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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_mdlib
57 #include "gromacs/commandline/filenm.h"
58 #include "gromacs/domdec/domdec.h"
59 #include "gromacs/domdec/domdec_struct.h"
60 #include "gromacs/ewald/ewald-utils.h"
61 #include "gromacs/ewald/pme.h"
62 #include "gromacs/fileio/checkpoint.h"
63 #include "gromacs/fileio/oenv.h"
64 #include "gromacs/fileio/tpxio.h"
65 #include "gromacs/gmxlib/network.h"
66 #include "gromacs/gpu_utils/gpu_utils.h"
67 #include "gromacs/hardware/cpuinfo.h"
68 #include "gromacs/hardware/detecthardware.h"
69 #include "gromacs/hardware/printhardware.h"
70 #include "gromacs/listed-forces/disre.h"
71 #include "gromacs/listed-forces/orires.h"
72 #include "gromacs/math/functions.h"
73 #include "gromacs/math/utilities.h"
74 #include "gromacs/math/vec.h"
75 #include "gromacs/mdlib/calc_verletbuf.h"
76 #include "gromacs/mdlib/constr.h"
77 #include "gromacs/mdlib/force.h"
78 #include "gromacs/mdlib/forcerec.h"
79 #include "gromacs/mdlib/gmx_omp_nthreads.h"
80 #include "gromacs/mdlib/integrator.h"
81 #include "gromacs/mdlib/main.h"
82 #include "gromacs/mdlib/md_support.h"
83 #include "gromacs/mdlib/mdatoms.h"
84 #include "gromacs/mdlib/mdrun.h"
85 #include "gromacs/mdlib/minimize.h"
86 #include "gromacs/mdlib/nb_verlet.h"
87 #include "gromacs/mdlib/nbnxn_search.h"
88 #include "gromacs/mdlib/nbnxn_tuning.h"
89 #include "gromacs/mdlib/qmmm.h"
90 #include "gromacs/mdlib/sighandler.h"
91 #include "gromacs/mdlib/sim_util.h"
92 #include "gromacs/mdlib/tpi.h"
93 #include "gromacs/mdrunutility/mdmodules.h"
94 #include "gromacs/mdrunutility/threadaffinity.h"
95 #include "gromacs/mdtypes/commrec.h"
96 #include "gromacs/mdtypes/inputrec.h"
97 #include "gromacs/mdtypes/md_enums.h"
98 #include "gromacs/mdtypes/observableshistory.h"
99 #include "gromacs/mdtypes/state.h"
100 #include "gromacs/pbcutil/pbc.h"
101 #include "gromacs/pulling/pull.h"
102 #include "gromacs/pulling/pull_rotation.h"
103 #include "gromacs/taskassignment/decidegpuusage.h"
104 #include "gromacs/taskassignment/resourcedivision.h"
105 #include "gromacs/taskassignment/taskassignment.h"
106 #include "gromacs/taskassignment/usergpuids.h"
107 #include "gromacs/timing/wallcycle.h"
108 #include "gromacs/topology/mtop_util.h"
109 #include "gromacs/trajectory/trajectoryframe.h"
110 #include "gromacs/utility/cstringutil.h"
111 #include "gromacs/utility/exceptions.h"
112 #include "gromacs/utility/fatalerror.h"
113 #include "gromacs/utility/filestream.h"
114 #include "gromacs/utility/gmxassert.h"
115 #include "gromacs/utility/gmxmpi.h"
116 #include "gromacs/utility/logger.h"
117 #include "gromacs/utility/loggerbuilder.h"
118 #include "gromacs/utility/pleasecite.h"
119 #include "gromacs/utility/programcontext.h"
120 #include "gromacs/utility/smalloc.h"
121 #include "gromacs/utility/stringutil.h"
129 #include "corewrap.h"
132 //! First step used in pressure scaling
133 gmx_int64_t deform_init_init_step_tpx
;
134 //! Initial box for pressure scaling
135 matrix deform_init_box_tpx
;
136 //! MPI variable for use in pressure scaling
137 tMPI_Thread_mutex_t deform_init_box_mutex
= TMPI_THREAD_MUTEX_INITIALIZER
;
142 void Mdrunner::reinitializeOnSpawnedThread()
144 // TODO This duplication is formally necessary if any thread might
145 // modify any memory in fnm or the pointers it contains. If the
146 // contents are ever provably const, then we can remove this
147 // allocation (and memory leak).
148 // TODO This should probably become part of a copy constructor for
150 fnm
= dup_tfn(nfile
, fnm
);
152 cr
= reinitialize_commrec_for_this_thread(cr
);
156 // Only the master rank writes to the log files
161 /*! \brief The callback used for running on spawned threads.
163 * Obtains the pointer to the master mdrunner object from the one
164 * argument permitted to the thread-launch API call, copies it to make
165 * a new runner for this thread, reinitializes necessary data, and
166 * proceeds to the simulation. */
167 static void mdrunner_start_fn(void *arg
)
171 auto masterMdrunner
= reinterpret_cast<const gmx::Mdrunner
*>(arg
);
172 /* copy the arg list to make sure that it's thread-local. This
173 doesn't copy pointed-to items, of course, but those are all
175 gmx::Mdrunner mdrunner
= *masterMdrunner
;
176 mdrunner
.reinitializeOnSpawnedThread();
179 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
;
183 /*! \brief Start thread-MPI threads.
185 * Called by mdrunner() to start a specific number of threads
186 * (including the main thread) for thread-parallel runs. This in turn
187 * calls mdrunner() for each thread. All options are the same as for
189 t_commrec
*Mdrunner::spawnThreads(int numThreadsToLaunch
)
192 /* first check whether we even need to start tMPI */
193 if (numThreadsToLaunch
< 2)
198 gmx::Mdrunner spawnedMdrunner
= *this;
199 // TODO This duplication is formally necessary if any thread might
200 // modify any memory in fnm or the pointers it contains. If the
201 // contents are ever provably const, then we can remove this
202 // allocation (and memory leak).
203 // TODO This should probably become part of a copy constructor for
205 spawnedMdrunner
.fnm
= dup_tfn(this->nfile
, fnm
);
208 /* now spawn new threads that start mdrunner_start_fn(), while
209 the main thread returns, we set thread affinity later */
210 if (tMPI_Init_fn(TRUE
, numThreadsToLaunch
, TMPI_AFFINITY_NONE
,
211 mdrunner_start_fn
, static_cast<void*>(&spawnedMdrunner
)) != TMPI_SUCCESS
)
213 GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
216 GMX_UNUSED_VALUE(mdrunner_start_fn
);
219 return reinitialize_commrec_for_this_thread(cr
);
224 /*! \brief Initialize variables for Verlet scheme simulation */
225 static void prepare_verlet_scheme(FILE *fplog
,
229 const gmx_mtop_t
*mtop
,
231 bool makeGpuPairList
,
232 const gmx::CpuInfo
&cpuinfo
)
234 /* For NVE simulations, we will retain the initial list buffer */
235 if (EI_DYNAMICS(ir
->eI
) &&
236 ir
->verletbuf_tol
> 0 &&
237 !(EI_MD(ir
->eI
) && ir
->etc
== etcNO
))
239 /* Update the Verlet buffer size for the current run setup */
241 /* Here we assume SIMD-enabled kernels are being used. But as currently
242 * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
243 * and 4x2 gives a larger buffer than 4x4, this is ok.
245 ListSetupType listType
= (makeGpuPairList
? ListSetupType::Gpu
: ListSetupType::CpuSimdWhenSupported
);
246 VerletbufListSetup listSetup
= verletbufGetSafeListSetup(listType
);
249 calc_verlet_buffer_size(mtop
, det(box
), ir
, ir
->nstlist
, ir
->nstlist
- 1, -1, &listSetup
, nullptr, &rlist_new
);
251 if (rlist_new
!= ir
->rlist
)
253 if (fplog
!= nullptr)
255 fprintf(fplog
, "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
256 ir
->rlist
, rlist_new
,
257 listSetup
.cluster_size_i
, listSetup
.cluster_size_j
);
259 ir
->rlist
= rlist_new
;
263 if (nstlist_cmdline
> 0 && (!EI_DYNAMICS(ir
->eI
) || ir
->verletbuf_tol
<= 0))
265 gmx_fatal(FARGS
, "Can not set nstlist without %s",
266 !EI_DYNAMICS(ir
->eI
) ? "dynamics" : "verlet-buffer-tolerance");
269 if (EI_DYNAMICS(ir
->eI
))
271 /* Set or try nstlist values */
272 increaseNstlist(fplog
, cr
, ir
, nstlist_cmdline
, mtop
, box
, makeGpuPairList
, cpuinfo
);
276 /*! \brief Override the nslist value in inputrec
278 * with value passed on the command line (if any)
280 static void override_nsteps_cmdline(const gmx::MDLogger
&mdlog
,
281 gmx_int64_t nsteps_cmdline
,
286 /* override with anything else than the default -2 */
287 if (nsteps_cmdline
> -2)
289 char sbuf_steps
[STEPSTRSIZE
];
290 char sbuf_msg
[STRLEN
];
292 ir
->nsteps
= nsteps_cmdline
;
293 if (EI_DYNAMICS(ir
->eI
) && nsteps_cmdline
!= -1)
295 sprintf(sbuf_msg
, "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
296 gmx_step_str(nsteps_cmdline
, sbuf_steps
),
297 fabs(nsteps_cmdline
*ir
->delta_t
));
301 sprintf(sbuf_msg
, "Overriding nsteps with value passed on the command line: %s steps",
302 gmx_step_str(nsteps_cmdline
, sbuf_steps
));
305 GMX_LOG(mdlog
.warning
).asParagraph().appendText(sbuf_msg
);
307 else if (nsteps_cmdline
< -2)
309 gmx_fatal(FARGS
, "Invalid nsteps value passed on the command line: %d",
312 /* Do nothing if nsteps_cmdline == -2 */
318 /*! \brief Return whether GPU acceleration of nonbondeds is useful with the given settings.
320 * If not, logs a message about falling back to CPU code. */
321 static bool gpuAccelerationOfNonbondedIsUseful(const MDLogger
&mdlog
,
322 const t_inputrec
*ir
,
325 if (doRerun
&& ir
->opts
.ngener
> 1)
327 /* Rerun execution time is dominated by I/O and pair search,
328 * so GPUs are not very useful, plus they do not support more
329 * than one energy group. If the user requested GPUs
330 * explicitly, a fatal error is given later. With non-reruns,
331 * we fall back to a single whole-of system energy group
332 * (which runs much faster than a multiple-energy-groups
333 * implementation would), and issue a note in the .log
334 * file. Users can re-run if they want the information. */
335 GMX_LOG(mdlog
.warning
).asParagraph().appendText("Multiple energy groups is not implemented for GPUs, so is not useful for this rerun, so falling back to the CPU");
342 //! \brief Return the correct integrator function.
343 static integrator_t
*my_integrator(unsigned int ei
)
352 if (!EI_DYNAMICS(ei
))
354 GMX_THROW(APIError("do_md integrator would be called for a non-dynamical integrator"));
369 GMX_THROW(APIError("do_tpi integrator would be called for a non-TPI integrator"));
373 GMX_THROW(NotImplementedError("SD2 integrator has been removed"));
375 GMX_THROW(APIError("Non existing integrator selected"));
379 //! Initializes the logger for mdrun.
380 static gmx::LoggerOwner
buildLogger(FILE *fplog
, const t_commrec
*cr
)
382 gmx::LoggerBuilder builder
;
383 if (fplog
!= nullptr)
385 builder
.addTargetFile(gmx::MDLogger::LogLevel::Info
, fplog
);
387 if (cr
== nullptr || SIMMASTER(cr
))
389 builder
.addTargetStream(gmx::MDLogger::LogLevel::Warning
,
390 &gmx::TextOutputFile::standardError());
392 return builder
.build();
395 //! Make a TaskTarget from an mdrun argument string.
396 static TaskTarget
findTaskTarget(const char *optionString
)
398 TaskTarget returnValue
= TaskTarget::Auto
;
400 if (strncmp(optionString
, "auto", 3) == 0)
402 returnValue
= TaskTarget::Auto
;
404 else if (strncmp(optionString
, "cpu", 3) == 0)
406 returnValue
= TaskTarget::Cpu
;
408 else if (strncmp(optionString
, "gpu", 3) == 0)
410 returnValue
= TaskTarget::Gpu
;
414 GMX_ASSERT(false, "Option string should have been checked for sanity already");
420 int Mdrunner::mdrunner()
423 gmx_ddbox_t ddbox
= {0};
424 int npme_major
, npme_minor
;
426 gmx_mtop_t
*mtop
= nullptr;
427 t_forcerec
*fr
= nullptr;
428 t_fcdata
*fcd
= nullptr;
429 real ewaldcoeff_q
= 0;
430 real ewaldcoeff_lj
= 0;
431 gmx_vsite_t
*vsite
= nullptr;
433 int nChargePerturbed
= -1, nTypePerturbed
= 0;
434 gmx_wallcycle_t wcycle
;
435 gmx_walltime_accounting_t walltime_accounting
= nullptr;
437 gmx_int64_t reset_counters
;
438 int nthreads_pme
= 1;
439 gmx_membed_t
* membed
= nullptr;
440 gmx_hw_info_t
*hwinfo
= nullptr;
442 /* CAUTION: threads may be started later on in this function, so
443 cr doesn't reflect the final parallel state right now */
444 gmx::MDModules mdModules
;
445 t_inputrec inputrecInstance
;
446 t_inputrec
*inputrec
= &inputrecInstance
;
449 if (mdrunOptions
.continuationOptions
.appendFiles
)
454 bool doMembed
= opt2bSet("-membed", nfile
, fnm
);
455 bool doRerun
= mdrunOptions
.rerun
;
457 // Handle task-assignment related user options.
458 EmulateGpuNonbonded emulateGpuNonbonded
= (getenv("GMX_EMULATE_GPU") != nullptr ?
459 EmulateGpuNonbonded::Yes
: EmulateGpuNonbonded::No
);
460 std::vector
<int> gpuIdsAvailable
;
463 gpuIdsAvailable
= parseUserGpuIds(hw_opt
.gpuIdsAvailable
);
464 // TODO We could put the GPU IDs into a std::map to find
465 // duplicates, but for the small numbers of IDs involved, this
466 // code is simple and fast.
467 for (size_t i
= 0; i
!= gpuIdsAvailable
.size(); ++i
)
469 for (size_t j
= i
+1; j
!= gpuIdsAvailable
.size(); ++j
)
471 if (gpuIdsAvailable
[i
] == gpuIdsAvailable
[j
])
473 GMX_THROW(InvalidInputError(formatString("The string of available GPU device IDs '%s' may not contain duplicate device IDs", hw_opt
.gpuIdsAvailable
.c_str())));
478 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
;
480 std::vector
<int> userGpuTaskAssignment
;
483 userGpuTaskAssignment
= parseUserGpuIds(hw_opt
.userGpuTaskAssignment
);
485 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
;
486 auto nonbondedTarget
= findTaskTarget(nbpu_opt
);
487 // TODO Connect these to actual mdrun arguments and some functionality
488 const char *pme_opt
= "cpu";
489 auto pmeTarget
= findTaskTarget(pme_opt
);
491 // TODO find a sensible home and behaviour for this
492 //const char *pme_fft_opt = "auto";
493 //auto pmeFftTarget = findTaskTarget(pme_fft_opt);
495 const PmeRunMode pmeRunMode
= PmeRunMode::CPU
;
496 //TODO this is a placeholder as PME on GPU is not permitted yet
497 //TODO should there exist a PmeRunMode::None value for consistency?
499 // Here we assume that SIMMASTER(cr) does not change even after the
500 // threads are started.
501 gmx::LoggerOwner
logOwner(buildLogger(fplog
, cr
));
502 gmx::MDLogger
mdlog(logOwner
.logger());
504 hwinfo
= gmx_detect_hardware(mdlog
, cr
);
506 gmx_print_detected_hardware(fplog
, cr
, mdlog
, hwinfo
);
508 std::vector
<int> gpuIdsToUse
;
509 auto compatibleGpus
= getCompatibleGpus(hwinfo
->gpu_info
);
510 if (gpuIdsAvailable
.empty())
512 gpuIdsToUse
= compatibleGpus
;
516 for (const auto &availableGpuId
: gpuIdsAvailable
)
518 bool availableGpuIsCompatible
= false;
519 for (const auto &compatibleGpuId
: compatibleGpus
)
521 if (availableGpuId
== compatibleGpuId
)
523 availableGpuIsCompatible
= true;
527 if (!availableGpuIsCompatible
)
529 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
);
531 gpuIdsToUse
.push_back(availableGpuId
);
535 if (fplog
!= nullptr)
537 /* Print references after all software/hardware printing */
538 please_cite(fplog
, "Abraham2015");
539 please_cite(fplog
, "Pall2015");
540 please_cite(fplog
, "Pronk2013");
541 please_cite(fplog
, "Hess2008b");
542 please_cite(fplog
, "Spoel2005a");
543 please_cite(fplog
, "Lindahl2001a");
544 please_cite(fplog
, "Berendsen95a");
547 std::unique_ptr
<t_state
> globalState
;
551 /* Only the master rank has the global state */
552 globalState
= std::unique_ptr
<t_state
>(new t_state
);
554 /* Read (nearly) all data required for the simulation */
555 read_tpx_state(ftp2fn(efTPR
, nfile
, fnm
), inputrec
, globalState
.get(), mtop
);
557 if (inputrec
->cutoff_scheme
!= ecutsVERLET
)
559 if (nstlist_cmdline
> 0)
561 gmx_fatal(FARGS
, "Can not set nstlist with the group cut-off scheme");
564 if (!compatibleGpus
.empty())
566 GMX_LOG(mdlog
.warning
).asParagraph().appendText(
567 "NOTE: GPU(s) found, but the current simulation can not use GPUs\n"
568 " To use a GPU, set the mdp option: cutoff-scheme = Verlet");
573 /* Check and update the hardware options for internal consistency */
574 check_and_update_hw_opt_1(&hw_opt
, cr
, domdecOptions
.numPmeRanks
);
576 /* Early check for externally set process affinity. */
577 gmx_check_thread_affinity_set(mdlog
, cr
,
578 &hw_opt
, hwinfo
->nthreads_hw_avail
, FALSE
);
580 if (GMX_THREAD_MPI
&& SIMMASTER(cr
))
582 if (domdecOptions
.numPmeRanks
> 0 && hw_opt
.nthreads_tmpi
<= 0)
584 gmx_fatal(FARGS
, "You need to explicitly specify the number of MPI threads (-ntmpi) when using separate PME ranks");
587 /* Since the master knows the cut-off scheme, update hw_opt for this.
588 * This is done later for normal MPI and also once more with tMPI
589 * for all tMPI ranks.
591 check_and_update_hw_opt_2(&hw_opt
, inputrec
->cutoff_scheme
);
593 bool useGpuForNonbonded
= false;
594 bool useGpuForPme
= false;
597 // If the user specified the number of ranks, then we must
598 // respect that, but in default mode, we need to allow for
599 // the number of GPUs to choose the number of ranks.
601 useGpuForNonbonded
= decideWhetherToUseGpusForNonbondedWithThreadMpi
602 (nonbondedTarget
, gpuIdsToUse
, userGpuTaskAssignment
, emulateGpuNonbonded
,
603 inputrec
->cutoff_scheme
== ecutsVERLET
,
604 gpuAccelerationOfNonbondedIsUseful(mdlog
, inputrec
, doRerun
),
605 hw_opt
.nthreads_tmpi
);
606 auto inputSystemHasPme
= EEL_PME(inputrec
->coulombtype
) || EVDW_PME(inputrec
->vdwtype
);
607 auto canUseGpuForPme
= inputSystemHasPme
&& pme_gpu_supports_input(inputrec
, nullptr);
608 useGpuForPme
= decideWhetherToUseGpusForPmeWithThreadMpi
609 (useGpuForNonbonded
, pmeTarget
, gpuIdsToUse
, userGpuTaskAssignment
,
610 canUseGpuForPme
, hw_opt
.nthreads_tmpi
);
612 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
;
613 /* Determine how many thread-MPI ranks to start.
615 * TODO Over-writing the user-supplied value here does
616 * prevent any possible subsequent checks from working
618 hw_opt
.nthreads_tmpi
= get_nthreads_mpi(hwinfo
,
627 // Now start the threads for thread MPI.
628 cr
= spawnThreads(hw_opt
.nthreads_tmpi
);
629 /* The main thread continues here with a new cr. We don't deallocate
630 the old cr because other threads may still be reading it. */
631 // TODO Both master and spawned threads call dup_tfn and
632 // reinitialize_commrec_for_this_thread. Find a way to express
635 /* END OF CAUTION: cr is now reliable */
639 /* now broadcast everything to the non-master nodes/threads: */
640 init_parallel(cr
, inputrec
, mtop
);
643 // Now each rank knows the inputrec that SIMMASTER read and used,
644 // and (if applicable) cr->nnodes has been assigned the number of
645 // thread-MPI ranks that have been chosen. The ranks can now all
646 // run the task-deciding functions and will agree on the result
647 // without needing to communicate.
649 // TODO Should we do the communication in debug mode to support
650 // having an assertion?
652 // Note that these variables describe only their own node.
653 bool useGpuForNonbonded
= false;
654 bool useGpuForPme
= false;
657 useGpuForNonbonded
= decideWhetherToUseGpusForNonbonded(nonbondedTarget
, gpuIdsToUse
, userGpuTaskAssignment
,
658 emulateGpuNonbonded
, inputrec
->cutoff_scheme
== ecutsVERLET
,
659 gpuAccelerationOfNonbondedIsUseful(mdlog
, inputrec
, doRerun
));
660 auto inputSystemHasPme
= EEL_PME(inputrec
->coulombtype
) || EVDW_PME(inputrec
->vdwtype
);
661 auto canUseGpuForPme
= inputSystemHasPme
&& pme_gpu_supports_input(inputrec
, nullptr);
662 useGpuForPme
= decideWhetherToUseGpusForPme(useGpuForNonbonded
, pmeTarget
, userGpuTaskAssignment
, canUseGpuForPme
, cr
->nnodes
);
664 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
;
666 // TODO: Error handling
667 mdModules
.assignOptionsToModules(*inputrec
->params
, nullptr);
669 if (fplog
!= nullptr)
671 pr_inputrec(fplog
, 0, "Input Parameters", inputrec
, FALSE
);
672 fprintf(fplog
, "\n");
677 /* now make sure the state is initialized and propagated */
678 set_state_entries(globalState
.get(), inputrec
);
681 /* NM and TPI parallelize over force/energy calculations, not atoms,
682 * so we need to initialize and broadcast the global state.
684 if (inputrec
->eI
== eiNM
|| inputrec
->eI
== eiTPI
)
688 globalState
= std::unique_ptr
<t_state
>(new t_state
);
690 broadcastStateWithoutDynamics(cr
, globalState
.get());
693 /* A parallel command line option consistency check that we can
694 only do after any threads have started. */
695 if (!PAR(cr
) && (domdecOptions
.numCells
[XX
] > 1 ||
696 domdecOptions
.numCells
[YY
] > 1 ||
697 domdecOptions
.numCells
[ZZ
] > 1 ||
698 domdecOptions
.numPmeRanks
> 0))
701 "The -dd or -npme option request a parallel simulation, "
703 "but %s was compiled without threads or MPI enabled"
706 "but the number of MPI-threads (option -ntmpi) is not set or is 1"
708 "but %s was not started through mpirun/mpiexec or only one rank was requested through mpirun/mpiexec"
711 , output_env_get_program_display_name(oenv
)
716 (EI_ENERGY_MINIMIZATION(inputrec
->eI
) || eiNM
== inputrec
->eI
))
718 gmx_fatal(FARGS
, "The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun");
721 if (can_use_allvsall(inputrec
, TRUE
, cr
, fplog
) && DOMAINDECOMP(cr
))
723 gmx_fatal(FARGS
, "All-vs-all loops do not work with domain decomposition, use a single MPI rank");
726 if (!(EEL_PME(inputrec
->coulombtype
) || EVDW_PME(inputrec
->vdwtype
)))
728 if (domdecOptions
.numPmeRanks
> 0)
730 gmx_fatal_collective(FARGS
, cr
->mpi_comm_mysim
, MASTER(cr
),
731 "PME-only ranks are requested, but the system does not use PME for electrostatics or LJ");
734 domdecOptions
.numPmeRanks
= 0;
737 if (useGpuForNonbonded
&& domdecOptions
.numPmeRanks
< 0)
739 /* With GPUs we don't automatically use PME-only ranks. PME ranks can
740 * improve performance with many threads per GPU, since our OpenMP
741 * scaling is bad, but it's difficult to automate the setup.
743 domdecOptions
.numPmeRanks
= 0;
749 fcRegisterSteps(inputrec
->nsteps
, inputrec
->init_step
);
753 /* NMR restraints must be initialized before load_checkpoint,
754 * since with time averaging the history is added to t_state.
755 * For proper consistency check we therefore need to extend
757 * So the PME-only nodes (if present) will also initialize
758 * the distance restraints.
762 /* This needs to be called before read_checkpoint to extend the state */
763 init_disres(fplog
, mtop
, inputrec
, cr
, fcd
, globalState
.get(), replExParams
.exchangeInterval
> 0);
765 init_orires(fplog
, mtop
, inputrec
, cr
, globalState
.get(), &(fcd
->orires
));
767 if (inputrecDeform(inputrec
))
769 /* Store the deform reference box before reading the checkpoint */
772 copy_mat(globalState
->box
, box
);
776 gmx_bcast(sizeof(box
), box
, cr
);
778 /* Because we do not have the update struct available yet
779 * in which the reference values should be stored,
780 * we store them temporarily in static variables.
781 * This should be thread safe, since they are only written once
782 * and with identical values.
784 tMPI_Thread_mutex_lock(&deform_init_box_mutex
);
785 deform_init_init_step_tpx
= inputrec
->init_step
;
786 copy_mat(box
, deform_init_box_tpx
);
787 tMPI_Thread_mutex_unlock(&deform_init_box_mutex
);
790 ObservablesHistory observablesHistory
= {};
792 ContinuationOptions
&continuationOptions
= mdrunOptions
.continuationOptions
;
794 if (continuationOptions
.startedFromCheckpoint
)
796 /* Check if checkpoint file exists before doing continuation.
797 * This way we can use identical input options for the first and subsequent runs...
801 load_checkpoint(opt2fn_master("-cpi", nfile
, fnm
, cr
), &fplog
,
802 cr
, domdecOptions
.numCells
,
803 inputrec
, globalState
.get(),
804 &bReadEkin
, &observablesHistory
,
805 continuationOptions
.appendFiles
,
806 continuationOptions
.appendFilesOptionSet
,
807 mdrunOptions
.reproducible
);
811 continuationOptions
.haveReadEkin
= true;
815 if (SIMMASTER(cr
) && continuationOptions
.appendFiles
)
817 gmx_log_open(ftp2fn(efLOG
, nfile
, fnm
), cr
,
818 continuationOptions
.appendFiles
, &fplog
);
819 logOwner
= buildLogger(fplog
, nullptr);
820 mdlog
= logOwner
.logger();
823 /* override nsteps with value set on the commamdline */
824 override_nsteps_cmdline(mdlog
, mdrunOptions
.numStepsCommandline
, inputrec
);
828 copy_mat(globalState
->box
, box
);
833 gmx_bcast(sizeof(box
), box
, cr
);
836 /* Update rlist and nstlist. */
837 if (inputrec
->cutoff_scheme
== ecutsVERLET
)
839 prepare_verlet_scheme(fplog
, cr
, inputrec
, nstlist_cmdline
, mtop
, box
,
840 useGpuForNonbonded
|| (emulateGpuNonbonded
== EmulateGpuNonbonded::Yes
), *hwinfo
->cpuInfo
);
843 if (PAR(cr
) && !(EI_TPI(inputrec
->eI
) ||
844 inputrec
->eI
== eiNM
))
846 const rvec
*xOnMaster
= (SIMMASTER(cr
) ? as_rvec_array(globalState
->x
.data()) : nullptr);
848 cr
->dd
= init_domain_decomposition(fplog
, cr
, domdecOptions
, mdrunOptions
,
851 &ddbox
, &npme_major
, &npme_minor
);
852 // Note that local state still does not exist yet.
856 /* PME, if used, is done on all nodes with 1D decomposition */
858 cr
->duty
= (DUTY_PP
| DUTY_PME
);
862 if (inputrec
->ePBC
== epbcSCREW
)
865 "pbc=%s is only implemented with domain decomposition",
866 epbc_names
[inputrec
->ePBC
]);
872 /* After possible communicator splitting in make_dd_communicators.
873 * we can set up the intra/inter node communication.
875 gmx_setup_nodecomm(fplog
, cr
);
878 /* Initialize per-physical-node MPI process/thread ID and counters. */
879 gmx_init_intranode_counters(cr
);
883 GMX_LOG(mdlog
.warning
).asParagraph().appendTextFormatted(
884 "This is simulation %d out of %d running as a composite GROMACS\n"
885 "multi-simulation job. Setup for this simulation:\n",
886 cr
->ms
->sim
, cr
->ms
->nsim
);
888 GMX_LOG(mdlog
.warning
).appendTextFormatted(
892 cr
->nnodes
== 1 ? "thread" : "threads"
894 cr
->nnodes
== 1 ? "process" : "processes"
900 /* Check and update hw_opt for the cut-off scheme */
901 check_and_update_hw_opt_2(&hw_opt
, inputrec
->cutoff_scheme
);
903 /* Check and update the number of OpenMP threads requested */
904 checkAndUpdateRequestedNumOpenmpThreads(&hw_opt
, *hwinfo
, cr
, pmeRunMode
, *mtop
);
906 gmx_omp_nthreads_init(mdlog
, cr
,
907 hwinfo
->nthreads_hw_avail
,
909 hw_opt
.nthreads_omp_pme
,
910 !thisRankHasDuty(cr
, DUTY_PP
),
911 inputrec
->cutoff_scheme
== ecutsVERLET
);
914 if (EI_TPI(inputrec
->eI
) &&
915 inputrec
->cutoff_scheme
== ecutsVERLET
)
917 gmx_feenableexcept();
921 // Build a data structure that expresses which kinds of non-bonded
922 // task are handled by this rank.
924 // TODO Later, this might become a loop over all registered modules
925 // relevant to the mdp inputs, to find those that have such tasks.
927 // TODO This could move before init_domain_decomposition() as part
928 // of refactoring that separates the responsibility for duty
929 // assignment from setup for communication between tasks, and
930 // setup for tasks handled with a domain (ie including short-ranged
931 // tasks, bonded tasks, etc.).
933 // Note that in general useGpuForNonbonded, etc. can have a value
934 // that is inconsistent with the presence of actual GPUs on any
935 // rank, and that is not known to be a problem until the
936 // duty of the ranks on a node become node.
938 // TODO Later we might need the concept of computeTasksOnThisRank,
939 // from which we construct gpuTasksOnThisRank.
941 // Currently the DD code assigns duty to ranks that can
942 // include PP work that currently can be executed on a single
943 // GPU, if present and compatible. This has to be coordinated
944 // across PP ranks on a node, with possible multiple devices
945 // or sharing devices on a node, either from the user
946 // selection, or automatically.
947 auto haveGpus
= !gpuIdsToUse
.empty();
948 std::vector
<GpuTask
> gpuTasksOnThisRank
;
949 if (thisRankHasDuty(cr
, DUTY_PP
))
951 if (useGpuForNonbonded
)
955 gpuTasksOnThisRank
.push_back(GpuTask::Nonbonded
);
957 else if (nonbondedTarget
== TaskTarget::Gpu
)
959 gmx_fatal(FARGS
, "Cannot run short-ranged nonbonded interactions on a GPU because there is none detected.");
963 // TODO cr->duty & DUTY_PME should imply that a PME algorithm is active, but currently does not.
964 if (EEL_PME(inputrec
->coulombtype
) && (thisRankHasDuty(cr
, DUTY_PME
)))
970 gpuTasksOnThisRank
.push_back(GpuTask::Pme
);
972 else if (pmeTarget
== TaskTarget::Gpu
)
974 gmx_fatal(FARGS
, "Cannot run PME on a GPU because there is none detected.");
979 GpuTaskAssignment gpuTaskAssignment
;
982 // Produce the task assignment for this rank.
983 gpuTaskAssignment
= runTaskAssignment(gpuIdsToUse
, userGpuTaskAssignment
, *hwinfo
,
984 mdlog
, cr
, gpuTasksOnThisRank
);
986 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
;
988 /* Prevent other ranks from continuing after an issue was found
989 * and reported as a fatal error.
991 * TODO This function implements a barrier so that MPI runtimes
992 * can organize an orderly shutdown if one of the ranks has had to
993 * issue a fatal error in various code already run. When we have
994 * MPI-aware error handling and reporting, this should be
999 MPI_Barrier(cr
->mpi_comm_mysim
);
1003 MPI_Barrier(cr
->ms
->mpi_comm_masters
);
1007 /* Now that we know the setup is consistent, check for efficiency */
1008 check_resource_division_efficiency(hwinfo
, hw_opt
.nthreads_tot
, !gpuTaskAssignment
.empty(), mdrunOptions
.ntompOptionIsSet
,
1011 gmx_device_info_t
*nonbondedDeviceInfo
= nullptr;
1012 int nonbondedDeviceId
= -1;
1013 if (thisRankHasDuty(cr
, DUTY_PP
))
1015 if (!gpuTaskAssignment
.empty())
1017 GMX_RELEASE_ASSERT(gpuTaskAssignment
.size() == 1, "A valid GPU assignment can only have one task per rank");
1018 GMX_RELEASE_ASSERT(gpuTaskAssignment
[0].task_
== gmx::GpuTask::Nonbonded
, "A valid GPU assignment can only include short-ranged tasks");
1019 nonbondedDeviceId
= gpuTaskAssignment
[0].deviceId_
;
1020 nonbondedDeviceInfo
= getDeviceInfo(hwinfo
->gpu_info
, nonbondedDeviceId
);
1024 if (DOMAINDECOMP(cr
))
1026 /* When we share GPUs over ranks, we need to know this for the DLB */
1027 dd_setup_dlb_resource_sharing(cr
, nonbondedDeviceId
);
1030 /* getting number of PP/PME threads
1031 PME: env variable should be read only on one node to make sure it is
1032 identical everywhere;
1034 nthreads_pme
= gmx_omp_nthreads_get(emntPME
);
1036 wcycle
= wallcycle_init(fplog
, mdrunOptions
.timingOptions
.resetStep
, cr
);
1040 /* Master synchronizes its value of reset_counters with all nodes
1041 * including PME only nodes */
1042 reset_counters
= wcycle_get_reset_counters(wcycle
);
1043 gmx_bcast_sim(sizeof(reset_counters
), &reset_counters
, cr
);
1044 wcycle_set_reset_counters(wcycle
, reset_counters
);
1047 // Membrane embedding must be initialized before we call init_forcerec()
1052 fprintf(stderr
, "Initializing membed");
1054 /* Note that membed cannot work in parallel because mtop is
1055 * changed here. Fix this if we ever want to make it run with
1056 * multiple ranks. */
1057 membed
= init_membed(fplog
, nfile
, fnm
, mtop
, inputrec
, globalState
.get(), cr
, &mdrunOptions
.checkpointOptions
.period
);
1060 std::unique_ptr
<MDAtoms
> mdAtoms
;
1063 if (thisRankHasDuty(cr
, DUTY_PP
))
1065 /* Initiate forcerecord */
1067 fr
->forceProviders
= mdModules
.initForceProviders();
1068 init_forcerec(fplog
, mdlog
, fr
, fcd
,
1069 inputrec
, mtop
, cr
, box
,
1070 opt2fn("-table", nfile
, fnm
),
1071 opt2fn("-tablep", nfile
, fnm
),
1072 getFilenm("-tableb", nfile
, fnm
),
1073 nonbondedDeviceInfo
,
1077 /* Initialize QM-MM */
1080 init_QMMMrec(cr
, mtop
, inputrec
, fr
);
1083 /* Initialize the mdAtoms structure.
1084 * mdAtoms is not filled with atom data,
1085 * as this can not be done now with domain decomposition.
1087 const bool useGpuForPme
= (pmeRunMode
== PmeRunMode::GPU
) || (pmeRunMode
== PmeRunMode::Hybrid
);
1088 mdAtoms
= makeMDAtoms(fplog
, *mtop
, *inputrec
, useGpuForPme
&& thisRankHasDuty(cr
, DUTY_PME
));
1091 // The pinning of coordinates in the global state object works, because we only use
1092 // PME on GPU without DD or on a separate PME rank, and because the local state pointer
1093 // points to the global state object without DD.
1094 // FIXME: MD and EM separately set up the local state - this should happen in the same function,
1095 // which should also perform the pinning.
1096 changePinningPolicy(&globalState
->x
, useGpuForPme
? PinningPolicy::CanBePinned
: PinningPolicy::CannotBePinned
);
1099 /* Initialize the virtual site communication */
1100 vsite
= initVsite(*mtop
, cr
);
1102 calc_shifts(box
, fr
->shift_vec
);
1104 /* With periodic molecules the charge groups should be whole at start up
1105 * and the virtual sites should not be far from their proper positions.
1107 if (!inputrec
->bContinuation
&& MASTER(cr
) &&
1108 !(inputrec
->ePBC
!= epbcNONE
&& inputrec
->bPeriodicMols
))
1110 /* Make molecules whole at start of run */
1111 if (fr
->ePBC
!= epbcNONE
)
1113 rvec
*xGlobal
= as_rvec_array(globalState
->x
.data());
1114 do_pbc_first_mtop(fplog
, inputrec
->ePBC
, box
, mtop
, xGlobal
);
1118 /* Correct initial vsite positions are required
1119 * for the initial distribution in the domain decomposition
1120 * and for the initial shell prediction.
1122 constructVsitesGlobal(*mtop
, globalState
->x
);
1126 if (EEL_PME(fr
->ic
->eeltype
) || EVDW_PME(fr
->ic
->vdwtype
))
1128 ewaldcoeff_q
= fr
->ic
->ewaldcoeff_q
;
1129 ewaldcoeff_lj
= fr
->ic
->ewaldcoeff_lj
;
1134 /* This is a PME only node */
1136 GMX_ASSERT(globalState
== nullptr, "We don't need the state on a PME only rank and expect it to be unitialized");
1138 ewaldcoeff_q
= calc_ewaldcoeff_q(inputrec
->rcoulomb
, inputrec
->ewald_rtol
);
1139 ewaldcoeff_lj
= calc_ewaldcoeff_lj(inputrec
->rvdw
, inputrec
->ewald_rtol_lj
);
1142 gmx_pme_t
*sepPmeData
= nullptr;
1143 // This reference hides the fact that PME data is owned by runner on PME-only ranks and by forcerec on other ranks
1144 GMX_ASSERT(thisRankHasDuty(cr
, DUTY_PP
) == (fr
!= nullptr), "Double-checking that only PME-only ranks have no forcerec");
1145 gmx_pme_t
* &pmedata
= fr
? fr
->pmedata
: sepPmeData
;
1147 if (hw_opt
.thread_affinity
!= threadaffOFF
)
1149 /* Before setting affinity, check whether the affinity has changed
1150 * - which indicates that probably the OpenMP library has changed it
1151 * since we first checked).
1153 gmx_check_thread_affinity_set(mdlog
, cr
,
1154 &hw_opt
, hwinfo
->nthreads_hw_avail
, TRUE
);
1157 /* threads on this MPI process or TMPI thread */
1158 if (thisRankHasDuty(cr
, DUTY_PP
))
1160 nthread_local
= gmx_omp_nthreads_get(emntNonbonded
);
1164 nthread_local
= gmx_omp_nthreads_get(emntPME
);
1167 /* Set the CPU affinity */
1168 gmx_set_thread_affinity(mdlog
, cr
, &hw_opt
, *hwinfo
->hardwareTopology
,
1169 nthread_local
, nullptr);
1172 /* Initiate PME if necessary,
1173 * either on all nodes or on dedicated PME nodes only. */
1174 if (EEL_PME(inputrec
->coulombtype
) || EVDW_PME(inputrec
->vdwtype
))
1176 if (mdAtoms
&& mdAtoms
->mdatoms())
1178 nChargePerturbed
= mdAtoms
->mdatoms()->nChargePerturbed
;
1179 if (EVDW_PME(inputrec
->vdwtype
))
1181 nTypePerturbed
= mdAtoms
->mdatoms()->nTypePerturbed
;
1184 if (cr
->npmenodes
> 0)
1186 /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
1187 gmx_bcast_sim(sizeof(nChargePerturbed
), &nChargePerturbed
, cr
);
1188 gmx_bcast_sim(sizeof(nTypePerturbed
), &nTypePerturbed
, cr
);
1191 if (thisRankHasDuty(cr
, DUTY_PME
))
1195 gmx_device_info_t
*pmeGpuInfo
= nullptr;
1196 pmedata
= gmx_pme_init(cr
, npme_major
, npme_minor
, inputrec
,
1197 mtop
? mtop
->natoms
: 0, nChargePerturbed
, nTypePerturbed
,
1198 mdrunOptions
.reproducible
,
1199 ewaldcoeff_q
, ewaldcoeff_lj
,
1201 pmeRunMode
, nullptr, pmeGpuInfo
, mdlog
);
1203 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
;
1208 if (EI_DYNAMICS(inputrec
->eI
))
1210 /* Turn on signal handling on all nodes */
1212 * (A user signal from the PME nodes (if any)
1213 * is communicated to the PP nodes.
1215 signal_handler_install();
1218 if (thisRankHasDuty(cr
, DUTY_PP
))
1220 /* Assumes uniform use of the number of OpenMP threads */
1221 walltime_accounting
= walltime_accounting_init(gmx_omp_nthreads_get(emntDefault
));
1223 if (inputrec
->bPull
)
1225 /* Initialize pull code */
1226 inputrec
->pull_work
=
1227 init_pull(fplog
, inputrec
->pull
, inputrec
, nfile
, fnm
,
1228 mtop
, cr
, oenv
, inputrec
->fepvals
->init_lambda
,
1229 EI_DYNAMICS(inputrec
->eI
) && MASTER(cr
),
1230 continuationOptions
);
1235 /* Initialize enforced rotation code */
1236 init_rot(fplog
, inputrec
, nfile
, fnm
, cr
, globalState
.get(), mtop
, oenv
, mdrunOptions
);
1239 /* Let init_constraints know whether we have essential dynamics constraints.
1240 * TODO: inputrec should tell us whether we use an algorithm, not a file option or the checkpoint
1242 bool doEdsam
= (opt2fn_null("-ei", nfile
, fnm
) != nullptr || observablesHistory
.edsamHistory
);
1244 constr
= init_constraints(fplog
, mtop
, inputrec
, doEdsam
, cr
);
1246 if (DOMAINDECOMP(cr
))
1248 GMX_RELEASE_ASSERT(fr
, "fr was NULL while cr->duty was DUTY_PP");
1249 /* This call is not included in init_domain_decomposition mainly
1250 * because fr->cginfo_mb is set later.
1252 dd_init_bondeds(fplog
, cr
->dd
, mtop
, vsite
, inputrec
,
1253 domdecOptions
.checkBondedInteractions
,
1257 /* Now do whatever the user wants us to do (how flexible...) */
1258 my_integrator(inputrec
->eI
) (fplog
, cr
, mdlog
, nfile
, fnm
,
1262 mdModules
.outputProvider(),
1266 &observablesHistory
,
1267 mdAtoms
.get(), nrnb
, wcycle
, fr
,
1270 walltime_accounting
);
1274 finish_rot(inputrec
->rot
);
1277 if (inputrec
->bPull
)
1279 finish_pull(inputrec
->pull_work
);
1285 GMX_RELEASE_ASSERT(pmedata
, "pmedata was NULL while cr->duty was not DUTY_PP");
1287 walltime_accounting
= walltime_accounting_init(gmx_omp_nthreads_get(emntPME
));
1288 gmx_pmeonly(pmedata
, cr
, nrnb
, wcycle
, walltime_accounting
, inputrec
, pmeRunMode
);
1291 wallcycle_stop(wcycle
, ewcRUN
);
1293 /* Finish up, write some stuff
1294 * if rerunMD, don't write last frame again
1296 finish_run(fplog
, mdlog
, cr
,
1297 inputrec
, nrnb
, wcycle
, walltime_accounting
,
1298 fr
? fr
->nbv
: nullptr,
1300 EI_DYNAMICS(inputrec
->eI
) && !MULTISIM(cr
));
1305 gmx_pme_destroy(pmedata
);
1309 /* Free GPU memory and context */
1310 free_gpu_resources(fr
, cr
, nonbondedDeviceInfo
);
1314 free_membed(membed
);
1317 gmx_hardware_info_free();
1319 /* Does what it says */
1320 print_date_and_time(fplog
, cr
->nodeid
, "Finished mdrun", gmx_gettime());
1321 walltime_accounting_destroy(walltime_accounting
);
1323 /* Close logfile already here if we were appending to it */
1324 if (MASTER(cr
) && continuationOptions
.appendFiles
)
1326 gmx_log_close(fplog
);
1329 rc
= (int)gmx_get_stop_condition();
1332 /* we need to join all threads. The sub-threads join when they
1333 exit this function, but the master thread needs to be told to
1335 if (PAR(cr
) && MASTER(cr
))