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39 * \brief Implements the MD runner routine calling all integrators.
41 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
42 * \ingroup module_mdrun
59 #include "gromacs/commandline/filenm.h"
60 #include "gromacs/domdec/builder.h"
61 #include "gromacs/domdec/domdec.h"
62 #include "gromacs/domdec/domdec_struct.h"
63 #include "gromacs/domdec/gpuhaloexchange.h"
64 #include "gromacs/domdec/localatomsetmanager.h"
65 #include "gromacs/domdec/partition.h"
66 #include "gromacs/ewald/ewald_utils.h"
67 #include "gromacs/ewald/pme.h"
68 #include "gromacs/ewald/pme_gpu_program.h"
69 #include "gromacs/ewald/pme_pp_comm_gpu.h"
70 #include "gromacs/fileio/checkpoint.h"
71 #include "gromacs/fileio/gmxfio.h"
72 #include "gromacs/fileio/oenv.h"
73 #include "gromacs/fileio/tpxio.h"
74 #include "gromacs/gmxlib/network.h"
75 #include "gromacs/gmxlib/nrnb.h"
76 #include "gromacs/gpu_utils/gpu_utils.h"
77 #include "gromacs/hardware/cpuinfo.h"
78 #include "gromacs/hardware/detecthardware.h"
79 #include "gromacs/hardware/printhardware.h"
80 #include "gromacs/imd/imd.h"
81 #include "gromacs/listed_forces/disre.h"
82 #include "gromacs/listed_forces/gpubonded.h"
83 #include "gromacs/listed_forces/orires.h"
84 #include "gromacs/math/functions.h"
85 #include "gromacs/math/utilities.h"
86 #include "gromacs/math/vec.h"
87 #include "gromacs/mdlib/boxdeformation.h"
88 #include "gromacs/mdlib/broadcaststructs.h"
89 #include "gromacs/mdlib/calc_verletbuf.h"
90 #include "gromacs/mdlib/dispersioncorrection.h"
91 #include "gromacs/mdlib/enerdata_utils.h"
92 #include "gromacs/mdlib/force.h"
93 #include "gromacs/mdlib/forcerec.h"
94 #include "gromacs/mdlib/gmx_omp_nthreads.h"
95 #include "gromacs/mdlib/makeconstraints.h"
96 #include "gromacs/mdlib/md_support.h"
97 #include "gromacs/mdlib/mdatoms.h"
98 #include "gromacs/mdlib/membed.h"
99 #include "gromacs/mdlib/qmmm.h"
100 #include "gromacs/mdlib/sighandler.h"
101 #include "gromacs/mdlib/stophandler.h"
102 #include "gromacs/mdrun/mdmodules.h"
103 #include "gromacs/mdrun/simulationcontext.h"
104 #include "gromacs/mdrunutility/handlerestart.h"
105 #include "gromacs/mdrunutility/logging.h"
106 #include "gromacs/mdrunutility/multisim.h"
107 #include "gromacs/mdrunutility/printtime.h"
108 #include "gromacs/mdrunutility/threadaffinity.h"
109 #include "gromacs/mdtypes/commrec.h"
110 #include "gromacs/mdtypes/enerdata.h"
111 #include "gromacs/mdtypes/fcdata.h"
112 #include "gromacs/mdtypes/group.h"
113 #include "gromacs/mdtypes/inputrec.h"
114 #include "gromacs/mdtypes/md_enums.h"
115 #include "gromacs/mdtypes/mdrunoptions.h"
116 #include "gromacs/mdtypes/observableshistory.h"
117 #include "gromacs/mdtypes/simulation_workload.h"
118 #include "gromacs/mdtypes/state.h"
119 #include "gromacs/mdtypes/state_propagator_data_gpu.h"
120 #include "gromacs/nbnxm/gpu_data_mgmt.h"
121 #include "gromacs/nbnxm/nbnxm.h"
122 #include "gromacs/nbnxm/pairlist_tuning.h"
123 #include "gromacs/pbcutil/pbc.h"
124 #include "gromacs/pulling/output.h"
125 #include "gromacs/pulling/pull.h"
126 #include "gromacs/pulling/pull_rotation.h"
127 #include "gromacs/restraint/manager.h"
128 #include "gromacs/restraint/restraintmdmodule.h"
129 #include "gromacs/restraint/restraintpotential.h"
130 #include "gromacs/swap/swapcoords.h"
131 #include "gromacs/taskassignment/decidegpuusage.h"
132 #include "gromacs/taskassignment/decidesimulationworkload.h"
133 #include "gromacs/taskassignment/resourcedivision.h"
134 #include "gromacs/taskassignment/taskassignment.h"
135 #include "gromacs/taskassignment/usergpuids.h"
136 #include "gromacs/timing/gpu_timing.h"
137 #include "gromacs/timing/wallcycle.h"
138 #include "gromacs/timing/wallcyclereporting.h"
139 #include "gromacs/topology/mtop_util.h"
140 #include "gromacs/trajectory/trajectoryframe.h"
141 #include "gromacs/utility/basenetwork.h"
142 #include "gromacs/utility/cstringutil.h"
143 #include "gromacs/utility/exceptions.h"
144 #include "gromacs/utility/fatalerror.h"
145 #include "gromacs/utility/filestream.h"
146 #include "gromacs/utility/gmxassert.h"
147 #include "gromacs/utility/gmxmpi.h"
148 #include "gromacs/utility/keyvaluetree.h"
149 #include "gromacs/utility/logger.h"
150 #include "gromacs/utility/loggerbuilder.h"
151 #include "gromacs/utility/mdmodulenotification.h"
152 #include "gromacs/utility/physicalnodecommunicator.h"
153 #include "gromacs/utility/pleasecite.h"
154 #include "gromacs/utility/programcontext.h"
155 #include "gromacs/utility/smalloc.h"
156 #include "gromacs/utility/stringutil.h"
158 #include "isimulator.h"
159 #include "replicaexchange.h"
160 #include "simulatorbuilder.h"
163 #include "corewrap.h"
169 /*! \brief Structure that holds boolean flags corresponding to the development
170 * features present enabled through environment variables.
173 struct DevelopmentFeatureFlags
175 //! True if the Buffer ops development feature is enabled
176 // TODO: when the trigger of the buffer ops offload is fully automated this should go away
177 bool enableGpuBufferOps = false;
178 //! If true, forces 'mdrun -update auto' default to 'gpu'
179 bool forceGpuUpdateDefaultOn = false;
180 //! True if the GPU halo exchange development feature is enabled
181 bool enableGpuHaloExchange = false;
182 //! True if the PME PP direct communication GPU development feature is enabled
183 bool enableGpuPmePPComm = false;
186 /*! \brief Manage any development feature flag variables encountered
188 * The use of dev features indicated by environment variables is
189 * logged in order to ensure that runs with such features enabled can
190 * be identified from their log and standard output. Any cross
191 * dependencies are also checked, and if unsatisfied, a fatal error
194 * Note that some development features overrides are applied already here:
195 * the GPU communication flags are set to false in non-tMPI and non-CUDA builds.
197 * \param[in] mdlog Logger object.
198 * \param[in] useGpuForNonbonded True if the nonbonded task is offloaded in this run.
199 * \param[in] useGpuForPme True if the PME task is offloaded in this run.
200 * \returns The object populated with development feature flags.
202 static DevelopmentFeatureFlags manageDevelopmentFeatures(const gmx::MDLogger &mdlog,
203 const bool useGpuForNonbonded,
204 const bool useGpuForPme)
206 DevelopmentFeatureFlags devFlags;
208 // Some builds of GCC 5 give false positive warnings that these
209 // getenv results are ignored when clearly they are used.
210 #pragma GCC diagnostic push
211 #pragma GCC diagnostic ignored "-Wunused-result"
212 devFlags.enableGpuBufferOps = (getenv("GMX_USE_GPU_BUFFER_OPS") != nullptr) && (GMX_GPU == GMX_GPU_CUDA) && useGpuForNonbonded;
213 devFlags.forceGpuUpdateDefaultOn = (getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") != nullptr);
214 devFlags.enableGpuHaloExchange = (getenv("GMX_GPU_DD_COMMS") != nullptr && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA));
215 devFlags.enableGpuPmePPComm = (getenv("GMX_GPU_PME_PP_COMMS") != nullptr && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA));
216 #pragma GCC diagnostic pop
218 if (devFlags.enableGpuBufferOps)
220 GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
221 "NOTE: This run uses the 'GPU buffer ops' feature, enabled by the GMX_USE_GPU_BUFFER_OPS environment variable.");
224 if (devFlags.enableGpuHaloExchange)
226 if (useGpuForNonbonded)
228 if (!devFlags.enableGpuBufferOps)
230 gmx_fatal(FARGS, "Cannot enable GPU halo exchange without GPU buffer operations, set GMX_USE_GPU_BUFFER_OPS=1\n");
232 GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
233 "NOTE: This run uses the 'GPU halo exchange' feature, enabled by the GMX_GPU_DD_COMMS environment variable.");
237 GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
238 "NOTE: GMX_GPU_DD_COMMS environment variable detected, but the 'GPU halo exchange' feature will not be enabled as nonbonded interactions are not offloaded.");
239 devFlags.enableGpuHaloExchange = false;
243 if (devFlags.forceGpuUpdateDefaultOn)
245 GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
246 "NOTE: This run will default to '-update gpu' as requested by the GMX_FORCE_UPDATE_DEFAULT_GPU environment variable.");
249 if (devFlags.enableGpuPmePPComm)
253 GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
254 "NOTE: This run uses the 'GPU PME-PP communications' feature, enabled by the GMX_GPU_PME_PP_COMMS environment variable.");
258 GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
259 "NOTE: GMX_GPU_PME_PP_COMMS environment variable detected, but the 'GPU PME-PP communications' feature was not enabled as PME is not offloaded to the GPU.");
260 devFlags.enableGpuPmePPComm = false;
267 /*! \brief Barrier for safe simultaneous thread access to mdrunner data
269 * Used to ensure that the master thread does not modify mdrunner during copy
270 * on the spawned threads. */
271 static void threadMpiMdrunnerAccessBarrier()
274 MPI_Barrier(MPI_COMM_WORLD);
278 Mdrunner Mdrunner::cloneOnSpawnedThread() const
280 auto newRunner = Mdrunner(std::make_unique<MDModules>());
282 // All runners in the same process share a restraint manager resource because it is
283 // part of the interface to the client code, which is associated only with the
284 // original thread. Handles to the same resources can be obtained by copy.
286 newRunner.restraintManager_ = std::make_unique<RestraintManager>(*restraintManager_);
289 // Copy members of master runner.
290 // \todo Replace with builder when Simulation context and/or runner phases are better defined.
291 // Ref https://redmine.gromacs.org/issues/2587 and https://redmine.gromacs.org/issues/2375
292 newRunner.hw_opt = hw_opt;
293 newRunner.filenames = filenames;
295 newRunner.oenv = oenv;
296 newRunner.mdrunOptions = mdrunOptions;
297 newRunner.domdecOptions = domdecOptions;
298 newRunner.nbpu_opt = nbpu_opt;
299 newRunner.pme_opt = pme_opt;
300 newRunner.pme_fft_opt = pme_fft_opt;
301 newRunner.bonded_opt = bonded_opt;
302 newRunner.update_opt = update_opt;
303 newRunner.nstlist_cmdline = nstlist_cmdline;
304 newRunner.replExParams = replExParams;
305 newRunner.pforce = pforce;
306 // Give the spawned thread the newly created valid communicator
307 // for the simulation.
308 newRunner.communicator = MPI_COMM_WORLD;
310 newRunner.startingBehavior = startingBehavior;
311 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>(*stopHandlerBuilder_);
313 threadMpiMdrunnerAccessBarrier();
318 /*! \brief The callback used for running on spawned threads.
320 * Obtains the pointer to the master mdrunner object from the one
321 * argument permitted to the thread-launch API call, copies it to make
322 * a new runner for this thread, reinitializes necessary data, and
323 * proceeds to the simulation. */
324 static void mdrunner_start_fn(const void *arg)
328 auto masterMdrunner = reinterpret_cast<const gmx::Mdrunner *>(arg);
329 /* copy the arg list to make sure that it's thread-local. This
330 doesn't copy pointed-to items, of course; fnm, cr and fplog
331 are reset in the call below, all others should be const. */
332 gmx::Mdrunner mdrunner = masterMdrunner->cloneOnSpawnedThread();
335 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
339 void Mdrunner::spawnThreads(int numThreadsToLaunch)
342 /* now spawn new threads that start mdrunner_start_fn(), while
343 the main thread returns. Thread affinity is handled later. */
344 if (tMPI_Init_fn(TRUE, numThreadsToLaunch, TMPI_AFFINITY_NONE,
345 mdrunner_start_fn, static_cast<const void*>(this)) != TMPI_SUCCESS)
347 GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
350 // Give the master thread the newly created valid communicator for
352 communicator = MPI_COMM_WORLD;
353 threadMpiMdrunnerAccessBarrier();
355 GMX_UNUSED_VALUE(numThreadsToLaunch);
356 GMX_UNUSED_VALUE(mdrunner_start_fn);
362 /*! \brief Initialize variables for Verlet scheme simulation */
363 static void prepare_verlet_scheme(FILE *fplog,
367 const gmx_mtop_t *mtop,
369 bool makeGpuPairList,
370 const gmx::CpuInfo &cpuinfo)
372 /* For NVE simulations, we will retain the initial list buffer */
373 if (EI_DYNAMICS(ir->eI) &&
374 ir->verletbuf_tol > 0 &&
375 !(EI_MD(ir->eI) && ir->etc == etcNO))
377 /* Update the Verlet buffer size for the current run setup */
379 /* Here we assume SIMD-enabled kernels are being used. But as currently
380 * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
381 * and 4x2 gives a larger buffer than 4x4, this is ok.
383 ListSetupType listType = (makeGpuPairList ? ListSetupType::Gpu : ListSetupType::CpuSimdWhenSupported);
384 VerletbufListSetup listSetup = verletbufGetSafeListSetup(listType);
386 const real rlist_new =
387 calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
389 if (rlist_new != ir->rlist)
391 if (fplog != nullptr)
393 fprintf(fplog, "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
394 ir->rlist, rlist_new,
395 listSetup.cluster_size_i, listSetup.cluster_size_j);
397 ir->rlist = rlist_new;
401 if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
403 gmx_fatal(FARGS, "Can not set nstlist without %s",
404 !EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
407 if (EI_DYNAMICS(ir->eI))
409 /* Set or try nstlist values */
410 increaseNstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, makeGpuPairList, cpuinfo);
414 /*! \brief Override the nslist value in inputrec
416 * with value passed on the command line (if any)
418 static void override_nsteps_cmdline(const gmx::MDLogger &mdlog,
419 int64_t nsteps_cmdline,
424 /* override with anything else than the default -2 */
425 if (nsteps_cmdline > -2)
427 char sbuf_steps[STEPSTRSIZE];
428 char sbuf_msg[STRLEN];
430 ir->nsteps = nsteps_cmdline;
431 if (EI_DYNAMICS(ir->eI) && nsteps_cmdline != -1)
433 sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
434 gmx_step_str(nsteps_cmdline, sbuf_steps),
435 fabs(nsteps_cmdline*ir->delta_t));
439 sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps",
440 gmx_step_str(nsteps_cmdline, sbuf_steps));
443 GMX_LOG(mdlog.warning).asParagraph().appendText(sbuf_msg);
445 else if (nsteps_cmdline < -2)
447 gmx_fatal(FARGS, "Invalid nsteps value passed on the command line: %" PRId64,
450 /* Do nothing if nsteps_cmdline == -2 */
456 /*! \brief Return whether GPU acceleration of nonbondeds is supported with the given settings.
458 * If not, and if a warning may be issued, logs a warning about
459 * falling back to CPU code. With thread-MPI, only the first
460 * call to this function should have \c issueWarning true. */
461 static bool gpuAccelerationOfNonbondedIsUseful(const MDLogger &mdlog,
462 const t_inputrec &ir,
465 bool gpuIsUseful = true;
468 if (ir.opts.ngener - ir.nwall > 1)
470 /* The GPU code does not support more than one energy group.
471 * If the user requested GPUs explicitly, a fatal error is given later.
475 "Multiple energy groups is not implemented for GPUs, falling back to the CPU. "
476 "For better performance, run on the GPU without energy groups and then do "
477 "gmx mdrun -rerun option on the trajectory with an energy group .tpr file.";
483 warning = "TPI is not implemented for GPUs.";
486 if (!gpuIsUseful && issueWarning)
488 GMX_LOG(mdlog.warning).asParagraph().appendText(warning);
494 //! Initializes the logger for mdrun.
495 static gmx::LoggerOwner buildLogger(FILE *fplog,
496 const bool isSimulationMasterRank)
498 gmx::LoggerBuilder builder;
499 if (fplog != nullptr)
501 builder.addTargetFile(gmx::MDLogger::LogLevel::Info, fplog);
503 if (isSimulationMasterRank)
505 builder.addTargetStream(gmx::MDLogger::LogLevel::Warning,
506 &gmx::TextOutputFile::standardError());
508 return builder.build();
511 //! Make a TaskTarget from an mdrun argument string.
512 static TaskTarget findTaskTarget(const char *optionString)
514 TaskTarget returnValue = TaskTarget::Auto;
516 if (strncmp(optionString, "auto", 3) == 0)
518 returnValue = TaskTarget::Auto;
520 else if (strncmp(optionString, "cpu", 3) == 0)
522 returnValue = TaskTarget::Cpu;
524 else if (strncmp(optionString, "gpu", 3) == 0)
526 returnValue = TaskTarget::Gpu;
530 GMX_ASSERT(false, "Option string should have been checked for sanity already");
536 //! Finish run, aggregate data to print performance info.
537 static void finish_run(FILE *fplog,
538 const gmx::MDLogger &mdlog,
540 const t_inputrec *inputrec,
541 t_nrnb nrnb[], gmx_wallcycle_t wcycle,
542 gmx_walltime_accounting_t walltime_accounting,
543 nonbonded_verlet_t *nbv,
544 const gmx_pme_t *pme,
548 double nbfs = 0, mflop = 0;
550 elapsed_time_over_all_ranks,
551 elapsed_time_over_all_threads,
552 elapsed_time_over_all_threads_over_all_ranks;
553 /* Control whether it is valid to print a report. Only the
554 simulation master may print, but it should not do so if the run
555 terminated e.g. before a scheduled reset step. This is
556 complicated by the fact that PME ranks are unaware of the
557 reason why they were sent a pmerecvqxFINISH. To avoid
558 communication deadlocks, we always do the communication for the
559 report, even if we've decided not to write the report, because
560 how long it takes to finish the run is not important when we've
561 decided not to report on the simulation performance.
563 Further, we only report performance for dynamical integrators,
564 because those are the only ones for which we plan to
565 consider doing any optimizations. */
566 bool printReport = EI_DYNAMICS(inputrec->eI) && SIMMASTER(cr);
568 if (printReport && !walltime_accounting_get_valid_finish(walltime_accounting))
570 GMX_LOG(mdlog.warning).asParagraph().appendText("Simulation ended prematurely, no performance report will be written.");
575 std::unique_ptr<t_nrnb> nrnbTotalStorage;
578 nrnbTotalStorage = std::make_unique<t_nrnb>();
579 nrnb_tot = nrnbTotalStorage.get();
581 MPI_Allreduce(nrnb->n, nrnb_tot->n, eNRNB, MPI_DOUBLE, MPI_SUM,
590 elapsed_time = walltime_accounting_get_time_since_reset(walltime_accounting);
591 elapsed_time_over_all_threads = walltime_accounting_get_time_since_reset_over_all_threads(walltime_accounting);
595 /* reduce elapsed_time over all MPI ranks in the current simulation */
596 MPI_Allreduce(&elapsed_time,
597 &elapsed_time_over_all_ranks,
598 1, MPI_DOUBLE, MPI_SUM,
600 elapsed_time_over_all_ranks /= cr->nnodes;
601 /* Reduce elapsed_time_over_all_threads over all MPI ranks in the
602 * current simulation. */
603 MPI_Allreduce(&elapsed_time_over_all_threads,
604 &elapsed_time_over_all_threads_over_all_ranks,
605 1, MPI_DOUBLE, MPI_SUM,
611 elapsed_time_over_all_ranks = elapsed_time;
612 elapsed_time_over_all_threads_over_all_ranks = elapsed_time_over_all_threads;
617 print_flop(fplog, nrnb_tot, &nbfs, &mflop);
620 if (thisRankHasDuty(cr, DUTY_PP) && DOMAINDECOMP(cr))
622 print_dd_statistics(cr, inputrec, fplog);
625 /* TODO Move the responsibility for any scaling by thread counts
626 * to the code that handled the thread region, so that there's a
627 * mechanism to keep cycle counting working during the transition
628 * to task parallelism. */
629 int nthreads_pp = gmx_omp_nthreads_get(emntNonbonded);
630 int nthreads_pme = gmx_omp_nthreads_get(emntPME);
631 wallcycle_scale_by_num_threads(wcycle, thisRankHasDuty(cr, DUTY_PME) && !thisRankHasDuty(cr, DUTY_PP), nthreads_pp, nthreads_pme);
632 auto cycle_sum(wallcycle_sum(cr, wcycle));
636 auto nbnxn_gpu_timings = (nbv != nullptr && nbv->useGpu()) ? Nbnxm::gpu_get_timings(nbv->gpu_nbv) : nullptr;
637 gmx_wallclock_gpu_pme_t pme_gpu_timings = {};
639 if (pme_gpu_task_enabled(pme))
641 pme_gpu_get_timings(pme, &pme_gpu_timings);
643 wallcycle_print(fplog, mdlog, cr->nnodes, cr->npmenodes, nthreads_pp, nthreads_pme,
644 elapsed_time_over_all_ranks,
649 if (EI_DYNAMICS(inputrec->eI))
651 delta_t = inputrec->delta_t;
656 print_perf(fplog, elapsed_time_over_all_threads_over_all_ranks,
657 elapsed_time_over_all_ranks,
658 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
659 delta_t, nbfs, mflop);
663 print_perf(stderr, elapsed_time_over_all_threads_over_all_ranks,
664 elapsed_time_over_all_ranks,
665 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
666 delta_t, nbfs, mflop);
671 int Mdrunner::mdrunner()
674 t_forcerec *fr = nullptr;
675 t_fcdata *fcd = nullptr;
676 real ewaldcoeff_q = 0;
677 real ewaldcoeff_lj = 0;
678 int nChargePerturbed = -1, nTypePerturbed = 0;
679 gmx_wallcycle_t wcycle;
680 gmx_walltime_accounting_t walltime_accounting = nullptr;
681 gmx_membed_t * membed = nullptr;
682 gmx_hw_info_t *hwinfo = nullptr;
684 /* CAUTION: threads may be started later on in this function, so
685 cr doesn't reflect the final parallel state right now */
688 /* TODO: inputrec should tell us whether we use an algorithm, not a file option */
689 const bool doEssentialDynamics = opt2bSet("-ei", filenames.size(), filenames.data());
690 const bool doMembed = opt2bSet("-membed", filenames.size(), filenames.data());
691 const bool doRerun = mdrunOptions.rerun;
693 // Handle task-assignment related user options.
694 EmulateGpuNonbonded emulateGpuNonbonded = (getenv("GMX_EMULATE_GPU") != nullptr ?
695 EmulateGpuNonbonded::Yes : EmulateGpuNonbonded::No);
697 std::vector<int> userGpuTaskAssignment;
700 userGpuTaskAssignment = parseUserTaskAssignmentString(hw_opt.userGpuTaskAssignment);
702 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
703 auto nonbondedTarget = findTaskTarget(nbpu_opt);
704 auto pmeTarget = findTaskTarget(pme_opt);
705 auto pmeFftTarget = findTaskTarget(pme_fft_opt);
706 auto bondedTarget = findTaskTarget(bonded_opt);
707 auto updateTarget = findTaskTarget(update_opt);
708 PmeRunMode pmeRunMode = PmeRunMode::None;
710 FILE *fplog = nullptr;
711 // If we are appending, we don't write log output because we need
712 // to check that the old log file matches what the checkpoint file
713 // expects. Otherwise, we should start to write log output now if
714 // there is a file ready for it.
715 if (logFileHandle != nullptr && startingBehavior != StartingBehavior::RestartWithAppending)
717 fplog = gmx_fio_getfp(logFileHandle);
719 const bool isSimulationMasterRank = findIsSimulationMasterRank(ms, communicator);
720 gmx::LoggerOwner logOwner(buildLogger(fplog, isSimulationMasterRank));
721 gmx::MDLogger mdlog(logOwner.logger());
723 // TODO The thread-MPI master rank makes a working
724 // PhysicalNodeCommunicator here, but it gets rebuilt by all ranks
725 // after the threads have been launched. This works because no use
726 // is made of that communicator until after the execution paths
727 // have rejoined. But it is likely that we can improve the way
728 // this is expressed, e.g. by expressly running detection only the
729 // master rank for thread-MPI, rather than relying on the mutex
730 // and reference count.
731 PhysicalNodeCommunicator physicalNodeComm(communicator, gmx_physicalnode_id_hash());
732 hwinfo = gmx_detect_hardware(mdlog, physicalNodeComm);
734 gmx_print_detected_hardware(fplog, isSimulationMasterRank && isMasterSim(ms), mdlog, hwinfo);
736 std::vector<int> gpuIdsToUse = makeGpuIdsToUse(hwinfo->gpu_info, hw_opt.gpuIdsAvailable);
738 // Print citation requests after all software/hardware printing
739 pleaseCiteGromacs(fplog);
741 // TODO Replace this by unique_ptr once t_inputrec is C++
742 t_inputrec inputrecInstance;
743 t_inputrec *inputrec = nullptr;
744 std::unique_ptr<t_state> globalState;
746 auto partialDeserializedTpr = std::make_unique<PartialDeserializedTprFile>();
748 if (isSimulationMasterRank)
750 /* Only the master rank has the global state */
751 globalState = std::make_unique<t_state>();
753 /* Read (nearly) all data required for the simulation
754 * and keep the partly serialized tpr contents to send to other ranks later
756 *partialDeserializedTpr = read_tpx_state(ftp2fn(efTPR, filenames.size(), filenames.data()), &inputrecInstance, globalState.get(), &mtop);
757 inputrec = &inputrecInstance;
760 /* Check and update the hardware options for internal consistency */
761 checkAndUpdateHardwareOptions(mdlog, &hw_opt, isSimulationMasterRank, domdecOptions.numPmeRanks, inputrec);
763 if (GMX_THREAD_MPI && isSimulationMasterRank)
765 bool useGpuForNonbonded = false;
766 bool useGpuForPme = false;
769 GMX_RELEASE_ASSERT(inputrec != nullptr, "Keep the compiler happy");
771 // If the user specified the number of ranks, then we must
772 // respect that, but in default mode, we need to allow for
773 // the number of GPUs to choose the number of ranks.
774 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
775 useGpuForNonbonded = decideWhetherToUseGpusForNonbondedWithThreadMpi
776 (nonbondedTarget, gpuIdsToUse, userGpuTaskAssignment, emulateGpuNonbonded,
777 canUseGpuForNonbonded,
778 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, GMX_THREAD_MPI),
779 hw_opt.nthreads_tmpi);
780 useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi
781 (useGpuForNonbonded, pmeTarget, gpuIdsToUse, userGpuTaskAssignment,
782 *hwinfo, *inputrec, mtop, hw_opt.nthreads_tmpi, domdecOptions.numPmeRanks);
785 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
787 /* Determine how many thread-MPI ranks to start.
789 * TODO Over-writing the user-supplied value here does
790 * prevent any possible subsequent checks from working
792 hw_opt.nthreads_tmpi = get_nthreads_mpi(hwinfo,
801 // Now start the threads for thread MPI.
802 spawnThreads(hw_opt.nthreads_tmpi);
803 // The spawned threads enter mdrunner() and execution of
804 // master and spawned threads joins at the end of this block.
805 physicalNodeComm = PhysicalNodeCommunicator(communicator, gmx_physicalnode_id_hash());
808 GMX_RELEASE_ASSERT(communicator == MPI_COMM_WORLD, "Must have valid world communicator");
809 CommrecHandle crHandle = init_commrec(communicator, ms);
810 t_commrec *cr = crHandle.get();
811 GMX_RELEASE_ASSERT(cr != nullptr, "Must have valid commrec");
815 /* now broadcast everything to the non-master nodes/threads: */
816 if (!isSimulationMasterRank)
818 inputrec = &inputrecInstance;
820 init_parallel(cr, inputrec, &mtop, partialDeserializedTpr.get());
822 GMX_RELEASE_ASSERT(inputrec != nullptr, "All ranks should have a valid inputrec now");
823 partialDeserializedTpr.reset(nullptr);
825 // Now the number of ranks is known to all ranks, and each knows
826 // the inputrec read by the master rank. The ranks can now all run
827 // the task-deciding functions and will agree on the result
828 // without needing to communicate.
830 // TODO Should we do the communication in debug mode to support
831 // having an assertion?
832 const bool useDomainDecomposition = (PAR(cr) && !(EI_TPI(inputrec->eI) ||
833 inputrec->eI == eiNM));
835 // Note that these variables describe only their own node.
837 // Note that when bonded interactions run on a GPU they always run
838 // alongside a nonbonded task, so do not influence task assignment
839 // even though they affect the force calculation workload.
840 bool useGpuForNonbonded = false;
841 bool useGpuForPme = false;
842 bool useGpuForBonded = false;
843 bool useGpuForUpdate = false;
844 bool gpusWereDetected = hwinfo->ngpu_compatible_tot > 0;
847 // It's possible that there are different numbers of GPUs on
848 // different nodes, which is the user's responsibility to
849 // handle. If unsuitable, we will notice that during task
851 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
852 useGpuForNonbonded = decideWhetherToUseGpusForNonbonded(nonbondedTarget, userGpuTaskAssignment,
854 canUseGpuForNonbonded,
855 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, !GMX_THREAD_MPI),
857 useGpuForPme = decideWhetherToUseGpusForPme(useGpuForNonbonded, pmeTarget, userGpuTaskAssignment,
858 *hwinfo, *inputrec, mtop,
859 cr->nnodes, domdecOptions.numPmeRanks,
861 auto canUseGpuForBonded = buildSupportsGpuBondeds(nullptr) && inputSupportsGpuBondeds(*inputrec, mtop, nullptr);
863 decideWhetherToUseGpusForBonded(useGpuForNonbonded, useGpuForPme,
864 bondedTarget, canUseGpuForBonded,
865 EVDW_PME(inputrec->vdwtype),
866 EEL_PME_EWALD(inputrec->coulombtype),
867 domdecOptions.numPmeRanks, gpusWereDetected);
869 pmeRunMode = (useGpuForPme ? PmeRunMode::GPU : PmeRunMode::CPU);
870 if (pmeRunMode == PmeRunMode::GPU)
872 if (pmeFftTarget == TaskTarget::Cpu)
874 pmeRunMode = PmeRunMode::Mixed;
877 else if (pmeFftTarget == TaskTarget::Gpu)
879 gmx_fatal(FARGS, "Assigning FFTs to GPU requires PME to be assigned to GPU as well. With PME on CPU you should not be using -pmefft.");
882 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
884 // Initialize development feature flags that enabled by environment variable
885 // and report those features that are enabled.
886 const DevelopmentFeatureFlags devFlags = manageDevelopmentFeatures(mdlog, useGpuForNonbonded, useGpuForPme);
888 // NOTE: The devFlags need decideWhetherToUseGpusForNonbonded(...) and decideWhetherToUseGpusForPme(...) for overrides,
889 // decideWhetherToUseGpuForUpdate() needs devFlags for the '-update auto' override, hence the interleaving.
890 // NOTE: When the simulationWork is constructed, the useGpuForUpdate overrides the devFlags.enableGpuBufferOps.
893 useGpuForUpdate = decideWhetherToUseGpuForUpdate(devFlags.forceGpuUpdateDefaultOn,
894 useDomainDecomposition,
900 gmx_mtop_interaction_count(mtop, IF_VSITE) > 0,
902 gmx_mtop_ftype_count(mtop, F_ORIRES) > 0,
903 replExParams.exchangeInterval > 0);
905 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
909 // TODO: hide restraint implementation details from Mdrunner.
910 // There is nothing unique about restraints at this point as far as the
911 // Mdrunner is concerned. The Mdrunner should just be getting a sequence of
912 // factory functions from the SimulationContext on which to call mdModules_->add().
913 // TODO: capture all restraints into a single RestraintModule, passed to the runner builder.
914 for (auto && restraint : restraintManager_->getRestraints())
916 auto module = RestraintMDModule::create(restraint,
918 mdModules_->add(std::move(module));
921 // TODO: Error handling
922 mdModules_->assignOptionsToModules(*inputrec->params, nullptr);
923 const auto &mdModulesNotifier = mdModules_->notifier().notifier_;
925 if (inputrec->internalParameters != nullptr)
927 mdModulesNotifier.notify(*inputrec->internalParameters);
930 if (fplog != nullptr)
932 pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
933 fprintf(fplog, "\n");
938 /* In rerun, set velocities to zero if present */
939 if (doRerun && ((globalState->flags & (1 << estV)) != 0))
941 // rerun does not use velocities
942 GMX_LOG(mdlog.info).asParagraph().appendText(
943 "Rerun trajectory contains velocities. Rerun does only evaluate "
944 "potential energy and forces. The velocities will be ignored.");
945 for (int i = 0; i < globalState->natoms; i++)
947 clear_rvec(globalState->v[i]);
949 globalState->flags &= ~(1 << estV);
952 /* now make sure the state is initialized and propagated */
953 set_state_entries(globalState.get(), inputrec);
956 /* NM and TPI parallelize over force/energy calculations, not atoms,
957 * so we need to initialize and broadcast the global state.
959 if (inputrec->eI == eiNM || inputrec->eI == eiTPI)
963 globalState = std::make_unique<t_state>();
965 broadcastStateWithoutDynamics(cr, globalState.get());
968 /* A parallel command line option consistency check that we can
969 only do after any threads have started. */
970 if (!PAR(cr) && (domdecOptions.numCells[XX] > 1 ||
971 domdecOptions.numCells[YY] > 1 ||
972 domdecOptions.numCells[ZZ] > 1 ||
973 domdecOptions.numPmeRanks > 0))
976 "The -dd or -npme option request a parallel simulation, "
978 "but %s was compiled without threads or MPI enabled", output_env_get_program_display_name(oenv));
980 "but the number of MPI-threads (option -ntmpi) is not set or is 1");
982 "but %s was not started through mpirun/mpiexec or only one rank was requested through mpirun/mpiexec", output_env_get_program_display_name(oenv));
987 (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
989 gmx_fatal(FARGS, "The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun");
992 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
994 if (domdecOptions.numPmeRanks > 0)
996 gmx_fatal_collective(FARGS, cr->mpi_comm_mysim, MASTER(cr),
997 "PME-only ranks are requested, but the system does not use PME for electrostatics or LJ");
1000 domdecOptions.numPmeRanks = 0;
1003 if (useGpuForNonbonded && domdecOptions.numPmeRanks < 0)
1005 /* With NB GPUs we don't automatically use PME-only CPU ranks. PME ranks can
1006 * improve performance with many threads per GPU, since our OpenMP
1007 * scaling is bad, but it's difficult to automate the setup.
1009 domdecOptions.numPmeRanks = 0;
1013 if (domdecOptions.numPmeRanks < 0)
1015 domdecOptions.numPmeRanks = 0;
1016 // TODO possibly print a note that one can opt-in for a separate PME GPU rank?
1020 GMX_RELEASE_ASSERT(domdecOptions.numPmeRanks <= 1, "PME GPU decomposition is not supported");
1027 fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
1031 /* NMR restraints must be initialized before load_checkpoint,
1032 * since with time averaging the history is added to t_state.
1033 * For proper consistency check we therefore need to extend
1035 * So the PME-only nodes (if present) will also initialize
1036 * the distance restraints.
1040 /* This needs to be called before read_checkpoint to extend the state */
1041 init_disres(fplog, &mtop, inputrec, cr, ms, fcd, globalState.get(), replExParams.exchangeInterval > 0);
1043 init_orires(fplog, &mtop, inputrec, cr, ms, globalState.get(), &(fcd->orires));
1045 auto deform = prepareBoxDeformation(globalState->box, cr, *inputrec);
1047 ObservablesHistory observablesHistory = {};
1049 if (startingBehavior != StartingBehavior::NewSimulation)
1051 /* Check if checkpoint file exists before doing continuation.
1052 * This way we can use identical input options for the first and subsequent runs...
1054 if (mdrunOptions.numStepsCommandline > -2)
1056 /* Temporarily set the number of steps to unlimited to avoid
1057 * triggering the nsteps check in load_checkpoint().
1058 * This hack will go away soon when the -nsteps option is removed.
1060 inputrec->nsteps = -1;
1063 load_checkpoint(opt2fn_master("-cpi", filenames.size(), filenames.data(), cr),
1065 cr, domdecOptions.numCells,
1066 inputrec, globalState.get(),
1067 &observablesHistory,
1068 mdrunOptions.reproducible, mdModules_->notifier());
1070 if (startingBehavior == StartingBehavior::RestartWithAppending && logFileHandle)
1072 // Now we can start normal logging to the truncated log file.
1073 fplog = gmx_fio_getfp(logFileHandle);
1074 prepareLogAppending(fplog);
1075 logOwner = buildLogger(fplog, MASTER(cr));
1076 mdlog = logOwner.logger();
1080 if (mdrunOptions.numStepsCommandline > -2)
1082 GMX_LOG(mdlog.info).asParagraph().
1083 appendText("The -nsteps functionality is deprecated, and may be removed in a future version. "
1084 "Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp file field.");
1086 /* override nsteps with value set on the commandline */
1087 override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec);
1091 copy_mat(globalState->box, box);
1096 gmx_bcast(sizeof(box), box, cr);
1099 if (inputrec->cutoff_scheme != ecutsVERLET)
1101 gmx_fatal(FARGS, "This group-scheme .tpr file can no longer be run by mdrun. Please update to the Verlet scheme, or use an earlier version of GROMACS if necessary.");
1103 /* Update rlist and nstlist. */
1104 prepare_verlet_scheme(fplog, cr, inputrec, nstlist_cmdline, &mtop, box,
1105 useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes), *hwinfo->cpuInfo);
1107 const bool prefer1DAnd1PulseDD = (devFlags.enableGpuHaloExchange && useGpuForNonbonded);
1108 // This builder is necessary while we have multi-part construction
1109 // of DD. Before DD is constructed, we use the existence of
1110 // the builder object to indicate that further construction of DD
1112 std::unique_ptr<DomainDecompositionBuilder> ddBuilder;
1113 if (useDomainDecomposition)
1115 ddBuilder = std::make_unique<DomainDecompositionBuilder>
1116 (mdlog, cr, domdecOptions, mdrunOptions,
1117 prefer1DAnd1PulseDD, mtop, *inputrec,
1118 box, positionsFromStatePointer(globalState.get()));
1122 /* PME, if used, is done on all nodes with 1D decomposition */
1124 cr->duty = (DUTY_PP | DUTY_PME);
1126 if (inputrec->ePBC == epbcSCREW)
1129 "pbc=screw is only implemented with domain decomposition");
1133 // Produce the task assignment for this rank.
1134 GpuTaskAssignmentsBuilder gpuTaskAssignmentsBuilder;
1135 GpuTaskAssignments gpuTaskAssignments =
1136 gpuTaskAssignmentsBuilder.build(gpuIdsToUse,
1137 userGpuTaskAssignment,
1148 thisRankHasDuty(cr, DUTY_PP),
1149 // TODO cr->duty & DUTY_PME should imply that a PME
1150 // algorithm is active, but currently does not.
1151 EEL_PME(inputrec->coulombtype) &&
1152 thisRankHasDuty(cr, DUTY_PME));
1154 const bool printHostName = (cr->nnodes > 1);
1155 gpuTaskAssignments.reportGpuUsage(mdlog, printHostName, useGpuForBonded, pmeRunMode);
1157 // If the user chose a task assignment, give them some hints
1158 // where appropriate.
1159 if (!userGpuTaskAssignment.empty())
1161 gpuTaskAssignments.logPerformanceHints(mdlog,
1162 ssize(gpuIdsToUse));
1165 // Get the device handles for the modules, nullptr when no task is assigned.
1166 gmx_device_info_t *nonbondedDeviceInfo = gpuTaskAssignments.initNonbondedDevice(cr);
1167 gmx_device_info_t *pmeDeviceInfo = gpuTaskAssignments.initPmeDevice();
1169 // TODO Initialize GPU streams here.
1171 // TODO Currently this is always built, yet DD partition code
1172 // checks if it is built before using it. Probably it should
1173 // become an MDModule that is made only when another module
1174 // requires it (e.g. pull, CompEl, density fitting), so that we
1175 // don't update the local atom sets unilaterally every step.
1176 LocalAtomSetManager atomSets;
1179 // TODO Pass the GPU streams to ddBuilder to use in buffer
1180 // transfers (e.g. halo exchange)
1181 cr->dd = ddBuilder->build(&atomSets);
1182 // The builder's job is done, so destruct it
1183 ddBuilder.reset(nullptr);
1184 // Note that local state still does not exist yet.
1189 /* After possible communicator splitting in make_dd_communicators.
1190 * we can set up the intra/inter node communication.
1192 gmx_setup_nodecomm(fplog, cr);
1198 GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
1199 "This is simulation %d out of %d running as a composite GROMACS\n"
1200 "multi-simulation job. Setup for this simulation:\n",
1203 GMX_LOG(mdlog.warning).appendTextFormatted(
1204 "Using %d MPI %s\n",
1207 cr->nnodes == 1 ? "thread" : "threads"
1209 cr->nnodes == 1 ? "process" : "processes"
1215 // If mdrun -pin auto honors any affinity setting that already
1216 // exists. If so, it is nice to provide feedback about whether
1217 // that existing affinity setting was from OpenMP or something
1218 // else, so we run this code both before and after we initialize
1219 // the OpenMP support.
1220 gmx_check_thread_affinity_set(mdlog,
1221 &hw_opt, hwinfo->nthreads_hw_avail, FALSE);
1222 /* Check and update the number of OpenMP threads requested */
1223 checkAndUpdateRequestedNumOpenmpThreads(&hw_opt, *hwinfo, cr, ms, physicalNodeComm.size_,
1224 pmeRunMode, mtop, *inputrec);
1226 gmx_omp_nthreads_init(mdlog, cr,
1227 hwinfo->nthreads_hw_avail,
1228 physicalNodeComm.size_,
1229 hw_opt.nthreads_omp,
1230 hw_opt.nthreads_omp_pme,
1231 !thisRankHasDuty(cr, DUTY_PP));
1233 // Enable FP exception detection, but not in
1234 // Release mode and not for compilers with known buggy FP
1235 // exception support (clang with any optimization) or suspected
1236 // buggy FP exception support (gcc 7.* with optimization).
1237 #if !defined NDEBUG && \
1238 !((defined __clang__ || (defined(__GNUC__) && !defined(__ICC) && __GNUC__ == 7)) \
1239 && defined __OPTIMIZE__)
1240 const bool bEnableFPE = true;
1242 const bool bEnableFPE = false;
1244 //FIXME - reconcile with gmx_feenableexcept() call from CommandLineModuleManager::run()
1247 gmx_feenableexcept();
1250 /* Now that we know the setup is consistent, check for efficiency */
1251 check_resource_division_efficiency(hwinfo,
1252 gpuTaskAssignments.thisRankHasAnyGpuTask(),
1253 mdrunOptions.ntompOptionIsSet,
1257 /* getting number of PP/PME threads on this MPI / tMPI rank.
1258 PME: env variable should be read only on one node to make sure it is
1259 identical everywhere;
1261 const int numThreadsOnThisRank =
1262 thisRankHasDuty(cr, DUTY_PP) ? gmx_omp_nthreads_get(emntNonbonded) : gmx_omp_nthreads_get(emntPME);
1263 checkHardwareOversubscription(numThreadsOnThisRank, cr->nodeid,
1264 *hwinfo->hardwareTopology,
1265 physicalNodeComm, mdlog);
1267 // Enable Peer access between GPUs where available
1268 // Only for DD, only master PP rank needs to perform setup, and only if thread MPI plus
1269 // any of the GPU communication features are active.
1270 if (DOMAINDECOMP(cr) && MASTER(cr) && thisRankHasDuty(cr, DUTY_PP) && GMX_THREAD_MPI &&
1271 (devFlags.enableGpuHaloExchange || devFlags.enableGpuPmePPComm))
1273 setupGpuDevicePeerAccess(gpuIdsToUse, mdlog);
1276 if (hw_opt.threadAffinity != ThreadAffinity::Off)
1278 /* Before setting affinity, check whether the affinity has changed
1279 * - which indicates that probably the OpenMP library has changed it
1280 * since we first checked).
1282 gmx_check_thread_affinity_set(mdlog,
1283 &hw_opt, hwinfo->nthreads_hw_avail, TRUE);
1285 int numThreadsOnThisNode, intraNodeThreadOffset;
1286 analyzeThreadsOnThisNode(physicalNodeComm, numThreadsOnThisRank, &numThreadsOnThisNode,
1287 &intraNodeThreadOffset);
1289 /* Set the CPU affinity */
1290 gmx_set_thread_affinity(mdlog, cr, &hw_opt, *hwinfo->hardwareTopology,
1291 numThreadsOnThisRank, numThreadsOnThisNode,
1292 intraNodeThreadOffset, nullptr);
1295 if (mdrunOptions.timingOptions.resetStep > -1)
1297 GMX_LOG(mdlog.info).asParagraph().
1298 appendText("The -resetstep functionality is deprecated, and may be removed in a future version.");
1300 wcycle = wallcycle_init(fplog, mdrunOptions.timingOptions.resetStep, cr);
1304 /* Master synchronizes its value of reset_counters with all nodes
1305 * including PME only nodes */
1306 int64_t reset_counters = wcycle_get_reset_counters(wcycle);
1307 gmx_bcast_sim(sizeof(reset_counters), &reset_counters, cr);
1308 wcycle_set_reset_counters(wcycle, reset_counters);
1311 // Membrane embedding must be initialized before we call init_forcerec()
1316 fprintf(stderr, "Initializing membed");
1318 /* Note that membed cannot work in parallel because mtop is
1319 * changed here. Fix this if we ever want to make it run with
1320 * multiple ranks. */
1321 membed = init_membed(fplog, filenames.size(), filenames.data(), &mtop, inputrec, globalState.get(), cr,
1323 .checkpointOptions.period);
1326 const bool thisRankHasPmeGpuTask = gpuTaskAssignments.thisRankHasPmeGpuTask();
1327 std::unique_ptr<MDAtoms> mdAtoms;
1328 std::unique_ptr<gmx_vsite_t> vsite;
1331 if (thisRankHasDuty(cr, DUTY_PP))
1333 mdModulesNotifier.notify(*cr);
1334 mdModulesNotifier.notify(&atomSets);
1335 mdModulesNotifier.notify(PeriodicBoundaryConditionType {inputrec->ePBC});
1336 mdModulesNotifier.notify(SimulationTimeStep { inputrec->delta_t });
1337 /* Initiate forcerecord */
1338 fr = new t_forcerec;
1339 fr->forceProviders = mdModules_->initForceProviders();
1340 init_forcerec(fplog, mdlog, fr, fcd,
1341 inputrec, &mtop, cr, box,
1342 opt2fn("-table", filenames.size(), filenames.data()),
1343 opt2fn("-tablep", filenames.size(), filenames.data()),
1344 opt2fns("-tableb", filenames.size(), filenames.data()),
1345 *hwinfo, nonbondedDeviceInfo,
1347 pmeRunMode == PmeRunMode::GPU && !thisRankHasDuty(cr, DUTY_PME),
1351 // TODO Move this to happen during domain decomposition setup,
1352 // once stream and event handling works well with that.
1353 // TODO remove need to pass local stream into GPU halo exchange - Redmine #3093
1354 if (havePPDomainDecomposition(cr) && prefer1DAnd1PulseDD && is1DAnd1PulseDD(*cr->dd))
1356 GMX_RELEASE_ASSERT(devFlags.enableGpuBufferOps, "Must use GMX_USE_GPU_BUFFER_OPS=1 to use GMX_GPU_DD_COMMS=1");
1357 void *streamLocal = Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::Local);
1358 void *streamNonLocal = Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::NonLocal);
1359 GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
1360 "NOTE: This run uses the 'GPU halo exchange' feature, enabled by the GMX_GPU_DD_COMMS environment variable.");
1361 cr->dd->gpuHaloExchange = std::make_unique<GpuHaloExchange>(cr->dd, cr->mpi_comm_mysim, streamLocal,
1365 /* Initialize the mdAtoms structure.
1366 * mdAtoms is not filled with atom data,
1367 * as this can not be done now with domain decomposition.
1369 mdAtoms = makeMDAtoms(fplog, mtop, *inputrec, thisRankHasPmeGpuTask);
1370 if (globalState && thisRankHasPmeGpuTask)
1372 // The pinning of coordinates in the global state object works, because we only use
1373 // PME on GPU without DD or on a separate PME rank, and because the local state pointer
1374 // points to the global state object without DD.
1375 // FIXME: MD and EM separately set up the local state - this should happen in the same function,
1376 // which should also perform the pinning.
1377 changePinningPolicy(&globalState->x, pme_get_pinning_policy());
1380 /* Initialize the virtual site communication */
1381 vsite = initVsite(mtop, cr);
1383 calc_shifts(box, fr->shift_vec);
1385 /* With periodic molecules the charge groups should be whole at start up
1386 * and the virtual sites should not be far from their proper positions.
1388 if (!inputrec->bContinuation && MASTER(cr) &&
1389 !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
1391 /* Make molecules whole at start of run */
1392 if (fr->ePBC != epbcNONE)
1394 do_pbc_first_mtop(fplog, inputrec->ePBC, box, &mtop, globalState->x.rvec_array());
1398 /* Correct initial vsite positions are required
1399 * for the initial distribution in the domain decomposition
1400 * and for the initial shell prediction.
1402 constructVsitesGlobal(mtop, globalState->x);
1406 if (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
1408 ewaldcoeff_q = fr->ic->ewaldcoeff_q;
1409 ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
1414 /* This is a PME only node */
1416 GMX_ASSERT(globalState == nullptr, "We don't need the state on a PME only rank and expect it to be unitialized");
1418 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
1419 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
1422 gmx_pme_t *sepPmeData = nullptr;
1423 // This reference hides the fact that PME data is owned by runner on PME-only ranks and by forcerec on other ranks
1424 GMX_ASSERT(thisRankHasDuty(cr, DUTY_PP) == (fr != nullptr), "Double-checking that only PME-only ranks have no forcerec");
1425 gmx_pme_t * &pmedata = fr ? fr->pmedata : sepPmeData;
1427 // TODO should live in ewald module once its testing is improved
1429 // Later, this program could contain kernels that might be later
1430 // re-used as auto-tuning progresses, or subsequent simulations
1432 PmeGpuProgramStorage pmeGpuProgram;
1433 if (thisRankHasPmeGpuTask)
1435 pmeGpuProgram = buildPmeGpuProgram(pmeDeviceInfo);
1438 /* Initiate PME if necessary,
1439 * either on all nodes or on dedicated PME nodes only. */
1440 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
1442 if (mdAtoms && mdAtoms->mdatoms())
1444 nChargePerturbed = mdAtoms->mdatoms()->nChargePerturbed;
1445 if (EVDW_PME(inputrec->vdwtype))
1447 nTypePerturbed = mdAtoms->mdatoms()->nTypePerturbed;
1450 if (cr->npmenodes > 0)
1452 /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
1453 gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
1454 gmx_bcast_sim(sizeof(nTypePerturbed), &nTypePerturbed, cr);
1457 if (thisRankHasDuty(cr, DUTY_PME))
1461 pmedata = gmx_pme_init(cr,
1462 getNumPmeDomains(cr->dd),
1464 nChargePerturbed != 0, nTypePerturbed != 0,
1465 mdrunOptions.reproducible,
1466 ewaldcoeff_q, ewaldcoeff_lj,
1467 gmx_omp_nthreads_get(emntPME),
1468 pmeRunMode, nullptr,
1469 pmeDeviceInfo, pmeGpuProgram.get(), mdlog);
1471 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1476 if (EI_DYNAMICS(inputrec->eI))
1478 /* Turn on signal handling on all nodes */
1480 * (A user signal from the PME nodes (if any)
1481 * is communicated to the PP nodes.
1483 signal_handler_install();
1486 pull_t *pull_work = nullptr;
1487 if (thisRankHasDuty(cr, DUTY_PP))
1489 /* Assumes uniform use of the number of OpenMP threads */
1490 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
1492 if (inputrec->bPull)
1494 /* Initialize pull code */
1496 init_pull(fplog, inputrec->pull, inputrec,
1497 &mtop, cr, &atomSets, inputrec->fepvals->init_lambda);
1498 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
1500 initPullHistory(pull_work, &observablesHistory);
1502 if (EI_DYNAMICS(inputrec->eI) && MASTER(cr))
1504 init_pull_output_files(pull_work,
1505 filenames.size(), filenames.data(), oenv,
1510 std::unique_ptr<EnforcedRotation> enforcedRotation;
1513 /* Initialize enforced rotation code */
1514 enforcedRotation = init_rot(fplog,
1527 t_swap *swap = nullptr;
1528 if (inputrec->eSwapCoords != eswapNO)
1530 /* Initialize ion swapping code */
1531 swap = init_swapcoords(fplog, inputrec,
1532 opt2fn_master("-swap", filenames.size(), filenames.data(), cr),
1533 &mtop, globalState.get(), &observablesHistory,
1534 cr, &atomSets, oenv, mdrunOptions,
1538 /* Let makeConstraints know whether we have essential dynamics constraints. */
1539 auto constr = makeConstraints(mtop, *inputrec, pull_work, doEssentialDynamics,
1540 fplog, *mdAtoms->mdatoms(),
1541 cr, ms, &nrnb, wcycle, fr->bMolPBC);
1543 /* Energy terms and groups */
1544 gmx_enerdata_t enerd(mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(), inputrec->fepvals->n_lambda);
1546 /* Kinetic energy data */
1547 gmx_ekindata_t ekind;
1548 init_ekindata(fplog, &mtop, &(inputrec->opts), &ekind, inputrec->cos_accel);
1550 /* Set up interactive MD (IMD) */
1551 auto imdSession = makeImdSession(inputrec, cr, wcycle, &enerd, ms, &mtop, mdlog,
1552 MASTER(cr) ? globalState->x.rvec_array() : nullptr,
1553 filenames.size(), filenames.data(), oenv, mdrunOptions.imdOptions,
1556 if (DOMAINDECOMP(cr))
1558 GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
1559 /* This call is not included in init_domain_decomposition mainly
1560 * because fr->cginfo_mb is set later.
1562 dd_init_bondeds(fplog, cr->dd, &mtop, vsite.get(), inputrec,
1563 domdecOptions.checkBondedInteractions,
1567 const bool inputIsCompatibleWithModularSimulator = ModularSimulator::isInputCompatible(
1569 inputrec, doRerun, vsite.get(), ms, replExParams,
1570 fcd, static_cast<int>(filenames.size()), filenames.data(),
1571 &observablesHistory, membed);
1573 const bool useModularSimulator = inputIsCompatibleWithModularSimulator && !(getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
1575 // TODO This is not the right place to manage the lifetime of
1576 // this data structure, but currently it's the easiest way to
1578 MdrunScheduleWorkload runScheduleWork;
1579 // Also populates the simulation constant workload description.
1580 runScheduleWork.simulationWork = createSimulationWorkload(useGpuForNonbonded,
1584 devFlags.enableGpuBufferOps,
1585 devFlags.enableGpuHaloExchange,
1586 devFlags.enableGpuPmePPComm);
1588 std::unique_ptr<gmx::StatePropagatorDataGpu> stateGpu;
1589 if (gpusWereDetected && ((useGpuForPme && thisRankHasDuty(cr, DUTY_PME)) || runScheduleWork.simulationWork.useGpuBufferOps))
1591 const void *pmeStream = pme_gpu_get_device_stream(fr->pmedata);
1592 const void *localStream = fr->nbv->gpu_nbv != nullptr ? Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::Local) : nullptr;
1593 const void *nonLocalStream = fr->nbv->gpu_nbv != nullptr ? Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::NonLocal) : nullptr;
1594 const void *deviceContext = pme_gpu_get_device_context(fr->pmedata);
1595 const int paddingSize = pme_gpu_get_padding_size(fr->pmedata);
1596 GpuApiCallBehavior transferKind = (inputrec->eI == eiMD && !doRerun && !useModularSimulator) ? GpuApiCallBehavior::Async : GpuApiCallBehavior::Sync;
1598 stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(pmeStream,
1604 fr->stateGpu = stateGpu.get();
1607 GMX_ASSERT(stopHandlerBuilder_, "Runner must provide StopHandlerBuilder to simulator.");
1608 SimulatorBuilder simulatorBuilder;
1610 // build and run simulator object based on user-input
1611 auto simulator = simulatorBuilder.build(
1612 inputIsCompatibleWithModularSimulator,
1613 fplog, cr, ms, mdlog, static_cast<int>(filenames.size()), filenames.data(),
1617 vsite.get(), constr.get(),
1618 enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr,
1620 mdModules_->outputProvider(),
1621 mdModules_->notifier(),
1622 inputrec, imdSession.get(), pull_work, swap, &mtop,
1625 &observablesHistory,
1626 mdAtoms.get(), &nrnb, wcycle, fr,
1632 walltime_accounting,
1633 std::move(stopHandlerBuilder_),
1637 if (inputrec->bPull)
1639 finish_pull(pull_work);
1641 finish_swapcoords(swap);
1645 GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
1647 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
1648 gmx_pmeonly(pmedata, cr, &nrnb, wcycle, walltime_accounting, inputrec, pmeRunMode);
1651 wallcycle_stop(wcycle, ewcRUN);
1653 /* Finish up, write some stuff
1654 * if rerunMD, don't write last frame again
1656 finish_run(fplog, mdlog, cr,
1657 inputrec, &nrnb, wcycle, walltime_accounting,
1658 fr ? fr->nbv.get() : nullptr,
1660 EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
1662 // clean up cycle counter
1663 wallcycle_destroy(wcycle);
1668 gmx_pme_destroy(pmedata);
1672 // FIXME: this is only here to manually unpin mdAtoms->chargeA_ and state->x,
1673 // before we destroy the GPU context(s) in free_gpu_resources().
1674 // Pinned buffers are associated with contexts in CUDA.
1675 // As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
1676 mdAtoms.reset(nullptr);
1677 globalState.reset(nullptr);
1678 mdModules_.reset(nullptr); // destruct force providers here as they might also use the GPU
1680 /* Free GPU memory and set a physical node tMPI barrier (which should eventually go away) */
1681 free_gpu_resources(fr, physicalNodeComm, hwinfo->gpu_info);
1682 free_gpu(nonbondedDeviceInfo);
1683 free_gpu(pmeDeviceInfo);
1684 done_forcerec(fr, mtop.molblock.size());
1689 free_membed(membed);
1692 /* Does what it says */
1693 print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
1694 walltime_accounting_destroy(walltime_accounting);
1696 // Ensure log file content is written
1699 gmx_fio_flush(logFileHandle);
1702 /* Reset FPEs (important for unit tests) by disabling them. Assumes no
1703 * exceptions were enabled before function was called. */
1706 gmx_fedisableexcept();
1709 auto rc = static_cast<int>(gmx_get_stop_condition());
1712 /* we need to join all threads. The sub-threads join when they
1713 exit this function, but the master thread needs to be told to
1715 if (PAR(cr) && MASTER(cr))
1723 Mdrunner::~Mdrunner()
1725 // Clean up of the Manager.
1726 // This will end up getting called on every thread-MPI rank, which is unnecessary,
1727 // but okay as long as threads synchronize some time before adding or accessing
1728 // a new set of restraints.
1729 if (restraintManager_)
1731 restraintManager_->clear();
1732 GMX_ASSERT(restraintManager_->countRestraints() == 0,
1733 "restraints added during runner life time should be cleared at runner destruction.");
1737 void Mdrunner::addPotential(std::shared_ptr<gmx::IRestraintPotential> puller,
1738 const std::string &name)
1740 GMX_ASSERT(restraintManager_, "Mdrunner must have a restraint manager.");
1741 // Not sure if this should be logged through the md logger or something else,
1742 // but it is helpful to have some sort of INFO level message sent somewhere.
1743 // std::cout << "Registering restraint named " << name << std::endl;
1745 // When multiple restraints are used, it may be wasteful to register them separately.
1746 // Maybe instead register an entire Restraint Manager as a force provider.
1747 restraintManager_->addToSpec(std::move(puller),
1751 Mdrunner::Mdrunner(std::unique_ptr<MDModules> mdModules)
1752 : mdModules_(std::move(mdModules))
1756 Mdrunner::Mdrunner(Mdrunner &&) noexcept = default;
1758 //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265
1759 Mdrunner &Mdrunner::operator=(Mdrunner && /*handle*/) noexcept(BUGFREE_NOEXCEPT_STRING) = default;
1761 class Mdrunner::BuilderImplementation
1764 BuilderImplementation() = delete;
1765 BuilderImplementation(std::unique_ptr<MDModules> mdModules,
1766 compat::not_null<SimulationContext*> context);
1767 ~BuilderImplementation();
1769 BuilderImplementation &setExtraMdrunOptions(const MdrunOptions &options,
1770 real forceWarningThreshold,
1771 StartingBehavior startingBehavior);
1773 void addDomdec(const DomdecOptions &options);
1775 void addVerletList(int nstlist);
1777 void addReplicaExchange(const ReplicaExchangeParameters ¶ms);
1779 void addNonBonded(const char* nbpu_opt);
1781 void addPME(const char* pme_opt_, const char* pme_fft_opt_);
1783 void addBondedTaskAssignment(const char* bonded_opt);
1785 void addUpdateTaskAssignment(const char* update_opt);
1787 void addHardwareOptions(const gmx_hw_opt_t &hardwareOptions);
1789 void addFilenames(ArrayRef <const t_filenm> filenames);
1791 void addOutputEnvironment(gmx_output_env_t* outputEnvironment);
1793 void addLogFile(t_fileio *logFileHandle);
1795 void addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
1801 // Default parameters copied from runner.h
1802 // \todo Clarify source(s) of default parameters.
1804 const char* nbpu_opt_ = nullptr;
1805 const char* pme_opt_ = nullptr;
1806 const char* pme_fft_opt_ = nullptr;
1807 const char *bonded_opt_ = nullptr;
1808 const char *update_opt_ = nullptr;
1810 MdrunOptions mdrunOptions_;
1812 DomdecOptions domdecOptions_;
1814 ReplicaExchangeParameters replicaExchangeParameters_;
1816 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
1819 //! Multisim communicator handle.
1820 gmx_multisim_t *multiSimulation_;
1822 //! mdrun communicator
1823 MPI_Comm communicator_ = MPI_COMM_NULL;
1825 //! Print a warning if any force is larger than this (in kJ/mol nm).
1826 real forceWarningThreshold_ = -1;
1828 //! Whether the simulation will start afresh, or restart with/without appending.
1829 StartingBehavior startingBehavior_ = StartingBehavior::NewSimulation;
1831 //! The modules that comprise the functionality of mdrun.
1832 std::unique_ptr<MDModules> mdModules_;
1834 //! \brief Parallelism information.
1835 gmx_hw_opt_t hardwareOptions_;
1837 //! filename options for simulation.
1838 ArrayRef<const t_filenm> filenames_;
1840 /*! \brief Handle to output environment.
1842 * \todo gmx_output_env_t needs lifetime management.
1844 gmx_output_env_t* outputEnvironment_ = nullptr;
1846 /*! \brief Non-owning handle to MD log file.
1848 * \todo Context should own output facilities for client.
1849 * \todo Improve log file handle management.
1851 * Code managing the FILE* relies on the ability to set it to
1852 * nullptr to check whether the filehandle is valid.
1854 t_fileio* logFileHandle_ = nullptr;
1857 * \brief Builder for simulation stop signal handler.
1859 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_ = nullptr;
1862 Mdrunner::BuilderImplementation::BuilderImplementation(std::unique_ptr<MDModules> mdModules,
1863 compat::not_null<SimulationContext*> context) :
1864 mdModules_(std::move(mdModules))
1866 communicator_ = context->communicator_;
1867 multiSimulation_ = context->multiSimulation_.get();
1870 Mdrunner::BuilderImplementation::~BuilderImplementation() = default;
1872 Mdrunner::BuilderImplementation &
1873 Mdrunner::BuilderImplementation::setExtraMdrunOptions(const MdrunOptions &options,
1874 const real forceWarningThreshold,
1875 const StartingBehavior startingBehavior)
1877 mdrunOptions_ = options;
1878 forceWarningThreshold_ = forceWarningThreshold;
1879 startingBehavior_ = startingBehavior;
1883 void Mdrunner::BuilderImplementation::addDomdec(const DomdecOptions &options)
1885 domdecOptions_ = options;
1888 void Mdrunner::BuilderImplementation::addVerletList(int nstlist)
1893 void Mdrunner::BuilderImplementation::addReplicaExchange(const ReplicaExchangeParameters ¶ms)
1895 replicaExchangeParameters_ = params;
1898 Mdrunner Mdrunner::BuilderImplementation::build()
1900 auto newRunner = Mdrunner(std::move(mdModules_));
1902 newRunner.mdrunOptions = mdrunOptions_;
1903 newRunner.pforce = forceWarningThreshold_;
1904 newRunner.startingBehavior = startingBehavior_;
1905 newRunner.domdecOptions = domdecOptions_;
1907 // \todo determine an invariant to check or confirm that all gmx_hw_opt_t objects are valid
1908 newRunner.hw_opt = hardwareOptions_;
1910 // No invariant to check. This parameter exists to optionally override other behavior.
1911 newRunner.nstlist_cmdline = nstlist_;
1913 newRunner.replExParams = replicaExchangeParameters_;
1915 newRunner.filenames = filenames_;
1917 newRunner.communicator = communicator_;
1919 // nullptr is a valid value for the multisim handle
1920 newRunner.ms = multiSimulation_;
1922 // \todo Clarify ownership and lifetime management for gmx_output_env_t
1923 // \todo Update sanity checking when output environment has clearly specified invariants.
1924 // Initialization and default values for oenv are not well specified in the current version.
1925 if (outputEnvironment_)
1927 newRunner.oenv = outputEnvironment_;
1931 GMX_THROW(gmx::APIError("MdrunnerBuilder::addOutputEnvironment() is required before build()"));
1934 newRunner.logFileHandle = logFileHandle_;
1938 newRunner.nbpu_opt = nbpu_opt_;
1942 GMX_THROW(gmx::APIError("MdrunnerBuilder::addNonBonded() is required before build()"));
1945 if (pme_opt_ && pme_fft_opt_)
1947 newRunner.pme_opt = pme_opt_;
1948 newRunner.pme_fft_opt = pme_fft_opt_;
1952 GMX_THROW(gmx::APIError("MdrunnerBuilder::addElectrostatics() is required before build()"));
1957 newRunner.bonded_opt = bonded_opt_;
1961 GMX_THROW(gmx::APIError("MdrunnerBuilder::addBondedTaskAssignment() is required before build()"));
1966 newRunner.update_opt = update_opt_;
1970 GMX_THROW(gmx::APIError("MdrunnerBuilder::addUpdateTaskAssignment() is required before build() "));
1974 newRunner.restraintManager_ = std::make_unique<gmx::RestraintManager>();
1976 if (stopHandlerBuilder_)
1978 newRunner.stopHandlerBuilder_ = std::move(stopHandlerBuilder_);
1982 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>();
1988 void Mdrunner::BuilderImplementation::addNonBonded(const char* nbpu_opt)
1990 nbpu_opt_ = nbpu_opt;
1993 void Mdrunner::BuilderImplementation::addPME(const char* pme_opt,
1994 const char* pme_fft_opt)
1997 pme_fft_opt_ = pme_fft_opt;
2000 void Mdrunner::BuilderImplementation::addBondedTaskAssignment(const char* bonded_opt)
2002 bonded_opt_ = bonded_opt;
2005 void Mdrunner::BuilderImplementation::addUpdateTaskAssignment(const char* update_opt)
2007 update_opt_ = update_opt;
2010 void Mdrunner::BuilderImplementation::addHardwareOptions(const gmx_hw_opt_t &hardwareOptions)
2012 hardwareOptions_ = hardwareOptions;
2015 void Mdrunner::BuilderImplementation::addFilenames(ArrayRef<const t_filenm> filenames)
2017 filenames_ = filenames;
2020 void Mdrunner::BuilderImplementation::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2022 outputEnvironment_ = outputEnvironment;
2025 void Mdrunner::BuilderImplementation::addLogFile(t_fileio *logFileHandle)
2027 logFileHandle_ = logFileHandle;
2030 void Mdrunner::BuilderImplementation::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2032 stopHandlerBuilder_ = std::move(builder);
2035 MdrunnerBuilder::MdrunnerBuilder(std::unique_ptr<MDModules> mdModules,
2036 compat::not_null<SimulationContext*> context) :
2037 impl_ {std::make_unique<Mdrunner::BuilderImplementation>(std::move(mdModules), context)}
2041 MdrunnerBuilder::~MdrunnerBuilder() = default;
2043 MdrunnerBuilder &MdrunnerBuilder::addSimulationMethod(const MdrunOptions &options,
2044 real forceWarningThreshold,
2045 const StartingBehavior startingBehavior)
2047 impl_->setExtraMdrunOptions(options, forceWarningThreshold, startingBehavior);
2051 MdrunnerBuilder &MdrunnerBuilder::addDomainDecomposition(const DomdecOptions &options)
2053 impl_->addDomdec(options);
2057 MdrunnerBuilder &MdrunnerBuilder::addNeighborList(int nstlist)
2059 impl_->addVerletList(nstlist);
2063 MdrunnerBuilder &MdrunnerBuilder::addReplicaExchange(const ReplicaExchangeParameters ¶ms)
2065 impl_->addReplicaExchange(params);
2069 MdrunnerBuilder &MdrunnerBuilder::addNonBonded(const char* nbpu_opt)
2071 impl_->addNonBonded(nbpu_opt);
2075 MdrunnerBuilder &MdrunnerBuilder::addElectrostatics(const char* pme_opt,
2076 const char* pme_fft_opt)
2078 // The builder method may become more general in the future, but in this version,
2079 // parameters for PME electrostatics are both required and the only parameters
2081 if (pme_opt && pme_fft_opt)
2083 impl_->addPME(pme_opt, pme_fft_opt);
2087 GMX_THROW(gmx::InvalidInputError("addElectrostatics() arguments must be non-null pointers."));
2092 MdrunnerBuilder &MdrunnerBuilder::addBondedTaskAssignment(const char* bonded_opt)
2094 impl_->addBondedTaskAssignment(bonded_opt);
2098 MdrunnerBuilder &MdrunnerBuilder::addUpdateTaskAssignment(const char* update_opt)
2100 impl_->addUpdateTaskAssignment(update_opt);
2104 Mdrunner MdrunnerBuilder::build()
2106 return impl_->build();
2109 MdrunnerBuilder &MdrunnerBuilder::addHardwareOptions(const gmx_hw_opt_t &hardwareOptions)
2111 impl_->addHardwareOptions(hardwareOptions);
2115 MdrunnerBuilder &MdrunnerBuilder::addFilenames(ArrayRef<const t_filenm> filenames)
2117 impl_->addFilenames(filenames);
2121 MdrunnerBuilder &MdrunnerBuilder::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2123 impl_->addOutputEnvironment(outputEnvironment);
2127 MdrunnerBuilder &MdrunnerBuilder::addLogFile(t_fileio *logFileHandle)
2129 impl_->addLogFile(logFileHandle);
2133 MdrunnerBuilder &MdrunnerBuilder::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2135 impl_->addStopHandlerBuilder(std::move(builder));
2139 MdrunnerBuilder::MdrunnerBuilder(MdrunnerBuilder &&) noexcept = default;
2141 MdrunnerBuilder &MdrunnerBuilder::operator=(MdrunnerBuilder &&) noexcept = default;