
1149 // don't update the local atom sets unilaterally every step.
1150 LocalAtomSetManager atomSets;
1153 // TODO Pass the GPU streams to ddBuilder to use in buffer
1154 // transfers (e.g. halo exchange)
1155 cr->dd = ddBuilder->build(&atomSets);
1156 // The builder's job is done, so destruct it
1157 ddBuilder.reset(nullptr);
1158 // Note that local state still does not exist yet.
1161 // The GPU update is decided here because we need to know whether the constraints or
1162 // SETTLEs can span accross the domain borders (i.e. whether or not update groups are
1163 // defined). This is only known after DD is initialized, hence decision on using GPU
1164 // update is done so late.
1167 const bool useUpdateGroups = cr->dd ? ddUsesUpdateGroups(*cr->dd) : false;
1169 useGpuForUpdate = decideWhetherToUseGpuForUpdate(
1170 devFlags.forceGpuUpdateDefault, useDomainDecomposition, useUpdateGroups, pmeRunMode,
1171 domdecOptions.numPmeRanks > 0, useGpuForNonbonded, updateTarget, gpusWereDetected,
1172 *inputrec, mtop, doEssentialDynamics, gmx_mtop_ftype_count(mtop, F_ORIRES) > 0,
1173 replExParams.exchangeInterval > 0, doRerun, mdlog);
1175 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1177 const bool printHostName = (cr->nnodes > 1);
1178 gpuTaskAssignments.reportGpuUsage(mdlog, printHostName, useGpuForBonded, pmeRunMode, useGpuForUpdate);
1180 // If the user chose a task assignment, give them some hints
1181 // where appropriate.
1182 if (!userGpuTaskAssignment.empty())
1184 gpuTaskAssignments.logPerformanceHints(mdlog, ssize(gpuIdsToUse));
1189 /* After possible communicator splitting in make_dd_communicators.
1190 * we can set up the intra/inter node communication.
1192 gmx_setup_nodecomm(fplog, cr);
1198 GMX_LOG(mdlog.warning)
1200 .appendTextFormatted(
1201 "This is simulation %d out of %d running as a composite GROMACS\n"
1202 "multi-simulation job. Setup for this simulation:\n",
1205 GMX_LOG(mdlog.warning)
1206 .appendTextFormatted("Using %d MPI %s\n", cr->nnodes,
1208 cr->nnodes == 1 ? "thread" : "threads"
1210 cr->nnodes == 1 ? "process" : "processes"
1216 // If mdrun -pin auto honors any affinity setting that already
1217 // exists. If so, it is nice to provide feedback about whether
1218 // that existing affinity setting was from OpenMP or something
1219 // else, so we run this code both before and after we initialize
1220 // the OpenMP support.
1221 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo->nthreads_hw_avail, FALSE);
1222 /* Check and update the number of OpenMP threads requested */
1223 checkAndUpdateRequestedNumOpenmpThreads(&hw_opt, *hwinfo, cr, ms, physicalNodeComm.size_,
1224 pmeRunMode, mtop, *inputrec);
1226 gmx_omp_nthreads_init(mdlog, cr, hwinfo->nthreads_hw_avail, physicalNodeComm.size_,
1227 hw_opt.nthreads_omp, hw_opt.nthreads_omp_pme, !thisRankHasDuty(cr, DUTY_PP));
1229 // Enable FP exception detection, but not in
1230 // Release mode and not for compilers with known buggy FP
1231 // exception support (clang with any optimization) or suspected
1232 // buggy FP exception support (gcc 7.* with optimization).
1233 #if !defined NDEBUG \
1234 && !((defined __clang__ || (defined(__GNUC__) && !defined(__ICC) && __GNUC__ == 7)) \
1235 && defined __OPTIMIZE__)
1236 const bool bEnableFPE = true;
1238 const bool bEnableFPE = false;
1240 // FIXME - reconcile with gmx_feenableexcept() call from CommandLineModuleManager::run()
1243 gmx_feenableexcept();
1246 /* Now that we know the setup is consistent, check for efficiency */
1247 check_resource_division_efficiency(hwinfo, gpuTaskAssignments.thisRankHasAnyGpuTask(),
1248 mdrunOptions.ntompOptionIsSet, cr, mdlog);
1250 /* getting number of PP/PME threads on this MPI / tMPI rank.
1251 PME: env variable should be read only on one node to make sure it is
1252 identical everywhere;
1254 const int numThreadsOnThisRank = thisRankHasDuty(cr, DUTY_PP) ? gmx_omp_nthreads_get(emntNonbonded)
1255 : gmx_omp_nthreads_get(emntPME);
1256 checkHardwareOversubscription(numThreadsOnThisRank, cr->nodeid, *hwinfo->hardwareTopology,
1257 physicalNodeComm, mdlog);
1259 // Enable Peer access between GPUs where available
1260 // Only for DD, only master PP rank needs to perform setup, and only if thread MPI plus
1261 // any of the GPU communication features are active.
1262 if (DOMAINDECOMP(cr) && MASTER(cr) && thisRankHasDuty(cr, DUTY_PP) && GMX_THREAD_MPI
1263 && (devFlags.enableGpuHaloExchange || devFlags.enableGpuPmePPComm))
1265 setupGpuDevicePeerAccess(gpuIdsToUse, mdlog);
1268 if (hw_opt.threadAffinity != ThreadAffinity::Off)
1270 /* Before setting affinity, check whether the affinity has changed
1271 * - which indicates that probably the OpenMP library has changed it
1272 * since we first checked).
1274 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo->nthreads_hw_avail, TRUE);
1276 int numThreadsOnThisNode, intraNodeThreadOffset;
1277 analyzeThreadsOnThisNode(physicalNodeComm, numThreadsOnThisRank, &numThreadsOnThisNode,
1278 &intraNodeThreadOffset);
1280 /* Set the CPU affinity */
1281 gmx_set_thread_affinity(mdlog, cr, &hw_opt, *hwinfo->hardwareTopology, numThreadsOnThisRank,
1282 numThreadsOnThisNode, intraNodeThreadOffset, nullptr);
1285 if (mdrunOptions.timingOptions.resetStep > -1)
1290 "The -resetstep functionality is deprecated, and may be removed in a "
1293 wcycle = wallcycle_init(fplog, mdrunOptions.timingOptions.resetStep, cr);
1297 /* Master synchronizes its value of reset_counters with all nodes
1298 * including PME only nodes */
1299 int64_t reset_counters = wcycle_get_reset_counters(wcycle);
1300 gmx_bcast_sim(sizeof(reset_counters), &reset_counters, cr);
1301 wcycle_set_reset_counters(wcycle, reset_counters);
1304 // Membrane embedding must be initialized before we call init_forcerec()
1309 fprintf(stderr, "Initializing membed");
1311 /* Note that membed cannot work in parallel because mtop is
1312 * changed here. Fix this if we ever want to make it run with
1313 * multiple ranks. */
1314 membed = init_membed(fplog, filenames.size(), filenames.data(), &mtop, inputrec,
1315 globalState.get(), cr, &mdrunOptions.checkpointOptions.period);
1318 const bool thisRankHasPmeGpuTask = gpuTaskAssignments.thisRankHasPmeGpuTask();
1319 std::unique_ptr<MDAtoms> mdAtoms;
1320 std::unique_ptr<gmx_vsite_t> vsite;
1323 if (thisRankHasDuty(cr, DUTY_PP))
1325 mdModulesNotifier.notify(*cr);
1326 mdModulesNotifier.notify(&atomSets);
1327 mdModulesNotifier.notify(PeriodicBoundaryConditionType{ inputrec->ePBC });
1328 mdModulesNotifier.notify(SimulationTimeStep{ inputrec->delta_t });
1329 /* Initiate forcerecord */
1330 fr = new t_forcerec;
1331 fr->forceProviders = mdModules_->initForceProviders();
1332 init_forcerec(fplog, mdlog, fr, fcd, inputrec, &mtop, cr, box,
1333 opt2fn("-table", filenames.size(), filenames.data()),
1334 opt2fn("-tablep", filenames.size(), filenames.data()),
1335 opt2fns("-tableb", filenames.size(), filenames.data()), *hwinfo,
1336 nonbondedDeviceInfo, useGpuForBonded,
1337 pmeRunMode == PmeRunMode::GPU && !thisRankHasDuty(cr, DUTY_PME), pforce, wcycle);
1339 // TODO Move this to happen during domain decomposition setup,
1340 // once stream and event handling works well with that.
1341 // TODO remove need to pass local stream into GPU halo exchange - Redmine #3093
1342 if (havePPDomainDecomposition(cr) && prefer1DAnd1PulseDD && is1DAnd1PulseDD(*cr->dd))
1344 GMX_RELEASE_ASSERT(devFlags.enableGpuBufferOps,
1345 "Must use GMX_USE_GPU_BUFFER_OPS=1 to use GMX_GPU_DD_COMMS=1");
1347 Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::Local);
1348 void* streamNonLocal =
1349 Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::NonLocal);
1350 GMX_LOG(mdlog.warning)
1352 .appendTextFormatted(
1353 "NOTE: This run uses the 'GPU halo exchange' feature, enabled by the "
1354 "GMX_GPU_DD_COMMS environment variable.");
1355 cr->dd->gpuHaloExchange = std::make_unique<GpuHaloExchange>(
1356 cr->dd, cr->mpi_comm_mysim, streamLocal, streamNonLocal);
1359 /* Initialize the mdAtoms structure.
1360 * mdAtoms is not filled with atom data,
1361 * as this can not be done now with domain decomposition.
1363 mdAtoms = makeMDAtoms(fplog, mtop, *inputrec, thisRankHasPmeGpuTask);
1364 if (globalState && thisRankHasPmeGpuTask)
1366 // The pinning of coordinates in the global state object works, because we only use
1367 // PME on GPU without DD or on a separate PME rank, and because the local state pointer
1368 // points to the global state object without DD.
1369 // FIXME: MD and EM separately set up the local state - this should happen in the same
1370 // function, which should also perform the pinning.
1371 changePinningPolicy(&globalState->x, pme_get_pinning_policy());
1374 /* Initialize the virtual site communication */
1375 vsite = initVsite(mtop, cr);
1377 calc_shifts(box, fr->shift_vec);
1379 /* With periodic molecules the charge groups should be whole at start up
1380 * and the virtual sites should not be far from their proper positions.
1382 if (!inputrec->bContinuation && MASTER(cr) && !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
1384 /* Make molecules whole at start of run */
1385 if (fr->ePBC != epbcNONE)
1387 do_pbc_first_mtop(fplog, inputrec->ePBC, box, &mtop, globalState->x.rvec_array());
1391 /* Correct initial vsite positions are required
1392 * for the initial distribution in the domain decomposition
1393 * and for the initial shell prediction.
1395 constructVsitesGlobal(mtop, globalState->x);
1399 if (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
1401 ewaldcoeff_q = fr->ic->ewaldcoeff_q;
1402 ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
1407 /* This is a PME only node */
1409 GMX_ASSERT(globalState == nullptr,
1410 "We don't need the state on a PME only rank and expect it to be unitialized");
1412 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
1413 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
1416 gmx_pme_t* sepPmeData = nullptr;
1417 // This reference hides the fact that PME data is owned by runner on PME-only ranks and by forcerec on other ranks
1418 GMX_ASSERT(thisRankHasDuty(cr, DUTY_PP) == (fr != nullptr),
1419 "Double-checking that only PME-only ranks have no forcerec");
1420 gmx_pme_t*& pmedata = fr ? fr->pmedata : sepPmeData;
1422 // TODO should live in ewald module once its testing is improved
1424 // Later, this program could contain kernels that might be later
1425 // re-used as auto-tuning progresses, or subsequent simulations
1427 PmeGpuProgramStorage pmeGpuProgram;
1428 if (thisRankHasPmeGpuTask)
1430 pmeGpuProgram = buildPmeGpuProgram(pmeDeviceInfo);
1433 /* Initiate PME if necessary,
1434 * either on all nodes or on dedicated PME nodes only. */
1435 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
1437 if (mdAtoms && mdAtoms->mdatoms())
1439 nChargePerturbed = mdAtoms->mdatoms()->nChargePerturbed;
1440 if (EVDW_PME(inputrec->vdwtype))
1442 nTypePerturbed = mdAtoms->mdatoms()->nTypePerturbed;
1445 if (cr->npmenodes > 0)
1447 /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
1448 gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
1449 gmx_bcast_sim(sizeof(nTypePerturbed), &nTypePerturbed, cr);
1452 if (thisRankHasDuty(cr, DUTY_PME))
1456 pmedata = gmx_pme_init(cr, getNumPmeDomains(cr->dd), inputrec, nChargePerturbed != 0,
1457 nTypePerturbed != 0, mdrunOptions.reproducible, ewaldcoeff_q,
1458 ewaldcoeff_lj, gmx_omp_nthreads_get(emntPME), pmeRunMode,
1459 nullptr, pmeDeviceInfo, pmeGpuProgram.get(), mdlog);
1461 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1466 if (EI_DYNAMICS(inputrec->eI))
1468 /* Turn on signal handling on all nodes */
1470 * (A user signal from the PME nodes (if any)
1471 * is communicated to the PP nodes.
1473 signal_handler_install();
1476 pull_t* pull_work = nullptr;
1477 if (thisRankHasDuty(cr, DUTY_PP))
1479 /* Assumes uniform use of the number of OpenMP threads */
1480 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
1482 if (inputrec->bPull)
1484 /* Initialize pull code */
1485 pull_work = init_pull(fplog, inputrec->pull, inputrec, &mtop, cr, &atomSets,
1486 inputrec->fepvals->init_lambda);
1487 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
1489 initPullHistory(pull_work, &observablesHistory);
1491 if (EI_DYNAMICS(inputrec->eI) && MASTER(cr))
1493 init_pull_output_files(pull_work, filenames.size(), filenames.data(), oenv, startingBehavior);
1497 std::unique_ptr<EnforcedRotation> enforcedRotation;
1500 /* Initialize enforced rotation code */
1502 init_rot(fplog, inputrec, filenames.size(), filenames.data(), cr, &atomSets,
1503 globalState.get(), &mtop, oenv, mdrunOptions, startingBehavior);
1506 t_swap* swap = nullptr;
1507 if (inputrec->eSwapCoords != eswapNO)
1509 /* Initialize ion swapping code */
1510 swap = init_swapcoords(fplog, inputrec,
1511 opt2fn_master("-swap", filenames.size(), filenames.data(), cr),
1512 &mtop, globalState.get(), &observablesHistory, cr, &atomSets,
1513 oenv, mdrunOptions, startingBehavior);
1516 /* Let makeConstraints know whether we have essential dynamics constraints. */
1517 auto constr = makeConstraints(mtop, *inputrec, pull_work, doEssentialDynamics, fplog,
1518 *mdAtoms->mdatoms(), cr, ms, &nrnb, wcycle, fr->bMolPBC);
1520 /* Energy terms and groups */
1521 gmx_enerdata_t enerd(mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
1522 inputrec->fepvals->n_lambda);
1524 /* Kinetic energy data */
1525 gmx_ekindata_t ekind;
1526 init_ekindata(fplog, &mtop, &(inputrec->opts), &ekind, inputrec->cos_accel);
1528 /* Set up interactive MD (IMD) */
1530 makeImdSession(inputrec, cr, wcycle, &enerd, ms, &mtop, mdlog,
1531 MASTER(cr) ? globalState->x.rvec_array() : nullptr, filenames.size(),
1532 filenames.data(), oenv, mdrunOptions.imdOptions, startingBehavior);
1534 if (DOMAINDECOMP(cr))
1536 GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
1537 /* This call is not included in init_domain_decomposition mainly
1538 * because fr->cginfo_mb is set later.
1540 dd_init_bondeds(fplog, cr->dd, &mtop, vsite.get(), inputrec,
1541 domdecOptions.checkBondedInteractions, fr->cginfo_mb);
1544 const bool inputIsCompatibleWithModularSimulator = ModularSimulator::isInputCompatible(
1545 false, inputrec, doRerun, vsite.get(), ms, replExParams, fcd,
1546 static_cast<int>(filenames.size()), filenames.data(), &observablesHistory, membed);
1548 const bool useModularSimulator = inputIsCompatibleWithModularSimulator
1549 && !(getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
1551 // TODO This is not the right place to manage the lifetime of
1552 // this data structure, but currently it's the easiest way to
1554 MdrunScheduleWorkload runScheduleWork;
1555 // Also populates the simulation constant workload description.
1556 runScheduleWork.simulationWork = createSimulationWorkload(
1557 useGpuForNonbonded, pmeRunMode, useGpuForBonded, useGpuForUpdate,
1558 devFlags.enableGpuBufferOps, devFlags.enableGpuHaloExchange,
1559 devFlags.enableGpuPmePPComm, haveEwaldSurfaceContribution(*inputrec));
1561 std::unique_ptr<gmx::StatePropagatorDataGpu> stateGpu;
1562 if (gpusWereDetected
1563 && ((useGpuForPme && thisRankHasDuty(cr, DUTY_PME))
1564 || runScheduleWork.simulationWork.useGpuBufferOps))
1566 const void* pmeStream = pme_gpu_get_device_stream(fr->pmedata);
1567 const void* localStream =
1568 fr->nbv->gpu_nbv != nullptr
1569 ? Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::Local)
1571 const void* nonLocalStream =
1572 fr->nbv->gpu_nbv != nullptr
1573 ? Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::NonLocal)
1575 const void* deviceContext = pme_gpu_get_device_context(fr->pmedata);
1576 const int paddingSize = pme_gpu_get_padding_size(fr->pmedata);
1577 GpuApiCallBehavior transferKind = (inputrec->eI == eiMD && !doRerun && !useModularSimulator)
1578 ? GpuApiCallBehavior::Async
1579 : GpuApiCallBehavior::Sync;
1581 stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(
1582 pmeStream, localStream, nonLocalStream, deviceContext, transferKind, paddingSize, wcycle);
1583 fr->stateGpu = stateGpu.get();
1586 GMX_ASSERT(stopHandlerBuilder_, "Runner must provide StopHandlerBuilder to simulator.");
1587 SimulatorBuilder simulatorBuilder;
1589 // build and run simulator object based on user-input
1590 auto simulator = simulatorBuilder.build(
1591 inputIsCompatibleWithModularSimulator, fplog, cr, ms, mdlog,
1592 static_cast<int>(filenames.size()), filenames.data(), oenv, mdrunOptions,
1593 startingBehavior, vsite.get(), constr.get(),
1594 enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr, deform.get(),
1595 mdModules_->outputProvider(), mdModules_->notifier(), inputrec, imdSession.get(),
1596 pull_work, swap, &mtop, fcd, globalState.get(), &observablesHistory, mdAtoms.get(),
1597 &nrnb, wcycle, fr, &enerd, &ekind, &runScheduleWork, replExParams, membed,
1598 walltime_accounting, std::move(stopHandlerBuilder_), doRerun);
1601 if (fr->pmePpCommGpu)
1603 // destroy object since it is no longer required. (This needs to be done while the GPU context still exists.)
1604 fr->pmePpCommGpu.reset();
1607 if (inputrec->bPull)
1609 finish_pull(pull_work);
1611 finish_swapcoords(swap);
1615 GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
1617 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
1618 gmx_pmeonly(pmedata, cr, &nrnb, wcycle, walltime_accounting, inputrec, pmeRunMode);
1621 wallcycle_stop(wcycle, ewcRUN);
1623 /* Finish up, write some stuff
1624 * if rerunMD, don't write last frame again
1626 finish_run(fplog, mdlog, cr, inputrec, &nrnb, wcycle, walltime_accounting,
1627 fr ? fr->nbv.get() : nullptr, pmedata, EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
1629 // clean up cycle counter
1630 wallcycle_destroy(wcycle);
1635 gmx_pme_destroy(pmedata);
1639 // FIXME: this is only here to manually unpin mdAtoms->chargeA_ and state->x,
1640 // before we destroy the GPU context(s) in free_gpu_resources().
1641 // Pinned buffers are associated with contexts in CUDA.
1642 // As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
1643 mdAtoms.reset(nullptr);
1644 globalState.reset(nullptr);
1645 mdModules_.reset(nullptr); // destruct force providers here as they might also use the GPU
1647 /* Free GPU memory and set a physical node tMPI barrier (which should eventually go away) */
1648 free_gpu_resources(fr, physicalNodeComm, hwinfo->gpu_info);
1649 free_gpu(nonbondedDeviceInfo);
1650 free_gpu(pmeDeviceInfo);
1651 done_forcerec(fr, mtop.molblock.size());
1656 free_membed(membed);
1659 /* Does what it says */
1660 print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
1661 walltime_accounting_destroy(walltime_accounting);
1663 // Ensure log file content is written
1666 gmx_fio_flush(logFileHandle);
1669 /* Reset FPEs (important for unit tests) by disabling them. Assumes no
1670 * exceptions were enabled before function was called. */
1673 gmx_fedisableexcept();
1676 auto rc = static_cast<int>(gmx_get_stop_condition());
1679 /* we need to join all threads. The sub-threads join when they
1680 exit this function, but the master thread needs to be told to
1682 if (PAR(cr) && MASTER(cr))
1690 Mdrunner::~Mdrunner()
1692 // Clean up of the Manager.
1693 // This will end up getting called on every thread-MPI rank, which is unnecessary,
1694 // but okay as long as threads synchronize some time before adding or accessing
1695 // a new set of restraints.
1696 if (restraintManager_)
1698 restraintManager_->clear();
1699 GMX_ASSERT(restraintManager_->countRestraints() == 0,
1700 "restraints added during runner life time should be cleared at runner "
1705 void Mdrunner::addPotential(std::shared_ptr<gmx::IRestraintPotential> puller, const std::string& name)
1707 GMX_ASSERT(restraintManager_, "Mdrunner must have a restraint manager.");
1708 // Not sure if this should be logged through the md logger or something else,
1709 // but it is helpful to have some sort of INFO level message sent somewhere.
1710 // std::cout << "Registering restraint named " << name << std::endl;
1712 // When multiple restraints are used, it may be wasteful to register them separately.
1713 // Maybe instead register an entire Restraint Manager as a force provider.
1714 restraintManager_->addToSpec(std::move(puller), name);
1717 Mdrunner::Mdrunner(std::unique_ptr<MDModules> mdModules) : mdModules_(std::move(mdModules)) {}
1719 Mdrunner::Mdrunner(Mdrunner&&) noexcept = default;
1721 //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265
1722 Mdrunner& Mdrunner::operator=(Mdrunner&& /*handle*/) noexcept(BUGFREE_NOEXCEPT_STRING) = default;
1724 class Mdrunner::BuilderImplementation
1727 BuilderImplementation() = delete;
1728 BuilderImplementation(std::unique_ptr<MDModules> mdModules, compat::not_null<SimulationContext*> context);
1729 ~BuilderImplementation();
1731 BuilderImplementation& setExtraMdrunOptions(const MdrunOptions& options,
1732 real forceWarningThreshold,
1733 StartingBehavior startingBehavior);
1735 void addDomdec(const DomdecOptions& options);
1737 void addVerletList(int nstlist);
1739 void addReplicaExchange(const ReplicaExchangeParameters& params);
1741 void addNonBonded(const char* nbpu_opt);
1743 void addPME(const char* pme_opt_, const char* pme_fft_opt_);
1745 void addBondedTaskAssignment(const char* bonded_opt);
1747 void addUpdateTaskAssignment(const char* update_opt);
1749 void addHardwareOptions(const gmx_hw_opt_t& hardwareOptions);
1751 void addFilenames(ArrayRef<const t_filenm> filenames);
1753 void addOutputEnvironment(gmx_output_env_t* outputEnvironment);
1755 void addLogFile(t_fileio* logFileHandle);
1757 void addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
1762 // Default parameters copied from runner.h
1763 // \todo Clarify source(s) of default parameters.
1765 const char* nbpu_opt_ = nullptr;
1766 const char* pme_opt_ = nullptr;
1767 const char* pme_fft_opt_ = nullptr;
1768 const char* bonded_opt_ = nullptr;
1769 const char* update_opt_ = nullptr;
1771 MdrunOptions mdrunOptions_;
1773 DomdecOptions domdecOptions_;
1775 ReplicaExchangeParameters replicaExchangeParameters_;
1777 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
1780 //! Multisim communicator handle.
1781 gmx_multisim_t* multiSimulation_;
1783 //! mdrun communicator
1784 MPI_Comm communicator_ = MPI_COMM_NULL;
1786 //! Print a warning if any force is larger than this (in kJ/mol nm).
1787 real forceWarningThreshold_ = -1;
1789 //! Whether the simulation will start afresh, or restart with/without appending.
1790 StartingBehavior startingBehavior_ = StartingBehavior::NewSimulation;
1792 //! The modules that comprise the functionality of mdrun.
1793 std::unique_ptr<MDModules> mdModules_;
1795 //! \brief Parallelism information.
1796 gmx_hw_opt_t hardwareOptions_;
1798 //! filename options for simulation.
1799 ArrayRef<const t_filenm> filenames_;
1801 /*! \brief Handle to output environment.
1803 * \todo gmx_output_env_t needs lifetime management.
1805 gmx_output_env_t* outputEnvironment_ = nullptr;
1807 /*! \brief Non-owning handle to MD log file.
1809 * \todo Context should own output facilities for client.
1810 * \todo Improve log file handle management.
1812 * Code managing the FILE* relies on the ability to set it to
1813 * nullptr to check whether the filehandle is valid.
1815 t_fileio* logFileHandle_ = nullptr;
1818 * \brief Builder for simulation stop signal handler.
1820 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_ = nullptr;
1823 Mdrunner::BuilderImplementation::BuilderImplementation(std::unique_ptr<MDModules> mdModules,
1824 compat::not_null<SimulationContext*> context) :
1825 mdModules_(std::move(mdModules))
1827 communicator_ = context->communicator_;
1828 multiSimulation_ = context->multiSimulation_.get();
1831 Mdrunner::BuilderImplementation::~BuilderImplementation() = default;
1833 Mdrunner::BuilderImplementation&
1834 Mdrunner::BuilderImplementation::setExtraMdrunOptions(const MdrunOptions& options,
1835 const real forceWarningThreshold,
1836 const StartingBehavior startingBehavior)
1838 mdrunOptions_ = options;
1839 forceWarningThreshold_ = forceWarningThreshold;
1840 startingBehavior_ = startingBehavior;
1844 void Mdrunner::BuilderImplementation::addDomdec(const DomdecOptions& options)
1846 domdecOptions_ = options;
1849 void Mdrunner::BuilderImplementation::addVerletList(int nstlist)
1854 void Mdrunner::BuilderImplementation::addReplicaExchange(const ReplicaExchangeParameters& params)
1856 replicaExchangeParameters_ = params;
1859 Mdrunner Mdrunner::BuilderImplementation::build()
1861 auto newRunner = Mdrunner(std::move(mdModules_));
1863 newRunner.mdrunOptions = mdrunOptions_;
1864 newRunner.pforce = forceWarningThreshold_;
1865 newRunner.startingBehavior = startingBehavior_;
1866 newRunner.domdecOptions = domdecOptions_;
1868 // \todo determine an invariant to check or confirm that all gmx_hw_opt_t objects are valid
1869 newRunner.hw_opt = hardwareOptions_;
1871 // No invariant to check. This parameter exists to optionally override other behavior.
1872 newRunner.nstlist_cmdline = nstlist_;
1874 newRunner.replExParams = replicaExchangeParameters_;
1876 newRunner.filenames = filenames_;
1878 newRunner.communicator = communicator_;
1880 // nullptr is a valid value for the multisim handle
1881 newRunner.ms = multiSimulation_;
1883 // \todo Clarify ownership and lifetime management for gmx_output_env_t
1884 // \todo Update sanity checking when output environment has clearly specified invariants.
1885 // Initialization and default values for oenv are not well specified in the current version.
1886 if (outputEnvironment_)
1888 newRunner.oenv = outputEnvironment_;
1892 GMX_THROW(gmx::APIError(
1893 "MdrunnerBuilder::addOutputEnvironment() is required before build()"));
1896 newRunner.logFileHandle = logFileHandle_;
1900 newRunner.nbpu_opt = nbpu_opt_;
1904 GMX_THROW(gmx::APIError("MdrunnerBuilder::addNonBonded() is required before build()"));
1907 if (pme_opt_ && pme_fft_opt_)
1909 newRunner.pme_opt = pme_opt_;
1910 newRunner.pme_fft_opt = pme_fft_opt_;
1914 GMX_THROW(gmx::APIError("MdrunnerBuilder::addElectrostatics() is required before build()"));
1919 newRunner.bonded_opt = bonded_opt_;
1923 GMX_THROW(gmx::APIError(
1924 "MdrunnerBuilder::addBondedTaskAssignment() is required before build()"));
1929 newRunner.update_opt = update_opt_;
1933 GMX_THROW(gmx::APIError(
1934 "MdrunnerBuilder::addUpdateTaskAssignment() is required before build() "));
1938 newRunner.restraintManager_ = std::make_unique<gmx::RestraintManager>();
1940 if (stopHandlerBuilder_)
1942 newRunner.stopHandlerBuilder_ = std::move(stopHandlerBuilder_);
1946 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>();
1952 void Mdrunner::BuilderImplementation::addNonBonded(const char* nbpu_opt)
1954 nbpu_opt_ = nbpu_opt;
1957 void Mdrunner::BuilderImplementation::addPME(const char* pme_opt, const char* pme_fft_opt)
1960 pme_fft_opt_ = pme_fft_opt;
1963 void Mdrunner::BuilderImplementation::addBondedTaskAssignment(const char* bonded_opt)
1965 bonded_opt_ = bonded_opt;
1968 void Mdrunner::BuilderImplementation::addUpdateTaskAssignment(const char* update_opt)
1970 update_opt_ = update_opt;
1973 void Mdrunner::BuilderImplementation::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
1975 hardwareOptions_ = hardwareOptions;
1978 void Mdrunner::BuilderImplementation::addFilenames(ArrayRef<const t_filenm> filenames)
1980 filenames_ = filenames;
1983 void Mdrunner::BuilderImplementation::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
1985 outputEnvironment_ = outputEnvironment;
1988 void Mdrunner::BuilderImplementation::addLogFile(t_fileio* logFileHandle)
1990 logFileHandle_ = logFileHandle;
1993 void Mdrunner::BuilderImplementation::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
1995 stopHandlerBuilder_ = std::move(builder);
1998 MdrunnerBuilder::MdrunnerBuilder(std::unique_ptr<MDModules> mdModules,
1999 compat::not_null<SimulationContext*> context) :
2000 impl_{ std::make_unique<Mdrunner::BuilderImplementation>(std::move(mdModules), context) }
2004 MdrunnerBuilder::~MdrunnerBuilder() = default;
2006 MdrunnerBuilder& MdrunnerBuilder::addSimulationMethod(const MdrunOptions& options,
2007 real forceWarningThreshold,
2008 const StartingBehavior startingBehavior)
2010 impl_->setExtraMdrunOptions(options, forceWarningThreshold, startingBehavior);
2014 MdrunnerBuilder& MdrunnerBuilder::addDomainDecomposition(const DomdecOptions& options)
2016 impl_->addDomdec(options);
2020 MdrunnerBuilder& MdrunnerBuilder::addNeighborList(int nstlist)
2022 impl_->addVerletList(nstlist);
2026 MdrunnerBuilder& MdrunnerBuilder::addReplicaExchange(const ReplicaExchangeParameters& params)
2028 impl_->addReplicaExchange(params);
2032 MdrunnerBuilder& MdrunnerBuilder::addNonBonded(const char* nbpu_opt)
2034 impl_->addNonBonded(nbpu_opt);
2038 MdrunnerBuilder& MdrunnerBuilder::addElectrostatics(const char* pme_opt, const char* pme_fft_opt)
2040 // The builder method may become more general in the future, but in this version,
2041 // parameters for PME electrostatics are both required and the only parameters
2043 if (pme_opt && pme_fft_opt)
2045 impl_->addPME(pme_opt, pme_fft_opt);
2050 gmx::InvalidInputError("addElectrostatics() arguments must be non-null pointers."));
2055 MdrunnerBuilder& MdrunnerBuilder::addBondedTaskAssignment(const char* bonded_opt)
2057 impl_->addBondedTaskAssignment(bonded_opt);
2061 MdrunnerBuilder& MdrunnerBuilder::addUpdateTaskAssignment(const char* update_opt)
2063 impl_->addUpdateTaskAssignment(update_opt);
2067 Mdrunner MdrunnerBuilder::build()
2069 return impl_->build();
2072 MdrunnerBuilder& MdrunnerBuilder::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2074 impl_->addHardwareOptions(hardwareOptions);
2078 MdrunnerBuilder& MdrunnerBuilder::addFilenames(ArrayRef<const t_filenm> filenames)
2080 impl_->addFilenames(filenames);
2084 MdrunnerBuilder& MdrunnerBuilder::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2086 impl_->addOutputEnvironment(outputEnvironment);
2090 MdrunnerBuilder& MdrunnerBuilder::addLogFile(t_fileio* logFileHandle)
2092 impl_->addLogFile(logFileHandle);
2096 MdrunnerBuilder& MdrunnerBuilder::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2098 impl_->addStopHandlerBuilder(std::move(builder));
2102 MdrunnerBuilder::MdrunnerBuilder(MdrunnerBuilder&&) noexcept = default;
2104 MdrunnerBuilder& MdrunnerBuilder::operator=(MdrunnerBuilder&&) noexcept = default;