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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/makebondedlinks.h"
66 #include "gromacs/domdec/partition.h"
67 #include "gromacs/domdec/reversetopology.h"
68 #include "gromacs/ewald/ewald_utils.h"
69 #include "gromacs/ewald/pme.h"
70 #include "gromacs/ewald/pme_gpu_program.h"
71 #include "gromacs/ewald/pme_only.h"
72 #include "gromacs/ewald/pme_pp_comm_gpu.h"
73 #include "gromacs/fileio/checkpoint.h"
74 #include "gromacs/fileio/gmxfio.h"
75 #include "gromacs/fileio/oenv.h"
76 #include "gromacs/fileio/tpxio.h"
77 #include "gromacs/gmxlib/network.h"
78 #include "gromacs/gmxlib/nrnb.h"
79 #include "gromacs/gpu_utils/device_stream_manager.h"
80 #include "gromacs/hardware/cpuinfo.h"
81 #include "gromacs/hardware/detecthardware.h"
82 #include "gromacs/hardware/device_management.h"
83 #include "gromacs/hardware/hardwaretopology.h"
84 #include "gromacs/hardware/printhardware.h"
85 #include "gromacs/imd/imd.h"
86 #include "gromacs/listed_forces/disre.h"
87 #include "gromacs/listed_forces/listed_forces_gpu.h"
88 #include "gromacs/listed_forces/listed_forces.h"
89 #include "gromacs/listed_forces/orires.h"
90 #include "gromacs/math/functions.h"
91 #include "gromacs/math/utilities.h"
92 #include "gromacs/math/vec.h"
93 #include "gromacs/mdlib/boxdeformation.h"
94 #include "gromacs/mdlib/broadcaststructs.h"
95 #include "gromacs/mdlib/calc_verletbuf.h"
96 #include "gromacs/mdlib/dispersioncorrection.h"
97 #include "gromacs/mdlib/enerdata_utils.h"
98 #include "gromacs/mdlib/force.h"
99 #include "gromacs/mdlib/forcerec.h"
100 #include "gromacs/mdlib/gmx_omp_nthreads.h"
101 #include "gromacs/mdlib/gpuforcereduction.h"
102 #include "gromacs/mdlib/makeconstraints.h"
103 #include "gromacs/mdlib/md_support.h"
104 #include "gromacs/mdlib/mdatoms.h"
105 #include "gromacs/mdlib/sighandler.h"
106 #include "gromacs/mdlib/stophandler.h"
107 #include "gromacs/mdlib/tgroup.h"
108 #include "gromacs/mdlib/updategroups.h"
109 #include "gromacs/mdlib/vsite.h"
110 #include "gromacs/mdrun/mdmodules.h"
111 #include "gromacs/mdrun/simulationcontext.h"
112 #include "gromacs/mdrun/simulationinput.h"
113 #include "gromacs/mdrun/simulationinputhandle.h"
114 #include "gromacs/mdrunutility/handlerestart.h"
115 #include "gromacs/mdrunutility/logging.h"
116 #include "gromacs/mdrunutility/multisim.h"
117 #include "gromacs/mdrunutility/printtime.h"
118 #include "gromacs/mdrunutility/threadaffinity.h"
119 #include "gromacs/mdtypes/checkpointdata.h"
120 #include "gromacs/mdtypes/commrec.h"
121 #include "gromacs/mdtypes/enerdata.h"
122 #include "gromacs/mdtypes/fcdata.h"
123 #include "gromacs/mdtypes/forcerec.h"
124 #include "gromacs/mdtypes/group.h"
125 #include "gromacs/mdtypes/inputrec.h"
126 #include "gromacs/mdtypes/interaction_const.h"
127 #include "gromacs/mdtypes/md_enums.h"
128 #include "gromacs/mdtypes/mdatom.h"
129 #include "gromacs/mdtypes/mdrunoptions.h"
130 #include "gromacs/mdtypes/observableshistory.h"
131 #include "gromacs/mdtypes/simulation_workload.h"
132 #include "gromacs/mdtypes/state.h"
133 #include "gromacs/mdtypes/state_propagator_data_gpu.h"
134 #include "gromacs/modularsimulator/modularsimulator.h"
135 #include "gromacs/nbnxm/gpu_data_mgmt.h"
136 #include "gromacs/nbnxm/nbnxm.h"
137 #include "gromacs/nbnxm/pairlist_tuning.h"
138 #include "gromacs/pbcutil/pbc.h"
139 #include "gromacs/pulling/output.h"
140 #include "gromacs/pulling/pull.h"
141 #include "gromacs/pulling/pull_rotation.h"
142 #include "gromacs/restraint/manager.h"
143 #include "gromacs/restraint/restraintmdmodule.h"
144 #include "gromacs/restraint/restraintpotential.h"
145 #include "gromacs/swap/swapcoords.h"
146 #include "gromacs/taskassignment/decidegpuusage.h"
147 #include "gromacs/taskassignment/decidesimulationworkload.h"
148 #include "gromacs/taskassignment/resourcedivision.h"
149 #include "gromacs/taskassignment/taskassignment.h"
150 #include "gromacs/taskassignment/usergpuids.h"
151 #include "gromacs/timing/gpu_timing.h"
152 #include "gromacs/timing/wallcycle.h"
153 #include "gromacs/timing/wallcyclereporting.h"
154 #include "gromacs/topology/mtop_util.h"
155 #include "gromacs/trajectory/trajectoryframe.h"
156 #include "gromacs/utility/basenetwork.h"
157 #include "gromacs/utility/cstringutil.h"
158 #include "gromacs/utility/exceptions.h"
159 #include "gromacs/utility/fatalerror.h"
160 #include "gromacs/utility/filestream.h"
161 #include "gromacs/utility/gmxassert.h"
162 #include "gromacs/utility/gmxmpi.h"
163 #include "gromacs/utility/keyvaluetree.h"
164 #include "gromacs/utility/logger.h"
165 #include "gromacs/utility/loggerbuilder.h"
166 #include "gromacs/utility/mdmodulesnotifiers.h"
167 #include "gromacs/utility/physicalnodecommunicator.h"
168 #include "gromacs/utility/pleasecite.h"
169 #include "gromacs/utility/programcontext.h"
170 #include "gromacs/utility/smalloc.h"
171 #include "gromacs/utility/stringutil.h"
172 #include "gromacs/utility/mpiinfo.h"
174 #include "isimulator.h"
175 #include "membedholder.h"
176 #include "replicaexchange.h"
177 #include "simulatorbuilder.h"
183 /*! \brief Manage any development feature flag variables encountered
185 * The use of dev features indicated by environment variables is
186 * logged in order to ensure that runs with such features enabled can
187 * be identified from their log and standard output. Any cross
188 * dependencies are also checked, and if unsatisfied, a fatal error
191 * Note that some development features overrides are applied already here:
192 * the GPU communication flags are set to false in non-tMPI and non-CUDA builds.
194 * \param[in] mdlog Logger object.
195 * \param[in] useGpuForNonbonded True if the nonbonded task is offloaded in this run.
196 * \param[in] pmeRunMode The PME run mode for this run
197 * \returns The object populated with development feature flags.
199 static DevelopmentFeatureFlags manageDevelopmentFeatures(const gmx::MDLogger& mdlog,
200 const bool useGpuForNonbonded,
201 const PmeRunMode pmeRunMode)
203 DevelopmentFeatureFlags devFlags;
205 devFlags.enableGpuBufferOps =
206 GMX_GPU_CUDA && useGpuForNonbonded && (getenv("GMX_USE_GPU_BUFFER_OPS") != nullptr);
207 devFlags.enableGpuHaloExchange = GMX_MPI && GMX_GPU_CUDA && getenv("GMX_GPU_DD_COMMS") != nullptr;
208 devFlags.forceGpuUpdateDefault = (getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") != nullptr) || GMX_FAHCORE;
209 devFlags.enableGpuPmePPComm = GMX_MPI && GMX_GPU_CUDA && getenv("GMX_GPU_PME_PP_COMMS") != nullptr;
211 // Direct GPU comm path is being used with CUDA_AWARE_MPI
212 // make sure underlying MPI implementation is CUDA-aware
213 if (!GMX_THREAD_MPI && (devFlags.enableGpuPmePPComm || devFlags.enableGpuHaloExchange))
215 const bool haveDetectedCudaAwareMpi =
216 (checkMpiCudaAwareSupport() == CudaAwareMpiStatus::Supported);
217 const bool forceCudaAwareMpi = (getenv("GMX_FORCE_CUDA_AWARE_MPI") != nullptr);
219 if (!haveDetectedCudaAwareMpi && forceCudaAwareMpi)
221 // CUDA-aware support not detected in MPI library but, user has forced it's use
222 GMX_LOG(mdlog.warning)
224 .appendTextFormatted(
225 "This run has forced use of 'CUDA-aware MPI'. "
226 "But, GROMACS cannot determine if underlying MPI "
227 "is CUDA-aware. GROMACS recommends use of latest openMPI version "
228 "for CUDA-aware support. "
229 "If you observe failures at runtime, try unsetting "
230 "GMX_FORCE_CUDA_AWARE_MPI environment variable.");
233 if (haveDetectedCudaAwareMpi || forceCudaAwareMpi)
235 devFlags.usingCudaAwareMpi = true;
236 GMX_LOG(mdlog.warning)
238 .appendTextFormatted(
239 "Using CUDA-aware MPI for 'GPU halo exchange' or 'GPU PME-PP "
240 "communications' feature.");
244 if (devFlags.enableGpuHaloExchange)
246 GMX_LOG(mdlog.warning)
248 .appendTextFormatted(
249 "GMX_GPU_DD_COMMS environment variable detected, but the 'GPU "
250 "halo exchange' feature will not be enabled as GROMACS couldn't "
251 "detect CUDA_aware support in underlying MPI implementation.");
252 devFlags.enableGpuHaloExchange = false;
254 if (devFlags.enableGpuPmePPComm)
256 GMX_LOG(mdlog.warning)
259 "GMX_GPU_PME_PP_COMMS environment variable detected, but the "
260 "'GPU PME-PP communications' feature will not be enabled as "
262 "detect CUDA_aware support in underlying MPI implementation.");
263 devFlags.enableGpuPmePPComm = false;
266 GMX_LOG(mdlog.warning)
268 .appendTextFormatted(
269 "GROMACS recommends use of latest OpenMPI version for CUDA-aware "
271 "If you are certain about CUDA-aware support in your MPI library, "
272 "you can force it's use by setting environment variable "
273 " GMX_FORCE_CUDA_AWARE_MPI.");
277 if (devFlags.enableGpuBufferOps)
279 GMX_LOG(mdlog.warning)
281 .appendTextFormatted(
282 "This run uses the 'GPU buffer ops' feature, enabled by the "
283 "GMX_USE_GPU_BUFFER_OPS environment variable.");
286 if (devFlags.forceGpuUpdateDefault)
288 GMX_LOG(mdlog.warning)
290 .appendTextFormatted(
291 "This run will default to '-update gpu' as requested by the "
292 "GMX_FORCE_UPDATE_DEFAULT_GPU environment variable. GPU update with domain "
293 "decomposition lacks substantial testing and should be used with caution.");
296 if (devFlags.enableGpuHaloExchange)
298 if (useGpuForNonbonded)
300 if (!devFlags.enableGpuBufferOps)
302 GMX_LOG(mdlog.warning)
304 .appendTextFormatted(
305 "Enabling GPU buffer operations required by GMX_GPU_DD_COMMS "
306 "(equivalent with GMX_USE_GPU_BUFFER_OPS=1).");
307 devFlags.enableGpuBufferOps = true;
309 GMX_LOG(mdlog.warning)
311 .appendTextFormatted(
312 "This run has requested the 'GPU halo exchange' feature, enabled by "
314 "GMX_GPU_DD_COMMS environment variable.");
318 GMX_LOG(mdlog.warning)
320 .appendTextFormatted(
321 "GMX_GPU_DD_COMMS environment variable detected, but the 'GPU "
322 "halo exchange' feature will not be enabled as nonbonded interactions "
323 "are not offloaded.");
324 devFlags.enableGpuHaloExchange = false;
328 if (devFlags.enableGpuPmePPComm)
330 if (pmeRunMode == PmeRunMode::GPU)
332 if (!devFlags.enableGpuBufferOps)
334 GMX_LOG(mdlog.warning)
336 .appendTextFormatted(
337 "Enabling GPU buffer operations required by GMX_GPU_PME_PP_COMMS "
338 "(equivalent with GMX_USE_GPU_BUFFER_OPS=1).");
339 devFlags.enableGpuBufferOps = true;
341 GMX_LOG(mdlog.warning)
343 .appendTextFormatted(
344 "This run uses the 'GPU PME-PP communications' feature, enabled "
345 "by the GMX_GPU_PME_PP_COMMS environment variable.");
349 std::string clarification;
350 if (pmeRunMode == PmeRunMode::Mixed)
353 "PME FFT and gather are not offloaded to the GPU (PME is running in mixed "
358 clarification = "PME is not offloaded to the GPU.";
360 GMX_LOG(mdlog.warning)
363 "GMX_GPU_PME_PP_COMMS environment variable detected, but the "
364 "'GPU PME-PP communications' feature was not enabled as "
366 devFlags.enableGpuPmePPComm = false;
373 /*! \brief Barrier for safe simultaneous thread access to mdrunner data
375 * Used to ensure that the master thread does not modify mdrunner during copy
376 * on the spawned threads. */
377 static void threadMpiMdrunnerAccessBarrier()
380 MPI_Barrier(MPI_COMM_WORLD);
384 Mdrunner Mdrunner::cloneOnSpawnedThread() const
386 auto newRunner = Mdrunner(std::make_unique<MDModules>());
388 // All runners in the same process share a restraint manager resource because it is
389 // part of the interface to the client code, which is associated only with the
390 // original thread. Handles to the same resources can be obtained by copy.
392 newRunner.restraintManager_ = std::make_unique<RestraintManager>(*restraintManager_);
395 // Copy members of master runner.
396 // \todo Replace with builder when Simulation context and/or runner phases are better defined.
397 // Ref https://gitlab.com/gromacs/gromacs/-/issues/2587 and https://gitlab.com/gromacs/gromacs/-/issues/2375
398 newRunner.hw_opt = hw_opt;
399 newRunner.filenames = filenames;
401 newRunner.hwinfo_ = hwinfo_;
402 newRunner.oenv = oenv;
403 newRunner.mdrunOptions = mdrunOptions;
404 newRunner.domdecOptions = domdecOptions;
405 newRunner.nbpu_opt = nbpu_opt;
406 newRunner.pme_opt = pme_opt;
407 newRunner.pme_fft_opt = pme_fft_opt;
408 newRunner.bonded_opt = bonded_opt;
409 newRunner.update_opt = update_opt;
410 newRunner.nstlist_cmdline = nstlist_cmdline;
411 newRunner.replExParams = replExParams;
412 newRunner.pforce = pforce;
413 // Give the spawned thread the newly created valid communicator
414 // for the simulation.
415 newRunner.libraryWorldCommunicator = MPI_COMM_WORLD;
416 newRunner.simulationCommunicator = MPI_COMM_WORLD;
418 newRunner.startingBehavior = startingBehavior;
419 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>(*stopHandlerBuilder_);
420 newRunner.inputHolder_ = inputHolder_;
422 threadMpiMdrunnerAccessBarrier();
427 /*! \brief The callback used for running on spawned threads.
429 * Obtains the pointer to the master mdrunner object from the one
430 * argument permitted to the thread-launch API call, copies it to make
431 * a new runner for this thread, reinitializes necessary data, and
432 * proceeds to the simulation. */
433 static void mdrunner_start_fn(const void* arg)
437 const auto* masterMdrunner = reinterpret_cast<const gmx::Mdrunner*>(arg);
438 /* copy the arg list to make sure that it's thread-local. This
439 doesn't copy pointed-to items, of course; fnm, cr and fplog
440 are reset in the call below, all others should be const. */
441 gmx::Mdrunner mdrunner = masterMdrunner->cloneOnSpawnedThread();
444 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
448 void Mdrunner::spawnThreads(int numThreadsToLaunch)
451 /* now spawn new threads that start mdrunner_start_fn(), while
452 the main thread returns. Thread affinity is handled later. */
453 if (tMPI_Init_fn(TRUE, numThreadsToLaunch, TMPI_AFFINITY_NONE, mdrunner_start_fn, static_cast<const void*>(this))
456 GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
459 // Give the master thread the newly created valid communicator for
461 libraryWorldCommunicator = MPI_COMM_WORLD;
462 simulationCommunicator = MPI_COMM_WORLD;
463 threadMpiMdrunnerAccessBarrier();
465 GMX_UNUSED_VALUE(numThreadsToLaunch);
466 GMX_UNUSED_VALUE(mdrunner_start_fn);
472 /*! \brief Initialize variables for Verlet scheme simulation */
473 static void prepare_verlet_scheme(FILE* fplog,
477 const gmx_mtop_t& mtop,
479 bool makeGpuPairList,
480 const gmx::CpuInfo& cpuinfo)
482 // We checked the cut-offs in grompp, but double-check here.
483 // We have PME+LJcutoff kernels for rcoulomb>rvdw.
484 if (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == VanDerWaalsType::Cut)
486 GMX_RELEASE_ASSERT(ir->rcoulomb >= ir->rvdw,
487 "With Verlet lists and PME we should have rcoulomb>=rvdw");
491 GMX_RELEASE_ASSERT(ir->rcoulomb == ir->rvdw,
492 "With Verlet lists and no PME rcoulomb and rvdw should be identical");
494 /* For NVE simulations, we will retain the initial list buffer */
495 if (EI_DYNAMICS(ir->eI) && ir->verletbuf_tol > 0
496 && !(EI_MD(ir->eI) && ir->etc == TemperatureCoupling::No))
498 /* Update the Verlet buffer size for the current run setup */
500 /* Here we assume SIMD-enabled kernels are being used. But as currently
501 * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
502 * and 4x2 gives a larger buffer than 4x4, this is ok.
504 ListSetupType listType =
505 (makeGpuPairList ? ListSetupType::Gpu : ListSetupType::CpuSimdWhenSupported);
506 VerletbufListSetup listSetup = verletbufGetSafeListSetup(listType);
508 const real rlist_new =
509 calcVerletBufferSize(mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
511 if (rlist_new != ir->rlist)
513 if (fplog != nullptr)
516 "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
519 listSetup.cluster_size_i,
520 listSetup.cluster_size_j);
522 ir->rlist = rlist_new;
526 if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
529 "Can not set nstlist without %s",
530 !EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
533 if (EI_DYNAMICS(ir->eI))
535 /* Set or try nstlist values */
536 increaseNstlist(fplog, cr, ir, nstlist_cmdline, &mtop, box, makeGpuPairList, cpuinfo);
540 /*! \brief Override the nslist value in inputrec
542 * with value passed on the command line (if any)
544 static void override_nsteps_cmdline(const gmx::MDLogger& mdlog, int64_t nsteps_cmdline, t_inputrec* ir)
548 /* override with anything else than the default -2 */
549 if (nsteps_cmdline > -2)
551 char sbuf_steps[STEPSTRSIZE];
552 char sbuf_msg[STRLEN];
554 ir->nsteps = nsteps_cmdline;
555 if (EI_DYNAMICS(ir->eI) && nsteps_cmdline != -1)
558 "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
559 gmx_step_str(nsteps_cmdline, sbuf_steps),
560 fabs(nsteps_cmdline * ir->delta_t));
565 "Overriding nsteps with value passed on the command line: %s steps",
566 gmx_step_str(nsteps_cmdline, sbuf_steps));
569 GMX_LOG(mdlog.warning).asParagraph().appendText(sbuf_msg);
571 else if (nsteps_cmdline < -2)
573 gmx_fatal(FARGS, "Invalid nsteps value passed on the command line: %" PRId64, nsteps_cmdline);
575 /* Do nothing if nsteps_cmdline == -2 */
581 /*! \brief Return whether GPU acceleration of nonbondeds is supported with the given settings.
583 * If not, and if a warning may be issued, logs a warning about
584 * falling back to CPU code. With thread-MPI, only the first
585 * call to this function should have \c issueWarning true. */
586 static bool gpuAccelerationOfNonbondedIsUseful(const MDLogger& mdlog, const t_inputrec& ir, bool issueWarning)
588 bool gpuIsUseful = true;
591 if (ir.opts.ngener - ir.nwall > 1)
593 /* The GPU code does not support more than one energy group.
594 * If the user requested GPUs explicitly, a fatal error is given later.
598 "Multiple energy groups is not implemented for GPUs, falling back to the CPU. "
599 "For better performance, run on the GPU without energy groups and then do "
600 "gmx mdrun -rerun option on the trajectory with an energy group .tpr file.";
606 warning = "TPI is not implemented for GPUs.";
609 if (!gpuIsUseful && issueWarning)
611 GMX_LOG(mdlog.warning).asParagraph().appendText(warning);
617 //! Initializes the logger for mdrun.
618 static gmx::LoggerOwner buildLogger(FILE* fplog, const bool isSimulationMasterRank)
620 gmx::LoggerBuilder builder;
621 if (fplog != nullptr)
623 builder.addTargetFile(gmx::MDLogger::LogLevel::Info, fplog);
625 if (isSimulationMasterRank)
627 builder.addTargetStream(gmx::MDLogger::LogLevel::Warning, &gmx::TextOutputFile::standardError());
629 return builder.build();
632 //! Make a TaskTarget from an mdrun argument string.
633 static TaskTarget findTaskTarget(const char* optionString)
635 TaskTarget returnValue = TaskTarget::Auto;
637 if (strncmp(optionString, "auto", 3) == 0)
639 returnValue = TaskTarget::Auto;
641 else if (strncmp(optionString, "cpu", 3) == 0)
643 returnValue = TaskTarget::Cpu;
645 else if (strncmp(optionString, "gpu", 3) == 0)
647 returnValue = TaskTarget::Gpu;
651 GMX_ASSERT(false, "Option string should have been checked for sanity already");
657 //! Finish run, aggregate data to print performance info.
658 static void finish_run(FILE* fplog,
659 const gmx::MDLogger& mdlog,
661 const t_inputrec& inputrec,
663 gmx_wallcycle* wcycle,
664 gmx_walltime_accounting_t walltime_accounting,
665 nonbonded_verlet_t* nbv,
666 const gmx_pme_t* pme,
670 double nbfs = 0, mflop = 0;
671 double elapsed_time, elapsed_time_over_all_ranks, elapsed_time_over_all_threads,
672 elapsed_time_over_all_threads_over_all_ranks;
673 /* Control whether it is valid to print a report. Only the
674 simulation master may print, but it should not do so if the run
675 terminated e.g. before a scheduled reset step. This is
676 complicated by the fact that PME ranks are unaware of the
677 reason why they were sent a pmerecvqxFINISH. To avoid
678 communication deadlocks, we always do the communication for the
679 report, even if we've decided not to write the report, because
680 how long it takes to finish the run is not important when we've
681 decided not to report on the simulation performance.
683 Further, we only report performance for dynamical integrators,
684 because those are the only ones for which we plan to
685 consider doing any optimizations. */
686 bool printReport = EI_DYNAMICS(inputrec.eI) && SIMMASTER(cr);
688 if (printReport && !walltime_accounting_get_valid_finish(walltime_accounting))
690 GMX_LOG(mdlog.warning)
692 .appendText("Simulation ended prematurely, no performance report will be written.");
697 std::unique_ptr<t_nrnb> nrnbTotalStorage;
700 nrnbTotalStorage = std::make_unique<t_nrnb>();
701 nrnb_tot = nrnbTotalStorage.get();
703 MPI_Allreduce(nrnb->n.data(), nrnb_tot->n.data(), eNRNB, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
711 elapsed_time = walltime_accounting_get_time_since_reset(walltime_accounting);
712 elapsed_time_over_all_threads =
713 walltime_accounting_get_time_since_reset_over_all_threads(walltime_accounting);
717 /* reduce elapsed_time over all MPI ranks in the current simulation */
718 MPI_Allreduce(&elapsed_time, &elapsed_time_over_all_ranks, 1, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
719 elapsed_time_over_all_ranks /= cr->nnodes;
720 /* Reduce elapsed_time_over_all_threads over all MPI ranks in the
721 * current simulation. */
722 MPI_Allreduce(&elapsed_time_over_all_threads,
723 &elapsed_time_over_all_threads_over_all_ranks,
732 elapsed_time_over_all_ranks = elapsed_time;
733 elapsed_time_over_all_threads_over_all_ranks = elapsed_time_over_all_threads;
738 print_flop(fplog, nrnb_tot, &nbfs, &mflop);
741 if (thisRankHasDuty(cr, DUTY_PP) && DOMAINDECOMP(cr))
743 print_dd_statistics(cr, inputrec, fplog);
746 /* TODO Move the responsibility for any scaling by thread counts
747 * to the code that handled the thread region, so that there's a
748 * mechanism to keep cycle counting working during the transition
749 * to task parallelism. */
750 int nthreads_pp = gmx_omp_nthreads_get(ModuleMultiThread::Nonbonded);
751 int nthreads_pme = gmx_omp_nthreads_get(ModuleMultiThread::Pme);
752 wallcycle_scale_by_num_threads(
753 wcycle, thisRankHasDuty(cr, DUTY_PME) && !thisRankHasDuty(cr, DUTY_PP), nthreads_pp, nthreads_pme);
754 auto cycle_sum(wallcycle_sum(cr, wcycle));
758 auto* nbnxn_gpu_timings =
759 (nbv != nullptr && nbv->useGpu()) ? Nbnxm::gpu_get_timings(nbv->gpu_nbv) : nullptr;
760 gmx_wallclock_gpu_pme_t pme_gpu_timings = {};
762 if (pme_gpu_task_enabled(pme))
764 pme_gpu_get_timings(pme, &pme_gpu_timings);
766 wallcycle_print(fplog,
772 elapsed_time_over_all_ranks,
778 if (EI_DYNAMICS(inputrec.eI))
780 delta_t = inputrec.delta_t;
786 elapsed_time_over_all_threads_over_all_ranks,
787 elapsed_time_over_all_ranks,
788 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
796 elapsed_time_over_all_threads_over_all_ranks,
797 elapsed_time_over_all_ranks,
798 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
806 int Mdrunner::mdrunner()
809 std::unique_ptr<t_forcerec> fr;
810 real ewaldcoeff_q = 0;
811 real ewaldcoeff_lj = 0;
812 int nChargePerturbed = -1, nTypePerturbed = 0;
813 gmx_walltime_accounting_t walltime_accounting = nullptr;
814 MembedHolder membedHolder(filenames.size(), filenames.data());
816 /* CAUTION: threads may be started later on in this function, so
817 cr doesn't reflect the final parallel state right now */
820 /* TODO: inputrec should tell us whether we use an algorithm, not a file option */
821 const bool doEssentialDynamics = opt2bSet("-ei", filenames.size(), filenames.data());
822 const bool doRerun = mdrunOptions.rerun;
824 // Handle task-assignment related user options.
825 EmulateGpuNonbonded emulateGpuNonbonded =
826 (getenv("GMX_EMULATE_GPU") != nullptr ? EmulateGpuNonbonded::Yes : EmulateGpuNonbonded::No);
828 std::vector<int> userGpuTaskAssignment;
831 userGpuTaskAssignment = parseUserTaskAssignmentString(hw_opt.userGpuTaskAssignment);
833 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
834 auto nonbondedTarget = findTaskTarget(nbpu_opt);
835 auto pmeTarget = findTaskTarget(pme_opt);
836 auto pmeFftTarget = findTaskTarget(pme_fft_opt);
837 auto bondedTarget = findTaskTarget(bonded_opt);
838 auto updateTarget = findTaskTarget(update_opt);
840 FILE* fplog = nullptr;
841 // If we are appending, we don't write log output because we need
842 // to check that the old log file matches what the checkpoint file
843 // expects. Otherwise, we should start to write log output now if
844 // there is a file ready for it.
845 if (logFileHandle != nullptr && startingBehavior != StartingBehavior::RestartWithAppending)
847 fplog = gmx_fio_getfp(logFileHandle);
849 const bool isSimulationMasterRank = findIsSimulationMasterRank(ms, simulationCommunicator);
850 gmx::LoggerOwner logOwner(buildLogger(fplog, isSimulationMasterRank));
851 gmx::MDLogger mdlog(logOwner.logger());
853 gmx_print_detected_hardware(fplog, isSimulationMasterRank && isMasterSim(ms), mdlog, hwinfo_);
855 std::vector<int> availableDevices =
856 makeListOfAvailableDevices(hwinfo_->deviceInfoList, hw_opt.devicesSelectedByUser);
857 const int numAvailableDevices = gmx::ssize(availableDevices);
859 // Print citation requests after all software/hardware printing
860 pleaseCiteGromacs(fplog);
862 // Note: legacy program logic relies on checking whether these pointers are assigned.
863 // Objects may or may not be allocated later.
864 std::unique_ptr<t_inputrec> inputrec;
865 std::unique_ptr<t_state> globalState;
867 auto partialDeserializedTpr = std::make_unique<PartialDeserializedTprFile>();
869 if (isSimulationMasterRank)
871 // Allocate objects to be initialized by later function calls.
872 /* Only the master rank has the global state */
873 globalState = std::make_unique<t_state>();
874 inputrec = std::make_unique<t_inputrec>();
876 /* Read (nearly) all data required for the simulation
877 * and keep the partly serialized tpr contents to send to other ranks later
879 applyGlobalSimulationState(
880 *inputHolder_.get(), partialDeserializedTpr.get(), globalState.get(), inputrec.get(), &mtop);
883 /* Check and update the hardware options for internal consistency */
884 checkAndUpdateHardwareOptions(
885 mdlog, &hw_opt, isSimulationMasterRank, domdecOptions.numPmeRanks, inputrec.get());
887 if (GMX_THREAD_MPI && isSimulationMasterRank)
889 bool useGpuForNonbonded = false;
890 bool useGpuForPme = false;
893 GMX_RELEASE_ASSERT(inputrec != nullptr, "Keep the compiler happy");
895 // If the user specified the number of ranks, then we must
896 // respect that, but in default mode, we need to allow for
897 // the number of GPUs to choose the number of ranks.
898 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
899 useGpuForNonbonded = decideWhetherToUseGpusForNonbondedWithThreadMpi(
901 numAvailableDevices > 0,
902 userGpuTaskAssignment,
904 canUseGpuForNonbonded,
905 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, GMX_THREAD_MPI),
906 hw_opt.nthreads_tmpi);
907 useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi(useGpuForNonbonded,
910 userGpuTaskAssignment,
913 hw_opt.nthreads_tmpi,
914 domdecOptions.numPmeRanks);
916 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
918 /* Determine how many thread-MPI ranks to start.
920 * TODO Over-writing the user-supplied value here does
921 * prevent any possible subsequent checks from working
923 hw_opt.nthreads_tmpi = get_nthreads_mpi(hwinfo_,
931 membedHolder.doMembed());
933 // Now start the threads for thread MPI.
934 spawnThreads(hw_opt.nthreads_tmpi);
935 // The spawned threads enter mdrunner() and execution of
936 // master and spawned threads joins at the end of this block.
939 GMX_RELEASE_ASSERT(ms || simulationCommunicator != MPI_COMM_NULL,
940 "Must have valid communicator unless running a multi-simulation");
941 CommrecHandle crHandle = init_commrec(simulationCommunicator);
942 t_commrec* cr = crHandle.get();
943 GMX_RELEASE_ASSERT(cr != nullptr, "Must have valid commrec");
945 PhysicalNodeCommunicator physicalNodeComm(libraryWorldCommunicator, gmx_physicalnode_id_hash());
947 // If we detected the topology on this system, double-check that it makes sense
948 if (hwinfo_->hardwareTopology->isThisSystem())
950 hardwareTopologyDoubleCheckDetection(mdlog, *hwinfo_->hardwareTopology);
955 /* now broadcast everything to the non-master nodes/threads: */
956 if (!isSimulationMasterRank)
958 // Until now, only the master rank has a non-null pointer.
959 // On non-master ranks, allocate the object that will receive data in the following call.
960 inputrec = std::make_unique<t_inputrec>();
962 init_parallel(cr->mpiDefaultCommunicator,
966 partialDeserializedTpr.get());
968 GMX_RELEASE_ASSERT(inputrec != nullptr, "All ranks should have a valid inputrec now");
969 partialDeserializedTpr.reset(nullptr);
972 !inputrec->useConstantAcceleration,
973 "Linear acceleration has been removed in GROMACS 2022, and was broken for many years "
974 "before that. Use GROMACS 4.5 or earlier if you need this feature.");
976 // Now the number of ranks is known to all ranks, and each knows
977 // the inputrec read by the master rank. The ranks can now all run
978 // the task-deciding functions and will agree on the result
979 // without needing to communicate.
980 const bool useDomainDecomposition =
981 (PAR(cr) && !(EI_TPI(inputrec->eI) || inputrec->eI == IntegrationAlgorithm::NM));
983 // Note that these variables describe only their own node.
985 // Note that when bonded interactions run on a GPU they always run
986 // alongside a nonbonded task, so do not influence task assignment
987 // even though they affect the force calculation workload.
988 bool useGpuForNonbonded = false;
989 bool useGpuForPme = false;
990 bool useGpuForBonded = false;
991 bool useGpuForUpdate = false;
992 bool gpusWereDetected = hwinfo_->ngpu_compatible_tot > 0;
995 // It's possible that there are different numbers of GPUs on
996 // different nodes, which is the user's responsibility to
997 // handle. If unsuitable, we will notice that during task
999 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
1000 useGpuForNonbonded = decideWhetherToUseGpusForNonbonded(
1002 userGpuTaskAssignment,
1003 emulateGpuNonbonded,
1004 canUseGpuForNonbonded,
1005 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, !GMX_THREAD_MPI),
1007 useGpuForPme = decideWhetherToUseGpusForPme(useGpuForNonbonded,
1009 userGpuTaskAssignment,
1012 cr->sizeOfDefaultCommunicator,
1013 domdecOptions.numPmeRanks,
1015 useGpuForBonded = decideWhetherToUseGpusForBonded(
1016 useGpuForNonbonded, useGpuForPme, bondedTarget, *inputrec, mtop, domdecOptions.numPmeRanks, gpusWereDetected);
1018 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1020 const PmeRunMode pmeRunMode = determinePmeRunMode(useGpuForPme, pmeFftTarget, *inputrec);
1022 // Initialize development feature flags that enabled by environment variable
1023 // and report those features that are enabled.
1024 const DevelopmentFeatureFlags devFlags =
1025 manageDevelopmentFeatures(mdlog, useGpuForNonbonded, pmeRunMode);
1027 const bool useModularSimulator = checkUseModularSimulator(false,
1034 doEssentialDynamics,
1035 membedHolder.doMembed());
1037 // Build restraints.
1038 // TODO: hide restraint implementation details from Mdrunner.
1039 // There is nothing unique about restraints at this point as far as the
1040 // Mdrunner is concerned. The Mdrunner should just be getting a sequence of
1041 // factory functions from the SimulationContext on which to call mdModules_->add().
1042 // TODO: capture all restraints into a single RestraintModule, passed to the runner builder.
1043 for (auto&& restraint : restraintManager_->getRestraints())
1045 auto module = RestraintMDModule::create(restraint, restraint->sites());
1046 mdModules_->add(std::move(module));
1049 // TODO: Error handling
1050 mdModules_->assignOptionsToModules(*inputrec->params, nullptr);
1051 // now that the MDModules know their options, they know which callbacks to sign up to
1052 mdModules_->subscribeToSimulationSetupNotifications();
1053 const auto& setupNotifier = mdModules_->notifiers().simulationSetupNotifier_;
1055 // Notify MdModules of existing logger
1056 setupNotifier.notify(mdlog);
1058 // Notify MdModules of internal parameters, saved into KVT
1059 if (inputrec->internalParameters != nullptr)
1061 setupNotifier.notify(*inputrec->internalParameters);
1064 // Let MdModules know the .tpr filename
1066 gmx::MdRunInputFilename mdRunInputFilename = { ftp2fn(efTPR, filenames.size(), filenames.data()) };
1067 setupNotifier.notify(mdRunInputFilename);
1070 if (fplog != nullptr)
1072 pr_inputrec(fplog, 0, "Input Parameters", inputrec.get(), FALSE);
1073 fprintf(fplog, "\n");
1078 /* In rerun, set velocities to zero if present */
1079 if (doRerun && ((globalState->flags & enumValueToBitMask(StateEntry::V)) != 0))
1081 // rerun does not use velocities
1085 "Rerun trajectory contains velocities. Rerun does only evaluate "
1086 "potential energy and forces. The velocities will be ignored.");
1087 for (int i = 0; i < globalState->natoms; i++)
1089 clear_rvec(globalState->v[i]);
1091 globalState->flags &= ~enumValueToBitMask(StateEntry::V);
1094 /* now make sure the state is initialized and propagated */
1095 set_state_entries(globalState.get(), inputrec.get(), useModularSimulator);
1098 /* NM and TPI parallelize over force/energy calculations, not atoms,
1099 * so we need to initialize and broadcast the global state.
1101 if (inputrec->eI == IntegrationAlgorithm::NM || inputrec->eI == IntegrationAlgorithm::TPI)
1105 globalState = std::make_unique<t_state>();
1107 broadcastStateWithoutDynamics(
1108 cr->mpiDefaultCommunicator, DOMAINDECOMP(cr), PAR(cr), globalState.get());
1111 /* A parallel command line option consistency check that we can
1112 only do after any threads have started. */
1114 && (domdecOptions.numCells[XX] > 1 || domdecOptions.numCells[YY] > 1
1115 || domdecOptions.numCells[ZZ] > 1 || domdecOptions.numPmeRanks > 0))
1118 "The -dd or -npme option request a parallel simulation, "
1120 "but %s was compiled without threads or MPI enabled",
1121 output_env_get_program_display_name(oenv));
1122 #elif GMX_THREAD_MPI
1123 "but the number of MPI-threads (option -ntmpi) is not set or is 1");
1125 "but %s was not started through mpirun/mpiexec or only one rank was requested "
1126 "through mpirun/mpiexec",
1127 output_env_get_program_display_name(oenv));
1131 if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || IntegrationAlgorithm::NM == inputrec->eI))
1134 "The .mdp file specified an energy mininization or normal mode algorithm, and "
1135 "these are not compatible with mdrun -rerun");
1138 /* NMR restraints must be initialized before load_checkpoint,
1139 * since with time averaging the history is added to t_state.
1140 * For proper consistency check we therefore need to extend
1142 * So the PME-only nodes (if present) will also initialize
1143 * the distance restraints.
1146 /* This needs to be called before read_checkpoint to extend the state */
1147 t_disresdata* disresdata;
1148 snew(disresdata, 1);
1152 DisResRunMode::MDRun,
1153 MASTER(cr) ? DDRole::Master : DDRole::Agent,
1154 PAR(cr) ? NumRanks::Multiple : NumRanks::Single,
1159 replExParams.exchangeInterval > 0);
1161 std::unique_ptr<t_oriresdata> oriresData;
1162 if (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0)
1164 oriresData = std::make_unique<t_oriresdata>(fplog, mtop, *inputrec, cr, ms, globalState.get());
1167 auto deform = prepareBoxDeformation(globalState != nullptr ? globalState->box : box,
1168 MASTER(cr) ? DDRole::Master : DDRole::Agent,
1169 PAR(cr) ? NumRanks::Multiple : NumRanks::Single,
1170 cr->mpi_comm_mygroup,
1174 /* We have to remember the generation's first step before reading checkpoint.
1175 This way, we can report to the F@H core both the generation's first step
1176 and the restored first step, thus making it able to distinguish between
1177 an interruption/resume and start of the n-th generation simulation.
1178 Having this information, the F@H core can correctly calculate and report
1181 int gen_first_step = 0;
1184 gen_first_step = inputrec->init_step;
1188 ObservablesHistory observablesHistory = {};
1190 auto modularSimulatorCheckpointData = std::make_unique<ReadCheckpointDataHolder>();
1191 if (startingBehavior != StartingBehavior::NewSimulation)
1193 /* Check if checkpoint file exists before doing continuation.
1194 * This way we can use identical input options for the first and subsequent runs...
1196 if (mdrunOptions.numStepsCommandline > -2)
1198 /* Temporarily set the number of steps to unlimited to avoid
1199 * triggering the nsteps check in load_checkpoint().
1200 * This hack will go away soon when the -nsteps option is removed.
1202 inputrec->nsteps = -1;
1205 // Finish applying initial simulation state information from external sources on all ranks.
1206 // Reconcile checkpoint file data with Mdrunner state established up to this point.
1207 applyLocalState(*inputHolder_.get(),
1210 domdecOptions.numCells,
1213 &observablesHistory,
1214 mdrunOptions.reproducible,
1215 mdModules_->notifiers(),
1216 modularSimulatorCheckpointData.get(),
1217 useModularSimulator);
1218 // TODO: (#3652) Synchronize filesystem state, SimulationInput contents, and program
1220 // on all code paths.
1221 // Write checkpoint or provide hook to update SimulationInput.
1222 // If there was a checkpoint file, SimulationInput contains more information
1223 // than if there wasn't. At this point, we have synchronized the in-memory
1224 // state with the filesystem state only for restarted simulations. We should
1225 // be calling applyLocalState unconditionally and expect that the completeness
1226 // of SimulationInput is not dependent on its creation method.
1228 if (startingBehavior == StartingBehavior::RestartWithAppending && logFileHandle)
1230 // Now we can start normal logging to the truncated log file.
1231 fplog = gmx_fio_getfp(logFileHandle);
1232 prepareLogAppending(fplog);
1233 logOwner = buildLogger(fplog, MASTER(cr));
1234 mdlog = logOwner.logger();
1241 fcRegisterSteps(inputrec->nsteps + inputrec->init_step, gen_first_step);
1245 if (mdrunOptions.numStepsCommandline > -2)
1250 "The -nsteps functionality is deprecated, and may be removed in a future "
1252 "Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp "
1255 /* override nsteps with value set on the commandline */
1256 override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec.get());
1258 if (isSimulationMasterRank)
1260 copy_mat(globalState->box, box);
1265 gmx_bcast(sizeof(box), box, cr->mpiDefaultCommunicator);
1268 if (inputrec->cutoff_scheme != CutoffScheme::Verlet)
1271 "This group-scheme .tpr file can no longer be run by mdrun. Please update to the "
1272 "Verlet scheme, or use an earlier version of GROMACS if necessary.");
1274 /* Update rlist and nstlist. */
1275 /* Note: prepare_verlet_scheme is calling increaseNstlist(...), which (while attempting to
1276 * increase rlist) tries to check if the newly chosen value fits with the DD scheme. As this is
1277 * run before any DD scheme is set up, this check is never executed. See #3334 for more details.
1279 prepare_verlet_scheme(fplog,
1285 useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes),
1288 // We need to decide on update groups early, as this affects
1289 // inter-domain communication distances.
1290 auto updateGroupingsPerMoleculeType = makeUpdateGroupingsPerMoleculeType(mtop);
1291 const real maxUpdateGroupRadius = computeMaxUpdateGroupRadius(
1292 mtop, updateGroupingsPerMoleculeType, maxReferenceTemperature(*inputrec));
1293 const real cutoffMargin = std::sqrt(max_cutoff2(inputrec->pbcType, box)) - inputrec->rlist;
1294 UpdateGroups updateGroups = makeUpdateGroups(mdlog,
1295 std::move(updateGroupingsPerMoleculeType),
1296 maxUpdateGroupRadius,
1297 useDomainDecomposition,
1298 systemHasConstraintsOrVsites(mtop),
1301 // This builder is necessary while we have multi-part construction
1302 // of DD. Before DD is constructed, we use the existence of
1303 // the builder object to indicate that further construction of DD
1305 std::unique_ptr<DomainDecompositionBuilder> ddBuilder;
1306 if (useDomainDecomposition)
1308 ddBuilder = std::make_unique<DomainDecompositionBuilder>(
1315 mdModules_->notifiers(),
1317 updateGroups.updateGroupingPerMoleculeType(),
1318 updateGroups.useUpdateGroups(),
1319 updateGroups.maxUpdateGroupRadius(),
1320 positionsFromStatePointer(globalState.get()),
1326 /* PME, if used, is done on all nodes with 1D decomposition */
1327 cr->nnodes = cr->sizeOfDefaultCommunicator;
1328 cr->sim_nodeid = cr->rankInDefaultCommunicator;
1329 cr->nodeid = cr->rankInDefaultCommunicator;
1331 cr->duty = (DUTY_PP | DUTY_PME);
1333 if (inputrec->pbcType == PbcType::Screw)
1335 gmx_fatal(FARGS, "pbc=screw is only implemented with domain decomposition");
1339 // Produce the task assignment for this rank - done after DD is constructed
1340 GpuTaskAssignments gpuTaskAssignments = GpuTaskAssignmentsBuilder::build(
1342 userGpuTaskAssignment,
1344 simulationCommunicator,
1352 thisRankHasDuty(cr, DUTY_PP),
1353 // TODO cr->duty & DUTY_PME should imply that a PME
1354 // algorithm is active, but currently does not.
1355 EEL_PME(inputrec->coulombtype) && thisRankHasDuty(cr, DUTY_PME));
1357 // Get the device handles for the modules, nullptr when no task is assigned.
1359 DeviceInformation* deviceInfo = gpuTaskAssignments.initDevice(&deviceId);
1361 // timing enabling - TODO put this in gpu_utils (even though generally this is just option handling?)
1362 bool useTiming = true;
1366 /* WARNING: CUDA timings are incorrect with multiple streams.
1367 * This is the main reason why they are disabled by default.
1369 // TODO: Consider turning on by default when we can detect nr of streams.
1370 useTiming = (getenv("GMX_ENABLE_GPU_TIMING") != nullptr);
1372 else if (GMX_GPU_OPENCL)
1374 useTiming = (getenv("GMX_DISABLE_GPU_TIMING") == nullptr);
1377 // TODO Currently this is always built, yet DD partition code
1378 // checks if it is built before using it. Probably it should
1379 // become an MDModule that is made only when another module
1380 // requires it (e.g. pull, CompEl, density fitting), so that we
1381 // don't update the local atom sets unilaterally every step.
1382 LocalAtomSetManager atomSets;
1385 // TODO Pass the GPU streams to ddBuilder to use in buffer
1386 // transfers (e.g. halo exchange)
1387 cr->dd = ddBuilder->build(&atomSets);
1388 // The builder's job is done, so destruct it
1389 ddBuilder.reset(nullptr);
1390 // Note that local state still does not exist yet.
1393 // The GPU update is decided here because we need to know whether the constraints or
1394 // SETTLEs can span accross the domain borders (i.e. whether or not update groups are
1395 // defined). This is only known after DD is initialized, hence decision on using GPU
1396 // update is done so late.
1399 const bool haveFrozenAtoms = inputrecFrozenAtoms(inputrec.get());
1401 useGpuForUpdate = decideWhetherToUseGpuForUpdate(useDomainDecomposition,
1402 updateGroups.useUpdateGroups(),
1404 domdecOptions.numPmeRanks > 0,
1410 doEssentialDynamics,
1411 gmx_mtop_ftype_count(mtop, F_ORIRES) > 0,
1417 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1419 const bool printHostName = (cr->nnodes > 1);
1420 gpuTaskAssignments.reportGpuUsage(mdlog, printHostName, useGpuForBonded, pmeRunMode, useGpuForUpdate);
1422 const bool disableNonbondedCalculation = (getenv("GMX_NO_NONBONDED") != nullptr);
1423 if (disableNonbondedCalculation)
1425 /* turn off non-bonded calculations */
1426 GMX_LOG(mdlog.warning)
1429 "Found environment variable GMX_NO_NONBONDED.\n"
1430 "Disabling nonbonded calculations.");
1433 MdrunScheduleWorkload runScheduleWork;
1435 bool useGpuDirectHalo = decideWhetherToUseGpuForHalo(devFlags,
1436 havePPDomainDecomposition(cr),
1438 useModularSimulator,
1440 EI_ENERGY_MINIMIZATION(inputrec->eI));
1442 // Also populates the simulation constant workload description.
1443 runScheduleWork.simulationWork = createSimulationWorkload(*inputrec,
1444 disableNonbondedCalculation,
1452 std::unique_ptr<DeviceStreamManager> deviceStreamManager = nullptr;
1454 if (deviceInfo != nullptr)
1456 if (DOMAINDECOMP(cr) && thisRankHasDuty(cr, DUTY_PP))
1458 dd_setup_dlb_resource_sharing(cr, deviceId);
1460 deviceStreamManager = std::make_unique<DeviceStreamManager>(
1461 *deviceInfo, havePPDomainDecomposition(cr), runScheduleWork.simulationWork, useTiming);
1464 // If the user chose a task assignment, give them some hints
1465 // where appropriate.
1466 if (!userGpuTaskAssignment.empty())
1468 gpuTaskAssignments.logPerformanceHints(mdlog, numAvailableDevices);
1473 /* After possible communicator splitting in make_dd_communicators.
1474 * we can set up the intra/inter node communication.
1476 gmx_setup_nodecomm(fplog, cr);
1482 GMX_LOG(mdlog.warning)
1484 .appendTextFormatted(
1485 "This is simulation %d out of %d running as a composite GROMACS\n"
1486 "multi-simulation job. Setup for this simulation:\n",
1487 ms->simulationIndex_,
1488 ms->numSimulations_);
1490 GMX_LOG(mdlog.warning)
1491 .appendTextFormatted("Using %d MPI %s\n",
1494 cr->nnodes == 1 ? "thread" : "threads"
1496 cr->nnodes == 1 ? "process" : "processes"
1502 // If mdrun -pin auto honors any affinity setting that already
1503 // exists. If so, it is nice to provide feedback about whether
1504 // that existing affinity setting was from OpenMP or something
1505 // else, so we run this code both before and after we initialize
1506 // the OpenMP support.
1507 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo_->nthreads_hw_avail, FALSE);
1508 /* Check and update the number of OpenMP threads requested */
1509 checkAndUpdateRequestedNumOpenmpThreads(
1510 &hw_opt, *hwinfo_, cr, ms, physicalNodeComm.size_, pmeRunMode, mtop, *inputrec);
1512 gmx_omp_nthreads_init(mdlog,
1514 hwinfo_->nthreads_hw_avail,
1515 physicalNodeComm.size_,
1516 hw_opt.nthreads_omp,
1517 hw_opt.nthreads_omp_pme,
1518 !thisRankHasDuty(cr, DUTY_PP));
1520 const bool bEnableFPE = gmxShouldEnableFPExceptions();
1521 // FIXME - reconcile with gmx_feenableexcept() call from CommandLineModuleManager::run()
1524 gmx_feenableexcept();
1527 /* Now that we know the setup is consistent, check for efficiency */
1528 check_resource_division_efficiency(
1529 hwinfo_, gpuTaskAssignments.thisRankHasAnyGpuTask(), mdrunOptions.ntompOptionIsSet, cr, mdlog);
1531 /* getting number of PP/PME threads on this MPI / tMPI rank.
1532 PME: env variable should be read only on one node to make sure it is
1533 identical everywhere;
1535 const int numThreadsOnThisRank = thisRankHasDuty(cr, DUTY_PP)
1536 ? gmx_omp_nthreads_get(ModuleMultiThread::Nonbonded)
1537 : gmx_omp_nthreads_get(ModuleMultiThread::Pme);
1538 checkHardwareOversubscription(
1539 numThreadsOnThisRank, cr->nodeid, *hwinfo_->hardwareTopology, physicalNodeComm, mdlog);
1541 // Enable Peer access between GPUs where available
1542 // Only for DD, only master PP rank needs to perform setup, and only if thread MPI plus
1543 // any of the GPU communication features are active.
1544 if (DOMAINDECOMP(cr) && MASTER(cr) && thisRankHasDuty(cr, DUTY_PP) && GMX_THREAD_MPI
1545 && (runScheduleWork.simulationWork.useGpuHaloExchange
1546 || runScheduleWork.simulationWork.useGpuPmePpCommunication))
1548 setupGpuDevicePeerAccess(gpuTaskAssignments.deviceIdsAssigned(), mdlog);
1551 if (hw_opt.threadAffinity != ThreadAffinity::Off)
1553 /* Before setting affinity, check whether the affinity has changed
1554 * - which indicates that probably the OpenMP library has changed it
1555 * since we first checked).
1557 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo_->nthreads_hw_avail, TRUE);
1559 int numThreadsOnThisNode, intraNodeThreadOffset;
1560 analyzeThreadsOnThisNode(
1561 physicalNodeComm, numThreadsOnThisRank, &numThreadsOnThisNode, &intraNodeThreadOffset);
1563 /* Set the CPU affinity */
1564 gmx_set_thread_affinity(mdlog,
1567 *hwinfo_->hardwareTopology,
1568 numThreadsOnThisRank,
1569 numThreadsOnThisNode,
1570 intraNodeThreadOffset,
1574 if (mdrunOptions.timingOptions.resetStep > -1)
1579 "The -resetstep functionality is deprecated, and may be removed in a "
1582 std::unique_ptr<gmx_wallcycle> wcycle =
1583 wallcycle_init(fplog, mdrunOptions.timingOptions.resetStep, cr);
1587 /* Master synchronizes its value of reset_counters with all nodes
1588 * including PME only nodes */
1589 int64_t reset_counters = wcycle_get_reset_counters(wcycle.get());
1590 gmx_bcast(sizeof(reset_counters), &reset_counters, cr->mpi_comm_mysim);
1591 wcycle_set_reset_counters(wcycle.get(), reset_counters);
1594 // Membrane embedding must be initialized before we call init_forcerec()
1595 membedHolder.initializeMembed(fplog,
1602 &mdrunOptions.checkpointOptions.period);
1604 const bool thisRankHasPmeGpuTask = gpuTaskAssignments.thisRankHasPmeGpuTask();
1605 std::unique_ptr<MDAtoms> mdAtoms;
1606 std::unique_ptr<VirtualSitesHandler> vsite;
1609 if (thisRankHasDuty(cr, DUTY_PP))
1611 setupNotifier.notify(*cr);
1612 setupNotifier.notify(&atomSets);
1613 setupNotifier.notify(mtop);
1614 setupNotifier.notify(inputrec->pbcType);
1615 setupNotifier.notify(SimulationTimeStep{ inputrec->delta_t });
1616 /* Initiate forcerecord */
1617 fr = std::make_unique<t_forcerec>();
1618 fr->forceProviders = mdModules_->initForceProviders();
1619 init_forcerec(fplog,
1621 runScheduleWork.simulationWork,
1627 opt2fn("-table", filenames.size(), filenames.data()),
1628 opt2fn("-tablep", filenames.size(), filenames.data()),
1629 opt2fns("-tableb", filenames.size(), filenames.data()),
1631 // Dirty hack, for fixing disres and orires should be made mdmodules
1632 fr->fcdata->disres = disresdata;
1633 fr->fcdata->orires.swap(oriresData);
1635 // Save a handle to device stream manager to use elsewhere in the code
1636 // TODO: Forcerec is not a correct place to store it.
1637 fr->deviceStreamManager = deviceStreamManager.get();
1639 if (runScheduleWork.simulationWork.useGpuPmePpCommunication && !thisRankHasDuty(cr, DUTY_PME))
1642 deviceStreamManager != nullptr,
1643 "GPU device stream manager should be valid in order to use PME-PP direct "
1646 deviceStreamManager->streamIsValid(DeviceStreamType::PmePpTransfer),
1647 "GPU PP-PME stream should be valid in order to use GPU PME-PP direct "
1649 fr->pmePpCommGpu = std::make_unique<gmx::PmePpCommGpu>(
1652 cr->dd->pmeForceReceiveBuffer,
1653 deviceStreamManager->context(),
1654 deviceStreamManager->stream(DeviceStreamType::PmePpTransfer));
1657 fr->nbv = Nbnxm::init_nb_verlet(mdlog,
1662 runScheduleWork.simulationWork.useGpuNonbonded,
1663 deviceStreamManager.get(),
1667 // TODO: Move the logic below to a GPU bonded builder
1668 if (runScheduleWork.simulationWork.useGpuBonded)
1670 GMX_RELEASE_ASSERT(deviceStreamManager != nullptr,
1671 "GPU device stream manager should be valid in order to use GPU "
1672 "version of bonded forces.");
1673 fr->listedForcesGpu = std::make_unique<ListedForcesGpu>(
1675 fr->ic->epsfac * fr->fudgeQQ,
1676 deviceStreamManager->context(),
1677 deviceStreamManager->bondedStream(havePPDomainDecomposition(cr)),
1681 /* Initialize the mdAtoms structure.
1682 * mdAtoms is not filled with atom data,
1683 * as this can not be done now with domain decomposition.
1685 mdAtoms = makeMDAtoms(fplog, mtop, *inputrec, thisRankHasPmeGpuTask);
1686 if (globalState && thisRankHasPmeGpuTask)
1688 // The pinning of coordinates in the global state object works, because we only use
1689 // PME on GPU without DD or on a separate PME rank, and because the local state pointer
1690 // points to the global state object without DD.
1691 // FIXME: MD and EM separately set up the local state - this should happen in the same
1692 // function, which should also perform the pinning.
1693 changePinningPolicy(&globalState->x, pme_get_pinning_policy());
1696 /* Initialize the virtual site communication */
1697 vsite = makeVirtualSitesHandler(
1698 mtop, cr, fr->pbcType, updateGroups.updateGroupingPerMoleculeType());
1700 calc_shifts(box, fr->shift_vec);
1702 /* With periodic molecules the charge groups should be whole at start up
1703 * and the virtual sites should not be far from their proper positions.
1705 if (!inputrec->bContinuation && MASTER(cr)
1706 && !(inputrec->pbcType != PbcType::No && inputrec->bPeriodicMols))
1708 /* Make molecules whole at start of run */
1709 if (fr->pbcType != PbcType::No)
1711 do_pbc_first_mtop(fplog, inputrec->pbcType, box, &mtop, globalState->x.rvec_array());
1715 /* Correct initial vsite positions are required
1716 * for the initial distribution in the domain decomposition
1717 * and for the initial shell prediction.
1719 constructVirtualSitesGlobal(mtop, globalState->x);
1722 // Make the DD reverse topology, now that any vsites that are present are available
1723 if (DOMAINDECOMP(cr))
1725 dd_make_reverse_top(fplog, cr->dd, mtop, vsite.get(), *inputrec, domdecOptions.ddBondedChecking);
1728 if (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
1730 ewaldcoeff_q = fr->ic->ewaldcoeff_q;
1731 ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
1736 /* This is a PME only node */
1738 GMX_ASSERT(globalState == nullptr,
1739 "We don't need the state on a PME only rank and expect it to be unitialized");
1741 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
1742 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
1745 gmx_pme_t* sepPmeData = nullptr;
1746 // This reference hides the fact that PME data is owned by runner on PME-only ranks and by forcerec on other ranks
1747 GMX_ASSERT(thisRankHasDuty(cr, DUTY_PP) == (fr != nullptr),
1748 "Double-checking that only PME-only ranks have no forcerec");
1749 gmx_pme_t*& pmedata = fr ? fr->pmedata : sepPmeData;
1751 // TODO should live in ewald module once its testing is improved
1753 // Later, this program could contain kernels that might be later
1754 // re-used as auto-tuning progresses, or subsequent simulations
1756 PmeGpuProgramStorage pmeGpuProgram;
1757 if (thisRankHasPmeGpuTask)
1760 (deviceStreamManager != nullptr),
1761 "GPU device stream manager should be initialized in order to use GPU for PME.");
1762 GMX_RELEASE_ASSERT((deviceInfo != nullptr),
1763 "GPU device should be initialized in order to use GPU for PME.");
1764 pmeGpuProgram = buildPmeGpuProgram(deviceStreamManager->context());
1767 /* Initiate PME if necessary,
1768 * either on all nodes or on dedicated PME nodes only. */
1769 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
1771 if (mdAtoms && mdAtoms->mdatoms())
1773 nChargePerturbed = mdAtoms->mdatoms()->nChargePerturbed;
1774 if (EVDW_PME(inputrec->vdwtype))
1776 nTypePerturbed = mdAtoms->mdatoms()->nTypePerturbed;
1779 if (cr->npmenodes > 0)
1781 /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
1782 gmx_bcast(sizeof(nChargePerturbed), &nChargePerturbed, cr->mpi_comm_mysim);
1783 gmx_bcast(sizeof(nTypePerturbed), &nTypePerturbed, cr->mpi_comm_mysim);
1786 if (thisRankHasDuty(cr, DUTY_PME))
1790 // TODO: This should be in the builder.
1791 GMX_RELEASE_ASSERT(!runScheduleWork.simulationWork.useGpuPme
1792 || (deviceStreamManager != nullptr),
1793 "Device stream manager should be valid in order to use GPU "
1796 !runScheduleWork.simulationWork.useGpuPme
1797 || deviceStreamManager->streamIsValid(DeviceStreamType::Pme),
1798 "GPU PME stream should be valid in order to use GPU version of PME.");
1800 const DeviceContext* deviceContext = runScheduleWork.simulationWork.useGpuPme
1801 ? &deviceStreamManager->context()
1803 const DeviceStream* pmeStream =
1804 runScheduleWork.simulationWork.useGpuPme
1805 ? &deviceStreamManager->stream(DeviceStreamType::Pme)
1808 pmedata = gmx_pme_init(cr,
1809 getNumPmeDomains(cr->dd),
1811 nChargePerturbed != 0,
1812 nTypePerturbed != 0,
1813 mdrunOptions.reproducible,
1816 gmx_omp_nthreads_get(ModuleMultiThread::Pme),
1821 pmeGpuProgram.get(),
1824 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1829 if (EI_DYNAMICS(inputrec->eI))
1831 /* Turn on signal handling on all nodes */
1833 * (A user signal from the PME nodes (if any)
1834 * is communicated to the PP nodes.
1836 signal_handler_install();
1839 pull_t* pull_work = nullptr;
1840 if (thisRankHasDuty(cr, DUTY_PP))
1842 /* Assumes uniform use of the number of OpenMP threads */
1843 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(ModuleMultiThread::Default));
1845 if (inputrec->bPull)
1847 /* Initialize pull code */
1848 pull_work = init_pull(fplog,
1849 inputrec->pull.get(),
1854 inputrec->fepvals->init_lambda);
1855 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
1857 initPullHistory(pull_work, &observablesHistory);
1859 if (EI_DYNAMICS(inputrec->eI) && MASTER(cr))
1861 init_pull_output_files(pull_work, filenames.size(), filenames.data(), oenv, startingBehavior);
1865 std::unique_ptr<EnforcedRotation> enforcedRotation;
1868 /* Initialize enforced rotation code */
1869 enforcedRotation = init_rot(fplog,
1882 t_swap* swap = nullptr;
1883 if (inputrec->eSwapCoords != SwapType::No)
1885 /* Initialize ion swapping code */
1886 swap = init_swapcoords(fplog,
1888 opt2fn_master("-swap", filenames.size(), filenames.data(), cr),
1891 &observablesHistory,
1899 /* Let makeConstraints know whether we have essential dynamics constraints. */
1900 auto constr = makeConstraints(mtop,
1903 doEssentialDynamics,
1906 updateGroups.useUpdateGroups(),
1912 /* Energy terms and groups */
1913 gmx_enerdata_t enerd(mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
1914 inputrec->fepvals->n_lambda);
1916 // cos acceleration is only supported by md, but older tpr
1917 // files might still combine it with other integrators
1918 GMX_RELEASE_ASSERT(inputrec->cos_accel == 0.0 || inputrec->eI == IntegrationAlgorithm::MD,
1919 "cos_acceleration is only supported by integrator=md");
1921 /* Kinetic energy data */
1922 gmx_ekindata_t ekind(inputrec->opts.ngtc,
1923 inputrec->cos_accel,
1924 gmx_omp_nthreads_get(ModuleMultiThread::Update));
1926 /* Set up interactive MD (IMD) */
1927 auto imdSession = makeImdSession(inputrec.get(),
1934 MASTER(cr) ? globalState->x : gmx::ArrayRef<gmx::RVec>(),
1938 mdrunOptions.imdOptions,
1941 if (DOMAINDECOMP(cr))
1943 GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
1944 /* This call is not included in init_domain_decomposition
1945 * because fr->atomInfoForEachMoleculeBlock is set later.
1947 makeBondedLinks(cr->dd, mtop, fr->atomInfoForEachMoleculeBlock);
1950 if (runScheduleWork.simulationWork.useGpuBufferOps)
1952 fr->gpuForceReduction[gmx::AtomLocality::Local] = std::make_unique<gmx::GpuForceReduction>(
1953 deviceStreamManager->context(),
1954 deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedLocal),
1956 fr->gpuForceReduction[gmx::AtomLocality::NonLocal] = std::make_unique<gmx::GpuForceReduction>(
1957 deviceStreamManager->context(),
1958 deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedNonLocal),
1962 std::unique_ptr<gmx::StatePropagatorDataGpu> stateGpu;
1963 if (gpusWereDetected
1964 && ((runScheduleWork.simulationWork.useGpuPme && thisRankHasDuty(cr, DUTY_PME))
1965 || runScheduleWork.simulationWork.useGpuBufferOps))
1967 GpuApiCallBehavior transferKind =
1968 (inputrec->eI == IntegrationAlgorithm::MD && !doRerun && !useModularSimulator)
1969 ? GpuApiCallBehavior::Async
1970 : GpuApiCallBehavior::Sync;
1971 GMX_RELEASE_ASSERT(deviceStreamManager != nullptr,
1972 "GPU device stream manager should be initialized to use GPU.");
1973 stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(
1974 *deviceStreamManager, transferKind, pme_gpu_get_block_size(fr->pmedata), wcycle.get());
1975 fr->stateGpu = stateGpu.get();
1978 GMX_ASSERT(stopHandlerBuilder_, "Runner must provide StopHandlerBuilder to simulator.");
1979 SimulatorBuilder simulatorBuilder;
1981 simulatorBuilder.add(SimulatorStateData(globalState.get(), &observablesHistory, &enerd, &ekind));
1982 simulatorBuilder.add(std::move(membedHolder));
1983 simulatorBuilder.add(std::move(stopHandlerBuilder_));
1984 simulatorBuilder.add(SimulatorConfig(mdrunOptions, startingBehavior, &runScheduleWork));
1987 simulatorBuilder.add(SimulatorEnv(fplog, cr, ms, mdlog, oenv));
1988 simulatorBuilder.add(Profiling(&nrnb, walltime_accounting, wcycle.get()));
1989 simulatorBuilder.add(ConstraintsParam(
1990 constr.get(), enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr, vsite.get()));
1991 // TODO: Separate `fr` to a separate add, and make the `build` handle the coupling sensibly.
1992 simulatorBuilder.add(LegacyInput(
1993 static_cast<int>(filenames.size()), filenames.data(), inputrec.get(), fr.get()));
1994 simulatorBuilder.add(ReplicaExchangeParameters(replExParams));
1995 simulatorBuilder.add(InteractiveMD(imdSession.get()));
1996 simulatorBuilder.add(SimulatorModules(mdModules_->outputProvider(), mdModules_->notifiers()));
1997 simulatorBuilder.add(CenterOfMassPulling(pull_work));
1998 // Todo move to an MDModule
1999 simulatorBuilder.add(IonSwapping(swap));
2000 simulatorBuilder.add(TopologyData(mtop, mdAtoms.get()));
2001 simulatorBuilder.add(BoxDeformationHandle(deform.get()));
2002 simulatorBuilder.add(std::move(modularSimulatorCheckpointData));
2004 // build and run simulator object based on user-input
2005 auto simulator = simulatorBuilder.build(useModularSimulator);
2008 if (fr->pmePpCommGpu)
2010 // destroy object since it is no longer required. (This needs to be done while the GPU context still exists.)
2011 fr->pmePpCommGpu.reset();
2014 if (inputrec->bPull)
2016 finish_pull(pull_work);
2018 finish_swapcoords(swap);
2022 GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
2024 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(ModuleMultiThread::Pme));
2025 gmx_pmeonly(pmedata,
2029 walltime_accounting,
2032 runScheduleWork.simulationWork.useGpuPmePpCommunication,
2033 deviceStreamManager.get());
2036 wallcycle_stop(wcycle.get(), WallCycleCounter::Run);
2038 /* Finish up, write some stuff
2039 * if rerunMD, don't write last frame again
2047 walltime_accounting,
2048 fr ? fr->nbv.get() : nullptr,
2050 EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
2053 deviceStreamManager.reset(nullptr);
2057 gmx_pme_destroy(pmedata);
2061 // FIXME: this is only here to manually unpin mdAtoms->chargeA_ and state->x,
2062 // before we destroy the GPU context(s)
2063 // Pinned buffers are associated with contexts in CUDA.
2064 // As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
2065 mdAtoms.reset(nullptr);
2066 globalState.reset(nullptr);
2067 mdModules_.reset(nullptr); // destruct force providers here as they might also use the GPU
2068 fr.reset(nullptr); // destruct forcerec before gpu
2069 // TODO convert to C++ so we can get rid of these frees
2072 if (!hwinfo_->deviceInfoList.empty())
2074 /* stop the GPU profiler (only CUDA) */
2078 /* With tMPI we need to wait for all ranks to finish deallocation before
2079 * destroying the CUDA context as some tMPI ranks may be sharing
2082 * This is not a concern in OpenCL where we use one context per rank.
2084 * Note: it is safe to not call the barrier on the ranks which do not use GPU,
2085 * but it is easier and more futureproof to call it on the whole node.
2087 * Note that this function needs to be called even if GPUs are not used
2088 * in this run because the PME ranks have no knowledge of whether GPUs
2089 * are used or not, but all ranks need to enter the barrier below.
2090 * \todo Remove this physical node barrier after making sure
2091 * that it's not needed anymore (with a shared GPU run).
2095 physicalNodeComm.barrier();
2098 if (!devFlags.usingCudaAwareMpi)
2100 // Don't reset GPU in case of CUDA-AWARE MPI
2101 // UCX creates CUDA buffers which are cleaned-up as part of MPI_Finalize()
2102 // resetting the device before MPI_Finalize() results in crashes inside UCX
2103 releaseDevice(deviceInfo);
2106 /* Does what it says */
2107 print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
2108 walltime_accounting_destroy(walltime_accounting);
2110 // Ensure log file content is written
2113 gmx_fio_flush(logFileHandle);
2116 /* Reset FPEs (important for unit tests) by disabling them. Assumes no
2117 * exceptions were enabled before function was called. */
2120 gmx_fedisableexcept();
2123 auto rc = static_cast<int>(gmx_get_stop_condition());
2126 /* we need to join all threads. The sub-threads join when they
2127 exit this function, but the master thread needs to be told to
2137 Mdrunner::~Mdrunner()
2139 // Clean up of the Manager.
2140 // This will end up getting called on every thread-MPI rank, which is unnecessary,
2141 // but okay as long as threads synchronize some time before adding or accessing
2142 // a new set of restraints.
2143 if (restraintManager_)
2145 restraintManager_->clear();
2146 GMX_ASSERT(restraintManager_->countRestraints() == 0,
2147 "restraints added during runner life time should be cleared at runner "
2152 void Mdrunner::addPotential(std::shared_ptr<gmx::IRestraintPotential> puller, const std::string& name)
2154 GMX_ASSERT(restraintManager_, "Mdrunner must have a restraint manager.");
2155 // Not sure if this should be logged through the md logger or something else,
2156 // but it is helpful to have some sort of INFO level message sent somewhere.
2157 // std::cout << "Registering restraint named " << name << std::endl;
2159 // When multiple restraints are used, it may be wasteful to register them separately.
2160 // Maybe instead register an entire Restraint Manager as a force provider.
2161 restraintManager_->addToSpec(std::move(puller), name);
2164 Mdrunner::Mdrunner(std::unique_ptr<MDModules> mdModules) : mdModules_(std::move(mdModules)) {}
2166 Mdrunner::Mdrunner(Mdrunner&&) noexcept = default;
2168 //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265 in CentOS 7
2169 Mdrunner& Mdrunner::operator=(Mdrunner&& /*handle*/) noexcept(BUGFREE_NOEXCEPT_STRING) = default;
2171 class Mdrunner::BuilderImplementation
2174 BuilderImplementation() = delete;
2175 BuilderImplementation(std::unique_ptr<MDModules> mdModules, compat::not_null<SimulationContext*> context);
2176 ~BuilderImplementation();
2178 BuilderImplementation& setExtraMdrunOptions(const MdrunOptions& options,
2179 real forceWarningThreshold,
2180 StartingBehavior startingBehavior);
2182 void addHardwareDetectionResult(const gmx_hw_info_t* hwinfo);
2184 void addDomdec(const DomdecOptions& options);
2186 void addInput(SimulationInputHandle inputHolder);
2188 void addVerletList(int nstlist);
2190 void addReplicaExchange(const ReplicaExchangeParameters& params);
2192 void addNonBonded(const char* nbpu_opt);
2194 void addPME(const char* pme_opt_, const char* pme_fft_opt_);
2196 void addBondedTaskAssignment(const char* bonded_opt);
2198 void addUpdateTaskAssignment(const char* update_opt);
2200 void addHardwareOptions(const gmx_hw_opt_t& hardwareOptions);
2202 void addFilenames(ArrayRef<const t_filenm> filenames);
2204 void addOutputEnvironment(gmx_output_env_t* outputEnvironment);
2206 void addLogFile(t_fileio* logFileHandle);
2208 void addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
2213 // Default parameters copied from runner.h
2214 // \todo Clarify source(s) of default parameters.
2216 const char* nbpu_opt_ = nullptr;
2217 const char* pme_opt_ = nullptr;
2218 const char* pme_fft_opt_ = nullptr;
2219 const char* bonded_opt_ = nullptr;
2220 const char* update_opt_ = nullptr;
2222 MdrunOptions mdrunOptions_;
2224 DomdecOptions domdecOptions_;
2226 ReplicaExchangeParameters replicaExchangeParameters_;
2228 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
2231 //! World communicator, used for hardware detection and task assignment
2232 MPI_Comm libraryWorldCommunicator_ = MPI_COMM_NULL;
2234 //! Multisim communicator handle.
2235 gmx_multisim_t* multiSimulation_;
2237 //! mdrun communicator
2238 MPI_Comm simulationCommunicator_ = MPI_COMM_NULL;
2240 //! Print a warning if any force is larger than this (in kJ/mol nm).
2241 real forceWarningThreshold_ = -1;
2243 //! Whether the simulation will start afresh, or restart with/without appending.
2244 StartingBehavior startingBehavior_ = StartingBehavior::NewSimulation;
2246 //! The modules that comprise the functionality of mdrun.
2247 std::unique_ptr<MDModules> mdModules_;
2249 //! Detected hardware.
2250 const gmx_hw_info_t* hwinfo_ = nullptr;
2252 //! \brief Parallelism information.
2253 gmx_hw_opt_t hardwareOptions_;
2255 //! filename options for simulation.
2256 ArrayRef<const t_filenm> filenames_;
2258 /*! \brief Handle to output environment.
2260 * \todo gmx_output_env_t needs lifetime management.
2262 gmx_output_env_t* outputEnvironment_ = nullptr;
2264 /*! \brief Non-owning handle to MD log file.
2266 * \todo Context should own output facilities for client.
2267 * \todo Improve log file handle management.
2269 * Code managing the FILE* relies on the ability to set it to
2270 * nullptr to check whether the filehandle is valid.
2272 t_fileio* logFileHandle_ = nullptr;
2275 * \brief Builder for simulation stop signal handler.
2277 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_ = nullptr;
2280 * \brief Sources for initial simulation state.
2282 * See issue #3652 for near-term refinements to the SimulationInput interface.
2284 * See issue #3379 for broader discussion on API aspects of simulation inputs and outputs.
2286 SimulationInputHandle inputHolder_;
2289 Mdrunner::BuilderImplementation::BuilderImplementation(std::unique_ptr<MDModules> mdModules,
2290 compat::not_null<SimulationContext*> context) :
2291 mdModules_(std::move(mdModules))
2293 libraryWorldCommunicator_ = context->libraryWorldCommunicator_;
2294 simulationCommunicator_ = context->simulationCommunicator_;
2295 multiSimulation_ = context->multiSimulation_.get();
2298 Mdrunner::BuilderImplementation::~BuilderImplementation() = default;
2300 Mdrunner::BuilderImplementation&
2301 Mdrunner::BuilderImplementation::setExtraMdrunOptions(const MdrunOptions& options,
2302 const real forceWarningThreshold,
2303 const StartingBehavior startingBehavior)
2305 mdrunOptions_ = options;
2306 forceWarningThreshold_ = forceWarningThreshold;
2307 startingBehavior_ = startingBehavior;
2311 void Mdrunner::BuilderImplementation::addDomdec(const DomdecOptions& options)
2313 domdecOptions_ = options;
2316 void Mdrunner::BuilderImplementation::addVerletList(int nstlist)
2321 void Mdrunner::BuilderImplementation::addReplicaExchange(const ReplicaExchangeParameters& params)
2323 replicaExchangeParameters_ = params;
2326 Mdrunner Mdrunner::BuilderImplementation::build()
2328 auto newRunner = Mdrunner(std::move(mdModules_));
2330 newRunner.mdrunOptions = mdrunOptions_;
2331 newRunner.pforce = forceWarningThreshold_;
2332 newRunner.startingBehavior = startingBehavior_;
2333 newRunner.domdecOptions = domdecOptions_;
2335 // \todo determine an invariant to check or confirm that all gmx_hw_opt_t objects are valid
2336 newRunner.hw_opt = hardwareOptions_;
2338 // No invariant to check. This parameter exists to optionally override other behavior.
2339 newRunner.nstlist_cmdline = nstlist_;
2341 newRunner.replExParams = replicaExchangeParameters_;
2343 newRunner.filenames = filenames_;
2345 newRunner.libraryWorldCommunicator = libraryWorldCommunicator_;
2347 newRunner.simulationCommunicator = simulationCommunicator_;
2349 // nullptr is a valid value for the multisim handle
2350 newRunner.ms = multiSimulation_;
2354 newRunner.hwinfo_ = hwinfo_;
2358 GMX_THROW(gmx::APIError(
2359 "MdrunnerBuilder::addHardwareDetectionResult() is required before build()"));
2364 newRunner.inputHolder_ = std::move(inputHolder_);
2368 GMX_THROW(gmx::APIError("MdrunnerBuilder::addInput() is required before build()."));
2371 // \todo Clarify ownership and lifetime management for gmx_output_env_t
2372 // \todo Update sanity checking when output environment has clearly specified invariants.
2373 // Initialization and default values for oenv are not well specified in the current version.
2374 if (outputEnvironment_)
2376 newRunner.oenv = outputEnvironment_;
2380 GMX_THROW(gmx::APIError(
2381 "MdrunnerBuilder::addOutputEnvironment() is required before build()"));
2384 newRunner.logFileHandle = logFileHandle_;
2388 newRunner.nbpu_opt = nbpu_opt_;
2392 GMX_THROW(gmx::APIError("MdrunnerBuilder::addNonBonded() is required before build()"));
2395 if (pme_opt_ && pme_fft_opt_)
2397 newRunner.pme_opt = pme_opt_;
2398 newRunner.pme_fft_opt = pme_fft_opt_;
2402 GMX_THROW(gmx::APIError("MdrunnerBuilder::addElectrostatics() is required before build()"));
2407 newRunner.bonded_opt = bonded_opt_;
2411 GMX_THROW(gmx::APIError(
2412 "MdrunnerBuilder::addBondedTaskAssignment() is required before build()"));
2417 newRunner.update_opt = update_opt_;
2421 GMX_THROW(gmx::APIError(
2422 "MdrunnerBuilder::addUpdateTaskAssignment() is required before build() "));
2426 newRunner.restraintManager_ = std::make_unique<gmx::RestraintManager>();
2428 if (stopHandlerBuilder_)
2430 newRunner.stopHandlerBuilder_ = std::move(stopHandlerBuilder_);
2434 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>();
2440 void Mdrunner::BuilderImplementation::addHardwareDetectionResult(const gmx_hw_info_t* hwinfo)
2445 void Mdrunner::BuilderImplementation::addNonBonded(const char* nbpu_opt)
2447 nbpu_opt_ = nbpu_opt;
2450 void Mdrunner::BuilderImplementation::addPME(const char* pme_opt, const char* pme_fft_opt)
2453 pme_fft_opt_ = pme_fft_opt;
2456 void Mdrunner::BuilderImplementation::addBondedTaskAssignment(const char* bonded_opt)
2458 bonded_opt_ = bonded_opt;
2461 void Mdrunner::BuilderImplementation::addUpdateTaskAssignment(const char* update_opt)
2463 update_opt_ = update_opt;
2466 void Mdrunner::BuilderImplementation::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2468 hardwareOptions_ = hardwareOptions;
2471 void Mdrunner::BuilderImplementation::addFilenames(ArrayRef<const t_filenm> filenames)
2473 filenames_ = filenames;
2476 void Mdrunner::BuilderImplementation::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2478 outputEnvironment_ = outputEnvironment;
2481 void Mdrunner::BuilderImplementation::addLogFile(t_fileio* logFileHandle)
2483 logFileHandle_ = logFileHandle;
2486 void Mdrunner::BuilderImplementation::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2488 stopHandlerBuilder_ = std::move(builder);
2491 void Mdrunner::BuilderImplementation::addInput(SimulationInputHandle inputHolder)
2493 inputHolder_ = std::move(inputHolder);
2496 MdrunnerBuilder::MdrunnerBuilder(std::unique_ptr<MDModules> mdModules,
2497 compat::not_null<SimulationContext*> context) :
2498 impl_{ std::make_unique<Mdrunner::BuilderImplementation>(std::move(mdModules), context) }
2502 MdrunnerBuilder::~MdrunnerBuilder() = default;
2504 MdrunnerBuilder& MdrunnerBuilder::addHardwareDetectionResult(const gmx_hw_info_t* hwinfo)
2506 impl_->addHardwareDetectionResult(hwinfo);
2510 MdrunnerBuilder& MdrunnerBuilder::addSimulationMethod(const MdrunOptions& options,
2511 real forceWarningThreshold,
2512 const StartingBehavior startingBehavior)
2514 impl_->setExtraMdrunOptions(options, forceWarningThreshold, startingBehavior);
2518 MdrunnerBuilder& MdrunnerBuilder::addDomainDecomposition(const DomdecOptions& options)
2520 impl_->addDomdec(options);
2524 MdrunnerBuilder& MdrunnerBuilder::addNeighborList(int nstlist)
2526 impl_->addVerletList(nstlist);
2530 MdrunnerBuilder& MdrunnerBuilder::addReplicaExchange(const ReplicaExchangeParameters& params)
2532 impl_->addReplicaExchange(params);
2536 MdrunnerBuilder& MdrunnerBuilder::addNonBonded(const char* nbpu_opt)
2538 impl_->addNonBonded(nbpu_opt);
2542 MdrunnerBuilder& MdrunnerBuilder::addElectrostatics(const char* pme_opt, const char* pme_fft_opt)
2544 // The builder method may become more general in the future, but in this version,
2545 // parameters for PME electrostatics are both required and the only parameters
2547 if (pme_opt && pme_fft_opt)
2549 impl_->addPME(pme_opt, pme_fft_opt);
2554 gmx::InvalidInputError("addElectrostatics() arguments must be non-null pointers."));
2559 MdrunnerBuilder& MdrunnerBuilder::addBondedTaskAssignment(const char* bonded_opt)
2561 impl_->addBondedTaskAssignment(bonded_opt);
2565 MdrunnerBuilder& MdrunnerBuilder::addUpdateTaskAssignment(const char* update_opt)
2567 impl_->addUpdateTaskAssignment(update_opt);
2571 Mdrunner MdrunnerBuilder::build()
2573 return impl_->build();
2576 MdrunnerBuilder& MdrunnerBuilder::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2578 impl_->addHardwareOptions(hardwareOptions);
2582 MdrunnerBuilder& MdrunnerBuilder::addFilenames(ArrayRef<const t_filenm> filenames)
2584 impl_->addFilenames(filenames);
2588 MdrunnerBuilder& MdrunnerBuilder::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2590 impl_->addOutputEnvironment(outputEnvironment);
2594 MdrunnerBuilder& MdrunnerBuilder::addLogFile(t_fileio* logFileHandle)
2596 impl_->addLogFile(logFileHandle);
2600 MdrunnerBuilder& MdrunnerBuilder::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2602 impl_->addStopHandlerBuilder(std::move(builder));
2606 MdrunnerBuilder& MdrunnerBuilder::addInput(SimulationInputHandle input)
2608 impl_->addInput(std::move(input));
2612 MdrunnerBuilder::MdrunnerBuilder(MdrunnerBuilder&&) noexcept = default;
2614 MdrunnerBuilder& MdrunnerBuilder::operator=(MdrunnerBuilder&&) noexcept = default;