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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
58 #include "gromacs/commandline/filenm.h"
59 #include "gromacs/compat/make_unique.h"
60 #include "gromacs/domdec/domdec.h"
61 #include "gromacs/domdec/domdec_struct.h"
62 #include "gromacs/domdec/localatomsetmanager.h"
63 #include "gromacs/ewald/ewald-utils.h"
64 #include "gromacs/ewald/pme.h"
65 #include "gromacs/ewald/pme-gpu-program.h"
66 #include "gromacs/fileio/checkpoint.h"
67 #include "gromacs/fileio/gmxfio.h"
68 #include "gromacs/fileio/oenv.h"
69 #include "gromacs/fileio/tpxio.h"
70 #include "gromacs/gmxlib/network.h"
71 #include "gromacs/gmxlib/nrnb.h"
72 #include "gromacs/gpu_utils/clfftinitializer.h"
73 #include "gromacs/gpu_utils/gpu_utils.h"
74 #include "gromacs/hardware/cpuinfo.h"
75 #include "gromacs/hardware/detecthardware.h"
76 #include "gromacs/hardware/printhardware.h"
77 #include "gromacs/listed-forces/disre.h"
78 #include "gromacs/listed-forces/manage-threading.h"
79 #include "gromacs/listed-forces/orires.h"
80 #include "gromacs/math/functions.h"
81 #include "gromacs/math/utilities.h"
82 #include "gromacs/math/vec.h"
83 #include "gromacs/mdlib/boxdeformation.h"
84 #include "gromacs/mdlib/calc_verletbuf.h"
85 #include "gromacs/mdlib/forcerec.h"
86 #include "gromacs/mdlib/gmx_omp_nthreads.h"
87 #include "gromacs/mdlib/makeconstraints.h"
88 #include "gromacs/mdlib/md_support.h"
89 #include "gromacs/mdlib/mdatoms.h"
90 #include "gromacs/mdlib/mdrun.h"
91 #include "gromacs/mdlib/membed.h"
92 #include "gromacs/mdlib/nb_verlet.h"
93 #include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
94 #include "gromacs/mdlib/nbnxn_search.h"
95 #include "gromacs/mdlib/nbnxn_tuning.h"
96 #include "gromacs/mdlib/qmmm.h"
97 #include "gromacs/mdlib/sighandler.h"
98 #include "gromacs/mdlib/sim_util.h"
99 #include "gromacs/mdlib/stophandler.h"
100 #include "gromacs/mdrun/legacymdrunoptions.h"
101 #include "gromacs/mdrun/logging.h"
102 #include "gromacs/mdrun/multisim.h"
103 #include "gromacs/mdrun/simulationcontext.h"
104 #include "gromacs/mdrunutility/mdmodules.h"
105 #include "gromacs/mdrunutility/threadaffinity.h"
106 #include "gromacs/mdtypes/commrec.h"
107 #include "gromacs/mdtypes/fcdata.h"
108 #include "gromacs/mdtypes/inputrec.h"
109 #include "gromacs/mdtypes/md_enums.h"
110 #include "gromacs/mdtypes/observableshistory.h"
111 #include "gromacs/mdtypes/state.h"
112 #include "gromacs/pbcutil/pbc.h"
113 #include "gromacs/pulling/output.h"
114 #include "gromacs/pulling/pull.h"
115 #include "gromacs/pulling/pull_rotation.h"
116 #include "gromacs/restraint/manager.h"
117 #include "gromacs/restraint/restraintmdmodule.h"
118 #include "gromacs/restraint/restraintpotential.h"
119 #include "gromacs/swap/swapcoords.h"
120 #include "gromacs/taskassignment/decidegpuusage.h"
121 #include "gromacs/taskassignment/resourcedivision.h"
122 #include "gromacs/taskassignment/taskassignment.h"
123 #include "gromacs/taskassignment/usergpuids.h"
124 #include "gromacs/timing/wallcycle.h"
125 #include "gromacs/topology/mtop_util.h"
126 #include "gromacs/trajectory/trajectoryframe.h"
127 #include "gromacs/utility/basenetwork.h"
128 #include "gromacs/utility/cstringutil.h"
129 #include "gromacs/utility/exceptions.h"
130 #include "gromacs/utility/fatalerror.h"
131 #include "gromacs/utility/filestream.h"
132 #include "gromacs/utility/gmxassert.h"
133 #include "gromacs/utility/gmxmpi.h"
134 #include "gromacs/utility/logger.h"
135 #include "gromacs/utility/loggerbuilder.h"
136 #include "gromacs/utility/physicalnodecommunicator.h"
137 #include "gromacs/utility/pleasecite.h"
138 #include "gromacs/utility/programcontext.h"
139 #include "gromacs/utility/smalloc.h"
140 #include "gromacs/utility/stringutil.h"
142 #include "integrator.h"
143 #include "replicaexchange.h"
146 #include "corewrap.h"
152 /*! \brief Barrier for safe simultaneous thread access to mdrunner data
154 * Used to ensure that the master thread does not modify mdrunner during copy
155 * on the spawned threads. */
156 static void threadMpiMdrunnerAccessBarrier()
159 MPI_Barrier(MPI_COMM_WORLD);
163 Mdrunner Mdrunner::cloneOnSpawnedThread() const
165 auto newRunner = Mdrunner();
167 // All runners in the same process share a restraint manager resource because it is
168 // part of the interface to the client code, which is associated only with the
169 // original thread. Handles to the same resources can be obtained by copy.
171 newRunner.restraintManager_ = compat::make_unique<RestraintManager>(*restraintManager_);
174 // Copy original cr pointer before master thread can pass the thread barrier
175 newRunner.cr = reinitialize_commrec_for_this_thread(cr);
177 // Copy members of master runner.
178 // \todo Replace with builder when Simulation context and/or runner phases are better defined.
179 // Ref https://redmine.gromacs.org/issues/2587 and https://redmine.gromacs.org/issues/2375
180 newRunner.hw_opt = hw_opt;
181 newRunner.filenames = filenames;
183 newRunner.oenv = oenv;
184 newRunner.mdrunOptions = mdrunOptions;
185 newRunner.domdecOptions = domdecOptions;
186 newRunner.nbpu_opt = nbpu_opt;
187 newRunner.pme_opt = pme_opt;
188 newRunner.pme_fft_opt = pme_fft_opt;
189 newRunner.bonded_opt = bonded_opt;
190 newRunner.nstlist_cmdline = nstlist_cmdline;
191 newRunner.replExParams = replExParams;
192 newRunner.pforce = pforce;
194 newRunner.stopHandlerBuilder_ = compat::make_unique<StopHandlerBuilder>(*stopHandlerBuilder_);
196 threadMpiMdrunnerAccessBarrier();
198 GMX_RELEASE_ASSERT(!MASTER(newRunner.cr), "cloneOnSpawnedThread should only be called on spawned threads");
203 /*! \brief The callback used for running on spawned threads.
205 * Obtains the pointer to the master mdrunner object from the one
206 * argument permitted to the thread-launch API call, copies it to make
207 * a new runner for this thread, reinitializes necessary data, and
208 * proceeds to the simulation. */
209 static void mdrunner_start_fn(const void *arg)
213 auto masterMdrunner = reinterpret_cast<const gmx::Mdrunner *>(arg);
214 /* copy the arg list to make sure that it's thread-local. This
215 doesn't copy pointed-to items, of course; fnm, cr and fplog
216 are reset in the call below, all others should be const. */
217 gmx::Mdrunner mdrunner = masterMdrunner->cloneOnSpawnedThread();
220 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
224 /*! \brief Start thread-MPI threads.
226 * Called by mdrunner() to start a specific number of threads
227 * (including the main thread) for thread-parallel runs. This in turn
228 * calls mdrunner() for each thread. All options are the same as for
230 t_commrec *Mdrunner::spawnThreads(int numThreadsToLaunch) const
233 /* first check whether we even need to start tMPI */
234 if (numThreadsToLaunch < 2)
240 /* now spawn new threads that start mdrunner_start_fn(), while
241 the main thread returns, we set thread affinity later */
242 if (tMPI_Init_fn(TRUE, numThreadsToLaunch, TMPI_AFFINITY_NONE,
243 mdrunner_start_fn, static_cast<const void*>(this)) != TMPI_SUCCESS)
245 GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
248 threadMpiMdrunnerAccessBarrier();
250 GMX_UNUSED_VALUE(mdrunner_start_fn);
253 return reinitialize_commrec_for_this_thread(cr);
258 /*! \brief Initialize variables for Verlet scheme simulation */
259 static void prepare_verlet_scheme(FILE *fplog,
263 const gmx_mtop_t *mtop,
265 bool makeGpuPairList,
266 const gmx::CpuInfo &cpuinfo)
268 /* For NVE simulations, we will retain the initial list buffer */
269 if (EI_DYNAMICS(ir->eI) &&
270 ir->verletbuf_tol > 0 &&
271 !(EI_MD(ir->eI) && ir->etc == etcNO))
273 /* Update the Verlet buffer size for the current run setup */
275 /* Here we assume SIMD-enabled kernels are being used. But as currently
276 * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
277 * and 4x2 gives a larger buffer than 4x4, this is ok.
279 ListSetupType listType = (makeGpuPairList ? ListSetupType::Gpu : ListSetupType::CpuSimdWhenSupported);
280 VerletbufListSetup listSetup = verletbufGetSafeListSetup(listType);
283 calc_verlet_buffer_size(mtop, det(box), ir, ir->nstlist, ir->nstlist - 1, -1, &listSetup, nullptr, &rlist_new);
285 if (rlist_new != ir->rlist)
287 if (fplog != nullptr)
289 fprintf(fplog, "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
290 ir->rlist, rlist_new,
291 listSetup.cluster_size_i, listSetup.cluster_size_j);
293 ir->rlist = rlist_new;
297 if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
299 gmx_fatal(FARGS, "Can not set nstlist without %s",
300 !EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
303 if (EI_DYNAMICS(ir->eI))
305 /* Set or try nstlist values */
306 increaseNstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, makeGpuPairList, cpuinfo);
310 /*! \brief Override the nslist value in inputrec
312 * with value passed on the command line (if any)
314 static void override_nsteps_cmdline(const gmx::MDLogger &mdlog,
315 int64_t nsteps_cmdline,
320 /* override with anything else than the default -2 */
321 if (nsteps_cmdline > -2)
323 char sbuf_steps[STEPSTRSIZE];
324 char sbuf_msg[STRLEN];
326 ir->nsteps = nsteps_cmdline;
327 if (EI_DYNAMICS(ir->eI) && nsteps_cmdline != -1)
329 sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
330 gmx_step_str(nsteps_cmdline, sbuf_steps),
331 fabs(nsteps_cmdline*ir->delta_t));
335 sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps",
336 gmx_step_str(nsteps_cmdline, sbuf_steps));
339 GMX_LOG(mdlog.warning).asParagraph().appendText(sbuf_msg);
341 else if (nsteps_cmdline < -2)
343 gmx_fatal(FARGS, "Invalid nsteps value passed on the command line: %" PRId64,
346 /* Do nothing if nsteps_cmdline == -2 */
352 /*! \brief Return whether GPU acceleration of nonbondeds is supported with the given settings.
354 * If not, and if a warning may be issued, logs a warning about
355 * falling back to CPU code. With thread-MPI, only the first
356 * call to this function should have \c issueWarning true. */
357 static bool gpuAccelerationOfNonbondedIsUseful(const MDLogger &mdlog,
358 const t_inputrec *ir,
361 if (ir->opts.ngener - ir->nwall > 1)
363 /* The GPU code does not support more than one energy group.
364 * If the user requested GPUs explicitly, a fatal error is given later.
368 GMX_LOG(mdlog.warning).asParagraph()
369 .appendText("Multiple energy groups is not implemented for GPUs, falling back to the CPU. "
370 "For better performance, run on the GPU without energy groups and then do "
371 "gmx mdrun -rerun option on the trajectory with an energy group .tpr file.");
378 //! Initializes the logger for mdrun.
379 static gmx::LoggerOwner buildLogger(FILE *fplog, const t_commrec *cr)
381 gmx::LoggerBuilder builder;
382 if (fplog != nullptr)
384 builder.addTargetFile(gmx::MDLogger::LogLevel::Info, fplog);
386 if (cr == nullptr || SIMMASTER(cr))
388 builder.addTargetStream(gmx::MDLogger::LogLevel::Warning,
389 &gmx::TextOutputFile::standardError());
391 return builder.build();
394 //! Make a TaskTarget from an mdrun argument string.
395 static TaskTarget findTaskTarget(const char *optionString)
397 TaskTarget returnValue = TaskTarget::Auto;
399 if (strncmp(optionString, "auto", 3) == 0)
401 returnValue = TaskTarget::Auto;
403 else if (strncmp(optionString, "cpu", 3) == 0)
405 returnValue = TaskTarget::Cpu;
407 else if (strncmp(optionString, "gpu", 3) == 0)
409 returnValue = TaskTarget::Gpu;
413 GMX_ASSERT(false, "Option string should have been checked for sanity already");
419 int Mdrunner::mdrunner()
423 t_forcerec *fr = nullptr;
424 t_fcdata *fcd = nullptr;
425 real ewaldcoeff_q = 0;
426 real ewaldcoeff_lj = 0;
427 int nChargePerturbed = -1, nTypePerturbed = 0;
428 gmx_wallcycle_t wcycle;
429 gmx_walltime_accounting_t walltime_accounting = nullptr;
431 int64_t reset_counters;
432 int nthreads_pme = 1;
433 gmx_membed_t * membed = nullptr;
434 gmx_hw_info_t *hwinfo = nullptr;
436 /* CAUTION: threads may be started later on in this function, so
437 cr doesn't reflect the final parallel state right now */
438 std::unique_ptr<gmx::MDModules> mdModules(new gmx::MDModules);
439 t_inputrec inputrecInstance;
440 t_inputrec *inputrec = &inputrecInstance;
443 bool doMembed = opt2bSet("-membed", filenames.size(), filenames.data());
444 bool doRerun = mdrunOptions.rerun;
446 // Handle task-assignment related user options.
447 EmulateGpuNonbonded emulateGpuNonbonded = (getenv("GMX_EMULATE_GPU") != nullptr ?
448 EmulateGpuNonbonded::Yes : EmulateGpuNonbonded::No);
449 std::vector<int> gpuIdsAvailable;
452 gpuIdsAvailable = parseUserGpuIds(hw_opt.gpuIdsAvailable);
453 // TODO We could put the GPU IDs into a std::map to find
454 // duplicates, but for the small numbers of IDs involved, this
455 // code is simple and fast.
456 for (size_t i = 0; i != gpuIdsAvailable.size(); ++i)
458 for (size_t j = i+1; j != gpuIdsAvailable.size(); ++j)
460 if (gpuIdsAvailable[i] == gpuIdsAvailable[j])
462 GMX_THROW(InvalidInputError(formatString("The string of available GPU device IDs '%s' may not contain duplicate device IDs", hw_opt.gpuIdsAvailable.c_str())));
467 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
469 std::vector<int> userGpuTaskAssignment;
472 userGpuTaskAssignment = parseUserGpuIds(hw_opt.userGpuTaskAssignment);
474 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
475 auto nonbondedTarget = findTaskTarget(nbpu_opt);
476 auto pmeTarget = findTaskTarget(pme_opt);
477 auto pmeFftTarget = findTaskTarget(pme_fft_opt);
478 auto bondedTarget = findTaskTarget(bonded_opt);
479 PmeRunMode pmeRunMode = PmeRunMode::None;
481 // Here we assume that SIMMASTER(cr) does not change even after the
482 // threads are started.
484 FILE *fplog = nullptr;
485 // If we are appending, we don't write log output because we need
486 // to check that the old log file matches what the checkpoint file
487 // expects. Otherwise, we should start to write log output now if
488 // there is a file ready for it.
489 if (logFileHandle != nullptr && !mdrunOptions.continuationOptions.appendFiles)
491 fplog = gmx_fio_getfp(logFileHandle);
493 gmx::LoggerOwner logOwner(buildLogger(fplog, cr));
494 gmx::MDLogger mdlog(logOwner.logger());
496 // TODO The thread-MPI master rank makes a working
497 // PhysicalNodeCommunicator here, but it gets rebuilt by all ranks
498 // after the threads have been launched. This works because no use
499 // is made of that communicator until after the execution paths
500 // have rejoined. But it is likely that we can improve the way
501 // this is expressed, e.g. by expressly running detection only the
502 // master rank for thread-MPI, rather than relying on the mutex
503 // and reference count.
504 PhysicalNodeCommunicator physicalNodeComm(MPI_COMM_WORLD, gmx_physicalnode_id_hash());
505 hwinfo = gmx_detect_hardware(mdlog, physicalNodeComm);
507 gmx_print_detected_hardware(fplog, cr, ms, mdlog, hwinfo);
509 std::vector<int> gpuIdsToUse;
510 auto compatibleGpus = getCompatibleGpus(hwinfo->gpu_info);
511 if (gpuIdsAvailable.empty())
513 gpuIdsToUse = compatibleGpus;
517 for (const auto &availableGpuId : gpuIdsAvailable)
519 bool availableGpuIsCompatible = false;
520 for (const auto &compatibleGpuId : compatibleGpus)
522 if (availableGpuId == compatibleGpuId)
524 availableGpuIsCompatible = true;
528 if (!availableGpuIsCompatible)
530 gmx_fatal(FARGS, "You limited the set of compatible GPUs to a set that included ID #%d, but that ID is not for a compatible GPU. List only compatible GPUs.", availableGpuId);
532 gpuIdsToUse.push_back(availableGpuId);
536 if (fplog != nullptr)
538 /* Print references after all software/hardware printing */
539 please_cite(fplog, "Abraham2015");
540 please_cite(fplog, "Pall2015");
541 please_cite(fplog, "Pronk2013");
542 please_cite(fplog, "Hess2008b");
543 please_cite(fplog, "Spoel2005a");
544 please_cite(fplog, "Lindahl2001a");
545 please_cite(fplog, "Berendsen95a");
546 writeSourceDoi(fplog);
549 std::unique_ptr<t_state> globalState;
553 /* Only the master rank has the global state */
554 globalState = compat::make_unique<t_state>();
556 /* Read (nearly) all data required for the simulation */
557 read_tpx_state(ftp2fn(efTPR, filenames.size(), filenames.data()), inputrec, globalState.get(), &mtop);
559 /* In rerun, set velocities to zero if present */
560 if (doRerun && ((globalState->flags & (1 << estV)) != 0))
562 // rerun does not use velocities
563 GMX_LOG(mdlog.info).asParagraph().appendText(
564 "Rerun trajectory contains velocities. Rerun does only evaluate "
565 "potential energy and forces. The velocities will be ignored.");
566 for (int i = 0; i < globalState->natoms; i++)
568 clear_rvec(globalState->v[i]);
570 globalState->flags &= ~(1 << estV);
573 if (inputrec->cutoff_scheme != ecutsVERLET)
575 if (nstlist_cmdline > 0)
577 gmx_fatal(FARGS, "Can not set nstlist with the group cut-off scheme");
580 if (!compatibleGpus.empty())
582 GMX_LOG(mdlog.warning).asParagraph().appendText(
583 "NOTE: GPU(s) found, but the current simulation can not use GPUs\n"
584 " To use a GPU, set the mdp option: cutoff-scheme = Verlet");
589 /* Check and update the hardware options for internal consistency */
590 check_and_update_hw_opt_1(mdlog, &hw_opt, cr, domdecOptions.numPmeRanks);
592 /* Early check for externally set process affinity. */
593 gmx_check_thread_affinity_set(mdlog, cr,
594 &hw_opt, hwinfo->nthreads_hw_avail, FALSE);
596 if (GMX_THREAD_MPI && SIMMASTER(cr))
598 if (domdecOptions.numPmeRanks > 0 && hw_opt.nthreads_tmpi <= 0)
600 gmx_fatal(FARGS, "You need to explicitly specify the number of MPI threads (-ntmpi) when using separate PME ranks");
603 /* Since the master knows the cut-off scheme, update hw_opt for this.
604 * This is done later for normal MPI and also once more with tMPI
605 * for all tMPI ranks.
607 check_and_update_hw_opt_2(&hw_opt, inputrec->cutoff_scheme);
609 bool useGpuForNonbonded = false;
610 bool useGpuForPme = false;
613 // If the user specified the number of ranks, then we must
614 // respect that, but in default mode, we need to allow for
615 // the number of GPUs to choose the number of ranks.
617 useGpuForNonbonded = decideWhetherToUseGpusForNonbondedWithThreadMpi
618 (nonbondedTarget, gpuIdsToUse, userGpuTaskAssignment, emulateGpuNonbonded,
619 inputrec->cutoff_scheme == ecutsVERLET,
620 gpuAccelerationOfNonbondedIsUseful(mdlog, inputrec, GMX_THREAD_MPI),
621 hw_opt.nthreads_tmpi);
622 auto canUseGpuForPme = pme_gpu_supports_build(nullptr) && pme_gpu_supports_input(*inputrec, mtop, nullptr);
623 useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi
624 (useGpuForNonbonded, pmeTarget, gpuIdsToUse, userGpuTaskAssignment,
625 canUseGpuForPme, hw_opt.nthreads_tmpi, domdecOptions.numPmeRanks);
628 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
630 /* Determine how many thread-MPI ranks to start.
632 * TODO Over-writing the user-supplied value here does
633 * prevent any possible subsequent checks from working
635 hw_opt.nthreads_tmpi = get_nthreads_mpi(hwinfo,
644 // Now start the threads for thread MPI.
645 cr = spawnThreads(hw_opt.nthreads_tmpi);
646 /* The main thread continues here with a new cr. We don't deallocate
647 the old cr because other threads may still be reading it. */
648 // TODO Both master and spawned threads call dup_tfn and
649 // reinitialize_commrec_for_this_thread. Find a way to express
651 physicalNodeComm = PhysicalNodeCommunicator(MPI_COMM_WORLD, gmx_physicalnode_id_hash());
653 // END OF CAUTION: cr and physicalNodeComm are now reliable
657 /* now broadcast everything to the non-master nodes/threads: */
658 init_parallel(cr, inputrec, &mtop);
661 // Now each rank knows the inputrec that SIMMASTER read and used,
662 // and (if applicable) cr->nnodes has been assigned the number of
663 // thread-MPI ranks that have been chosen. The ranks can now all
664 // run the task-deciding functions and will agree on the result
665 // without needing to communicate.
667 // TODO Should we do the communication in debug mode to support
668 // having an assertion?
670 // Note that these variables describe only their own node.
672 // Note that when bonded interactions run on a GPU they always run
673 // alongside a nonbonded task, so do not influence task assignment
674 // even though they affect the force calculation schedule.
675 bool useGpuForNonbonded = false;
676 bool useGpuForPme = false;
677 bool useGpuForBonded = false;
680 // It's possible that there are different numbers of GPUs on
681 // different nodes, which is the user's responsibilty to
682 // handle. If unsuitable, we will notice that during task
684 bool gpusWereDetected = hwinfo->ngpu_compatible_tot > 0;
685 bool usingVerletScheme = inputrec->cutoff_scheme == ecutsVERLET;
686 useGpuForNonbonded = decideWhetherToUseGpusForNonbonded(nonbondedTarget, userGpuTaskAssignment,
687 emulateGpuNonbonded, usingVerletScheme,
688 gpuAccelerationOfNonbondedIsUseful(mdlog, inputrec, !GMX_THREAD_MPI),
690 auto canUseGpuForPme = pme_gpu_supports_build(nullptr) && pme_gpu_supports_input(*inputrec, mtop, nullptr);
691 useGpuForPme = decideWhetherToUseGpusForPme(useGpuForNonbonded, pmeTarget, userGpuTaskAssignment,
692 canUseGpuForPme, cr->nnodes, domdecOptions.numPmeRanks,
694 auto canUseGpuForBonded = buildSupportsGpuBondeds(nullptr) && inputSupportsGpuBondeds(*inputrec, mtop, nullptr);
696 decideWhetherToUseGpusForBonded(useGpuForNonbonded, useGpuForPme, usingVerletScheme,
697 bondedTarget, canUseGpuForBonded, cr->nnodes,
698 domdecOptions.numPmeRanks, gpusWereDetected);
700 pmeRunMode = (useGpuForPme ? PmeRunMode::GPU : PmeRunMode::CPU);
701 if (pmeRunMode == PmeRunMode::GPU)
703 if (pmeFftTarget == TaskTarget::Cpu)
705 pmeRunMode = PmeRunMode::Mixed;
708 else if (pmeFftTarget == TaskTarget::Gpu)
710 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.");
713 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
716 // TODO: hide restraint implementation details from Mdrunner.
717 // There is nothing unique about restraints at this point as far as the
718 // Mdrunner is concerned. The Mdrunner should just be getting a sequence of
719 // factory functions from the SimulationContext on which to call mdModules->add().
720 // TODO: capture all restraints into a single RestraintModule, passed to the runner builder.
721 for (auto && restraint : restraintManager_->getRestraints())
723 auto module = RestraintMDModule::create(restraint,
725 mdModules->add(std::move(module));
728 // TODO: Error handling
729 mdModules->assignOptionsToModules(*inputrec->params, nullptr);
731 if (fplog != nullptr)
733 pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
734 fprintf(fplog, "\n");
739 /* now make sure the state is initialized and propagated */
740 set_state_entries(globalState.get(), inputrec);
743 /* NM and TPI parallelize over force/energy calculations, not atoms,
744 * so we need to initialize and broadcast the global state.
746 if (inputrec->eI == eiNM || inputrec->eI == eiTPI)
750 globalState = compat::make_unique<t_state>();
752 broadcastStateWithoutDynamics(cr, globalState.get());
755 /* A parallel command line option consistency check that we can
756 only do after any threads have started. */
757 if (!PAR(cr) && (domdecOptions.numCells[XX] > 1 ||
758 domdecOptions.numCells[YY] > 1 ||
759 domdecOptions.numCells[ZZ] > 1 ||
760 domdecOptions.numPmeRanks > 0))
763 "The -dd or -npme option request a parallel simulation, "
765 "but %s was compiled without threads or MPI enabled", output_env_get_program_display_name(oenv));
768 "but the number of MPI-threads (option -ntmpi) is not set or is 1");
770 "but %s was not started through mpirun/mpiexec or only one rank was requested through mpirun/mpiexec", output_env_get_program_display_name(oenv));
776 (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
778 gmx_fatal(FARGS, "The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun");
781 if (can_use_allvsall(inputrec, TRUE, cr, fplog) && DOMAINDECOMP(cr))
783 gmx_fatal(FARGS, "All-vs-all loops do not work with domain decomposition, use a single MPI rank");
786 if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
788 if (domdecOptions.numPmeRanks > 0)
790 gmx_fatal_collective(FARGS, cr->mpi_comm_mysim, MASTER(cr),
791 "PME-only ranks are requested, but the system does not use PME for electrostatics or LJ");
794 domdecOptions.numPmeRanks = 0;
797 if (useGpuForNonbonded && domdecOptions.numPmeRanks < 0)
799 /* With NB GPUs we don't automatically use PME-only CPU ranks. PME ranks can
800 * improve performance with many threads per GPU, since our OpenMP
801 * scaling is bad, but it's difficult to automate the setup.
803 domdecOptions.numPmeRanks = 0;
807 if (domdecOptions.numPmeRanks < 0)
809 domdecOptions.numPmeRanks = 0;
810 // TODO possibly print a note that one can opt-in for a separate PME GPU rank?
814 GMX_RELEASE_ASSERT(domdecOptions.numPmeRanks <= 1, "PME GPU decomposition is not supported");
821 fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
825 /* NMR restraints must be initialized before load_checkpoint,
826 * since with time averaging the history is added to t_state.
827 * For proper consistency check we therefore need to extend
829 * So the PME-only nodes (if present) will also initialize
830 * the distance restraints.
834 /* This needs to be called before read_checkpoint to extend the state */
835 init_disres(fplog, &mtop, inputrec, cr, ms, fcd, globalState.get(), replExParams.exchangeInterval > 0);
837 init_orires(fplog, &mtop, inputrec, cr, ms, globalState.get(), &(fcd->orires));
839 auto deform = prepareBoxDeformation(globalState->box, cr, *inputrec);
841 ObservablesHistory observablesHistory = {};
843 ContinuationOptions &continuationOptions = mdrunOptions.continuationOptions;
845 if (continuationOptions.startedFromCheckpoint)
847 /* Check if checkpoint file exists before doing continuation.
848 * This way we can use identical input options for the first and subsequent runs...
852 load_checkpoint(opt2fn_master("-cpi", filenames.size(), filenames.data(), cr),
854 cr, domdecOptions.numCells,
855 inputrec, globalState.get(),
856 &bReadEkin, &observablesHistory,
857 continuationOptions.appendFiles,
858 continuationOptions.appendFilesOptionSet,
859 mdrunOptions.reproducible);
863 continuationOptions.haveReadEkin = true;
866 if (continuationOptions.appendFiles && logFileHandle)
868 // Now we can start normal logging to the truncated log file.
869 fplog = gmx_fio_getfp(logFileHandle);
870 prepareLogAppending(cr->nodeid, cr->nnodes, fplog);
871 logOwner = buildLogger(fplog, cr);
872 mdlog = logOwner.logger();
876 if (mdrunOptions.numStepsCommandline > -2)
878 GMX_LOG(mdlog.info).asParagraph().
879 appendText("The -nsteps functionality is deprecated, and may be removed in a future version. "
880 "Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp file field.");
882 /* override nsteps with value set on the commamdline */
883 override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec);
887 copy_mat(globalState->box, box);
892 gmx_bcast(sizeof(box), box, cr);
895 /* Update rlist and nstlist. */
896 if (inputrec->cutoff_scheme == ecutsVERLET)
898 prepare_verlet_scheme(fplog, cr, inputrec, nstlist_cmdline, &mtop, box,
899 useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes), *hwinfo->cpuInfo);
902 LocalAtomSetManager atomSets;
904 if (PAR(cr) && !(EI_TPI(inputrec->eI) ||
905 inputrec->eI == eiNM))
907 cr->dd = init_domain_decomposition(mdlog, cr, domdecOptions, mdrunOptions,
909 box, positionsFromStatePointer(globalState.get()),
911 // Note that local state still does not exist yet.
915 /* PME, if used, is done on all nodes with 1D decomposition */
917 cr->duty = (DUTY_PP | DUTY_PME);
919 if (inputrec->ePBC == epbcSCREW)
922 "pbc=screw is only implemented with domain decomposition");
928 /* After possible communicator splitting in make_dd_communicators.
929 * we can set up the intra/inter node communication.
931 gmx_setup_nodecomm(fplog, cr);
937 GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
938 "This is simulation %d out of %d running as a composite GROMACS\n"
939 "multi-simulation job. Setup for this simulation:\n",
942 GMX_LOG(mdlog.warning).appendTextFormatted(
946 cr->nnodes == 1 ? "thread" : "threads"
948 cr->nnodes == 1 ? "process" : "processes"
954 /* Check and update hw_opt for the cut-off scheme */
955 check_and_update_hw_opt_2(&hw_opt, inputrec->cutoff_scheme);
957 /* Check and update the number of OpenMP threads requested */
958 checkAndUpdateRequestedNumOpenmpThreads(&hw_opt, *hwinfo, cr, ms, physicalNodeComm.size_,
961 gmx_omp_nthreads_init(mdlog, cr,
962 hwinfo->nthreads_hw_avail,
963 physicalNodeComm.size_,
965 hw_opt.nthreads_omp_pme,
966 !thisRankHasDuty(cr, DUTY_PP),
967 inputrec->cutoff_scheme == ecutsVERLET);
969 // Enable FP exception detection for the Verlet scheme, but not in
970 // Release mode and not for compilers with known buggy FP
971 // exception support (clang with any optimization) or suspected
972 // buggy FP exception support (gcc 7.* with optimization).
973 #if !defined NDEBUG && \
974 !((defined __clang__ || (defined(__GNUC__) && !defined(__ICC) && __GNUC__ == 7)) \
975 && defined __OPTIMIZE__)
976 const bool bEnableFPE = inputrec->cutoff_scheme == ecutsVERLET;
978 const bool bEnableFPE = false;
980 //FIXME - reconcile with gmx_feenableexcept() call from CommandLineModuleManager::run()
983 gmx_feenableexcept();
986 // Build a data structure that expresses which kinds of non-bonded
987 // task are handled by this rank.
989 // TODO Later, this might become a loop over all registered modules
990 // relevant to the mdp inputs, to find those that have such tasks.
992 // TODO This could move before init_domain_decomposition() as part
993 // of refactoring that separates the responsibility for duty
994 // assignment from setup for communication between tasks, and
995 // setup for tasks handled with a domain (ie including short-ranged
996 // tasks, bonded tasks, etc.).
998 // Note that in general useGpuForNonbonded, etc. can have a value
999 // that is inconsistent with the presence of actual GPUs on any
1000 // rank, and that is not known to be a problem until the
1001 // duty of the ranks on a node become known.
1003 // TODO Later we might need the concept of computeTasksOnThisRank,
1004 // from which we construct gpuTasksOnThisRank.
1006 // Currently the DD code assigns duty to ranks that can
1007 // include PP work that currently can be executed on a single
1008 // GPU, if present and compatible. This has to be coordinated
1009 // across PP ranks on a node, with possible multiple devices
1010 // or sharing devices on a node, either from the user
1011 // selection, or automatically.
1012 auto haveGpus = !gpuIdsToUse.empty();
1013 std::vector<GpuTask> gpuTasksOnThisRank;
1014 if (thisRankHasDuty(cr, DUTY_PP))
1016 if (useGpuForNonbonded)
1018 // Note that any bonded tasks on a GPU always accompany a
1022 gpuTasksOnThisRank.push_back(GpuTask::Nonbonded);
1024 else if (nonbondedTarget == TaskTarget::Gpu)
1026 gmx_fatal(FARGS, "Cannot run short-ranged nonbonded interactions on a GPU because there is none detected.");
1028 else if (bondedTarget == TaskTarget::Gpu)
1030 gmx_fatal(FARGS, "Cannot run bonded interactions on a GPU because there is none detected.");
1034 // TODO cr->duty & DUTY_PME should imply that a PME algorithm is active, but currently does not.
1035 if (EEL_PME(inputrec->coulombtype) && (thisRankHasDuty(cr, DUTY_PME)))
1041 gpuTasksOnThisRank.push_back(GpuTask::Pme);
1043 else if (pmeTarget == TaskTarget::Gpu)
1045 gmx_fatal(FARGS, "Cannot run PME on a GPU because there is none detected.");
1050 GpuTaskAssignment gpuTaskAssignment;
1053 // Produce the task assignment for this rank.
1054 gpuTaskAssignment = runTaskAssignment(gpuIdsToUse, userGpuTaskAssignment, *hwinfo,
1055 mdlog, cr, ms, physicalNodeComm, gpuTasksOnThisRank,
1056 useGpuForBonded, pmeRunMode);
1058 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1060 /* Prevent other ranks from continuing after an issue was found
1061 * and reported as a fatal error.
1063 * TODO This function implements a barrier so that MPI runtimes
1064 * can organize an orderly shutdown if one of the ranks has had to
1065 * issue a fatal error in various code already run. When we have
1066 * MPI-aware error handling and reporting, this should be
1071 MPI_Barrier(cr->mpi_comm_mysim);
1077 MPI_Barrier(ms->mpi_comm_masters);
1079 /* We need another barrier to prevent non-master ranks from contiuing
1080 * when an error occured in a different simulation.
1082 MPI_Barrier(cr->mpi_comm_mysim);
1086 /* Now that we know the setup is consistent, check for efficiency */
1087 check_resource_division_efficiency(hwinfo, !gpuTaskAssignment.empty(), mdrunOptions.ntompOptionIsSet,
1090 gmx_device_info_t *nonbondedDeviceInfo = nullptr;
1092 if (thisRankHasDuty(cr, DUTY_PP))
1094 // This works because only one task of each type is currently permitted.
1095 auto nbGpuTaskMapping = std::find_if(gpuTaskAssignment.begin(), gpuTaskAssignment.end(),
1096 hasTaskType<GpuTask::Nonbonded>);
1097 if (nbGpuTaskMapping != gpuTaskAssignment.end())
1099 int nonbondedDeviceId = nbGpuTaskMapping->deviceId_;
1100 nonbondedDeviceInfo = getDeviceInfo(hwinfo->gpu_info, nonbondedDeviceId);
1101 init_gpu(nonbondedDeviceInfo);
1103 if (DOMAINDECOMP(cr))
1105 /* When we share GPUs over ranks, we need to know this for the DLB */
1106 dd_setup_dlb_resource_sharing(cr, nonbondedDeviceId);
1112 std::unique_ptr<ClfftInitializer> initializedClfftLibrary;
1114 gmx_device_info_t *pmeDeviceInfo = nullptr;
1115 // Later, this program could contain kernels that might be later
1116 // re-used as auto-tuning progresses, or subsequent simulations
1118 PmeGpuProgramStorage pmeGpuProgram;
1119 // This works because only one task of each type is currently permitted.
1120 auto pmeGpuTaskMapping = std::find_if(gpuTaskAssignment.begin(), gpuTaskAssignment.end(), hasTaskType<GpuTask::Pme>);
1121 const bool thisRankHasPmeGpuTask = (pmeGpuTaskMapping != gpuTaskAssignment.end());
1122 if (thisRankHasPmeGpuTask)
1124 pmeDeviceInfo = getDeviceInfo(hwinfo->gpu_info, pmeGpuTaskMapping->deviceId_);
1125 init_gpu(pmeDeviceInfo);
1126 pmeGpuProgram = buildPmeGpuProgram(pmeDeviceInfo);
1127 // TODO It would be nice to move this logic into the factory
1128 // function. See Redmine #2535.
1129 bool isMasterThread = !GMX_THREAD_MPI || MASTER(cr);
1130 if (pmeRunMode == PmeRunMode::GPU && !initializedClfftLibrary && isMasterThread)
1132 initializedClfftLibrary = initializeClfftLibrary();
1136 /* getting number of PP/PME threads
1137 PME: env variable should be read only on one node to make sure it is
1138 identical everywhere;
1140 nthreads_pme = gmx_omp_nthreads_get(emntPME);
1142 int numThreadsOnThisRank;
1143 /* threads on this MPI process or TMPI thread */
1144 if (thisRankHasDuty(cr, DUTY_PP))
1146 numThreadsOnThisRank = gmx_omp_nthreads_get(emntNonbonded);
1150 numThreadsOnThisRank = nthreads_pme;
1153 checkHardwareOversubscription(numThreadsOnThisRank, cr->nodeid,
1154 *hwinfo->hardwareTopology,
1155 physicalNodeComm, mdlog);
1157 if (hw_opt.thread_affinity != threadaffOFF)
1159 /* Before setting affinity, check whether the affinity has changed
1160 * - which indicates that probably the OpenMP library has changed it
1161 * since we first checked).
1163 gmx_check_thread_affinity_set(mdlog, cr,
1164 &hw_opt, hwinfo->nthreads_hw_avail, TRUE);
1166 int numThreadsOnThisNode, intraNodeThreadOffset;
1167 analyzeThreadsOnThisNode(physicalNodeComm, numThreadsOnThisRank, &numThreadsOnThisNode,
1168 &intraNodeThreadOffset);
1170 /* Set the CPU affinity */
1171 gmx_set_thread_affinity(mdlog, cr, &hw_opt, *hwinfo->hardwareTopology,
1172 numThreadsOnThisRank, numThreadsOnThisNode,
1173 intraNodeThreadOffset, nullptr);
1176 if (mdrunOptions.timingOptions.resetStep > -1)
1178 GMX_LOG(mdlog.info).asParagraph().
1179 appendText("The -resetstep functionality is deprecated, and may be removed in a future version.");
1181 wcycle = wallcycle_init(fplog, mdrunOptions.timingOptions.resetStep, cr);
1185 /* Master synchronizes its value of reset_counters with all nodes
1186 * including PME only nodes */
1187 reset_counters = wcycle_get_reset_counters(wcycle);
1188 gmx_bcast_sim(sizeof(reset_counters), &reset_counters, cr);
1189 wcycle_set_reset_counters(wcycle, reset_counters);
1192 // Membrane embedding must be initialized before we call init_forcerec()
1197 fprintf(stderr, "Initializing membed");
1199 /* Note that membed cannot work in parallel because mtop is
1200 * changed here. Fix this if we ever want to make it run with
1201 * multiple ranks. */
1202 membed = init_membed(fplog, filenames.size(), filenames.data(), &mtop, inputrec, globalState.get(), cr,
1204 .checkpointOptions.period);
1207 std::unique_ptr<MDAtoms> mdAtoms;
1208 std::unique_ptr<gmx_vsite_t> vsite;
1211 if (thisRankHasDuty(cr, DUTY_PP))
1213 /* Initiate forcerecord */
1215 fr->forceProviders = mdModules->initForceProviders();
1216 init_forcerec(fplog, mdlog, fr, fcd,
1217 inputrec, &mtop, cr, box,
1218 opt2fn("-table", filenames.size(), filenames.data()),
1219 opt2fn("-tablep", filenames.size(), filenames.data()),
1220 opt2fns("-tableb", filenames.size(), filenames.data()),
1221 *hwinfo, nonbondedDeviceInfo,
1226 /* Initialize QM-MM */
1229 GMX_LOG(mdlog.info).asParagraph().
1230 appendText("Large parts of the QM/MM support is deprecated, and may be removed in a future "
1231 "version. Please get in touch with the developers if you find the support useful, "
1232 "as help is needed if the functionality is to continue to be available.");
1233 init_QMMMrec(cr, &mtop, inputrec, fr);
1236 /* Initialize the mdAtoms structure.
1237 * mdAtoms is not filled with atom data,
1238 * as this can not be done now with domain decomposition.
1240 mdAtoms = makeMDAtoms(fplog, mtop, *inputrec, thisRankHasPmeGpuTask);
1241 if (globalState && thisRankHasPmeGpuTask)
1243 // The pinning of coordinates in the global state object works, because we only use
1244 // PME on GPU without DD or on a separate PME rank, and because the local state pointer
1245 // points to the global state object without DD.
1246 // FIXME: MD and EM separately set up the local state - this should happen in the same function,
1247 // which should also perform the pinning.
1248 changePinningPolicy(&globalState->x, pme_get_pinning_policy());
1251 /* Initialize the virtual site communication */
1252 vsite = initVsite(mtop, cr);
1254 calc_shifts(box, fr->shift_vec);
1256 /* With periodic molecules the charge groups should be whole at start up
1257 * and the virtual sites should not be far from their proper positions.
1259 if (!inputrec->bContinuation && MASTER(cr) &&
1260 !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
1262 /* Make molecules whole at start of run */
1263 if (fr->ePBC != epbcNONE)
1265 do_pbc_first_mtop(fplog, inputrec->ePBC, box, &mtop, globalState->x.rvec_array());
1269 /* Correct initial vsite positions are required
1270 * for the initial distribution in the domain decomposition
1271 * and for the initial shell prediction.
1273 constructVsitesGlobal(mtop, globalState->x);
1277 if (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
1279 ewaldcoeff_q = fr->ic->ewaldcoeff_q;
1280 ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
1285 /* This is a PME only node */
1287 GMX_ASSERT(globalState == nullptr, "We don't need the state on a PME only rank and expect it to be unitialized");
1289 ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
1290 ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
1293 gmx_pme_t *sepPmeData = nullptr;
1294 // This reference hides the fact that PME data is owned by runner on PME-only ranks and by forcerec on other ranks
1295 GMX_ASSERT(thisRankHasDuty(cr, DUTY_PP) == (fr != nullptr), "Double-checking that only PME-only ranks have no forcerec");
1296 gmx_pme_t * &pmedata = fr ? fr->pmedata : sepPmeData;
1298 /* Initiate PME if necessary,
1299 * either on all nodes or on dedicated PME nodes only. */
1300 if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
1302 if (mdAtoms && mdAtoms->mdatoms())
1304 nChargePerturbed = mdAtoms->mdatoms()->nChargePerturbed;
1305 if (EVDW_PME(inputrec->vdwtype))
1307 nTypePerturbed = mdAtoms->mdatoms()->nTypePerturbed;
1310 if (cr->npmenodes > 0)
1312 /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
1313 gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
1314 gmx_bcast_sim(sizeof(nTypePerturbed), &nTypePerturbed, cr);
1317 if (thisRankHasDuty(cr, DUTY_PME))
1321 pmedata = gmx_pme_init(cr,
1322 getNumPmeDomains(cr->dd),
1324 mtop.natoms, nChargePerturbed != 0, nTypePerturbed != 0,
1325 mdrunOptions.reproducible,
1326 ewaldcoeff_q, ewaldcoeff_lj,
1328 pmeRunMode, nullptr,
1329 pmeDeviceInfo, pmeGpuProgram.get(), mdlog);
1331 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1336 if (EI_DYNAMICS(inputrec->eI))
1338 /* Turn on signal handling on all nodes */
1340 * (A user signal from the PME nodes (if any)
1341 * is communicated to the PP nodes.
1343 signal_handler_install();
1346 if (thisRankHasDuty(cr, DUTY_PP))
1348 /* Assumes uniform use of the number of OpenMP threads */
1349 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
1351 if (inputrec->bPull)
1353 /* Initialize pull code */
1354 inputrec->pull_work =
1355 init_pull(fplog, inputrec->pull, inputrec,
1356 &mtop, cr, &atomSets, inputrec->fepvals->init_lambda);
1357 if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
1359 initPullHistory(inputrec->pull_work, &observablesHistory);
1361 if (EI_DYNAMICS(inputrec->eI) && MASTER(cr))
1363 init_pull_output_files(inputrec->pull_work,
1364 filenames.size(), filenames.data(), oenv,
1365 continuationOptions);
1369 std::unique_ptr<EnforcedRotation> enforcedRotation;
1372 /* Initialize enforced rotation code */
1373 enforcedRotation = init_rot(fplog,
1385 if (inputrec->eSwapCoords != eswapNO)
1387 /* Initialize ion swapping code */
1388 init_swapcoords(fplog, inputrec, opt2fn_master("-swap", filenames.size(), filenames.data(), cr),
1389 &mtop, globalState.get(), &observablesHistory,
1390 cr, &atomSets, oenv, mdrunOptions);
1393 /* Let makeConstraints know whether we have essential dynamics constraints.
1394 * TODO: inputrec should tell us whether we use an algorithm, not a file option or the checkpoint
1396 bool doEssentialDynamics = (opt2fn_null("-ei", filenames.size(), filenames.data()) != nullptr
1397 || observablesHistory.edsamHistory);
1398 auto constr = makeConstraints(mtop, *inputrec, doEssentialDynamics,
1399 fplog, *mdAtoms->mdatoms(),
1400 cr, *ms, nrnb, wcycle, fr->bMolPBC);
1402 if (DOMAINDECOMP(cr))
1404 GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
1405 /* This call is not included in init_domain_decomposition mainly
1406 * because fr->cginfo_mb is set later.
1408 dd_init_bondeds(fplog, cr->dd, &mtop, vsite.get(), inputrec,
1409 domdecOptions.checkBondedInteractions,
1413 GMX_ASSERT(stopHandlerBuilder_, "Runner must provide StopHandlerBuilder to integrator.");
1414 /* Now do whatever the user wants us to do (how flexible...) */
1415 Integrator integrator {
1416 fplog, cr, ms, mdlog, static_cast<int>(filenames.size()), filenames.data(),
1419 vsite.get(), constr.get(),
1420 enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr,
1422 mdModules->outputProvider(),
1426 &observablesHistory,
1427 mdAtoms.get(), nrnb, wcycle, fr,
1430 walltime_accounting,
1431 std::move(stopHandlerBuilder_)
1433 integrator.run(inputrec->eI, doRerun);
1435 if (inputrec->bPull)
1437 finish_pull(inputrec->pull_work);
1443 GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
1445 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
1446 gmx_pmeonly(pmedata, cr, nrnb, wcycle, walltime_accounting, inputrec, pmeRunMode);
1449 wallcycle_stop(wcycle, ewcRUN);
1451 /* Finish up, write some stuff
1452 * if rerunMD, don't write last frame again
1454 finish_run(fplog, mdlog, cr,
1455 inputrec, nrnb, wcycle, walltime_accounting,
1456 fr ? fr->nbv : nullptr,
1458 EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
1463 gmx_pme_destroy(pmedata);
1467 // FIXME: this is only here to manually unpin mdAtoms->chargeA_ and state->x,
1468 // before we destroy the GPU context(s) in free_gpu_resources().
1469 // Pinned buffers are associated with contexts in CUDA.
1470 // As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
1471 mdAtoms.reset(nullptr);
1472 globalState.reset(nullptr);
1473 mdModules.reset(nullptr); // destruct force providers here as they might also use the GPU
1475 /* Free GPU memory and set a physical node tMPI barrier (which should eventually go away) */
1476 free_gpu_resources(fr, physicalNodeComm);
1477 free_gpu(nonbondedDeviceInfo);
1478 free_gpu(pmeDeviceInfo);
1479 done_forcerec(fr, mtop.molblock.size(), mtop.groups.grps[egcENER].nr);
1484 free_membed(membed);
1487 gmx_hardware_info_free();
1489 /* Does what it says */
1490 print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
1491 walltime_accounting_destroy(walltime_accounting);
1494 // Ensure log file content is written
1497 gmx_fio_flush(logFileHandle);
1500 /* Reset FPEs (important for unit tests) by disabling them. Assumes no
1501 * exceptions were enabled before function was called. */
1504 gmx_fedisableexcept();
1507 rc = static_cast<int>(gmx_get_stop_condition());
1510 /* we need to join all threads. The sub-threads join when they
1511 exit this function, but the master thread needs to be told to
1513 if (PAR(cr) && MASTER(cr))
1523 Mdrunner::~Mdrunner()
1525 // Clean up of the Manager.
1526 // This will end up getting called on every thread-MPI rank, which is unnecessary,
1527 // but okay as long as threads synchronize some time before adding or accessing
1528 // a new set of restraints.
1529 if (restraintManager_)
1531 restraintManager_->clear();
1532 GMX_ASSERT(restraintManager_->countRestraints() == 0,
1533 "restraints added during runner life time should be cleared at runner destruction.");
1537 void Mdrunner::addPotential(std::shared_ptr<gmx::IRestraintPotential> puller,
1540 GMX_ASSERT(restraintManager_, "Mdrunner must have a restraint manager.");
1541 // Not sure if this should be logged through the md logger or something else,
1542 // but it is helpful to have some sort of INFO level message sent somewhere.
1543 // std::cout << "Registering restraint named " << name << std::endl;
1545 // When multiple restraints are used, it may be wasteful to register them separately.
1546 // Maybe instead register an entire Restraint Manager as a force provider.
1547 restraintManager_->addToSpec(std::move(puller),
1551 Mdrunner::Mdrunner(Mdrunner &&) noexcept = default;
1553 //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265
1554 Mdrunner &Mdrunner::operator=(Mdrunner && /*handle*/) noexcept(BUGFREE_NOEXCEPT_STRING) = default;
1556 class Mdrunner::BuilderImplementation
1559 BuilderImplementation() = delete;
1560 explicit BuilderImplementation(SimulationContext* context);
1561 ~BuilderImplementation();
1563 BuilderImplementation &setExtraMdrunOptions(const MdrunOptions &options,
1564 real forceWarningThreshold);
1566 void addDomdec(const DomdecOptions &options);
1568 void addVerletList(int nstlist);
1570 void addReplicaExchange(const ReplicaExchangeParameters ¶ms);
1572 void addMultiSim(gmx_multisim_t* multisim);
1574 void addNonBonded(const char* nbpu_opt);
1576 void addPME(const char* pme_opt_, const char* pme_fft_opt_);
1578 void addBondedTaskAssignment(const char* bonded_opt);
1580 void addHardwareOptions(const gmx_hw_opt_t &hardwareOptions);
1582 void addFilenames(ArrayRef <const t_filenm> filenames);
1584 void addOutputEnvironment(gmx_output_env_t* outputEnvironment);
1586 void addLogFile(t_fileio *logFileHandle);
1588 void addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
1593 // Default parameters copied from runner.h
1594 // \todo Clarify source(s) of default parameters.
1596 const char* nbpu_opt_ = nullptr;
1597 const char* pme_opt_ = nullptr;
1598 const char* pme_fft_opt_ = nullptr;
1599 const char *bonded_opt_ = nullptr;
1601 MdrunOptions mdrunOptions_;
1603 DomdecOptions domdecOptions_;
1605 ReplicaExchangeParameters replicaExchangeParameters_;
1607 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
1610 //! Non-owning multisim communicator handle.
1611 std::unique_ptr<gmx_multisim_t*> multisim_ = nullptr;
1613 //! Print a warning if any force is larger than this (in kJ/mol nm).
1614 real forceWarningThreshold_ = -1;
1616 /*! \brief Non-owning pointer to SimulationContext (owned and managed by client)
1619 * \todo Establish robust protocol to make sure resources remain valid.
1620 * SimulationContext will likely be separated into multiple layers for
1621 * different levels of access and different phases of execution. Ref
1622 * https://redmine.gromacs.org/issues/2375
1623 * https://redmine.gromacs.org/issues/2587
1625 SimulationContext* context_ = nullptr;
1627 //! \brief Parallelism information.
1628 gmx_hw_opt_t hardwareOptions_;
1630 //! filename options for simulation.
1631 ArrayRef<const t_filenm> filenames_;
1633 /*! \brief Handle to output environment.
1635 * \todo gmx_output_env_t needs lifetime management.
1637 gmx_output_env_t* outputEnvironment_ = nullptr;
1639 /*! \brief Non-owning handle to MD log file.
1641 * \todo Context should own output facilities for client.
1642 * \todo Improve log file handle management.
1644 * Code managing the FILE* relies on the ability to set it to
1645 * nullptr to check whether the filehandle is valid.
1647 t_fileio* logFileHandle_ = nullptr;
1650 * \brief Builder for simulation stop signal handler.
1652 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_ = nullptr;
1655 Mdrunner::BuilderImplementation::BuilderImplementation(SimulationContext* context) :
1658 GMX_ASSERT(context_, "Bug found. It should not be possible to construct builder without a valid context.");
1661 Mdrunner::BuilderImplementation::~BuilderImplementation() = default;
1663 Mdrunner::BuilderImplementation &
1664 Mdrunner::BuilderImplementation::setExtraMdrunOptions(const MdrunOptions &options,
1665 real forceWarningThreshold)
1667 mdrunOptions_ = options;
1668 forceWarningThreshold_ = forceWarningThreshold;
1672 void Mdrunner::BuilderImplementation::addDomdec(const DomdecOptions &options)
1674 domdecOptions_ = options;
1677 void Mdrunner::BuilderImplementation::addVerletList(int nstlist)
1682 void Mdrunner::BuilderImplementation::addReplicaExchange(const ReplicaExchangeParameters ¶ms)
1684 replicaExchangeParameters_ = params;
1687 void Mdrunner::BuilderImplementation::addMultiSim(gmx_multisim_t* multisim)
1689 multisim_ = compat::make_unique<gmx_multisim_t*>(multisim);
1692 Mdrunner Mdrunner::BuilderImplementation::build()
1694 auto newRunner = Mdrunner();
1696 GMX_ASSERT(context_, "Bug found. It should not be possible to call build() without a valid context.");
1698 newRunner.mdrunOptions = mdrunOptions_;
1699 newRunner.domdecOptions = domdecOptions_;
1701 // \todo determine an invariant to check or confirm that all gmx_hw_opt_t objects are valid
1702 newRunner.hw_opt = hardwareOptions_;
1704 // No invariant to check. This parameter exists to optionally override other behavior.
1705 newRunner.nstlist_cmdline = nstlist_;
1707 newRunner.replExParams = replicaExchangeParameters_;
1709 newRunner.filenames = filenames_;
1711 GMX_ASSERT(context_->communicationRecord_, "SimulationContext communications not initialized.");
1712 newRunner.cr = context_->communicationRecord_;
1716 // nullptr is a valid value for the multisim handle, so we don't check the pointed-to pointer.
1717 newRunner.ms = *multisim_;
1721 GMX_THROW(gmx::APIError("MdrunnerBuilder::addMultiSim() is required before build()"));
1724 // \todo Clarify ownership and lifetime management for gmx_output_env_t
1725 // \todo Update sanity checking when output environment has clearly specified invariants.
1726 // Initialization and default values for oenv are not well specified in the current version.
1727 if (outputEnvironment_)
1729 newRunner.oenv = outputEnvironment_;
1733 GMX_THROW(gmx::APIError("MdrunnerBuilder::addOutputEnvironment() is required before build()"));
1736 newRunner.logFileHandle = logFileHandle_;
1740 newRunner.nbpu_opt = nbpu_opt_;
1744 GMX_THROW(gmx::APIError("MdrunnerBuilder::addNonBonded() is required before build()"));
1747 if (pme_opt_ && pme_fft_opt_)
1749 newRunner.pme_opt = pme_opt_;
1750 newRunner.pme_fft_opt = pme_fft_opt_;
1754 GMX_THROW(gmx::APIError("MdrunnerBuilder::addElectrostatics() is required before build()"));
1759 newRunner.bonded_opt = bonded_opt_;
1763 GMX_THROW(gmx::APIError("MdrunnerBuilder::addBondedTaskAssignment() is required before build()"));
1766 newRunner.restraintManager_ = compat::make_unique<gmx::RestraintManager>();
1768 if (stopHandlerBuilder_)
1770 newRunner.stopHandlerBuilder_ = std::move(stopHandlerBuilder_);
1774 newRunner.stopHandlerBuilder_ = compat::make_unique<StopHandlerBuilder>();
1780 void Mdrunner::BuilderImplementation::addNonBonded(const char* nbpu_opt)
1782 nbpu_opt_ = nbpu_opt;
1785 void Mdrunner::BuilderImplementation::addPME(const char* pme_opt,
1786 const char* pme_fft_opt)
1789 pme_fft_opt_ = pme_fft_opt;
1792 void Mdrunner::BuilderImplementation::addBondedTaskAssignment(const char* bonded_opt)
1794 bonded_opt_ = bonded_opt;
1797 void Mdrunner::BuilderImplementation::addHardwareOptions(const gmx_hw_opt_t &hardwareOptions)
1799 hardwareOptions_ = hardwareOptions;
1802 void Mdrunner::BuilderImplementation::addFilenames(ArrayRef<const t_filenm> filenames)
1804 filenames_ = filenames;
1807 void Mdrunner::BuilderImplementation::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
1809 outputEnvironment_ = outputEnvironment;
1812 void Mdrunner::BuilderImplementation::addLogFile(t_fileio *logFileHandle)
1814 logFileHandle_ = logFileHandle;
1817 void Mdrunner::BuilderImplementation::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
1819 stopHandlerBuilder_ = std::move(builder);
1822 MdrunnerBuilder::MdrunnerBuilder(compat::not_null<SimulationContext*> context) :
1823 impl_ {gmx::compat::make_unique<Mdrunner::BuilderImplementation>(context)}
1827 MdrunnerBuilder::~MdrunnerBuilder() = default;
1829 MdrunnerBuilder &MdrunnerBuilder::addSimulationMethod(const MdrunOptions &options,
1830 real forceWarningThreshold)
1832 impl_->setExtraMdrunOptions(options, forceWarningThreshold);
1836 MdrunnerBuilder &MdrunnerBuilder::addDomainDecomposition(const DomdecOptions &options)
1838 impl_->addDomdec(options);
1842 MdrunnerBuilder &MdrunnerBuilder::addNeighborList(int nstlist)
1844 impl_->addVerletList(nstlist);
1848 MdrunnerBuilder &MdrunnerBuilder::addReplicaExchange(const ReplicaExchangeParameters ¶ms)
1850 impl_->addReplicaExchange(params);
1854 MdrunnerBuilder &MdrunnerBuilder::addMultiSim(gmx_multisim_t* multisim)
1856 impl_->addMultiSim(multisim);
1860 MdrunnerBuilder &MdrunnerBuilder::addNonBonded(const char* nbpu_opt)
1862 impl_->addNonBonded(nbpu_opt);
1866 MdrunnerBuilder &MdrunnerBuilder::addElectrostatics(const char* pme_opt,
1867 const char* pme_fft_opt)
1869 // The builder method may become more general in the future, but in this version,
1870 // parameters for PME electrostatics are both required and the only parameters
1872 if (pme_opt && pme_fft_opt)
1874 impl_->addPME(pme_opt, pme_fft_opt);
1878 GMX_THROW(gmx::InvalidInputError("addElectrostatics() arguments must be non-null pointers."));
1883 MdrunnerBuilder &MdrunnerBuilder::addBondedTaskAssignment(const char* bonded_opt)
1885 impl_->addBondedTaskAssignment(bonded_opt);
1889 Mdrunner MdrunnerBuilder::build()
1891 return impl_->build();
1894 MdrunnerBuilder &MdrunnerBuilder::addHardwareOptions(const gmx_hw_opt_t &hardwareOptions)
1896 impl_->addHardwareOptions(hardwareOptions);
1900 MdrunnerBuilder &MdrunnerBuilder::addFilenames(ArrayRef<const t_filenm> filenames)
1902 impl_->addFilenames(filenames);
1906 MdrunnerBuilder &MdrunnerBuilder::addOutputEnvironment(gmx_output_env_t* outputEnvironment)
1908 impl_->addOutputEnvironment(outputEnvironment);
1912 MdrunnerBuilder &MdrunnerBuilder::addLogFile(t_fileio *logFileHandle)
1914 impl_->addLogFile(logFileHandle);
1918 MdrunnerBuilder &MdrunnerBuilder::addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder)
1920 impl_->addStopHandlerBuilder(std::move(builder));
1924 MdrunnerBuilder::MdrunnerBuilder(MdrunnerBuilder &&) noexcept = default;
1926 MdrunnerBuilder &MdrunnerBuilder::operator=(MdrunnerBuilder &&) noexcept = default;