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35 /*! \libinternal \file
37 * \brief Declares the routine running the inetgrators.
39 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
40 * \ingroup module_mdrun
42 #ifndef GMX_MDRUN_RUNNER_H
43 #define GMX_MDRUN_RUNNER_H
50 #include "gromacs/commandline/filenm.h"
51 #include "gromacs/compat/pointers.h"
52 #include "gromacs/domdec/options.h"
53 #include "gromacs/hardware/hw_info.h"
54 #include "gromacs/math/vec.h"
55 #include "gromacs/mdrun/mdmodules.h"
56 #include "gromacs/mdrun/simulationinputhandle.h"
57 #include "gromacs/mdrunutility/handlerestart.h"
58 #include "gromacs/mdtypes/mdrunoptions.h"
59 #include "gromacs/utility/arrayref.h"
60 #include "gromacs/utility/basedefinitions.h"
61 #include "gromacs/utility/gmxmpi.h"
62 #include "gromacs/utility/real.h"
64 #include "replicaexchange.h"
66 struct gmx_multisim_t;
67 struct gmx_output_env_t;
68 struct ReplicaExchangeParameters;
74 // Todo: move to forward declaration headers...
76 class IRestraintPotential; // defined in restraint/restraintpotential.h
77 class RestraintManager;
78 class SimulationContext;
79 class StopHandlerBuilder;
81 /*! \libinternal \brief Runner object for supporting setup and execution of mdrun.
83 * This class has responsibility for the lifetime of data structures
84 * that exist for the life of the simulation, e.g. for logging and
87 * It is also responsible for initializing data members that
88 * e.g. correspond to values potentially set by commmand-line
89 * options. Later these will be obtained directly from modules, and
90 * the results of command-line option handling returned directly to
91 * the modules, rather than propagated to them by data members of this
94 * \todo Most of the attributes should be declared by specific modules
95 * as command-line options. Accordingly, they do not conform to the
96 * naming scheme, because that would make for a lot of noise in the
97 * diff, only to have it change again when the options move to their
100 * \todo Preparing logging and MPI contexts could probably be a
101 * higher-level responsibility, so that an Mdrunner would get made
102 * without needing to re-initialize these components (as currently
103 * happens always for the master rank, and differently for the spawned
104 * ranks with thread-MPI).
106 * \ingroup module_mdrun
111 /*! \brief Builder class to manage object creation.
113 * This class is a member of gmx::Mdrunner so that it can initialize
114 * private members of gmx::Mdrunner.
116 * It is non-trivial to establish an initialized gmx::Mdrunner invariant,
117 * so objects can be obtained by clients using a Builder or a move.
118 * Clients cannot default initialize or copy gmx::Mdrunner.
120 class BuilderImplementation;
125 * \brief Copy not allowed.
127 * An Mdrunner has unique resources and it is not clear whether any of
128 * one of those resources should be duplicated or shared unless the
129 * specific use case is known. Either build a fresh runner or use a
130 * helper function for clearly indicated behavior. API clarification may
131 * allow unambiguous initialization by copy in future versions.
135 Mdrunner(const Mdrunner&) = delete;
136 Mdrunner& operator=(const Mdrunner&) = delete;
140 * \brief Mdrunner objects can be passed by value via move semantics.
142 * \param handle runner instance to be moved from.
145 Mdrunner(Mdrunner&& handle) noexcept;
146 Mdrunner& operator=(Mdrunner&& handle) noexcept;
149 /*! \brief Driver routine, that calls the different simulation methods. */
151 * Currently, thread-MPI does not spawn threads until during mdrunner() and parallelism
152 * is not initialized until some time during this call...
157 * \brief Add a potential to be evaluated during MD integration.
159 * \param restraint MD restraint potential to apply
160 * \param name User-friendly plain-text name to uniquely identify the puller
162 * This implementation attaches an object providing the gmx::IRestraintPotential
164 * \todo Mdrunner should fetch such resources from the SimulationContext
165 * rather than offering this public interface.
167 void addPotential(std::shared_ptr<IRestraintPotential> restraint, const std::string& name);
169 /*! \brief Prepare the thread-MPI communicator to have \c
170 * numThreadsToLaunch ranks, by spawning new thread-MPI
173 * Called by mdrunner() to start a specific number of threads
174 * (including the main thread) for thread-parallel runs. This
175 * in turn calls mdrunner() for each thread. */
176 void spawnThreads(int numThreadsToLaunch);
178 /*! \brief Initializes a new Mdrunner from the master.
180 * Run this method in a new thread from a master runner to get additional
181 * workers on spawned threads.
183 * \returns New Mdrunner instance suitable for thread-MPI work on new ranks.
186 * \todo clarify (multiple) invariants during MD runner start-up.
187 * The runner state before and after launching threads is distinct enough that
188 * it should be codified in the invariants of different classes. That would
189 * mean that the object returned by this method would be of a different type
190 * than the object held by the client up to the point of call, and its name
191 * would be changed to "launchOnSpawnedThread" or something not including the
194 Mdrunner cloneOnSpawnedThread() const;
197 /*! \brief Constructor. */
198 explicit Mdrunner(std::unique_ptr<MDModules> mdModules);
200 //! Parallelism-related user options.
203 //! Filenames and properties from command-line argument values.
204 ArrayRef<const t_filenm> filenames;
206 /*! \brief Output context for writing text files
209 * \todo push this data member down when the information can be queried from an encapsulated resource.
211 gmx_output_env_t* oenv = nullptr;
212 //! Ongoing collection of mdrun options
213 MdrunOptions mdrunOptions;
214 //! Options for the domain decomposition.
215 DomdecOptions domdecOptions;
217 /*! \brief Target short-range interations for "cpu", "gpu", or "auto". Default is "auto".
220 * \todo replace with string or enum class and initialize with sensible value.
222 const char* nbpu_opt = nullptr;
224 /*! \brief Target long-range interactions for "cpu", "gpu", or "auto". Default is "auto".
227 * \todo replace with string or enum class and initialize with sensible value.
229 const char* pme_opt = nullptr;
231 /*! \brief Target long-range interactions FFT/solve stages for "cpu", "gpu", or "auto". Default is "auto".
234 * \todo replace with string or enum class and initialize with sensible value.
236 const char* pme_fft_opt = nullptr;
238 /*! \brief Target bonded interations for "cpu", "gpu", or "auto". Default is "auto".
241 * \todo replace with string or enum class and initialize with sensible value.
243 const char* bonded_opt = nullptr;
245 /*! \brief Target update calculation for "cpu", "gpu", or "auto". Default is "auto".
248 * \todo replace with string or enum class and initialize with sensible value.
250 const char* update_opt = nullptr;
252 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
253 int nstlist_cmdline = 0;
254 //! Parameters for replica-exchange simulations.
255 ReplicaExchangeParameters replExParams;
256 //! Print a warning if any force is larger than this (in kJ/mol nm).
259 //! Handle to file used for logging.
260 LogFilePtr logFileGuard = nullptr;
261 //! \brief Non-owning handle to file used for logging.
262 t_fileio* logFileHandle = nullptr;
264 /*! \brief Non-owning handle to world communication data structure for task assigment.
266 * With real MPI, gets a value from the SimulationContext
267 * supplied to the MdrunnerBuilder. With thread-MPI gets a
268 * value after threads have been spawned. */
269 MPI_Comm libraryWorldCommunicator = MPI_COMM_NULL;
271 /*! \brief Non-owning handle to communication data structure for the current simulation.
273 * With real MPI, gets a value from the SimulationContext
274 * supplied to the MdrunnerBuilder. With thread-MPI gets a
275 * value after threads have been spawned. */
276 MPI_Comm simulationCommunicator = MPI_COMM_NULL;
278 //! \brief Non-owning handle to multi-simulation handler.
279 gmx_multisim_t* ms = nullptr;
281 //! Whether the simulation will start afresh, or restart with/without appending.
282 StartingBehavior startingBehavior = StartingBehavior::NewSimulation;
285 * \brief Handle to restraints manager for the current process.
288 * Use opaque pointer for this implementation detail.
290 std::unique_ptr<RestraintManager> restraintManager_;
293 * \brief Builder for stop signal handler
295 * Optionally provided through MdrunnerBuilder. Client may create a
296 * StopHandlerBuilder and register any number of signal providers before
297 * launching the Mdrunner.
299 * Default is an empty signal handler that will have local signal issuers
300 * added after being passed into the integrator.
303 * We do not need a full type specification here, so we use an opaque pointer.
305 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_;
306 //! The modules that comprise mdrun.
307 std::unique_ptr<MDModules> mdModules_;
310 * \brief Holds simulation input specification provided by client, if any.
312 * If present on any instance (rank) of a simulation runner, an identical
313 * (or compatible) SimulationInput must be held on all cooperating instances.
315 SimulationInputHandle inputHolder_;
319 * \brief Build a gmx::Mdrunner.
321 * Client code (such as `gmx mdrun`) uses this builder to get an initialized Mdrunner.
323 * A builder allows the library to ensure that client code cannot obtain an
324 * uninitialized or partially initialized runner by refusing to build() if the
325 * client has not provided sufficient or self-consistent direction. Director
326 * code can be implemented for different user interfaces, encapsulating any
327 * run-time functionality that does not belong in the library MD code, such
328 * as command-line option processing or interfacing to external libraries.
330 * \ingroup module_mdrun
334 * The initial Builder implementation is neither extensible at run time nor
335 * at compile time. Future implementations should evolve to compose the runner,
336 * rather than just consolidating the parameters for initialization, but there
337 * is not yet a firm design for how flexibly module code will be coupled to
338 * the builder and how much of the client interface will be in this Builder
339 * versus Builders provided by the various modules.
341 * The named components for the initial builder implementation are descriptive
342 * of the state of mdrun at the time, and are not intended to be prescriptive of
344 * The probable course of GROMACS development is for the modular components that
345 * support MD simulation to independently express their input parameters (required
346 * and optional) and to provide some sort of help to the UI for input preparation.
347 * If each module provides or aids the instantiation of a Director
348 * for the client code, the Directors could be constructed with a handle to this
349 * Builder and it would not need a public interface.
351 * As the modules are more clearly encapsulated, each module can provide its own
352 * builder, user interface helpers, and/or composable Director code.
353 * The runner and client code will also have to be updated as appropriate
354 * default behavior is clarified for
355 * (a) default behavior of client when user does not provide input,
356 * (b) default behavior of builder when client does not provide input, and
357 * (c) default behavior of runner when builder does not provide input.
359 class MdrunnerBuilder final
363 * \brief Constructor requires a handle to a SimulationContext to share.
365 * \param mdModules The handle to the set of modules active in mdrun
366 * \param context Required handle to simulation context
368 * The calling code must guarantee that the
369 * pointer remains valid for the lifetime of the builder, and that the
370 * resources retrieved from the context remain valid for the lifetime of
371 * the runner produced.
373 explicit MdrunnerBuilder(std::unique_ptr<MDModules> mdModules,
374 compat::not_null<SimulationContext*> context);
377 MdrunnerBuilder() = delete;
378 MdrunnerBuilder(const MdrunnerBuilder&) = delete;
379 MdrunnerBuilder& operator=(const MdrunnerBuilder&) = delete;
382 /*! \brief Allow transfer of ownership with move semantics.
384 * \param builder source object to transfer.
388 MdrunnerBuilder(MdrunnerBuilder&& builder) noexcept;
389 MdrunnerBuilder& operator=(MdrunnerBuilder&& builder) noexcept;
393 * \brief Get ownership of an initialized gmx::Mdrunner.
395 * After build() is called, the Builder object should not be used
396 * again. It is an error to call build without first calling all builder
397 * methods described as "required."
399 * \return A new Mdrunner.
401 * \throws APIError if a required component has not been added before calling build().
406 * \brief Set up non-bonded short-range force calculations.
408 * Required. Director code must provide valid options for the non-bonded
409 * interaction code. The builder does not apply any defaults.
411 * \param nbpu_opt Target short-range interactions for "cpu", "gpu", or "auto".
413 * Calling must guarantee that the pointed-to C string is valid through
417 * \todo Replace with string or enum that we can have sensible defaults for.
418 * \todo Either the Builder or modular Director code should provide sensible defaults.
420 MdrunnerBuilder& addNonBonded(const char* nbpu_opt);
423 * \brief Set up long-range electrostatics calculations.
425 * Required. Director code should provide valid options for PME electrostatics,
426 * whether or not PME electrostatics are used. The builder does not apply
427 * any defaults, so client code should be prepared to provide (e.g.) "auto"
428 * in the event no user input or logic provides an alternative argument.
430 * \param pme_opt Target long-range interactions for "cpu", "gpu", or "auto".
431 * \param pme_fft_opt Target long-range interactions FFT/solve stages for "cpu", "gpu", or "auto".
433 * Calling must guarantee that the pointed-to C strings are valid through
437 * The arguments are passed as references to elements of arrays of C strings.
438 * \todo Replace with modern strings or (better) enum classes.
439 * \todo Make optional and/or encapsulate into electrostatics module.
441 MdrunnerBuilder& addElectrostatics(const char* pme_opt, const char* pme_fft_opt);
444 * \brief Assign responsibility for tasks for bonded interactions.
446 * Required. Director code should provide valid options for
447 * bonded interaction task assignment, whether or not such
448 * interactions are present. The builder does not apply any
449 * defaults, so client code should be prepared to provide
450 * (e.g.) "auto" in the event no user input or logic provides
451 * an alternative argument.
453 * \param bonded_opt Target bonded interactions for "cpu", "gpu", or "auto".
455 * Calling must guarantee that the pointed-to C strings are valid through
459 * The arguments are passed as references to elements of arrays of C strings.
460 * \todo Replace with modern strings or (better) enum classes.
461 * \todo Make optional and/or encapsulate into task assignment module.
463 MdrunnerBuilder& addBondedTaskAssignment(const char* bonded_opt);
466 * Assign responsibility for tasks for update and constrain calculation.
468 * Required. Director code should provide valid options for
469 * update and constraint task assignment. The builder does not apply any
470 * defaults, so client code should be prepared to provide
471 * (e.g.) "auto" in the event no user input or logic provides
472 * an alternative argument.
474 * \param[in] update_opt Target update calculation for "cpu", "gpu", or "auto".
476 * Calling must guarantee that the pointed-to C strings are valid through
480 * The arguments are passed as references to elements of arrays of C strings.
481 * \todo Replace with modern strings or (better) enum classes.
482 * \todo Make optional and/or encapsulate into task assignment module.
484 MdrunnerBuilder& addUpdateTaskAssignment(const char* update_opt);
487 * \brief Set MD options not owned by some other module.
489 * Optional. Override simulation parameters
491 * \param options structure to copy
492 * \param forceWarningThreshold Print a warning if any force is larger than this (in kJ/mol nm) (default -1)
493 * \param startingBehavior Whether the simulation will start afresh, or restart with/without appending.
496 * \todo Map these parameters to more appropriate encapsulating types.
497 * Find a better way to indicate "unspecified" than a magic value of the parameter type.
499 MdrunnerBuilder& addSimulationMethod(const MdrunOptions& options,
500 real forceWarningThreshold,
501 StartingBehavior startingBehavior);
504 * \brief Set the domain decomposition module.
506 * Optional. Overrides default constructed DomdecOptions if provided.
508 * \param options options with which to construct domain decomposition.
511 * \todo revisit whether we should be passing this parameter struct or a higher-level handle of some sort.
513 MdrunnerBuilder& addDomainDecomposition(const DomdecOptions& options);
516 * \brief Set Verlet list manager.
518 * Optional. Neighbor list existence, type, and parameters are mostly determined
519 * by the simulation parameters loaded elsewhere. This is just an override.
521 * \param rebuildInterval override for the duration of a neighbor list with the Verlet scheme.
523 MdrunnerBuilder& addNeighborList(int rebuildInterval);
526 * \brief Set replica exchange manager.
528 * Optional. For guidance on preparing a valid ReplicaExchangeParameters
529 * value, refer to the details in mdrun.cpp, the `t_pargs pa[]` defined there,
530 * and the action of parse_common_args() with regards to that structure.
531 * If not provided by client, a default constructed ReplicaExchangeParameters
534 * \param params parameters with which to set up replica exchange.
537 * \todo revisit whether we should be passing this parameter struct or a higher-level handle of some sort.
539 MdrunnerBuilder& addReplicaExchange(const ReplicaExchangeParameters& params);
542 * \brief Specify parameters determining hardware resource allocation.
544 * Optional. If not provided, default-constructed gmx_hw_opt_t will be used.
546 * \param hardwareOptions Parallelism-related user options.
548 MdrunnerBuilder& addHardwareOptions(const gmx_hw_opt_t& hardwareOptions);
551 * \brief Provide the filenames options structure with option values chosen
553 * Required. The object is assumed to have been updated by
554 * parse_common_args or equivalent.
556 * \param filenames Filenames and properties from command-line argument values or defaults.
559 * \todo Modules should manage their own filename options and defaults.
561 MdrunnerBuilder& addFilenames(ArrayRef<const t_filenm> filenames);
564 * \brief Provide parameters for setting up output environment.
566 * Required. Handle is assumed to have been produced by output_env_init
567 * as in parse_common_args.
569 * \param outputEnvironment Output context for writing text files.
572 * \todo Allow client code to set up output environment and provide as a resource.
573 * This parameter is used to set up resources that are dependent on the execution
574 * environment and API context. Such resources should be retrieved by the simulator
575 * from a client-provided resource, but currently the resources are only fully
576 * initialized in Mdrunner.
578 MdrunnerBuilder& addOutputEnvironment(gmx_output_env_t* outputEnvironment);
581 * \brief Provide the filehandle pointer to be used for the MD log.
583 * Required. Either nullptr if no log should be written, or
584 * valid and open reading for writing.
586 * \param logFileHandle Non-owning handle to file used for logging.
589 MdrunnerBuilder& addLogFile(t_fileio* logFileHandle);
592 * \brief Provide a StopHandlerBuilder for the MD stop signal handling.
594 * Optional. Defaults to empty.
596 * Client may provide additional (non-default) issuers of simulation stop
597 * signals by preconfiguring the StopHandlerBuilder used later when the
602 MdrunnerBuilder& addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
605 * \brief Acquire a handle to the SimulationInput.
607 * Required. SimulationInput will be taking responsibility for some of the
608 * input provided through other methods, such as addFilenames.
610 * See also issue https://gitlab.com/gromacs/gromacs/-/issues/3374
612 * \param input Shared ownership of a SimulationInput.
614 MdrunnerBuilder& addInput(SimulationInputHandle input);
619 std::unique_ptr<Mdrunner::BuilderImplementation> impl_;
624 #endif // GMX_MDRUN_RUNNER_H