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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/arrayref.h"
59 #include "gromacs/utility/basedefinitions.h"
60 #include "gromacs/utility/gmxmpi.h"
61 #include "gromacs/utility/real.h"
63 #include "replicaexchange.h"
65 struct gmx_multisim_t;
66 struct gmx_output_env_t;
67 struct ReplicaExchangeParameters;
73 // Todo: move to forward declaration headers...
75 class IRestraintPotential; // defined in restraint/restraintpotential.h
76 class RestraintManager;
77 class SimulationContext;
78 class StopHandlerBuilder;
80 //! Work-around for GCC bug 58265
81 constexpr bool BUGFREE_NOEXCEPT_STRING = std::is_nothrow_move_assignable<std::string>::value;
83 /*! \libinternal \brief Runner object for supporting setup and execution of mdrun.
85 * This class has responsibility for the lifetime of data structures
86 * that exist for the life of the simulation, e.g. for logging and
89 * It is also responsible for initializing data members that
90 * e.g. correspond to values potentially set by commmand-line
91 * options. Later these will be obtained directly from modules, and
92 * the results of command-line option handling returned directly to
93 * the modules, rather than propagated to them by data members of this
96 * \todo Most of the attributes should be declared by specific modules
97 * as command-line options. Accordingly, they do not conform to the
98 * naming scheme, because that would make for a lot of noise in the
99 * diff, only to have it change again when the options move to their
102 * \todo Preparing logging and MPI contexts could probably be a
103 * higher-level responsibility, so that an Mdrunner would get made
104 * without needing to re-initialize these components (as currently
105 * happens always for the master rank, and differently for the spawned
106 * ranks with thread-MPI).
108 * \ingroup module_mdrun
113 /*! \brief Builder class to manage object creation.
115 * This class is a member of gmx::Mdrunner so that it can initialize
116 * private members of gmx::Mdrunner.
118 * It is non-trivial to establish an initialized gmx::Mdrunner invariant,
119 * so objects can be obtained by clients using a Builder or a move.
120 * Clients cannot default initialize or copy gmx::Mdrunner.
122 class BuilderImplementation;
127 * \brief Copy not allowed.
129 * An Mdrunner has unique resources and it is not clear whether any of
130 * one of those resources should be duplicated or shared unless the
131 * specific use case is known. Either build a fresh runner or use a
132 * helper function for clearly indicated behavior. API clarification may
133 * allow unambiguous initialization by copy in future versions.
137 Mdrunner(const Mdrunner&) = delete;
138 Mdrunner& operator=(const Mdrunner&) = delete;
142 * \brief Mdrunner objects can be passed by value via move semantics.
144 * \param handle runner instance to be moved from.
147 Mdrunner(Mdrunner&& handle) noexcept;
148 //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265
149 Mdrunner& operator=(Mdrunner&& handle) noexcept(BUGFREE_NOEXCEPT_STRING);
152 /*! \brief Driver routine, that calls the different simulation methods. */
154 * Currently, thread-MPI does not spawn threads until during mdrunner() and parallelism
155 * is not initialized until some time during this call...
160 * \brief Add a potential to be evaluated during MD integration.
162 * \param restraint MD restraint potential to apply
163 * \param name User-friendly plain-text name to uniquely identify the puller
165 * This implementation attaches an object providing the gmx::IRestraintPotential
167 * \todo Mdrunner should fetch such resources from the SimulationContext
168 * rather than offering this public interface.
170 void addPotential(std::shared_ptr<IRestraintPotential> restraint, const std::string& name);
172 /*! \brief Prepare the thread-MPI communicator to have \c
173 * numThreadsToLaunch ranks, by spawning new thread-MPI
176 * Called by mdrunner() to start a specific number of threads
177 * (including the main thread) for thread-parallel runs. This
178 * in turn calls mdrunner() for each thread. */
179 void spawnThreads(int numThreadsToLaunch);
181 /*! \brief Initializes a new Mdrunner from the master.
183 * Run this method in a new thread from a master runner to get additional
184 * workers on spawned threads.
186 * \returns New Mdrunner instance suitable for thread-MPI work on new ranks.
189 * \todo clarify (multiple) invariants during MD runner start-up.
190 * The runner state before and after launching threads is distinct enough that
191 * it should be codified in the invariants of different classes. That would
192 * mean that the object returned by this method would be of a different type
193 * than the object held by the client up to the point of call, and its name
194 * would be changed to "launchOnSpawnedThread" or something not including the
197 Mdrunner cloneOnSpawnedThread() const;
200 /*! \brief Constructor. */
201 explicit Mdrunner(std::unique_ptr<MDModules> mdModules);
203 //! Parallelism-related user options.
206 //! Filenames and properties from command-line argument values.
207 ArrayRef<const t_filenm> filenames;
209 /*! \brief Output context for writing text files
212 * \todo push this data member down when the information can be queried from an encapsulated resource.
214 gmx_output_env_t* oenv = nullptr;
215 //! Ongoing collection of mdrun options
216 MdrunOptions mdrunOptions;
217 //! Options for the domain decomposition.
218 DomdecOptions domdecOptions;
220 /*! \brief Target short-range interations for "cpu", "gpu", or "auto". Default is "auto".
223 * \todo replace with string or enum class and initialize with sensible value.
225 const char* nbpu_opt = nullptr;
227 /*! \brief Target long-range interactions for "cpu", "gpu", or "auto". Default is "auto".
230 * \todo replace with string or enum class and initialize with sensible value.
232 const char* pme_opt = nullptr;
234 /*! \brief Target long-range interactions FFT/solve stages for "cpu", "gpu", or "auto". Default is "auto".
237 * \todo replace with string or enum class and initialize with sensible value.
239 const char* pme_fft_opt = nullptr;
241 /*! \brief Target bonded interations for "cpu", "gpu", or "auto". Default is "auto".
244 * \todo replace with string or enum class and initialize with sensible value.
246 const char* bonded_opt = nullptr;
248 /*! \brief Target update calculation for "cpu", "gpu", or "auto". Default is "auto".
251 * \todo replace with string or enum class and initialize with sensible value.
253 const char* update_opt = nullptr;
255 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
256 int nstlist_cmdline = 0;
257 //! Parameters for replica-exchange simulations.
258 ReplicaExchangeParameters replExParams;
259 //! Print a warning if any force is larger than this (in kJ/mol nm).
262 //! Handle to file used for logging.
263 LogFilePtr logFileGuard = nullptr;
264 //! \brief Non-owning handle to file used for logging.
265 t_fileio* logFileHandle = nullptr;
267 /*! \brief Non-owning handle to communication data structure.
269 * With real MPI, gets a value from the SimulationContext
270 * supplied to the MdrunnerBuilder. With thread-MPI gets a
271 * value after threads have been spawned. */
272 MPI_Comm communicator = MPI_COMM_NULL;
274 //! \brief Non-owning handle to multi-simulation handler.
275 gmx_multisim_t* ms = nullptr;
277 //! Whether the simulation will start afresh, or restart with/without appending.
278 StartingBehavior startingBehavior = StartingBehavior::NewSimulation;
281 * \brief Handle to restraints manager for the current process.
284 * Use opaque pointer for this implementation detail.
286 std::unique_ptr<RestraintManager> restraintManager_;
289 * \brief Builder for stop signal handler
291 * Optionally provided through MdrunnerBuilder. Client may create a
292 * StopHandlerBuilder and register any number of signal providers before
293 * launching the Mdrunner.
295 * Default is an empty signal handler that will have local signal issuers
296 * added after being passed into the integrator.
299 * We do not need a full type specification here, so we use an opaque pointer.
301 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_;
302 //! The modules that comprise mdrun.
303 std::unique_ptr<MDModules> mdModules_;
307 * \brief Build a gmx::Mdrunner.
309 * Client code (such as `gmx mdrun`) uses this builder to get an initialized Mdrunner.
311 * A builder allows the library to ensure that client code cannot obtain an
312 * uninitialized or partially initialized runner by refusing to build() if the
313 * client has not provided sufficient or self-consistent direction. Director
314 * code can be implemented for different user interfaces, encapsulating any
315 * run-time functionality that does not belong in the library MD code, such
316 * as command-line option processing or interfacing to external libraries.
318 * \ingroup module_mdrun
322 * The initial Builder implementation is neither extensible at run time nor
323 * at compile time. Future implementations should evolve to compose the runner,
324 * rather than just consolidating the parameters for initialization, but there
325 * is not yet a firm design for how flexibly module code will be coupled to
326 * the builder and how much of the client interface will be in this Builder
327 * versus Builders provided by the various modules.
329 * The named components for the initial builder implementation are descriptive
330 * of the state of mdrun at the time, and are not intended to be prescriptive of
332 * The probable course of GROMACS development is for the modular components that
333 * support MD simulation to independently express their input parameters (required
334 * and optional) and to provide some sort of help to the UI for input preparation.
335 * If each module provides or aids the instantiation of a Director
336 * for the client code, the Directors could be constructed with a handle to this
337 * Builder and it would not need a public interface.
339 * As the modules are more clearly encapsulated, each module can provide its own
340 * builder, user interface helpers, and/or composable Director code.
341 * The runner and client code will also have to be updated as appropriate
342 * default behavior is clarified for
343 * (a) default behavior of client when user does not provide input,
344 * (b) default behavior of builder when client does not provide input, and
345 * (c) default behavior of runner when builder does not provide input.
347 class MdrunnerBuilder final
351 * \brief Constructor requires a handle to a SimulationContext to share.
353 * \param mdModules The handle to the set of modules active in mdrun
354 * \param context Required handle to simulation context
356 * The calling code must guarantee that the
357 * pointer remains valid for the lifetime of the builder, and that the
358 * resources retrieved from the context remain valid for the lifetime of
359 * the runner produced.
361 explicit MdrunnerBuilder(std::unique_ptr<MDModules> mdModules,
362 compat::not_null<SimulationContext*> context);
365 MdrunnerBuilder() = delete;
366 MdrunnerBuilder(const MdrunnerBuilder&) = delete;
367 MdrunnerBuilder& operator=(const MdrunnerBuilder&) = delete;
370 /*! \brief Allow transfer of ownership with move semantics.
372 * \param builder source object to transfer.
376 MdrunnerBuilder(MdrunnerBuilder&& builder) noexcept;
377 MdrunnerBuilder& operator=(MdrunnerBuilder&& builder) noexcept;
381 * \brief Get ownership of an initialized gmx::Mdrunner.
383 * After build() is called, the Builder object should not be used
384 * again. It is an error to call build without first calling all builder
385 * methods described as "required."
387 * \return A new Mdrunner.
389 * \throws APIError if a required component has not been added before calling build().
394 * \brief Set up non-bonded short-range force calculations.
396 * Required. Director code must provide valid options for the non-bonded
397 * interaction code. The builder does not apply any defaults.
399 * \param nbpu_opt Target short-range interactions for "cpu", "gpu", or "auto".
401 * Calling must guarantee that the pointed-to C string is valid through
405 * \todo Replace with string or enum that we can have sensible defaults for.
406 * \todo Either the Builder or modular Director code should provide sensible defaults.
408 MdrunnerBuilder& addNonBonded(const char* nbpu_opt);
411 * \brief Set up long-range electrostatics calculations.
413 * Required. Director code should provide valid options for PME electrostatics,
414 * whether or not PME electrostatics are used. The builder does not apply
415 * any defaults, so client code should be prepared to provide (e.g.) "auto"
416 * in the event no user input or logic provides an alternative argument.
418 * \param pme_opt Target long-range interactions for "cpu", "gpu", or "auto".
419 * \param pme_fft_opt Target long-range interactions FFT/solve stages for "cpu", "gpu", or "auto".
421 * Calling must guarantee that the pointed-to C strings are valid through
425 * The arguments are passed as references to elements of arrays of C strings.
426 * \todo Replace with modern strings or (better) enum classes.
427 * \todo Make optional and/or encapsulate into electrostatics module.
429 MdrunnerBuilder& addElectrostatics(const char* pme_opt, const char* pme_fft_opt);
432 * \brief Assign responsibility for tasks for bonded interactions.
434 * Required. Director code should provide valid options for
435 * bonded interaction task assignment, whether or not such
436 * interactions are present. The builder does not apply any
437 * defaults, so client code should be prepared to provide
438 * (e.g.) "auto" in the event no user input or logic provides
439 * an alternative argument.
441 * \param bonded_opt Target bonded interactions for "cpu", "gpu", or "auto".
443 * Calling must guarantee that the pointed-to C strings are valid through
447 * The arguments are passed as references to elements of arrays of C strings.
448 * \todo Replace with modern strings or (better) enum classes.
449 * \todo Make optional and/or encapsulate into task assignment module.
451 MdrunnerBuilder& addBondedTaskAssignment(const char* bonded_opt);
454 * Assign responsibility for tasks for update and constrain calculation.
456 * Required. Director code should provide valid options for
457 * update and constraint task assignment. The builder does not apply any
458 * defaults, so client code should be prepared to provide
459 * (e.g.) "auto" in the event no user input or logic provides
460 * an alternative argument.
462 * \param[in] update_opt Target update calculation for "cpu", "gpu", or "auto".
464 * Calling must guarantee that the pointed-to C strings are valid through
468 * The arguments are passed as references to elements of arrays of C strings.
469 * \todo Replace with modern strings or (better) enum classes.
470 * \todo Make optional and/or encapsulate into task assignment module.
472 MdrunnerBuilder& addUpdateTaskAssignment(const char* update_opt);
475 * \brief Set MD options not owned by some other module.
477 * Optional. Override simulation parameters
479 * \param options structure to copy
480 * \param forceWarningThreshold Print a warning if any force is larger than this (in kJ/mol nm) (default -1)
481 * \param startingBehavior Whether the simulation will start afresh, or restart with/without appending.
484 * \todo Map these parameters to more appropriate encapsulating types.
485 * Find a better way to indicate "unspecified" than a magic value of the parameter type.
487 MdrunnerBuilder& addSimulationMethod(const MdrunOptions& options,
488 real forceWarningThreshold,
489 StartingBehavior startingBehavior);
492 * \brief Set the domain decomposition module.
494 * Optional. Overrides default constructed DomdecOptions if provided.
496 * \param options options with which to construct domain decomposition.
499 * \todo revisit whether we should be passing this parameter struct or a higher-level handle of some sort.
501 MdrunnerBuilder& addDomainDecomposition(const DomdecOptions& options);
504 * \brief Set Verlet list manager.
506 * Optional. Neighbor list existence, type, and parameters are mostly determined
507 * by the simulation parameters loaded elsewhere. This is just an override.
509 * \param rebuildInterval override for the duration of a neighbor list with the Verlet scheme.
511 MdrunnerBuilder& addNeighborList(int rebuildInterval);
514 * \brief Set replica exchange manager.
516 * Optional. For guidance on preparing a valid ReplicaExchangeParameters
517 * value, refer to the details in mdrun.cpp, the `t_pargs pa[]` defined there,
518 * and the action of parse_common_args() with regards to that structure.
519 * If not provided by client, a default constructed ReplicaExchangeParameters
522 * \param params parameters with which to set up replica exchange.
525 * \todo revisit whether we should be passing this parameter struct or a higher-level handle of some sort.
527 MdrunnerBuilder& addReplicaExchange(const ReplicaExchangeParameters& params);
530 * \brief Specify parameters determining hardware resource allocation.
532 * Optional. If not provided, default-constructed gmx_hw_opt_t will be used.
534 * \param hardwareOptions Parallelism-related user options.
536 MdrunnerBuilder& addHardwareOptions(const gmx_hw_opt_t& hardwareOptions);
539 * \brief Provide the filenames options structure with option values chosen
541 * Required. The object is assumed to have been updated by
542 * parse_common_args or equivalent.
544 * \param filenames Filenames and properties from command-line argument values or defaults.
547 * \todo Modules should manage their own filename options and defaults.
549 MdrunnerBuilder& addFilenames(ArrayRef<const t_filenm> filenames);
552 * \brief Provide parameters for setting up output environment.
554 * Required. Handle is assumed to have been produced by output_env_init
555 * as in parse_common_args.
557 * \param outputEnvironment Output context for writing text files.
560 * \todo Allow client code to set up output environment and provide as a resource.
561 * This parameter is used to set up resources that are dependent on the execution
562 * environment and API context. Such resources should be retrieved by the simulator
563 * from a client-provided resource, but currently the resources are only fully
564 * initialized in Mdrunner.
566 MdrunnerBuilder& addOutputEnvironment(gmx_output_env_t* outputEnvironment);
569 * \brief Provide the filehandle pointer to be used for the MD log.
571 * Required. Either nullptr if no log should be written, or
572 * valid and open reading for writing.
574 * \param logFileHandle Non-owning handle to file used for logging.
577 MdrunnerBuilder& addLogFile(t_fileio* logFileHandle);
580 * \brief Provide a StopHandlerBuilder for the MD stop signal handling.
582 * Optional. Defaults to empty.
584 * Client may provide additional (non-default) issuers of simulation stop
585 * signals by preconfiguring the StopHandlerBuilder used later when the
590 MdrunnerBuilder& addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
595 std::unique_ptr<Mdrunner::BuilderImplementation> impl_;
600 #endif // GMX_MDRUN_RUNNER_H