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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/fileio/checkpoint.h"
70 #include "gromacs/fileio/gmxfio.h"
71 #include "gromacs/fileio/oenv.h"
72 #include "gromacs/fileio/tpxio.h"
73 #include "gromacs/gmxlib/network.h"
74 #include "gromacs/gmxlib/nrnb.h"
75 #include "gromacs/gpu_utils/gpu_utils.h"
76 #include "gromacs/hardware/cpuinfo.h"
77 #include "gromacs/hardware/detecthardware.h"
78 #include "gromacs/hardware/printhardware.h"
79 #include "gromacs/imd/imd.h"
80 #include "gromacs/listed_forces/disre.h"
81 #include "gromacs/listed_forces/gpubonded.h"
82 #include "gromacs/listed_forces/orires.h"
83 #include "gromacs/math/functions.h"
84 #include "gromacs/math/utilities.h"
85 #include "gromacs/math/vec.h"
86 #include "gromacs/mdlib/boxdeformation.h"
87 #include "gromacs/mdlib/broadcaststructs.h"
88 #include "gromacs/mdlib/calc_verletbuf.h"
89 #include "gromacs/mdlib/dispersioncorrection.h"
90 #include "gromacs/mdlib/enerdata_utils.h"
91 #include "gromacs/mdlib/force.h"
92 #include "gromacs/mdlib/forcerec.h"
93 #include "gromacs/mdlib/gmx_omp_nthreads.h"
94 #include "gromacs/mdlib/makeconstraints.h"
95 #include "gromacs/mdlib/md_support.h"
96 #include "gromacs/mdlib/mdatoms.h"
97 #include "gromacs/mdlib/membed.h"
98 #include "gromacs/mdlib/qmmm.h"
99 #include "gromacs/mdlib/sighandler.h"
100 #include "gromacs/mdlib/stophandler.h"
101 #include "gromacs/mdrun/mdmodules.h"
102 #include "gromacs/mdrun/simulationcontext.h"
103 #include "gromacs/mdrunutility/handlerestart.h"
104 #include "gromacs/mdrunutility/logging.h"
105 #include "gromacs/mdrunutility/multisim.h"
106 #include "gromacs/mdrunutility/printtime.h"
107 #include "gromacs/mdrunutility/threadaffinity.h"
108 #include "gromacs/mdtypes/commrec.h"
109 #include "gromacs/mdtypes/enerdata.h"
110 #include "gromacs/mdtypes/fcdata.h"
111 #include "gromacs/mdtypes/group.h"
112 #include "gromacs/mdtypes/inputrec.h"
113 #include "gromacs/mdtypes/md_enums.h"
114 #include "gromacs/mdtypes/mdrunoptions.h"
115 #include "gromacs/mdtypes/observableshistory.h"
116 #include "gromacs/mdtypes/simulation_workload.h"
117 #include "gromacs/mdtypes/state.h"
118 #include "gromacs/mdtypes/state_propagator_data_gpu.h"
119 #include "gromacs/nbnxm/gpu_data_mgmt.h"
120 #include "gromacs/nbnxm/nbnxm.h"
121 #include "gromacs/nbnxm/pairlist_tuning.h"
122 #include "gromacs/pbcutil/pbc.h"
123 #include "gromacs/pulling/output.h"
124 #include "gromacs/pulling/pull.h"
125 #include "gromacs/pulling/pull_rotation.h"
126 #include "gromacs/restraint/manager.h"
127 #include "gromacs/restraint/restraintmdmodule.h"
128 #include "gromacs/restraint/restraintpotential.h"
129 #include "gromacs/swap/swapcoords.h"
130 #include "gromacs/taskassignment/decidegpuusage.h"
131 #include "gromacs/taskassignment/decidesimulationworkload.h"
132 #include "gromacs/taskassignment/resourcedivision.h"
133 #include "gromacs/taskassignment/taskassignment.h"
134 #include "gromacs/taskassignment/usergpuids.h"
135 #include "gromacs/timing/gpu_timing.h"
136 #include "gromacs/timing/wallcycle.h"
137 #include "gromacs/timing/wallcyclereporting.h"
138 #include "gromacs/topology/mtop_util.h"
139 #include "gromacs/trajectory/trajectoryframe.h"
140 #include "gromacs/utility/basenetwork.h"
141 #include "gromacs/utility/cstringutil.h"
142 #include "gromacs/utility/exceptions.h"
143 #include "gromacs/utility/fatalerror.h"
144 #include "gromacs/utility/filestream.h"
145 #include "gromacs/utility/gmxassert.h"
146 #include "gromacs/utility/gmxmpi.h"
147 #include "gromacs/utility/keyvaluetree.h"
148 #include "gromacs/utility/logger.h"
149 #include "gromacs/utility/loggerbuilder.h"
150 #include "gromacs/utility/mdmodulenotification.h"
151 #include "gromacs/utility/physicalnodecommunicator.h"
152 #include "gromacs/utility/pleasecite.h"
153 #include "gromacs/utility/programcontext.h"
154 #include "gromacs/utility/smalloc.h"
155 #include "gromacs/utility/stringutil.h"
157 #include "isimulator.h"
158 #include "replicaexchange.h"
159 #include "simulatorbuilder.h"
162 #include "corewrap.h"
168 /*! \brief Structure that holds boolean flags corresponding to the development
169 * features present enabled through environemnt variables.
172 struct DevelopmentFeatureFlags
174 ///! True if the Buffer ops development feature is enabled
175 // TODO: when the trigger of the buffer ops offload is fully automated this should go away
176 bool enableGpuBufferOps = false;
177 ///! True if the update-constraints development feature is enabled
178 // TODO This needs to be reomved when the code gets cleaned up of GMX_UPDATE_CONSTRAIN_GPU
179 bool useGpuUpdateConstrain = false;
180 ///! True if the GPU halo exchange development feature is enabled
181 bool enableGpuHaloExchange = false;
182 ///! True if the PME PP direct commuinication 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 * \returns The object populated with development feature flags.
201 static DevelopmentFeatureFlags manageDevelopmentFeatures(const gmx::MDLogger &mdlog,
202 const bool useGpuForNonbonded)
204 DevelopmentFeatureFlags devFlags;
206 devFlags.enableGpuBufferOps = (getenv("GMX_USE_GPU_BUFFER_OPS") != nullptr) && (GMX_GPU == GMX_GPU_CUDA) && useGpuForNonbonded;
207 devFlags.useGpuUpdateConstrain = (getenv("GMX_UPDATE_CONSTRAIN_GPU") != nullptr);
208 devFlags.enableGpuHaloExchange = (getenv("GMX_GPU_DD_COMMS") != nullptr && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA));
209 devFlags.enableGpuPmePPComm = (getenv("GMX_GPU_DD_COMMS") != nullptr && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA));
211 if (devFlags.enableGpuBufferOps)
213 GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
214 "NOTE: This run uses the 'GPU buffer ops' feature, enabled by the GMX_USE_GPU_BUFFER_OPS environment variable.");
217 if (devFlags.enableGpuHaloExchange)
219 if (!devFlags.enableGpuBufferOps)
221 gmx_fatal(FARGS, "Cannot enable GPU halo exchange without GPU buffer operations, set GMX_USE_GPU_BUFFER_OPS=1\n");
225 if (devFlags.useGpuUpdateConstrain)
227 GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
228 "NOTE: This run uses the 'GPU update/constraints' feature, enabled by the GMX_UPDATE_CONSTRAIN_GPU environment variable.");
234 /*! \brief Barrier for safe simultaneous thread access to mdrunner data
236 * Used to ensure that the master thread does not modify mdrunner during copy
237 * on the spawned threads. */
238 static void threadMpiMdrunnerAccessBarrier()
241 MPI_Barrier(MPI_COMM_WORLD);
245 Mdrunner Mdrunner::cloneOnSpawnedThread() const
247 auto newRunner = Mdrunner(std::make_unique<MDModules>());
249 // All runners in the same process share a restraint manager resource because it is
250 // part of the interface to the client code, which is associated only with the
251 // original thread. Handles to the same resources can be obtained by copy.
253 newRunner.restraintManager_ = std::make_unique<RestraintManager>(*restraintManager_);
256 // Copy members of master runner.
257 // \todo Replace with builder when Simulation context and/or runner phases are better defined.
258 // Ref https://redmine.gromacs.org/issues/2587 and https://redmine.gromacs.org/issues/2375
259 newRunner.hw_opt = hw_opt;
260 newRunner.filenames = filenames;
262 newRunner.oenv = oenv;
263 newRunner.mdrunOptions = mdrunOptions;
264 newRunner.domdecOptions = domdecOptions;
265 newRunner.nbpu_opt = nbpu_opt;
266 newRunner.pme_opt = pme_opt;
267 newRunner.pme_fft_opt = pme_fft_opt;
268 newRunner.bonded_opt = bonded_opt;
269 newRunner.update_opt = update_opt;
270 newRunner.nstlist_cmdline = nstlist_cmdline;
271 newRunner.replExParams = replExParams;
272 newRunner.pforce = pforce;
273 // Give the spawned thread the newly created valid communicator
274 // for the simulation.
275 newRunner.communicator = MPI_COMM_WORLD;
277 newRunner.startingBehavior = startingBehavior;
278 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>(*stopHandlerBuilder_);
280 threadMpiMdrunnerAccessBarrier();
285 /*! \brief The callback used for running on spawned threads.
287 * Obtains the pointer to the master mdrunner object from the one
288 * argument permitted to the thread-launch API call, copies it to make
289 * a new runner for this thread, reinitializes necessary data, and
290 * proceeds to the simulation. */
291 static void mdrunner_start_fn(const void *arg)
295 auto masterMdrunner = reinterpret_cast<const gmx::Mdrunner *>(arg);
296 /* copy the arg list to make sure that it's thread-local. This
297 doesn't copy pointed-to items, of course; fnm, cr and fplog
298 are reset in the call below, all others should be const. */
299 gmx::Mdrunner mdrunner = masterMdrunner->cloneOnSpawnedThread();
302 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
306 void Mdrunner::spawnThreads(int numThreadsToLaunch)
309 /* now spawn new threads that start mdrunner_start_fn(), while
310 the main thread returns. Thread affinity is handled later. */
311 if (tMPI_Init_fn(TRUE, numThreadsToLaunch, TMPI_AFFINITY_NONE,
312 mdrunner_start_fn, static_cast<const void*>(this)) != TMPI_SUCCESS)
314 GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
317 // Give the master thread the newly created valid communicator for
319 communicator = MPI_COMM_WORLD;
320 threadMpiMdrunnerAccessBarrier();
322 GMX_UNUSED_VALUE(numThreadsToLaunch);
323 GMX_UNUSED_VALUE(mdrunner_start_fn);
329 /*! \brief Initialize variables for Verlet scheme simulation */
330 static void prepare_verlet_scheme(FILE *fplog,
334 const gmx_mtop_t *mtop,
336 bool makeGpuPairList,
337 const gmx::CpuInfo &cpuinfo)
339 /* For NVE simulations, we will retain the initial list buffer */
340 if (EI_DYNAMICS(ir->eI) &&
341 ir->verletbuf_tol > 0 &&
342 !(EI_MD(ir->eI) && ir->etc == etcNO))
344 /* Update the Verlet buffer size for the current run setup */
346 /* Here we assume SIMD-enabled kernels are being used. But as currently
347 * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
348 * and 4x2 gives a larger buffer than 4x4, this is ok.
350 ListSetupType listType = (makeGpuPairList ? ListSetupType::Gpu : ListSetupType::CpuSimdWhenSupported);
351 VerletbufListSetup listSetup = verletbufGetSafeListSetup(listType);
353 const real rlist_new =
354 calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
356 if (rlist_new != ir->rlist)
358 if (fplog != nullptr)
360 fprintf(fplog, "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
361 ir->rlist, rlist_new,
362 listSetup.cluster_size_i, listSetup.cluster_size_j);
364 ir->rlist = rlist_new;
368 if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
370 gmx_fatal(FARGS, "Can not set nstlist without %s",
371 !EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
374 if (EI_DYNAMICS(ir->eI))
376 /* Set or try nstlist values */
377 increaseNstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, makeGpuPairList, cpuinfo);
381 /*! \brief Override the nslist value in inputrec
383 * with value passed on the command line (if any)
385 static void override_nsteps_cmdline(const gmx::MDLogger &mdlog,
386 int64_t nsteps_cmdline,
391 /* override with anything else than the default -2 */
392 if (nsteps_cmdline > -2)
394 char sbuf_steps[STEPSTRSIZE];
395 char sbuf_msg[STRLEN];
397 ir->nsteps = nsteps_cmdline;
398 if (EI_DYNAMICS(ir->eI) && nsteps_cmdline != -1)
400 sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
401 gmx_step_str(nsteps_cmdline, sbuf_steps),
402 fabs(nsteps_cmdline*ir->delta_t));
406 sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps",
407 gmx_step_str(nsteps_cmdline, sbuf_steps));
410 GMX_LOG(mdlog.warning).asParagraph().appendText(sbuf_msg);
412 else if (nsteps_cmdline < -2)
414 gmx_fatal(FARGS, "Invalid nsteps value passed on the command line: %" PRId64,
417 /* Do nothing if nsteps_cmdline == -2 */
423 /*! \brief Return whether GPU acceleration of nonbondeds is supported with the given settings.
425 * If not, and if a warning may be issued, logs a warning about
426 * falling back to CPU code. With thread-MPI, only the first
427 * call to this function should have \c issueWarning true. */
428 static bool gpuAccelerationOfNonbondedIsUseful(const MDLogger &mdlog,
429 const t_inputrec &ir,
432 bool gpuIsUseful = true;
435 if (ir.opts.ngener - ir.nwall > 1)
437 /* The GPU code does not support more than one energy group.
438 * If the user requested GPUs explicitly, a fatal error is given later.
442 "Multiple energy groups is not implemented for GPUs, falling back to the CPU. "
443 "For better performance, run on the GPU without energy groups and then do "
444 "gmx mdrun -rerun option on the trajectory with an energy group .tpr file.";
450 warning = "TPI is not implemented for GPUs.";
453 if (!gpuIsUseful && issueWarning)
455 GMX_LOG(mdlog.warning).asParagraph().appendText(warning);
461 //! Initializes the logger for mdrun.
462 static gmx::LoggerOwner buildLogger(FILE *fplog,
463 const bool isSimulationMasterRank)
465 gmx::LoggerBuilder builder;
466 if (fplog != nullptr)
468 builder.addTargetFile(gmx::MDLogger::LogLevel::Info, fplog);
470 if (isSimulationMasterRank)
472 builder.addTargetStream(gmx::MDLogger::LogLevel::Warning,
473 &gmx::TextOutputFile::standardError());
475 return builder.build();
478 //! Make a TaskTarget from an mdrun argument string.
479 static TaskTarget findTaskTarget(const char *optionString)
481 TaskTarget returnValue = TaskTarget::Auto;
483 if (strncmp(optionString, "auto", 3) == 0)
485 returnValue = TaskTarget::Auto;
487 else if (strncmp(optionString, "cpu", 3) == 0)
489 returnValue = TaskTarget::Cpu;
491 else if (strncmp(optionString, "gpu", 3) == 0)
493 returnValue = TaskTarget::Gpu;
497 GMX_ASSERT(false, "Option string should have been checked for sanity already");
503 //! Finish run, aggregate data to print performance info.
504 static void finish_run(FILE *fplog,
505 const gmx::MDLogger &mdlog,
507 const t_inputrec *inputrec,
508 t_nrnb nrnb[], gmx_wallcycle_t wcycle,
509 gmx_walltime_accounting_t walltime_accounting,
510 nonbonded_verlet_t *nbv,
511 const gmx_pme_t *pme,
515 double nbfs = 0, mflop = 0;
517 elapsed_time_over_all_ranks,
518 elapsed_time_over_all_threads,
519 elapsed_time_over_all_threads_over_all_ranks;
520 /* Control whether it is valid to print a report. Only the
521 simulation master may print, but it should not do so if the run
522 terminated e.g. before a scheduled reset step. This is
523 complicated by the fact that PME ranks are unaware of the
524 reason why they were sent a pmerecvqxFINISH. To avoid
525 communication deadlocks, we always do the communication for the
526 report, even if we've decided not to write the report, because
527 how long it takes to finish the run is not important when we've
528 decided not to report on the simulation performance.
530 Further, we only report performance for dynamical integrators,
531 because those are the only ones for which we plan to
532 consider doing any optimizations. */
533 bool printReport = EI_DYNAMICS(inputrec->eI) && SIMMASTER(cr);
535 if (printReport && !walltime_accounting_get_valid_finish(walltime_accounting))
537 GMX_LOG(mdlog.warning).asParagraph().appendText("Simulation ended prematurely, no performance report will be written.");
542 std::unique_ptr<t_nrnb> nrnbTotalStorage;
545 nrnbTotalStorage = std::make_unique<t_nrnb>();
546 nrnb_tot = nrnbTotalStorage.get();
548 MPI_Allreduce(nrnb->n, nrnb_tot->n, eNRNB, MPI_DOUBLE, MPI_SUM,
557 elapsed_time = walltime_accounting_get_time_since_reset(walltime_accounting);
558 elapsed_time_over_all_threads = walltime_accounting_get_time_since_reset_over_all_threads(walltime_accounting);
562 /* reduce elapsed_time over all MPI ranks in the current simulation */
563 MPI_Allreduce(&elapsed_time,
564 &elapsed_time_over_all_ranks,
565 1, MPI_DOUBLE, MPI_SUM,
567 elapsed_time_over_all_ranks /= cr->nnodes;
568 /* Reduce elapsed_time_over_all_threads over all MPI ranks in the
569 * current simulation. */
570 MPI_Allreduce(&elapsed_time_over_all_threads,
571 &elapsed_time_over_all_threads_over_all_ranks,
572 1, MPI_DOUBLE, MPI_SUM,
578 elapsed_time_over_all_ranks = elapsed_time;
579 elapsed_time_over_all_threads_over_all_ranks = elapsed_time_over_all_threads;
584 print_flop(fplog, nrnb_tot, &nbfs, &mflop);
587 if (thisRankHasDuty(cr, DUTY_PP) && DOMAINDECOMP(cr))
589 print_dd_statistics(cr, inputrec, fplog);
592 /* TODO Move the responsibility for any scaling by thread counts
593 * to the code that handled the thread region, so that there's a
594 * mechanism to keep cycle counting working during the transition
595 * to task parallelism. */
596 int nthreads_pp = gmx_omp_nthreads_get(emntNonbonded);
597 int nthreads_pme = gmx_omp_nthreads_get(emntPME);
598 wallcycle_scale_by_num_threads(wcycle, thisRankHasDuty(cr, DUTY_PME) && !thisRankHasDuty(cr, DUTY_PP), nthreads_pp, nthreads_pme);
599 auto cycle_sum(wallcycle_sum(cr, wcycle));
603 auto nbnxn_gpu_timings = (nbv != nullptr && nbv->useGpu()) ? Nbnxm::gpu_get_timings(nbv->gpu_nbv) : nullptr;
604 gmx_wallclock_gpu_pme_t pme_gpu_timings = {};
606 if (pme_gpu_task_enabled(pme))
608 pme_gpu_get_timings(pme, &pme_gpu_timings);
610 wallcycle_print(fplog, mdlog, cr->nnodes, cr->npmenodes, nthreads_pp, nthreads_pme,
611 elapsed_time_over_all_ranks,
616 if (EI_DYNAMICS(inputrec->eI))
618 delta_t = inputrec->delta_t;
623 print_perf(fplog, elapsed_time_over_all_threads_over_all_ranks,
624 elapsed_time_over_all_ranks,
625 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
626 delta_t, nbfs, mflop);
630 print_perf(stderr, elapsed_time_over_all_threads_over_all_ranks,
631 elapsed_time_over_all_ranks,
632 walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
633 delta_t, nbfs, mflop);
638 int Mdrunner::mdrunner()
641 t_forcerec *fr = nullptr;
642 t_fcdata *fcd = nullptr;
643 real ewaldcoeff_q = 0;
644 real ewaldcoeff_lj = 0;
645 int nChargePerturbed = -1, nTypePerturbed = 0;
646 gmx_wallcycle_t wcycle;
647 gmx_walltime_accounting_t walltime_accounting = nullptr;
648 gmx_membed_t * membed = nullptr;
649 gmx_hw_info_t *hwinfo = nullptr;
651 /* CAUTION: threads may be started later on in this function, so
652 cr doesn't reflect the final parallel state right now */
655 bool doMembed = opt2bSet("-membed", filenames.size(), filenames.data());
656 bool doRerun = mdrunOptions.rerun;
658 // Handle task-assignment related user options.
659 EmulateGpuNonbonded emulateGpuNonbonded = (getenv("GMX_EMULATE_GPU") != nullptr ?
660 EmulateGpuNonbonded::Yes : EmulateGpuNonbonded::No);
662 std::vector<int> userGpuTaskAssignment;
665 userGpuTaskAssignment = parseUserTaskAssignmentString(hw_opt.userGpuTaskAssignment);
667 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
668 auto nonbondedTarget = findTaskTarget(nbpu_opt);
669 auto pmeTarget = findTaskTarget(pme_opt);
670 auto pmeFftTarget = findTaskTarget(pme_fft_opt);
671 auto bondedTarget = findTaskTarget(bonded_opt);
672 auto updateTarget = findTaskTarget(update_opt);
673 PmeRunMode pmeRunMode = PmeRunMode::None;
675 FILE *fplog = nullptr;
676 // If we are appending, we don't write log output because we need
677 // to check that the old log file matches what the checkpoint file
678 // expects. Otherwise, we should start to write log output now if
679 // there is a file ready for it.
680 if (logFileHandle != nullptr && startingBehavior != StartingBehavior::RestartWithAppending)
682 fplog = gmx_fio_getfp(logFileHandle);
684 const bool isSimulationMasterRank = findIsSimulationMasterRank(ms, communicator);
685 gmx::LoggerOwner logOwner(buildLogger(fplog, isSimulationMasterRank));
686 gmx::MDLogger mdlog(logOwner.logger());
688 // TODO The thread-MPI master rank makes a working
689 // PhysicalNodeCommunicator here, but it gets rebuilt by all ranks
690 // after the threads have been launched. This works because no use
691 // is made of that communicator until after the execution paths
692 // have rejoined. But it is likely that we can improve the way
693 // this is expressed, e.g. by expressly running detection only the
694 // master rank for thread-MPI, rather than relying on the mutex
695 // and reference count.
696 PhysicalNodeCommunicator physicalNodeComm(communicator, gmx_physicalnode_id_hash());
697 hwinfo = gmx_detect_hardware(mdlog, physicalNodeComm);
699 gmx_print_detected_hardware(fplog, isSimulationMasterRank && isMasterSim(ms), mdlog, hwinfo);
701 std::vector<int> gpuIdsToUse = makeGpuIdsToUse(hwinfo->gpu_info, hw_opt.gpuIdsAvailable);
703 // Print citation requests after all software/hardware printing
704 pleaseCiteGromacs(fplog);
706 // TODO Replace this by unique_ptr once t_inputrec is C++
707 t_inputrec inputrecInstance;
708 t_inputrec *inputrec = nullptr;
709 std::unique_ptr<t_state> globalState;
711 auto partialDeserializedTpr = std::make_unique<PartialDeserializedTprFile>();
713 if (isSimulationMasterRank)
715 /* Only the master rank has the global state */
716 globalState = std::make_unique<t_state>();
718 /* Read (nearly) all data required for the simulation
719 * and keep the partly serialized tpr contents to send to other ranks later
721 *partialDeserializedTpr = read_tpx_state(ftp2fn(efTPR, filenames.size(), filenames.data()), &inputrecInstance, globalState.get(), &mtop);
722 inputrec = &inputrecInstance;
725 /* Check and update the hardware options for internal consistency */
726 checkAndUpdateHardwareOptions(mdlog, &hw_opt, isSimulationMasterRank, domdecOptions.numPmeRanks, inputrec);
728 if (GMX_THREAD_MPI && isSimulationMasterRank)
730 bool useGpuForNonbonded = false;
731 bool useGpuForPme = false;
734 GMX_RELEASE_ASSERT(inputrec != nullptr, "Keep the compiler happy");
736 // If the user specified the number of ranks, then we must
737 // respect that, but in default mode, we need to allow for
738 // the number of GPUs to choose the number of ranks.
739 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
740 useGpuForNonbonded = decideWhetherToUseGpusForNonbondedWithThreadMpi
741 (nonbondedTarget, gpuIdsToUse, userGpuTaskAssignment, emulateGpuNonbonded,
742 canUseGpuForNonbonded,
743 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, GMX_THREAD_MPI),
744 hw_opt.nthreads_tmpi);
745 useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi
746 (useGpuForNonbonded, pmeTarget, gpuIdsToUse, userGpuTaskAssignment,
747 *hwinfo, *inputrec, mtop, hw_opt.nthreads_tmpi, domdecOptions.numPmeRanks);
750 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
752 /* Determine how many thread-MPI ranks to start.
754 * TODO Over-writing the user-supplied value here does
755 * prevent any possible subsequent checks from working
757 hw_opt.nthreads_tmpi = get_nthreads_mpi(hwinfo,
766 // Now start the threads for thread MPI.
767 spawnThreads(hw_opt.nthreads_tmpi);
768 // The spawned threads enter mdrunner() and execution of
769 // master and spawned threads joins at the end of this block.
770 physicalNodeComm = PhysicalNodeCommunicator(communicator, gmx_physicalnode_id_hash());
773 GMX_RELEASE_ASSERT(communicator == MPI_COMM_WORLD, "Must have valid world communicator");
774 CommrecHandle crHandle = init_commrec(communicator, ms);
775 t_commrec *cr = crHandle.get();
776 GMX_RELEASE_ASSERT(cr != nullptr, "Must have valid commrec");
780 /* now broadcast everything to the non-master nodes/threads: */
781 if (!isSimulationMasterRank)
783 inputrec = &inputrecInstance;
785 init_parallel(cr, inputrec, &mtop, partialDeserializedTpr.get());
787 GMX_RELEASE_ASSERT(inputrec != nullptr, "All ranks should have a valid inputrec now");
788 partialDeserializedTpr.reset(nullptr);
790 // Now the number of ranks is known to all ranks, and each knows
791 // the inputrec read by the master rank. The ranks can now all run
792 // the task-deciding functions and will agree on the result
793 // without needing to communicate.
795 // TODO Should we do the communication in debug mode to support
796 // having an assertion?
798 // Note that these variables describe only their own node.
800 // Note that when bonded interactions run on a GPU they always run
801 // alongside a nonbonded task, so do not influence task assignment
802 // even though they affect the force calculation workload.
803 bool useGpuForNonbonded = false;
804 bool useGpuForPme = false;
805 bool useGpuForBonded = false;
806 bool useGpuForUpdate = false;
807 bool gpusWereDetected = hwinfo->ngpu_compatible_tot > 0;
810 // It's possible that there are different numbers of GPUs on
811 // different nodes, which is the user's responsibility to
812 // handle. If unsuitable, we will notice that during task
814 auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
815 useGpuForNonbonded = decideWhetherToUseGpusForNonbonded(nonbondedTarget, userGpuTaskAssignment,
817 canUseGpuForNonbonded,
818 gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, !GMX_THREAD_MPI),
820 useGpuForPme = decideWhetherToUseGpusForPme(useGpuForNonbonded, pmeTarget, userGpuTaskAssignment,
821 *hwinfo, *inputrec, mtop,
822 cr->nnodes, domdecOptions.numPmeRanks,
824 auto canUseGpuForBonded = buildSupportsGpuBondeds(nullptr) && inputSupportsGpuBondeds(*inputrec, mtop, nullptr);
826 decideWhetherToUseGpusForBonded(useGpuForNonbonded, useGpuForPme,
827 bondedTarget, canUseGpuForBonded,
828 EVDW_PME(inputrec->vdwtype),
829 EEL_PME_EWALD(inputrec->coulombtype),
830 domdecOptions.numPmeRanks, gpusWereDetected);
832 pmeRunMode = (useGpuForPme ? PmeRunMode::GPU : PmeRunMode::CPU);
833 if (pmeRunMode == PmeRunMode::GPU)
835 if (pmeFftTarget == TaskTarget::Cpu)
837 pmeRunMode = PmeRunMode::Mixed;
840 else if (pmeFftTarget == TaskTarget::Gpu)
842 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.");
845 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
847 // Initialize development feature flags that enabled by environment variable
848 // and report those features that are enabled.
849 const DevelopmentFeatureFlags devFlags = manageDevelopmentFeatures(mdlog, useGpuForNonbonded);
852 // TODO: hide restraint implementation details from Mdrunner.
853 // There is nothing unique about restraints at this point as far as the
854 // Mdrunner is concerned. The Mdrunner should just be getting a sequence of
855 // factory functions from the SimulationContext on which to call mdModules_->add().
856 // TODO: capture all restraints into a single RestraintModule, passed to the runner builder.
857 for (auto && restraint : restraintManager_->getRestraints())
859 auto module = RestraintMDModule::create(restraint,
861 mdModules_->add(std::move(module));
864 // TODO: Error handling
865 mdModules_->assignOptionsToModules(*inputrec->params, nullptr);
866 const auto &mdModulesNotifier = mdModules_->notifier().notifier_;
868 if (inputrec->internalParameters != nullptr)
870 mdModulesNotifier.notify(*inputrec->internalParameters);
873 if (fplog != nullptr)
875 pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
876 fprintf(fplog, "\n");
881 /* In rerun, set velocities to zero if present */
882 if (doRerun && ((globalState->flags & (1 << estV)) != 0))
884 // rerun does not use velocities
885 GMX_LOG(mdlog.info).asParagraph().appendText(
886 "Rerun trajectory contains velocities. Rerun does only evaluate "
887 "potential energy and forces. The velocities will be ignored.");
888 for (int i = 0; i < globalState->natoms; i++)
890 clear_rvec(globalState->v[i]);
892 globalState->flags &= ~(1 << estV);
895 /* now make sure the state is initialized and propagated */
896 set_state_entries(globalState.get(), inputrec);
899 /* NM and TPI parallelize over force/energy calculations, not atoms,
900 * so we need to initialize and broadcast the global state.
902 if (inputrec->eI == eiNM || inputrec->eI == eiTPI)
906 globalState = std::make_unique<t_state>();
908 broadcastStateWithoutDynamics(cr, globalState.get());
911 /* A parallel command line option consistency check that we can
912 only do after any threads have started. */
913 if (!PAR(cr) && (domdecOptions.numCells[XX] > 1 ||
914 domdecOptions.numCells[YY] > 1 ||
915 domdecOptions.numCells[ZZ] > 1 ||
916 domdecOptions.numPmeRanks > 0))
919 "The -dd or -npme option request a parallel simulation, "
921 "but %s was compiled without threads or MPI enabled", output_env_get_program_display_name(oenv));
923 "but the number of MPI-threads (option -ntmpi) is not set or is 1");
925 "but %s was not started through mpirun/mpiexec or only one rank was requested through mpirun/mpiexec", output_env_get_program_display_name(oenv));
930 (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
932 gmx_fatal(FARGS, "The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun");
935 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
937 if (domdecOptions.numPmeRanks > 0)
939 gmx_fatal_collective(FARGS, cr->mpi_comm_mysim, MASTER(cr),
940 "PME-only ranks are requested, but the system does not use PME for electrostatics or LJ");
943 domdecOptions.numPmeRanks = 0;
946 if (useGpuForNonbonded && domdecOptions.numPmeRanks < 0)
948 /* With NB GPUs we don't automatically use PME-only CPU ranks. PME ranks can
949 * improve performance with many threads per GPU, since our OpenMP
950 * scaling is bad, but it's difficult to automate the setup.
952 domdecOptions.numPmeRanks = 0;
956 if (domdecOptions.numPmeRanks < 0)
958 domdecOptions.numPmeRanks = 0;
959 // TODO possibly print a note that one can opt-in for a separate PME GPU rank?
963 GMX_RELEASE_ASSERT(domdecOptions.numPmeRanks <= 1, "PME GPU decomposition is not supported");
970 fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
974 /* NMR restraints must be initialized before load_checkpoint,
975 * since with time averaging the history is added to t_state.
976 * For proper consistency check we therefore need to extend
978 * So the PME-only nodes (if present) will also initialize
979 * the distance restraints.
983 /* This needs to be called before read_checkpoint to extend the state */
984 init_disres(fplog, &mtop, inputrec, cr, ms, fcd, globalState.get(), replExParams.exchangeInterval > 0);
986 init_orires(fplog, &mtop, inputrec, cr, ms, globalState.get(), &(fcd->orires));
988 auto deform = prepareBoxDeformation(globalState->box, cr, *inputrec);
990 ObservablesHistory observablesHistory = {};
992 if (startingBehavior != StartingBehavior::NewSimulation)
994 /* Check if checkpoint file exists before doing continuation.
995 * This way we can use identical input options for the first and subsequent runs...
997 if (mdrunOptions.numStepsCommandline > -2)
999 /* Temporarily set the number of steps to unlimited to avoid
1000 * triggering the nsteps check in load_checkpoint().
1001 * This hack will go away soon when the -nsteps option is removed.
1003 inputrec->nsteps = -1;
1006 load_checkpoint(opt2fn_master("-cpi", filenames.size(), filenames.data(), cr),
1008 cr, domdecOptions.numCells,
1009 inputrec, globalState.get(),
1010 &observablesHistory,
1011 mdrunOptions.reproducible, mdModules_->notifier());
1013 if (startingBehavior == StartingBehavior::RestartWithAppending && logFileHandle)
1015 // Now we can start normal logging to the truncated log file.
1016 fplog = gmx_fio_getfp(logFileHandle);
1017 prepareLogAppending(fplog);
1018 logOwner = buildLogger(fplog, MASTER(cr));
1019 mdlog = logOwner.logger();
1023 if (mdrunOptions.numStepsCommandline > -2)
1025 GMX_LOG(mdlog.info).asParagraph().
1026 appendText("The -nsteps functionality is deprecated, and may be removed in a future version. "
1027 "Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp file field.");
1029 /* override nsteps with value set on the commandline */
1030 override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec);
1034 copy_mat(globalState->box, box);
1039 gmx_bcast(sizeof(box), box, cr);
1042 if (inputrec->cutoff_scheme != ecutsVERLET)
1044 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.");
1046 /* Update rlist and nstlist. */
1047 prepare_verlet_scheme(fplog, cr, inputrec, nstlist_cmdline, &mtop, box,
1048 useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes), *hwinfo->cpuInfo);
1050 const bool prefer1DAnd1PulseDD = (devFlags.enableGpuHaloExchange && useGpuForNonbonded);
1051 // This builder is necessary while we have multi-part construction
1052 // of DD. Before DD is constructed, we use the existence of
1053 // the builder object to indicate that further construction of DD
1055 std::unique_ptr<DomainDecompositionBuilder> ddBuilder;
1056 if (PAR(cr) && !(EI_TPI(inputrec->eI) ||
1057 inputrec->eI == eiNM))
1059 ddBuilder = std::make_unique<DomainDecompositionBuilder>
1060 (mdlog, cr, domdecOptions, mdrunOptions,
1061 prefer1DAnd1PulseDD, mtop, *inputrec,
1062 box, positionsFromStatePointer(globalState.get()));
1066 /* PME, if used, is done on all nodes with 1D decomposition */
1068 cr->duty = (DUTY_PP | DUTY_PME);
1070 if (inputrec->ePBC == epbcSCREW)
1073 "pbc=screw is only implemented with domain decomposition");
1077 // Produce the task assignment for this rank.
1078 GpuTaskAssignmentsBuilder gpuTaskAssignmentsBuilder;
1079 GpuTaskAssignments gpuTaskAssignments =
1080 gpuTaskAssignmentsBuilder.build(gpuIdsToUse,
1081 userGpuTaskAssignment,
1092 thisRankHasDuty(cr, DUTY_PP),
1093 // TODO cr->duty & DUTY_PME should imply that a PME
1094 // algorithm is active, but currently does not.
1095 EEL_PME(inputrec->coulombtype) &&
1096 thisRankHasDuty(cr, DUTY_PME));
1098 const bool printHostName = (cr->nnodes > 1);
1099 gpuTaskAssignments.reportGpuUsage(mdlog, printHostName, useGpuForBonded, pmeRunMode);
1101 // If the user chose a task assignment, give them some hints
1102 // where appropriate.
1103 if (!userGpuTaskAssignment.empty())
1105 gpuTaskAssignments.logPerformanceHints(mdlog,
1106 ssize(gpuIdsToUse));
1109 // Get the device handles for the modules, nullptr when no task is assigned.
1110 gmx_device_info_t *nonbondedDeviceInfo = gpuTaskAssignments.initNonbondedDevice(cr);
1111 gmx_device_info_t *pmeDeviceInfo = gpuTaskAssignments.initPmeDevice();
1113 // TODO Initialize GPU streams here.
1115 // TODO Currently this is always built, yet DD partition code
1116 // checks if it is built before using it. Probably it should
1117 // become an MDModule that is made only when another module
1118 // requires it (e.g. pull, CompEl, density fitting), so that we
1119 // don't update the local atom sets unilaterally every step.
1120 LocalAtomSetManager atomSets;
1123 // TODO Pass the GPU streams to ddBuilder to use in buffer
1124 // transfers (e.g. halo exchange)
1125 cr->dd = ddBuilder->build(&atomSets);
1126 // The builder's job is done, so destruct it
1127 ddBuilder.reset(nullptr);
1128 // Note that local state still does not exist yet.
1133 /* After possible communicator splitting in make_dd_communicators.
1134 * we can set up the intra/inter node communication.
1136 gmx_setup_nodecomm(fplog, cr);
1142 GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
1143 "This is simulation %d out of %d running as a composite GROMACS\n"
1144 "multi-simulation job. Setup for this simulation:\n",
1147 GMX_LOG(mdlog.warning).appendTextFormatted(
1148 "Using %d MPI %s\n",
1151 cr->nnodes == 1 ? "thread" : "threads"
1153 cr->nnodes == 1 ? "process" : "processes"
1159 // If mdrun -pin auto honors any affinity setting that already
1160 // exists. If so, it is nice to provide feedback about whether
1161 // that existing affinity setting was from OpenMP or something
1162 // else, so we run this code both before and after we initialize
1163 // the OpenMP support.
1164 gmx_check_thread_affinity_set(mdlog,
1165 &hw_opt, hwinfo->nthreads_hw_avail, FALSE);
1166 /* Check and update the number of OpenMP threads requested */
1167 checkAndUpdateRequestedNumOpenmpThreads(&hw_opt, *hwinfo, cr, ms, physicalNodeComm.size_,
1168 pmeRunMode, mtop, *inputrec);
1170 gmx_omp_nthreads_init(mdlog, cr,
1171 hwinfo->nthreads_hw_avail,
1172 physicalNodeComm.size_,
1173 hw_opt.nthreads_omp,
1174 hw_opt.nthreads_omp_pme,
1175 !thisRankHasDuty(cr, DUTY_PP));
1177 // Enable FP exception detection, but not in
1178 // Release mode and not for compilers with known buggy FP
1179 // exception support (clang with any optimization) or suspected
1180 // buggy FP exception support (gcc 7.* with optimization).
1181 #if !defined NDEBUG && \
1182 !((defined __clang__ || (defined(__GNUC__) && !defined(__ICC) && __GNUC__ == 7)) \
1183 && defined __OPTIMIZE__)
1184 const bool bEnableFPE = true;
1186 const bool bEnableFPE = false;
1188 //FIXME - reconcile with gmx_feenableexcept() call from CommandLineModuleManager::run()
1191 gmx_feenableexcept();
1194 /* Now that we know the setup is consistent, check for efficiency */
1195 check_resource_division_efficiency(hwinfo,
1196 gpuTaskAssignments.thisRankHasAnyGpuTask(),
1197 mdrunOptions.ntompOptionIsSet,
1201 /* getting number of PP/PME threads on this MPI / tMPI rank.
1202 PME: env variable should be read only on one node to make sure it is
1203 identical everywhere;
1205 const int numThreadsOnThisRank =
1206 thisRankHasDuty(cr, DUTY_PP) ? gmx_omp_nthreads_get(emntNonbonded) : gmx_omp_nthreads_get(emntPME);
1207 checkHardwareOversubscription(numThreadsOnThisRank, cr->nodeid,
1208 *hwinfo->hardwareTopology,
1209 physicalNodeComm, mdlog);
1211 if (hw_opt.threadAffinity != ThreadAffinity::Off)
1213 /* Before setting affinity, check whether the affinity has changed
1214 * - which indicates that probably the OpenMP library has changed it
1215 * since we first checked).
1217 gmx_check_thread_affinity_set(mdlog,
1218 &hw_opt, hwinfo->nthreads_hw_avail, TRUE);
1220 int numThreadsOnThisNode, intraNodeThreadOffset;
1221 analyzeThreadsOnThisNode(physicalNodeComm, numThreadsOnThisRank, &numThreadsOnThisNode,
1222 &intraNodeThreadOffset);
1224 /* Set the CPU affinity */
1225 gmx_set_thread_affinity(mdlog, cr, &hw_opt, *hwinfo->hardwareTopology,
1226 numThreadsOnThisRank, numThreadsOnThisNode,
1227 intraNodeThreadOffset, nullptr);
1230 if (mdrunOptions.timingOptions.resetStep > -1)
1232 GMX_LOG(mdlog.info).asParagraph().
1233 appendText("The -resetstep functionality is deprecated, and may be removed in a future version.");
1235 wcycle = wallcycle_init(fplog, mdrunOptions.timingOptions.resetStep, cr);
1239 /* Master synchronizes its value of reset_counters with all nodes
1240 * including PME only nodes */
1241 int64_t reset_counters = wcycle_get_reset_counters(wcycle);
1242 gmx_bcast_sim(sizeof(reset_counters), &reset_counters, cr);
1243 wcycle_set_reset_counters(wcycle, reset_counters);
1246 // Membrane embedding must be initialized before we call init_forcerec()
1251 fprintf(stderr, "Initializing membed");
1253 /* Note that membed cannot work in parallel because mtop is
1254 * changed here. Fix this if we ever want to make it run with
1255 * multiple ranks. */
1256 membed = init_membed(fplog, filenames.size(), filenames.data(), &mtop, inputrec, globalState.get(), cr,
1258 .checkpointOptions.period);
1261 const bool thisRankHasPmeGpuTask = gpuTaskAssignments.thisRankHasPmeGpuTask();
1262 std::unique_ptr<MDAtoms> mdAtoms;
1263 std::unique_ptr<gmx_vsite_t> vsite;
1266 if (thisRankHasDuty(cr, DUTY_PP))
1268 mdModulesNotifier.notify(*cr);
1269 mdModulesNotifier.notify(&atomSets);
1270 mdModulesNotifier.notify(PeriodicBoundaryConditionType {inputrec->ePBC});
1271 /* Initiate forcerecord */
1272 fr = new t_forcerec;
1273 fr->forceProviders = mdModules_->initForceProviders();
1274 init_forcerec(fplog, mdlog, fr, fcd,
1275 inputrec, &mtop, cr, box,
1276 opt2fn("-table", filenames.size(), filenames.data()),
1277 opt2fn("-tablep", filenames.size(), filenames.data()),
1278 opt2fns("-tableb", filenames.size(), filenames.data()),
1279 *hwinfo, nonbondedDeviceInfo,
1284 // TODO Move this to happen during domain decomposition setup,
1285 // once stream and event handling works well with that.
1286 // TODO remove need to pass local stream into GPU halo exchange - Redmine #3093
1287 if (havePPDomainDecomposition(cr) && prefer1DAnd1PulseDD && is1DAnd1PulseDD(*cr->dd))
1289 GMX_RELEASE_ASSERT(devFlags.enableGpuBufferOps, "Must use GMX_GPU_BUFFER_OPS=1 to use GMX_GPU_DD_COMMS=1");
1290 void *streamLocal = Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, Nbnxm::InteractionLocality::Local);
1291 void *streamNonLocal = Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, Nbnxm::InteractionLocality::NonLocal);
1292 void *coordinatesOnDeviceEvent = fr->nbv->get_x_on_device_event();
1293 GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
1294 "NOTE: This run uses the 'GPU halo exchange' feature, enabled by the GMX_GPU_DD_COMMS environment variable.");
1295 cr->dd->gpuHaloExchange = std::make_unique<GpuHaloExchange>(cr->dd, cr->mpi_comm_mysim, streamLocal,
1296 streamNonLocal, coordinatesOnDeviceEvent);
1299 /* Initialize the mdAtoms structure.
1300 * mdAtoms is not filled with atom data,
1301 * as this can not be done now with domain decomposition.
1303 mdAtoms = makeMDAtoms(fplog, mtop, *inputrec, thisRankHasPmeGpuTask);
1304 if (globalState && thisRankHasPmeGpuTask)
1306 // The pinning of coordinates in the global state object works, because we only use
1307 // PME on GPU without DD or on a separate PME rank, and because the local state pointer
1308 // points to the global state object without DD.
1309 // FIXME: MD and EM separately set up the local state - this should happen in the same function,
1310 // which should also perform the pinning.
1311 changePinningPolicy(&globalState->x, pme_get_pinning_policy());
1314 /* Initialize the virtual site communication */
1315 vsite = initVsite(mtop, cr);
1317 calc_shifts(box, fr->shift_vec);
1319 /* With periodic molecules the charge groups should be whole at start up
1320 * and the virtual sites should not be far from their proper positions.
1322 if (!inputrec->bContinuation && MASTER(cr) &&
1323 !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
1325 /* Make molecules whole at start of run */
1326 if (fr->ePBC != epbcNONE)
1328 do_pbc_first_mtop(fplog, inputrec->ePBC, box, &mtop, globalState->x.rvec_array());
1332 /* Correct initial vsite positions are required
1333 * for the initial distribution in the domain decomposition
1334 * and for the initial shell prediction.
1336 constructVsitesGlobal(mtop, globalState->x);
1340 if (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
1342 ewaldcoeff_q = fr->ic->ewaldcoeff_q;
1343 ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
1348 /* This is a PME only node */
1350 GMX_ASSERT(globalState == nullptr, "We don't need the state on a PME only rank and expect it to be unitialized");
1352 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
1353 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
1356 gmx_pme_t *sepPmeData = nullptr;
1357 // This reference hides the fact that PME data is owned by runner on PME-only ranks and by forcerec on other ranks
1358 GMX_ASSERT(thisRankHasDuty(cr, DUTY_PP) == (fr != nullptr), "Double-checking that only PME-only ranks have no forcerec");
1359 gmx_pme_t * &pmedata = fr ? fr->pmedata : sepPmeData;
1361 // TODO should live in ewald module once its testing is improved
1363 // Later, this program could contain kernels that might be later
1364 // re-used as auto-tuning progresses, or subsequent simulations
1366 PmeGpuProgramStorage pmeGpuProgram;
1367 if (thisRankHasPmeGpuTask)
1369 pmeGpuProgram = buildPmeGpuProgram(pmeDeviceInfo);
1372 /* Initiate PME if necessary,
1373 * either on all nodes or on dedicated PME nodes only. */
1374 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
1376 if (mdAtoms && mdAtoms->mdatoms())
1378 nChargePerturbed = mdAtoms->mdatoms()->nChargePerturbed;
1379 if (EVDW_PME(inputrec->vdwtype))
1381 nTypePerturbed = mdAtoms->mdatoms()->nTypePerturbed;
1384 if (cr->npmenodes > 0)
1386 /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
1387 gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
1388 gmx_bcast_sim(sizeof(nTypePerturbed), &nTypePerturbed, cr);
1391 if (thisRankHasDuty(cr, DUTY_PME))
1395 pmedata = gmx_pme_init(cr,
1396 getNumPmeDomains(cr->dd),
1398 nChargePerturbed != 0, nTypePerturbed != 0,
1399 mdrunOptions.reproducible,
1400 ewaldcoeff_q, ewaldcoeff_lj,
1401 gmx_omp_nthreads_get(emntPME),
1402 pmeRunMode, nullptr,
1403 pmeDeviceInfo, pmeGpuProgram.get(), mdlog);
1405 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1410 if (EI_DYNAMICS(inputrec->eI))
1412 /* Turn on signal handling on all nodes */
1414 * (A user signal from the PME nodes (if any)
1415 * is communicated to the PP nodes.
1417 signal_handler_install();
1420 pull_t *pull_work = nullptr;
1421 if (thisRankHasDuty(cr, DUTY_PP))
1423 /* Assumes uniform use of the number of OpenMP threads */
1424 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
1426 if (inputrec->bPull)
1428 /* Initialize pull code */
1430 init_pull(fplog, inputrec->pull, inputrec,
1431 &mtop, cr, &atomSets, inputrec->fepvals->init_lambda);
1432 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
1434 initPullHistory(pull_work, &observablesHistory);
1436 if (EI_DYNAMICS(inputrec->eI) && MASTER(cr))
1438 init_pull_output_files(pull_work,
1439 filenames.size(), filenames.data(), oenv,
1444 std::unique_ptr<EnforcedRotation> enforcedRotation;
1447 /* Initialize enforced rotation code */
1448 enforcedRotation = init_rot(fplog,
1461 t_swap *swap = nullptr;
1462 if (inputrec->eSwapCoords != eswapNO)
1464 /* Initialize ion swapping code */
1465 swap = init_swapcoords(fplog, inputrec,
1466 opt2fn_master("-swap", filenames.size(), filenames.data(), cr),
1467 &mtop, globalState.get(), &observablesHistory,
1468 cr, &atomSets, oenv, mdrunOptions,
1472 /* Let makeConstraints know whether we have essential dynamics constraints.
1473 * TODO: inputrec should tell us whether we use an algorithm, not a file option or the checkpoint
1475 bool doEssentialDynamics = (opt2fn_null("-ei", filenames.size(), filenames.data()) != nullptr
1476 || observablesHistory.edsamHistory);
1477 auto constr = makeConstraints(mtop, *inputrec, pull_work, doEssentialDynamics,
1478 fplog, *mdAtoms->mdatoms(),
1479 cr, ms, &nrnb, wcycle, fr->bMolPBC);
1481 /* Energy terms and groups */
1482 gmx_enerdata_t enerd(mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(), inputrec->fepvals->n_lambda);
1484 /* Kinetic energy data */
1485 gmx_ekindata_t ekind;
1486 init_ekindata(fplog, &mtop, &(inputrec->opts), &ekind, inputrec->cos_accel);
1488 /* Set up interactive MD (IMD) */
1489 auto imdSession = makeImdSession(inputrec, cr, wcycle, &enerd, ms, &mtop, mdlog,
1490 MASTER(cr) ? globalState->x.rvec_array() : nullptr,
1491 filenames.size(), filenames.data(), oenv, mdrunOptions.imdOptions,
1494 if (DOMAINDECOMP(cr))
1496 GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
1497 /* This call is not included in init_domain_decomposition mainly
1498 * because fr->cginfo_mb is set later.
1500 dd_init_bondeds(fplog, cr->dd, &mtop, vsite.get(), inputrec,
1501 domdecOptions.checkBondedInteractions,
1505 if (updateTarget == TaskTarget::Gpu)
1509 gmx_fatal(FARGS, "It is currently not possible to redirect the calculation "
1510 "of update and constraints to the GPU!");
1514 // Before we start the actual simulator, try if we can run the update task on the GPU.
1515 useGpuForUpdate = decideWhetherToUseGpuForUpdate(DOMAINDECOMP(cr),
1518 devFlags.enableGpuBufferOps,
1523 doEssentialDynamics,
1524 fcd->orires.nr != 0,
1525 fcd->disres.nsystems != 0);
1527 const bool inputIsCompatibleWithModularSimulator = ModularSimulator::isInputCompatible(
1529 inputrec, doRerun, vsite.get(), ms, replExParams,
1530 fcd, static_cast<int>(filenames.size()), filenames.data(),
1531 &observablesHistory, membed);
1533 const bool useModularSimulator = inputIsCompatibleWithModularSimulator && !(getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
1535 std::unique_ptr<gmx::StatePropagatorDataGpu> stateGpu;
1536 if (gpusWereDetected && ((useGpuForPme && thisRankHasDuty(cr, DUTY_PME)) || devFlags.enableGpuBufferOps))
1538 const void *pmeStream = pme_gpu_get_device_stream(fr->pmedata);
1539 const void *localStream = fr->nbv->gpu_nbv != nullptr ? Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, Nbnxm::InteractionLocality::Local) : nullptr;
1540 const void *nonLocalStream = fr->nbv->gpu_nbv != nullptr ? Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, Nbnxm::InteractionLocality::NonLocal) : nullptr;
1541 const void *deviceContext = pme_gpu_get_device_context(fr->pmedata);
1542 const int paddingSize = pme_gpu_get_padding_size(fr->pmedata);
1543 GpuApiCallBehavior transferKind = (inputrec->eI == eiMD && !doRerun && !useModularSimulator) ? GpuApiCallBehavior::Async : GpuApiCallBehavior::Sync;
1545 stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(pmeStream,
1551 fr->stateGpu = stateGpu.get();
1554 // TODO This is not the right place to manage the lifetime of
1555 // this data structure, but currently it's the easiest way to
1557 MdrunScheduleWorkload runScheduleWork;
1558 // Also populates the simulation constant workload description.
1559 runScheduleWork.simulationWork = createSimulationWorkload(useGpuForNonbonded,
1561 (pmeRunMode == PmeRunMode::GPU),
1564 devFlags.enableGpuBufferOps,
1565 devFlags.enableGpuHaloExchange,
1566 devFlags.enableGpuPmePPComm);
1569 GMX_ASSERT(stopHandlerBuilder_, "Runner must provide StopHandlerBuilder to simulator.");
1570 SimulatorBuilder simulatorBuilder;
1572 // build and run simulator object based on user-input
1573 auto simulator = simulatorBuilder.build(
1574 inputIsCompatibleWithModularSimulator,
1575 fplog, cr, ms, mdlog, static_cast<int>(filenames.size()), filenames.data(),
1579 vsite.get(), constr.get(),
1580 enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr,
1582 mdModules_->outputProvider(),
1583 mdModules_->notifier(),
1584 inputrec, imdSession.get(), pull_work, swap, &mtop,
1587 &observablesHistory,
1588 mdAtoms.get(), &nrnb, wcycle, fr,
1594 walltime_accounting,
1595 std::move(stopHandlerBuilder_),
1599 if (inputrec->bPull)
1601 finish_pull(pull_work);
1603 finish_swapcoords(swap);
1607 GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
1609 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
1610 gmx_pmeonly(pmedata, cr, &nrnb, wcycle, walltime_accounting, inputrec, pmeRunMode);
1613 wallcycle_stop(wcycle, ewcRUN);
1615 /* Finish up, write some stuff
1616 * if rerunMD, don't write last frame again
1618 finish_run(fplog, mdlog, cr,
1619 inputrec, &nrnb, wcycle, walltime_accounting,
1620 fr ? fr->nbv.get() : nullptr,
1622 EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
1624 // clean up cycle counter
1625 wallcycle_destroy(wcycle);
1630 gmx_pme_destroy(pmedata);
1634 // FIXME: this is only here to manually unpin mdAtoms->chargeA_ and state->x,
1635 // before we destroy the GPU context(s) in free_gpu_resources().
1636 // Pinned buffers are associated with contexts in CUDA.
1637 // As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
1638 mdAtoms.reset(nullptr);
1639 globalState.reset(nullptr);
1640 mdModules_.reset(nullptr); // destruct force providers here as they might also use the GPU
1642 /* Free GPU memory and set a physical node tMPI barrier (which should eventually go away) */
1643 free_gpu_resources(fr, physicalNodeComm, hwinfo->gpu_info);
1644 free_gpu(nonbondedDeviceInfo);
1645 free_gpu(pmeDeviceInfo);
1646 done_forcerec(fr, mtop.molblock.size());
1651 free_membed(membed);
1654 /* Does what it says */
1655 print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
1656 walltime_accounting_destroy(walltime_accounting);
1658 // Ensure log file content is written
1661 gmx_fio_flush(logFileHandle);
1664 /* Reset FPEs (important for unit tests) by disabling them. Assumes no
1665 * exceptions were enabled before function was called. */
1668 gmx_fedisableexcept();
1671 auto rc = static_cast<int>(gmx_get_stop_condition());
1674 /* we need to join all threads. The sub-threads join when they
1675 exit this function, but the master thread needs to be told to
1677 if (PAR(cr) && MASTER(cr))
1685 Mdrunner::~Mdrunner()
1687 // Clean up of the Manager.
1688 // This will end up getting called on every thread-MPI rank, which is unnecessary,
1689 // but okay as long as threads synchronize some time before adding or accessing
1690 // a new set of restraints.
1691 if (restraintManager_)
1693 restraintManager_->clear();
1694 GMX_ASSERT(restraintManager_->countRestraints() == 0,
1695 "restraints added during runner life time should be cleared at runner destruction.");
1699 void Mdrunner::addPotential(std::shared_ptr<gmx::IRestraintPotential> puller,
1700 const std::string &name)
1702 GMX_ASSERT(restraintManager_, "Mdrunner must have a restraint manager.");
1703 // Not sure if this should be logged through the md logger or something else,
1704 // but it is helpful to have some sort of INFO level message sent somewhere.
1705 // std::cout << "Registering restraint named " << name << std::endl;
1707 // When multiple restraints are used, it may be wasteful to register them separately.
1708 // Maybe instead register an entire Restraint Manager as a force provider.
1709 restraintManager_->addToSpec(std::move(puller),
1713 Mdrunner::Mdrunner(std::unique_ptr<MDModules> mdModules)
1714 : mdModules_(std::move(mdModules))
1718 Mdrunner::Mdrunner(Mdrunner &&) noexcept = default;
1720 //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265
1721 Mdrunner &Mdrunner::operator=(Mdrunner && /*handle*/) noexcept(BUGFREE_NOEXCEPT_STRING) = default;
1723 class Mdrunner::BuilderImplementation
1726 BuilderImplementation() = delete;
1727 BuilderImplementation(std::unique_ptr<MDModules> mdModules,
1728 compat::not_null<SimulationContext*> context);
1729 ~BuilderImplementation();
1731 BuilderImplementation &setExtraMdrunOptions(const MdrunOptions &options,
1732 real forceWarningThreshold,
1733 StartingBehavior startingBehavior);
1735 void addDomdec(const DomdecOptions &options);
1737 void addVerletList(int nstlist);
1739 void addReplicaExchange(const ReplicaExchangeParameters ¶ms);
1741 void addNonBonded(const char* nbpu_opt);
1743 void addPME(const char* pme_opt_, const char* pme_fft_opt_);
1745 void addBondedTaskAssignment(const char* bonded_opt);
1747 void addUpdateTaskAssignment(const char* update_opt);
1749 void addHardwareOptions(const gmx_hw_opt_t &hardwareOptions);
1751 void addFilenames(ArrayRef <const t_filenm> filenames);
1753 void addOutputEnvironment(gmx_output_env_t* outputEnvironment);
1755 void addLogFile(t_fileio *logFileHandle);
1757 void addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
1763 // Default parameters copied from runner.h
1764 // \todo Clarify source(s) of default parameters.
1766 const char* nbpu_opt_ = nullptr;
1767 const char* pme_opt_ = nullptr;
1768 const char* pme_fft_opt_ = nullptr;
1769 const char *bonded_opt_ = nullptr;
1770 const char *update_opt_ = nullptr;
1772 MdrunOptions mdrunOptions_;
1774 DomdecOptions domdecOptions_;
1776 ReplicaExchangeParameters replicaExchangeParameters_;
1778 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
1781 //! Multisim communicator handle.
1782 gmx_multisim_t *multiSimulation_;
1784 //! mdrun communicator
1785 MPI_Comm communicator_ = MPI_COMM_NULL;
1787 //! Print a warning if any force is larger than this (in kJ/mol nm).
1788 real forceWarningThreshold_ = -1;
1790 //! Whether the simulation will start afresh, or restart with/without appending.
1791 StartingBehavior startingBehavior_ = StartingBehavior::NewSimulation;
1793 //! The modules that comprise the functionality of mdrun.
1794 std::unique_ptr<MDModules> mdModules_;
1796 //! \brief Parallelism information.
1797 gmx_hw_opt_t hardwareOptions_;
1799 //! filename options for simulation.
1800 ArrayRef<const t_filenm> filenames_;
1802 /*! \brief Handle to output environment.
1804 * \todo gmx_output_env_t needs lifetime management.
1806 gmx_output_env_t* outputEnvironment_ = nullptr;
1808 /*! \brief Non-owning handle to MD log file.
1810 * \todo Context should own output facilities for client.
1811 * \todo Improve log file handle management.
1813 * Code managing the FILE* relies on the ability to set it to
1814 * nullptr to check whether the filehandle is valid.
1816 t_fileio* logFileHandle_ = nullptr;
1819 * \brief Builder for simulation stop signal handler.
1821 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_ = nullptr;
1824 Mdrunner::BuilderImplementation::BuilderImplementation(std::unique_ptr<MDModules> mdModules,
1825 compat::not_null<SimulationContext*> context) :
1826 mdModules_(std::move(mdModules))
1828 communicator_ = context->communicator_;
1829 multiSimulation_ = context->multiSimulation_.get();
1832 Mdrunner::BuilderImplementation::~BuilderImplementation() = default;
1834 Mdrunner::BuilderImplementation &
1835 Mdrunner::BuilderImplementation::setExtraMdrunOptions(const MdrunOptions &options,
1836 const real forceWarningThreshold,
1837 const StartingBehavior startingBehavior)
1839 mdrunOptions_ = options;
1840 forceWarningThreshold_ = forceWarningThreshold;
1841 startingBehavior_ = startingBehavior;
1845 void Mdrunner::BuilderImplementation::addDomdec(const DomdecOptions &options)
1847 domdecOptions_ = options;
1850 void Mdrunner::BuilderImplementation::addVerletList(int nstlist)
1855 void Mdrunner::BuilderImplementation::addReplicaExchange(const ReplicaExchangeParameters ¶ms)
1857 replicaExchangeParameters_ = params;
1860 Mdrunner Mdrunner::BuilderImplementation::build()
1862 auto newRunner = Mdrunner(std::move(mdModules_));
1864 newRunner.mdrunOptions = mdrunOptions_;
1865 newRunner.pforce = forceWarningThreshold_;
1866 newRunner.startingBehavior = startingBehavior_;
1867 newRunner.domdecOptions = domdecOptions_;
1869 // \todo determine an invariant to check or confirm that all gmx_hw_opt_t objects are valid
1870 newRunner.hw_opt = hardwareOptions_;
1872 // No invariant to check. This parameter exists to optionally override other behavior.
1873 newRunner.nstlist_cmdline = nstlist_;
1875 newRunner.replExParams = replicaExchangeParameters_;
1877 newRunner.filenames = filenames_;
1879 newRunner.communicator = communicator_;
1881 // nullptr is a valid value for the multisim handle
1882 newRunner.ms = multiSimulation_;
1884 // \todo Clarify ownership and lifetime management for gmx_output_env_t
1885 // \todo Update sanity checking when output environment has clearly specified invariants.
1886 // Initialization and default values for oenv are not well specified in the current version.
1887 if (outputEnvironment_)
1889 newRunner.oenv = outputEnvironment_;
1893 GMX_THROW(gmx::APIError("MdrunnerBuilder::addOutputEnvironment() is required before build()"));
1896 newRunner.logFileHandle = logFileHandle_;
1900 newRunner.nbpu_opt = nbpu_opt_;
1904 GMX_THROW(gmx::APIError("MdrunnerBuilder::addNonBonded() is required before build()"));
1907 if (pme_opt_ && pme_fft_opt_)
1909 newRunner.pme_opt = pme_opt_;
1910 newRunner.pme_fft_opt = pme_fft_opt_;
1914 GMX_THROW(gmx::APIError("MdrunnerBuilder::addElectrostatics() is required before build()"));
1919 newRunner.bonded_opt = bonded_opt_;
1923 GMX_THROW(gmx::APIError("MdrunnerBuilder::addBondedTaskAssignment() is required before build()"));
1928 newRunner.update_opt = update_opt_;
1932 GMX_THROW(gmx::APIError("MdrunnerBuilder::addUpdateTaskAssignment() is required before build() "));
1936 newRunner.restraintManager_ = std::make_unique<gmx::RestraintManager>();
1938 if (stopHandlerBuilder_)
1940 newRunner.stopHandlerBuilder_ = std::move(stopHandlerBuilder_);
1944 newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>();
1950 void Mdrunner::BuilderImplementation::addNonBonded(const char* nbpu_opt)
1952 nbpu_opt_ = nbpu_opt;
1955 void Mdrunner::BuilderImplementation::addPME(const char* pme_opt,
1956 const char* pme_fft_opt)
1959 pme_fft_opt_ = pme_fft_opt;
1962 void Mdrunner::BuilderImplementation::addBondedTaskAssignment(const char* bonded_opt)
1964 bonded_opt_ = bonded_opt;
1967 void Mdrunner::BuilderImplementation::addUpdateTaskAssignment(const char* update_opt)
1969 update_opt_ = update_opt;
1972 void Mdrunner::BuilderImplementation::addHardwareOptions(const gmx_hw_opt_t &hardwareOptions)
1974 hardwareOptions_ = hardwareOptions;
1977 void Mdrunner::BuilderImplementation::addFilenames(ArrayRef<const t_filenm> filenames)
1979 filenames_ = filenames;
1982 void Mdrunner::BuilderImplementation::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
1984 outputEnvironment_ = outputEnvironment;
1987 void Mdrunner::BuilderImplementation::addLogFile(t_fileio *logFileHandle)
1989 logFileHandle_ = logFileHandle;
1992 void Mdrunner::BuilderImplementation::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
1994 stopHandlerBuilder_ = std::move(builder);
1997 MdrunnerBuilder::MdrunnerBuilder(std::unique_ptr<MDModules> mdModules,
1998 compat::not_null<SimulationContext*> context) :
1999 impl_ {std::make_unique<Mdrunner::BuilderImplementation>(std::move(mdModules), context)}
2003 MdrunnerBuilder::~MdrunnerBuilder() = default;
2005 MdrunnerBuilder &MdrunnerBuilder::addSimulationMethod(const MdrunOptions &options,
2006 real forceWarningThreshold,
2007 const StartingBehavior startingBehavior)
2009 impl_->setExtraMdrunOptions(options, forceWarningThreshold, startingBehavior);
2013 MdrunnerBuilder &MdrunnerBuilder::addDomainDecomposition(const DomdecOptions &options)
2015 impl_->addDomdec(options);
2019 MdrunnerBuilder &MdrunnerBuilder::addNeighborList(int nstlist)
2021 impl_->addVerletList(nstlist);
2025 MdrunnerBuilder &MdrunnerBuilder::addReplicaExchange(const ReplicaExchangeParameters ¶ms)
2027 impl_->addReplicaExchange(params);
2031 MdrunnerBuilder &MdrunnerBuilder::addNonBonded(const char* nbpu_opt)
2033 impl_->addNonBonded(nbpu_opt);
2037 MdrunnerBuilder &MdrunnerBuilder::addElectrostatics(const char* pme_opt,
2038 const char* pme_fft_opt)
2040 // The builder method may become more general in the future, but in this version,
2041 // parameters for PME electrostatics are both required and the only parameters
2043 if (pme_opt && pme_fft_opt)
2045 impl_->addPME(pme_opt, pme_fft_opt);
2049 GMX_THROW(gmx::InvalidInputError("addElectrostatics() arguments must be non-null pointers."));
2054 MdrunnerBuilder &MdrunnerBuilder::addBondedTaskAssignment(const char* bonded_opt)
2056 impl_->addBondedTaskAssignment(bonded_opt);
2060 MdrunnerBuilder &MdrunnerBuilder::addUpdateTaskAssignment(const char* update_opt)
2062 impl_->addUpdateTaskAssignment(update_opt);
2066 Mdrunner MdrunnerBuilder::build()
2068 return impl_->build();
2071 MdrunnerBuilder &MdrunnerBuilder::addHardwareOptions(const gmx_hw_opt_t &hardwareOptions)
2073 impl_->addHardwareOptions(hardwareOptions);
2077 MdrunnerBuilder &MdrunnerBuilder::addFilenames(ArrayRef<const t_filenm> filenames)
2079 impl_->addFilenames(filenames);
2083 MdrunnerBuilder &MdrunnerBuilder::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
2085 impl_->addOutputEnvironment(outputEnvironment);
2089 MdrunnerBuilder &MdrunnerBuilder::addLogFile(t_fileio *logFileHandle)
2091 impl_->addLogFile(logFileHandle);
2095 MdrunnerBuilder &MdrunnerBuilder::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
2097 impl_->addStopHandlerBuilder(std::move(builder));
2101 MdrunnerBuilder::MdrunnerBuilder(MdrunnerBuilder &&) noexcept = default;
2103 MdrunnerBuilder &MdrunnerBuilder::operator=(MdrunnerBuilder &&) noexcept = default;