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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/mdrunutility/handlerestart.h"
57 #include "gromacs/mdtypes/mdrunoptions.h"
58 #include "gromacs/utility/basedefinitions.h"
59 #include "gromacs/utility/gmxmpi.h"
60 #include "gromacs/utility/real.h"
62 #include "replicaexchange.h"
64 struct gmx_multisim_t;
65 struct gmx_output_env_t;
66 struct ReplicaExchangeParameters;
72 // Todo: move to forward declaration headers...
74 class IRestraintPotential; // defined in restraint/restraintpotential.h
75 class RestraintManager;
76 class SimulationContext;
77 class StopHandlerBuilder;
79 //! Work-around for GCC bug 58265
80 constexpr bool BUGFREE_NOEXCEPT_STRING = std::is_nothrow_move_assignable<std::string>::value;
82 /*! \libinternal \brief Runner object for supporting setup and execution of mdrun.
84 * This class has responsibility for the lifetime of data structures
85 * that exist for the life of the simulation, e.g. for logging and
88 * It is also responsible for initializing data members that
89 * e.g. correspond to values potentially set by commmand-line
90 * options. Later these will be obtained directly from modules, and
91 * the results of command-line option handling returned directly to
92 * the modules, rather than propagated to them by data members of this
95 * \todo Most of the attributes should be declared by specific modules
96 * as command-line options. Accordingly, they do not conform to the
97 * naming scheme, because that would make for a lot of noise in the
98 * diff, only to have it change again when the options move to their
101 * \todo Preparing logging and MPI contexts could probably be a
102 * higher-level responsibility, so that an Mdrunner would get made
103 * without needing to re-initialize these components (as currently
104 * happens always for the master rank, and differently for the spawned
105 * ranks with thread-MPI).
107 * \ingroup module_mdrun
112 /*! \brief Builder class to manage object creation.
114 * This class is a member of gmx::Mdrunner so that it can initialize
115 * private members of gmx::Mdrunner.
117 * It is non-trivial to establish an initialized gmx::Mdrunner invariant,
118 * so objects can be obtained by clients using a Builder or a move.
119 * Clients cannot default initialize or copy gmx::Mdrunner.
121 class BuilderImplementation;
126 * \brief Copy not allowed.
128 * An Mdrunner has unique resources and it is not clear whether any of
129 * one of those resources should be duplicated or shared unless the
130 * specific use case is known. Either build a fresh runner or use a
131 * helper function for clearly indicated behavior. API clarification may
132 * allow unambiguous initialization by copy in future versions.
136 Mdrunner(const Mdrunner&) = delete;
137 Mdrunner& operator=(const Mdrunner&) = delete;
141 * \brief Mdrunner objects can be passed by value via move semantics.
143 * \param handle runner instance to be moved from.
146 Mdrunner(Mdrunner&& handle) noexcept;
147 //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265
148 Mdrunner& operator=(Mdrunner&& handle) noexcept(BUGFREE_NOEXCEPT_STRING);
151 /*! \brief Driver routine, that calls the different simulation methods. */
153 * Currently, thread-MPI does not spawn threads until during mdrunner() and parallelism
154 * is not initialized until some time during this call...
159 * \brief Add a potential to be evaluated during MD integration.
161 * \param restraint MD restraint potential to apply
162 * \param name User-friendly plain-text name to uniquely identify the puller
164 * This implementation attaches an object providing the gmx::IRestraintPotential
166 * \todo Mdrunner should fetch such resources from the SimulationContext
167 * rather than offering this public interface.
169 void addPotential(std::shared_ptr<IRestraintPotential> restraint, const std::string& name);
171 /*! \brief Prepare the thread-MPI communicator to have \c
172 * numThreadsToLaunch ranks, by spawning new thread-MPI
175 * Called by mdrunner() to start a specific number of threads
176 * (including the main thread) for thread-parallel runs. This
177 * in turn calls mdrunner() for each thread. */
178 void spawnThreads(int numThreadsToLaunch);
180 /*! \brief Initializes a new Mdrunner from the master.
182 * Run this method in a new thread from a master runner to get additional
183 * workers on spawned threads.
185 * \returns New Mdrunner instance suitable for thread-MPI work on new ranks.
188 * \todo clarify (multiple) invariants during MD runner start-up.
189 * The runner state before and after launching threads is distinct enough that
190 * it should be codified in the invariants of different classes. That would
191 * mean that the object returned by this method would be of a different type
192 * than the object held by the client up to the point of call, and its name
193 * would be changed to "launchOnSpawnedThread" or something not including the
196 Mdrunner cloneOnSpawnedThread() const;
199 /*! \brief Constructor. */
200 explicit Mdrunner(std::unique_ptr<MDModules> mdModules);
202 //! Parallelism-related user options.
205 //! Filenames and properties from command-line argument values.
206 ArrayRef<const t_filenm> filenames;
208 /*! \brief Output context for writing text files
211 * \todo push this data member down when the information can be queried from an encapsulated resource.
213 gmx_output_env_t* oenv = nullptr;
214 //! Ongoing collection of mdrun options
215 MdrunOptions mdrunOptions;
216 //! Options for the domain decomposition.
217 DomdecOptions domdecOptions;
219 /*! \brief Target short-range interations for "cpu", "gpu", or "auto". Default is "auto".
222 * \todo replace with string or enum class and initialize with sensible value.
224 const char* nbpu_opt = nullptr;
226 /*! \brief Target long-range interactions for "cpu", "gpu", or "auto". Default is "auto".
229 * \todo replace with string or enum class and initialize with sensible value.
231 const char* pme_opt = nullptr;
233 /*! \brief Target long-range interactions FFT/solve stages for "cpu", "gpu", or "auto". Default is "auto".
236 * \todo replace with string or enum class and initialize with sensible value.
238 const char* pme_fft_opt = nullptr;
240 /*! \brief Target bonded interations for "cpu", "gpu", or "auto". Default is "auto".
243 * \todo replace with string or enum class and initialize with sensible value.
245 const char* bonded_opt = nullptr;
247 /*! \brief Target update calculation for "cpu", "gpu", or "auto". Default is "auto".
250 * \todo replace with string or enum class and initialize with sensible value.
252 const char* update_opt = nullptr;
254 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
255 int nstlist_cmdline = 0;
256 //! Parameters for replica-exchange simulations.
257 ReplicaExchangeParameters replExParams;
258 //! Print a warning if any force is larger than this (in kJ/mol nm).
261 //! Handle to file used for logging.
262 LogFilePtr logFileGuard = nullptr;
263 //! \brief Non-owning handle to file used for logging.
264 t_fileio* logFileHandle = nullptr;
266 /*! \brief Non-owning handle to communication data structure.
268 * With real MPI, gets a value from the SimulationContext
269 * supplied to the MdrunnerBuilder. With thread-MPI gets a
270 * value after threads have been spawned. */
271 MPI_Comm communicator = MPI_COMM_NULL;
273 //! \brief Non-owning handle to multi-simulation handler.
274 gmx_multisim_t* ms = nullptr;
276 //! Whether the simulation will start afresh, or restart with/without appending.
277 StartingBehavior startingBehavior = StartingBehavior::NewSimulation;
280 * \brief Handle to restraints manager for the current process.
283 * Use opaque pointer for this implementation detail.
285 std::unique_ptr<RestraintManager> restraintManager_;
288 * \brief Builder for stop signal handler
290 * Optionally provided through MdrunnerBuilder. Client may create a
291 * StopHandlerBuilder and register any number of signal providers before
292 * launching the Mdrunner.
294 * Default is an empty signal handler that will have local signal issuers
295 * added after being passed into the integrator.
298 * We do not need a full type specification here, so we use an opaque pointer.
300 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_;
301 //! The modules that comprise mdrun.
302 std::unique_ptr<MDModules> mdModules_;
306 * \brief Build a gmx::Mdrunner.
308 * Client code (such as `gmx mdrun`) uses this builder to get an initialized Mdrunner.
310 * A builder allows the library to ensure that client code cannot obtain an
311 * uninitialized or partially initialized runner by refusing to build() if the
312 * client has not provided sufficient or self-consistent direction. Director
313 * code can be implemented for different user interfaces, encapsulating any
314 * run-time functionality that does not belong in the library MD code, such
315 * as command-line option processing or interfacing to external libraries.
317 * \ingroup module_mdrun
321 * The initial Builder implementation is neither extensible at run time nor
322 * at compile time. Future implementations should evolve to compose the runner,
323 * rather than just consolidating the parameters for initialization, but there
324 * is not yet a firm design for how flexibly module code will be coupled to
325 * the builder and how much of the client interface will be in this Builder
326 * versus Builders provided by the various modules.
328 * The named components for the initial builder implementation are descriptive
329 * of the state of mdrun at the time, and are not intended to be prescriptive of
331 * The probable course of GROMACS development is for the modular components that
332 * support MD simulation to independently express their input parameters (required
333 * and optional) and to provide some sort of help to the UI for input preparation.
334 * If each module provides or aids the instantiation of a Director
335 * for the client code, the Directors could be constructed with a handle to this
336 * Builder and it would not need a public interface.
338 * As the modules are more clearly encapsulated, each module can provide its own
339 * builder, user interface helpers, and/or composable Director code.
340 * The runner and client code will also have to be updated as appropriate
341 * default behavior is clarified for
342 * (a) default behavior of client when user does not provide input,
343 * (b) default behavior of builder when client does not provide input, and
344 * (c) default behavior of runner when builder does not provide input.
346 class MdrunnerBuilder final
350 * \brief Constructor requires a handle to a SimulationContext to share.
352 * \param mdModules The handle to the set of modules active in mdrun
353 * \param context Required handle to simulation context
355 * The calling code must guarantee that the
356 * pointer remains valid for the lifetime of the builder, and that the
357 * resources retrieved from the context remain valid for the lifetime of
358 * the runner produced.
360 explicit MdrunnerBuilder(std::unique_ptr<MDModules> mdModules,
361 compat::not_null<SimulationContext*> context);
364 MdrunnerBuilder() = delete;
365 MdrunnerBuilder(const MdrunnerBuilder&) = delete;
366 MdrunnerBuilder& operator=(const MdrunnerBuilder&) = delete;
369 /*! \brief Allow transfer of ownership with move semantics.
371 * \param builder source object to transfer.
375 MdrunnerBuilder(MdrunnerBuilder&& builder) noexcept;
376 MdrunnerBuilder& operator=(MdrunnerBuilder&& builder) noexcept;
380 * \brief Get ownership of an initialized gmx::Mdrunner.
382 * After build() is called, the Builder object should not be used
383 * again. It is an error to call build without first calling all builder
384 * methods described as "required."
386 * \return A new Mdrunner.
388 * \throws APIError if a required component has not been added before calling build().
393 * \brief Set up non-bonded short-range force calculations.
395 * Required. Director code must provide valid options for the non-bonded
396 * interaction code. The builder does not apply any defaults.
398 * \param nbpu_opt Target short-range interactions for "cpu", "gpu", or "auto".
400 * Calling must guarantee that the pointed-to C string is valid through
404 * \todo Replace with string or enum that we can have sensible defaults for.
405 * \todo Either the Builder or modular Director code should provide sensible defaults.
407 MdrunnerBuilder& addNonBonded(const char* nbpu_opt);
410 * \brief Set up long-range electrostatics calculations.
412 * Required. Director code should provide valid options for PME electrostatics,
413 * whether or not PME electrostatics are used. The builder does not apply
414 * any defaults, so client code should be prepared to provide (e.g.) "auto"
415 * in the event no user input or logic provides an alternative argument.
417 * \param pme_opt Target long-range interactions for "cpu", "gpu", or "auto".
418 * \param pme_fft_opt Target long-range interactions FFT/solve stages for "cpu", "gpu", or "auto".
420 * Calling must guarantee that the pointed-to C strings are valid through
424 * The arguments are passed as references to elements of arrays of C strings.
425 * \todo Replace with modern strings or (better) enum classes.
426 * \todo Make optional and/or encapsulate into electrostatics module.
428 MdrunnerBuilder& addElectrostatics(const char* pme_opt, const char* pme_fft_opt);
431 * \brief Assign responsibility for tasks for bonded interactions.
433 * Required. Director code should provide valid options for
434 * bonded interaction task assignment, whether or not such
435 * interactions are present. The builder does not apply any
436 * defaults, so client code should be prepared to provide
437 * (e.g.) "auto" in the event no user input or logic provides
438 * an alternative argument.
440 * \param bonded_opt Target bonded interactions for "cpu", "gpu", or "auto".
442 * Calling must guarantee that the pointed-to C strings are valid through
446 * The arguments are passed as references to elements of arrays of C strings.
447 * \todo Replace with modern strings or (better) enum classes.
448 * \todo Make optional and/or encapsulate into task assignment module.
450 MdrunnerBuilder& addBondedTaskAssignment(const char* bonded_opt);
453 * Assign responsibility for tasks for update and constrain calculation.
455 * Required. Director code should provide valid options for
456 * update and constraint task assignment. The builder does not apply any
457 * defaults, so client code should be prepared to provide
458 * (e.g.) "auto" in the event no user input or logic provides
459 * an alternative argument.
461 * \param[in] update_opt Target update calculation for "cpu", "gpu", or "auto".
463 * Calling must guarantee that the pointed-to C strings are valid through
467 * The arguments are passed as references to elements of arrays of C strings.
468 * \todo Replace with modern strings or (better) enum classes.
469 * \todo Make optional and/or encapsulate into task assignment module.
471 MdrunnerBuilder& addUpdateTaskAssignment(const char* update_opt);
474 * \brief Set MD options not owned by some other module.
476 * Optional. Override simulation parameters
478 * \param options structure to copy
479 * \param forceWarningThreshold Print a warning if any force is larger than this (in kJ/mol nm) (default -1)
480 * \param startingBehavior Whether the simulation will start afresh, or restart with/without appending.
483 * \todo Map these parameters to more appropriate encapsulating types.
484 * Find a better way to indicate "unspecified" than a magic value of the parameter type.
486 MdrunnerBuilder& addSimulationMethod(const MdrunOptions& options,
487 real forceWarningThreshold,
488 StartingBehavior startingBehavior);
491 * \brief Set the domain decomposition module.
493 * Optional. Overrides default constructed DomdecOptions if provided.
495 * \param options options with which to construct domain decomposition.
498 * \todo revisit whether we should be passing this parameter struct or a higher-level handle of some sort.
500 MdrunnerBuilder& addDomainDecomposition(const DomdecOptions& options);
503 * \brief Set Verlet list manager.
505 * Optional. Neighbor list existence, type, and parameters are mostly determined
506 * by the simulation parameters loaded elsewhere. This is just an override.
508 * \param rebuildInterval override for the duration of a neighbor list with the Verlet scheme.
510 MdrunnerBuilder& addNeighborList(int rebuildInterval);
513 * \brief Set replica exchange manager.
515 * Optional. For guidance on preparing a valid ReplicaExchangeParameters
516 * value, refer to the details in mdrun.cpp, the `t_pargs pa[]` defined there,
517 * and the action of parse_common_args() with regards to that structure.
518 * If not provided by client, a default constructed ReplicaExchangeParameters
521 * \param params parameters with which to set up replica exchange.
524 * \todo revisit whether we should be passing this parameter struct or a higher-level handle of some sort.
526 MdrunnerBuilder& addReplicaExchange(const ReplicaExchangeParameters& params);
529 * \brief Specify parameters determining hardware resource allocation.
531 * Optional. If not provided, default-constructed gmx_hw_opt_t will be used.
533 * \param hardwareOptions Parallelism-related user options.
535 MdrunnerBuilder& addHardwareOptions(const gmx_hw_opt_t& hardwareOptions);
538 * \brief Provide the filenames options structure with option values chosen
540 * Required. The object is assumed to have been updated by
541 * parse_common_args or equivalent.
543 * \param filenames Filenames and properties from command-line argument values or defaults.
546 * \todo Modules should manage their own filename options and defaults.
548 MdrunnerBuilder& addFilenames(ArrayRef<const t_filenm> filenames);
551 * \brief Provide parameters for setting up output environment.
553 * Required. Handle is assumed to have been produced by output_env_init
554 * as in parse_common_args.
556 * \param outputEnvironment Output context for writing text files.
559 * \todo Allow client code to set up output environment and provide as a resource.
560 * This parameter is used to set up resources that are dependent on the execution
561 * environment and API context. Such resources should be retrieved by the simulator
562 * from a client-provided resource, but currently the resources are only fully
563 * initialized in Mdrunner.
565 MdrunnerBuilder& addOutputEnvironment(gmx_output_env_t* outputEnvironment);
568 * \brief Provide the filehandle pointer to be used for the MD log.
570 * Required. Either nullptr if no log should be written, or
571 * valid and open reading for writing.
573 * \param logFileHandle Non-owning handle to file used for logging.
576 MdrunnerBuilder& addLogFile(t_fileio* logFileHandle);
579 * \brief Provide a StopHandlerBuilder for the MD stop signal handling.
581 * Optional. Defaults to empty.
583 * Client may provide additional (non-default) issuers of simulation stop
584 * signals by preconfiguring the StopHandlerBuilder used later when the
589 MdrunnerBuilder& addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
594 std::unique_ptr<Mdrunner::BuilderImplementation> impl_;
599 #endif // GMX_MDRUN_RUNNER_H