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39 * \brief Implements the MD runner routine calling all integrators.
41 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
42 * \ingroup module_mdrun
59 #include "gromacs/commandline/filenm.h"
60 #include "gromacs/domdec/builder.h"
61 #include "gromacs/domdec/domdec.h"
62 #include "gromacs/domdec/domdec_struct.h"
63 #include "gromacs/domdec/gpuhaloexchange.h"
64 #include "gromacs/domdec/localatomsetmanager.h"
65 #include "gromacs/domdec/partition.h"
66 #include "gromacs/ewald/ewald_utils.h"
67 #include "gromacs/ewald/pme_gpu_program.h"
68 #include "gromacs/ewald/pme_only.h"
69 #include "gromacs/ewald/pme_pp_comm_gpu.h"
70 #include "gromacs/fileio/checkpoint.h"
71 #include "gromacs/fileio/gmxfio.h"
72 #include "gromacs/fileio/oenv.h"
73 #include "gromacs/fileio/tpxio.h"
74 #include "gromacs/gmxlib/network.h"
75 #include "gromacs/gmxlib/nrnb.h"
76 #include "gromacs/gpu_utils/device_stream_manager.h"
77 #include "gromacs/hardware/cpuinfo.h"
78 #include "gromacs/hardware/detecthardware.h"
79 #include "gromacs/hardware/device_management.h"
80 #include "gromacs/hardware/hardwaretopology.h"
81 #include "gromacs/hardware/printhardware.h"
82 #include "gromacs/imd/imd.h"
83 #include "gromacs/listed_forces/disre.h"
84 #include "gromacs/listed_forces/gpubonded.h"
85 #include "gromacs/listed_forces/listed_forces.h"
86 #include "gromacs/listed_forces/orires.h"
87 #include "gromacs/math/functions.h"
88 #include "gromacs/math/utilities.h"
89 #include "gromacs/math/vec.h"
90 #include "gromacs/mdlib/boxdeformation.h"
91 #include "gromacs/mdlib/broadcaststructs.h"
92 #include "gromacs/mdlib/calc_verletbuf.h"
93 #include "gromacs/mdlib/dispersioncorrection.h"
94 #include "gromacs/mdlib/enerdata_utils.h"
95 #include "gromacs/mdlib/force.h"
96 #include "gromacs/mdlib/forcerec.h"
97 #include "gromacs/mdlib/gmx_omp_nthreads.h"
98 #include "gromacs/mdlib/gpuforcereduction.h"
99 #include "gromacs/mdlib/makeconstraints.h"
100 #include "gromacs/mdlib/md_support.h"
101 #include "gromacs/mdlib/mdatoms.h"
102 #include "gromacs/mdlib/sighandler.h"
103 #include "gromacs/mdlib/stophandler.h"
104 #include "gromacs/mdlib/tgroup.h"
105 #include "gromacs/mdlib/updategroups.h"
106 #include "gromacs/mdlib/vsite.h"
107 #include "gromacs/mdrun/mdmodules.h"
108 #include "gromacs/mdrun/simulationcontext.h"
109 #include "gromacs/mdrun/simulationinput.h"
110 #include "gromacs/mdrun/simulationinputhandle.h"
111 #include "gromacs/mdrunutility/handlerestart.h"
112 #include "gromacs/mdrunutility/logging.h"
113 #include "gromacs/mdrunutility/multisim.h"
114 #include "gromacs/mdrunutility/printtime.h"
115 #include "gromacs/mdrunutility/threadaffinity.h"
116 #include "gromacs/mdtypes/checkpointdata.h"
117 #include "gromacs/mdtypes/commrec.h"
118 #include "gromacs/mdtypes/enerdata.h"
119 #include "gromacs/mdtypes/fcdata.h"
120 #include "gromacs/mdtypes/forcerec.h"
121 #include "gromacs/mdtypes/group.h"
122 #include "gromacs/mdtypes/inputrec.h"
123 #include "gromacs/mdtypes/interaction_const.h"
124 #include "gromacs/mdtypes/md_enums.h"
125 #include "gromacs/mdtypes/mdatom.h"
126 #include "gromacs/mdtypes/mdrunoptions.h"
127 #include "gromacs/mdtypes/observableshistory.h"
128 #include "gromacs/mdtypes/simulation_workload.h"
129 #include "gromacs/mdtypes/state.h"
130 #include "gromacs/mdtypes/state_propagator_data_gpu.h"
131 #include "gromacs/modularsimulator/modularsimulator.h"
132 #include "gromacs/nbnxm/gpu_data_mgmt.h"
133 #include "gromacs/nbnxm/nbnxm.h"
134 #include "gromacs/nbnxm/pairlist_tuning.h"
135 #include "gromacs/pbcutil/pbc.h"
136 #include "gromacs/pulling/output.h"
137 #include "gromacs/pulling/pull.h"
138 #include "gromacs/pulling/pull_rotation.h"
139 #include "gromacs/restraint/manager.h"
140 #include "gromacs/restraint/restraintmdmodule.h"
141 #include "gromacs/restraint/restraintpotential.h"
142 #include "gromacs/swap/swapcoords.h"
143 #include "gromacs/taskassignment/decidegpuusage.h"
144 #include "gromacs/taskassignment/decidesimulationworkload.h"
145 #include "gromacs/taskassignment/resourcedivision.h"
146 #include "gromacs/taskassignment/taskassignment.h"
147 #include "gromacs/taskassignment/usergpuids.h"
148 #include "gromacs/timing/gpu_timing.h"
149 #include "gromacs/timing/wallcycle.h"
150 #include "gromacs/timing/wallcyclereporting.h"
151 #include "gromacs/topology/mtop_util.h"
152 #include "gromacs/trajectory/trajectoryframe.h"
153 #include "gromacs/utility/basenetwork.h"
154 #include "gromacs/utility/cstringutil.h"
155 #include "gromacs/utility/exceptions.h"
156 #include "gromacs/utility/fatalerror.h"
157 #include "gromacs/utility/filestream.h"
158 #include "gromacs/utility/gmxassert.h"
159 #include "gromacs/utility/gmxmpi.h"
160 #include "gromacs/utility/keyvaluetree.h"
161 #include "gromacs/utility/logger.h"
162 #include "gromacs/utility/loggerbuilder.h"
163 #include "gromacs/utility/mdmodulenotification.h"
164 #include "gromacs/utility/physicalnodecommunicator.h"
165 #include "gromacs/utility/pleasecite.h"
166 #include "gromacs/utility/programcontext.h"
167 #include "gromacs/utility/smalloc.h"
168 #include "gromacs/utility/stringutil.h"
170 #include "isimulator.h"
171 #include "membedholder.h"
172 #include "replicaexchange.h"
173 #include "simulatorbuilder.h"
179 /*! \brief Manage any development feature flag variables encountered
181 * The use of dev features indicated by environment variables is
182 * logged in order to ensure that runs with such features enabled can
183 * be identified from their log and standard output. Any cross
184 * dependencies are also checked, and if unsatisfied, a fatal error
187 * Note that some development features overrides are applied already here:
188 * the GPU communication flags are set to false in non-tMPI and non-CUDA builds.
190 * \param[in] mdlog Logger object.
191 * \param[in] useGpuForNonbonded True if the nonbonded task is offloaded in this run.
192 * \param[in] pmeRunMode The PME run mode for this run
193 * \returns The object populated with development feature flags.
195 static DevelopmentFeatureFlags manageDevelopmentFeatures(const gmx::MDLogger& mdlog,
196 const bool useGpuForNonbonded,
197 const PmeRunMode pmeRunMode)
199 DevelopmentFeatureFlags devFlags;
201 // Some builds of GCC 5 give false positive warnings that these
202 // getenv results are ignored when clearly they are used.
203 #pragma GCC diagnostic push
204 #pragma GCC diagnostic ignored "-Wunused-result"
206 devFlags.enableGpuBufferOps =
207 GMX_GPU_CUDA && useGpuForNonbonded && (getenv("GMX_USE_GPU_BUFFER_OPS") != nullptr);
208 devFlags.enableGpuHaloExchange = GMX_GPU_CUDA && GMX_THREAD_MPI && getenv("GMX_GPU_DD_COMMS") != nullptr;
209 devFlags.forceGpuUpdateDefault = (getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") != nullptr) || GMX_FAHCORE;
210 devFlags.enableGpuPmePPComm =
211 GMX_GPU_CUDA && GMX_THREAD_MPI && getenv("GMX_GPU_PME_PP_COMMS") != nullptr;
213 #pragma GCC diagnostic pop
215 if (devFlags.enableGpuBufferOps)
217 GMX_LOG(mdlog.warning)
219 .appendTextFormatted(
220 "This run uses the 'GPU buffer ops' feature, enabled by the "
221 "GMX_USE_GPU_BUFFER_OPS environment variable.");
224 if (devFlags.forceGpuUpdateDefault)
226 GMX_LOG(mdlog.warning)
228 .appendTextFormatted(
229 "This run will default to '-update gpu' as requested by the "
230 "GMX_FORCE_UPDATE_DEFAULT_GPU environment variable. GPU update with domain "
231 "decomposition lacks substantial testing and should be used with caution.");
234 if (devFlags.enableGpuHaloExchange)
236 if (useGpuForNonbonded)
238 if (!devFlags.enableGpuBufferOps)
240 GMX_LOG(mdlog.warning)
242 .appendTextFormatted(
243 "Enabling GPU buffer operations required by GMX_GPU_DD_COMMS "
244 "(equivalent with GMX_USE_GPU_BUFFER_OPS=1).");
245 devFlags.enableGpuBufferOps = true;
247 GMX_LOG(mdlog.warning)
249 .appendTextFormatted(
250 "This run has requested the 'GPU halo exchange' feature, enabled by "
252 "GMX_GPU_DD_COMMS environment variable.");
256 GMX_LOG(mdlog.warning)
258 .appendTextFormatted(
259 "GMX_GPU_DD_COMMS environment variable detected, but the 'GPU "
260 "halo exchange' feature will not be enabled as nonbonded interactions "
261 "are not offloaded.");
262 devFlags.enableGpuHaloExchange = false;
266 if (devFlags.enableGpuPmePPComm)
268 if (pmeRunMode == PmeRunMode::GPU)
270 if (!devFlags.enableGpuBufferOps)
272 GMX_LOG(mdlog.warning)
274 .appendTextFormatted(
275 "Enabling GPU buffer operations required by GMX_GPU_PME_PP_COMMS "
276 "(equivalent with GMX_USE_GPU_BUFFER_OPS=1).");
277 devFlags.enableGpuBufferOps = true;
279 GMX_LOG(mdlog.warning)
281 .appendTextFormatted(
282 "This run uses the 'GPU PME-PP communications' feature, enabled "
283 "by the GMX_GPU_PME_PP_COMMS environment variable.");
287 std::string clarification;
288 if (pmeRunMode == PmeRunMode::Mixed)
291 "PME FFT and gather are not offloaded to the GPU (PME is running in mixed "
296 clarification = "PME is not offloaded to the GPU.";
298 GMX_LOG(mdlog.warning)
301 "GMX_GPU_PME_PP_COMMS environment variable detected, but the "
302 "'GPU PME-PP communications' feature was not enabled as "
304 devFlags.enableGpuPmePPComm = false;
311 /*! \brief Barrier for safe simultaneous thread access to mdrunner data
313 * Used to ensure that the master thread does not modify mdrunner during copy
314 * on the spawned threads. */
315 static void threadMpiMdrunnerAccessBarrier()
318 MPI_Barrier(MPI_COMM_WORLD);
322 Mdrunner Mdrunner::cloneOnSpawnedThread() const
324 auto newRunner = Mdrunner(std::make_unique<MDModules>());
326 // All runners in the same process share a restraint manager resource because it is
327 // part of the interface to the client code, which is associated only with the
328 // original thread. Handles to the same resources can be obtained by copy.
330 newRunner.restraintManager_ = std::make_unique<RestraintManager>(*restraintManager_);
333 // Copy members of master runner.
334 // \todo Replace with builder when Simulation context and/or runner phases are better defined.
335 // Ref https://gitlab.com/gromacs/gromacs/-/issues/2587 and https://gitlab.com/gromacs/gromacs/-/issues/2375
336 newRunner.hw_opt = hw_opt;
337 newRunner.filenames = filenames;
339 newRunner.hwinfo_ = hwinfo_;
340 newRunner.oenv = oenv;
341 newRunner.mdrunOptions = mdrunOptions;
342 newRunner.domdecOptions = domdecOptions;
343 newRunner.nbpu_opt = nbpu_opt;
344 newRunner.pme_opt = pme_opt;
345 newRunner.pme_fft_opt = pme_fft_opt;
346 newRunner.bonded_opt = bonded_opt;
347 newRunner.update_opt = update_opt;
348 newRunner.nstlist_cmdline = nstlist_cmdline;
349 newRunner.replExParams = replExParams;
350 newRunner.pforce = pforce;
351 // Give the spawned thread the newly created valid communicator
352 // for the simulation.
353 newRunner.libraryWorldCommunicator = MPI_COMM_WORLD;
354 newRunner.simulationCommunicator = MPI_COMM_WORLD;
356 newRunner.startingBehavior = startingBehavior;
357 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>(*stopHandlerBuilder_);
358 newRunner.inputHolder_ = inputHolder_;
360 threadMpiMdrunnerAccessBarrier();
365 /*! \brief The callback used for running on spawned threads.
367 * Obtains the pointer to the master mdrunner object from the one
368 * argument permitted to the thread-launch API call, copies it to make
369 * a new runner for this thread, reinitializes necessary data, and
370 * proceeds to the simulation. */
371 static void mdrunner_start_fn(const void* arg)
375 auto masterMdrunner = reinterpret_cast<const gmx::Mdrunner*>(arg);
376 /* copy the arg list to make sure that it's thread-local. This
377 doesn't copy pointed-to items, of course; fnm, cr and fplog
378 are reset in the call below, all others should be const. */
379 gmx::Mdrunner mdrunner = masterMdrunner->cloneOnSpawnedThread();
382 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
386 void Mdrunner::spawnThreads(int numThreadsToLaunch)
389 /* now spawn new threads that start mdrunner_start_fn(), while
390 the main thread returns. Thread affinity is handled later. */
391 if (tMPI_Init_fn(TRUE, numThreadsToLaunch, TMPI_AFFINITY_NONE, mdrunner_start_fn, static_cast<const void*>(this))
394 GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
397 // Give the master thread the newly created valid communicator for
399 libraryWorldCommunicator = MPI_COMM_WORLD;
400 simulationCommunicator = MPI_COMM_WORLD;
401 threadMpiMdrunnerAccessBarrier();
403 GMX_UNUSED_VALUE(numThreadsToLaunch);
404 GMX_UNUSED_VALUE(mdrunner_start_fn);
410 /*! \brief Initialize variables for Verlet scheme simulation */
411 static void prepare_verlet_scheme(FILE* fplog,
415 const gmx_mtop_t* mtop,
417 bool makeGpuPairList,
418 const gmx::CpuInfo& cpuinfo)
420 // We checked the cut-offs in grompp, but double-check here.
421 // We have PME+LJcutoff kernels for rcoulomb>rvdw.
422 if (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == eelCUT)
424 GMX_RELEASE_ASSERT(ir->rcoulomb >= ir->rvdw,
425 "With Verlet lists and PME we should have rcoulomb>=rvdw");
429 GMX_RELEASE_ASSERT(ir->rcoulomb == ir->rvdw,
430 "With Verlet lists and no PME rcoulomb and rvdw should be identical");
432 /* For NVE simulations, we will retain the initial list buffer */
433 if (EI_DYNAMICS(ir->eI) && ir->verletbuf_tol > 0 && !(EI_MD(ir->eI) && ir->etc == etcNO))
435 /* Update the Verlet buffer size for the current run setup */
437 /* Here we assume SIMD-enabled kernels are being used. But as currently
438 * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
439 * and 4x2 gives a larger buffer than 4x4, this is ok.
441 ListSetupType listType =
442 (makeGpuPairList ? ListSetupType::Gpu : ListSetupType::CpuSimdWhenSupported);
443 VerletbufListSetup listSetup = verletbufGetSafeListSetup(listType);
445 const real rlist_new =
446 calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
448 if (rlist_new != ir->rlist)
450 if (fplog != nullptr)
453 "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
456 listSetup.cluster_size_i,
457 listSetup.cluster_size_j);
459 ir->rlist = rlist_new;
463 if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
466 "Can not set nstlist without %s",
467 !EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
470 if (EI_DYNAMICS(ir->eI))
472 /* Set or try nstlist values */
473 increaseNstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, makeGpuPairList, cpuinfo);
477 /*! \brief Override the nslist value in inputrec
479 * with value passed on the command line (if any)
481 static void override_nsteps_cmdline(const gmx::MDLogger& mdlog, int64_t nsteps_cmdline, t_inputrec* ir)
485 /* override with anything else than the default -2 */
486 if (nsteps_cmdline > -2)
488 char sbuf_steps[STEPSTRSIZE];
489 char sbuf_msg[STRLEN];
491 ir->nsteps = nsteps_cmdline;
492 if (EI_DYNAMICS(ir->eI) && nsteps_cmdline != -1)
495 "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
496 gmx_step_str(nsteps_cmdline, sbuf_steps),
497 fabs(nsteps_cmdline * ir->delta_t));
502 "Overriding nsteps with value passed on the command line: %s steps",
503 gmx_step_str(nsteps_cmdline, sbuf_steps));
506 GMX_LOG(mdlog.warning).asParagraph().appendText(sbuf_msg);
508 else if (nsteps_cmdline < -2)
510 gmx_fatal(FARGS, "Invalid nsteps value passed on the command line: %" PRId64, nsteps_cmdline);
512 /* Do nothing if nsteps_cmdline == -2 */
518 /*! \brief Return whether GPU acceleration of nonbondeds is supported with the given settings.
520 * If not, and if a warning may be issued, logs a warning about
521 * falling back to CPU code. With thread-MPI, only the first
522 * call to this function should have \c issueWarning true. */
523 static bool gpuAccelerationOfNonbondedIsUseful(const MDLogger& mdlog, const t_inputrec& ir, bool issueWarning)
525 bool gpuIsUseful = true;
528 if (ir.opts.ngener - ir.nwall > 1)
530 /* The GPU code does not support more than one energy group.
531 * If the user requested GPUs explicitly, a fatal error is given later.
535 "Multiple energy groups is not implemented for GPUs, falling back to the CPU. "
536 "For better performance, run on the GPU without energy groups and then do "
537 "gmx mdrun -rerun option on the trajectory with an energy group .tpr file.";
543 warning = "TPI is not implemented for GPUs.";
546 if (!gpuIsUseful && issueWarning)
548 GMX_LOG(mdlog.warning).asParagraph().appendText(warning);
554 //! Initializes the logger for mdrun.
555 static gmx::LoggerOwner buildLogger(FILE* fplog, const bool isSimulationMasterRank)
557 gmx::LoggerBuilder builder;
558 if (fplog != nullptr)
560 builder.addTargetFile(gmx::MDLogger::LogLevel::Info, fplog);
562 if (isSimulationMasterRank)
564 builder.addTargetStream(gmx::MDLogger::LogLevel::Warning, &gmx::TextOutputFile::standardError());
566 return builder.build();
569 //! Make a TaskTarget from an mdrun argument string.
570 static TaskTarget findTaskTarget(const char* optionString)
572 TaskTarget returnValue = TaskTarget::Auto;
574 if (strncmp(optionString, "auto", 3) == 0)
576 returnValue = TaskTarget::Auto;
578 else if (strncmp(optionString, "cpu", 3) == 0)
580 returnValue = TaskTarget::Cpu;
582 else if (strncmp(optionString, "gpu", 3) == 0)
584 returnValue = TaskTarget::Gpu;
588 GMX_ASSERT(false, "Option string should have been checked for sanity already");
594 //! Finish run, aggregate data to print performance info.
595 static void finish_run(FILE* fplog,
596 const gmx::MDLogger& mdlog,
598 const t_inputrec* inputrec,
600 gmx_wallcycle_t wcycle,
601 gmx_walltime_accounting_t walltime_accounting,
602 nonbonded_verlet_t* nbv,
603 const gmx_pme_t* pme,
607 double nbfs = 0, mflop = 0;
608 double elapsed_time, elapsed_time_over_all_ranks, elapsed_time_over_all_threads,
609 elapsed_time_over_all_threads_over_all_ranks;
610 /* Control whether it is valid to print a report. Only the
611 simulation master may print, but it should not do so if the run
612 terminated e.g. before a scheduled reset step. This is
613 complicated by the fact that PME ranks are unaware of the
614 reason why they were sent a pmerecvqxFINISH. To avoid
615 communication deadlocks, we always do the communication for the
616 report, even if we've decided not to write the report, because
617 how long it takes to finish the run is not important when we've
618 decided not to report on the simulation performance.
620 Further, we only report performance for dynamical integrators,
621 because those are the only ones for which we plan to
622 consider doing any optimizations. */
623 bool printReport = EI_DYNAMICS(inputrec->eI) && SIMMASTER(cr);
625 if (printReport && !walltime_accounting_get_valid_finish(walltime_accounting))
627 GMX_LOG(mdlog.warning)
629 .appendText("Simulation ended prematurely, no performance report will be written.");
634 std::unique_ptr<t_nrnb> nrnbTotalStorage;
637 nrnbTotalStorage = std::make_unique<t_nrnb>();
638 nrnb_tot = nrnbTotalStorage.get();
640 MPI_Allreduce(nrnb->n, nrnb_tot->n, eNRNB, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
648 elapsed_time = walltime_accounting_get_time_since_reset(walltime_accounting);
649 elapsed_time_over_all_threads =
650 walltime_accounting_get_time_since_reset_over_all_threads(walltime_accounting);
654 /* reduce elapsed_time over all MPI ranks in the current simulation */
655 MPI_Allreduce(&elapsed_time, &elapsed_time_over_all_ranks, 1, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
656 elapsed_time_over_all_ranks /= cr->nnodes;
657 /* Reduce elapsed_time_over_all_threads over all MPI ranks in the
658 * current simulation. */
659 MPI_Allreduce(&elapsed_time_over_all_threads,
660 &elapsed_time_over_all_threads_over_all_ranks,
669 elapsed_time_over_all_ranks = elapsed_time;
670 elapsed_time_over_all_threads_over_all_ranks = elapsed_time_over_all_threads;
675 print_flop(fplog, nrnb_tot, &nbfs, &mflop);
678 if (thisRankHasDuty(cr, DUTY_PP) && DOMAINDECOMP(cr))
680 print_dd_statistics(cr, inputrec, fplog);
683 /* TODO Move the responsibility for any scaling by thread counts
684 * to the code that handled the thread region, so that there's a
685 * mechanism to keep cycle counting working during the transition
686 * to task parallelism. */
687 int nthreads_pp = gmx_omp_nthreads_get(emntNonbonded);
688 int nthreads_pme = gmx_omp_nthreads_get(emntPME);
689 wallcycle_scale_by_num_threads(
690 wcycle, thisRankHasDuty(cr, DUTY_PME) && !thisRankHasDuty(cr, DUTY_PP), nthreads_pp, nthreads_pme);
691 auto cycle_sum(wallcycle_sum(cr, wcycle));
695 auto nbnxn_gpu_timings =
696 (nbv != nullptr && nbv->useGpu()) ? Nbnxm::gpu_get_timings(nbv->gpu_nbv) : nullptr;
697 gmx_wallclock_gpu_pme_t pme_gpu_timings = {};
699 if (pme_gpu_task_enabled(pme))
701 pme_gpu_get_timings(pme, &pme_gpu_timings);
703 wallcycle_print(fplog,
709 elapsed_time_over_all_ranks,
715 if (EI_DYNAMICS(inputrec->eI))
717 delta_t = inputrec->delta_t;
723 elapsed_time_over_all_threads_over_all_ranks,
724 elapsed_time_over_all_ranks,
725 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
733 elapsed_time_over_all_threads_over_all_ranks,
734 elapsed_time_over_all_ranks,
735 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
743 int Mdrunner::mdrunner()
746 t_forcerec* fr = nullptr;
747 real ewaldcoeff_q = 0;
748 real ewaldcoeff_lj = 0;
749 int nChargePerturbed = -1, nTypePerturbed = 0;
750 gmx_wallcycle_t wcycle;
751 gmx_walltime_accounting_t walltime_accounting = nullptr;
752 MembedHolder membedHolder(filenames.size(), filenames.data());
754 /* CAUTION: threads may be started later on in this function, so
755 cr doesn't reflect the final parallel state right now */
758 /* TODO: inputrec should tell us whether we use an algorithm, not a file option */
759 const bool doEssentialDynamics = opt2bSet("-ei", filenames.size(), filenames.data());
760 const bool doRerun = mdrunOptions.rerun;
762 // Handle task-assignment related user options.
763 EmulateGpuNonbonded emulateGpuNonbonded =
764 (getenv("GMX_EMULATE_GPU") != nullptr ? EmulateGpuNonbonded::Yes : EmulateGpuNonbonded::No);
766 std::vector<int> userGpuTaskAssignment;
769 userGpuTaskAssignment = parseUserTaskAssignmentString(hw_opt.userGpuTaskAssignment);
771 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
772 auto nonbondedTarget = findTaskTarget(nbpu_opt);
773 auto pmeTarget = findTaskTarget(pme_opt);
774 auto pmeFftTarget = findTaskTarget(pme_fft_opt);
775 auto bondedTarget = findTaskTarget(bonded_opt);
776 auto updateTarget = findTaskTarget(update_opt);
778 FILE* fplog = nullptr;
779 // If we are appending, we don't write log output because we need
780 // to check that the old log file matches what the checkpoint file
781 // expects. Otherwise, we should start to write log output now if
782 // there is a file ready for it.
783 if (logFileHandle != nullptr && startingBehavior != StartingBehavior::RestartWithAppending)
785 fplog = gmx_fio_getfp(logFileHandle);
787 const bool isSimulationMasterRank = findIsSimulationMasterRank(ms, simulationCommunicator);
788 gmx::LoggerOwner logOwner(buildLogger(fplog, isSimulationMasterRank));
789 gmx::MDLogger mdlog(logOwner.logger());
791 gmx_print_detected_hardware(fplog, isSimulationMasterRank && isMasterSim(ms), mdlog, hwinfo_);
793 std::vector<int> gpuIdsToUse = makeGpuIdsToUse(hwinfo_->deviceInfoList, hw_opt.gpuIdsAvailable);
794 const int numDevicesToUse = gmx::ssize(gpuIdsToUse);
796 // Print citation requests after all software/hardware printing
797 pleaseCiteGromacs(fplog);
799 // Note: legacy program logic relies on checking whether these pointers are assigned.
800 // Objects may or may not be allocated later.
801 std::unique_ptr<t_inputrec> inputrec;
802 std::unique_ptr<t_state> globalState;
804 auto partialDeserializedTpr = std::make_unique<PartialDeserializedTprFile>();
806 if (isSimulationMasterRank)
808 // Allocate objects to be initialized by later function calls.
809 /* Only the master rank has the global state */
810 globalState = std::make_unique<t_state>();
811 inputrec = std::make_unique<t_inputrec>();
813 /* Read (nearly) all data required for the simulation
814 * and keep the partly serialized tpr contents to send to other ranks later
816 applyGlobalSimulationState(
817 *inputHolder_.get(), partialDeserializedTpr.get(), globalState.get(), inputrec.get(), &mtop);
820 /* Check and update the hardware options for internal consistency */
821 checkAndUpdateHardwareOptions(
822 mdlog, &hw_opt, isSimulationMasterRank, domdecOptions.numPmeRanks, inputrec.get());
824 if (GMX_THREAD_MPI && isSimulationMasterRank)
826 bool useGpuForNonbonded = false;
827 bool useGpuForPme = false;
830 GMX_RELEASE_ASSERT(inputrec != nullptr, "Keep the compiler happy");
832 // If the user specified the number of ranks, then we must
833 // respect that, but in default mode, we need to allow for
834 // the number of GPUs to choose the number of ranks.
835 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
836 useGpuForNonbonded = decideWhetherToUseGpusForNonbondedWithThreadMpi(
839 userGpuTaskAssignment,
841 canUseGpuForNonbonded,
842 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, GMX_THREAD_MPI),
843 hw_opt.nthreads_tmpi);
844 useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi(useGpuForNonbonded,
847 userGpuTaskAssignment,
850 hw_opt.nthreads_tmpi,
851 domdecOptions.numPmeRanks);
853 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
855 /* Determine how many thread-MPI ranks to start.
857 * TODO Over-writing the user-supplied value here does
858 * prevent any possible subsequent checks from working
860 hw_opt.nthreads_tmpi = get_nthreads_mpi(hwinfo_,
868 membedHolder.doMembed());
870 // Now start the threads for thread MPI.
871 spawnThreads(hw_opt.nthreads_tmpi);
872 // The spawned threads enter mdrunner() and execution of
873 // master and spawned threads joins at the end of this block.
876 GMX_RELEASE_ASSERT(ms || simulationCommunicator != MPI_COMM_NULL,
877 "Must have valid communicator unless running a multi-simulation");
878 CommrecHandle crHandle = init_commrec(simulationCommunicator);
879 t_commrec* cr = crHandle.get();
880 GMX_RELEASE_ASSERT(cr != nullptr, "Must have valid commrec");
882 PhysicalNodeCommunicator physicalNodeComm(libraryWorldCommunicator, gmx_physicalnode_id_hash());
884 // If we detected the topology on this system, double-check that it makes sense
885 if (hwinfo_->hardwareTopology->isThisSystem())
887 hardwareTopologyDoubleCheckDetection(mdlog, *hwinfo_->hardwareTopology);
892 /* now broadcast everything to the non-master nodes/threads: */
893 if (!isSimulationMasterRank)
895 // Until now, only the master rank has a non-null pointer.
896 // On non-master ranks, allocate the object that will receive data in the following call.
897 inputrec = std::make_unique<t_inputrec>();
899 init_parallel(cr->mpiDefaultCommunicator,
903 partialDeserializedTpr.get());
905 GMX_RELEASE_ASSERT(inputrec != nullptr, "All ranks should have a valid inputrec now");
906 partialDeserializedTpr.reset(nullptr);
909 !inputrec->useConstantAcceleration,
910 "Linear acceleration has been removed in GROMACS 2022, and was broken for many years "
911 "before that. Use GROMACS 4.5 or earlier if you need this feature.");
913 // Now the number of ranks is known to all ranks, and each knows
914 // the inputrec read by the master rank. The ranks can now all run
915 // the task-deciding functions and will agree on the result
916 // without needing to communicate.
917 const bool useDomainDecomposition = (PAR(cr) && !(EI_TPI(inputrec->eI) || inputrec->eI == eiNM));
919 // Note that these variables describe only their own node.
921 // Note that when bonded interactions run on a GPU they always run
922 // alongside a nonbonded task, so do not influence task assignment
923 // even though they affect the force calculation workload.
924 bool useGpuForNonbonded = false;
925 bool useGpuForPme = false;
926 bool useGpuForBonded = false;
927 bool useGpuForUpdate = false;
928 bool gpusWereDetected = hwinfo_->ngpu_compatible_tot > 0;
931 // It's possible that there are different numbers of GPUs on
932 // different nodes, which is the user's responsibility to
933 // handle. If unsuitable, we will notice that during task
935 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
936 useGpuForNonbonded = decideWhetherToUseGpusForNonbonded(
938 userGpuTaskAssignment,
940 canUseGpuForNonbonded,
941 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, !GMX_THREAD_MPI),
943 useGpuForPme = decideWhetherToUseGpusForPme(useGpuForNonbonded,
945 userGpuTaskAssignment,
948 cr->sizeOfDefaultCommunicator,
949 domdecOptions.numPmeRanks,
951 useGpuForBonded = decideWhetherToUseGpusForBonded(
952 useGpuForNonbonded, useGpuForPme, bondedTarget, *inputrec, mtop, domdecOptions.numPmeRanks, gpusWereDetected);
954 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
956 const PmeRunMode pmeRunMode = determinePmeRunMode(useGpuForPme, pmeFftTarget, *inputrec);
958 // Initialize development feature flags that enabled by environment variable
959 // and report those features that are enabled.
960 const DevelopmentFeatureFlags devFlags =
961 manageDevelopmentFeatures(mdlog, useGpuForNonbonded, pmeRunMode);
963 const bool useModularSimulator = checkUseModularSimulator(false,
971 membedHolder.doMembed());
974 // TODO: hide restraint implementation details from Mdrunner.
975 // There is nothing unique about restraints at this point as far as the
976 // Mdrunner is concerned. The Mdrunner should just be getting a sequence of
977 // factory functions from the SimulationContext on which to call mdModules_->add().
978 // TODO: capture all restraints into a single RestraintModule, passed to the runner builder.
979 for (auto&& restraint : restraintManager_->getRestraints())
981 auto module = RestraintMDModule::create(restraint, restraint->sites());
982 mdModules_->add(std::move(module));
985 // TODO: Error handling
986 mdModules_->assignOptionsToModules(*inputrec->params, nullptr);
987 // now that the MdModules know their options, they know which callbacks to sign up to
988 mdModules_->subscribeToSimulationSetupNotifications();
989 const auto& mdModulesNotifier = mdModules_->notifier().simulationSetupNotifications_;
991 if (inputrec->internalParameters != nullptr)
993 mdModulesNotifier.notify(*inputrec->internalParameters);
996 if (fplog != nullptr)
998 pr_inputrec(fplog, 0, "Input Parameters", inputrec.get(), FALSE);
999 fprintf(fplog, "\n");
1004 /* In rerun, set velocities to zero if present */
1005 if (doRerun && ((globalState->flags & (1 << estV)) != 0))
1007 // rerun does not use velocities
1011 "Rerun trajectory contains velocities. Rerun does only evaluate "
1012 "potential energy and forces. The velocities will be ignored.");
1013 for (int i = 0; i < globalState->natoms; i++)
1015 clear_rvec(globalState->v[i]);
1017 globalState->flags &= ~(1 << estV);
1020 /* now make sure the state is initialized and propagated */
1021 set_state_entries(globalState.get(), inputrec.get(), useModularSimulator);
1024 /* NM and TPI parallelize over force/energy calculations, not atoms,
1025 * so we need to initialize and broadcast the global state.
1027 if (inputrec->eI == eiNM || inputrec->eI == eiTPI)
1031 globalState = std::make_unique<t_state>();
1033 broadcastStateWithoutDynamics(
1034 cr->mpiDefaultCommunicator, DOMAINDECOMP(cr), PAR(cr), globalState.get());
1037 /* A parallel command line option consistency check that we can
1038 only do after any threads have started. */
1040 && (domdecOptions.numCells[XX] > 1 || domdecOptions.numCells[YY] > 1
1041 || domdecOptions.numCells[ZZ] > 1 || domdecOptions.numPmeRanks > 0))
1044 "The -dd or -npme option request a parallel simulation, "
1046 "but %s was compiled without threads or MPI enabled",
1047 output_env_get_program_display_name(oenv));
1048 #elif GMX_THREAD_MPI
1049 "but the number of MPI-threads (option -ntmpi) is not set or is 1");
1051 "but %s was not started through mpirun/mpiexec or only one rank was requested "
1052 "through mpirun/mpiexec",
1053 output_env_get_program_display_name(oenv));
1057 if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
1060 "The .mdp file specified an energy mininization or normal mode algorithm, and "
1061 "these are not compatible with mdrun -rerun");
1064 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
1066 if (domdecOptions.numPmeRanks > 0)
1068 gmx_fatal_collective(FARGS,
1069 cr->mpiDefaultCommunicator,
1071 "PME-only ranks are requested, but the system does not use PME "
1072 "for electrostatics or LJ");
1075 domdecOptions.numPmeRanks = 0;
1078 if (useGpuForNonbonded && domdecOptions.numPmeRanks < 0)
1080 /* With NB GPUs we don't automatically use PME-only CPU ranks. PME ranks can
1081 * improve performance with many threads per GPU, since our OpenMP
1082 * scaling is bad, but it's difficult to automate the setup.
1084 domdecOptions.numPmeRanks = 0;
1088 if (domdecOptions.numPmeRanks < 0)
1090 domdecOptions.numPmeRanks = 0;
1091 // TODO possibly print a note that one can opt-in for a separate PME GPU rank?
1095 GMX_RELEASE_ASSERT(domdecOptions.numPmeRanks <= 1,
1096 "PME GPU decomposition is not supported");
1100 /* NMR restraints must be initialized before load_checkpoint,
1101 * since with time averaging the history is added to t_state.
1102 * For proper consistency check we therefore need to extend
1104 * So the PME-only nodes (if present) will also initialize
1105 * the distance restraints.
1108 /* This needs to be called before read_checkpoint to extend the state */
1109 t_disresdata* disresdata;
1110 snew(disresdata, 1);
1114 DisResRunMode::MDRun,
1115 MASTER(cr) ? DDRole::Master : DDRole::Agent,
1116 PAR(cr) ? NumRanks::Multiple : NumRanks::Single,
1121 replExParams.exchangeInterval > 0);
1123 t_oriresdata* oriresdata;
1124 snew(oriresdata, 1);
1125 init_orires(fplog, &mtop, inputrec.get(), cr, ms, globalState.get(), oriresdata);
1127 auto deform = prepareBoxDeformation(globalState != nullptr ? globalState->box : box,
1128 MASTER(cr) ? DDRole::Master : DDRole::Agent,
1129 PAR(cr) ? NumRanks::Multiple : NumRanks::Single,
1130 cr->mpi_comm_mygroup,
1134 /* We have to remember the generation's first step before reading checkpoint.
1135 This way, we can report to the F@H core both the generation's first step
1136 and the restored first step, thus making it able to distinguish between
1137 an interruption/resume and start of the n-th generation simulation.
1138 Having this information, the F@H core can correctly calculate and report
1141 int gen_first_step = 0;
1144 gen_first_step = inputrec->init_step;
1148 ObservablesHistory observablesHistory = {};
1150 auto modularSimulatorCheckpointData = std::make_unique<ReadCheckpointDataHolder>();
1151 if (startingBehavior != StartingBehavior::NewSimulation)
1153 /* Check if checkpoint file exists before doing continuation.
1154 * This way we can use identical input options for the first and subsequent runs...
1156 if (mdrunOptions.numStepsCommandline > -2)
1158 /* Temporarily set the number of steps to unlimited to avoid
1159 * triggering the nsteps check in load_checkpoint().
1160 * This hack will go away soon when the -nsteps option is removed.
1162 inputrec->nsteps = -1;
1165 // Finish applying initial simulation state information from external sources on all ranks.
1166 // Reconcile checkpoint file data with Mdrunner state established up to this point.
1167 applyLocalState(*inputHolder_.get(),
1170 domdecOptions.numCells,
1173 &observablesHistory,
1174 mdrunOptions.reproducible,
1175 mdModules_->notifier(),
1176 modularSimulatorCheckpointData.get(),
1177 useModularSimulator);
1178 // TODO: (#3652) Synchronize filesystem state, SimulationInput contents, and program
1180 // on all code paths.
1181 // Write checkpoint or provide hook to update SimulationInput.
1182 // If there was a checkpoint file, SimulationInput contains more information
1183 // than if there wasn't. At this point, we have synchronized the in-memory
1184 // state with the filesystem state only for restarted simulations. We should
1185 // be calling applyLocalState unconditionally and expect that the completeness
1186 // of SimulationInput is not dependent on its creation method.
1188 if (startingBehavior == StartingBehavior::RestartWithAppending && logFileHandle)
1190 // Now we can start normal logging to the truncated log file.
1191 fplog = gmx_fio_getfp(logFileHandle);
1192 prepareLogAppending(fplog);
1193 logOwner = buildLogger(fplog, MASTER(cr));
1194 mdlog = logOwner.logger();
1201 fcRegisterSteps(inputrec->nsteps + inputrec->init_step, gen_first_step);
1205 if (mdrunOptions.numStepsCommandline > -2)
1210 "The -nsteps functionality is deprecated, and may be removed in a future "
1212 "Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp "
1215 /* override nsteps with value set on the commandline */
1216 override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec.get());
1218 if (isSimulationMasterRank)
1220 copy_mat(globalState->box, box);
1225 gmx_bcast(sizeof(box), box, cr->mpiDefaultCommunicator);
1228 if (inputrec->cutoff_scheme != ecutsVERLET)
1231 "This group-scheme .tpr file can no longer be run by mdrun. Please update to the "
1232 "Verlet scheme, or use an earlier version of GROMACS if necessary.");
1234 /* Update rlist and nstlist. */
1235 /* Note: prepare_verlet_scheme is calling increaseNstlist(...), which (while attempting to
1236 * increase rlist) tries to check if the newly chosen value fits with the DD scheme. As this is
1237 * run before any DD scheme is set up, this check is never executed. See #3334 for more details.
1239 prepare_verlet_scheme(fplog,
1245 useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes),
1248 // This builder is necessary while we have multi-part construction
1249 // of DD. Before DD is constructed, we use the existence of
1250 // the builder object to indicate that further construction of DD
1252 std::unique_ptr<DomainDecompositionBuilder> ddBuilder;
1253 if (useDomainDecomposition)
1255 ddBuilder = std::make_unique<DomainDecompositionBuilder>(
1263 positionsFromStatePointer(globalState.get()));
1267 /* PME, if used, is done on all nodes with 1D decomposition */
1268 cr->nnodes = cr->sizeOfDefaultCommunicator;
1269 cr->sim_nodeid = cr->rankInDefaultCommunicator;
1270 cr->nodeid = cr->rankInDefaultCommunicator;
1272 cr->duty = (DUTY_PP | DUTY_PME);
1274 if (inputrec->pbcType == PbcType::Screw)
1276 gmx_fatal(FARGS, "pbc=screw is only implemented with domain decomposition");
1280 // Produce the task assignment for this rank - done after DD is constructed
1281 GpuTaskAssignments gpuTaskAssignments = GpuTaskAssignmentsBuilder::build(
1283 userGpuTaskAssignment,
1285 simulationCommunicator,
1293 thisRankHasDuty(cr, DUTY_PP),
1294 // TODO cr->duty & DUTY_PME should imply that a PME
1295 // algorithm is active, but currently does not.
1296 EEL_PME(inputrec->coulombtype) && thisRankHasDuty(cr, DUTY_PME));
1298 // Get the device handles for the modules, nullptr when no task is assigned.
1300 DeviceInformation* deviceInfo = gpuTaskAssignments.initDevice(&deviceId);
1302 // timing enabling - TODO put this in gpu_utils (even though generally this is just option handling?)
1303 bool useTiming = true;
1307 /* WARNING: CUDA timings are incorrect with multiple streams.
1308 * This is the main reason why they are disabled by default.
1310 // TODO: Consider turning on by default when we can detect nr of streams.
1311 useTiming = (getenv("GMX_ENABLE_GPU_TIMING") != nullptr);
1313 else if (GMX_GPU_OPENCL)
1315 useTiming = (getenv("GMX_DISABLE_GPU_TIMING") == nullptr);
1318 // TODO Currently this is always built, yet DD partition code
1319 // checks if it is built before using it. Probably it should
1320 // become an MDModule that is made only when another module
1321 // requires it (e.g. pull, CompEl, density fitting), so that we
1322 // don't update the local atom sets unilaterally every step.
1323 LocalAtomSetManager atomSets;
1326 // TODO Pass the GPU streams to ddBuilder to use in buffer
1327 // transfers (e.g. halo exchange)
1328 cr->dd = ddBuilder->build(&atomSets);
1329 // The builder's job is done, so destruct it
1330 ddBuilder.reset(nullptr);
1331 // Note that local state still does not exist yet.
1334 // The GPU update is decided here because we need to know whether the constraints or
1335 // SETTLEs can span accross the domain borders (i.e. whether or not update groups are
1336 // defined). This is only known after DD is initialized, hence decision on using GPU
1337 // update is done so late.
1340 const bool useUpdateGroups = cr->dd ? ddUsesUpdateGroups(*cr->dd) : false;
1342 useGpuForUpdate = decideWhetherToUseGpuForUpdate(useDomainDecomposition,
1345 domdecOptions.numPmeRanks > 0,
1351 doEssentialDynamics,
1352 gmx_mtop_ftype_count(mtop, F_ORIRES) > 0,
1353 replExParams.exchangeInterval > 0,
1358 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1360 const bool printHostName = (cr->nnodes > 1);
1361 gpuTaskAssignments.reportGpuUsage(mdlog, printHostName, useGpuForBonded, pmeRunMode, useGpuForUpdate);
1363 const bool disableNonbondedCalculation = (getenv("GMX_NO_NONBONDED") != nullptr);
1364 if (disableNonbondedCalculation)
1366 /* turn off non-bonded calculations */
1367 GMX_LOG(mdlog.warning)
1370 "Found environment variable GMX_NO_NONBONDED.\n"
1371 "Disabling nonbonded calculations.");
1374 MdrunScheduleWorkload runScheduleWork;
1376 bool useGpuDirectHalo = decideWhetherToUseGpuForHalo(devFlags,
1377 havePPDomainDecomposition(cr),
1379 useModularSimulator,
1381 EI_ENERGY_MINIMIZATION(inputrec->eI));
1383 // Also populates the simulation constant workload description.
1384 runScheduleWork.simulationWork = createSimulationWorkload(*inputrec,
1385 disableNonbondedCalculation,
1393 std::unique_ptr<DeviceStreamManager> deviceStreamManager = nullptr;
1395 if (deviceInfo != nullptr)
1397 if (DOMAINDECOMP(cr) && thisRankHasDuty(cr, DUTY_PP))
1399 dd_setup_dlb_resource_sharing(cr, deviceId);
1401 deviceStreamManager = std::make_unique<DeviceStreamManager>(
1402 *deviceInfo, havePPDomainDecomposition(cr), runScheduleWork.simulationWork, useTiming);
1405 // If the user chose a task assignment, give them some hints
1406 // where appropriate.
1407 if (!userGpuTaskAssignment.empty())
1409 gpuTaskAssignments.logPerformanceHints(mdlog, numDevicesToUse);
1414 /* After possible communicator splitting in make_dd_communicators.
1415 * we can set up the intra/inter node communication.
1417 gmx_setup_nodecomm(fplog, cr);
1423 GMX_LOG(mdlog.warning)
1425 .appendTextFormatted(
1426 "This is simulation %d out of %d running as a composite GROMACS\n"
1427 "multi-simulation job. Setup for this simulation:\n",
1428 ms->simulationIndex_,
1429 ms->numSimulations_);
1431 GMX_LOG(mdlog.warning)
1432 .appendTextFormatted("Using %d MPI %s\n",
1435 cr->nnodes == 1 ? "thread" : "threads"
1437 cr->nnodes == 1 ? "process" : "processes"
1443 // If mdrun -pin auto honors any affinity setting that already
1444 // exists. If so, it is nice to provide feedback about whether
1445 // that existing affinity setting was from OpenMP or something
1446 // else, so we run this code both before and after we initialize
1447 // the OpenMP support.
1448 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo_->nthreads_hw_avail, FALSE);
1449 /* Check and update the number of OpenMP threads requested */
1450 checkAndUpdateRequestedNumOpenmpThreads(
1451 &hw_opt, *hwinfo_, cr, ms, physicalNodeComm.size_, pmeRunMode, mtop, *inputrec);
1453 gmx_omp_nthreads_init(mdlog,
1455 hwinfo_->nthreads_hw_avail,
1456 physicalNodeComm.size_,
1457 hw_opt.nthreads_omp,
1458 hw_opt.nthreads_omp_pme,
1459 !thisRankHasDuty(cr, DUTY_PP));
1461 // Enable FP exception detection, but not in
1462 // Release mode and not for compilers with known buggy FP
1463 // exception support (clang with any optimization) or suspected
1464 // buggy FP exception support (gcc 7.* with optimization).
1465 #if !defined NDEBUG \
1466 && !((defined __clang__ || (defined(__GNUC__) && !defined(__ICC) && __GNUC__ == 7)) \
1467 && defined __OPTIMIZE__)
1468 const bool bEnableFPE = true;
1470 const bool bEnableFPE = false;
1472 // FIXME - reconcile with gmx_feenableexcept() call from CommandLineModuleManager::run()
1475 gmx_feenableexcept();
1478 /* Now that we know the setup is consistent, check for efficiency */
1479 check_resource_division_efficiency(
1480 hwinfo_, gpuTaskAssignments.thisRankHasAnyGpuTask(), mdrunOptions.ntompOptionIsSet, cr, mdlog);
1482 /* getting number of PP/PME threads on this MPI / tMPI rank.
1483 PME: env variable should be read only on one node to make sure it is
1484 identical everywhere;
1486 const int numThreadsOnThisRank = thisRankHasDuty(cr, DUTY_PP) ? gmx_omp_nthreads_get(emntNonbonded)
1487 : gmx_omp_nthreads_get(emntPME);
1488 checkHardwareOversubscription(
1489 numThreadsOnThisRank, cr->nodeid, *hwinfo_->hardwareTopology, physicalNodeComm, mdlog);
1491 // Enable Peer access between GPUs where available
1492 // Only for DD, only master PP rank needs to perform setup, and only if thread MPI plus
1493 // any of the GPU communication features are active.
1494 if (DOMAINDECOMP(cr) && MASTER(cr) && thisRankHasDuty(cr, DUTY_PP) && GMX_THREAD_MPI
1495 && (runScheduleWork.simulationWork.useGpuHaloExchange
1496 || runScheduleWork.simulationWork.useGpuPmePpCommunication))
1498 setupGpuDevicePeerAccess(gpuIdsToUse, mdlog);
1501 if (hw_opt.threadAffinity != ThreadAffinity::Off)
1503 /* Before setting affinity, check whether the affinity has changed
1504 * - which indicates that probably the OpenMP library has changed it
1505 * since we first checked).
1507 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo_->nthreads_hw_avail, TRUE);
1509 int numThreadsOnThisNode, intraNodeThreadOffset;
1510 analyzeThreadsOnThisNode(
1511 physicalNodeComm, numThreadsOnThisRank, &numThreadsOnThisNode, &intraNodeThreadOffset);
1513 /* Set the CPU affinity */
1514 gmx_set_thread_affinity(mdlog,
1517 *hwinfo_->hardwareTopology,
1518 numThreadsOnThisRank,
1519 numThreadsOnThisNode,
1520 intraNodeThreadOffset,
1524 if (mdrunOptions.timingOptions.resetStep > -1)
1529 "The -resetstep functionality is deprecated, and may be removed in a "
1532 wcycle = wallcycle_init(fplog, mdrunOptions.timingOptions.resetStep, cr);
1536 /* Master synchronizes its value of reset_counters with all nodes
1537 * including PME only nodes */
1538 int64_t reset_counters = wcycle_get_reset_counters(wcycle);
1539 gmx_bcast(sizeof(reset_counters), &reset_counters, cr->mpi_comm_mysim);
1540 wcycle_set_reset_counters(wcycle, reset_counters);
1543 // Membrane embedding must be initialized before we call init_forcerec()
1544 membedHolder.initializeMembed(fplog,
1551 &mdrunOptions.checkpointOptions.period);
1553 const bool thisRankHasPmeGpuTask = gpuTaskAssignments.thisRankHasPmeGpuTask();
1554 std::unique_ptr<MDAtoms> mdAtoms;
1555 std::unique_ptr<VirtualSitesHandler> vsite;
1556 std::unique_ptr<GpuBonded> gpuBonded;
1559 if (thisRankHasDuty(cr, DUTY_PP))
1561 mdModulesNotifier.notify(*cr);
1562 mdModulesNotifier.notify(&atomSets);
1563 mdModulesNotifier.notify(inputrec->pbcType);
1564 mdModulesNotifier.notify(SimulationTimeStep{ inputrec->delta_t });
1565 /* Initiate forcerecord */
1566 fr = new t_forcerec;
1567 fr->forceProviders = mdModules_->initForceProviders();
1568 init_forcerec(fplog,
1575 opt2fn("-table", filenames.size(), filenames.data()),
1576 opt2fn("-tablep", filenames.size(), filenames.data()),
1577 opt2fns("-tableb", filenames.size(), filenames.data()),
1579 // Dirty hack, for fixing disres and orires should be made mdmodules
1580 fr->fcdata->disres = disresdata;
1581 fr->fcdata->orires = oriresdata;
1583 // Save a handle to device stream manager to use elsewhere in the code
1584 // TODO: Forcerec is not a correct place to store it.
1585 fr->deviceStreamManager = deviceStreamManager.get();
1587 if (runScheduleWork.simulationWork.useGpuPmePpCommunication && !thisRankHasDuty(cr, DUTY_PME))
1590 deviceStreamManager != nullptr,
1591 "GPU device stream manager should be valid in order to use PME-PP direct "
1594 deviceStreamManager->streamIsValid(DeviceStreamType::PmePpTransfer),
1595 "GPU PP-PME stream should be valid in order to use GPU PME-PP direct "
1597 fr->pmePpCommGpu = std::make_unique<gmx::PmePpCommGpu>(
1600 deviceStreamManager->context(),
1601 deviceStreamManager->stream(DeviceStreamType::PmePpTransfer));
1604 fr->nbv = Nbnxm::init_nb_verlet(mdlog,
1609 runScheduleWork.simulationWork.useGpuNonbonded,
1610 deviceStreamManager.get(),
1614 // TODO: Move the logic below to a GPU bonded builder
1615 if (runScheduleWork.simulationWork.useGpuBonded)
1617 GMX_RELEASE_ASSERT(deviceStreamManager != nullptr,
1618 "GPU device stream manager should be valid in order to use GPU "
1619 "version of bonded forces.");
1620 gpuBonded = std::make_unique<GpuBonded>(
1622 fr->ic->epsfac * fr->fudgeQQ,
1623 deviceStreamManager->context(),
1624 deviceStreamManager->bondedStream(havePPDomainDecomposition(cr)),
1626 fr->gpuBonded = gpuBonded.get();
1629 /* Initialize the mdAtoms structure.
1630 * mdAtoms is not filled with atom data,
1631 * as this can not be done now with domain decomposition.
1633 mdAtoms = makeMDAtoms(fplog, mtop, *inputrec, thisRankHasPmeGpuTask);
1634 if (globalState && thisRankHasPmeGpuTask)
1636 // The pinning of coordinates in the global state object works, because we only use
1637 // PME on GPU without DD or on a separate PME rank, and because the local state pointer
1638 // points to the global state object without DD.
1639 // FIXME: MD and EM separately set up the local state - this should happen in the same
1640 // function, which should also perform the pinning.
1641 changePinningPolicy(&globalState->x, pme_get_pinning_policy());
1644 /* Initialize the virtual site communication */
1645 vsite = makeVirtualSitesHandler(mtop, cr, fr->pbcType);
1647 calc_shifts(box, fr->shift_vec);
1649 /* With periodic molecules the charge groups should be whole at start up
1650 * and the virtual sites should not be far from their proper positions.
1652 if (!inputrec->bContinuation && MASTER(cr)
1653 && !(inputrec->pbcType != PbcType::No && inputrec->bPeriodicMols))
1655 /* Make molecules whole at start of run */
1656 if (fr->pbcType != PbcType::No)
1658 do_pbc_first_mtop(fplog, inputrec->pbcType, box, &mtop, globalState->x.rvec_array());
1662 /* Correct initial vsite positions are required
1663 * for the initial distribution in the domain decomposition
1664 * and for the initial shell prediction.
1666 constructVirtualSitesGlobal(mtop, globalState->x);
1670 if (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
1672 ewaldcoeff_q = fr->ic->ewaldcoeff_q;
1673 ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
1678 /* This is a PME only node */
1680 GMX_ASSERT(globalState == nullptr,
1681 "We don't need the state on a PME only rank and expect it to be unitialized");
1683 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
1684 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
1687 gmx_pme_t* sepPmeData = nullptr;
1688 // This reference hides the fact that PME data is owned by runner on PME-only ranks and by forcerec on other ranks
1689 GMX_ASSERT(thisRankHasDuty(cr, DUTY_PP) == (fr != nullptr),
1690 "Double-checking that only PME-only ranks have no forcerec");
1691 gmx_pme_t*& pmedata = fr ? fr->pmedata : sepPmeData;
1693 // TODO should live in ewald module once its testing is improved
1695 // Later, this program could contain kernels that might be later
1696 // re-used as auto-tuning progresses, or subsequent simulations
1698 PmeGpuProgramStorage pmeGpuProgram;
1699 if (thisRankHasPmeGpuTask)
1702 (deviceStreamManager != nullptr),
1703 "GPU device stream manager should be initialized in order to use GPU for PME.");
1704 GMX_RELEASE_ASSERT((deviceInfo != nullptr),
1705 "GPU device should be initialized in order to use GPU for PME.");
1706 pmeGpuProgram = buildPmeGpuProgram(deviceStreamManager->context());
1709 /* Initiate PME if necessary,
1710 * either on all nodes or on dedicated PME nodes only. */
1711 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
1713 if (mdAtoms && mdAtoms->mdatoms())
1715 nChargePerturbed = mdAtoms->mdatoms()->nChargePerturbed;
1716 if (EVDW_PME(inputrec->vdwtype))
1718 nTypePerturbed = mdAtoms->mdatoms()->nTypePerturbed;
1721 if (cr->npmenodes > 0)
1723 /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
1724 gmx_bcast(sizeof(nChargePerturbed), &nChargePerturbed, cr->mpi_comm_mysim);
1725 gmx_bcast(sizeof(nTypePerturbed), &nTypePerturbed, cr->mpi_comm_mysim);
1728 if (thisRankHasDuty(cr, DUTY_PME))
1732 // TODO: This should be in the builder.
1733 GMX_RELEASE_ASSERT(!runScheduleWork.simulationWork.useGpuPme
1734 || (deviceStreamManager != nullptr),
1735 "Device stream manager should be valid in order to use GPU "
1738 !runScheduleWork.simulationWork.useGpuPme
1739 || deviceStreamManager->streamIsValid(DeviceStreamType::Pme),
1740 "GPU PME stream should be valid in order to use GPU version of PME.");
1742 const DeviceContext* deviceContext = runScheduleWork.simulationWork.useGpuPme
1743 ? &deviceStreamManager->context()
1745 const DeviceStream* pmeStream =
1746 runScheduleWork.simulationWork.useGpuPme
1747 ? &deviceStreamManager->stream(DeviceStreamType::Pme)
1750 pmedata = gmx_pme_init(cr,
1751 getNumPmeDomains(cr->dd),
1753 nChargePerturbed != 0,
1754 nTypePerturbed != 0,
1755 mdrunOptions.reproducible,
1758 gmx_omp_nthreads_get(emntPME),
1763 pmeGpuProgram.get(),
1766 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1771 if (EI_DYNAMICS(inputrec->eI))
1773 /* Turn on signal handling on all nodes */
1775 * (A user signal from the PME nodes (if any)
1776 * is communicated to the PP nodes.
1778 signal_handler_install();
1781 pull_t* pull_work = nullptr;
1782 if (thisRankHasDuty(cr, DUTY_PP))
1784 /* Assumes uniform use of the number of OpenMP threads */
1785 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
1787 if (inputrec->bPull)
1789 /* Initialize pull code */
1790 pull_work = init_pull(fplog,
1791 inputrec->pull.get(),
1796 inputrec->fepvals->init_lambda);
1797 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
1799 initPullHistory(pull_work, &observablesHistory);
1801 if (EI_DYNAMICS(inputrec->eI) && MASTER(cr))
1803 init_pull_output_files(pull_work, filenames.size(), filenames.data(), oenv, startingBehavior);
1807 std::unique_ptr<EnforcedRotation> enforcedRotation;
1810 /* Initialize enforced rotation code */
1811 enforcedRotation = init_rot(fplog,
1824 t_swap* swap = nullptr;
1825 if (inputrec->eSwapCoords != eswapNO)
1827 /* Initialize ion swapping code */
1828 swap = init_swapcoords(fplog,
1830 opt2fn_master("-swap", filenames.size(), filenames.data(), cr),
1833 &observablesHistory,
1841 /* Let makeConstraints know whether we have essential dynamics constraints. */
1842 auto constr = makeConstraints(
1843 mtop, *inputrec, pull_work, doEssentialDynamics, fplog, cr, ms, &nrnb, wcycle, fr->bMolPBC);
1845 /* Energy terms and groups */
1846 gmx_enerdata_t enerd(mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
1847 inputrec->fepvals->n_lambda);
1849 /* Kinetic energy data */
1850 gmx_ekindata_t ekind;
1851 init_ekindata(fplog, &(inputrec->opts), &ekind, inputrec->cos_accel);
1853 /* Set up interactive MD (IMD) */
1854 auto imdSession = makeImdSession(inputrec.get(),
1861 MASTER(cr) ? globalState->x.rvec_array() : nullptr,
1865 mdrunOptions.imdOptions,
1868 if (DOMAINDECOMP(cr))
1870 GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
1871 /* This call is not included in init_domain_decomposition mainly
1872 * because fr->cginfo_mb is set later.
1874 dd_init_bondeds(fplog,
1879 domdecOptions.checkBondedInteractions,
1883 if (runScheduleWork.simulationWork.useGpuBufferOps)
1885 fr->gpuForceReduction[gmx::AtomLocality::Local] = std::make_unique<gmx::GpuForceReduction>(
1886 deviceStreamManager->context(),
1887 deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedLocal),
1889 fr->gpuForceReduction[gmx::AtomLocality::NonLocal] = std::make_unique<gmx::GpuForceReduction>(
1890 deviceStreamManager->context(),
1891 deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedNonLocal),
1895 std::unique_ptr<gmx::StatePropagatorDataGpu> stateGpu;
1896 if (gpusWereDetected
1897 && ((runScheduleWork.simulationWork.useGpuPme && thisRankHasDuty(cr, DUTY_PME))
1898 || runScheduleWork.simulationWork.useGpuBufferOps))
1900 GpuApiCallBehavior transferKind = (inputrec->eI == eiMD && !doRerun && !useModularSimulator)
1901 ? GpuApiCallBehavior::Async
1902 : GpuApiCallBehavior::Sync;
1903 GMX_RELEASE_ASSERT(deviceStreamManager != nullptr,
1904 "GPU device stream manager should be initialized to use GPU.");
1905 stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(
1906 *deviceStreamManager, transferKind, pme_gpu_get_block_size(fr->pmedata), wcycle);
1907 fr->stateGpu = stateGpu.get();
1910 GMX_ASSERT(stopHandlerBuilder_, "Runner must provide StopHandlerBuilder to simulator.");
1911 SimulatorBuilder simulatorBuilder;
1913 simulatorBuilder.add(SimulatorStateData(globalState.get(), &observablesHistory, &enerd, &ekind));
1914 simulatorBuilder.add(std::move(membedHolder));
1915 simulatorBuilder.add(std::move(stopHandlerBuilder_));
1916 simulatorBuilder.add(SimulatorConfig(mdrunOptions, startingBehavior, &runScheduleWork));
1919 simulatorBuilder.add(SimulatorEnv(fplog, cr, ms, mdlog, oenv));
1920 simulatorBuilder.add(Profiling(&nrnb, walltime_accounting, wcycle));
1921 simulatorBuilder.add(ConstraintsParam(
1922 constr.get(), enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr, vsite.get()));
1923 // TODO: Separate `fr` to a separate add, and make the `build` handle the coupling sensibly.
1924 simulatorBuilder.add(LegacyInput(
1925 static_cast<int>(filenames.size()), filenames.data(), inputrec.get(), fr));
1926 simulatorBuilder.add(ReplicaExchangeParameters(replExParams));
1927 simulatorBuilder.add(InteractiveMD(imdSession.get()));
1928 simulatorBuilder.add(SimulatorModules(mdModules_->outputProvider(), mdModules_->notifier()));
1929 simulatorBuilder.add(CenterOfMassPulling(pull_work));
1930 // Todo move to an MDModule
1931 simulatorBuilder.add(IonSwapping(swap));
1932 simulatorBuilder.add(TopologyData(&mtop, mdAtoms.get()));
1933 simulatorBuilder.add(BoxDeformationHandle(deform.get()));
1934 simulatorBuilder.add(std::move(modularSimulatorCheckpointData));
1936 // build and run simulator object based on user-input
1937 auto simulator = simulatorBuilder.build(useModularSimulator);
1940 if (fr->pmePpCommGpu)
1942 // destroy object since it is no longer required. (This needs to be done while the GPU context still exists.)
1943 fr->pmePpCommGpu.reset();
1946 if (inputrec->bPull)
1948 finish_pull(pull_work);
1950 finish_swapcoords(swap);
1954 GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
1956 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
1957 gmx_pmeonly(pmedata,
1961 walltime_accounting,
1964 deviceStreamManager.get());
1967 wallcycle_stop(wcycle, ewcRUN);
1969 /* Finish up, write some stuff
1970 * if rerunMD, don't write last frame again
1978 walltime_accounting,
1979 fr ? fr->nbv.get() : nullptr,
1981 EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
1983 // clean up cycle counter
1984 wallcycle_destroy(wcycle);
1986 deviceStreamManager.reset(nullptr);
1990 gmx_pme_destroy(pmedata);
1994 // FIXME: this is only here to manually unpin mdAtoms->chargeA_ and state->x,
1995 // before we destroy the GPU context(s)
1996 // Pinned buffers are associated with contexts in CUDA.
1997 // As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
1998 mdAtoms.reset(nullptr);
1999 globalState.reset(nullptr);
2000 mdModules_.reset(nullptr); // destruct force providers here as they might also use the GPU
2001 gpuBonded.reset(nullptr);
2002 /* Free pinned buffers in *fr */
2005 // TODO convert to C++ so we can get rid of these frees
2009 if (!hwinfo_->deviceInfoList.empty())
2011 /* stop the GPU profiler (only CUDA) */
2015 /* With tMPI we need to wait for all ranks to finish deallocation before
2016 * destroying the CUDA context as some tMPI ranks may be sharing
2019 * This is not a concern in OpenCL where we use one context per rank.
2021 * Note: it is safe to not call the barrier on the ranks which do not use GPU,
2022 * but it is easier and more futureproof to call it on the whole node.
2024 * Note that this function needs to be called even if GPUs are not used
2025 * in this run because the PME ranks have no knowledge of whether GPUs
2026 * are used or not, but all ranks need to enter the barrier below.
2027 * \todo Remove this physical node barrier after making sure
2028 * that it's not needed anymore (with a shared GPU run).
2032 physicalNodeComm.barrier();
2034 releaseDevice(deviceInfo);
2036 /* Does what it says */
2037 print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
2038 walltime_accounting_destroy(walltime_accounting);
2040 // Ensure log file content is written
2043 gmx_fio_flush(logFileHandle);
2046 /* Reset FPEs (important for unit tests) by disabling them. Assumes no
2047 * exceptions were enabled before function was called. */
2050 gmx_fedisableexcept();
2053 auto rc = static_cast<int>(gmx_get_stop_condition());
2056 /* we need to join all threads. The sub-threads join when they
2057 exit this function, but the master thread needs to be told to
2067 Mdrunner::~Mdrunner()
2069 // Clean up of the Manager.
2070 // This will end up getting called on every thread-MPI rank, which is unnecessary,
2071 // but okay as long as threads synchronize some time before adding or accessing
2072 // a new set of restraints.
2073 if (restraintManager_)
2075 restraintManager_->clear();
2076 GMX_ASSERT(restraintManager_->countRestraints() == 0,
2077 "restraints added during runner life time should be cleared at runner "
2082 void Mdrunner::addPotential(std::shared_ptr<gmx::IRestraintPotential> puller, const std::string& name)
2084 GMX_ASSERT(restraintManager_, "Mdrunner must have a restraint manager.");
2085 // Not sure if this should be logged through the md logger or something else,
2086 // but it is helpful to have some sort of INFO level message sent somewhere.
2087 // std::cout << "Registering restraint named " << name << std::endl;
2089 // When multiple restraints are used, it may be wasteful to register them separately.
2090 // Maybe instead register an entire Restraint Manager as a force provider.
2091 restraintManager_->addToSpec(std::move(puller), name);
2094 Mdrunner::Mdrunner(std::unique_ptr<MDModules> mdModules) : mdModules_(std::move(mdModules)) {}
2096 Mdrunner::Mdrunner(Mdrunner&&) noexcept = default;
2098 //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265 in CentOS 7
2099 Mdrunner& Mdrunner::operator=(Mdrunner&& /*handle*/) noexcept(BUGFREE_NOEXCEPT_STRING) = default;
2101 class Mdrunner::BuilderImplementation
2104 BuilderImplementation() = delete;
2105 BuilderImplementation(std::unique_ptr<MDModules> mdModules, compat::not_null<SimulationContext*> context);
2106 ~BuilderImplementation();
2108 BuilderImplementation& setExtraMdrunOptions(const MdrunOptions& options,
2109 real forceWarningThreshold,
2110 StartingBehavior startingBehavior);
2112 void addHardwareDetectionResult(const gmx_hw_info_t* hwinfo);
2114 void addDomdec(const DomdecOptions& options);
2116 void addInput(SimulationInputHandle inputHolder);
2118 void addVerletList(int nstlist);
2120 void addReplicaExchange(const ReplicaExchangeParameters& params);
2122 void addNonBonded(const char* nbpu_opt);
2124 void addPME(const char* pme_opt_, const char* pme_fft_opt_);
2126 void addBondedTaskAssignment(const char* bonded_opt);
2128 void addUpdateTaskAssignment(const char* update_opt);
2130 void addHardwareOptions(const gmx_hw_opt_t& hardwareOptions);
2132 void addFilenames(ArrayRef<const t_filenm> filenames);
2134 void addOutputEnvironment(gmx_output_env_t* outputEnvironment);
2136 void addLogFile(t_fileio* logFileHandle);
2138 void addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
2143 // Default parameters copied from runner.h
2144 // \todo Clarify source(s) of default parameters.
2146 const char* nbpu_opt_ = nullptr;
2147 const char* pme_opt_ = nullptr;
2148 const char* pme_fft_opt_ = nullptr;
2149 const char* bonded_opt_ = nullptr;
2150 const char* update_opt_ = nullptr;
2152 MdrunOptions mdrunOptions_;
2154 DomdecOptions domdecOptions_;
2156 ReplicaExchangeParameters replicaExchangeParameters_;
2158 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
2161 //! World communicator, used for hardware detection and task assignment
2162 MPI_Comm libraryWorldCommunicator_ = MPI_COMM_NULL;
2164 //! Multisim communicator handle.
2165 gmx_multisim_t* multiSimulation_;
2167 //! mdrun communicator
2168 MPI_Comm simulationCommunicator_ = MPI_COMM_NULL;
2170 //! Print a warning if any force is larger than this (in kJ/mol nm).
2171 real forceWarningThreshold_ = -1;
2173 //! Whether the simulation will start afresh, or restart with/without appending.
2174 StartingBehavior startingBehavior_ = StartingBehavior::NewSimulation;
2176 //! The modules that comprise the functionality of mdrun.
2177 std::unique_ptr<MDModules> mdModules_;
2179 //! Detected hardware.
2180 const gmx_hw_info_t* hwinfo_ = nullptr;
2182 //! \brief Parallelism information.
2183 gmx_hw_opt_t hardwareOptions_;
2185 //! filename options for simulation.
2186 ArrayRef<const t_filenm> filenames_;
2188 /*! \brief Handle to output environment.
2190 * \todo gmx_output_env_t needs lifetime management.
2192 gmx_output_env_t* outputEnvironment_ = nullptr;
2194 /*! \brief Non-owning handle to MD log file.
2196 * \todo Context should own output facilities for client.
2197 * \todo Improve log file handle management.
2199 * Code managing the FILE* relies on the ability to set it to
2200 * nullptr to check whether the filehandle is valid.
2202 t_fileio* logFileHandle_ = nullptr;
2205 * \brief Builder for simulation stop signal handler.
2207 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_ = nullptr;
2210 * \brief Sources for initial simulation state.
2212 * See issue #3652 for near-term refinements to the SimulationInput interface.
2214 * See issue #3379 for broader discussion on API aspects of simulation inputs and outputs.
2216 SimulationInputHandle inputHolder_;
2219 Mdrunner::BuilderImplementation::BuilderImplementation(std::unique_ptr<MDModules> mdModules,
2220 compat::not_null<SimulationContext*> context) :
2221 mdModules_(std::move(mdModules))
2223 libraryWorldCommunicator_ = context->libraryWorldCommunicator_;
2224 simulationCommunicator_ = context->simulationCommunicator_;
2225 multiSimulation_ = context->multiSimulation_.get();
2228 Mdrunner::BuilderImplementation::~BuilderImplementation() = default;
2230 Mdrunner::BuilderImplementation&
2231 Mdrunner::BuilderImplementation::setExtraMdrunOptions(const MdrunOptions& options,
2232 const real forceWarningThreshold,
2233 const StartingBehavior startingBehavior)
2235 mdrunOptions_ = options;
2236 forceWarningThreshold_ = forceWarningThreshold;
2237 startingBehavior_ = startingBehavior;
2241 void Mdrunner::BuilderImplementation::addDomdec(const DomdecOptions& options)
2243 domdecOptions_ = options;
2246 void Mdrunner::BuilderImplementation::addVerletList(int nstlist)
2251 void Mdrunner::BuilderImplementation::addReplicaExchange(const ReplicaExchangeParameters& params)
2253 replicaExchangeParameters_ = params;
2256 Mdrunner Mdrunner::BuilderImplementation::build()
2258 auto newRunner = Mdrunner(std::move(mdModules_));
2260 newRunner.mdrunOptions = mdrunOptions_;
2261 newRunner.pforce = forceWarningThreshold_;
2262 newRunner.startingBehavior = startingBehavior_;
2263 newRunner.domdecOptions = domdecOptions_;
2265 // \todo determine an invariant to check or confirm that all gmx_hw_opt_t objects are valid
2266 newRunner.hw_opt = hardwareOptions_;
2268 // No invariant to check. This parameter exists to optionally override other behavior.
2269 newRunner.nstlist_cmdline = nstlist_;
2271 newRunner.replExParams = replicaExchangeParameters_;
2273 newRunner.filenames = filenames_;
2275 newRunner.libraryWorldCommunicator = libraryWorldCommunicator_;
2277 newRunner.simulationCommunicator = simulationCommunicator_;
2279 // nullptr is a valid value for the multisim handle
2280 newRunner.ms = multiSimulation_;
2284 newRunner.hwinfo_ = hwinfo_;
2288 GMX_THROW(gmx::APIError(
2289 "MdrunnerBuilder::addHardwareDetectionResult() is required before build()"));
2294 newRunner.inputHolder_ = std::move(inputHolder_);
2298 GMX_THROW(gmx::APIError("MdrunnerBuilder::addInput() is required before build()."));
2301 // \todo Clarify ownership and lifetime management for gmx_output_env_t
2302 // \todo Update sanity checking when output environment has clearly specified invariants.
2303 // Initialization and default values for oenv are not well specified in the current version.
2304 if (outputEnvironment_)
2306 newRunner.oenv = outputEnvironment_;
2310 GMX_THROW(gmx::APIError(
2311 "MdrunnerBuilder::addOutputEnvironment() is required before build()"));
2314 newRunner.logFileHandle = logFileHandle_;
2318 newRunner.nbpu_opt = nbpu_opt_;
2322 GMX_THROW(gmx::APIError("MdrunnerBuilder::addNonBonded() is required before build()"));
2325 if (pme_opt_ && pme_fft_opt_)
2327 newRunner.pme_opt = pme_opt_;
2328 newRunner.pme_fft_opt = pme_fft_opt_;
2332 GMX_THROW(gmx::APIError("MdrunnerBuilder::addElectrostatics() is required before build()"));
2337 newRunner.bonded_opt = bonded_opt_;
2341 GMX_THROW(gmx::APIError(
2342 "MdrunnerBuilder::addBondedTaskAssignment() is required before build()"));
2347 newRunner.update_opt = update_opt_;
2351 GMX_THROW(gmx::APIError(
2352 "MdrunnerBuilder::addUpdateTaskAssignment() is required before build() "));
2356 newRunner.restraintManager_ = std::make_unique<gmx::RestraintManager>();
2358 if (stopHandlerBuilder_)
2360 newRunner.stopHandlerBuilder_ = std::move(stopHandlerBuilder_);
2364 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>();
2370 void Mdrunner::BuilderImplementation::addHardwareDetectionResult(const gmx_hw_info_t* hwinfo)
2375 void Mdrunner::BuilderImplementation::addNonBonded(const char* nbpu_opt)
2377 nbpu_opt_ = nbpu_opt;
2380 void Mdrunner::BuilderImplementation::addPME(const char* pme_opt, const char* pme_fft_opt)
2383 pme_fft_opt_ = pme_fft_opt;
2386 void Mdrunner::BuilderImplementation::addBondedTaskAssignment(const char* bonded_opt)
2388 bonded_opt_ = bonded_opt;
2391 void Mdrunner::BuilderImplementation::addUpdateTaskAssignment(const char* update_opt)
2393 update_opt_ = update_opt;
2396 void Mdrunner::BuilderImplementation::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2398 hardwareOptions_ = hardwareOptions;
2401 void Mdrunner::BuilderImplementation::addFilenames(ArrayRef<const t_filenm> filenames)
2403 filenames_ = filenames;
2406 void Mdrunner::BuilderImplementation::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2408 outputEnvironment_ = outputEnvironment;
2411 void Mdrunner::BuilderImplementation::addLogFile(t_fileio* logFileHandle)
2413 logFileHandle_ = logFileHandle;
2416 void Mdrunner::BuilderImplementation::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2418 stopHandlerBuilder_ = std::move(builder);
2421 void Mdrunner::BuilderImplementation::addInput(SimulationInputHandle inputHolder)
2423 inputHolder_ = std::move(inputHolder);
2426 MdrunnerBuilder::MdrunnerBuilder(std::unique_ptr<MDModules> mdModules,
2427 compat::not_null<SimulationContext*> context) :
2428 impl_{ std::make_unique<Mdrunner::BuilderImplementation>(std::move(mdModules), context) }
2432 MdrunnerBuilder::~MdrunnerBuilder() = default;
2434 MdrunnerBuilder& MdrunnerBuilder::addHardwareDetectionResult(const gmx_hw_info_t* hwinfo)
2436 impl_->addHardwareDetectionResult(hwinfo);
2440 MdrunnerBuilder& MdrunnerBuilder::addSimulationMethod(const MdrunOptions& options,
2441 real forceWarningThreshold,
2442 const StartingBehavior startingBehavior)
2444 impl_->setExtraMdrunOptions(options, forceWarningThreshold, startingBehavior);
2448 MdrunnerBuilder& MdrunnerBuilder::addDomainDecomposition(const DomdecOptions& options)
2450 impl_->addDomdec(options);
2454 MdrunnerBuilder& MdrunnerBuilder::addNeighborList(int nstlist)
2456 impl_->addVerletList(nstlist);
2460 MdrunnerBuilder& MdrunnerBuilder::addReplicaExchange(const ReplicaExchangeParameters& params)
2462 impl_->addReplicaExchange(params);
2466 MdrunnerBuilder& MdrunnerBuilder::addNonBonded(const char* nbpu_opt)
2468 impl_->addNonBonded(nbpu_opt);
2472 MdrunnerBuilder& MdrunnerBuilder::addElectrostatics(const char* pme_opt, const char* pme_fft_opt)
2474 // The builder method may become more general in the future, but in this version,
2475 // parameters for PME electrostatics are both required and the only parameters
2477 if (pme_opt && pme_fft_opt)
2479 impl_->addPME(pme_opt, pme_fft_opt);
2484 gmx::InvalidInputError("addElectrostatics() arguments must be non-null pointers."));
2489 MdrunnerBuilder& MdrunnerBuilder::addBondedTaskAssignment(const char* bonded_opt)
2491 impl_->addBondedTaskAssignment(bonded_opt);
2495 MdrunnerBuilder& MdrunnerBuilder::addUpdateTaskAssignment(const char* update_opt)
2497 impl_->addUpdateTaskAssignment(update_opt);
2501 Mdrunner MdrunnerBuilder::build()
2503 return impl_->build();
2506 MdrunnerBuilder& MdrunnerBuilder::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2508 impl_->addHardwareOptions(hardwareOptions);
2512 MdrunnerBuilder& MdrunnerBuilder::addFilenames(ArrayRef<const t_filenm> filenames)
2514 impl_->addFilenames(filenames);
2518 MdrunnerBuilder& MdrunnerBuilder::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2520 impl_->addOutputEnvironment(outputEnvironment);
2524 MdrunnerBuilder& MdrunnerBuilder::addLogFile(t_fileio* logFileHandle)
2526 impl_->addLogFile(logFileHandle);
2530 MdrunnerBuilder& MdrunnerBuilder::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2532 impl_->addStopHandlerBuilder(std::move(builder));
2536 MdrunnerBuilder& MdrunnerBuilder::addInput(SimulationInputHandle input)
2538 impl_->addInput(std::move(input));
2542 MdrunnerBuilder::MdrunnerBuilder(MdrunnerBuilder&&) noexcept = default;
2544 MdrunnerBuilder& MdrunnerBuilder::operator=(MdrunnerBuilder&&) noexcept = default;