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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_context.h"
77 #include "gromacs/gpu_utils/device_stream_manager.h"
78 #include "gromacs/hardware/cpuinfo.h"
79 #include "gromacs/hardware/detecthardware.h"
80 #include "gromacs/hardware/device_management.h"
81 #include "gromacs/hardware/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/makeconstraints.h"
99 #include "gromacs/mdlib/md_support.h"
100 #include "gromacs/mdlib/mdatoms.h"
101 #include "gromacs/mdlib/sighandler.h"
102 #include "gromacs/mdlib/stophandler.h"
103 #include "gromacs/mdlib/tgroup.h"
104 #include "gromacs/mdlib/updategroups.h"
105 #include "gromacs/mdlib/vsite.h"
106 #include "gromacs/mdrun/mdmodules.h"
107 #include "gromacs/mdrun/simulationcontext.h"
108 #include "gromacs/mdrunutility/handlerestart.h"
109 #include "gromacs/mdrunutility/logging.h"
110 #include "gromacs/mdrunutility/multisim.h"
111 #include "gromacs/mdrunutility/printtime.h"
112 #include "gromacs/mdrunutility/threadaffinity.h"
113 #include "gromacs/mdtypes/commrec.h"
114 #include "gromacs/mdtypes/enerdata.h"
115 #include "gromacs/mdtypes/fcdata.h"
116 #include "gromacs/mdtypes/forcerec.h"
117 #include "gromacs/mdtypes/group.h"
118 #include "gromacs/mdtypes/inputrec.h"
119 #include "gromacs/mdtypes/interaction_const.h"
120 #include "gromacs/mdtypes/md_enums.h"
121 #include "gromacs/mdtypes/mdatom.h"
122 #include "gromacs/mdtypes/mdrunoptions.h"
123 #include "gromacs/mdtypes/observableshistory.h"
124 #include "gromacs/mdtypes/simulation_workload.h"
125 #include "gromacs/mdtypes/state.h"
126 #include "gromacs/mdtypes/state_propagator_data_gpu.h"
127 #include "gromacs/modularsimulator/modularsimulator.h"
128 #include "gromacs/nbnxm/gpu_data_mgmt.h"
129 #include "gromacs/nbnxm/nbnxm.h"
130 #include "gromacs/nbnxm/pairlist_tuning.h"
131 #include "gromacs/pbcutil/pbc.h"
132 #include "gromacs/pulling/output.h"
133 #include "gromacs/pulling/pull.h"
134 #include "gromacs/pulling/pull_rotation.h"
135 #include "gromacs/restraint/manager.h"
136 #include "gromacs/restraint/restraintmdmodule.h"
137 #include "gromacs/restraint/restraintpotential.h"
138 #include "gromacs/swap/swapcoords.h"
139 #include "gromacs/taskassignment/decidegpuusage.h"
140 #include "gromacs/taskassignment/decidesimulationworkload.h"
141 #include "gromacs/taskassignment/resourcedivision.h"
142 #include "gromacs/taskassignment/taskassignment.h"
143 #include "gromacs/taskassignment/usergpuids.h"
144 #include "gromacs/timing/gpu_timing.h"
145 #include "gromacs/timing/wallcycle.h"
146 #include "gromacs/timing/wallcyclereporting.h"
147 #include "gromacs/topology/mtop_util.h"
148 #include "gromacs/trajectory/trajectoryframe.h"
149 #include "gromacs/utility/basenetwork.h"
150 #include "gromacs/utility/cstringutil.h"
151 #include "gromacs/utility/exceptions.h"
152 #include "gromacs/utility/fatalerror.h"
153 #include "gromacs/utility/filestream.h"
154 #include "gromacs/utility/gmxassert.h"
155 #include "gromacs/utility/gmxmpi.h"
156 #include "gromacs/utility/keyvaluetree.h"
157 #include "gromacs/utility/logger.h"
158 #include "gromacs/utility/loggerbuilder.h"
159 #include "gromacs/utility/mdmodulenotification.h"
160 #include "gromacs/utility/physicalnodecommunicator.h"
161 #include "gromacs/utility/pleasecite.h"
162 #include "gromacs/utility/programcontext.h"
163 #include "gromacs/utility/smalloc.h"
164 #include "gromacs/utility/stringutil.h"
166 #include "isimulator.h"
167 #include "membedholder.h"
168 #include "replicaexchange.h"
169 #include "simulatorbuilder.h"
172 # include "corewrap.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.enableGpuPmePPComm =
210 GMX_GPU_CUDA && GMX_THREAD_MPI && getenv("GMX_GPU_PME_PP_COMMS") != nullptr;
212 #pragma GCC diagnostic pop
214 if (devFlags.enableGpuBufferOps)
216 GMX_LOG(mdlog.warning)
218 .appendTextFormatted(
219 "This run uses the 'GPU buffer ops' feature, enabled by the "
220 "GMX_USE_GPU_BUFFER_OPS environment variable.");
223 if (devFlags.forceGpuUpdateDefault)
225 GMX_LOG(mdlog.warning)
227 .appendTextFormatted(
228 "This run will default to '-update gpu' as requested by the "
229 "GMX_FORCE_UPDATE_DEFAULT_GPU environment variable. GPU update with domain "
230 "decomposition lacks substantial testing and should be used with caution.");
233 if (devFlags.enableGpuHaloExchange)
235 if (useGpuForNonbonded)
237 if (!devFlags.enableGpuBufferOps)
239 GMX_LOG(mdlog.warning)
241 .appendTextFormatted(
242 "Enabling GPU buffer operations required by GMX_GPU_DD_COMMS "
243 "(equivalent with GMX_USE_GPU_BUFFER_OPS=1).");
244 devFlags.enableGpuBufferOps = true;
246 GMX_LOG(mdlog.warning)
248 .appendTextFormatted(
249 "This run has requested the 'GPU halo exchange' feature, enabled by "
251 "GMX_GPU_DD_COMMS environment variable.");
255 GMX_LOG(mdlog.warning)
257 .appendTextFormatted(
258 "GMX_GPU_DD_COMMS environment variable detected, but the 'GPU "
259 "halo exchange' feature will not be enabled as nonbonded interactions "
260 "are not offloaded.");
261 devFlags.enableGpuHaloExchange = false;
265 if (devFlags.enableGpuPmePPComm)
267 if (pmeRunMode == PmeRunMode::GPU)
269 if (!devFlags.enableGpuBufferOps)
271 GMX_LOG(mdlog.warning)
273 .appendTextFormatted(
274 "Enabling GPU buffer operations required by GMX_GPU_PME_PP_COMMS "
275 "(equivalent with GMX_USE_GPU_BUFFER_OPS=1).");
276 devFlags.enableGpuBufferOps = true;
278 GMX_LOG(mdlog.warning)
280 .appendTextFormatted(
281 "This run uses the 'GPU PME-PP communications' feature, enabled "
282 "by the GMX_GPU_PME_PP_COMMS environment variable.");
286 std::string clarification;
287 if (pmeRunMode == PmeRunMode::Mixed)
290 "PME FFT and gather are not offloaded to the GPU (PME is running in mixed "
295 clarification = "PME is not offloaded to the GPU.";
297 GMX_LOG(mdlog.warning)
300 "GMX_GPU_PME_PP_COMMS environment variable detected, but the "
301 "'GPU PME-PP communications' feature was not enabled as "
303 devFlags.enableGpuPmePPComm = false;
310 /*! \brief Barrier for safe simultaneous thread access to mdrunner data
312 * Used to ensure that the master thread does not modify mdrunner during copy
313 * on the spawned threads. */
314 static void threadMpiMdrunnerAccessBarrier()
317 MPI_Barrier(MPI_COMM_WORLD);
321 Mdrunner Mdrunner::cloneOnSpawnedThread() const
323 auto newRunner = Mdrunner(std::make_unique<MDModules>());
325 // All runners in the same process share a restraint manager resource because it is
326 // part of the interface to the client code, which is associated only with the
327 // original thread. Handles to the same resources can be obtained by copy.
329 newRunner.restraintManager_ = std::make_unique<RestraintManager>(*restraintManager_);
332 // Copy members of master runner.
333 // \todo Replace with builder when Simulation context and/or runner phases are better defined.
334 // Ref https://gitlab.com/gromacs/gromacs/-/issues/2587 and https://gitlab.com/gromacs/gromacs/-/issues/2375
335 newRunner.hw_opt = hw_opt;
336 newRunner.filenames = filenames;
338 newRunner.oenv = oenv;
339 newRunner.mdrunOptions = mdrunOptions;
340 newRunner.domdecOptions = domdecOptions;
341 newRunner.nbpu_opt = nbpu_opt;
342 newRunner.pme_opt = pme_opt;
343 newRunner.pme_fft_opt = pme_fft_opt;
344 newRunner.bonded_opt = bonded_opt;
345 newRunner.update_opt = update_opt;
346 newRunner.nstlist_cmdline = nstlist_cmdline;
347 newRunner.replExParams = replExParams;
348 newRunner.pforce = pforce;
349 // Give the spawned thread the newly created valid communicator
350 // for the simulation.
351 newRunner.communicator = MPI_COMM_WORLD;
353 newRunner.startingBehavior = startingBehavior;
354 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>(*stopHandlerBuilder_);
356 threadMpiMdrunnerAccessBarrier();
361 /*! \brief The callback used for running on spawned threads.
363 * Obtains the pointer to the master mdrunner object from the one
364 * argument permitted to the thread-launch API call, copies it to make
365 * a new runner for this thread, reinitializes necessary data, and
366 * proceeds to the simulation. */
367 static void mdrunner_start_fn(const void* arg)
371 auto masterMdrunner = reinterpret_cast<const gmx::Mdrunner*>(arg);
372 /* copy the arg list to make sure that it's thread-local. This
373 doesn't copy pointed-to items, of course; fnm, cr and fplog
374 are reset in the call below, all others should be const. */
375 gmx::Mdrunner mdrunner = masterMdrunner->cloneOnSpawnedThread();
378 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
382 void Mdrunner::spawnThreads(int numThreadsToLaunch)
385 /* now spawn new threads that start mdrunner_start_fn(), while
386 the main thread returns. Thread affinity is handled later. */
387 if (tMPI_Init_fn(TRUE, numThreadsToLaunch, TMPI_AFFINITY_NONE, mdrunner_start_fn,
388 static_cast<const void*>(this))
391 GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
394 // Give the master thread the newly created valid communicator for
396 communicator = MPI_COMM_WORLD;
397 threadMpiMdrunnerAccessBarrier();
399 GMX_UNUSED_VALUE(numThreadsToLaunch);
400 GMX_UNUSED_VALUE(mdrunner_start_fn);
406 /*! \brief Initialize variables for Verlet scheme simulation */
407 static void prepare_verlet_scheme(FILE* fplog,
411 const gmx_mtop_t* mtop,
413 bool makeGpuPairList,
414 const gmx::CpuInfo& cpuinfo)
416 // We checked the cut-offs in grompp, but double-check here.
417 // We have PME+LJcutoff kernels for rcoulomb>rvdw.
418 if (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == eelCUT)
420 GMX_RELEASE_ASSERT(ir->rcoulomb >= ir->rvdw,
421 "With Verlet lists and PME we should have rcoulomb>=rvdw");
425 GMX_RELEASE_ASSERT(ir->rcoulomb == ir->rvdw,
426 "With Verlet lists and no PME rcoulomb and rvdw should be identical");
428 /* For NVE simulations, we will retain the initial list buffer */
429 if (EI_DYNAMICS(ir->eI) && ir->verletbuf_tol > 0 && !(EI_MD(ir->eI) && ir->etc == etcNO))
431 /* Update the Verlet buffer size for the current run setup */
433 /* Here we assume SIMD-enabled kernels are being used. But as currently
434 * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
435 * and 4x2 gives a larger buffer than 4x4, this is ok.
437 ListSetupType listType =
438 (makeGpuPairList ? ListSetupType::Gpu : ListSetupType::CpuSimdWhenSupported);
439 VerletbufListSetup listSetup = verletbufGetSafeListSetup(listType);
441 const real rlist_new =
442 calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
444 if (rlist_new != ir->rlist)
446 if (fplog != nullptr)
449 "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
450 ir->rlist, rlist_new, listSetup.cluster_size_i, listSetup.cluster_size_j);
452 ir->rlist = rlist_new;
456 if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
458 gmx_fatal(FARGS, "Can not set nstlist without %s",
459 !EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
462 if (EI_DYNAMICS(ir->eI))
464 /* Set or try nstlist values */
465 increaseNstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, makeGpuPairList, cpuinfo);
469 /*! \brief Override the nslist value in inputrec
471 * with value passed on the command line (if any)
473 static void override_nsteps_cmdline(const gmx::MDLogger& mdlog, int64_t nsteps_cmdline, t_inputrec* ir)
477 /* override with anything else than the default -2 */
478 if (nsteps_cmdline > -2)
480 char sbuf_steps[STEPSTRSIZE];
481 char sbuf_msg[STRLEN];
483 ir->nsteps = nsteps_cmdline;
484 if (EI_DYNAMICS(ir->eI) && nsteps_cmdline != -1)
487 "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
488 gmx_step_str(nsteps_cmdline, sbuf_steps), fabs(nsteps_cmdline * ir->delta_t));
492 sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps",
493 gmx_step_str(nsteps_cmdline, sbuf_steps));
496 GMX_LOG(mdlog.warning).asParagraph().appendText(sbuf_msg);
498 else if (nsteps_cmdline < -2)
500 gmx_fatal(FARGS, "Invalid nsteps value passed on the command line: %" PRId64, nsteps_cmdline);
502 /* Do nothing if nsteps_cmdline == -2 */
508 /*! \brief Return whether GPU acceleration of nonbondeds is supported with the given settings.
510 * If not, and if a warning may be issued, logs a warning about
511 * falling back to CPU code. With thread-MPI, only the first
512 * call to this function should have \c issueWarning true. */
513 static bool gpuAccelerationOfNonbondedIsUseful(const MDLogger& mdlog, const t_inputrec& ir, bool issueWarning)
515 bool gpuIsUseful = true;
518 if (ir.opts.ngener - ir.nwall > 1)
520 /* The GPU code does not support more than one energy group.
521 * If the user requested GPUs explicitly, a fatal error is given later.
525 "Multiple energy groups is not implemented for GPUs, falling back to the CPU. "
526 "For better performance, run on the GPU without energy groups and then do "
527 "gmx mdrun -rerun option on the trajectory with an energy group .tpr file.";
533 warning = "TPI is not implemented for GPUs.";
536 if (!gpuIsUseful && issueWarning)
538 GMX_LOG(mdlog.warning).asParagraph().appendText(warning);
544 //! Initializes the logger for mdrun.
545 static gmx::LoggerOwner buildLogger(FILE* fplog, const bool isSimulationMasterRank)
547 gmx::LoggerBuilder builder;
548 if (fplog != nullptr)
550 builder.addTargetFile(gmx::MDLogger::LogLevel::Info, fplog);
552 if (isSimulationMasterRank)
554 builder.addTargetStream(gmx::MDLogger::LogLevel::Warning, &gmx::TextOutputFile::standardError());
556 return builder.build();
559 //! Make a TaskTarget from an mdrun argument string.
560 static TaskTarget findTaskTarget(const char* optionString)
562 TaskTarget returnValue = TaskTarget::Auto;
564 if (strncmp(optionString, "auto", 3) == 0)
566 returnValue = TaskTarget::Auto;
568 else if (strncmp(optionString, "cpu", 3) == 0)
570 returnValue = TaskTarget::Cpu;
572 else if (strncmp(optionString, "gpu", 3) == 0)
574 returnValue = TaskTarget::Gpu;
578 GMX_ASSERT(false, "Option string should have been checked for sanity already");
584 //! Finish run, aggregate data to print performance info.
585 static void finish_run(FILE* fplog,
586 const gmx::MDLogger& mdlog,
588 const t_inputrec* inputrec,
590 gmx_wallcycle_t wcycle,
591 gmx_walltime_accounting_t walltime_accounting,
592 nonbonded_verlet_t* nbv,
593 const gmx_pme_t* pme,
597 double nbfs = 0, mflop = 0;
598 double elapsed_time, elapsed_time_over_all_ranks, elapsed_time_over_all_threads,
599 elapsed_time_over_all_threads_over_all_ranks;
600 /* Control whether it is valid to print a report. Only the
601 simulation master may print, but it should not do so if the run
602 terminated e.g. before a scheduled reset step. This is
603 complicated by the fact that PME ranks are unaware of the
604 reason why they were sent a pmerecvqxFINISH. To avoid
605 communication deadlocks, we always do the communication for the
606 report, even if we've decided not to write the report, because
607 how long it takes to finish the run is not important when we've
608 decided not to report on the simulation performance.
610 Further, we only report performance for dynamical integrators,
611 because those are the only ones for which we plan to
612 consider doing any optimizations. */
613 bool printReport = EI_DYNAMICS(inputrec->eI) && SIMMASTER(cr);
615 if (printReport && !walltime_accounting_get_valid_finish(walltime_accounting))
617 GMX_LOG(mdlog.warning)
619 .appendText("Simulation ended prematurely, no performance report will be written.");
624 std::unique_ptr<t_nrnb> nrnbTotalStorage;
627 nrnbTotalStorage = std::make_unique<t_nrnb>();
628 nrnb_tot = nrnbTotalStorage.get();
630 MPI_Allreduce(nrnb->n, nrnb_tot->n, eNRNB, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
638 elapsed_time = walltime_accounting_get_time_since_reset(walltime_accounting);
639 elapsed_time_over_all_threads =
640 walltime_accounting_get_time_since_reset_over_all_threads(walltime_accounting);
644 /* reduce elapsed_time over all MPI ranks in the current simulation */
645 MPI_Allreduce(&elapsed_time, &elapsed_time_over_all_ranks, 1, MPI_DOUBLE, MPI_SUM,
647 elapsed_time_over_all_ranks /= cr->nnodes;
648 /* Reduce elapsed_time_over_all_threads over all MPI ranks in the
649 * current simulation. */
650 MPI_Allreduce(&elapsed_time_over_all_threads, &elapsed_time_over_all_threads_over_all_ranks,
651 1, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
656 elapsed_time_over_all_ranks = elapsed_time;
657 elapsed_time_over_all_threads_over_all_ranks = elapsed_time_over_all_threads;
662 print_flop(fplog, nrnb_tot, &nbfs, &mflop);
665 if (thisRankHasDuty(cr, DUTY_PP) && DOMAINDECOMP(cr))
667 print_dd_statistics(cr, inputrec, fplog);
670 /* TODO Move the responsibility for any scaling by thread counts
671 * to the code that handled the thread region, so that there's a
672 * mechanism to keep cycle counting working during the transition
673 * to task parallelism. */
674 int nthreads_pp = gmx_omp_nthreads_get(emntNonbonded);
675 int nthreads_pme = gmx_omp_nthreads_get(emntPME);
676 wallcycle_scale_by_num_threads(wcycle, thisRankHasDuty(cr, DUTY_PME) && !thisRankHasDuty(cr, DUTY_PP),
677 nthreads_pp, nthreads_pme);
678 auto cycle_sum(wallcycle_sum(cr, wcycle));
682 auto nbnxn_gpu_timings =
683 (nbv != nullptr && nbv->useGpu()) ? Nbnxm::gpu_get_timings(nbv->gpu_nbv) : nullptr;
684 gmx_wallclock_gpu_pme_t pme_gpu_timings = {};
686 if (pme_gpu_task_enabled(pme))
688 pme_gpu_get_timings(pme, &pme_gpu_timings);
690 wallcycle_print(fplog, mdlog, cr->nnodes, cr->npmenodes, nthreads_pp, nthreads_pme,
691 elapsed_time_over_all_ranks, wcycle, cycle_sum, nbnxn_gpu_timings,
694 if (EI_DYNAMICS(inputrec->eI))
696 delta_t = inputrec->delta_t;
701 print_perf(fplog, elapsed_time_over_all_threads_over_all_ranks, elapsed_time_over_all_ranks,
702 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
703 delta_t, nbfs, mflop);
707 print_perf(stderr, elapsed_time_over_all_threads_over_all_ranks, elapsed_time_over_all_ranks,
708 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
709 delta_t, nbfs, mflop);
714 int Mdrunner::mdrunner()
717 t_forcerec* fr = nullptr;
718 real ewaldcoeff_q = 0;
719 real ewaldcoeff_lj = 0;
720 int nChargePerturbed = -1, nTypePerturbed = 0;
721 gmx_wallcycle_t wcycle;
722 gmx_walltime_accounting_t walltime_accounting = nullptr;
723 MembedHolder membedHolder(filenames.size(), filenames.data());
724 gmx_hw_info_t* hwinfo = nullptr;
726 /* CAUTION: threads may be started later on in this function, so
727 cr doesn't reflect the final parallel state right now */
730 /* TODO: inputrec should tell us whether we use an algorithm, not a file option */
731 const bool doEssentialDynamics = opt2bSet("-ei", filenames.size(), filenames.data());
732 const bool doRerun = mdrunOptions.rerun;
734 // Handle task-assignment related user options.
735 EmulateGpuNonbonded emulateGpuNonbonded =
736 (getenv("GMX_EMULATE_GPU") != nullptr ? EmulateGpuNonbonded::Yes : EmulateGpuNonbonded::No);
738 std::vector<int> userGpuTaskAssignment;
741 userGpuTaskAssignment = parseUserTaskAssignmentString(hw_opt.userGpuTaskAssignment);
743 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
744 auto nonbondedTarget = findTaskTarget(nbpu_opt);
745 auto pmeTarget = findTaskTarget(pme_opt);
746 auto pmeFftTarget = findTaskTarget(pme_fft_opt);
747 auto bondedTarget = findTaskTarget(bonded_opt);
748 auto updateTarget = findTaskTarget(update_opt);
750 FILE* fplog = nullptr;
751 // If we are appending, we don't write log output because we need
752 // to check that the old log file matches what the checkpoint file
753 // expects. Otherwise, we should start to write log output now if
754 // there is a file ready for it.
755 if (logFileHandle != nullptr && startingBehavior != StartingBehavior::RestartWithAppending)
757 fplog = gmx_fio_getfp(logFileHandle);
759 const bool isSimulationMasterRank = findIsSimulationMasterRank(ms, communicator);
760 gmx::LoggerOwner logOwner(buildLogger(fplog, isSimulationMasterRank));
761 gmx::MDLogger mdlog(logOwner.logger());
763 // TODO The thread-MPI master rank makes a working
764 // PhysicalNodeCommunicator here, but it gets rebuilt by all ranks
765 // after the threads have been launched. This works because no use
766 // is made of that communicator until after the execution paths
767 // have rejoined. But it is likely that we can improve the way
768 // this is expressed, e.g. by expressly running detection only the
769 // master rank for thread-MPI, rather than relying on the mutex
770 // and reference count.
771 PhysicalNodeCommunicator physicalNodeComm(communicator, gmx_physicalnode_id_hash());
772 hwinfo = gmx_detect_hardware(mdlog, physicalNodeComm);
774 gmx_print_detected_hardware(fplog, isSimulationMasterRank && isMasterSim(ms), mdlog, hwinfo);
776 std::vector<int> gpuIdsToUse = makeGpuIdsToUse(hwinfo->gpu_info, hw_opt.gpuIdsAvailable);
778 // Print citation requests after all software/hardware printing
779 pleaseCiteGromacs(fplog);
781 // Note: legacy program logic relies on checking whether these pointers are assigned.
782 // Objects may or may not be allocated later.
783 std::unique_ptr<t_inputrec> inputrec;
784 std::unique_ptr<t_state> globalState;
786 auto partialDeserializedTpr = std::make_unique<PartialDeserializedTprFile>();
788 if (isSimulationMasterRank)
790 // Allocate objects to be initialized by later function calls.
791 /* Only the master rank has the global state */
792 globalState = std::make_unique<t_state>();
793 inputrec = std::make_unique<t_inputrec>();
795 /* Read (nearly) all data required for the simulation
796 * and keep the partly serialized tpr contents to send to other ranks later
798 *partialDeserializedTpr = read_tpx_state(ftp2fn(efTPR, filenames.size(), filenames.data()),
799 inputrec.get(), globalState.get(), &mtop);
802 /* Check and update the hardware options for internal consistency */
803 checkAndUpdateHardwareOptions(mdlog, &hw_opt, isSimulationMasterRank, domdecOptions.numPmeRanks,
806 if (GMX_THREAD_MPI && isSimulationMasterRank)
808 bool useGpuForNonbonded = false;
809 bool useGpuForPme = false;
812 GMX_RELEASE_ASSERT(inputrec != nullptr, "Keep the compiler happy");
814 // If the user specified the number of ranks, then we must
815 // respect that, but in default mode, we need to allow for
816 // the number of GPUs to choose the number of ranks.
817 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
818 useGpuForNonbonded = decideWhetherToUseGpusForNonbondedWithThreadMpi(
819 nonbondedTarget, gpuIdsToUse, userGpuTaskAssignment, emulateGpuNonbonded,
820 canUseGpuForNonbonded,
821 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, GMX_THREAD_MPI),
822 hw_opt.nthreads_tmpi);
823 useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi(
824 useGpuForNonbonded, pmeTarget, gpuIdsToUse, userGpuTaskAssignment, *hwinfo,
825 *inputrec, hw_opt.nthreads_tmpi, domdecOptions.numPmeRanks);
827 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
829 /* Determine how many thread-MPI ranks to start.
831 * TODO Over-writing the user-supplied value here does
832 * prevent any possible subsequent checks from working
834 hw_opt.nthreads_tmpi =
835 get_nthreads_mpi(hwinfo, &hw_opt, gpuIdsToUse, useGpuForNonbonded, useGpuForPme,
836 inputrec.get(), &mtop, mdlog, membedHolder.doMembed());
838 // Now start the threads for thread MPI.
839 spawnThreads(hw_opt.nthreads_tmpi);
840 // The spawned threads enter mdrunner() and execution of
841 // master and spawned threads joins at the end of this block.
842 physicalNodeComm = PhysicalNodeCommunicator(communicator, gmx_physicalnode_id_hash());
845 GMX_RELEASE_ASSERT(ms || communicator == MPI_COMM_WORLD,
846 "Must have valid world communicator unless running a multi-simulation");
847 CommrecHandle crHandle = init_commrec(communicator);
848 t_commrec* cr = crHandle.get();
849 GMX_RELEASE_ASSERT(cr != nullptr, "Must have valid commrec");
853 /* now broadcast everything to the non-master nodes/threads: */
854 if (!isSimulationMasterRank)
856 // Until now, only the master rank has a non-null pointer.
857 // On non-master ranks, allocate the object that will receive data in the following call.
858 inputrec = std::make_unique<t_inputrec>();
860 init_parallel(cr->mpiDefaultCommunicator, MASTER(cr), inputrec.get(), &mtop,
861 partialDeserializedTpr.get());
863 GMX_RELEASE_ASSERT(inputrec != nullptr, "All ranks should have a valid inputrec now");
864 partialDeserializedTpr.reset(nullptr);
866 // Now the number of ranks is known to all ranks, and each knows
867 // the inputrec read by the master rank. The ranks can now all run
868 // the task-deciding functions and will agree on the result
869 // without needing to communicate.
870 const bool useDomainDecomposition = (PAR(cr) && !(EI_TPI(inputrec->eI) || inputrec->eI == eiNM));
872 // Note that these variables describe only their own node.
874 // Note that when bonded interactions run on a GPU they always run
875 // alongside a nonbonded task, so do not influence task assignment
876 // even though they affect the force calculation workload.
877 bool useGpuForNonbonded = false;
878 bool useGpuForPme = false;
879 bool useGpuForBonded = false;
880 bool useGpuForUpdate = false;
881 bool gpusWereDetected = hwinfo->ngpu_compatible_tot > 0;
884 // It's possible that there are different numbers of GPUs on
885 // different nodes, which is the user's responsibility to
886 // handle. If unsuitable, we will notice that during task
888 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
889 useGpuForNonbonded = decideWhetherToUseGpusForNonbonded(
890 nonbondedTarget, userGpuTaskAssignment, emulateGpuNonbonded, canUseGpuForNonbonded,
891 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, !GMX_THREAD_MPI), gpusWereDetected);
892 useGpuForPme = decideWhetherToUseGpusForPme(
893 useGpuForNonbonded, pmeTarget, userGpuTaskAssignment, *hwinfo, *inputrec,
894 cr->sizeOfDefaultCommunicator, domdecOptions.numPmeRanks, gpusWereDetected);
895 auto canUseGpuForBonded = buildSupportsGpuBondeds(nullptr)
896 && inputSupportsGpuBondeds(*inputrec, mtop, nullptr);
897 useGpuForBonded = decideWhetherToUseGpusForBonded(
898 useGpuForNonbonded, useGpuForPme, bondedTarget, canUseGpuForBonded,
899 EVDW_PME(inputrec->vdwtype), EEL_PME_EWALD(inputrec->coulombtype),
900 domdecOptions.numPmeRanks, gpusWereDetected);
902 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
904 const PmeRunMode pmeRunMode = determinePmeRunMode(useGpuForPme, pmeFftTarget, *inputrec);
906 // Initialize development feature flags that enabled by environment variable
907 // and report those features that are enabled.
908 const DevelopmentFeatureFlags devFlags =
909 manageDevelopmentFeatures(mdlog, useGpuForNonbonded, pmeRunMode);
911 const bool useModularSimulator =
912 checkUseModularSimulator(false, inputrec.get(), doRerun, mtop, ms, replExParams,
913 nullptr, doEssentialDynamics, membedHolder.doMembed());
916 // TODO: hide restraint implementation details from Mdrunner.
917 // There is nothing unique about restraints at this point as far as the
918 // Mdrunner is concerned. The Mdrunner should just be getting a sequence of
919 // factory functions from the SimulationContext on which to call mdModules_->add().
920 // TODO: capture all restraints into a single RestraintModule, passed to the runner builder.
921 for (auto&& restraint : restraintManager_->getRestraints())
923 auto module = RestraintMDModule::create(restraint, restraint->sites());
924 mdModules_->add(std::move(module));
927 // TODO: Error handling
928 mdModules_->assignOptionsToModules(*inputrec->params, nullptr);
929 // now that the MdModules know their options, they know which callbacks to sign up to
930 mdModules_->subscribeToSimulationSetupNotifications();
931 const auto& mdModulesNotifier = mdModules_->notifier().simulationSetupNotifications_;
933 if (inputrec->internalParameters != nullptr)
935 mdModulesNotifier.notify(*inputrec->internalParameters);
938 if (fplog != nullptr)
940 pr_inputrec(fplog, 0, "Input Parameters", inputrec.get(), FALSE);
941 fprintf(fplog, "\n");
946 /* In rerun, set velocities to zero if present */
947 if (doRerun && ((globalState->flags & (1 << estV)) != 0))
949 // rerun does not use velocities
953 "Rerun trajectory contains velocities. Rerun does only evaluate "
954 "potential energy and forces. The velocities will be ignored.");
955 for (int i = 0; i < globalState->natoms; i++)
957 clear_rvec(globalState->v[i]);
959 globalState->flags &= ~(1 << estV);
962 /* now make sure the state is initialized and propagated */
963 set_state_entries(globalState.get(), inputrec.get(), useModularSimulator);
966 /* NM and TPI parallelize over force/energy calculations, not atoms,
967 * so we need to initialize and broadcast the global state.
969 if (inputrec->eI == eiNM || inputrec->eI == eiTPI)
973 globalState = std::make_unique<t_state>();
975 broadcastStateWithoutDynamics(cr->mpiDefaultCommunicator, DOMAINDECOMP(cr), PAR(cr),
979 /* A parallel command line option consistency check that we can
980 only do after any threads have started. */
982 && (domdecOptions.numCells[XX] > 1 || domdecOptions.numCells[YY] > 1
983 || domdecOptions.numCells[ZZ] > 1 || domdecOptions.numPmeRanks > 0))
986 "The -dd or -npme option request a parallel simulation, "
988 "but %s was compiled without threads or MPI enabled",
989 output_env_get_program_display_name(oenv));
991 "but the number of MPI-threads (option -ntmpi) is not set or is 1");
993 "but %s was not started through mpirun/mpiexec or only one rank was requested "
994 "through mpirun/mpiexec",
995 output_env_get_program_display_name(oenv));
999 if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
1002 "The .mdp file specified an energy mininization or normal mode algorithm, and "
1003 "these are not compatible with mdrun -rerun");
1006 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
1008 if (domdecOptions.numPmeRanks > 0)
1010 gmx_fatal_collective(FARGS, cr->mpiDefaultCommunicator, MASTER(cr),
1011 "PME-only ranks are requested, but the system does not use PME "
1012 "for electrostatics or LJ");
1015 domdecOptions.numPmeRanks = 0;
1018 if (useGpuForNonbonded && domdecOptions.numPmeRanks < 0)
1020 /* With NB GPUs we don't automatically use PME-only CPU ranks. PME ranks can
1021 * improve performance with many threads per GPU, since our OpenMP
1022 * scaling is bad, but it's difficult to automate the setup.
1024 domdecOptions.numPmeRanks = 0;
1028 if (domdecOptions.numPmeRanks < 0)
1030 domdecOptions.numPmeRanks = 0;
1031 // TODO possibly print a note that one can opt-in for a separate PME GPU rank?
1035 GMX_RELEASE_ASSERT(domdecOptions.numPmeRanks <= 1,
1036 "PME GPU decomposition is not supported");
1043 fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
1047 /* NMR restraints must be initialized before load_checkpoint,
1048 * since with time averaging the history is added to t_state.
1049 * For proper consistency check we therefore need to extend
1051 * So the PME-only nodes (if present) will also initialize
1052 * the distance restraints.
1055 /* This needs to be called before read_checkpoint to extend the state */
1056 t_disresdata* disresdata;
1057 snew(disresdata, 1);
1058 init_disres(fplog, &mtop, inputrec.get(), DisResRunMode::MDRun,
1059 MASTER(cr) ? DDRole::Master : DDRole::Agent,
1060 PAR(cr) ? NumRanks::Multiple : NumRanks::Single, cr->mpi_comm_mysim, ms, disresdata,
1061 globalState.get(), replExParams.exchangeInterval > 0);
1063 t_oriresdata* oriresdata;
1064 snew(oriresdata, 1);
1065 init_orires(fplog, &mtop, inputrec.get(), cr, ms, globalState.get(), oriresdata);
1067 auto deform = prepareBoxDeformation(
1068 globalState != nullptr ? globalState->box : box, MASTER(cr) ? DDRole::Master : DDRole::Agent,
1069 PAR(cr) ? NumRanks::Multiple : NumRanks::Single, cr->mpi_comm_mygroup, *inputrec);
1071 ObservablesHistory observablesHistory = {};
1073 if (startingBehavior != StartingBehavior::NewSimulation)
1075 /* Check if checkpoint file exists before doing continuation.
1076 * This way we can use identical input options for the first and subsequent runs...
1078 if (mdrunOptions.numStepsCommandline > -2)
1080 /* Temporarily set the number of steps to unlimited to avoid
1081 * triggering the nsteps check in load_checkpoint().
1082 * This hack will go away soon when the -nsteps option is removed.
1084 inputrec->nsteps = -1;
1087 load_checkpoint(opt2fn_master("-cpi", filenames.size(), filenames.data(), cr),
1088 logFileHandle, cr, domdecOptions.numCells, inputrec.get(), globalState.get(),
1089 &observablesHistory, mdrunOptions.reproducible, mdModules_->notifier());
1091 if (startingBehavior == StartingBehavior::RestartWithAppending && logFileHandle)
1093 // Now we can start normal logging to the truncated log file.
1094 fplog = gmx_fio_getfp(logFileHandle);
1095 prepareLogAppending(fplog);
1096 logOwner = buildLogger(fplog, MASTER(cr));
1097 mdlog = logOwner.logger();
1101 if (mdrunOptions.numStepsCommandline > -2)
1106 "The -nsteps functionality is deprecated, and may be removed in a future "
1108 "Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp "
1111 /* override nsteps with value set on the commandline */
1112 override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec.get());
1114 if (isSimulationMasterRank)
1116 copy_mat(globalState->box, box);
1121 gmx_bcast(sizeof(box), box, cr->mpiDefaultCommunicator);
1124 if (inputrec->cutoff_scheme != ecutsVERLET)
1127 "This group-scheme .tpr file can no longer be run by mdrun. Please update to the "
1128 "Verlet scheme, or use an earlier version of GROMACS if necessary.");
1130 /* Update rlist and nstlist. */
1131 /* Note: prepare_verlet_scheme is calling increaseNstlist(...), which (while attempting to
1132 * increase rlist) tries to check if the newly chosen value fits with the DD scheme. As this is
1133 * run before any DD scheme is set up, this check is never executed. See #3334 for more details.
1135 prepare_verlet_scheme(fplog, cr, inputrec.get(), nstlist_cmdline, &mtop, box,
1136 useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes),
1139 const bool prefer1DAnd1PulseDD = (devFlags.enableGpuHaloExchange && useGpuForNonbonded);
1140 // This builder is necessary while we have multi-part construction
1141 // of DD. Before DD is constructed, we use the existence of
1142 // the builder object to indicate that further construction of DD
1144 std::unique_ptr<DomainDecompositionBuilder> ddBuilder;
1145 if (useDomainDecomposition)
1147 ddBuilder = std::make_unique<DomainDecompositionBuilder>(
1148 mdlog, cr, domdecOptions, mdrunOptions, prefer1DAnd1PulseDD, mtop, *inputrec, box,
1149 positionsFromStatePointer(globalState.get()));
1153 /* PME, if used, is done on all nodes with 1D decomposition */
1154 cr->nnodes = cr->sizeOfDefaultCommunicator;
1155 cr->sim_nodeid = cr->rankInDefaultCommunicator;
1156 cr->nodeid = cr->rankInDefaultCommunicator;
1158 cr->duty = (DUTY_PP | DUTY_PME);
1160 if (inputrec->pbcType == PbcType::Screw)
1162 gmx_fatal(FARGS, "pbc=screw is only implemented with domain decomposition");
1166 // Produce the task assignment for this rank - done after DD is constructed
1167 GpuTaskAssignments gpuTaskAssignments = GpuTaskAssignmentsBuilder::build(
1168 gpuIdsToUse, userGpuTaskAssignment, *hwinfo, communicator, physicalNodeComm,
1169 nonbondedTarget, pmeTarget, bondedTarget, updateTarget, useGpuForNonbonded,
1170 useGpuForPme, thisRankHasDuty(cr, DUTY_PP),
1171 // TODO cr->duty & DUTY_PME should imply that a PME
1172 // algorithm is active, but currently does not.
1173 EEL_PME(inputrec->coulombtype) && thisRankHasDuty(cr, DUTY_PME));
1175 // Get the device handles for the modules, nullptr when no task is assigned.
1177 DeviceInformation* deviceInfo = gpuTaskAssignments.initDevice(&deviceId);
1179 // timing enabling - TODO put this in gpu_utils (even though generally this is just option handling?)
1180 bool useTiming = true;
1184 /* WARNING: CUDA timings are incorrect with multiple streams.
1185 * This is the main reason why they are disabled by default.
1187 // TODO: Consider turning on by default when we can detect nr of streams.
1188 useTiming = (getenv("GMX_ENABLE_GPU_TIMING") != nullptr);
1190 else if (GMX_GPU_OPENCL)
1192 useTiming = (getenv("GMX_DISABLE_GPU_TIMING") == nullptr);
1195 // TODO Currently this is always built, yet DD partition code
1196 // checks if it is built before using it. Probably it should
1197 // become an MDModule that is made only when another module
1198 // requires it (e.g. pull, CompEl, density fitting), so that we
1199 // don't update the local atom sets unilaterally every step.
1200 LocalAtomSetManager atomSets;
1203 // TODO Pass the GPU streams to ddBuilder to use in buffer
1204 // transfers (e.g. halo exchange)
1205 cr->dd = ddBuilder->build(&atomSets);
1206 // The builder's job is done, so destruct it
1207 ddBuilder.reset(nullptr);
1208 // Note that local state still does not exist yet.
1211 // The GPU update is decided here because we need to know whether the constraints or
1212 // SETTLEs can span accross the domain borders (i.e. whether or not update groups are
1213 // defined). This is only known after DD is initialized, hence decision on using GPU
1214 // update is done so late.
1217 const bool useUpdateGroups = cr->dd ? ddUsesUpdateGroups(*cr->dd) : false;
1219 useGpuForUpdate = decideWhetherToUseGpuForUpdate(
1220 useDomainDecomposition, useUpdateGroups, pmeRunMode, domdecOptions.numPmeRanks > 0,
1221 useGpuForNonbonded, updateTarget, gpusWereDetected, *inputrec, mtop,
1222 doEssentialDynamics, gmx_mtop_ftype_count(mtop, F_ORIRES) > 0,
1223 replExParams.exchangeInterval > 0, doRerun, devFlags, mdlog);
1225 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1227 const bool printHostName = (cr->nnodes > 1);
1228 gpuTaskAssignments.reportGpuUsage(mdlog, printHostName, useGpuForBonded, pmeRunMode, useGpuForUpdate);
1230 std::unique_ptr<DeviceStreamManager> deviceStreamManager = nullptr;
1232 if (deviceInfo != nullptr)
1234 if (DOMAINDECOMP(cr) && thisRankHasDuty(cr, DUTY_PP))
1236 dd_setup_dlb_resource_sharing(cr, deviceId);
1238 deviceStreamManager = std::make_unique<DeviceStreamManager>(
1239 *deviceInfo, useGpuForPme, useGpuForNonbonded, havePPDomainDecomposition(cr),
1240 useGpuForUpdate, useTiming);
1243 // If the user chose a task assignment, give them some hints
1244 // where appropriate.
1245 if (!userGpuTaskAssignment.empty())
1247 gpuTaskAssignments.logPerformanceHints(mdlog, ssize(gpuIdsToUse));
1252 /* After possible communicator splitting in make_dd_communicators.
1253 * we can set up the intra/inter node communication.
1255 gmx_setup_nodecomm(fplog, cr);
1261 GMX_LOG(mdlog.warning)
1263 .appendTextFormatted(
1264 "This is simulation %d out of %d running as a composite GROMACS\n"
1265 "multi-simulation job. Setup for this simulation:\n",
1266 ms->simulationIndex_, ms->numSimulations_);
1268 GMX_LOG(mdlog.warning)
1269 .appendTextFormatted("Using %d MPI %s\n", cr->nnodes,
1271 cr->nnodes == 1 ? "thread" : "threads"
1273 cr->nnodes == 1 ? "process" : "processes"
1279 // If mdrun -pin auto honors any affinity setting that already
1280 // exists. If so, it is nice to provide feedback about whether
1281 // that existing affinity setting was from OpenMP or something
1282 // else, so we run this code both before and after we initialize
1283 // the OpenMP support.
1284 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo->nthreads_hw_avail, FALSE);
1285 /* Check and update the number of OpenMP threads requested */
1286 checkAndUpdateRequestedNumOpenmpThreads(&hw_opt, *hwinfo, cr, ms, physicalNodeComm.size_,
1287 pmeRunMode, mtop, *inputrec);
1289 gmx_omp_nthreads_init(mdlog, cr, hwinfo->nthreads_hw_avail, physicalNodeComm.size_,
1290 hw_opt.nthreads_omp, hw_opt.nthreads_omp_pme, !thisRankHasDuty(cr, DUTY_PP));
1292 // Enable FP exception detection, but not in
1293 // Release mode and not for compilers with known buggy FP
1294 // exception support (clang with any optimization) or suspected
1295 // buggy FP exception support (gcc 7.* with optimization).
1296 #if !defined NDEBUG \
1297 && !((defined __clang__ || (defined(__GNUC__) && !defined(__ICC) && __GNUC__ == 7)) \
1298 && defined __OPTIMIZE__)
1299 const bool bEnableFPE = true;
1301 const bool bEnableFPE = false;
1303 // FIXME - reconcile with gmx_feenableexcept() call from CommandLineModuleManager::run()
1306 gmx_feenableexcept();
1309 /* Now that we know the setup is consistent, check for efficiency */
1310 check_resource_division_efficiency(hwinfo, gpuTaskAssignments.thisRankHasAnyGpuTask(),
1311 mdrunOptions.ntompOptionIsSet, cr, mdlog);
1313 /* getting number of PP/PME threads on this MPI / tMPI rank.
1314 PME: env variable should be read only on one node to make sure it is
1315 identical everywhere;
1317 const int numThreadsOnThisRank = thisRankHasDuty(cr, DUTY_PP) ? gmx_omp_nthreads_get(emntNonbonded)
1318 : gmx_omp_nthreads_get(emntPME);
1319 checkHardwareOversubscription(numThreadsOnThisRank, cr->nodeid, *hwinfo->hardwareTopology,
1320 physicalNodeComm, mdlog);
1322 // Enable Peer access between GPUs where available
1323 // Only for DD, only master PP rank needs to perform setup, and only if thread MPI plus
1324 // any of the GPU communication features are active.
1325 if (DOMAINDECOMP(cr) && MASTER(cr) && thisRankHasDuty(cr, DUTY_PP) && GMX_THREAD_MPI
1326 && (devFlags.enableGpuHaloExchange || devFlags.enableGpuPmePPComm))
1328 setupGpuDevicePeerAccess(gpuIdsToUse, mdlog);
1331 if (hw_opt.threadAffinity != ThreadAffinity::Off)
1333 /* Before setting affinity, check whether the affinity has changed
1334 * - which indicates that probably the OpenMP library has changed it
1335 * since we first checked).
1337 gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo->nthreads_hw_avail, TRUE);
1339 int numThreadsOnThisNode, intraNodeThreadOffset;
1340 analyzeThreadsOnThisNode(physicalNodeComm, numThreadsOnThisRank, &numThreadsOnThisNode,
1341 &intraNodeThreadOffset);
1343 /* Set the CPU affinity */
1344 gmx_set_thread_affinity(mdlog, cr, &hw_opt, *hwinfo->hardwareTopology, numThreadsOnThisRank,
1345 numThreadsOnThisNode, intraNodeThreadOffset, nullptr);
1348 if (mdrunOptions.timingOptions.resetStep > -1)
1353 "The -resetstep functionality is deprecated, and may be removed in a "
1356 wcycle = wallcycle_init(fplog, mdrunOptions.timingOptions.resetStep, cr);
1360 /* Master synchronizes its value of reset_counters with all nodes
1361 * including PME only nodes */
1362 int64_t reset_counters = wcycle_get_reset_counters(wcycle);
1363 gmx_bcast(sizeof(reset_counters), &reset_counters, cr->mpi_comm_mysim);
1364 wcycle_set_reset_counters(wcycle, reset_counters);
1367 // Membrane embedding must be initialized before we call init_forcerec()
1368 membedHolder.initializeMembed(fplog, filenames.size(), filenames.data(), &mtop, inputrec.get(),
1369 globalState.get(), cr, &mdrunOptions.checkpointOptions.period);
1371 const bool thisRankHasPmeGpuTask = gpuTaskAssignments.thisRankHasPmeGpuTask();
1372 std::unique_ptr<MDAtoms> mdAtoms;
1373 std::unique_ptr<VirtualSitesHandler> vsite;
1374 std::unique_ptr<GpuBonded> gpuBonded;
1377 if (thisRankHasDuty(cr, DUTY_PP))
1379 mdModulesNotifier.notify(*cr);
1380 mdModulesNotifier.notify(&atomSets);
1381 mdModulesNotifier.notify(inputrec->pbcType);
1382 mdModulesNotifier.notify(SimulationTimeStep{ inputrec->delta_t });
1383 /* Initiate forcerecord */
1384 fr = new t_forcerec;
1385 fr->forceProviders = mdModules_->initForceProviders();
1386 init_forcerec(fplog, mdlog, fr, inputrec.get(), &mtop, cr, box,
1387 opt2fn("-table", filenames.size(), filenames.data()),
1388 opt2fn("-tablep", filenames.size(), filenames.data()),
1389 opt2fns("-tableb", filenames.size(), filenames.data()), pforce);
1390 // Dirty hack, for fixing disres and orires should be made mdmodules
1391 fr->listedForces->fcdata().disres = disresdata;
1392 fr->listedForces->fcdata().orires = oriresdata;
1394 // Save a handle to device stream manager to use elsewhere in the code
1395 // TODO: Forcerec is not a correct place to store it.
1396 fr->deviceStreamManager = deviceStreamManager.get();
1398 if (devFlags.enableGpuPmePPComm && !thisRankHasDuty(cr, DUTY_PME))
1401 deviceStreamManager != nullptr,
1402 "GPU device stream manager should be valid in order to use PME-PP direct "
1405 deviceStreamManager->streamIsValid(DeviceStreamType::PmePpTransfer),
1406 "GPU PP-PME stream should be valid in order to use GPU PME-PP direct "
1408 fr->pmePpCommGpu = std::make_unique<gmx::PmePpCommGpu>(
1409 cr->mpi_comm_mysim, cr->dd->pme_nodeid, deviceStreamManager->context(),
1410 deviceStreamManager->stream(DeviceStreamType::PmePpTransfer));
1413 fr->nbv = Nbnxm::init_nb_verlet(mdlog, inputrec.get(), fr, cr, *hwinfo, useGpuForNonbonded,
1414 deviceStreamManager.get(), &mtop, box, wcycle);
1415 // TODO: Move the logic below to a GPU bonded builder
1416 if (useGpuForBonded)
1418 GMX_RELEASE_ASSERT(deviceStreamManager != nullptr,
1419 "GPU device stream manager should be valid in order to use GPU "
1420 "version of bonded forces.");
1421 gpuBonded = std::make_unique<GpuBonded>(
1422 mtop.ffparams, fr->ic->epsfac * fr->fudgeQQ, deviceStreamManager->context(),
1423 deviceStreamManager->bondedStream(havePPDomainDecomposition(cr)), wcycle);
1424 fr->gpuBonded = gpuBonded.get();
1427 /* Initialize the mdAtoms structure.
1428 * mdAtoms is not filled with atom data,
1429 * as this can not be done now with domain decomposition.
1431 mdAtoms = makeMDAtoms(fplog, mtop, *inputrec, thisRankHasPmeGpuTask);
1432 if (globalState && thisRankHasPmeGpuTask)
1434 // The pinning of coordinates in the global state object works, because we only use
1435 // PME on GPU without DD or on a separate PME rank, and because the local state pointer
1436 // points to the global state object without DD.
1437 // FIXME: MD and EM separately set up the local state - this should happen in the same
1438 // function, which should also perform the pinning.
1439 changePinningPolicy(&globalState->x, pme_get_pinning_policy());
1442 /* Initialize the virtual site communication */
1443 vsite = makeVirtualSitesHandler(mtop, cr, fr->pbcType);
1445 calc_shifts(box, fr->shift_vec);
1447 /* With periodic molecules the charge groups should be whole at start up
1448 * and the virtual sites should not be far from their proper positions.
1450 if (!inputrec->bContinuation && MASTER(cr)
1451 && !(inputrec->pbcType != PbcType::No && inputrec->bPeriodicMols))
1453 /* Make molecules whole at start of run */
1454 if (fr->pbcType != PbcType::No)
1456 do_pbc_first_mtop(fplog, inputrec->pbcType, box, &mtop, globalState->x.rvec_array());
1460 /* Correct initial vsite positions are required
1461 * for the initial distribution in the domain decomposition
1462 * and for the initial shell prediction.
1464 constructVirtualSitesGlobal(mtop, globalState->x);
1468 if (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
1470 ewaldcoeff_q = fr->ic->ewaldcoeff_q;
1471 ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
1476 /* This is a PME only node */
1478 GMX_ASSERT(globalState == nullptr,
1479 "We don't need the state on a PME only rank and expect it to be unitialized");
1481 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
1482 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
1485 gmx_pme_t* sepPmeData = nullptr;
1486 // This reference hides the fact that PME data is owned by runner on PME-only ranks and by forcerec on other ranks
1487 GMX_ASSERT(thisRankHasDuty(cr, DUTY_PP) == (fr != nullptr),
1488 "Double-checking that only PME-only ranks have no forcerec");
1489 gmx_pme_t*& pmedata = fr ? fr->pmedata : sepPmeData;
1491 // TODO should live in ewald module once its testing is improved
1493 // Later, this program could contain kernels that might be later
1494 // re-used as auto-tuning progresses, or subsequent simulations
1496 PmeGpuProgramStorage pmeGpuProgram;
1497 if (thisRankHasPmeGpuTask)
1500 (deviceStreamManager != nullptr),
1501 "GPU device stream manager should be initialized in order to use GPU for PME.");
1502 GMX_RELEASE_ASSERT((deviceInfo != nullptr),
1503 "GPU device should be initialized in order to use GPU for PME.");
1504 pmeGpuProgram = buildPmeGpuProgram(deviceStreamManager->context());
1507 /* Initiate PME if necessary,
1508 * either on all nodes or on dedicated PME nodes only. */
1509 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
1511 if (mdAtoms && mdAtoms->mdatoms())
1513 nChargePerturbed = mdAtoms->mdatoms()->nChargePerturbed;
1514 if (EVDW_PME(inputrec->vdwtype))
1516 nTypePerturbed = mdAtoms->mdatoms()->nTypePerturbed;
1519 if (cr->npmenodes > 0)
1521 /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
1522 gmx_bcast(sizeof(nChargePerturbed), &nChargePerturbed, cr->mpi_comm_mysim);
1523 gmx_bcast(sizeof(nTypePerturbed), &nTypePerturbed, cr->mpi_comm_mysim);
1526 if (thisRankHasDuty(cr, DUTY_PME))
1530 // TODO: This should be in the builder.
1531 GMX_RELEASE_ASSERT(!useGpuForPme || (deviceStreamManager != nullptr),
1532 "Device stream manager should be valid in order to use GPU "
1535 !useGpuForPme || deviceStreamManager->streamIsValid(DeviceStreamType::Pme),
1536 "GPU PME stream should be valid in order to use GPU version of PME.");
1538 const DeviceContext* deviceContext =
1539 useGpuForPme ? &deviceStreamManager->context() : nullptr;
1540 const DeviceStream* pmeStream =
1541 useGpuForPme ? &deviceStreamManager->stream(DeviceStreamType::Pme) : nullptr;
1543 pmedata = gmx_pme_init(cr, getNumPmeDomains(cr->dd), inputrec.get(),
1544 nChargePerturbed != 0, nTypePerturbed != 0,
1545 mdrunOptions.reproducible, ewaldcoeff_q, ewaldcoeff_lj,
1546 gmx_omp_nthreads_get(emntPME), pmeRunMode, nullptr,
1547 deviceContext, pmeStream, pmeGpuProgram.get(), mdlog);
1549 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1554 if (EI_DYNAMICS(inputrec->eI))
1556 /* Turn on signal handling on all nodes */
1558 * (A user signal from the PME nodes (if any)
1559 * is communicated to the PP nodes.
1561 signal_handler_install();
1564 pull_t* pull_work = nullptr;
1565 if (thisRankHasDuty(cr, DUTY_PP))
1567 /* Assumes uniform use of the number of OpenMP threads */
1568 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
1570 if (inputrec->bPull)
1572 /* Initialize pull code */
1573 pull_work = init_pull(fplog, inputrec->pull, inputrec.get(), &mtop, cr, &atomSets,
1574 inputrec->fepvals->init_lambda);
1575 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
1577 initPullHistory(pull_work, &observablesHistory);
1579 if (EI_DYNAMICS(inputrec->eI) && MASTER(cr))
1581 init_pull_output_files(pull_work, filenames.size(), filenames.data(), oenv, startingBehavior);
1585 std::unique_ptr<EnforcedRotation> enforcedRotation;
1588 /* Initialize enforced rotation code */
1589 enforcedRotation = init_rot(fplog, inputrec.get(), filenames.size(), filenames.data(),
1590 cr, &atomSets, globalState.get(), &mtop, oenv, mdrunOptions,
1594 t_swap* swap = nullptr;
1595 if (inputrec->eSwapCoords != eswapNO)
1597 /* Initialize ion swapping code */
1598 swap = init_swapcoords(fplog, inputrec.get(),
1599 opt2fn_master("-swap", filenames.size(), filenames.data(), cr),
1600 &mtop, globalState.get(), &observablesHistory, cr, &atomSets,
1601 oenv, mdrunOptions, startingBehavior);
1604 /* Let makeConstraints know whether we have essential dynamics constraints. */
1605 auto constr = makeConstraints(mtop, *inputrec, pull_work, doEssentialDynamics, fplog, cr,
1606 ms, &nrnb, wcycle, fr->bMolPBC);
1608 /* Energy terms and groups */
1609 gmx_enerdata_t enerd(mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
1610 inputrec->fepvals->n_lambda);
1612 /* Kinetic energy data */
1613 gmx_ekindata_t ekind;
1614 init_ekindata(fplog, &mtop, &(inputrec->opts), &ekind, inputrec->cos_accel);
1616 /* Set up interactive MD (IMD) */
1618 makeImdSession(inputrec.get(), cr, wcycle, &enerd, ms, &mtop, mdlog,
1619 MASTER(cr) ? globalState->x.rvec_array() : nullptr, filenames.size(),
1620 filenames.data(), oenv, mdrunOptions.imdOptions, startingBehavior);
1622 if (DOMAINDECOMP(cr))
1624 GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
1625 /* This call is not included in init_domain_decomposition mainly
1626 * because fr->cginfo_mb is set later.
1628 dd_init_bondeds(fplog, cr->dd, mtop, vsite.get(), inputrec.get(),
1629 domdecOptions.checkBondedInteractions, fr->cginfo_mb);
1632 // TODO This is not the right place to manage the lifetime of
1633 // this data structure, but currently it's the easiest way to
1635 MdrunScheduleWorkload runScheduleWork;
1636 // Also populates the simulation constant workload description.
1637 runScheduleWork.simulationWork =
1638 createSimulationWorkload(*inputrec, useGpuForNonbonded, pmeRunMode, useGpuForBonded,
1639 useGpuForUpdate, devFlags.enableGpuBufferOps,
1640 devFlags.enableGpuHaloExchange, devFlags.enableGpuPmePPComm);
1642 std::unique_ptr<gmx::StatePropagatorDataGpu> stateGpu;
1643 if (gpusWereDetected
1644 && ((useGpuForPme && thisRankHasDuty(cr, DUTY_PME))
1645 || runScheduleWork.simulationWork.useGpuBufferOps))
1647 GpuApiCallBehavior transferKind = (inputrec->eI == eiMD && !doRerun && !useModularSimulator)
1648 ? GpuApiCallBehavior::Async
1649 : GpuApiCallBehavior::Sync;
1650 GMX_RELEASE_ASSERT(deviceStreamManager != nullptr,
1651 "GPU device stream manager should be initialized to use GPU.");
1652 stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(
1653 *deviceStreamManager, transferKind, pme_gpu_get_block_size(fr->pmedata), wcycle);
1654 fr->stateGpu = stateGpu.get();
1657 GMX_ASSERT(stopHandlerBuilder_, "Runner must provide StopHandlerBuilder to simulator.");
1658 SimulatorBuilder simulatorBuilder;
1660 simulatorBuilder.add(SimulatorStateData(globalState.get(), &observablesHistory, &enerd, &ekind));
1661 simulatorBuilder.add(std::move(membedHolder));
1662 simulatorBuilder.add(std::move(stopHandlerBuilder_));
1663 simulatorBuilder.add(SimulatorConfig(mdrunOptions, startingBehavior, &runScheduleWork));
1666 simulatorBuilder.add(SimulatorEnv(fplog, cr, ms, mdlog, oenv));
1667 simulatorBuilder.add(Profiling(&nrnb, walltime_accounting, wcycle));
1668 simulatorBuilder.add(ConstraintsParam(
1669 constr.get(), enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr,
1671 // TODO: Separate `fr` to a separate add, and make the `build` handle the coupling sensibly.
1672 simulatorBuilder.add(LegacyInput(static_cast<int>(filenames.size()), filenames.data(),
1673 inputrec.get(), fr));
1674 simulatorBuilder.add(ReplicaExchangeParameters(replExParams));
1675 simulatorBuilder.add(InteractiveMD(imdSession.get()));
1676 simulatorBuilder.add(SimulatorModules(mdModules_->outputProvider(), mdModules_->notifier()));
1677 simulatorBuilder.add(CenterOfMassPulling(pull_work));
1678 // Todo move to an MDModule
1679 simulatorBuilder.add(IonSwapping(swap));
1680 simulatorBuilder.add(TopologyData(&mtop, mdAtoms.get()));
1681 simulatorBuilder.add(BoxDeformationHandle(deform.get()));
1683 // build and run simulator object based on user-input
1684 auto simulator = simulatorBuilder.build(useModularSimulator);
1687 if (fr->pmePpCommGpu)
1689 // destroy object since it is no longer required. (This needs to be done while the GPU context still exists.)
1690 fr->pmePpCommGpu.reset();
1693 if (inputrec->bPull)
1695 finish_pull(pull_work);
1697 finish_swapcoords(swap);
1701 GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
1703 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
1704 gmx_pmeonly(pmedata, cr, &nrnb, wcycle, walltime_accounting, inputrec.get(), pmeRunMode,
1705 deviceStreamManager.get());
1708 wallcycle_stop(wcycle, ewcRUN);
1710 /* Finish up, write some stuff
1711 * if rerunMD, don't write last frame again
1713 finish_run(fplog, mdlog, cr, inputrec.get(), &nrnb, wcycle, walltime_accounting,
1714 fr ? fr->nbv.get() : nullptr, pmedata, EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
1716 // clean up cycle counter
1717 wallcycle_destroy(wcycle);
1719 deviceStreamManager.reset(nullptr);
1723 gmx_pme_destroy(pmedata);
1727 // FIXME: this is only here to manually unpin mdAtoms->chargeA_ and state->x,
1728 // before we destroy the GPU context(s) in free_gpu().
1729 // Pinned buffers are associated with contexts in CUDA.
1730 // As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
1731 mdAtoms.reset(nullptr);
1732 globalState.reset(nullptr);
1733 mdModules_.reset(nullptr); // destruct force providers here as they might also use the GPU
1734 gpuBonded.reset(nullptr);
1735 /* Free pinned buffers in *fr */
1738 // TODO convert to C++ so we can get rid of these frees
1742 if (hwinfo->gpu_info.n_dev > 0)
1744 /* stop the GPU profiler (only CUDA) */
1748 /* With tMPI we need to wait for all ranks to finish deallocation before
1749 * destroying the CUDA context in free_gpu() as some tMPI ranks may be sharing
1752 * This is not a concern in OpenCL where we use one context per rank which
1753 * is freed in nbnxn_gpu_free().
1755 * Note: it is safe to not call the barrier on the ranks which do not use GPU,
1756 * but it is easier and more futureproof to call it on the whole node.
1758 * Note that this function needs to be called even if GPUs are not used
1759 * in this run because the PME ranks have no knowledge of whether GPUs
1760 * are used or not, but all ranks need to enter the barrier below.
1761 * \todo Remove this physical node barrier after making sure
1762 * that it's not needed anymore (with a shared GPU run).
1766 physicalNodeComm.barrier();
1769 free_gpu(deviceInfo);
1771 /* Does what it says */
1772 print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
1773 walltime_accounting_destroy(walltime_accounting);
1775 // Ensure log file content is written
1778 gmx_fio_flush(logFileHandle);
1781 /* Reset FPEs (important for unit tests) by disabling them. Assumes no
1782 * exceptions were enabled before function was called. */
1785 gmx_fedisableexcept();
1788 auto rc = static_cast<int>(gmx_get_stop_condition());
1791 /* we need to join all threads. The sub-threads join when they
1792 exit this function, but the master thread needs to be told to
1802 Mdrunner::~Mdrunner()
1804 // Clean up of the Manager.
1805 // This will end up getting called on every thread-MPI rank, which is unnecessary,
1806 // but okay as long as threads synchronize some time before adding or accessing
1807 // a new set of restraints.
1808 if (restraintManager_)
1810 restraintManager_->clear();
1811 GMX_ASSERT(restraintManager_->countRestraints() == 0,
1812 "restraints added during runner life time should be cleared at runner "
1817 void Mdrunner::addPotential(std::shared_ptr<gmx::IRestraintPotential> puller, const std::string& name)
1819 GMX_ASSERT(restraintManager_, "Mdrunner must have a restraint manager.");
1820 // Not sure if this should be logged through the md logger or something else,
1821 // but it is helpful to have some sort of INFO level message sent somewhere.
1822 // std::cout << "Registering restraint named " << name << std::endl;
1824 // When multiple restraints are used, it may be wasteful to register them separately.
1825 // Maybe instead register an entire Restraint Manager as a force provider.
1826 restraintManager_->addToSpec(std::move(puller), name);
1829 Mdrunner::Mdrunner(std::unique_ptr<MDModules> mdModules) : mdModules_(std::move(mdModules)) {}
1831 Mdrunner::Mdrunner(Mdrunner&&) noexcept = default;
1833 Mdrunner& Mdrunner::operator=(Mdrunner&& /*handle*/) noexcept = default;
1835 class Mdrunner::BuilderImplementation
1838 BuilderImplementation() = delete;
1839 BuilderImplementation(std::unique_ptr<MDModules> mdModules, compat::not_null<SimulationContext*> context);
1840 ~BuilderImplementation();
1842 BuilderImplementation& setExtraMdrunOptions(const MdrunOptions& options,
1843 real forceWarningThreshold,
1844 StartingBehavior startingBehavior);
1846 void addDomdec(const DomdecOptions& options);
1848 void addVerletList(int nstlist);
1850 void addReplicaExchange(const ReplicaExchangeParameters& params);
1852 void addNonBonded(const char* nbpu_opt);
1854 void addPME(const char* pme_opt_, const char* pme_fft_opt_);
1856 void addBondedTaskAssignment(const char* bonded_opt);
1858 void addUpdateTaskAssignment(const char* update_opt);
1860 void addHardwareOptions(const gmx_hw_opt_t& hardwareOptions);
1862 void addFilenames(ArrayRef<const t_filenm> filenames);
1864 void addOutputEnvironment(gmx_output_env_t* outputEnvironment);
1866 void addLogFile(t_fileio* logFileHandle);
1868 void addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
1873 // Default parameters copied from runner.h
1874 // \todo Clarify source(s) of default parameters.
1876 const char* nbpu_opt_ = nullptr;
1877 const char* pme_opt_ = nullptr;
1878 const char* pme_fft_opt_ = nullptr;
1879 const char* bonded_opt_ = nullptr;
1880 const char* update_opt_ = nullptr;
1882 MdrunOptions mdrunOptions_;
1884 DomdecOptions domdecOptions_;
1886 ReplicaExchangeParameters replicaExchangeParameters_;
1888 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
1891 //! Multisim communicator handle.
1892 gmx_multisim_t* multiSimulation_;
1894 //! mdrun communicator
1895 MPI_Comm communicator_ = MPI_COMM_NULL;
1897 //! Print a warning if any force is larger than this (in kJ/mol nm).
1898 real forceWarningThreshold_ = -1;
1900 //! Whether the simulation will start afresh, or restart with/without appending.
1901 StartingBehavior startingBehavior_ = StartingBehavior::NewSimulation;
1903 //! The modules that comprise the functionality of mdrun.
1904 std::unique_ptr<MDModules> mdModules_;
1906 //! \brief Parallelism information.
1907 gmx_hw_opt_t hardwareOptions_;
1909 //! filename options for simulation.
1910 ArrayRef<const t_filenm> filenames_;
1912 /*! \brief Handle to output environment.
1914 * \todo gmx_output_env_t needs lifetime management.
1916 gmx_output_env_t* outputEnvironment_ = nullptr;
1918 /*! \brief Non-owning handle to MD log file.
1920 * \todo Context should own output facilities for client.
1921 * \todo Improve log file handle management.
1923 * Code managing the FILE* relies on the ability to set it to
1924 * nullptr to check whether the filehandle is valid.
1926 t_fileio* logFileHandle_ = nullptr;
1929 * \brief Builder for simulation stop signal handler.
1931 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_ = nullptr;
1934 Mdrunner::BuilderImplementation::BuilderImplementation(std::unique_ptr<MDModules> mdModules,
1935 compat::not_null<SimulationContext*> context) :
1936 mdModules_(std::move(mdModules))
1938 communicator_ = context->communicator_;
1939 multiSimulation_ = context->multiSimulation_.get();
1942 Mdrunner::BuilderImplementation::~BuilderImplementation() = default;
1944 Mdrunner::BuilderImplementation&
1945 Mdrunner::BuilderImplementation::setExtraMdrunOptions(const MdrunOptions& options,
1946 const real forceWarningThreshold,
1947 const StartingBehavior startingBehavior)
1949 mdrunOptions_ = options;
1950 forceWarningThreshold_ = forceWarningThreshold;
1951 startingBehavior_ = startingBehavior;
1955 void Mdrunner::BuilderImplementation::addDomdec(const DomdecOptions& options)
1957 domdecOptions_ = options;
1960 void Mdrunner::BuilderImplementation::addVerletList(int nstlist)
1965 void Mdrunner::BuilderImplementation::addReplicaExchange(const ReplicaExchangeParameters& params)
1967 replicaExchangeParameters_ = params;
1970 Mdrunner Mdrunner::BuilderImplementation::build()
1972 auto newRunner = Mdrunner(std::move(mdModules_));
1974 newRunner.mdrunOptions = mdrunOptions_;
1975 newRunner.pforce = forceWarningThreshold_;
1976 newRunner.startingBehavior = startingBehavior_;
1977 newRunner.domdecOptions = domdecOptions_;
1979 // \todo determine an invariant to check or confirm that all gmx_hw_opt_t objects are valid
1980 newRunner.hw_opt = hardwareOptions_;
1982 // No invariant to check. This parameter exists to optionally override other behavior.
1983 newRunner.nstlist_cmdline = nstlist_;
1985 newRunner.replExParams = replicaExchangeParameters_;
1987 newRunner.filenames = filenames_;
1989 newRunner.communicator = communicator_;
1991 // nullptr is a valid value for the multisim handle
1992 newRunner.ms = multiSimulation_;
1994 // \todo Clarify ownership and lifetime management for gmx_output_env_t
1995 // \todo Update sanity checking when output environment has clearly specified invariants.
1996 // Initialization and default values for oenv are not well specified in the current version.
1997 if (outputEnvironment_)
1999 newRunner.oenv = outputEnvironment_;
2003 GMX_THROW(gmx::APIError(
2004 "MdrunnerBuilder::addOutputEnvironment() is required before build()"));
2007 newRunner.logFileHandle = logFileHandle_;
2011 newRunner.nbpu_opt = nbpu_opt_;
2015 GMX_THROW(gmx::APIError("MdrunnerBuilder::addNonBonded() is required before build()"));
2018 if (pme_opt_ && pme_fft_opt_)
2020 newRunner.pme_opt = pme_opt_;
2021 newRunner.pme_fft_opt = pme_fft_opt_;
2025 GMX_THROW(gmx::APIError("MdrunnerBuilder::addElectrostatics() is required before build()"));
2030 newRunner.bonded_opt = bonded_opt_;
2034 GMX_THROW(gmx::APIError(
2035 "MdrunnerBuilder::addBondedTaskAssignment() is required before build()"));
2040 newRunner.update_opt = update_opt_;
2044 GMX_THROW(gmx::APIError(
2045 "MdrunnerBuilder::addUpdateTaskAssignment() is required before build() "));
2049 newRunner.restraintManager_ = std::make_unique<gmx::RestraintManager>();
2051 if (stopHandlerBuilder_)
2053 newRunner.stopHandlerBuilder_ = std::move(stopHandlerBuilder_);
2057 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>();
2063 void Mdrunner::BuilderImplementation::addNonBonded(const char* nbpu_opt)
2065 nbpu_opt_ = nbpu_opt;
2068 void Mdrunner::BuilderImplementation::addPME(const char* pme_opt, const char* pme_fft_opt)
2071 pme_fft_opt_ = pme_fft_opt;
2074 void Mdrunner::BuilderImplementation::addBondedTaskAssignment(const char* bonded_opt)
2076 bonded_opt_ = bonded_opt;
2079 void Mdrunner::BuilderImplementation::addUpdateTaskAssignment(const char* update_opt)
2081 update_opt_ = update_opt;
2084 void Mdrunner::BuilderImplementation::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2086 hardwareOptions_ = hardwareOptions;
2089 void Mdrunner::BuilderImplementation::addFilenames(ArrayRef<const t_filenm> filenames)
2091 filenames_ = filenames;
2094 void Mdrunner::BuilderImplementation::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2096 outputEnvironment_ = outputEnvironment;
2099 void Mdrunner::BuilderImplementation::addLogFile(t_fileio* logFileHandle)
2101 logFileHandle_ = logFileHandle;
2104 void Mdrunner::BuilderImplementation::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2106 stopHandlerBuilder_ = std::move(builder);
2109 MdrunnerBuilder::MdrunnerBuilder(std::unique_ptr<MDModules> mdModules,
2110 compat::not_null<SimulationContext*> context) :
2111 impl_{ std::make_unique<Mdrunner::BuilderImplementation>(std::move(mdModules), context) }
2115 MdrunnerBuilder::~MdrunnerBuilder() = default;
2117 MdrunnerBuilder& MdrunnerBuilder::addSimulationMethod(const MdrunOptions& options,
2118 real forceWarningThreshold,
2119 const StartingBehavior startingBehavior)
2121 impl_->setExtraMdrunOptions(options, forceWarningThreshold, startingBehavior);
2125 MdrunnerBuilder& MdrunnerBuilder::addDomainDecomposition(const DomdecOptions& options)
2127 impl_->addDomdec(options);
2131 MdrunnerBuilder& MdrunnerBuilder::addNeighborList(int nstlist)
2133 impl_->addVerletList(nstlist);
2137 MdrunnerBuilder& MdrunnerBuilder::addReplicaExchange(const ReplicaExchangeParameters& params)
2139 impl_->addReplicaExchange(params);
2143 MdrunnerBuilder& MdrunnerBuilder::addNonBonded(const char* nbpu_opt)
2145 impl_->addNonBonded(nbpu_opt);
2149 MdrunnerBuilder& MdrunnerBuilder::addElectrostatics(const char* pme_opt, const char* pme_fft_opt)
2151 // The builder method may become more general in the future, but in this version,
2152 // parameters for PME electrostatics are both required and the only parameters
2154 if (pme_opt && pme_fft_opt)
2156 impl_->addPME(pme_opt, pme_fft_opt);
2161 gmx::InvalidInputError("addElectrostatics() arguments must be non-null pointers."));
2166 MdrunnerBuilder& MdrunnerBuilder::addBondedTaskAssignment(const char* bonded_opt)
2168 impl_->addBondedTaskAssignment(bonded_opt);
2172 MdrunnerBuilder& MdrunnerBuilder::addUpdateTaskAssignment(const char* update_opt)
2174 impl_->addUpdateTaskAssignment(update_opt);
2178 Mdrunner MdrunnerBuilder::build()
2180 return impl_->build();
2183 MdrunnerBuilder& MdrunnerBuilder::addHardwareOptions(const gmx_hw_opt_t& hardwareOptions)
2185 impl_->addHardwareOptions(hardwareOptions);
2189 MdrunnerBuilder& MdrunnerBuilder::addFilenames(ArrayRef<const t_filenm> filenames)
2191 impl_->addFilenames(filenames);
2195 MdrunnerBuilder& MdrunnerBuilder::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2197 impl_->addOutputEnvironment(outputEnvironment);
2201 MdrunnerBuilder& MdrunnerBuilder::addLogFile(t_fileio* logFileHandle)
2203 impl_->addLogFile(logFileHandle);
2207 MdrunnerBuilder& MdrunnerBuilder::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2209 impl_->addStopHandlerBuilder(std::move(builder));
2213 MdrunnerBuilder::MdrunnerBuilder(MdrunnerBuilder&&) noexcept = default;
2215 MdrunnerBuilder& MdrunnerBuilder::operator=(MdrunnerBuilder&&) noexcept = default;