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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);
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.
854 // TODO Should we do the communication in debug mode to support
855 // having an assertion?
856 const bool useDomainDecomposition = (PAR(cr) && !(EI_TPI(inputrec->eI) || inputrec->eI == eiNM));
858 // Note that these variables describe only their own node.
860 // Note that when bonded interactions run on a GPU they always run
861 // alongside a nonbonded task, so do not influence task assignment
862 // even though they affect the force calculation workload.
863 bool useGpuForNonbonded = false;
864 bool useGpuForPme = false;
865 bool useGpuForBonded = false;
866 bool useGpuForUpdate = false;
867 bool gpusWereDetected = hwinfo->ngpu_compatible_tot > 0;
870 // It's possible that there are different numbers of GPUs on
871 // different nodes, which is the user's responsibility to
872 // handle. If unsuitable, we will notice that during task
874 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
875 useGpuForNonbonded = decideWhetherToUseGpusForNonbonded(
876 nonbondedTarget, userGpuTaskAssignment, emulateGpuNonbonded, canUseGpuForNonbonded,
877 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, !GMX_THREAD_MPI), gpusWereDetected);
878 useGpuForPme = decideWhetherToUseGpusForPme(
879 useGpuForNonbonded, pmeTarget, userGpuTaskAssignment, *hwinfo, *inputrec, mtop,
880 cr->nnodes, domdecOptions.numPmeRanks, gpusWereDetected);
881 auto canUseGpuForBonded = buildSupportsGpuBondeds(nullptr)
882 && inputSupportsGpuBondeds(*inputrec, mtop, nullptr);
883 useGpuForBonded = decideWhetherToUseGpusForBonded(
884 useGpuForNonbonded, useGpuForPme, bondedTarget, canUseGpuForBonded,
885 EVDW_PME(inputrec->vdwtype), EEL_PME_EWALD(inputrec->coulombtype),
886 domdecOptions.numPmeRanks, gpusWereDetected);
888 pmeRunMode = (useGpuForPme ? PmeRunMode::GPU : PmeRunMode::CPU);
889 if (pmeRunMode == PmeRunMode::GPU)
891 if (pmeFftTarget == TaskTarget::Cpu)
893 pmeRunMode = PmeRunMode::Mixed;
896 else if (pmeFftTarget == TaskTarget::Gpu)
899 "Assigning FFTs to GPU requires PME to be assigned to GPU as well. With PME "
900 "on CPU you should not be using -pmefft.");
903 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
905 // Initialize development feature flags that enabled by environment variable
906 // and report those features that are enabled.
907 const DevelopmentFeatureFlags devFlags =
908 manageDevelopmentFeatures(mdlog, useGpuForNonbonded, pmeRunMode);
911 // TODO: hide restraint implementation details from Mdrunner.
912 // There is nothing unique about restraints at this point as far as the
913 // Mdrunner is concerned. The Mdrunner should just be getting a sequence of
914 // factory functions from the SimulationContext on which to call mdModules_->add().
915 // TODO: capture all restraints into a single RestraintModule, passed to the runner builder.
916 for (auto&& restraint : restraintManager_->getRestraints())
918 auto module = RestraintMDModule::create(restraint, restraint->sites());
919 mdModules_->add(std::move(module));
922 // TODO: Error handling
923 mdModules_->assignOptionsToModules(*inputrec->params, nullptr);
924 const auto& mdModulesNotifier = mdModules_->notifier().notifier_;
926 if (inputrec->internalParameters != nullptr)
928 mdModulesNotifier.notify(*inputrec->internalParameters);
931 if (fplog != nullptr)
933 pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
934 fprintf(fplog, "\n");
939 /* In rerun, set velocities to zero if present */
940 if (doRerun && ((globalState->flags & (1 << estV)) != 0))
942 // rerun does not use velocities
946 "Rerun trajectory contains velocities. Rerun does only evaluate "
947 "potential energy and forces. The velocities will be ignored.");
948 for (int i = 0; i < globalState->natoms; i++)
950 clear_rvec(globalState->v[i]);
952 globalState->flags &= ~(1 << estV);
955 /* now make sure the state is initialized and propagated */
956 set_state_entries(globalState.get(), inputrec);
959 /* NM and TPI parallelize over force/energy calculations, not atoms,
960 * so we need to initialize and broadcast the global state.
962 if (inputrec->eI == eiNM || inputrec->eI == eiTPI)
966 globalState = std::make_unique<t_state>();
968 broadcastStateWithoutDynamics(cr, globalState.get());
971 /* A parallel command line option consistency check that we can
972 only do after any threads have started. */
974 && (domdecOptions.numCells[XX] > 1 || domdecOptions.numCells[YY] > 1
975 || domdecOptions.numCells[ZZ] > 1 || domdecOptions.numPmeRanks > 0))
978 "The -dd or -npme option request a parallel simulation, "
980 "but %s was compiled without threads or MPI enabled",
981 output_env_get_program_display_name(oenv));
983 "but the number of MPI-threads (option -ntmpi) is not set or is 1");
985 "but %s was not started through mpirun/mpiexec or only one rank was requested "
986 "through mpirun/mpiexec",
987 output_env_get_program_display_name(oenv));
991 if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
994 "The .mdp file specified an energy mininization or normal mode algorithm, and "
995 "these are not compatible with mdrun -rerun");
998 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
1000 if (domdecOptions.numPmeRanks > 0)
1002 gmx_fatal_collective(FARGS, cr->mpi_comm_mysim, MASTER(cr),
1003 "PME-only ranks are requested, but the system does not use PME "
1004 "for electrostatics or LJ");
1007 domdecOptions.numPmeRanks = 0;
1010 if (useGpuForNonbonded && domdecOptions.numPmeRanks < 0)
1012 /* With NB GPUs we don't automatically use PME-only CPU ranks. PME ranks can
1013 * improve performance with many threads per GPU, since our OpenMP
1014 * scaling is bad, but it's difficult to automate the setup.
1016 domdecOptions.numPmeRanks = 0;
1020 if (domdecOptions.numPmeRanks < 0)
1022 domdecOptions.numPmeRanks = 0;
1023 // TODO possibly print a note that one can opt-in for a separate PME GPU rank?
1027 GMX_RELEASE_ASSERT(domdecOptions.numPmeRanks <= 1,
1028 "PME GPU decomposition is not supported");
1035 fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
1039 /* NMR restraints must be initialized before load_checkpoint,
1040 * since with time averaging the history is added to t_state.
1041 * For proper consistency check we therefore need to extend
1043 * So the PME-only nodes (if present) will also initialize
1044 * the distance restraints.
1048 /* This needs to be called before read_checkpoint to extend the state */
1049 init_disres(fplog, &mtop, inputrec, cr, ms, fcd, globalState.get(), replExParams.exchangeInterval > 0);
1051 init_orires(fplog, &mtop, inputrec, cr, ms, globalState.get(), &(fcd->orires));
1053 auto deform = prepareBoxDeformation(globalState->box, cr, *inputrec);
1055 ObservablesHistory observablesHistory = {};
1057 if (startingBehavior != StartingBehavior::NewSimulation)
1059 /* Check if checkpoint file exists before doing continuation.
1060 * This way we can use identical input options for the first and subsequent runs...
1062 if (mdrunOptions.numStepsCommandline > -2)
1064 /* Temporarily set the number of steps to unlimited to avoid
1065 * triggering the nsteps check in load_checkpoint().
1066 * This hack will go away soon when the -nsteps option is removed.
1068 inputrec->nsteps = -1;
1071 load_checkpoint(opt2fn_master("-cpi", filenames.size(), filenames.data(), cr),
1072 logFileHandle, cr, domdecOptions.numCells, inputrec, globalState.get(),
1073 &observablesHistory, mdrunOptions.reproducible, mdModules_->notifier());
1075 if (startingBehavior == StartingBehavior::RestartWithAppending && logFileHandle)
1077 // Now we can start normal logging to the truncated log file.
1078 fplog = gmx_fio_getfp(logFileHandle);
1079 prepareLogAppending(fplog);
1080 logOwner = buildLogger(fplog, MASTER(cr));
1081 mdlog = logOwner.logger();
1085 if (mdrunOptions.numStepsCommandline > -2)
1090 "The -nsteps functionality is deprecated, and may be removed in a future "
1092 "Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp "
1095 /* override nsteps with value set on the commandline */
1096 override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec);
1100 copy_mat(globalState->box, box);
1105 gmx_bcast(sizeof(box), box, cr);
1108 if (inputrec->cutoff_scheme != ecutsVERLET)
1111 "This group-scheme .tpr file can no longer be run by mdrun. Please update to the "
1112 "Verlet scheme, or use an earlier version of GROMACS if necessary.");
1114 /* Update rlist and nstlist. */
1115 prepare_verlet_scheme(fplog, cr, inputrec, nstlist_cmdline, &mtop, box,
1116 useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes),
1119 const bool prefer1DAnd1PulseDD = (devFlags.enableGpuHaloExchange && useGpuForNonbonded);
1120 // This builder is necessary while we have multi-part construction
1121 // of DD. Before DD is constructed, we use the existence of
1122 // the builder object to indicate that further construction of DD
1124 std::unique_ptr<DomainDecompositionBuilder> ddBuilder;
1125 if (useDomainDecomposition)
1127 ddBuilder = std::make_unique<DomainDecompositionBuilder>(
1128 mdlog, cr, domdecOptions, mdrunOptions, prefer1DAnd1PulseDD, mtop, *inputrec, box,
1129 positionsFromStatePointer(globalState.get()));
1133 /* PME, if used, is done on all nodes with 1D decomposition */
1135 cr->duty = (DUTY_PP | DUTY_PME);
1137 if (inputrec->ePBC == epbcSCREW)
1139 gmx_fatal(FARGS, "pbc=screw is only implemented with domain decomposition");
1143 // Produce the task assignment for this rank.
1144 GpuTaskAssignmentsBuilder gpuTaskAssignmentsBuilder;
1145 GpuTaskAssignments gpuTaskAssignments = gpuTaskAssignmentsBuilder.build(
1146 gpuIdsToUse, userGpuTaskAssignment, *hwinfo, communicator, physicalNodeComm,
1147 nonbondedTarget, pmeTarget, bondedTarget, updateTarget, useGpuForNonbonded,
1148 useGpuForPme, thisRankHasDuty(cr, DUTY_PP),
1149 // TODO cr->duty & DUTY_PME should imply that a PME
1150 // algorithm is active, but currently does not.
1151 EEL_PME(inputrec->coulombtype) && thisRankHasDuty(cr, DUTY_PME));
1153 // Get the device handles for the modules, nullptr when no task is assigned.
1154 gmx_device_info_t* nonbondedDeviceInfo = gpuTaskAssignments.initNonbondedDevice(cr);
1155 gmx_device_info_t* pmeDeviceInfo = gpuTaskAssignments.initPmeDevice();
1157 // TODO Initialize GPU streams here.
1159 // TODO Currently this is always built, yet DD partition code
1160 // checks if it is built before using it. Probably it should
1161 // become an MDModule that is made only when another module
1162 // requires it (e.g. pull, CompEl, density fitting), so that we
1163 // don't update the local atom sets unilaterally every step.
1164 LocalAtomSetManager atomSets;
1167 // TODO Pass the GPU streams to ddBuilder to use in buffer
1168 // transfers (e.g. halo exchange)
1169 cr->dd = ddBuilder->build(&atomSets);
1170 // The builder's job is done, so destruct it
1171 ddBuilder.reset(nullptr);
1172 // Note that local state still does not exist yet.
1175 // The GPU update is decided here because we need to know whether the constraints or
1176 // SETTLEs can span accross the domain borders (i.e. whether or not update groups are
1177 // defined). This is only known after DD is initialized, hence decision on using GPU
1178 // update is done so late.
1181 const bool useUpdateGroups = cr->dd ? ddUsesUpdateGroups(*cr->dd) : false;
1183 useGpuForUpdate = decideWhetherToUseGpuForUpdate(
1184 devFlags.forceGpuUpdateDefault, useDomainDecomposition, useUpdateGroups, pmeRunMode,
1185 domdecOptions.numPmeRanks > 0, useGpuForNonbonded, updateTarget, gpusWereDetected,
1186 *inputrec, mtop, doEssentialDynamics, gmx_mtop_ftype_count(mtop, F_ORIRES) > 0,
1187 replExParams.exchangeInterval > 0, doRerun, mdlog);
1189 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1191 const bool printHostName = (cr->nnodes > 1);
1192 gpuTaskAssignments.reportGpuUsage(mdlog, printHostName, useGpuForBonded, pmeRunMode, useGpuForUpdate);
1194 // If the user chose a task assignment, give them some hints
1195 // where appropriate.
1196 if (!userGpuTaskAssignment.empty())
1198 gpuTaskAssignments.logPerformanceHints(mdlog, ssize(gpuIdsToUse));
1203 /* After possible communicator splitting in make_dd_communicators.
1204 * we can set up the intra/inter node communication.
1206 gmx_setup_nodecomm(fplog, cr);
1212 GMX_LOG(mdlog.warning)
1214 .appendTextFormatted(
1215 "This is simulation %d out of %d running as a composite GROMACS\n"
1216 "multi-simulation job. Setup for this simulation:\n",
1219 GMX_LOG(mdlog.warning)
1220 .appendTextFormatted("Using %d MPI %s\n", cr->nnodes,
1222 cr->nnodes == 1 ? "thread" : "threads"
1224 cr->nnodes == 1 ? "process" : "processes"
1230 // If mdrun -pin auto honors any affinity setting that already
1231 // exists. If so, it is nice to provide feedback about whether
1232 // that existing affinity setting was from OpenMP or something
1233 // else, so we run this code both before and after we initialize
1234 // the OpenMP support.
1235 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo->nthreads_hw_avail, FALSE);
1236 /* Check and update the number of OpenMP threads requested */
1237 checkAndUpdateRequestedNumOpenmpThreads(&hw_opt, *hwinfo, cr, ms, physicalNodeComm.size_,
1238 pmeRunMode, mtop, *inputrec);
1240 gmx_omp_nthreads_init(mdlog, cr, hwinfo->nthreads_hw_avail, physicalNodeComm.size_,
1241 hw_opt.nthreads_omp, hw_opt.nthreads_omp_pme, !thisRankHasDuty(cr, DUTY_PP));
1243 // Enable FP exception detection, but not in
1244 // Release mode and not for compilers with known buggy FP
1245 // exception support (clang with any optimization) or suspected
1246 // buggy FP exception support (gcc 7.* with optimization).
1247 #if !defined NDEBUG \
1248 && !((defined __clang__ || (defined(__GNUC__) && !defined(__ICC) && __GNUC__ == 7)) \
1249 && defined __OPTIMIZE__)
1250 const bool bEnableFPE = true;
1252 const bool bEnableFPE = false;
1254 // FIXME - reconcile with gmx_feenableexcept() call from CommandLineModuleManager::run()
1257 gmx_feenableexcept();
1260 /* Now that we know the setup is consistent, check for efficiency */
1261 check_resource_division_efficiency(hwinfo, gpuTaskAssignments.thisRankHasAnyGpuTask(),
1262 mdrunOptions.ntompOptionIsSet, cr, mdlog);
1264 /* getting number of PP/PME threads on this MPI / tMPI rank.
1265 PME: env variable should be read only on one node to make sure it is
1266 identical everywhere;
1268 const int numThreadsOnThisRank = thisRankHasDuty(cr, DUTY_PP) ? gmx_omp_nthreads_get(emntNonbonded)
1269 : gmx_omp_nthreads_get(emntPME);
1270 checkHardwareOversubscription(numThreadsOnThisRank, cr->nodeid, *hwinfo->hardwareTopology,
1271 physicalNodeComm, mdlog);
1273 // Enable Peer access between GPUs where available
1274 // Only for DD, only master PP rank needs to perform setup, and only if thread MPI plus
1275 // any of the GPU communication features are active.
1276 if (DOMAINDECOMP(cr) && MASTER(cr) && thisRankHasDuty(cr, DUTY_PP) && GMX_THREAD_MPI
1277 && (devFlags.enableGpuHaloExchange || devFlags.enableGpuPmePPComm))
1279 setupGpuDevicePeerAccess(gpuIdsToUse, mdlog);
1282 if (hw_opt.threadAffinity != ThreadAffinity::Off)
1284 /* Before setting affinity, check whether the affinity has changed
1285 * - which indicates that probably the OpenMP library has changed it
1286 * since we first checked).
1288 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo->nthreads_hw_avail, TRUE);
1290 int numThreadsOnThisNode, intraNodeThreadOffset;
1291 analyzeThreadsOnThisNode(physicalNodeComm, numThreadsOnThisRank, &numThreadsOnThisNode,
1292 &intraNodeThreadOffset);
1294 /* Set the CPU affinity */
1295 gmx_set_thread_affinity(mdlog, cr, &hw_opt, *hwinfo->hardwareTopology, numThreadsOnThisRank,
1296 numThreadsOnThisNode, intraNodeThreadOffset, nullptr);
1299 if (mdrunOptions.timingOptions.resetStep > -1)
1304 "The -resetstep functionality is deprecated, and may be removed in a "
1307 wcycle = wallcycle_init(fplog, mdrunOptions.timingOptions.resetStep, cr);
1311 /* Master synchronizes its value of reset_counters with all nodes
1312 * including PME only nodes */
1313 int64_t reset_counters = wcycle_get_reset_counters(wcycle);
1314 gmx_bcast_sim(sizeof(reset_counters), &reset_counters, cr);
1315 wcycle_set_reset_counters(wcycle, reset_counters);
1318 // Membrane embedding must be initialized before we call init_forcerec()
1323 fprintf(stderr, "Initializing membed");
1325 /* Note that membed cannot work in parallel because mtop is
1326 * changed here. Fix this if we ever want to make it run with
1327 * multiple ranks. */
1328 membed = init_membed(fplog, filenames.size(), filenames.data(), &mtop, inputrec,
1329 globalState.get(), cr, &mdrunOptions.checkpointOptions.period);
1332 const bool thisRankHasPmeGpuTask = gpuTaskAssignments.thisRankHasPmeGpuTask();
1333 std::unique_ptr<MDAtoms> mdAtoms;
1334 std::unique_ptr<gmx_vsite_t> vsite;
1337 if (thisRankHasDuty(cr, DUTY_PP))
1339 mdModulesNotifier.notify(*cr);
1340 mdModulesNotifier.notify(&atomSets);
1341 mdModulesNotifier.notify(PeriodicBoundaryConditionType{ inputrec->ePBC });
1342 mdModulesNotifier.notify(SimulationTimeStep{ inputrec->delta_t });
1343 /* Initiate forcerecord */
1344 fr = new t_forcerec;
1345 fr->forceProviders = mdModules_->initForceProviders();
1346 init_forcerec(fplog, mdlog, fr, fcd, inputrec, &mtop, cr, box,
1347 opt2fn("-table", filenames.size(), filenames.data()),
1348 opt2fn("-tablep", filenames.size(), filenames.data()),
1349 opt2fns("-tableb", filenames.size(), filenames.data()), *hwinfo,
1350 nonbondedDeviceInfo, useGpuForBonded,
1351 pmeRunMode == PmeRunMode::GPU && !thisRankHasDuty(cr, DUTY_PME), pforce, wcycle);
1353 // TODO Move this to happen during domain decomposition setup,
1354 // once stream and event handling works well with that.
1355 // TODO remove need to pass local stream into GPU halo exchange - Redmine #3093
1356 if (havePPDomainDecomposition(cr) && prefer1DAnd1PulseDD && is1DAnd1PulseDD(*cr->dd))
1358 GMX_RELEASE_ASSERT(devFlags.enableGpuBufferOps,
1359 "Must use GMX_USE_GPU_BUFFER_OPS=1 to use GMX_GPU_DD_COMMS=1");
1361 Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::Local);
1362 void* streamNonLocal =
1363 Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::NonLocal);
1364 GMX_LOG(mdlog.warning)
1366 .appendTextFormatted(
1367 "NOTE: This run uses the 'GPU halo exchange' feature, enabled by the "
1368 "GMX_GPU_DD_COMMS environment variable.");
1369 cr->dd->gpuHaloExchange = std::make_unique<GpuHaloExchange>(
1370 cr->dd, cr->mpi_comm_mysim, streamLocal, streamNonLocal);
1373 /* Initialize the mdAtoms structure.
1374 * mdAtoms is not filled with atom data,
1375 * as this can not be done now with domain decomposition.
1377 mdAtoms = makeMDAtoms(fplog, mtop, *inputrec, thisRankHasPmeGpuTask);
1378 if (globalState && thisRankHasPmeGpuTask)
1380 // The pinning of coordinates in the global state object works, because we only use
1381 // PME on GPU without DD or on a separate PME rank, and because the local state pointer
1382 // points to the global state object without DD.
1383 // FIXME: MD and EM separately set up the local state - this should happen in the same
1384 // function, which should also perform the pinning.
1385 changePinningPolicy(&globalState->x, pme_get_pinning_policy());
1388 /* Initialize the virtual site communication */
1389 vsite = initVsite(mtop, cr);
1391 calc_shifts(box, fr->shift_vec);
1393 /* With periodic molecules the charge groups should be whole at start up
1394 * and the virtual sites should not be far from their proper positions.
1396 if (!inputrec->bContinuation && MASTER(cr) && !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
1398 /* Make molecules whole at start of run */
1399 if (fr->ePBC != epbcNONE)
1401 do_pbc_first_mtop(fplog, inputrec->ePBC, box, &mtop, globalState->x.rvec_array());
1405 /* Correct initial vsite positions are required
1406 * for the initial distribution in the domain decomposition
1407 * and for the initial shell prediction.
1409 constructVsitesGlobal(mtop, globalState->x);
1413 if (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
1415 ewaldcoeff_q = fr->ic->ewaldcoeff_q;
1416 ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
1421 /* This is a PME only node */
1423 GMX_ASSERT(globalState == nullptr,
1424 "We don't need the state on a PME only rank and expect it to be unitialized");
1426 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
1427 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
1430 gmx_pme_t* sepPmeData = nullptr;
1431 // This reference hides the fact that PME data is owned by runner on PME-only ranks and by forcerec on other ranks
1432 GMX_ASSERT(thisRankHasDuty(cr, DUTY_PP) == (fr != nullptr),
1433 "Double-checking that only PME-only ranks have no forcerec");
1434 gmx_pme_t*& pmedata = fr ? fr->pmedata : sepPmeData;
1436 // TODO should live in ewald module once its testing is improved
1438 // Later, this program could contain kernels that might be later
1439 // re-used as auto-tuning progresses, or subsequent simulations
1441 PmeGpuProgramStorage pmeGpuProgram;
1442 if (thisRankHasPmeGpuTask)
1444 pmeGpuProgram = buildPmeGpuProgram(pmeDeviceInfo);
1447 /* Initiate PME if necessary,
1448 * either on all nodes or on dedicated PME nodes only. */
1449 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
1451 if (mdAtoms && mdAtoms->mdatoms())
1453 nChargePerturbed = mdAtoms->mdatoms()->nChargePerturbed;
1454 if (EVDW_PME(inputrec->vdwtype))
1456 nTypePerturbed = mdAtoms->mdatoms()->nTypePerturbed;
1459 if (cr->npmenodes > 0)
1461 /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
1462 gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
1463 gmx_bcast_sim(sizeof(nTypePerturbed), &nTypePerturbed, cr);
1466 if (thisRankHasDuty(cr, DUTY_PME))
1470 pmedata = gmx_pme_init(cr, getNumPmeDomains(cr->dd), inputrec, nChargePerturbed != 0,
1471 nTypePerturbed != 0, mdrunOptions.reproducible, ewaldcoeff_q,
1472 ewaldcoeff_lj, gmx_omp_nthreads_get(emntPME), pmeRunMode,
1473 nullptr, pmeDeviceInfo, pmeGpuProgram.get(), mdlog);
1475 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1480 if (EI_DYNAMICS(inputrec->eI))
1482 /* Turn on signal handling on all nodes */
1484 * (A user signal from the PME nodes (if any)
1485 * is communicated to the PP nodes.
1487 signal_handler_install();
1490 pull_t* pull_work = nullptr;
1491 if (thisRankHasDuty(cr, DUTY_PP))
1493 /* Assumes uniform use of the number of OpenMP threads */
1494 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
1496 if (inputrec->bPull)
1498 /* Initialize pull code */
1499 pull_work = init_pull(fplog, inputrec->pull, inputrec, &mtop, cr, &atomSets,
1500 inputrec->fepvals->init_lambda);
1501 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
1503 initPullHistory(pull_work, &observablesHistory);
1505 if (EI_DYNAMICS(inputrec->eI) && MASTER(cr))
1507 init_pull_output_files(pull_work, filenames.size(), filenames.data(), oenv, startingBehavior);
1511 std::unique_ptr<EnforcedRotation> enforcedRotation;
1514 /* Initialize enforced rotation code */
1516 init_rot(fplog, inputrec, filenames.size(), filenames.data(), cr, &atomSets,
1517 globalState.get(), &mtop, oenv, mdrunOptions, startingBehavior);
1520 t_swap* swap = nullptr;
1521 if (inputrec->eSwapCoords != eswapNO)
1523 /* Initialize ion swapping code */
1524 swap = init_swapcoords(fplog, inputrec,
1525 opt2fn_master("-swap", filenames.size(), filenames.data(), cr),
1526 &mtop, globalState.get(), &observablesHistory, cr, &atomSets,
1527 oenv, mdrunOptions, startingBehavior);
1530 /* Let makeConstraints know whether we have essential dynamics constraints. */
1531 auto constr = makeConstraints(mtop, *inputrec, pull_work, doEssentialDynamics, fplog,
1532 *mdAtoms->mdatoms(), cr, ms, &nrnb, wcycle, fr->bMolPBC);
1534 /* Energy terms and groups */
1535 gmx_enerdata_t enerd(mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
1536 inputrec->fepvals->n_lambda);
1538 /* Kinetic energy data */
1539 gmx_ekindata_t ekind;
1540 init_ekindata(fplog, &mtop, &(inputrec->opts), &ekind, inputrec->cos_accel);
1542 /* Set up interactive MD (IMD) */
1544 makeImdSession(inputrec, cr, wcycle, &enerd, ms, &mtop, mdlog,
1545 MASTER(cr) ? globalState->x.rvec_array() : nullptr, filenames.size(),
1546 filenames.data(), oenv, mdrunOptions.imdOptions, startingBehavior);
1548 if (DOMAINDECOMP(cr))
1550 GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
1551 /* This call is not included in init_domain_decomposition mainly
1552 * because fr->cginfo_mb is set later.
1554 dd_init_bondeds(fplog, cr->dd, &mtop, vsite.get(), inputrec,
1555 domdecOptions.checkBondedInteractions, fr->cginfo_mb);
1558 const bool inputIsCompatibleWithModularSimulator = ModularSimulator::isInputCompatible(
1559 false, inputrec, doRerun, vsite.get(), ms, replExParams, fcd,
1560 static_cast<int>(filenames.size()), filenames.data(), &observablesHistory, membed);
1562 const bool useModularSimulator = inputIsCompatibleWithModularSimulator
1563 && !(getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
1565 // TODO This is not the right place to manage the lifetime of
1566 // this data structure, but currently it's the easiest way to
1568 MdrunScheduleWorkload runScheduleWork;
1569 // Also populates the simulation constant workload description.
1570 runScheduleWork.simulationWork = createSimulationWorkload(
1571 useGpuForNonbonded, pmeRunMode, useGpuForBonded, useGpuForUpdate,
1572 devFlags.enableGpuBufferOps, devFlags.enableGpuHaloExchange,
1573 devFlags.enableGpuPmePPComm, haveEwaldSurfaceContribution(*inputrec));
1575 std::unique_ptr<gmx::StatePropagatorDataGpu> stateGpu;
1576 if (gpusWereDetected
1577 && ((useGpuForPme && thisRankHasDuty(cr, DUTY_PME))
1578 || runScheduleWork.simulationWork.useGpuBufferOps))
1580 const void* pmeStream = pme_gpu_get_device_stream(fr->pmedata);
1581 const void* localStream =
1582 fr->nbv->gpu_nbv != nullptr
1583 ? Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::Local)
1585 const void* nonLocalStream =
1586 fr->nbv->gpu_nbv != nullptr
1587 ? Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::NonLocal)
1589 const void* deviceContext = pme_gpu_get_device_context(fr->pmedata);
1590 const int paddingSize = pme_gpu_get_padding_size(fr->pmedata);
1591 GpuApiCallBehavior transferKind = (inputrec->eI == eiMD && !doRerun && !useModularSimulator)
1592 ? GpuApiCallBehavior::Async
1593 : GpuApiCallBehavior::Sync;
1595 stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(
1596 pmeStream, localStream, nonLocalStream, deviceContext, transferKind, paddingSize, wcycle);
1597 fr->stateGpu = stateGpu.get();
1600 GMX_ASSERT(stopHandlerBuilder_, "Runner must provide StopHandlerBuilder to simulator.");
1601 SimulatorBuilder simulatorBuilder;
1603 // build and run simulator object based on user-input
1604 auto simulator = simulatorBuilder.build(
1605 inputIsCompatibleWithModularSimulator, fplog, cr, ms, mdlog,
1606 static_cast<int>(filenames.size()), filenames.data(), oenv, mdrunOptions,
1607 startingBehavior, vsite.get(), constr.get(),
1608 enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr, deform.get(),
1609 mdModules_->outputProvider(), mdModules_->notifier(), inputrec, imdSession.get(),
1610 pull_work, swap, &mtop, fcd, globalState.get(), &observablesHistory, mdAtoms.get(),
1611 &nrnb, wcycle, fr, &enerd, &ekind, &runScheduleWork, replExParams, membed,
1612 walltime_accounting, std::move(stopHandlerBuilder_), doRerun);
1615 if (fr->pmePpCommGpu)
1617 // destroy object since it is no longer required. (This needs to be done while the GPU context still exists.)
1618 fr->pmePpCommGpu.reset();
1621 if (inputrec->bPull)
1623 finish_pull(pull_work);
1625 finish_swapcoords(swap);
1629 GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
1631 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
1632 gmx_pmeonly(pmedata, cr, &nrnb, wcycle, walltime_accounting, inputrec, pmeRunMode);
1635 wallcycle_stop(wcycle, ewcRUN);
1637 /* Finish up, write some stuff
1638 * if rerunMD, don't write last frame again
1640 finish_run(fplog, mdlog, cr, inputrec, &nrnb, wcycle, walltime_accounting,
1641 fr ? fr->nbv.get() : nullptr, pmedata, EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
1643 // clean up cycle counter
1644 wallcycle_destroy(wcycle);
1649 gmx_pme_destroy(pmedata);
1653 // FIXME: this is only here to manually unpin mdAtoms->chargeA_ and state->x,
1654 // before we destroy the GPU context(s) in free_gpu_resources().
1655 // Pinned buffers are associated with contexts in CUDA.
1656 // As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
1657 mdAtoms.reset(nullptr);
1658 globalState.reset(nullptr);
1659 mdModules_.reset(nullptr); // destruct force providers here as they might also use the GPU
1661 /* Free GPU memory and set a physical node tMPI barrier (which should eventually go away) */
1662 free_gpu_resources(fr, physicalNodeComm, hwinfo->gpu_info);
1663 free_gpu(nonbondedDeviceInfo);
1664 free_gpu(pmeDeviceInfo);
1665 done_forcerec(fr, mtop.molblock.size());
1670 free_membed(membed);
1673 /* Does what it says */
1674 print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
1675 walltime_accounting_destroy(walltime_accounting);
1677 // Ensure log file content is written
1680 gmx_fio_flush(logFileHandle);
1683 /* Reset FPEs (important for unit tests) by disabling them. Assumes no
1684 * exceptions were enabled before function was called. */
1687 gmx_fedisableexcept();
1690 auto rc = static_cast<int>(gmx_get_stop_condition());
1693 /* we need to join all threads. The sub-threads join when they
1694 exit this function, but the master thread needs to be told to
1696 if (PAR(cr) && MASTER(cr))
1704 Mdrunner::~Mdrunner()
1706 // Clean up of the Manager.
1707 // This will end up getting called on every thread-MPI rank, which is unnecessary,
1708 // but okay as long as threads synchronize some time before adding or accessing
1709 // a new set of restraints.
1710 if (restraintManager_)
1712 restraintManager_->clear();
1713 GMX_ASSERT(restraintManager_->countRestraints() == 0,
1714 "restraints added during runner life time should be cleared at runner "
1719 void Mdrunner::addPotential(std::shared_ptr<gmx::IRestraintPotential> puller, const std::string& name)
1721 GMX_ASSERT(restraintManager_, "Mdrunner must have a restraint manager.");
1722 // Not sure if this should be logged through the md logger or something else,
1723 // but it is helpful to have some sort of INFO level message sent somewhere.
1724 // std::cout << "Registering restraint named " << name << std::endl;
1726 // When multiple restraints are used, it may be wasteful to register them separately.
1727 // Maybe instead register an entire Restraint Manager as a force provider.
1728 restraintManager_->addToSpec(std::move(puller), name);
1731 Mdrunner::Mdrunner(std::unique_ptr<MDModules> mdModules) : mdModules_(std::move(mdModules)) {}
1733 Mdrunner::Mdrunner(Mdrunner&&) noexcept = default;
1735 //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265
1736 Mdrunner& Mdrunner::operator=(Mdrunner&& /*handle*/) noexcept(BUGFREE_NOEXCEPT_STRING) = default;
1738 class Mdrunner::BuilderImplementation
1741 BuilderImplementation() = delete;
1742 BuilderImplementation(std::unique_ptr<MDModules> mdModules, compat::not_null<SimulationContext*> context);
1743 ~BuilderImplementation();
1745 BuilderImplementation& setExtraMdrunOptions(const MdrunOptions& options,
1746 real forceWarningThreshold,
1747 StartingBehavior startingBehavior);
1749 void addDomdec(const DomdecOptions& options);
1751 void addVerletList(int nstlist);
1753 void addReplicaExchange(const ReplicaExchangeParameters& params);
1755 void addNonBonded(const char* nbpu_opt);
1757 void addPME(const char* pme_opt_, const char* pme_fft_opt_);
1759 void addBondedTaskAssignment(const char* bonded_opt);
1761 void addUpdateTaskAssignment(const char* update_opt);
1763 void addHardwareOptions(const gmx_hw_opt_t& hardwareOptions);
1765 void addFilenames(ArrayRef<const t_filenm> filenames);
1767 void addOutputEnvironment(gmx_output_env_t* outputEnvironment);
1769 void addLogFile(t_fileio* logFileHandle);
1771 void addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
1776 // Default parameters copied from runner.h
1777 // \todo Clarify source(s) of default parameters.
1779 const char* nbpu_opt_ = nullptr;
1780 const char* pme_opt_ = nullptr;
1781 const char* pme_fft_opt_ = nullptr;
1782 const char* bonded_opt_ = nullptr;
1783 const char* update_opt_ = nullptr;
1785 MdrunOptions mdrunOptions_;
1787 DomdecOptions domdecOptions_;
1789 ReplicaExchangeParameters replicaExchangeParameters_;
1791 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
1794 //! Multisim communicator handle.
1795 gmx_multisim_t* multiSimulation_;
1797 //! mdrun communicator
1798 MPI_Comm communicator_ = MPI_COMM_NULL;
1800 //! Print a warning if any force is larger than this (in kJ/mol nm).
1801 real forceWarningThreshold_ = -1;
1803 //! Whether the simulation will start afresh, or restart with/without appending.
1804 StartingBehavior startingBehavior_ = StartingBehavior::NewSimulation;
1806 //! The modules that comprise the functionality of mdrun.
1807 std::unique_ptr<MDModules> mdModules_;
1809 //! \brief Parallelism information.
1810 gmx_hw_opt_t hardwareOptions_;
1812 //! filename options for simulation.
1813 ArrayRef<const t_filenm> filenames_;
1815 /*! \brief Handle to output environment.
1817 * \todo gmx_output_env_t needs lifetime management.
1819 gmx_output_env_t* outputEnvironment_ = nullptr;
1821 /*! \brief Non-owning handle to MD log file.
1823 * \todo Context should own output facilities for client.
1824 * \todo Improve log file handle management.
1826 * Code managing the FILE* relies on the ability to set it to
1827 * nullptr to check whether the filehandle is valid.
1829 t_fileio* logFileHandle_ = nullptr;
1832 * \brief Builder for simulation stop signal handler.
1834 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_ = nullptr;
1837 Mdrunner::BuilderImplementation::BuilderImplementation(std::unique_ptr<MDModules> mdModules,
1838 compat::not_null<SimulationContext*> context) :
1839 mdModules_(std::move(mdModules))
1841 communicator_ = context->communicator_;
1842 multiSimulation_ = context->multiSimulation_.get();
1845 Mdrunner::BuilderImplementation::~BuilderImplementation() = default;
1847 Mdrunner::BuilderImplementation&
1848 Mdrunner::BuilderImplementation::setExtraMdrunOptions(const MdrunOptions& options,
1849 const real forceWarningThreshold,
1850 const StartingBehavior startingBehavior)
1852 mdrunOptions_ = options;
1853 forceWarningThreshold_ = forceWarningThreshold;
1854 startingBehavior_ = startingBehavior;
1858 void Mdrunner::BuilderImplementation::addDomdec(const DomdecOptions& options)
1860 domdecOptions_ = options;
1863 void Mdrunner::BuilderImplementation::addVerletList(int nstlist)
1868 void Mdrunner::BuilderImplementation::addReplicaExchange(const ReplicaExchangeParameters& params)
1870 replicaExchangeParameters_ = params;
1873 Mdrunner Mdrunner::BuilderImplementation::build()
1875 auto newRunner = Mdrunner(std::move(mdModules_));
1877 newRunner.mdrunOptions = mdrunOptions_;
1878 newRunner.pforce = forceWarningThreshold_;
1879 newRunner.startingBehavior = startingBehavior_;
1880 newRunner.domdecOptions = domdecOptions_;
1882 // \todo determine an invariant to check or confirm that all gmx_hw_opt_t objects are valid
1883 newRunner.hw_opt = hardwareOptions_;
1885 // No invariant to check. This parameter exists to optionally override other behavior.
1886 newRunner.nstlist_cmdline = nstlist_;
1888 newRunner.replExParams = replicaExchangeParameters_;
1890 newRunner.filenames = filenames_;
1892 newRunner.communicator = communicator_;
1894 // nullptr is a valid value for the multisim handle
1895 newRunner.ms = multiSimulation_;
1897 // \todo Clarify ownership and lifetime management for gmx_output_env_t
1898 // \todo Update sanity checking when output environment has clearly specified invariants.
1899 // Initialization and default values for oenv are not well specified in the current version.
1900 if (outputEnvironment_)
1902 newRunner.oenv = outputEnvironment_;
1906 GMX_THROW(gmx::APIError(
1907 "MdrunnerBuilder::addOutputEnvironment() is required before build()"));
1910 newRunner.logFileHandle = logFileHandle_;
1914 newRunner.nbpu_opt = nbpu_opt_;
1918 GMX_THROW(gmx::APIError("MdrunnerBuilder::addNonBonded() is required before build()"));
1921 if (pme_opt_ && pme_fft_opt_)
1923 newRunner.pme_opt = pme_opt_;
1924 newRunner.pme_fft_opt = pme_fft_opt_;
1928 GMX_THROW(gmx::APIError("MdrunnerBuilder::addElectrostatics() is required before build()"));
1933 newRunner.bonded_opt = bonded_opt_;
1937 GMX_THROW(gmx::APIError(
1938 "MdrunnerBuilder::addBondedTaskAssignment() is required before build()"));
1943 newRunner.update_opt = update_opt_;
1947 GMX_THROW(gmx::APIError(
1948 "MdrunnerBuilder::addUpdateTaskAssignment() is required before build() "));
1952 newRunner.restraintManager_ = std::make_unique<gmx::RestraintManager>();
1954 if (stopHandlerBuilder_)
1956 newRunner.stopHandlerBuilder_ = std::move(stopHandlerBuilder_);
1960 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>();
1966 void Mdrunner::BuilderImplementation::addNonBonded(const char* nbpu_opt)
1968 nbpu_opt_ = nbpu_opt;
1971 void Mdrunner::BuilderImplementation::addPME(const char* pme_opt, const char* pme_fft_opt)
1974 pme_fft_opt_ = pme_fft_opt;
1977 void Mdrunner::BuilderImplementation::addBondedTaskAssignment(const char* bonded_opt)
1979 bonded_opt_ = bonded_opt;
1982 void Mdrunner::BuilderImplementation::addUpdateTaskAssignment(const char* update_opt)
1984 update_opt_ = update_opt;
1987 void Mdrunner::BuilderImplementation::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
1989 hardwareOptions_ = hardwareOptions;
1992 void Mdrunner::BuilderImplementation::addFilenames(ArrayRef<const t_filenm> filenames)
1994 filenames_ = filenames;
1997 void Mdrunner::BuilderImplementation::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
1999 outputEnvironment_ = outputEnvironment;
2002 void Mdrunner::BuilderImplementation::addLogFile(t_fileio* logFileHandle)
2004 logFileHandle_ = logFileHandle;
2007 void Mdrunner::BuilderImplementation::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2009 stopHandlerBuilder_ = std::move(builder);
2012 MdrunnerBuilder::MdrunnerBuilder(std::unique_ptr<MDModules> mdModules,
2013 compat::not_null<SimulationContext*> context) :
2014 impl_{ std::make_unique<Mdrunner::BuilderImplementation>(std::move(mdModules), context) }
2018 MdrunnerBuilder::~MdrunnerBuilder() = default;
2020 MdrunnerBuilder& MdrunnerBuilder::addSimulationMethod(const MdrunOptions& options,
2021 real forceWarningThreshold,
2022 const StartingBehavior startingBehavior)
2024 impl_->setExtraMdrunOptions(options, forceWarningThreshold, startingBehavior);
2028 MdrunnerBuilder& MdrunnerBuilder::addDomainDecomposition(const DomdecOptions& options)
2030 impl_->addDomdec(options);
2034 MdrunnerBuilder& MdrunnerBuilder::addNeighborList(int nstlist)
2036 impl_->addVerletList(nstlist);
2040 MdrunnerBuilder& MdrunnerBuilder::addReplicaExchange(const ReplicaExchangeParameters& params)
2042 impl_->addReplicaExchange(params);
2046 MdrunnerBuilder& MdrunnerBuilder::addNonBonded(const char* nbpu_opt)
2048 impl_->addNonBonded(nbpu_opt);
2052 MdrunnerBuilder& MdrunnerBuilder::addElectrostatics(const char* pme_opt, const char* pme_fft_opt)
2054 // The builder method may become more general in the future, but in this version,
2055 // parameters for PME electrostatics are both required and the only parameters
2057 if (pme_opt && pme_fft_opt)
2059 impl_->addPME(pme_opt, pme_fft_opt);
2064 gmx::InvalidInputError("addElectrostatics() arguments must be non-null pointers."));
2069 MdrunnerBuilder& MdrunnerBuilder::addBondedTaskAssignment(const char* bonded_opt)
2071 impl_->addBondedTaskAssignment(bonded_opt);
2075 MdrunnerBuilder& MdrunnerBuilder::addUpdateTaskAssignment(const char* update_opt)
2077 impl_->addUpdateTaskAssignment(update_opt);
2081 Mdrunner MdrunnerBuilder::build()
2083 return impl_->build();
2086 MdrunnerBuilder& MdrunnerBuilder::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2088 impl_->addHardwareOptions(hardwareOptions);
2092 MdrunnerBuilder& MdrunnerBuilder::addFilenames(ArrayRef<const t_filenm> filenames)
2094 impl_->addFilenames(filenames);
2098 MdrunnerBuilder& MdrunnerBuilder::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2100 impl_->addOutputEnvironment(outputEnvironment);
2104 MdrunnerBuilder& MdrunnerBuilder::addLogFile(t_fileio* logFileHandle)
2106 impl_->addLogFile(logFileHandle);
2110 MdrunnerBuilder& MdrunnerBuilder::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2112 impl_->addStopHandlerBuilder(std::move(builder));
2116 MdrunnerBuilder::MdrunnerBuilder(MdrunnerBuilder&&) noexcept = default;
2118 MdrunnerBuilder& MdrunnerBuilder::operator=(MdrunnerBuilder&&) noexcept = default;