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39 * \brief Implements the MD runner routine calling all integrators.
41 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
42 * \ingroup module_mdrun
59 #include "gromacs/commandline/filenm.h"
60 #include "gromacs/domdec/builder.h"
61 #include "gromacs/domdec/domdec.h"
62 #include "gromacs/domdec/domdec_struct.h"
63 #include "gromacs/domdec/gpuhaloexchange.h"
64 #include "gromacs/domdec/localatomsetmanager.h"
65 #include "gromacs/domdec/partition.h"
66 #include "gromacs/ewald/ewald_utils.h"
67 #include "gromacs/ewald/pme_gpu_program.h"
68 #include "gromacs/ewald/pme_only.h"
69 #include "gromacs/ewald/pme_pp_comm_gpu.h"
70 #include "gromacs/fileio/checkpoint.h"
71 #include "gromacs/fileio/gmxfio.h"
72 #include "gromacs/fileio/oenv.h"
73 #include "gromacs/fileio/tpxio.h"
74 #include "gromacs/gmxlib/network.h"
75 #include "gromacs/gmxlib/nrnb.h"
76 #include "gromacs/gpu_utils/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);
737 PmeRunMode pmeRunMode = PmeRunMode::None;
739 FILE* fplog = nullptr;
740 // If we are appending, we don't write log output because we need
741 // to check that the old log file matches what the checkpoint file
742 // expects. Otherwise, we should start to write log output now if
743 // there is a file ready for it.
744 if (logFileHandle != nullptr && startingBehavior != StartingBehavior::RestartWithAppending)
746 fplog = gmx_fio_getfp(logFileHandle);
748 const bool isSimulationMasterRank = findIsSimulationMasterRank(ms, communicator);
749 gmx::LoggerOwner logOwner(buildLogger(fplog, isSimulationMasterRank));
750 gmx::MDLogger mdlog(logOwner.logger());
752 // TODO The thread-MPI master rank makes a working
753 // PhysicalNodeCommunicator here, but it gets rebuilt by all ranks
754 // after the threads have been launched. This works because no use
755 // is made of that communicator until after the execution paths
756 // have rejoined. But it is likely that we can improve the way
757 // this is expressed, e.g. by expressly running detection only the
758 // master rank for thread-MPI, rather than relying on the mutex
759 // and reference count.
760 PhysicalNodeCommunicator physicalNodeComm(communicator, gmx_physicalnode_id_hash());
761 hwinfo = gmx_detect_hardware(mdlog, physicalNodeComm);
763 gmx_print_detected_hardware(fplog, isSimulationMasterRank && isMasterSim(ms), mdlog, hwinfo);
765 std::vector<int> gpuIdsToUse = makeGpuIdsToUse(hwinfo->gpu_info, hw_opt.gpuIdsAvailable);
767 // Print citation requests after all software/hardware printing
768 pleaseCiteGromacs(fplog);
770 // TODO Replace this by unique_ptr once t_inputrec is C++
771 t_inputrec inputrecInstance;
772 t_inputrec* inputrec = nullptr;
773 std::unique_ptr<t_state> globalState;
775 auto partialDeserializedTpr = std::make_unique<PartialDeserializedTprFile>();
777 if (isSimulationMasterRank)
779 /* Only the master rank has the global state */
780 globalState = std::make_unique<t_state>();
782 /* Read (nearly) all data required for the simulation
783 * and keep the partly serialized tpr contents to send to other ranks later
785 *partialDeserializedTpr = read_tpx_state(ftp2fn(efTPR, filenames.size(), filenames.data()),
786 &inputrecInstance, globalState.get(), &mtop);
787 inputrec = &inputrecInstance;
790 /* Check and update the hardware options for internal consistency */
791 checkAndUpdateHardwareOptions(mdlog, &hw_opt, isSimulationMasterRank, domdecOptions.numPmeRanks,
794 if (GMX_THREAD_MPI && isSimulationMasterRank)
796 bool useGpuForNonbonded = false;
797 bool useGpuForPme = false;
800 GMX_RELEASE_ASSERT(inputrec != nullptr, "Keep the compiler happy");
802 // If the user specified the number of ranks, then we must
803 // respect that, but in default mode, we need to allow for
804 // the number of GPUs to choose the number of ranks.
805 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
806 useGpuForNonbonded = decideWhetherToUseGpusForNonbondedWithThreadMpi(
807 nonbondedTarget, gpuIdsToUse, userGpuTaskAssignment, emulateGpuNonbonded,
808 canUseGpuForNonbonded,
809 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, GMX_THREAD_MPI),
810 hw_opt.nthreads_tmpi);
811 useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi(
812 useGpuForNonbonded, pmeTarget, gpuIdsToUse, userGpuTaskAssignment, *hwinfo,
813 *inputrec, mtop, hw_opt.nthreads_tmpi, domdecOptions.numPmeRanks);
815 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
817 /* Determine how many thread-MPI ranks to start.
819 * TODO Over-writing the user-supplied value here does
820 * prevent any possible subsequent checks from working
822 hw_opt.nthreads_tmpi = get_nthreads_mpi(hwinfo, &hw_opt, gpuIdsToUse, useGpuForNonbonded,
823 useGpuForPme, inputrec, &mtop, mdlog, doMembed);
825 // Now start the threads for thread MPI.
826 spawnThreads(hw_opt.nthreads_tmpi);
827 // The spawned threads enter mdrunner() and execution of
828 // master and spawned threads joins at the end of this block.
829 physicalNodeComm = PhysicalNodeCommunicator(communicator, gmx_physicalnode_id_hash());
832 GMX_RELEASE_ASSERT(communicator == MPI_COMM_WORLD, "Must have valid world communicator");
833 CommrecHandle crHandle = init_commrec(communicator, ms);
834 t_commrec* cr = crHandle.get();
835 GMX_RELEASE_ASSERT(cr != nullptr, "Must have valid commrec");
839 /* now broadcast everything to the non-master nodes/threads: */
840 if (!isSimulationMasterRank)
842 inputrec = &inputrecInstance;
844 init_parallel(cr, inputrec, &mtop, partialDeserializedTpr.get());
846 GMX_RELEASE_ASSERT(inputrec != nullptr, "All ranks should have a valid inputrec now");
847 partialDeserializedTpr.reset(nullptr);
849 // Now the number of ranks is known to all ranks, and each knows
850 // the inputrec read by the master rank. The ranks can now all run
851 // the task-deciding functions and will agree on the result
852 // without needing to communicate.
853 const bool useDomainDecomposition = (PAR(cr) && !(EI_TPI(inputrec->eI) || inputrec->eI == eiNM));
855 // Note that these variables describe only their own node.
857 // Note that when bonded interactions run on a GPU they always run
858 // alongside a nonbonded task, so do not influence task assignment
859 // even though they affect the force calculation workload.
860 bool useGpuForNonbonded = false;
861 bool useGpuForPme = false;
862 bool useGpuForBonded = false;
863 bool useGpuForUpdate = false;
864 bool gpusWereDetected = hwinfo->ngpu_compatible_tot > 0;
867 // It's possible that there are different numbers of GPUs on
868 // different nodes, which is the user's responsibility to
869 // handle. If unsuitable, we will notice that during task
871 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
872 useGpuForNonbonded = decideWhetherToUseGpusForNonbonded(
873 nonbondedTarget, userGpuTaskAssignment, emulateGpuNonbonded, canUseGpuForNonbonded,
874 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, !GMX_THREAD_MPI), gpusWereDetected);
875 useGpuForPme = decideWhetherToUseGpusForPme(
876 useGpuForNonbonded, pmeTarget, userGpuTaskAssignment, *hwinfo, *inputrec, mtop,
877 cr->nnodes, domdecOptions.numPmeRanks, gpusWereDetected);
878 auto canUseGpuForBonded = buildSupportsGpuBondeds(nullptr)
879 && inputSupportsGpuBondeds(*inputrec, mtop, nullptr);
880 useGpuForBonded = decideWhetherToUseGpusForBonded(
881 useGpuForNonbonded, useGpuForPme, bondedTarget, canUseGpuForBonded,
882 EVDW_PME(inputrec->vdwtype), EEL_PME_EWALD(inputrec->coulombtype),
883 domdecOptions.numPmeRanks, gpusWereDetected);
885 pmeRunMode = (useGpuForPme ? PmeRunMode::GPU : PmeRunMode::CPU);
886 if (pmeRunMode == PmeRunMode::GPU)
888 if (pmeFftTarget == TaskTarget::Cpu)
890 pmeRunMode = PmeRunMode::Mixed;
893 else if (pmeFftTarget == TaskTarget::Gpu)
896 "Assigning FFTs to GPU requires PME to be assigned to GPU as well. With PME "
897 "on CPU you should not be using -pmefft.");
900 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
902 // Initialize development feature flags that enabled by environment variable
903 // and report those features that are enabled.
904 const DevelopmentFeatureFlags devFlags =
905 manageDevelopmentFeatures(mdlog, useGpuForNonbonded, pmeRunMode);
908 // TODO: hide restraint implementation details from Mdrunner.
909 // There is nothing unique about restraints at this point as far as the
910 // Mdrunner is concerned. The Mdrunner should just be getting a sequence of
911 // factory functions from the SimulationContext on which to call mdModules_->add().
912 // TODO: capture all restraints into a single RestraintModule, passed to the runner builder.
913 for (auto&& restraint : restraintManager_->getRestraints())
915 auto module = RestraintMDModule::create(restraint, restraint->sites());
916 mdModules_->add(std::move(module));
919 // TODO: Error handling
920 mdModules_->assignOptionsToModules(*inputrec->params, nullptr);
921 const auto& mdModulesNotifier = mdModules_->notifier().notifier_;
923 if (inputrec->internalParameters != nullptr)
925 mdModulesNotifier.notify(*inputrec->internalParameters);
928 if (fplog != nullptr)
930 pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
931 fprintf(fplog, "\n");
936 /* In rerun, set velocities to zero if present */
937 if (doRerun && ((globalState->flags & (1 << estV)) != 0))
939 // rerun does not use velocities
943 "Rerun trajectory contains velocities. Rerun does only evaluate "
944 "potential energy and forces. The velocities will be ignored.");
945 for (int i = 0; i < globalState->natoms; i++)
947 clear_rvec(globalState->v[i]);
949 globalState->flags &= ~(1 << estV);
952 /* now make sure the state is initialized and propagated */
953 set_state_entries(globalState.get(), inputrec);
956 /* NM and TPI parallelize over force/energy calculations, not atoms,
957 * so we need to initialize and broadcast the global state.
959 if (inputrec->eI == eiNM || inputrec->eI == eiTPI)
963 globalState = std::make_unique<t_state>();
965 broadcastStateWithoutDynamics(cr, globalState.get());
968 /* A parallel command line option consistency check that we can
969 only do after any threads have started. */
971 && (domdecOptions.numCells[XX] > 1 || domdecOptions.numCells[YY] > 1
972 || domdecOptions.numCells[ZZ] > 1 || domdecOptions.numPmeRanks > 0))
975 "The -dd or -npme option request a parallel simulation, "
977 "but %s was compiled without threads or MPI enabled",
978 output_env_get_program_display_name(oenv));
980 "but the number of MPI-threads (option -ntmpi) is not set or is 1");
982 "but %s was not started through mpirun/mpiexec or only one rank was requested "
983 "through mpirun/mpiexec",
984 output_env_get_program_display_name(oenv));
988 if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
991 "The .mdp file specified an energy mininization or normal mode algorithm, and "
992 "these are not compatible with mdrun -rerun");
995 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
997 if (domdecOptions.numPmeRanks > 0)
999 gmx_fatal_collective(FARGS, cr->mpi_comm_mysim, MASTER(cr),
1000 "PME-only ranks are requested, but the system does not use PME "
1001 "for electrostatics or LJ");
1004 domdecOptions.numPmeRanks = 0;
1007 if (useGpuForNonbonded && domdecOptions.numPmeRanks < 0)
1009 /* With NB GPUs we don't automatically use PME-only CPU ranks. PME ranks can
1010 * improve performance with many threads per GPU, since our OpenMP
1011 * scaling is bad, but it's difficult to automate the setup.
1013 domdecOptions.numPmeRanks = 0;
1017 if (domdecOptions.numPmeRanks < 0)
1019 domdecOptions.numPmeRanks = 0;
1020 // TODO possibly print a note that one can opt-in for a separate PME GPU rank?
1024 GMX_RELEASE_ASSERT(domdecOptions.numPmeRanks <= 1,
1025 "PME GPU decomposition is not supported");
1032 fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
1036 /* NMR restraints must be initialized before load_checkpoint,
1037 * since with time averaging the history is added to t_state.
1038 * For proper consistency check we therefore need to extend
1040 * So the PME-only nodes (if present) will also initialize
1041 * the distance restraints.
1045 /* This needs to be called before read_checkpoint to extend the state */
1046 init_disres(fplog, &mtop, inputrec, cr, ms, fcd, globalState.get(), replExParams.exchangeInterval > 0);
1048 init_orires(fplog, &mtop, inputrec, cr, ms, globalState.get(), &(fcd->orires));
1050 auto deform = prepareBoxDeformation(globalState->box, cr, *inputrec);
1052 ObservablesHistory observablesHistory = {};
1054 if (startingBehavior != StartingBehavior::NewSimulation)
1056 /* Check if checkpoint file exists before doing continuation.
1057 * This way we can use identical input options for the first and subsequent runs...
1059 if (mdrunOptions.numStepsCommandline > -2)
1061 /* Temporarily set the number of steps to unlimited to avoid
1062 * triggering the nsteps check in load_checkpoint().
1063 * This hack will go away soon when the -nsteps option is removed.
1065 inputrec->nsteps = -1;
1068 load_checkpoint(opt2fn_master("-cpi", filenames.size(), filenames.data(), cr),
1069 logFileHandle, cr, domdecOptions.numCells, inputrec, globalState.get(),
1070 &observablesHistory, mdrunOptions.reproducible, mdModules_->notifier());
1072 if (startingBehavior == StartingBehavior::RestartWithAppending && logFileHandle)
1074 // Now we can start normal logging to the truncated log file.
1075 fplog = gmx_fio_getfp(logFileHandle);
1076 prepareLogAppending(fplog);
1077 logOwner = buildLogger(fplog, MASTER(cr));
1078 mdlog = logOwner.logger();
1082 if (mdrunOptions.numStepsCommandline > -2)
1087 "The -nsteps functionality is deprecated, and may be removed in a future "
1089 "Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp "
1092 /* override nsteps with value set on the commandline */
1093 override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec);
1097 copy_mat(globalState->box, box);
1102 gmx_bcast(sizeof(box), box, cr);
1105 if (inputrec->cutoff_scheme != ecutsVERLET)
1108 "This group-scheme .tpr file can no longer be run by mdrun. Please update to the "
1109 "Verlet scheme, or use an earlier version of GROMACS if necessary.");
1111 /* Update rlist and nstlist. */
1112 prepare_verlet_scheme(fplog, cr, inputrec, nstlist_cmdline, &mtop, box,
1113 useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes),
1116 const bool prefer1DAnd1PulseDD = (devFlags.enableGpuHaloExchange && useGpuForNonbonded);
1117 // This builder is necessary while we have multi-part construction
1118 // of DD. Before DD is constructed, we use the existence of
1119 // the builder object to indicate that further construction of DD
1121 std::unique_ptr<DomainDecompositionBuilder> ddBuilder;
1122 if (useDomainDecomposition)
1124 ddBuilder = std::make_unique<DomainDecompositionBuilder>(
1125 mdlog, cr, domdecOptions, mdrunOptions, prefer1DAnd1PulseDD, mtop, *inputrec, box,
1126 positionsFromStatePointer(globalState.get()));
1130 /* PME, if used, is done on all nodes with 1D decomposition */
1132 cr->duty = (DUTY_PP | DUTY_PME);
1134 if (inputrec->ePBC == epbcSCREW)
1136 gmx_fatal(FARGS, "pbc=screw is only implemented with domain decomposition");
1140 // Produce the task assignment for this rank.
1141 GpuTaskAssignmentsBuilder gpuTaskAssignmentsBuilder;
1142 GpuTaskAssignments gpuTaskAssignments = gpuTaskAssignmentsBuilder.build(
1143 gpuIdsToUse, userGpuTaskAssignment, *hwinfo, cr, ms, physicalNodeComm, nonbondedTarget,
1144 pmeTarget, bondedTarget, updateTarget, useGpuForNonbonded, useGpuForPme,
1145 thisRankHasDuty(cr, DUTY_PP),
1146 // TODO cr->duty & DUTY_PME should imply that a PME
1147 // algorithm is active, but currently does not.
1148 EEL_PME(inputrec->coulombtype) && thisRankHasDuty(cr, DUTY_PME));
1150 const bool printHostName = (cr->nnodes > 1);
1151 gpuTaskAssignments.reportGpuUsage(mdlog, printHostName, useGpuForBonded, pmeRunMode);
1153 // If the user chose a task assignment, give them some hints
1154 // where appropriate.
1155 if (!userGpuTaskAssignment.empty())
1157 gpuTaskAssignments.logPerformanceHints(mdlog, ssize(gpuIdsToUse));
1160 // Get the device handles for the modules, nullptr when no task is assigned.
1161 gmx_device_info_t* nonbondedDeviceInfo = gpuTaskAssignments.initNonbondedDevice(cr);
1162 gmx_device_info_t* pmeDeviceInfo = gpuTaskAssignments.initPmeDevice();
1164 // TODO Initialize GPU streams here.
1166 // TODO Currently this is always built, yet DD partition code
1167 // checks if it is built before using it. Probably it should
1168 // become an MDModule that is made only when another module
1169 // requires it (e.g. pull, CompEl, density fitting), so that we
1170 // don't update the local atom sets unilaterally every step.
1171 LocalAtomSetManager atomSets;
1174 // TODO Pass the GPU streams to ddBuilder to use in buffer
1175 // transfers (e.g. halo exchange)
1176 cr->dd = ddBuilder->build(&atomSets);
1177 // The builder's job is done, so destruct it
1178 ddBuilder.reset(nullptr);
1179 // Note that local state still does not exist yet.
1182 // The GPU update is decided here because we need to know whether the constraints or
1183 // SETTLEs can span accross the domain borders (i.e. whether or not update groups are
1184 // defined). This is only known after DD is initialized, hence decision on using GPU
1185 // update is done so late.
1188 const bool useUpdateGroups = cr->dd ? ddUsesUpdateGroups(*cr->dd) : false;
1190 useGpuForUpdate = decideWhetherToUseGpuForUpdate(
1191 devFlags.forceGpuUpdateDefault, useDomainDecomposition, useUpdateGroups, pmeRunMode,
1192 domdecOptions.numPmeRanks > 0, useGpuForNonbonded, updateTarget, gpusWereDetected,
1193 *inputrec, mtop, doEssentialDynamics, gmx_mtop_ftype_count(mtop, F_ORIRES) > 0,
1194 replExParams.exchangeInterval > 0, doRerun, mdlog);
1196 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1200 /* After possible communicator splitting in make_dd_communicators.
1201 * we can set up the intra/inter node communication.
1203 gmx_setup_nodecomm(fplog, cr);
1209 GMX_LOG(mdlog.warning)
1211 .appendTextFormatted(
1212 "This is simulation %d out of %d running as a composite GROMACS\n"
1213 "multi-simulation job. Setup for this simulation:\n",
1216 GMX_LOG(mdlog.warning)
1217 .appendTextFormatted("Using %d MPI %s\n", cr->nnodes,
1219 cr->nnodes == 1 ? "thread" : "threads"
1221 cr->nnodes == 1 ? "process" : "processes"
1227 // If mdrun -pin auto honors any affinity setting that already
1228 // exists. If so, it is nice to provide feedback about whether
1229 // that existing affinity setting was from OpenMP or something
1230 // else, so we run this code both before and after we initialize
1231 // the OpenMP support.
1232 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo->nthreads_hw_avail, FALSE);
1233 /* Check and update the number of OpenMP threads requested */
1234 checkAndUpdateRequestedNumOpenmpThreads(&hw_opt, *hwinfo, cr, ms, physicalNodeComm.size_,
1235 pmeRunMode, mtop, *inputrec);
1237 gmx_omp_nthreads_init(mdlog, cr, hwinfo->nthreads_hw_avail, physicalNodeComm.size_,
1238 hw_opt.nthreads_omp, hw_opt.nthreads_omp_pme, !thisRankHasDuty(cr, DUTY_PP));
1240 // Enable FP exception detection, but not in
1241 // Release mode and not for compilers with known buggy FP
1242 // exception support (clang with any optimization) or suspected
1243 // buggy FP exception support (gcc 7.* with optimization).
1244 #if !defined NDEBUG \
1245 && !((defined __clang__ || (defined(__GNUC__) && !defined(__ICC) && __GNUC__ == 7)) \
1246 && defined __OPTIMIZE__)
1247 const bool bEnableFPE = true;
1249 const bool bEnableFPE = false;
1251 // FIXME - reconcile with gmx_feenableexcept() call from CommandLineModuleManager::run()
1254 gmx_feenableexcept();
1257 /* Now that we know the setup is consistent, check for efficiency */
1258 check_resource_division_efficiency(hwinfo, gpuTaskAssignments.thisRankHasAnyGpuTask(),
1259 mdrunOptions.ntompOptionIsSet, cr, mdlog);
1261 /* getting number of PP/PME threads on this MPI / tMPI rank.
1262 PME: env variable should be read only on one node to make sure it is
1263 identical everywhere;
1265 const int numThreadsOnThisRank = thisRankHasDuty(cr, DUTY_PP) ? gmx_omp_nthreads_get(emntNonbonded)
1266 : gmx_omp_nthreads_get(emntPME);
1267 checkHardwareOversubscription(numThreadsOnThisRank, cr->nodeid, *hwinfo->hardwareTopology,
1268 physicalNodeComm, mdlog);
1270 // Enable Peer access between GPUs where available
1271 // Only for DD, only master PP rank needs to perform setup, and only if thread MPI plus
1272 // any of the GPU communication features are active.
1273 if (DOMAINDECOMP(cr) && MASTER(cr) && thisRankHasDuty(cr, DUTY_PP) && GMX_THREAD_MPI
1274 && (devFlags.enableGpuHaloExchange || devFlags.enableGpuPmePPComm))
1276 setupGpuDevicePeerAccess(gpuIdsToUse, mdlog);
1279 if (hw_opt.threadAffinity != ThreadAffinity::Off)
1281 /* Before setting affinity, check whether the affinity has changed
1282 * - which indicates that probably the OpenMP library has changed it
1283 * since we first checked).
1285 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo->nthreads_hw_avail, TRUE);
1287 int numThreadsOnThisNode, intraNodeThreadOffset;
1288 analyzeThreadsOnThisNode(physicalNodeComm, numThreadsOnThisRank, &numThreadsOnThisNode,
1289 &intraNodeThreadOffset);
1291 /* Set the CPU affinity */
1292 gmx_set_thread_affinity(mdlog, cr, &hw_opt, *hwinfo->hardwareTopology, numThreadsOnThisRank,
1293 numThreadsOnThisNode, intraNodeThreadOffset, nullptr);
1296 if (mdrunOptions.timingOptions.resetStep > -1)
1301 "The -resetstep functionality is deprecated, and may be removed in a "
1304 wcycle = wallcycle_init(fplog, mdrunOptions.timingOptions.resetStep, cr);
1308 /* Master synchronizes its value of reset_counters with all nodes
1309 * including PME only nodes */
1310 int64_t reset_counters = wcycle_get_reset_counters(wcycle);
1311 gmx_bcast_sim(sizeof(reset_counters), &reset_counters, cr);
1312 wcycle_set_reset_counters(wcycle, reset_counters);
1315 // Membrane embedding must be initialized before we call init_forcerec()
1320 fprintf(stderr, "Initializing membed");
1322 /* Note that membed cannot work in parallel because mtop is
1323 * changed here. Fix this if we ever want to make it run with
1324 * multiple ranks. */
1325 membed = init_membed(fplog, filenames.size(), filenames.data(), &mtop, inputrec,
1326 globalState.get(), cr, &mdrunOptions.checkpointOptions.period);
1329 const bool thisRankHasPmeGpuTask = gpuTaskAssignments.thisRankHasPmeGpuTask();
1330 std::unique_ptr<MDAtoms> mdAtoms;
1331 std::unique_ptr<gmx_vsite_t> vsite;
1334 if (thisRankHasDuty(cr, DUTY_PP))
1336 mdModulesNotifier.notify(*cr);
1337 mdModulesNotifier.notify(&atomSets);
1338 mdModulesNotifier.notify(PeriodicBoundaryConditionType{ inputrec->ePBC });
1339 mdModulesNotifier.notify(SimulationTimeStep{ inputrec->delta_t });
1340 /* Initiate forcerecord */
1341 fr = new t_forcerec;
1342 fr->forceProviders = mdModules_->initForceProviders();
1343 init_forcerec(fplog, mdlog, fr, fcd, inputrec, &mtop, cr, box,
1344 opt2fn("-table", filenames.size(), filenames.data()),
1345 opt2fn("-tablep", filenames.size(), filenames.data()),
1346 opt2fns("-tableb", filenames.size(), filenames.data()), *hwinfo,
1347 nonbondedDeviceInfo, useGpuForBonded,
1348 pmeRunMode == PmeRunMode::GPU && !thisRankHasDuty(cr, DUTY_PME), pforce, wcycle);
1350 // TODO Move this to happen during domain decomposition setup,
1351 // once stream and event handling works well with that.
1352 // TODO remove need to pass local stream into GPU halo exchange - Redmine #3093
1353 if (havePPDomainDecomposition(cr) && prefer1DAnd1PulseDD && is1DAnd1PulseDD(*cr->dd))
1355 GMX_RELEASE_ASSERT(devFlags.enableGpuBufferOps,
1356 "Must use GMX_USE_GPU_BUFFER_OPS=1 to use GMX_GPU_DD_COMMS=1");
1358 Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::Local);
1359 void* streamNonLocal =
1360 Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::NonLocal);
1361 GMX_LOG(mdlog.warning)
1363 .appendTextFormatted(
1364 "NOTE: This run uses the 'GPU halo exchange' feature, enabled by the "
1365 "GMX_GPU_DD_COMMS environment variable.");
1366 cr->dd->gpuHaloExchange = std::make_unique<GpuHaloExchange>(
1367 cr->dd, cr->mpi_comm_mysim, streamLocal, streamNonLocal);
1370 /* Initialize the mdAtoms structure.
1371 * mdAtoms is not filled with atom data,
1372 * as this can not be done now with domain decomposition.
1374 mdAtoms = makeMDAtoms(fplog, mtop, *inputrec, thisRankHasPmeGpuTask);
1375 if (globalState && thisRankHasPmeGpuTask)
1377 // The pinning of coordinates in the global state object works, because we only use
1378 // PME on GPU without DD or on a separate PME rank, and because the local state pointer
1379 // points to the global state object without DD.
1380 // FIXME: MD and EM separately set up the local state - this should happen in the same
1381 // function, which should also perform the pinning.
1382 changePinningPolicy(&globalState->x, pme_get_pinning_policy());
1385 /* Initialize the virtual site communication */
1386 vsite = initVsite(mtop, cr);
1388 calc_shifts(box, fr->shift_vec);
1390 /* With periodic molecules the charge groups should be whole at start up
1391 * and the virtual sites should not be far from their proper positions.
1393 if (!inputrec->bContinuation && MASTER(cr) && !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
1395 /* Make molecules whole at start of run */
1396 if (fr->ePBC != epbcNONE)
1398 do_pbc_first_mtop(fplog, inputrec->ePBC, box, &mtop, globalState->x.rvec_array());
1402 /* Correct initial vsite positions are required
1403 * for the initial distribution in the domain decomposition
1404 * and for the initial shell prediction.
1406 constructVsitesGlobal(mtop, globalState->x);
1410 if (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
1412 ewaldcoeff_q = fr->ic->ewaldcoeff_q;
1413 ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
1418 /* This is a PME only node */
1420 GMX_ASSERT(globalState == nullptr,
1421 "We don't need the state on a PME only rank and expect it to be unitialized");
1423 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
1424 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
1427 gmx_pme_t* sepPmeData = nullptr;
1428 // This reference hides the fact that PME data is owned by runner on PME-only ranks and by forcerec on other ranks
1429 GMX_ASSERT(thisRankHasDuty(cr, DUTY_PP) == (fr != nullptr),
1430 "Double-checking that only PME-only ranks have no forcerec");
1431 gmx_pme_t*& pmedata = fr ? fr->pmedata : sepPmeData;
1433 // TODO should live in ewald module once its testing is improved
1435 // Later, this program could contain kernels that might be later
1436 // re-used as auto-tuning progresses, or subsequent simulations
1438 PmeGpuProgramStorage pmeGpuProgram;
1439 if (thisRankHasPmeGpuTask)
1441 pmeGpuProgram = buildPmeGpuProgram(pmeDeviceInfo);
1444 /* Initiate PME if necessary,
1445 * either on all nodes or on dedicated PME nodes only. */
1446 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
1448 if (mdAtoms && mdAtoms->mdatoms())
1450 nChargePerturbed = mdAtoms->mdatoms()->nChargePerturbed;
1451 if (EVDW_PME(inputrec->vdwtype))
1453 nTypePerturbed = mdAtoms->mdatoms()->nTypePerturbed;
1456 if (cr->npmenodes > 0)
1458 /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
1459 gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
1460 gmx_bcast_sim(sizeof(nTypePerturbed), &nTypePerturbed, cr);
1463 if (thisRankHasDuty(cr, DUTY_PME))
1467 pmedata = gmx_pme_init(cr, getNumPmeDomains(cr->dd), inputrec, nChargePerturbed != 0,
1468 nTypePerturbed != 0, mdrunOptions.reproducible, ewaldcoeff_q,
1469 ewaldcoeff_lj, gmx_omp_nthreads_get(emntPME), pmeRunMode,
1470 nullptr, pmeDeviceInfo, pmeGpuProgram.get(), mdlog);
1472 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1477 if (EI_DYNAMICS(inputrec->eI))
1479 /* Turn on signal handling on all nodes */
1481 * (A user signal from the PME nodes (if any)
1482 * is communicated to the PP nodes.
1484 signal_handler_install();
1487 pull_t* pull_work = nullptr;
1488 if (thisRankHasDuty(cr, DUTY_PP))
1490 /* Assumes uniform use of the number of OpenMP threads */
1491 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
1493 if (inputrec->bPull)
1495 /* Initialize pull code */
1496 pull_work = init_pull(fplog, inputrec->pull, inputrec, &mtop, cr, &atomSets,
1497 inputrec->fepvals->init_lambda);
1498 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
1500 initPullHistory(pull_work, &observablesHistory);
1502 if (EI_DYNAMICS(inputrec->eI) && MASTER(cr))
1504 init_pull_output_files(pull_work, filenames.size(), filenames.data(), oenv, startingBehavior);
1508 std::unique_ptr<EnforcedRotation> enforcedRotation;
1511 /* Initialize enforced rotation code */
1513 init_rot(fplog, inputrec, filenames.size(), filenames.data(), cr, &atomSets,
1514 globalState.get(), &mtop, oenv, mdrunOptions, startingBehavior);
1517 t_swap* swap = nullptr;
1518 if (inputrec->eSwapCoords != eswapNO)
1520 /* Initialize ion swapping code */
1521 swap = init_swapcoords(fplog, inputrec,
1522 opt2fn_master("-swap", filenames.size(), filenames.data(), cr),
1523 &mtop, globalState.get(), &observablesHistory, cr, &atomSets,
1524 oenv, mdrunOptions, startingBehavior);
1527 /* Let makeConstraints know whether we have essential dynamics constraints. */
1528 auto constr = makeConstraints(mtop, *inputrec, pull_work, doEssentialDynamics, fplog,
1529 *mdAtoms->mdatoms(), cr, ms, &nrnb, wcycle, fr->bMolPBC);
1531 /* Energy terms and groups */
1532 gmx_enerdata_t enerd(mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
1533 inputrec->fepvals->n_lambda);
1535 /* Kinetic energy data */
1536 gmx_ekindata_t ekind;
1537 init_ekindata(fplog, &mtop, &(inputrec->opts), &ekind, inputrec->cos_accel);
1539 /* Set up interactive MD (IMD) */
1541 makeImdSession(inputrec, cr, wcycle, &enerd, ms, &mtop, mdlog,
1542 MASTER(cr) ? globalState->x.rvec_array() : nullptr, filenames.size(),
1543 filenames.data(), oenv, mdrunOptions.imdOptions, startingBehavior);
1545 if (DOMAINDECOMP(cr))
1547 GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
1548 /* This call is not included in init_domain_decomposition mainly
1549 * because fr->cginfo_mb is set later.
1551 dd_init_bondeds(fplog, cr->dd, mtop, vsite.get(), inputrec,
1552 domdecOptions.checkBondedInteractions, fr->cginfo_mb);
1555 const bool inputIsCompatibleWithModularSimulator = ModularSimulator::isInputCompatible(
1556 false, inputrec, doRerun, vsite.get(), ms, replExParams, fcd,
1557 static_cast<int>(filenames.size()), filenames.data(), &observablesHistory, membed);
1559 const bool useModularSimulator = inputIsCompatibleWithModularSimulator
1560 && !(getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
1562 // TODO This is not the right place to manage the lifetime of
1563 // this data structure, but currently it's the easiest way to
1565 MdrunScheduleWorkload runScheduleWork;
1566 // Also populates the simulation constant workload description.
1567 runScheduleWork.simulationWork = createSimulationWorkload(
1568 useGpuForNonbonded, pmeRunMode, useGpuForBonded, useGpuForUpdate,
1569 devFlags.enableGpuBufferOps, devFlags.enableGpuHaloExchange,
1570 devFlags.enableGpuPmePPComm, haveEwaldSurfaceContribution(*inputrec));
1572 std::unique_ptr<gmx::StatePropagatorDataGpu> stateGpu;
1573 if (gpusWereDetected
1574 && ((useGpuForPme && thisRankHasDuty(cr, DUTY_PME))
1575 || runScheduleWork.simulationWork.useGpuBufferOps))
1577 const void* pmeStream = pme_gpu_get_device_stream(fr->pmedata);
1578 const void* localStream =
1579 fr->nbv->gpu_nbv != nullptr
1580 ? Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::Local)
1582 const void* nonLocalStream =
1583 fr->nbv->gpu_nbv != nullptr
1584 ? Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::NonLocal)
1586 const void* deviceContext = pme_gpu_get_device_context(fr->pmedata);
1587 const int paddingSize = pme_gpu_get_padding_size(fr->pmedata);
1588 GpuApiCallBehavior transferKind = (inputrec->eI == eiMD && !doRerun && !useModularSimulator)
1589 ? GpuApiCallBehavior::Async
1590 : GpuApiCallBehavior::Sync;
1592 stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(
1593 pmeStream, localStream, nonLocalStream, deviceContext, transferKind, paddingSize, wcycle);
1594 fr->stateGpu = stateGpu.get();
1597 GMX_ASSERT(stopHandlerBuilder_, "Runner must provide StopHandlerBuilder to simulator.");
1598 SimulatorBuilder simulatorBuilder;
1600 // build and run simulator object based on user-input
1601 auto simulator = simulatorBuilder.build(
1602 inputIsCompatibleWithModularSimulator, fplog, cr, ms, mdlog,
1603 static_cast<int>(filenames.size()), filenames.data(), oenv, mdrunOptions,
1604 startingBehavior, vsite.get(), constr.get(),
1605 enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr, deform.get(),
1606 mdModules_->outputProvider(), mdModules_->notifier(), inputrec, imdSession.get(),
1607 pull_work, swap, &mtop, fcd, globalState.get(), &observablesHistory, mdAtoms.get(),
1608 &nrnb, wcycle, fr, &enerd, &ekind, &runScheduleWork, replExParams, membed,
1609 walltime_accounting, std::move(stopHandlerBuilder_), doRerun);
1612 if (fr->pmePpCommGpu)
1614 // destroy object since it is no longer required. (This needs to be done while the GPU context still exists.)
1615 fr->pmePpCommGpu.reset();
1618 if (inputrec->bPull)
1620 finish_pull(pull_work);
1622 finish_swapcoords(swap);
1626 GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
1628 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
1629 gmx_pmeonly(pmedata, cr, &nrnb, wcycle, walltime_accounting, inputrec, pmeRunMode);
1632 wallcycle_stop(wcycle, ewcRUN);
1634 /* Finish up, write some stuff
1635 * if rerunMD, don't write last frame again
1637 finish_run(fplog, mdlog, cr, inputrec, &nrnb, wcycle, walltime_accounting,
1638 fr ? fr->nbv.get() : nullptr, pmedata, EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
1640 // clean up cycle counter
1641 wallcycle_destroy(wcycle);
1646 gmx_pme_destroy(pmedata);
1650 // FIXME: this is only here to manually unpin mdAtoms->chargeA_ and state->x,
1651 // before we destroy the GPU context(s) in free_gpu().
1652 // Pinned buffers are associated with contexts in CUDA.
1653 // As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
1654 mdAtoms.reset(nullptr);
1655 globalState.reset(nullptr);
1656 mdModules_.reset(nullptr); // destruct force providers here as they might also use the GPU
1657 /* Free pinned buffers in *fr */
1661 if (hwinfo->gpu_info.n_dev > 0)
1663 /* stop the GPU profiler (only CUDA) */
1667 /* With tMPI we need to wait for all ranks to finish deallocation before
1668 * destroying the CUDA context in free_gpu() as some tMPI ranks may be sharing
1671 * This is not a concern in OpenCL where we use one context per rank which
1672 * is freed in nbnxn_gpu_free().
1674 * Note: it is safe to not call the barrier on the ranks which do not use GPU,
1675 * but it is easier and more futureproof to call it on the whole node.
1677 * Note that this function needs to be called even if GPUs are not used
1678 * in this run because the PME ranks have no knowledge of whether GPUs
1679 * are used or not, but all ranks need to enter the barrier below.
1680 * \todo Remove this physical node barrier after making sure
1681 * that it's not needed anymore (with a shared GPU run).
1685 physicalNodeComm.barrier();
1688 free_gpu(nonbondedDeviceInfo);
1689 free_gpu(pmeDeviceInfo);
1694 free_membed(membed);
1697 /* Does what it says */
1698 print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
1699 walltime_accounting_destroy(walltime_accounting);
1701 // Ensure log file content is written
1704 gmx_fio_flush(logFileHandle);
1707 /* Reset FPEs (important for unit tests) by disabling them. Assumes no
1708 * exceptions were enabled before function was called. */
1711 gmx_fedisableexcept();
1714 auto rc = static_cast<int>(gmx_get_stop_condition());
1717 /* we need to join all threads. The sub-threads join when they
1718 exit this function, but the master thread needs to be told to
1720 if (PAR(cr) && MASTER(cr))
1728 Mdrunner::~Mdrunner()
1730 // Clean up of the Manager.
1731 // This will end up getting called on every thread-MPI rank, which is unnecessary,
1732 // but okay as long as threads synchronize some time before adding or accessing
1733 // a new set of restraints.
1734 if (restraintManager_)
1736 restraintManager_->clear();
1737 GMX_ASSERT(restraintManager_->countRestraints() == 0,
1738 "restraints added during runner life time should be cleared at runner "
1743 void Mdrunner::addPotential(std::shared_ptr<gmx::IRestraintPotential> puller, const std::string& name)
1745 GMX_ASSERT(restraintManager_, "Mdrunner must have a restraint manager.");
1746 // Not sure if this should be logged through the md logger or something else,
1747 // but it is helpful to have some sort of INFO level message sent somewhere.
1748 // std::cout << "Registering restraint named " << name << std::endl;
1750 // When multiple restraints are used, it may be wasteful to register them separately.
1751 // Maybe instead register an entire Restraint Manager as a force provider.
1752 restraintManager_->addToSpec(std::move(puller), name);
1755 Mdrunner::Mdrunner(std::unique_ptr<MDModules> mdModules) : mdModules_(std::move(mdModules)) {}
1757 Mdrunner::Mdrunner(Mdrunner&&) noexcept = default;
1759 //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265
1760 Mdrunner& Mdrunner::operator=(Mdrunner&& /*handle*/) noexcept(BUGFREE_NOEXCEPT_STRING) = default;
1762 class Mdrunner::BuilderImplementation
1765 BuilderImplementation() = delete;
1766 BuilderImplementation(std::unique_ptr<MDModules> mdModules, compat::not_null<SimulationContext*> context);
1767 ~BuilderImplementation();
1769 BuilderImplementation& setExtraMdrunOptions(const MdrunOptions& options,
1770 real forceWarningThreshold,
1771 StartingBehavior startingBehavior);
1773 void addDomdec(const DomdecOptions& options);
1775 void addVerletList(int nstlist);
1777 void addReplicaExchange(const ReplicaExchangeParameters& params);
1779 void addNonBonded(const char* nbpu_opt);
1781 void addPME(const char* pme_opt_, const char* pme_fft_opt_);
1783 void addBondedTaskAssignment(const char* bonded_opt);
1785 void addUpdateTaskAssignment(const char* update_opt);
1787 void addHardwareOptions(const gmx_hw_opt_t& hardwareOptions);
1789 void addFilenames(ArrayRef<const t_filenm> filenames);
1791 void addOutputEnvironment(gmx_output_env_t* outputEnvironment);
1793 void addLogFile(t_fileio* logFileHandle);
1795 void addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
1800 // Default parameters copied from runner.h
1801 // \todo Clarify source(s) of default parameters.
1803 const char* nbpu_opt_ = nullptr;
1804 const char* pme_opt_ = nullptr;
1805 const char* pme_fft_opt_ = nullptr;
1806 const char* bonded_opt_ = nullptr;
1807 const char* update_opt_ = nullptr;
1809 MdrunOptions mdrunOptions_;
1811 DomdecOptions domdecOptions_;
1813 ReplicaExchangeParameters replicaExchangeParameters_;
1815 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
1818 //! Multisim communicator handle.
1819 gmx_multisim_t* multiSimulation_;
1821 //! mdrun communicator
1822 MPI_Comm communicator_ = MPI_COMM_NULL;
1824 //! Print a warning if any force is larger than this (in kJ/mol nm).
1825 real forceWarningThreshold_ = -1;
1827 //! Whether the simulation will start afresh, or restart with/without appending.
1828 StartingBehavior startingBehavior_ = StartingBehavior::NewSimulation;
1830 //! The modules that comprise the functionality of mdrun.
1831 std::unique_ptr<MDModules> mdModules_;
1833 //! \brief Parallelism information.
1834 gmx_hw_opt_t hardwareOptions_;
1836 //! filename options for simulation.
1837 ArrayRef<const t_filenm> filenames_;
1839 /*! \brief Handle to output environment.
1841 * \todo gmx_output_env_t needs lifetime management.
1843 gmx_output_env_t* outputEnvironment_ = nullptr;
1845 /*! \brief Non-owning handle to MD log file.
1847 * \todo Context should own output facilities for client.
1848 * \todo Improve log file handle management.
1850 * Code managing the FILE* relies on the ability to set it to
1851 * nullptr to check whether the filehandle is valid.
1853 t_fileio* logFileHandle_ = nullptr;
1856 * \brief Builder for simulation stop signal handler.
1858 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_ = nullptr;
1861 Mdrunner::BuilderImplementation::BuilderImplementation(std::unique_ptr<MDModules> mdModules,
1862 compat::not_null<SimulationContext*> context) :
1863 mdModules_(std::move(mdModules))
1865 communicator_ = context->communicator_;
1866 multiSimulation_ = context->multiSimulation_.get();
1869 Mdrunner::BuilderImplementation::~BuilderImplementation() = default;
1871 Mdrunner::BuilderImplementation&
1872 Mdrunner::BuilderImplementation::setExtraMdrunOptions(const MdrunOptions& options,
1873 const real forceWarningThreshold,
1874 const StartingBehavior startingBehavior)
1876 mdrunOptions_ = options;
1877 forceWarningThreshold_ = forceWarningThreshold;
1878 startingBehavior_ = startingBehavior;
1882 void Mdrunner::BuilderImplementation::addDomdec(const DomdecOptions& options)
1884 domdecOptions_ = options;
1887 void Mdrunner::BuilderImplementation::addVerletList(int nstlist)
1892 void Mdrunner::BuilderImplementation::addReplicaExchange(const ReplicaExchangeParameters& params)
1894 replicaExchangeParameters_ = params;
1897 Mdrunner Mdrunner::BuilderImplementation::build()
1899 auto newRunner = Mdrunner(std::move(mdModules_));
1901 newRunner.mdrunOptions = mdrunOptions_;
1902 newRunner.pforce = forceWarningThreshold_;
1903 newRunner.startingBehavior = startingBehavior_;
1904 newRunner.domdecOptions = domdecOptions_;
1906 // \todo determine an invariant to check or confirm that all gmx_hw_opt_t objects are valid
1907 newRunner.hw_opt = hardwareOptions_;
1909 // No invariant to check. This parameter exists to optionally override other behavior.
1910 newRunner.nstlist_cmdline = nstlist_;
1912 newRunner.replExParams = replicaExchangeParameters_;
1914 newRunner.filenames = filenames_;
1916 newRunner.communicator = communicator_;
1918 // nullptr is a valid value for the multisim handle
1919 newRunner.ms = multiSimulation_;
1921 // \todo Clarify ownership and lifetime management for gmx_output_env_t
1922 // \todo Update sanity checking when output environment has clearly specified invariants.
1923 // Initialization and default values for oenv are not well specified in the current version.
1924 if (outputEnvironment_)
1926 newRunner.oenv = outputEnvironment_;
1930 GMX_THROW(gmx::APIError(
1931 "MdrunnerBuilder::addOutputEnvironment() is required before build()"));
1934 newRunner.logFileHandle = logFileHandle_;
1938 newRunner.nbpu_opt = nbpu_opt_;
1942 GMX_THROW(gmx::APIError("MdrunnerBuilder::addNonBonded() is required before build()"));
1945 if (pme_opt_ && pme_fft_opt_)
1947 newRunner.pme_opt = pme_opt_;
1948 newRunner.pme_fft_opt = pme_fft_opt_;
1952 GMX_THROW(gmx::APIError("MdrunnerBuilder::addElectrostatics() is required before build()"));
1957 newRunner.bonded_opt = bonded_opt_;
1961 GMX_THROW(gmx::APIError(
1962 "MdrunnerBuilder::addBondedTaskAssignment() is required before build()"));
1967 newRunner.update_opt = update_opt_;
1971 GMX_THROW(gmx::APIError(
1972 "MdrunnerBuilder::addUpdateTaskAssignment() is required before build() "));
1976 newRunner.restraintManager_ = std::make_unique<gmx::RestraintManager>();
1978 if (stopHandlerBuilder_)
1980 newRunner.stopHandlerBuilder_ = std::move(stopHandlerBuilder_);
1984 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>();
1990 void Mdrunner::BuilderImplementation::addNonBonded(const char* nbpu_opt)
1992 nbpu_opt_ = nbpu_opt;
1995 void Mdrunner::BuilderImplementation::addPME(const char* pme_opt, const char* pme_fft_opt)
1998 pme_fft_opt_ = pme_fft_opt;
2001 void Mdrunner::BuilderImplementation::addBondedTaskAssignment(const char* bonded_opt)
2003 bonded_opt_ = bonded_opt;
2006 void Mdrunner::BuilderImplementation::addUpdateTaskAssignment(const char* update_opt)
2008 update_opt_ = update_opt;
2011 void Mdrunner::BuilderImplementation::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2013 hardwareOptions_ = hardwareOptions;
2016 void Mdrunner::BuilderImplementation::addFilenames(ArrayRef<const t_filenm> filenames)
2018 filenames_ = filenames;
2021 void Mdrunner::BuilderImplementation::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2023 outputEnvironment_ = outputEnvironment;
2026 void Mdrunner::BuilderImplementation::addLogFile(t_fileio* logFileHandle)
2028 logFileHandle_ = logFileHandle;
2031 void Mdrunner::BuilderImplementation::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2033 stopHandlerBuilder_ = std::move(builder);
2036 MdrunnerBuilder::MdrunnerBuilder(std::unique_ptr<MDModules> mdModules,
2037 compat::not_null<SimulationContext*> context) :
2038 impl_{ std::make_unique<Mdrunner::BuilderImplementation>(std::move(mdModules), context) }
2042 MdrunnerBuilder::~MdrunnerBuilder() = default;
2044 MdrunnerBuilder& MdrunnerBuilder::addSimulationMethod(const MdrunOptions& options,
2045 real forceWarningThreshold,
2046 const StartingBehavior startingBehavior)
2048 impl_->setExtraMdrunOptions(options, forceWarningThreshold, startingBehavior);
2052 MdrunnerBuilder& MdrunnerBuilder::addDomainDecomposition(const DomdecOptions& options)
2054 impl_->addDomdec(options);
2058 MdrunnerBuilder& MdrunnerBuilder::addNeighborList(int nstlist)
2060 impl_->addVerletList(nstlist);
2064 MdrunnerBuilder& MdrunnerBuilder::addReplicaExchange(const ReplicaExchangeParameters& params)
2066 impl_->addReplicaExchange(params);
2070 MdrunnerBuilder& MdrunnerBuilder::addNonBonded(const char* nbpu_opt)
2072 impl_->addNonBonded(nbpu_opt);
2076 MdrunnerBuilder& MdrunnerBuilder::addElectrostatics(const char* pme_opt, const char* pme_fft_opt)
2078 // The builder method may become more general in the future, but in this version,
2079 // parameters for PME electrostatics are both required and the only parameters
2081 if (pme_opt && pme_fft_opt)
2083 impl_->addPME(pme_opt, pme_fft_opt);
2088 gmx::InvalidInputError("addElectrostatics() arguments must be non-null pointers."));
2093 MdrunnerBuilder& MdrunnerBuilder::addBondedTaskAssignment(const char* bonded_opt)
2095 impl_->addBondedTaskAssignment(bonded_opt);
2099 MdrunnerBuilder& MdrunnerBuilder::addUpdateTaskAssignment(const char* update_opt)
2101 impl_->addUpdateTaskAssignment(update_opt);
2105 Mdrunner MdrunnerBuilder::build()
2107 return impl_->build();
2110 MdrunnerBuilder& MdrunnerBuilder::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2112 impl_->addHardwareOptions(hardwareOptions);
2116 MdrunnerBuilder& MdrunnerBuilder::addFilenames(ArrayRef<const t_filenm> filenames)
2118 impl_->addFilenames(filenames);
2122 MdrunnerBuilder& MdrunnerBuilder::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2124 impl_->addOutputEnvironment(outputEnvironment);
2128 MdrunnerBuilder& MdrunnerBuilder::addLogFile(t_fileio* logFileHandle)
2130 impl_->addLogFile(logFileHandle);
2134 MdrunnerBuilder& MdrunnerBuilder::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2136 impl_->addStopHandlerBuilder(std::move(builder));
2140 MdrunnerBuilder::MdrunnerBuilder(MdrunnerBuilder&&) noexcept = default;
2142 MdrunnerBuilder& MdrunnerBuilder::operator=(MdrunnerBuilder&&) noexcept = default;