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39 * \brief Implements the MD runner routine calling all integrators.
41 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
42 * \ingroup module_mdrun
59 #include "gromacs/commandline/filenm.h"
60 #include "gromacs/domdec/builder.h"
61 #include "gromacs/domdec/domdec.h"
62 #include "gromacs/domdec/domdec_struct.h"
63 #include "gromacs/domdec/gpuhaloexchange.h"
64 #include "gromacs/domdec/localatomsetmanager.h"
65 #include "gromacs/domdec/partition.h"
66 #include "gromacs/ewald/ewald_utils.h"
67 #include "gromacs/ewald/pme.h"
68 #include "gromacs/ewald/pme_gpu_program.h"
69 #include "gromacs/ewald/pme_only.h"
70 #include "gromacs/ewald/pme_pp_comm_gpu.h"
71 #include "gromacs/fileio/checkpoint.h"
72 #include "gromacs/fileio/gmxfio.h"
73 #include "gromacs/fileio/oenv.h"
74 #include "gromacs/fileio/tpxio.h"
75 #include "gromacs/gmxlib/network.h"
76 #include "gromacs/gmxlib/nrnb.h"
77 #include "gromacs/gpu_utils/device_stream_manager.h"
78 #include "gromacs/hardware/cpuinfo.h"
79 #include "gromacs/hardware/detecthardware.h"
80 #include "gromacs/hardware/device_management.h"
81 #include "gromacs/hardware/hardwaretopology.h"
82 #include "gromacs/hardware/printhardware.h"
83 #include "gromacs/imd/imd.h"
84 #include "gromacs/listed_forces/disre.h"
85 #include "gromacs/listed_forces/gpubonded.h"
86 #include "gromacs/listed_forces/listed_forces.h"
87 #include "gromacs/listed_forces/orires.h"
88 #include "gromacs/math/functions.h"
89 #include "gromacs/math/utilities.h"
90 #include "gromacs/math/vec.h"
91 #include "gromacs/mdlib/boxdeformation.h"
92 #include "gromacs/mdlib/broadcaststructs.h"
93 #include "gromacs/mdlib/calc_verletbuf.h"
94 #include "gromacs/mdlib/dispersioncorrection.h"
95 #include "gromacs/mdlib/enerdata_utils.h"
96 #include "gromacs/mdlib/force.h"
97 #include "gromacs/mdlib/forcerec.h"
98 #include "gromacs/mdlib/gmx_omp_nthreads.h"
99 #include "gromacs/mdlib/gpuforcereduction.h"
100 #include "gromacs/mdlib/makeconstraints.h"
101 #include "gromacs/mdlib/md_support.h"
102 #include "gromacs/mdlib/mdatoms.h"
103 #include "gromacs/mdlib/sighandler.h"
104 #include "gromacs/mdlib/stophandler.h"
105 #include "gromacs/mdlib/tgroup.h"
106 #include "gromacs/mdlib/updategroups.h"
107 #include "gromacs/mdlib/vsite.h"
108 #include "gromacs/mdrun/mdmodules.h"
109 #include "gromacs/mdrun/simulationcontext.h"
110 #include "gromacs/mdrun/simulationinput.h"
111 #include "gromacs/mdrun/simulationinputhandle.h"
112 #include "gromacs/mdrunutility/handlerestart.h"
113 #include "gromacs/mdrunutility/logging.h"
114 #include "gromacs/mdrunutility/multisim.h"
115 #include "gromacs/mdrunutility/printtime.h"
116 #include "gromacs/mdrunutility/threadaffinity.h"
117 #include "gromacs/mdtypes/checkpointdata.h"
118 #include "gromacs/mdtypes/commrec.h"
119 #include "gromacs/mdtypes/enerdata.h"
120 #include "gromacs/mdtypes/fcdata.h"
121 #include "gromacs/mdtypes/forcerec.h"
122 #include "gromacs/mdtypes/group.h"
123 #include "gromacs/mdtypes/inputrec.h"
124 #include "gromacs/mdtypes/interaction_const.h"
125 #include "gromacs/mdtypes/md_enums.h"
126 #include "gromacs/mdtypes/mdatom.h"
127 #include "gromacs/mdtypes/mdrunoptions.h"
128 #include "gromacs/mdtypes/observableshistory.h"
129 #include "gromacs/mdtypes/simulation_workload.h"
130 #include "gromacs/mdtypes/state.h"
131 #include "gromacs/mdtypes/state_propagator_data_gpu.h"
132 #include "gromacs/modularsimulator/modularsimulator.h"
133 #include "gromacs/nbnxm/gpu_data_mgmt.h"
134 #include "gromacs/nbnxm/nbnxm.h"
135 #include "gromacs/nbnxm/pairlist_tuning.h"
136 #include "gromacs/pbcutil/pbc.h"
137 #include "gromacs/pulling/output.h"
138 #include "gromacs/pulling/pull.h"
139 #include "gromacs/pulling/pull_rotation.h"
140 #include "gromacs/restraint/manager.h"
141 #include "gromacs/restraint/restraintmdmodule.h"
142 #include "gromacs/restraint/restraintpotential.h"
143 #include "gromacs/swap/swapcoords.h"
144 #include "gromacs/taskassignment/decidegpuusage.h"
145 #include "gromacs/taskassignment/decidesimulationworkload.h"
146 #include "gromacs/taskassignment/resourcedivision.h"
147 #include "gromacs/taskassignment/taskassignment.h"
148 #include "gromacs/taskassignment/usergpuids.h"
149 #include "gromacs/timing/gpu_timing.h"
150 #include "gromacs/timing/wallcycle.h"
151 #include "gromacs/timing/wallcyclereporting.h"
152 #include "gromacs/topology/mtop_util.h"
153 #include "gromacs/trajectory/trajectoryframe.h"
154 #include "gromacs/utility/basenetwork.h"
155 #include "gromacs/utility/cstringutil.h"
156 #include "gromacs/utility/exceptions.h"
157 #include "gromacs/utility/fatalerror.h"
158 #include "gromacs/utility/filestream.h"
159 #include "gromacs/utility/gmxassert.h"
160 #include "gromacs/utility/gmxmpi.h"
161 #include "gromacs/utility/keyvaluetree.h"
162 #include "gromacs/utility/logger.h"
163 #include "gromacs/utility/loggerbuilder.h"
164 #include "gromacs/utility/mdmodulenotification.h"
165 #include "gromacs/utility/physicalnodecommunicator.h"
166 #include "gromacs/utility/pleasecite.h"
167 #include "gromacs/utility/programcontext.h"
168 #include "gromacs/utility/smalloc.h"
169 #include "gromacs/utility/stringutil.h"
171 #include "isimulator.h"
172 #include "membedholder.h"
173 #include "replicaexchange.h"
174 #include "simulatorbuilder.h"
180 /*! \brief Manage any development feature flag variables encountered
182 * The use of dev features indicated by environment variables is
183 * logged in order to ensure that runs with such features enabled can
184 * be identified from their log and standard output. Any cross
185 * dependencies are also checked, and if unsatisfied, a fatal error
188 * Note that some development features overrides are applied already here:
189 * the GPU communication flags are set to false in non-tMPI and non-CUDA builds.
191 * \param[in] mdlog Logger object.
192 * \param[in] useGpuForNonbonded True if the nonbonded task is offloaded in this run.
193 * \param[in] pmeRunMode The PME run mode for this run
194 * \returns The object populated with development feature flags.
196 static DevelopmentFeatureFlags manageDevelopmentFeatures(const gmx::MDLogger& mdlog,
197 const bool useGpuForNonbonded,
198 const PmeRunMode pmeRunMode)
200 DevelopmentFeatureFlags devFlags;
202 // Some builds of GCC 5 give false positive warnings that these
203 // getenv results are ignored when clearly they are used.
204 #pragma GCC diagnostic push
205 #pragma GCC diagnostic ignored "-Wunused-result"
207 devFlags.enableGpuBufferOps =
208 GMX_GPU_CUDA && useGpuForNonbonded && (getenv("GMX_USE_GPU_BUFFER_OPS") != nullptr);
209 devFlags.enableGpuHaloExchange = GMX_GPU_CUDA && GMX_THREAD_MPI && getenv("GMX_GPU_DD_COMMS") != nullptr;
210 devFlags.forceGpuUpdateDefault = (getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") != nullptr) || GMX_FAHCORE;
211 devFlags.enableGpuPmePPComm =
212 GMX_GPU_CUDA && GMX_THREAD_MPI && getenv("GMX_GPU_PME_PP_COMMS") != nullptr;
214 #pragma GCC diagnostic pop
216 if (devFlags.enableGpuBufferOps)
218 GMX_LOG(mdlog.warning)
220 .appendTextFormatted(
221 "This run uses the 'GPU buffer ops' feature, enabled by the "
222 "GMX_USE_GPU_BUFFER_OPS environment variable.");
225 if (devFlags.forceGpuUpdateDefault)
227 GMX_LOG(mdlog.warning)
229 .appendTextFormatted(
230 "This run will default to '-update gpu' as requested by the "
231 "GMX_FORCE_UPDATE_DEFAULT_GPU environment variable. GPU update with domain "
232 "decomposition lacks substantial testing and should be used with caution.");
235 if (devFlags.enableGpuHaloExchange)
237 if (useGpuForNonbonded)
239 if (!devFlags.enableGpuBufferOps)
241 GMX_LOG(mdlog.warning)
243 .appendTextFormatted(
244 "Enabling GPU buffer operations required by GMX_GPU_DD_COMMS "
245 "(equivalent with GMX_USE_GPU_BUFFER_OPS=1).");
246 devFlags.enableGpuBufferOps = true;
248 GMX_LOG(mdlog.warning)
250 .appendTextFormatted(
251 "This run has requested the 'GPU halo exchange' feature, enabled by "
253 "GMX_GPU_DD_COMMS environment variable.");
257 GMX_LOG(mdlog.warning)
259 .appendTextFormatted(
260 "GMX_GPU_DD_COMMS environment variable detected, but the 'GPU "
261 "halo exchange' feature will not be enabled as nonbonded interactions "
262 "are not offloaded.");
263 devFlags.enableGpuHaloExchange = false;
267 if (devFlags.enableGpuPmePPComm)
269 if (pmeRunMode == PmeRunMode::GPU)
271 if (!devFlags.enableGpuBufferOps)
273 GMX_LOG(mdlog.warning)
275 .appendTextFormatted(
276 "Enabling GPU buffer operations required by GMX_GPU_PME_PP_COMMS "
277 "(equivalent with GMX_USE_GPU_BUFFER_OPS=1).");
278 devFlags.enableGpuBufferOps = true;
280 GMX_LOG(mdlog.warning)
282 .appendTextFormatted(
283 "This run uses the 'GPU PME-PP communications' feature, enabled "
284 "by the GMX_GPU_PME_PP_COMMS environment variable.");
288 std::string clarification;
289 if (pmeRunMode == PmeRunMode::Mixed)
292 "PME FFT and gather are not offloaded to the GPU (PME is running in mixed "
297 clarification = "PME is not offloaded to the GPU.";
299 GMX_LOG(mdlog.warning)
302 "GMX_GPU_PME_PP_COMMS environment variable detected, but the "
303 "'GPU PME-PP communications' feature was not enabled as "
305 devFlags.enableGpuPmePPComm = false;
312 /*! \brief Barrier for safe simultaneous thread access to mdrunner data
314 * Used to ensure that the master thread does not modify mdrunner during copy
315 * on the spawned threads. */
316 static void threadMpiMdrunnerAccessBarrier()
319 MPI_Barrier(MPI_COMM_WORLD);
323 Mdrunner Mdrunner::cloneOnSpawnedThread() const
325 auto newRunner = Mdrunner(std::make_unique<MDModules>());
327 // All runners in the same process share a restraint manager resource because it is
328 // part of the interface to the client code, which is associated only with the
329 // original thread. Handles to the same resources can be obtained by copy.
331 newRunner.restraintManager_ = std::make_unique<RestraintManager>(*restraintManager_);
334 // Copy members of master runner.
335 // \todo Replace with builder when Simulation context and/or runner phases are better defined.
336 // Ref https://gitlab.com/gromacs/gromacs/-/issues/2587 and https://gitlab.com/gromacs/gromacs/-/issues/2375
337 newRunner.hw_opt = hw_opt;
338 newRunner.filenames = filenames;
340 newRunner.hwinfo_ = hwinfo_;
341 newRunner.oenv = oenv;
342 newRunner.mdrunOptions = mdrunOptions;
343 newRunner.domdecOptions = domdecOptions;
344 newRunner.nbpu_opt = nbpu_opt;
345 newRunner.pme_opt = pme_opt;
346 newRunner.pme_fft_opt = pme_fft_opt;
347 newRunner.bonded_opt = bonded_opt;
348 newRunner.update_opt = update_opt;
349 newRunner.nstlist_cmdline = nstlist_cmdline;
350 newRunner.replExParams = replExParams;
351 newRunner.pforce = pforce;
352 // Give the spawned thread the newly created valid communicator
353 // for the simulation.
354 newRunner.libraryWorldCommunicator = MPI_COMM_WORLD;
355 newRunner.simulationCommunicator = MPI_COMM_WORLD;
357 newRunner.startingBehavior = startingBehavior;
358 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>(*stopHandlerBuilder_);
359 newRunner.inputHolder_ = inputHolder_;
361 threadMpiMdrunnerAccessBarrier();
366 /*! \brief The callback used for running on spawned threads.
368 * Obtains the pointer to the master mdrunner object from the one
369 * argument permitted to the thread-launch API call, copies it to make
370 * a new runner for this thread, reinitializes necessary data, and
371 * proceeds to the simulation. */
372 static void mdrunner_start_fn(const void* arg)
376 auto masterMdrunner = reinterpret_cast<const gmx::Mdrunner*>(arg);
377 /* copy the arg list to make sure that it's thread-local. This
378 doesn't copy pointed-to items, of course; fnm, cr and fplog
379 are reset in the call below, all others should be const. */
380 gmx::Mdrunner mdrunner = masterMdrunner->cloneOnSpawnedThread();
383 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
387 void Mdrunner::spawnThreads(int numThreadsToLaunch)
390 /* now spawn new threads that start mdrunner_start_fn(), while
391 the main thread returns. Thread affinity is handled later. */
392 if (tMPI_Init_fn(TRUE, numThreadsToLaunch, TMPI_AFFINITY_NONE, mdrunner_start_fn, static_cast<const void*>(this))
395 GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
398 // Give the master thread the newly created valid communicator for
400 libraryWorldCommunicator = MPI_COMM_WORLD;
401 simulationCommunicator = MPI_COMM_WORLD;
402 threadMpiMdrunnerAccessBarrier();
404 GMX_UNUSED_VALUE(numThreadsToLaunch);
405 GMX_UNUSED_VALUE(mdrunner_start_fn);
411 /*! \brief Initialize variables for Verlet scheme simulation */
412 static void prepare_verlet_scheme(FILE* fplog,
416 const gmx_mtop_t* mtop,
418 bool makeGpuPairList,
419 const gmx::CpuInfo& cpuinfo)
421 // We checked the cut-offs in grompp, but double-check here.
422 // We have PME+LJcutoff kernels for rcoulomb>rvdw.
423 if (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == eelCUT)
425 GMX_RELEASE_ASSERT(ir->rcoulomb >= ir->rvdw,
426 "With Verlet lists and PME we should have rcoulomb>=rvdw");
430 GMX_RELEASE_ASSERT(ir->rcoulomb == ir->rvdw,
431 "With Verlet lists and no PME rcoulomb and rvdw should be identical");
433 /* For NVE simulations, we will retain the initial list buffer */
434 if (EI_DYNAMICS(ir->eI) && ir->verletbuf_tol > 0 && !(EI_MD(ir->eI) && ir->etc == etcNO))
436 /* Update the Verlet buffer size for the current run setup */
438 /* Here we assume SIMD-enabled kernels are being used. But as currently
439 * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
440 * and 4x2 gives a larger buffer than 4x4, this is ok.
442 ListSetupType listType =
443 (makeGpuPairList ? ListSetupType::Gpu : ListSetupType::CpuSimdWhenSupported);
444 VerletbufListSetup listSetup = verletbufGetSafeListSetup(listType);
446 const real rlist_new =
447 calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
449 if (rlist_new != ir->rlist)
451 if (fplog != nullptr)
454 "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
457 listSetup.cluster_size_i,
458 listSetup.cluster_size_j);
460 ir->rlist = rlist_new;
464 if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
467 "Can not set nstlist without %s",
468 !EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
471 if (EI_DYNAMICS(ir->eI))
473 /* Set or try nstlist values */
474 increaseNstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, makeGpuPairList, cpuinfo);
478 /*! \brief Override the nslist value in inputrec
480 * with value passed on the command line (if any)
482 static void override_nsteps_cmdline(const gmx::MDLogger& mdlog, int64_t nsteps_cmdline, t_inputrec* ir)
486 /* override with anything else than the default -2 */
487 if (nsteps_cmdline > -2)
489 char sbuf_steps[STEPSTRSIZE];
490 char sbuf_msg[STRLEN];
492 ir->nsteps = nsteps_cmdline;
493 if (EI_DYNAMICS(ir->eI) && nsteps_cmdline != -1)
496 "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
497 gmx_step_str(nsteps_cmdline, sbuf_steps),
498 fabs(nsteps_cmdline * ir->delta_t));
503 "Overriding nsteps with value passed on the command line: %s steps",
504 gmx_step_str(nsteps_cmdline, sbuf_steps));
507 GMX_LOG(mdlog.warning).asParagraph().appendText(sbuf_msg);
509 else if (nsteps_cmdline < -2)
511 gmx_fatal(FARGS, "Invalid nsteps value passed on the command line: %" PRId64, nsteps_cmdline);
513 /* Do nothing if nsteps_cmdline == -2 */
519 /*! \brief Return whether GPU acceleration of nonbondeds is supported with the given settings.
521 * If not, and if a warning may be issued, logs a warning about
522 * falling back to CPU code. With thread-MPI, only the first
523 * call to this function should have \c issueWarning true. */
524 static bool gpuAccelerationOfNonbondedIsUseful(const MDLogger& mdlog, const t_inputrec& ir, bool issueWarning)
526 bool gpuIsUseful = true;
529 if (ir.opts.ngener - ir.nwall > 1)
531 /* The GPU code does not support more than one energy group.
532 * If the user requested GPUs explicitly, a fatal error is given later.
536 "Multiple energy groups is not implemented for GPUs, falling back to the CPU. "
537 "For better performance, run on the GPU without energy groups and then do "
538 "gmx mdrun -rerun option on the trajectory with an energy group .tpr file.";
544 warning = "TPI is not implemented for GPUs.";
547 if (!gpuIsUseful && issueWarning)
549 GMX_LOG(mdlog.warning).asParagraph().appendText(warning);
555 //! Initializes the logger for mdrun.
556 static gmx::LoggerOwner buildLogger(FILE* fplog, const bool isSimulationMasterRank)
558 gmx::LoggerBuilder builder;
559 if (fplog != nullptr)
561 builder.addTargetFile(gmx::MDLogger::LogLevel::Info, fplog);
563 if (isSimulationMasterRank)
565 builder.addTargetStream(gmx::MDLogger::LogLevel::Warning, &gmx::TextOutputFile::standardError());
567 return builder.build();
570 //! Make a TaskTarget from an mdrun argument string.
571 static TaskTarget findTaskTarget(const char* optionString)
573 TaskTarget returnValue = TaskTarget::Auto;
575 if (strncmp(optionString, "auto", 3) == 0)
577 returnValue = TaskTarget::Auto;
579 else if (strncmp(optionString, "cpu", 3) == 0)
581 returnValue = TaskTarget::Cpu;
583 else if (strncmp(optionString, "gpu", 3) == 0)
585 returnValue = TaskTarget::Gpu;
589 GMX_ASSERT(false, "Option string should have been checked for sanity already");
595 //! Finish run, aggregate data to print performance info.
596 static void finish_run(FILE* fplog,
597 const gmx::MDLogger& mdlog,
599 const t_inputrec* inputrec,
601 gmx_wallcycle_t wcycle,
602 gmx_walltime_accounting_t walltime_accounting,
603 nonbonded_verlet_t* nbv,
604 const gmx_pme_t* pme,
608 double nbfs = 0, mflop = 0;
609 double elapsed_time, elapsed_time_over_all_ranks, elapsed_time_over_all_threads,
610 elapsed_time_over_all_threads_over_all_ranks;
611 /* Control whether it is valid to print a report. Only the
612 simulation master may print, but it should not do so if the run
613 terminated e.g. before a scheduled reset step. This is
614 complicated by the fact that PME ranks are unaware of the
615 reason why they were sent a pmerecvqxFINISH. To avoid
616 communication deadlocks, we always do the communication for the
617 report, even if we've decided not to write the report, because
618 how long it takes to finish the run is not important when we've
619 decided not to report on the simulation performance.
621 Further, we only report performance for dynamical integrators,
622 because those are the only ones for which we plan to
623 consider doing any optimizations. */
624 bool printReport = EI_DYNAMICS(inputrec->eI) && SIMMASTER(cr);
626 if (printReport && !walltime_accounting_get_valid_finish(walltime_accounting))
628 GMX_LOG(mdlog.warning)
630 .appendText("Simulation ended prematurely, no performance report will be written.");
635 std::unique_ptr<t_nrnb> nrnbTotalStorage;
638 nrnbTotalStorage = std::make_unique<t_nrnb>();
639 nrnb_tot = nrnbTotalStorage.get();
641 MPI_Allreduce(nrnb->n, nrnb_tot->n, eNRNB, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
649 elapsed_time = walltime_accounting_get_time_since_reset(walltime_accounting);
650 elapsed_time_over_all_threads =
651 walltime_accounting_get_time_since_reset_over_all_threads(walltime_accounting);
655 /* reduce elapsed_time over all MPI ranks in the current simulation */
656 MPI_Allreduce(&elapsed_time, &elapsed_time_over_all_ranks, 1, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
657 elapsed_time_over_all_ranks /= cr->nnodes;
658 /* Reduce elapsed_time_over_all_threads over all MPI ranks in the
659 * current simulation. */
660 MPI_Allreduce(&elapsed_time_over_all_threads,
661 &elapsed_time_over_all_threads_over_all_ranks,
670 elapsed_time_over_all_ranks = elapsed_time;
671 elapsed_time_over_all_threads_over_all_ranks = elapsed_time_over_all_threads;
676 print_flop(fplog, nrnb_tot, &nbfs, &mflop);
679 if (thisRankHasDuty(cr, DUTY_PP) && DOMAINDECOMP(cr))
681 print_dd_statistics(cr, inputrec, fplog);
684 /* TODO Move the responsibility for any scaling by thread counts
685 * to the code that handled the thread region, so that there's a
686 * mechanism to keep cycle counting working during the transition
687 * to task parallelism. */
688 int nthreads_pp = gmx_omp_nthreads_get(emntNonbonded);
689 int nthreads_pme = gmx_omp_nthreads_get(emntPME);
690 wallcycle_scale_by_num_threads(
691 wcycle, thisRankHasDuty(cr, DUTY_PME) && !thisRankHasDuty(cr, DUTY_PP), nthreads_pp, nthreads_pme);
692 auto cycle_sum(wallcycle_sum(cr, wcycle));
696 auto nbnxn_gpu_timings =
697 (nbv != nullptr && nbv->useGpu()) ? Nbnxm::gpu_get_timings(nbv->gpu_nbv) : nullptr;
698 gmx_wallclock_gpu_pme_t pme_gpu_timings = {};
700 if (pme_gpu_task_enabled(pme))
702 pme_gpu_get_timings(pme, &pme_gpu_timings);
704 wallcycle_print(fplog,
710 elapsed_time_over_all_ranks,
716 if (EI_DYNAMICS(inputrec->eI))
718 delta_t = inputrec->delta_t;
724 elapsed_time_over_all_threads_over_all_ranks,
725 elapsed_time_over_all_ranks,
726 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
734 elapsed_time_over_all_threads_over_all_ranks,
735 elapsed_time_over_all_ranks,
736 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
744 int Mdrunner::mdrunner()
747 t_forcerec* fr = nullptr;
748 real ewaldcoeff_q = 0;
749 real ewaldcoeff_lj = 0;
750 int nChargePerturbed = -1, nTypePerturbed = 0;
751 gmx_wallcycle_t wcycle;
752 gmx_walltime_accounting_t walltime_accounting = nullptr;
753 MembedHolder membedHolder(filenames.size(), filenames.data());
755 /* CAUTION: threads may be started later on in this function, so
756 cr doesn't reflect the final parallel state right now */
759 /* TODO: inputrec should tell us whether we use an algorithm, not a file option */
760 const bool doEssentialDynamics = opt2bSet("-ei", filenames.size(), filenames.data());
761 const bool doRerun = mdrunOptions.rerun;
763 // Handle task-assignment related user options.
764 EmulateGpuNonbonded emulateGpuNonbonded =
765 (getenv("GMX_EMULATE_GPU") != nullptr ? EmulateGpuNonbonded::Yes : EmulateGpuNonbonded::No);
767 std::vector<int> userGpuTaskAssignment;
770 userGpuTaskAssignment = parseUserTaskAssignmentString(hw_opt.userGpuTaskAssignment);
772 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
773 auto nonbondedTarget = findTaskTarget(nbpu_opt);
774 auto pmeTarget = findTaskTarget(pme_opt);
775 auto pmeFftTarget = findTaskTarget(pme_fft_opt);
776 auto bondedTarget = findTaskTarget(bonded_opt);
777 auto updateTarget = findTaskTarget(update_opt);
779 FILE* fplog = nullptr;
780 // If we are appending, we don't write log output because we need
781 // to check that the old log file matches what the checkpoint file
782 // expects. Otherwise, we should start to write log output now if
783 // there is a file ready for it.
784 if (logFileHandle != nullptr && startingBehavior != StartingBehavior::RestartWithAppending)
786 fplog = gmx_fio_getfp(logFileHandle);
788 const bool isSimulationMasterRank = findIsSimulationMasterRank(ms, simulationCommunicator);
789 gmx::LoggerOwner logOwner(buildLogger(fplog, isSimulationMasterRank));
790 gmx::MDLogger mdlog(logOwner.logger());
792 gmx_print_detected_hardware(fplog, isSimulationMasterRank && isMasterSim(ms), mdlog, hwinfo_);
794 std::vector<int> gpuIdsToUse = makeGpuIdsToUse(hwinfo_->deviceInfoList, hw_opt.gpuIdsAvailable);
795 const int numDevicesToUse = gmx::ssize(gpuIdsToUse);
797 // Print citation requests after all software/hardware printing
798 pleaseCiteGromacs(fplog);
800 // Note: legacy program logic relies on checking whether these pointers are assigned.
801 // Objects may or may not be allocated later.
802 std::unique_ptr<t_inputrec> inputrec;
803 std::unique_ptr<t_state> globalState;
805 auto partialDeserializedTpr = std::make_unique<PartialDeserializedTprFile>();
807 if (isSimulationMasterRank)
809 // Allocate objects to be initialized by later function calls.
810 /* Only the master rank has the global state */
811 globalState = std::make_unique<t_state>();
812 inputrec = std::make_unique<t_inputrec>();
814 /* Read (nearly) all data required for the simulation
815 * and keep the partly serialized tpr contents to send to other ranks later
817 applyGlobalSimulationState(
818 *inputHolder_.get(), partialDeserializedTpr.get(), globalState.get(), inputrec.get(), &mtop);
821 /* Check and update the hardware options for internal consistency */
822 checkAndUpdateHardwareOptions(
823 mdlog, &hw_opt, isSimulationMasterRank, domdecOptions.numPmeRanks, inputrec.get());
825 if (GMX_THREAD_MPI && isSimulationMasterRank)
827 bool useGpuForNonbonded = false;
828 bool useGpuForPme = false;
831 GMX_RELEASE_ASSERT(inputrec != nullptr, "Keep the compiler happy");
833 // If the user specified the number of ranks, then we must
834 // respect that, but in default mode, we need to allow for
835 // the number of GPUs to choose the number of ranks.
836 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
837 useGpuForNonbonded = decideWhetherToUseGpusForNonbondedWithThreadMpi(
840 userGpuTaskAssignment,
842 canUseGpuForNonbonded,
843 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, GMX_THREAD_MPI),
844 hw_opt.nthreads_tmpi);
845 useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi(useGpuForNonbonded,
848 userGpuTaskAssignment,
851 hw_opt.nthreads_tmpi,
852 domdecOptions.numPmeRanks);
854 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
856 /* Determine how many thread-MPI ranks to start.
858 * TODO Over-writing the user-supplied value here does
859 * prevent any possible subsequent checks from working
861 hw_opt.nthreads_tmpi = get_nthreads_mpi(hwinfo_,
869 membedHolder.doMembed());
871 // Now start the threads for thread MPI.
872 spawnThreads(hw_opt.nthreads_tmpi);
873 // The spawned threads enter mdrunner() and execution of
874 // master and spawned threads joins at the end of this block.
877 GMX_RELEASE_ASSERT(ms || simulationCommunicator != MPI_COMM_NULL,
878 "Must have valid communicator unless running a multi-simulation");
879 CommrecHandle crHandle = init_commrec(simulationCommunicator);
880 t_commrec* cr = crHandle.get();
881 GMX_RELEASE_ASSERT(cr != nullptr, "Must have valid commrec");
883 PhysicalNodeCommunicator physicalNodeComm(libraryWorldCommunicator, gmx_physicalnode_id_hash());
885 // If we detected the topology on this system, double-check that it makes sense
886 if (hwinfo_->hardwareTopology->isThisSystem())
888 hardwareTopologyDoubleCheckDetection(mdlog, *hwinfo_->hardwareTopology);
893 /* now broadcast everything to the non-master nodes/threads: */
894 if (!isSimulationMasterRank)
896 // Until now, only the master rank has a non-null pointer.
897 // On non-master ranks, allocate the object that will receive data in the following call.
898 inputrec = std::make_unique<t_inputrec>();
900 init_parallel(cr->mpiDefaultCommunicator,
904 partialDeserializedTpr.get());
906 GMX_RELEASE_ASSERT(inputrec != nullptr, "All ranks should have a valid inputrec now");
907 partialDeserializedTpr.reset(nullptr);
910 !inputrec->useConstantAcceleration,
911 "Linear acceleration has been removed in GROMACS 2022, and was broken for many years "
912 "before that. Use GROMACS 4.5 or earlier if you need this feature.");
914 // Now the number of ranks is known to all ranks, and each knows
915 // the inputrec read by the master rank. The ranks can now all run
916 // the task-deciding functions and will agree on the result
917 // without needing to communicate.
918 const bool useDomainDecomposition = (PAR(cr) && !(EI_TPI(inputrec->eI) || inputrec->eI == eiNM));
920 // Note that these variables describe only their own node.
922 // Note that when bonded interactions run on a GPU they always run
923 // alongside a nonbonded task, so do not influence task assignment
924 // even though they affect the force calculation workload.
925 bool useGpuForNonbonded = false;
926 bool useGpuForPme = false;
927 bool useGpuForBonded = false;
928 bool useGpuForUpdate = false;
929 bool gpusWereDetected = hwinfo_->ngpu_compatible_tot > 0;
932 // It's possible that there are different numbers of GPUs on
933 // different nodes, which is the user's responsibility to
934 // handle. If unsuitable, we will notice that during task
936 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
937 useGpuForNonbonded = decideWhetherToUseGpusForNonbonded(
939 userGpuTaskAssignment,
941 canUseGpuForNonbonded,
942 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, !GMX_THREAD_MPI),
944 useGpuForPme = decideWhetherToUseGpusForPme(useGpuForNonbonded,
946 userGpuTaskAssignment,
949 cr->sizeOfDefaultCommunicator,
950 domdecOptions.numPmeRanks,
952 useGpuForBonded = decideWhetherToUseGpusForBonded(
953 useGpuForNonbonded, useGpuForPme, bondedTarget, *inputrec, mtop, domdecOptions.numPmeRanks, gpusWereDetected);
955 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
957 const PmeRunMode pmeRunMode = determinePmeRunMode(useGpuForPme, pmeFftTarget, *inputrec);
959 // Initialize development feature flags that enabled by environment variable
960 // and report those features that are enabled.
961 const DevelopmentFeatureFlags devFlags =
962 manageDevelopmentFeatures(mdlog, useGpuForNonbonded, pmeRunMode);
964 const bool useModularSimulator = checkUseModularSimulator(false,
972 membedHolder.doMembed());
975 // TODO: hide restraint implementation details from Mdrunner.
976 // There is nothing unique about restraints at this point as far as the
977 // Mdrunner is concerned. The Mdrunner should just be getting a sequence of
978 // factory functions from the SimulationContext on which to call mdModules_->add().
979 // TODO: capture all restraints into a single RestraintModule, passed to the runner builder.
980 for (auto&& restraint : restraintManager_->getRestraints())
982 auto module = RestraintMDModule::create(restraint, restraint->sites());
983 mdModules_->add(std::move(module));
986 // TODO: Error handling
987 mdModules_->assignOptionsToModules(*inputrec->params, nullptr);
988 // now that the MdModules know their options, they know which callbacks to sign up to
989 mdModules_->subscribeToSimulationSetupNotifications();
990 const auto& mdModulesNotifier = mdModules_->notifier().simulationSetupNotifications_;
992 if (inputrec->internalParameters != nullptr)
994 mdModulesNotifier.notify(*inputrec->internalParameters);
997 if (fplog != nullptr)
999 pr_inputrec(fplog, 0, "Input Parameters", inputrec.get(), FALSE);
1000 fprintf(fplog, "\n");
1005 /* In rerun, set velocities to zero if present */
1006 if (doRerun && ((globalState->flags & (1 << estV)) != 0))
1008 // rerun does not use velocities
1012 "Rerun trajectory contains velocities. Rerun does only evaluate "
1013 "potential energy and forces. The velocities will be ignored.");
1014 for (int i = 0; i < globalState->natoms; i++)
1016 clear_rvec(globalState->v[i]);
1018 globalState->flags &= ~(1 << estV);
1021 /* now make sure the state is initialized and propagated */
1022 set_state_entries(globalState.get(), inputrec.get(), useModularSimulator);
1025 /* NM and TPI parallelize over force/energy calculations, not atoms,
1026 * so we need to initialize and broadcast the global state.
1028 if (inputrec->eI == eiNM || inputrec->eI == eiTPI)
1032 globalState = std::make_unique<t_state>();
1034 broadcastStateWithoutDynamics(
1035 cr->mpiDefaultCommunicator, DOMAINDECOMP(cr), PAR(cr), globalState.get());
1038 /* A parallel command line option consistency check that we can
1039 only do after any threads have started. */
1041 && (domdecOptions.numCells[XX] > 1 || domdecOptions.numCells[YY] > 1
1042 || domdecOptions.numCells[ZZ] > 1 || domdecOptions.numPmeRanks > 0))
1045 "The -dd or -npme option request a parallel simulation, "
1047 "but %s was compiled without threads or MPI enabled",
1048 output_env_get_program_display_name(oenv));
1049 #elif GMX_THREAD_MPI
1050 "but the number of MPI-threads (option -ntmpi) is not set or is 1");
1052 "but %s was not started through mpirun/mpiexec or only one rank was requested "
1053 "through mpirun/mpiexec",
1054 output_env_get_program_display_name(oenv));
1058 if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
1061 "The .mdp file specified an energy mininization or normal mode algorithm, and "
1062 "these are not compatible with mdrun -rerun");
1065 /* Object for collecting reasons for not using PME-only ranks */
1066 SeparatePmeRanksPermitted separatePmeRanksPermitted;
1068 /* Permit MDModules to notify whether they want to use PME-only ranks */
1069 mdModulesNotifier.notify(&separatePmeRanksPermitted);
1071 /* If simulation is not using PME then disable PME-only ranks */
1072 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
1074 separatePmeRanksPermitted.disablePmeRanks(
1075 "PME-only ranks are requested, but the system does not use PME "
1076 "for electrostatics or LJ");
1079 /* With NB GPUs we don't automatically use PME-only CPU ranks. PME ranks can
1080 * improve performance with many threads per GPU, since our OpenMP
1081 * scaling is bad, but it's difficult to automate the setup.
1083 if (useGpuForNonbonded && domdecOptions.numPmeRanks < 0)
1085 separatePmeRanksPermitted.disablePmeRanks(
1086 "PME-only CPU ranks are not automatically used when "
1087 "non-bonded interactions are computed on GPUs");
1090 /* If GPU is used for PME then only 1 PME rank is permitted */
1091 if (useGpuForPme && (domdecOptions.numPmeRanks < 0 || domdecOptions.numPmeRanks > 1))
1093 separatePmeRanksPermitted.disablePmeRanks(
1094 "PME GPU decomposition is not supported. Only one separate PME-only GPU rank "
1098 /* Disable PME-only ranks if some parts of the code requested so and it's up to GROMACS to decide */
1099 if (!separatePmeRanksPermitted.permitSeparatePmeRanks() && domdecOptions.numPmeRanks < 0)
1101 domdecOptions.numPmeRanks = 0;
1104 .appendText("Simulation will not use PME-only ranks because: "
1105 + separatePmeRanksPermitted.reasonsWhyDisabled());
1108 /* If some parts of the code could not use PME-only ranks and
1109 * user explicitly used mdrun -npme option then throw an error */
1110 if (!separatePmeRanksPermitted.permitSeparatePmeRanks() && domdecOptions.numPmeRanks > 0)
1112 gmx_fatal_collective(FARGS,
1113 cr->mpiDefaultCommunicator,
1115 "Requested -npme %d option is not viable because: %s",
1116 domdecOptions.numPmeRanks,
1117 separatePmeRanksPermitted.reasonsWhyDisabled().c_str());
1120 /* NMR restraints must be initialized before load_checkpoint,
1121 * since with time averaging the history is added to t_state.
1122 * For proper consistency check we therefore need to extend
1124 * So the PME-only nodes (if present) will also initialize
1125 * the distance restraints.
1128 /* This needs to be called before read_checkpoint to extend the state */
1129 t_disresdata* disresdata;
1130 snew(disresdata, 1);
1134 DisResRunMode::MDRun,
1135 MASTER(cr) ? DDRole::Master : DDRole::Agent,
1136 PAR(cr) ? NumRanks::Multiple : NumRanks::Single,
1141 replExParams.exchangeInterval > 0);
1143 t_oriresdata* oriresdata;
1144 snew(oriresdata, 1);
1145 init_orires(fplog, &mtop, inputrec.get(), cr, ms, globalState.get(), oriresdata);
1147 auto deform = prepareBoxDeformation(globalState != nullptr ? globalState->box : box,
1148 MASTER(cr) ? DDRole::Master : DDRole::Agent,
1149 PAR(cr) ? NumRanks::Multiple : NumRanks::Single,
1150 cr->mpi_comm_mygroup,
1154 /* We have to remember the generation's first step before reading checkpoint.
1155 This way, we can report to the F@H core both the generation's first step
1156 and the restored first step, thus making it able to distinguish between
1157 an interruption/resume and start of the n-th generation simulation.
1158 Having this information, the F@H core can correctly calculate and report
1161 int gen_first_step = 0;
1164 gen_first_step = inputrec->init_step;
1168 ObservablesHistory observablesHistory = {};
1170 auto modularSimulatorCheckpointData = std::make_unique<ReadCheckpointDataHolder>();
1171 if (startingBehavior != StartingBehavior::NewSimulation)
1173 /* Check if checkpoint file exists before doing continuation.
1174 * This way we can use identical input options for the first and subsequent runs...
1176 if (mdrunOptions.numStepsCommandline > -2)
1178 /* Temporarily set the number of steps to unlimited to avoid
1179 * triggering the nsteps check in load_checkpoint().
1180 * This hack will go away soon when the -nsteps option is removed.
1182 inputrec->nsteps = -1;
1185 // Finish applying initial simulation state information from external sources on all ranks.
1186 // Reconcile checkpoint file data with Mdrunner state established up to this point.
1187 applyLocalState(*inputHolder_.get(),
1190 domdecOptions.numCells,
1193 &observablesHistory,
1194 mdrunOptions.reproducible,
1195 mdModules_->notifier(),
1196 modularSimulatorCheckpointData.get(),
1197 useModularSimulator);
1198 // TODO: (#3652) Synchronize filesystem state, SimulationInput contents, and program
1200 // on all code paths.
1201 // Write checkpoint or provide hook to update SimulationInput.
1202 // If there was a checkpoint file, SimulationInput contains more information
1203 // than if there wasn't. At this point, we have synchronized the in-memory
1204 // state with the filesystem state only for restarted simulations. We should
1205 // be calling applyLocalState unconditionally and expect that the completeness
1206 // of SimulationInput is not dependent on its creation method.
1208 if (startingBehavior == StartingBehavior::RestartWithAppending && logFileHandle)
1210 // Now we can start normal logging to the truncated log file.
1211 fplog = gmx_fio_getfp(logFileHandle);
1212 prepareLogAppending(fplog);
1213 logOwner = buildLogger(fplog, MASTER(cr));
1214 mdlog = logOwner.logger();
1221 fcRegisterSteps(inputrec->nsteps + inputrec->init_step, gen_first_step);
1225 if (mdrunOptions.numStepsCommandline > -2)
1230 "The -nsteps functionality is deprecated, and may be removed in a future "
1232 "Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp "
1235 /* override nsteps with value set on the commandline */
1236 override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec.get());
1238 if (isSimulationMasterRank)
1240 copy_mat(globalState->box, box);
1245 gmx_bcast(sizeof(box), box, cr->mpiDefaultCommunicator);
1248 if (inputrec->cutoff_scheme != ecutsVERLET)
1251 "This group-scheme .tpr file can no longer be run by mdrun. Please update to the "
1252 "Verlet scheme, or use an earlier version of GROMACS if necessary.");
1254 /* Update rlist and nstlist. */
1255 /* Note: prepare_verlet_scheme is calling increaseNstlist(...), which (while attempting to
1256 * increase rlist) tries to check if the newly chosen value fits with the DD scheme. As this is
1257 * run before any DD scheme is set up, this check is never executed. See #3334 for more details.
1259 prepare_verlet_scheme(fplog,
1265 useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes),
1268 // This builder is necessary while we have multi-part construction
1269 // of DD. Before DD is constructed, we use the existence of
1270 // the builder object to indicate that further construction of DD
1272 std::unique_ptr<DomainDecompositionBuilder> ddBuilder;
1273 if (useDomainDecomposition)
1275 ddBuilder = std::make_unique<DomainDecompositionBuilder>(
1283 positionsFromStatePointer(globalState.get()));
1287 /* PME, if used, is done on all nodes with 1D decomposition */
1288 cr->nnodes = cr->sizeOfDefaultCommunicator;
1289 cr->sim_nodeid = cr->rankInDefaultCommunicator;
1290 cr->nodeid = cr->rankInDefaultCommunicator;
1292 cr->duty = (DUTY_PP | DUTY_PME);
1294 if (inputrec->pbcType == PbcType::Screw)
1296 gmx_fatal(FARGS, "pbc=screw is only implemented with domain decomposition");
1300 // Produce the task assignment for this rank - done after DD is constructed
1301 GpuTaskAssignments gpuTaskAssignments = GpuTaskAssignmentsBuilder::build(
1303 userGpuTaskAssignment,
1305 simulationCommunicator,
1313 thisRankHasDuty(cr, DUTY_PP),
1314 // TODO cr->duty & DUTY_PME should imply that a PME
1315 // algorithm is active, but currently does not.
1316 EEL_PME(inputrec->coulombtype) && thisRankHasDuty(cr, DUTY_PME));
1318 // Get the device handles for the modules, nullptr when no task is assigned.
1320 DeviceInformation* deviceInfo = gpuTaskAssignments.initDevice(&deviceId);
1322 // timing enabling - TODO put this in gpu_utils (even though generally this is just option handling?)
1323 bool useTiming = true;
1327 /* WARNING: CUDA timings are incorrect with multiple streams.
1328 * This is the main reason why they are disabled by default.
1330 // TODO: Consider turning on by default when we can detect nr of streams.
1331 useTiming = (getenv("GMX_ENABLE_GPU_TIMING") != nullptr);
1333 else if (GMX_GPU_OPENCL)
1335 useTiming = (getenv("GMX_DISABLE_GPU_TIMING") == nullptr);
1338 // TODO Currently this is always built, yet DD partition code
1339 // checks if it is built before using it. Probably it should
1340 // become an MDModule that is made only when another module
1341 // requires it (e.g. pull, CompEl, density fitting), so that we
1342 // don't update the local atom sets unilaterally every step.
1343 LocalAtomSetManager atomSets;
1346 // TODO Pass the GPU streams to ddBuilder to use in buffer
1347 // transfers (e.g. halo exchange)
1348 cr->dd = ddBuilder->build(&atomSets);
1349 // The builder's job is done, so destruct it
1350 ddBuilder.reset(nullptr);
1351 // Note that local state still does not exist yet.
1354 // The GPU update is decided here because we need to know whether the constraints or
1355 // SETTLEs can span accross the domain borders (i.e. whether or not update groups are
1356 // defined). This is only known after DD is initialized, hence decision on using GPU
1357 // update is done so late.
1360 const bool useUpdateGroups = cr->dd ? ddUsesUpdateGroups(*cr->dd) : false;
1362 useGpuForUpdate = decideWhetherToUseGpuForUpdate(useDomainDecomposition,
1365 domdecOptions.numPmeRanks > 0,
1371 doEssentialDynamics,
1372 gmx_mtop_ftype_count(mtop, F_ORIRES) > 0,
1373 replExParams.exchangeInterval > 0,
1378 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1380 const bool printHostName = (cr->nnodes > 1);
1381 gpuTaskAssignments.reportGpuUsage(mdlog, printHostName, useGpuForBonded, pmeRunMode, useGpuForUpdate);
1383 const bool disableNonbondedCalculation = (getenv("GMX_NO_NONBONDED") != nullptr);
1384 if (disableNonbondedCalculation)
1386 /* turn off non-bonded calculations */
1387 GMX_LOG(mdlog.warning)
1390 "Found environment variable GMX_NO_NONBONDED.\n"
1391 "Disabling nonbonded calculations.");
1394 MdrunScheduleWorkload runScheduleWork;
1396 bool useGpuDirectHalo = decideWhetherToUseGpuForHalo(devFlags,
1397 havePPDomainDecomposition(cr),
1399 useModularSimulator,
1401 EI_ENERGY_MINIMIZATION(inputrec->eI));
1403 // Also populates the simulation constant workload description.
1404 runScheduleWork.simulationWork = createSimulationWorkload(*inputrec,
1405 disableNonbondedCalculation,
1413 std::unique_ptr<DeviceStreamManager> deviceStreamManager = nullptr;
1415 if (deviceInfo != nullptr)
1417 if (DOMAINDECOMP(cr) && thisRankHasDuty(cr, DUTY_PP))
1419 dd_setup_dlb_resource_sharing(cr, deviceId);
1421 deviceStreamManager = std::make_unique<DeviceStreamManager>(
1422 *deviceInfo, havePPDomainDecomposition(cr), runScheduleWork.simulationWork, useTiming);
1425 // If the user chose a task assignment, give them some hints
1426 // where appropriate.
1427 if (!userGpuTaskAssignment.empty())
1429 gpuTaskAssignments.logPerformanceHints(mdlog, numDevicesToUse);
1434 /* After possible communicator splitting in make_dd_communicators.
1435 * we can set up the intra/inter node communication.
1437 gmx_setup_nodecomm(fplog, cr);
1443 GMX_LOG(mdlog.warning)
1445 .appendTextFormatted(
1446 "This is simulation %d out of %d running as a composite GROMACS\n"
1447 "multi-simulation job. Setup for this simulation:\n",
1448 ms->simulationIndex_,
1449 ms->numSimulations_);
1451 GMX_LOG(mdlog.warning)
1452 .appendTextFormatted("Using %d MPI %s\n",
1455 cr->nnodes == 1 ? "thread" : "threads"
1457 cr->nnodes == 1 ? "process" : "processes"
1463 // If mdrun -pin auto honors any affinity setting that already
1464 // exists. If so, it is nice to provide feedback about whether
1465 // that existing affinity setting was from OpenMP or something
1466 // else, so we run this code both before and after we initialize
1467 // the OpenMP support.
1468 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo_->nthreads_hw_avail, FALSE);
1469 /* Check and update the number of OpenMP threads requested */
1470 checkAndUpdateRequestedNumOpenmpThreads(
1471 &hw_opt, *hwinfo_, cr, ms, physicalNodeComm.size_, pmeRunMode, mtop, *inputrec);
1473 gmx_omp_nthreads_init(mdlog,
1475 hwinfo_->nthreads_hw_avail,
1476 physicalNodeComm.size_,
1477 hw_opt.nthreads_omp,
1478 hw_opt.nthreads_omp_pme,
1479 !thisRankHasDuty(cr, DUTY_PP));
1481 const bool bEnableFPE = gmxShouldEnableFPExceptions();
1482 // FIXME - reconcile with gmx_feenableexcept() call from CommandLineModuleManager::run()
1485 gmx_feenableexcept();
1488 /* Now that we know the setup is consistent, check for efficiency */
1489 check_resource_division_efficiency(
1490 hwinfo_, gpuTaskAssignments.thisRankHasAnyGpuTask(), mdrunOptions.ntompOptionIsSet, cr, mdlog);
1492 /* getting number of PP/PME threads on this MPI / tMPI rank.
1493 PME: env variable should be read only on one node to make sure it is
1494 identical everywhere;
1496 const int numThreadsOnThisRank = thisRankHasDuty(cr, DUTY_PP) ? gmx_omp_nthreads_get(emntNonbonded)
1497 : gmx_omp_nthreads_get(emntPME);
1498 checkHardwareOversubscription(
1499 numThreadsOnThisRank, cr->nodeid, *hwinfo_->hardwareTopology, physicalNodeComm, mdlog);
1501 // Enable Peer access between GPUs where available
1502 // Only for DD, only master PP rank needs to perform setup, and only if thread MPI plus
1503 // any of the GPU communication features are active.
1504 if (DOMAINDECOMP(cr) && MASTER(cr) && thisRankHasDuty(cr, DUTY_PP) && GMX_THREAD_MPI
1505 && (runScheduleWork.simulationWork.useGpuHaloExchange
1506 || runScheduleWork.simulationWork.useGpuPmePpCommunication))
1508 setupGpuDevicePeerAccess(gpuIdsToUse, mdlog);
1511 if (hw_opt.threadAffinity != ThreadAffinity::Off)
1513 /* Before setting affinity, check whether the affinity has changed
1514 * - which indicates that probably the OpenMP library has changed it
1515 * since we first checked).
1517 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo_->nthreads_hw_avail, TRUE);
1519 int numThreadsOnThisNode, intraNodeThreadOffset;
1520 analyzeThreadsOnThisNode(
1521 physicalNodeComm, numThreadsOnThisRank, &numThreadsOnThisNode, &intraNodeThreadOffset);
1523 /* Set the CPU affinity */
1524 gmx_set_thread_affinity(mdlog,
1527 *hwinfo_->hardwareTopology,
1528 numThreadsOnThisRank,
1529 numThreadsOnThisNode,
1530 intraNodeThreadOffset,
1534 if (mdrunOptions.timingOptions.resetStep > -1)
1539 "The -resetstep functionality is deprecated, and may be removed in a "
1542 wcycle = wallcycle_init(fplog, mdrunOptions.timingOptions.resetStep, cr);
1546 /* Master synchronizes its value of reset_counters with all nodes
1547 * including PME only nodes */
1548 int64_t reset_counters = wcycle_get_reset_counters(wcycle);
1549 gmx_bcast(sizeof(reset_counters), &reset_counters, cr->mpi_comm_mysim);
1550 wcycle_set_reset_counters(wcycle, reset_counters);
1553 // Membrane embedding must be initialized before we call init_forcerec()
1554 membedHolder.initializeMembed(fplog,
1561 &mdrunOptions.checkpointOptions.period);
1563 const bool thisRankHasPmeGpuTask = gpuTaskAssignments.thisRankHasPmeGpuTask();
1564 std::unique_ptr<MDAtoms> mdAtoms;
1565 std::unique_ptr<VirtualSitesHandler> vsite;
1566 std::unique_ptr<GpuBonded> gpuBonded;
1569 if (thisRankHasDuty(cr, DUTY_PP))
1571 mdModulesNotifier.notify(*cr);
1572 mdModulesNotifier.notify(&atomSets);
1573 mdModulesNotifier.notify(mtop);
1574 mdModulesNotifier.notify(inputrec->pbcType);
1575 mdModulesNotifier.notify(SimulationTimeStep{ inputrec->delta_t });
1576 /* Initiate forcerecord */
1577 fr = new t_forcerec;
1578 fr->forceProviders = mdModules_->initForceProviders();
1579 init_forcerec(fplog,
1586 opt2fn("-table", filenames.size(), filenames.data()),
1587 opt2fn("-tablep", filenames.size(), filenames.data()),
1588 opt2fns("-tableb", filenames.size(), filenames.data()),
1590 // Dirty hack, for fixing disres and orires should be made mdmodules
1591 fr->fcdata->disres = disresdata;
1592 fr->fcdata->orires = oriresdata;
1594 // Save a handle to device stream manager to use elsewhere in the code
1595 // TODO: Forcerec is not a correct place to store it.
1596 fr->deviceStreamManager = deviceStreamManager.get();
1598 if (runScheduleWork.simulationWork.useGpuPmePpCommunication && !thisRankHasDuty(cr, DUTY_PME))
1601 deviceStreamManager != nullptr,
1602 "GPU device stream manager should be valid in order to use PME-PP direct "
1605 deviceStreamManager->streamIsValid(DeviceStreamType::PmePpTransfer),
1606 "GPU PP-PME stream should be valid in order to use GPU PME-PP direct "
1608 fr->pmePpCommGpu = std::make_unique<gmx::PmePpCommGpu>(
1611 deviceStreamManager->context(),
1612 deviceStreamManager->stream(DeviceStreamType::PmePpTransfer));
1615 fr->nbv = Nbnxm::init_nb_verlet(mdlog,
1620 runScheduleWork.simulationWork.useGpuNonbonded,
1621 deviceStreamManager.get(),
1625 // TODO: Move the logic below to a GPU bonded builder
1626 if (runScheduleWork.simulationWork.useGpuBonded)
1628 GMX_RELEASE_ASSERT(deviceStreamManager != nullptr,
1629 "GPU device stream manager should be valid in order to use GPU "
1630 "version of bonded forces.");
1631 gpuBonded = std::make_unique<GpuBonded>(
1633 fr->ic->epsfac * fr->fudgeQQ,
1634 deviceStreamManager->context(),
1635 deviceStreamManager->bondedStream(havePPDomainDecomposition(cr)),
1637 fr->gpuBonded = gpuBonded.get();
1640 /* Initialize the mdAtoms structure.
1641 * mdAtoms is not filled with atom data,
1642 * as this can not be done now with domain decomposition.
1644 mdAtoms = makeMDAtoms(fplog, mtop, *inputrec, thisRankHasPmeGpuTask);
1645 if (globalState && thisRankHasPmeGpuTask)
1647 // The pinning of coordinates in the global state object works, because we only use
1648 // PME on GPU without DD or on a separate PME rank, and because the local state pointer
1649 // points to the global state object without DD.
1650 // FIXME: MD and EM separately set up the local state - this should happen in the same
1651 // function, which should also perform the pinning.
1652 changePinningPolicy(&globalState->x, pme_get_pinning_policy());
1655 /* Initialize the virtual site communication */
1656 vsite = makeVirtualSitesHandler(mtop, cr, fr->pbcType);
1658 calc_shifts(box, fr->shift_vec);
1660 /* With periodic molecules the charge groups should be whole at start up
1661 * and the virtual sites should not be far from their proper positions.
1663 if (!inputrec->bContinuation && MASTER(cr)
1664 && !(inputrec->pbcType != PbcType::No && inputrec->bPeriodicMols))
1666 /* Make molecules whole at start of run */
1667 if (fr->pbcType != PbcType::No)
1669 do_pbc_first_mtop(fplog, inputrec->pbcType, box, &mtop, globalState->x.rvec_array());
1673 /* Correct initial vsite positions are required
1674 * for the initial distribution in the domain decomposition
1675 * and for the initial shell prediction.
1677 constructVirtualSitesGlobal(mtop, globalState->x);
1681 if (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
1683 ewaldcoeff_q = fr->ic->ewaldcoeff_q;
1684 ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
1689 /* This is a PME only node */
1691 GMX_ASSERT(globalState == nullptr,
1692 "We don't need the state on a PME only rank and expect it to be unitialized");
1694 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
1695 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
1698 gmx_pme_t* sepPmeData = nullptr;
1699 // This reference hides the fact that PME data is owned by runner on PME-only ranks and by forcerec on other ranks
1700 GMX_ASSERT(thisRankHasDuty(cr, DUTY_PP) == (fr != nullptr),
1701 "Double-checking that only PME-only ranks have no forcerec");
1702 gmx_pme_t*& pmedata = fr ? fr->pmedata : sepPmeData;
1704 // TODO should live in ewald module once its testing is improved
1706 // Later, this program could contain kernels that might be later
1707 // re-used as auto-tuning progresses, or subsequent simulations
1709 PmeGpuProgramStorage pmeGpuProgram;
1710 if (thisRankHasPmeGpuTask)
1713 (deviceStreamManager != nullptr),
1714 "GPU device stream manager should be initialized in order to use GPU for PME.");
1715 GMX_RELEASE_ASSERT((deviceInfo != nullptr),
1716 "GPU device should be initialized in order to use GPU for PME.");
1717 pmeGpuProgram = buildPmeGpuProgram(deviceStreamManager->context());
1720 /* Initiate PME if necessary,
1721 * either on all nodes or on dedicated PME nodes only. */
1722 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
1724 if (mdAtoms && mdAtoms->mdatoms())
1726 nChargePerturbed = mdAtoms->mdatoms()->nChargePerturbed;
1727 if (EVDW_PME(inputrec->vdwtype))
1729 nTypePerturbed = mdAtoms->mdatoms()->nTypePerturbed;
1732 if (cr->npmenodes > 0)
1734 /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
1735 gmx_bcast(sizeof(nChargePerturbed), &nChargePerturbed, cr->mpi_comm_mysim);
1736 gmx_bcast(sizeof(nTypePerturbed), &nTypePerturbed, cr->mpi_comm_mysim);
1739 if (thisRankHasDuty(cr, DUTY_PME))
1743 // TODO: This should be in the builder.
1744 GMX_RELEASE_ASSERT(!runScheduleWork.simulationWork.useGpuPme
1745 || (deviceStreamManager != nullptr),
1746 "Device stream manager should be valid in order to use GPU "
1749 !runScheduleWork.simulationWork.useGpuPme
1750 || deviceStreamManager->streamIsValid(DeviceStreamType::Pme),
1751 "GPU PME stream should be valid in order to use GPU version of PME.");
1753 const DeviceContext* deviceContext = runScheduleWork.simulationWork.useGpuPme
1754 ? &deviceStreamManager->context()
1756 const DeviceStream* pmeStream =
1757 runScheduleWork.simulationWork.useGpuPme
1758 ? &deviceStreamManager->stream(DeviceStreamType::Pme)
1761 pmedata = gmx_pme_init(cr,
1762 getNumPmeDomains(cr->dd),
1764 nChargePerturbed != 0,
1765 nTypePerturbed != 0,
1766 mdrunOptions.reproducible,
1769 gmx_omp_nthreads_get(emntPME),
1774 pmeGpuProgram.get(),
1777 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1782 if (EI_DYNAMICS(inputrec->eI))
1784 /* Turn on signal handling on all nodes */
1786 * (A user signal from the PME nodes (if any)
1787 * is communicated to the PP nodes.
1789 signal_handler_install();
1792 pull_t* pull_work = nullptr;
1793 if (thisRankHasDuty(cr, DUTY_PP))
1795 /* Assumes uniform use of the number of OpenMP threads */
1796 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
1798 if (inputrec->bPull)
1800 /* Initialize pull code */
1801 pull_work = init_pull(fplog,
1802 inputrec->pull.get(),
1807 inputrec->fepvals->init_lambda);
1808 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
1810 initPullHistory(pull_work, &observablesHistory);
1812 if (EI_DYNAMICS(inputrec->eI) && MASTER(cr))
1814 init_pull_output_files(pull_work, filenames.size(), filenames.data(), oenv, startingBehavior);
1818 std::unique_ptr<EnforcedRotation> enforcedRotation;
1821 /* Initialize enforced rotation code */
1822 enforcedRotation = init_rot(fplog,
1835 t_swap* swap = nullptr;
1836 if (inputrec->eSwapCoords != eswapNO)
1838 /* Initialize ion swapping code */
1839 swap = init_swapcoords(fplog,
1841 opt2fn_master("-swap", filenames.size(), filenames.data(), cr),
1844 &observablesHistory,
1852 /* Let makeConstraints know whether we have essential dynamics constraints. */
1853 auto constr = makeConstraints(
1854 mtop, *inputrec, pull_work, doEssentialDynamics, fplog, cr, ms, &nrnb, wcycle, fr->bMolPBC);
1856 /* Energy terms and groups */
1857 gmx_enerdata_t enerd(mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
1858 inputrec->fepvals->n_lambda);
1860 /* Kinetic energy data */
1861 gmx_ekindata_t ekind;
1862 init_ekindata(fplog, &(inputrec->opts), &ekind, inputrec->cos_accel);
1864 /* Set up interactive MD (IMD) */
1865 auto imdSession = makeImdSession(inputrec.get(),
1872 MASTER(cr) ? globalState->x.rvec_array() : nullptr,
1876 mdrunOptions.imdOptions,
1879 if (DOMAINDECOMP(cr))
1881 GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
1882 /* This call is not included in init_domain_decomposition mainly
1883 * because fr->cginfo_mb is set later.
1885 dd_init_bondeds(fplog,
1890 domdecOptions.checkBondedInteractions,
1894 if (runScheduleWork.simulationWork.useGpuBufferOps)
1896 fr->gpuForceReduction[gmx::AtomLocality::Local] = std::make_unique<gmx::GpuForceReduction>(
1897 deviceStreamManager->context(),
1898 deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedLocal),
1900 fr->gpuForceReduction[gmx::AtomLocality::NonLocal] = std::make_unique<gmx::GpuForceReduction>(
1901 deviceStreamManager->context(),
1902 deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedNonLocal),
1906 std::unique_ptr<gmx::StatePropagatorDataGpu> stateGpu;
1907 if (gpusWereDetected
1908 && ((runScheduleWork.simulationWork.useGpuPme && thisRankHasDuty(cr, DUTY_PME))
1909 || runScheduleWork.simulationWork.useGpuBufferOps))
1911 GpuApiCallBehavior transferKind = (inputrec->eI == eiMD && !doRerun && !useModularSimulator)
1912 ? GpuApiCallBehavior::Async
1913 : GpuApiCallBehavior::Sync;
1914 GMX_RELEASE_ASSERT(deviceStreamManager != nullptr,
1915 "GPU device stream manager should be initialized to use GPU.");
1916 stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(
1917 *deviceStreamManager, transferKind, pme_gpu_get_block_size(fr->pmedata), wcycle);
1918 fr->stateGpu = stateGpu.get();
1921 GMX_ASSERT(stopHandlerBuilder_, "Runner must provide StopHandlerBuilder to simulator.");
1922 SimulatorBuilder simulatorBuilder;
1924 simulatorBuilder.add(SimulatorStateData(globalState.get(), &observablesHistory, &enerd, &ekind));
1925 simulatorBuilder.add(std::move(membedHolder));
1926 simulatorBuilder.add(std::move(stopHandlerBuilder_));
1927 simulatorBuilder.add(SimulatorConfig(mdrunOptions, startingBehavior, &runScheduleWork));
1930 simulatorBuilder.add(SimulatorEnv(fplog, cr, ms, mdlog, oenv));
1931 simulatorBuilder.add(Profiling(&nrnb, walltime_accounting, wcycle));
1932 simulatorBuilder.add(ConstraintsParam(
1933 constr.get(), enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr, vsite.get()));
1934 // TODO: Separate `fr` to a separate add, and make the `build` handle the coupling sensibly.
1935 simulatorBuilder.add(LegacyInput(
1936 static_cast<int>(filenames.size()), filenames.data(), inputrec.get(), fr));
1937 simulatorBuilder.add(ReplicaExchangeParameters(replExParams));
1938 simulatorBuilder.add(InteractiveMD(imdSession.get()));
1939 simulatorBuilder.add(SimulatorModules(mdModules_->outputProvider(), mdModules_->notifier()));
1940 simulatorBuilder.add(CenterOfMassPulling(pull_work));
1941 // Todo move to an MDModule
1942 simulatorBuilder.add(IonSwapping(swap));
1943 simulatorBuilder.add(TopologyData(&mtop, mdAtoms.get()));
1944 simulatorBuilder.add(BoxDeformationHandle(deform.get()));
1945 simulatorBuilder.add(std::move(modularSimulatorCheckpointData));
1947 // build and run simulator object based on user-input
1948 auto simulator = simulatorBuilder.build(useModularSimulator);
1951 if (fr->pmePpCommGpu)
1953 // destroy object since it is no longer required. (This needs to be done while the GPU context still exists.)
1954 fr->pmePpCommGpu.reset();
1957 if (inputrec->bPull)
1959 finish_pull(pull_work);
1961 finish_swapcoords(swap);
1965 GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
1967 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
1968 gmx_pmeonly(pmedata,
1972 walltime_accounting,
1975 deviceStreamManager.get());
1978 wallcycle_stop(wcycle, ewcRUN);
1980 /* Finish up, write some stuff
1981 * if rerunMD, don't write last frame again
1989 walltime_accounting,
1990 fr ? fr->nbv.get() : nullptr,
1992 EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
1994 // clean up cycle counter
1995 wallcycle_destroy(wcycle);
1997 deviceStreamManager.reset(nullptr);
2001 gmx_pme_destroy(pmedata);
2005 // FIXME: this is only here to manually unpin mdAtoms->chargeA_ and state->x,
2006 // before we destroy the GPU context(s)
2007 // Pinned buffers are associated with contexts in CUDA.
2008 // As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
2009 mdAtoms.reset(nullptr);
2010 globalState.reset(nullptr);
2011 mdModules_.reset(nullptr); // destruct force providers here as they might also use the GPU
2012 gpuBonded.reset(nullptr);
2013 /* Free pinned buffers in *fr */
2016 // TODO convert to C++ so we can get rid of these frees
2020 if (!hwinfo_->deviceInfoList.empty())
2022 /* stop the GPU profiler (only CUDA) */
2026 /* With tMPI we need to wait for all ranks to finish deallocation before
2027 * destroying the CUDA context as some tMPI ranks may be sharing
2030 * This is not a concern in OpenCL where we use one context per rank.
2032 * Note: it is safe to not call the barrier on the ranks which do not use GPU,
2033 * but it is easier and more futureproof to call it on the whole node.
2035 * Note that this function needs to be called even if GPUs are not used
2036 * in this run because the PME ranks have no knowledge of whether GPUs
2037 * are used or not, but all ranks need to enter the barrier below.
2038 * \todo Remove this physical node barrier after making sure
2039 * that it's not needed anymore (with a shared GPU run).
2043 physicalNodeComm.barrier();
2045 releaseDevice(deviceInfo);
2047 /* Does what it says */
2048 print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
2049 walltime_accounting_destroy(walltime_accounting);
2051 // Ensure log file content is written
2054 gmx_fio_flush(logFileHandle);
2057 /* Reset FPEs (important for unit tests) by disabling them. Assumes no
2058 * exceptions were enabled before function was called. */
2061 gmx_fedisableexcept();
2064 auto rc = static_cast<int>(gmx_get_stop_condition());
2067 /* we need to join all threads. The sub-threads join when they
2068 exit this function, but the master thread needs to be told to
2078 Mdrunner::~Mdrunner()
2080 // Clean up of the Manager.
2081 // This will end up getting called on every thread-MPI rank, which is unnecessary,
2082 // but okay as long as threads synchronize some time before adding or accessing
2083 // a new set of restraints.
2084 if (restraintManager_)
2086 restraintManager_->clear();
2087 GMX_ASSERT(restraintManager_->countRestraints() == 0,
2088 "restraints added during runner life time should be cleared at runner "
2093 void Mdrunner::addPotential(std::shared_ptr<gmx::IRestraintPotential> puller, const std::string& name)
2095 GMX_ASSERT(restraintManager_, "Mdrunner must have a restraint manager.");
2096 // Not sure if this should be logged through the md logger or something else,
2097 // but it is helpful to have some sort of INFO level message sent somewhere.
2098 // std::cout << "Registering restraint named " << name << std::endl;
2100 // When multiple restraints are used, it may be wasteful to register them separately.
2101 // Maybe instead register an entire Restraint Manager as a force provider.
2102 restraintManager_->addToSpec(std::move(puller), name);
2105 Mdrunner::Mdrunner(std::unique_ptr<MDModules> mdModules) : mdModules_(std::move(mdModules)) {}
2107 Mdrunner::Mdrunner(Mdrunner&&) noexcept = default;
2109 //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265 in CentOS 7
2110 Mdrunner& Mdrunner::operator=(Mdrunner&& /*handle*/) noexcept(BUGFREE_NOEXCEPT_STRING) = default;
2112 class Mdrunner::BuilderImplementation
2115 BuilderImplementation() = delete;
2116 BuilderImplementation(std::unique_ptr<MDModules> mdModules, compat::not_null<SimulationContext*> context);
2117 ~BuilderImplementation();
2119 BuilderImplementation& setExtraMdrunOptions(const MdrunOptions& options,
2120 real forceWarningThreshold,
2121 StartingBehavior startingBehavior);
2123 void addHardwareDetectionResult(const gmx_hw_info_t* hwinfo);
2125 void addDomdec(const DomdecOptions& options);
2127 void addInput(SimulationInputHandle inputHolder);
2129 void addVerletList(int nstlist);
2131 void addReplicaExchange(const ReplicaExchangeParameters& params);
2133 void addNonBonded(const char* nbpu_opt);
2135 void addPME(const char* pme_opt_, const char* pme_fft_opt_);
2137 void addBondedTaskAssignment(const char* bonded_opt);
2139 void addUpdateTaskAssignment(const char* update_opt);
2141 void addHardwareOptions(const gmx_hw_opt_t& hardwareOptions);
2143 void addFilenames(ArrayRef<const t_filenm> filenames);
2145 void addOutputEnvironment(gmx_output_env_t* outputEnvironment);
2147 void addLogFile(t_fileio* logFileHandle);
2149 void addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
2154 // Default parameters copied from runner.h
2155 // \todo Clarify source(s) of default parameters.
2157 const char* nbpu_opt_ = nullptr;
2158 const char* pme_opt_ = nullptr;
2159 const char* pme_fft_opt_ = nullptr;
2160 const char* bonded_opt_ = nullptr;
2161 const char* update_opt_ = nullptr;
2163 MdrunOptions mdrunOptions_;
2165 DomdecOptions domdecOptions_;
2167 ReplicaExchangeParameters replicaExchangeParameters_;
2169 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
2172 //! World communicator, used for hardware detection and task assignment
2173 MPI_Comm libraryWorldCommunicator_ = MPI_COMM_NULL;
2175 //! Multisim communicator handle.
2176 gmx_multisim_t* multiSimulation_;
2178 //! mdrun communicator
2179 MPI_Comm simulationCommunicator_ = MPI_COMM_NULL;
2181 //! Print a warning if any force is larger than this (in kJ/mol nm).
2182 real forceWarningThreshold_ = -1;
2184 //! Whether the simulation will start afresh, or restart with/without appending.
2185 StartingBehavior startingBehavior_ = StartingBehavior::NewSimulation;
2187 //! The modules that comprise the functionality of mdrun.
2188 std::unique_ptr<MDModules> mdModules_;
2190 //! Detected hardware.
2191 const gmx_hw_info_t* hwinfo_ = nullptr;
2193 //! \brief Parallelism information.
2194 gmx_hw_opt_t hardwareOptions_;
2196 //! filename options for simulation.
2197 ArrayRef<const t_filenm> filenames_;
2199 /*! \brief Handle to output environment.
2201 * \todo gmx_output_env_t needs lifetime management.
2203 gmx_output_env_t* outputEnvironment_ = nullptr;
2205 /*! \brief Non-owning handle to MD log file.
2207 * \todo Context should own output facilities for client.
2208 * \todo Improve log file handle management.
2210 * Code managing the FILE* relies on the ability to set it to
2211 * nullptr to check whether the filehandle is valid.
2213 t_fileio* logFileHandle_ = nullptr;
2216 * \brief Builder for simulation stop signal handler.
2218 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_ = nullptr;
2221 * \brief Sources for initial simulation state.
2223 * See issue #3652 for near-term refinements to the SimulationInput interface.
2225 * See issue #3379 for broader discussion on API aspects of simulation inputs and outputs.
2227 SimulationInputHandle inputHolder_;
2230 Mdrunner::BuilderImplementation::BuilderImplementation(std::unique_ptr<MDModules> mdModules,
2231 compat::not_null<SimulationContext*> context) :
2232 mdModules_(std::move(mdModules))
2234 libraryWorldCommunicator_ = context->libraryWorldCommunicator_;
2235 simulationCommunicator_ = context->simulationCommunicator_;
2236 multiSimulation_ = context->multiSimulation_.get();
2239 Mdrunner::BuilderImplementation::~BuilderImplementation() = default;
2241 Mdrunner::BuilderImplementation&
2242 Mdrunner::BuilderImplementation::setExtraMdrunOptions(const MdrunOptions& options,
2243 const real forceWarningThreshold,
2244 const StartingBehavior startingBehavior)
2246 mdrunOptions_ = options;
2247 forceWarningThreshold_ = forceWarningThreshold;
2248 startingBehavior_ = startingBehavior;
2252 void Mdrunner::BuilderImplementation::addDomdec(const DomdecOptions& options)
2254 domdecOptions_ = options;
2257 void Mdrunner::BuilderImplementation::addVerletList(int nstlist)
2262 void Mdrunner::BuilderImplementation::addReplicaExchange(const ReplicaExchangeParameters& params)
2264 replicaExchangeParameters_ = params;
2267 Mdrunner Mdrunner::BuilderImplementation::build()
2269 auto newRunner = Mdrunner(std::move(mdModules_));
2271 newRunner.mdrunOptions = mdrunOptions_;
2272 newRunner.pforce = forceWarningThreshold_;
2273 newRunner.startingBehavior = startingBehavior_;
2274 newRunner.domdecOptions = domdecOptions_;
2276 // \todo determine an invariant to check or confirm that all gmx_hw_opt_t objects are valid
2277 newRunner.hw_opt = hardwareOptions_;
2279 // No invariant to check. This parameter exists to optionally override other behavior.
2280 newRunner.nstlist_cmdline = nstlist_;
2282 newRunner.replExParams = replicaExchangeParameters_;
2284 newRunner.filenames = filenames_;
2286 newRunner.libraryWorldCommunicator = libraryWorldCommunicator_;
2288 newRunner.simulationCommunicator = simulationCommunicator_;
2290 // nullptr is a valid value for the multisim handle
2291 newRunner.ms = multiSimulation_;
2295 newRunner.hwinfo_ = hwinfo_;
2299 GMX_THROW(gmx::APIError(
2300 "MdrunnerBuilder::addHardwareDetectionResult() is required before build()"));
2305 newRunner.inputHolder_ = std::move(inputHolder_);
2309 GMX_THROW(gmx::APIError("MdrunnerBuilder::addInput() is required before build()."));
2312 // \todo Clarify ownership and lifetime management for gmx_output_env_t
2313 // \todo Update sanity checking when output environment has clearly specified invariants.
2314 // Initialization and default values for oenv are not well specified in the current version.
2315 if (outputEnvironment_)
2317 newRunner.oenv = outputEnvironment_;
2321 GMX_THROW(gmx::APIError(
2322 "MdrunnerBuilder::addOutputEnvironment() is required before build()"));
2325 newRunner.logFileHandle = logFileHandle_;
2329 newRunner.nbpu_opt = nbpu_opt_;
2333 GMX_THROW(gmx::APIError("MdrunnerBuilder::addNonBonded() is required before build()"));
2336 if (pme_opt_ && pme_fft_opt_)
2338 newRunner.pme_opt = pme_opt_;
2339 newRunner.pme_fft_opt = pme_fft_opt_;
2343 GMX_THROW(gmx::APIError("MdrunnerBuilder::addElectrostatics() is required before build()"));
2348 newRunner.bonded_opt = bonded_opt_;
2352 GMX_THROW(gmx::APIError(
2353 "MdrunnerBuilder::addBondedTaskAssignment() is required before build()"));
2358 newRunner.update_opt = update_opt_;
2362 GMX_THROW(gmx::APIError(
2363 "MdrunnerBuilder::addUpdateTaskAssignment() is required before build() "));
2367 newRunner.restraintManager_ = std::make_unique<gmx::RestraintManager>();
2369 if (stopHandlerBuilder_)
2371 newRunner.stopHandlerBuilder_ = std::move(stopHandlerBuilder_);
2375 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>();
2381 void Mdrunner::BuilderImplementation::addHardwareDetectionResult(const gmx_hw_info_t* hwinfo)
2386 void Mdrunner::BuilderImplementation::addNonBonded(const char* nbpu_opt)
2388 nbpu_opt_ = nbpu_opt;
2391 void Mdrunner::BuilderImplementation::addPME(const char* pme_opt, const char* pme_fft_opt)
2394 pme_fft_opt_ = pme_fft_opt;
2397 void Mdrunner::BuilderImplementation::addBondedTaskAssignment(const char* bonded_opt)
2399 bonded_opt_ = bonded_opt;
2402 void Mdrunner::BuilderImplementation::addUpdateTaskAssignment(const char* update_opt)
2404 update_opt_ = update_opt;
2407 void Mdrunner::BuilderImplementation::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2409 hardwareOptions_ = hardwareOptions;
2412 void Mdrunner::BuilderImplementation::addFilenames(ArrayRef<const t_filenm> filenames)
2414 filenames_ = filenames;
2417 void Mdrunner::BuilderImplementation::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2419 outputEnvironment_ = outputEnvironment;
2422 void Mdrunner::BuilderImplementation::addLogFile(t_fileio* logFileHandle)
2424 logFileHandle_ = logFileHandle;
2427 void Mdrunner::BuilderImplementation::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2429 stopHandlerBuilder_ = std::move(builder);
2432 void Mdrunner::BuilderImplementation::addInput(SimulationInputHandle inputHolder)
2434 inputHolder_ = std::move(inputHolder);
2437 MdrunnerBuilder::MdrunnerBuilder(std::unique_ptr<MDModules> mdModules,
2438 compat::not_null<SimulationContext*> context) :
2439 impl_{ std::make_unique<Mdrunner::BuilderImplementation>(std::move(mdModules), context) }
2443 MdrunnerBuilder::~MdrunnerBuilder() = default;
2445 MdrunnerBuilder& MdrunnerBuilder::addHardwareDetectionResult(const gmx_hw_info_t* hwinfo)
2447 impl_->addHardwareDetectionResult(hwinfo);
2451 MdrunnerBuilder& MdrunnerBuilder::addSimulationMethod(const MdrunOptions& options,
2452 real forceWarningThreshold,
2453 const StartingBehavior startingBehavior)
2455 impl_->setExtraMdrunOptions(options, forceWarningThreshold, startingBehavior);
2459 MdrunnerBuilder& MdrunnerBuilder::addDomainDecomposition(const DomdecOptions& options)
2461 impl_->addDomdec(options);
2465 MdrunnerBuilder& MdrunnerBuilder::addNeighborList(int nstlist)
2467 impl_->addVerletList(nstlist);
2471 MdrunnerBuilder& MdrunnerBuilder::addReplicaExchange(const ReplicaExchangeParameters& params)
2473 impl_->addReplicaExchange(params);
2477 MdrunnerBuilder& MdrunnerBuilder::addNonBonded(const char* nbpu_opt)
2479 impl_->addNonBonded(nbpu_opt);
2483 MdrunnerBuilder& MdrunnerBuilder::addElectrostatics(const char* pme_opt, const char* pme_fft_opt)
2485 // The builder method may become more general in the future, but in this version,
2486 // parameters for PME electrostatics are both required and the only parameters
2488 if (pme_opt && pme_fft_opt)
2490 impl_->addPME(pme_opt, pme_fft_opt);
2495 gmx::InvalidInputError("addElectrostatics() arguments must be non-null pointers."));
2500 MdrunnerBuilder& MdrunnerBuilder::addBondedTaskAssignment(const char* bonded_opt)
2502 impl_->addBondedTaskAssignment(bonded_opt);
2506 MdrunnerBuilder& MdrunnerBuilder::addUpdateTaskAssignment(const char* update_opt)
2508 impl_->addUpdateTaskAssignment(update_opt);
2512 Mdrunner MdrunnerBuilder::build()
2514 return impl_->build();
2517 MdrunnerBuilder& MdrunnerBuilder::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2519 impl_->addHardwareOptions(hardwareOptions);
2523 MdrunnerBuilder& MdrunnerBuilder::addFilenames(ArrayRef<const t_filenm> filenames)
2525 impl_->addFilenames(filenames);
2529 MdrunnerBuilder& MdrunnerBuilder::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2531 impl_->addOutputEnvironment(outputEnvironment);
2535 MdrunnerBuilder& MdrunnerBuilder::addLogFile(t_fileio* logFileHandle)
2537 impl_->addLogFile(logFileHandle);
2541 MdrunnerBuilder& MdrunnerBuilder::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2543 impl_->addStopHandlerBuilder(std::move(builder));
2547 MdrunnerBuilder& MdrunnerBuilder::addInput(SimulationInputHandle input)
2549 impl_->addInput(std::move(input));
2553 MdrunnerBuilder::MdrunnerBuilder(MdrunnerBuilder&&) noexcept = default;
2555 MdrunnerBuilder& MdrunnerBuilder::operator=(MdrunnerBuilder&&) noexcept = default;