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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/domdec/options.h"
52 #include "gromacs/hardware/hw_info.h"
53 #include "gromacs/math/vec.h"
54 #include "gromacs/mdrun/mdmodules.h"
55 #include "gromacs/mdrunutility/handlerestart.h"
56 #include "gromacs/mdtypes/mdrunoptions.h"
57 #include "gromacs/utility/basedefinitions.h"
58 #include "gromacs/utility/real.h"
60 #include "replicaexchange.h"
62 struct gmx_output_env_t;
63 struct ReplicaExchangeParameters;
70 // Todo: move to forward declaration headers...
72 class IRestraintPotential; // defined in restraint/restraintpotential.h
73 class RestraintManager;
74 class SimulationContext;
75 class StopHandlerBuilder;
77 //! Work-around for GCC bug 58265
78 constexpr bool BUGFREE_NOEXCEPT_STRING = std::is_nothrow_move_assignable<std::string>::value;
80 /*! \libinternal \brief Runner object for supporting setup and execution of mdrun.
82 * This class has responsibility for the lifetime of data structures
83 * that exist for the life of the simulation, e.g. for logging and
86 * It is also responsible for initializing data members that
87 * e.g. correspond to values potentially set by commmand-line
88 * options. Later these will be obtained directly from modules, and
89 * the results of command-line option handling returned directly to
90 * the modules, rather than propagated to them by data members of this
93 * \todo Most of the attributes should be declared by specific modules
94 * as command-line options. Accordingly, they do not conform to the
95 * naming scheme, because that would make for a lot of noise in the
96 * diff, only to have it change again when the options move to their
99 * \todo Preparing logging and MPI contexts could probably be a
100 * higher-level responsibility, so that an Mdrunner would get made
101 * without needing to re-initialize these components (as currently
102 * happens always for the master rank, and differently for the spawned
103 * ranks with thread-MPI).
105 * \ingroup module_mdrun
110 /*! \brief Builder class to manage object creation.
112 * This class is a member of gmx::Mdrunner so that it can initialize
113 * private members of gmx::Mdrunner.
115 * It is non-trivial to establish an initialized gmx::Mdrunner invariant,
116 * so objects can be obtained by clients using a Builder or a move.
117 * Clients cannot default initialize or copy gmx::Mdrunner.
119 class BuilderImplementation;
124 * \brief Copy not allowed.
126 * An Mdrunner has unique resources and it is not clear whether any of
127 * one of those resources should be duplicated or shared unless the
128 * specific use case is known. Either build a fresh runner or use a
129 * helper function for clearly indicated behavior. API clarification may
130 * allow unambiguous initialization by copy in future versions.
134 Mdrunner(const Mdrunner &) = delete;
135 Mdrunner &operator=(const Mdrunner &) = delete;
139 * \brief Mdrunner objects can be passed by value via move semantics.
141 * \param handle runner instance to be moved from.
144 Mdrunner(Mdrunner &&handle) noexcept;
145 //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265
146 Mdrunner &operator=(Mdrunner &&handle) noexcept(BUGFREE_NOEXCEPT_STRING);
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,
168 const std::string &name);
170 //! Called when thread-MPI spawns threads.
171 t_commrec *spawnThreads(int numThreadsToLaunch) const;
173 /*! \brief Initializes a new Mdrunner from the master.
175 * Run this method in a new thread from a master runner to get additional
176 * workers on spawned threads.
178 * \returns New Mdrunner instance suitable for thread-MPI work on new ranks.
181 * \todo clarify (multiple) invariants during MD runner start-up.
182 * The runner state before and after launching threads is distinct enough that
183 * it should be codified in the invariants of different classes. That would
184 * mean that the object returned by this method would be of a different type
185 * than the object held by the client up to the point of call, and its name
186 * would be changed to "launchOnSpawnedThread" or something not including the
189 Mdrunner cloneOnSpawnedThread() const;
192 /*! \brief Constructor. */
193 explicit Mdrunner(std::unique_ptr<MDModules> mdModules);
195 //! Parallelism-related user options.
198 //! Filenames and properties from command-line argument values.
199 ArrayRef<const t_filenm> filenames;
201 /*! \brief Output context for writing text files
204 * \todo push this data member down when the information can be queried from an encapsulated resource.
206 gmx_output_env_t *oenv = nullptr;
207 //! Ongoing collection of mdrun options
208 MdrunOptions mdrunOptions;
209 //! Options for the domain decomposition.
210 DomdecOptions domdecOptions;
212 /*! \brief Target short-range interations for "cpu", "gpu", or "auto". Default is "auto".
215 * \todo replace with string or enum class and initialize with sensible value.
217 const char *nbpu_opt = nullptr;
219 /*! \brief Target long-range interactions for "cpu", "gpu", or "auto". Default is "auto".
222 * \todo replace with string or enum class and initialize with sensible value.
224 const char *pme_opt = nullptr;
226 /*! \brief Target long-range interactions FFT/solve stages 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_fft_opt = nullptr;
233 /*! \brief Target bonded interations for "cpu", "gpu", or "auto". Default is "auto".
236 * \todo replace with string or enum class and initialize with sensible value.
238 const char *bonded_opt = nullptr;
240 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
241 int nstlist_cmdline = 0;
242 //! Parameters for replica-exchange simulations.
243 ReplicaExchangeParameters replExParams;
244 //! Print a warning if any force is larger than this (in kJ/mol nm).
247 //! Handle to file used for logging.
248 LogFilePtr logFileGuard = nullptr;
249 //! \brief Non-owning handle to file used for logging.
250 t_fileio *logFileHandle = nullptr;
252 //! \brief Non-owning handle to communication data structure.
253 t_commrec *cr = nullptr;
255 //! \brief Non-owning handle to multi-simulation handler.
256 gmx_multisim_t *ms = nullptr;
258 //! Whether the simulation will start afresh, or restart with/without appending.
259 StartingBehavior startingBehavior = StartingBehavior::NewSimulation;
262 * \brief Handle to restraints manager for the current process.
265 * Use opaque pointer for this implementation detail.
267 std::unique_ptr<RestraintManager> restraintManager_;
270 * \brief Builder for stop signal handler
272 * Optionally provided through MdrunnerBuilder. Client may create a
273 * StopHandlerBuilder and register any number of signal providers before
274 * launching the Mdrunner.
276 * Default is an empty signal handler that will have local signal issuers
277 * added after being passed into the integrator.
280 * We do not need a full type specification here, so we use an opaque pointer.
282 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_;
283 //! The modules that comprise mdrun.
284 std::unique_ptr<MDModules> mdModules_;
288 * \brief Build a gmx::Mdrunner.
290 * Client code (such as `gmx mdrun`) uses this builder to get an initialized Mdrunner.
292 * A builder allows the library to ensure that client code cannot obtain an
293 * uninitialized or partially initialized runner by refusing to build() if the
294 * client has not provided sufficient or self-consistent direction. Director
295 * code can be implemented for different user interfaces, encapsulating any
296 * run-time functionality that does not belong in the library MD code, such
297 * as command-line option processing or interfacing to external libraries.
299 * \ingroup module_mdrun
303 * The initial Builder implementation is neither extensible at run time nor
304 * at compile time. Future implementations should evolve to compose the runner,
305 * rather than just consolidating the parameters for initialization, but there
306 * is not yet a firm design for how flexibly module code will be coupled to
307 * the builder and how much of the client interface will be in this Builder
308 * versus Builders provided by the various modules.
310 * The named components for the initial builder implementation are descriptive
311 * of the state of mdrun at the time, and are not intended to be prescriptive of
313 * The probable course of GROMACS development is for the modular components that
314 * support MD simulation to independently express their input parameters (required
315 * and optional) and to provide some sort of help to the UI for input preparation.
316 * If each module provides or aids the instantiation of a Director
317 * for the client code, the Directors could be constructed with a handle to this
318 * Builder and it would not need a public interface.
320 * As the modules are more clearly encapsulated, each module can provide its own
321 * builder, user interface helpers, and/or composable Director code.
322 * The runner and client code will also have to be updated as appropriate
323 * default behavior is clarified for
324 * (a) default behavior of client when user does not provide input,
325 * (b) default behavior of builder when client does not provide input, and
326 * (c) default behavior of runner when builder does not provide input.
328 class MdrunnerBuilder final
332 * \brief Constructor requires a handle to a SimulationContext to share.
334 * \param mdModules The handle to the set of modules active in mdrun
336 * The calling code must guarantee that the
337 * pointer remains valid for the lifetime of the builder, and that the
338 * resources retrieved from the context remain valid for the lifetime of
339 * the runner produced.
341 explicit MdrunnerBuilder(std::unique_ptr<MDModules> mdModules);
344 MdrunnerBuilder() = delete;
345 MdrunnerBuilder(const MdrunnerBuilder&) = delete;
346 MdrunnerBuilder &operator=(const MdrunnerBuilder &) = delete;
349 /*! \brief Allow transfer of ownership with move semantics.
351 * \param builder source object to transfer.
355 MdrunnerBuilder(MdrunnerBuilder && builder) noexcept;
356 MdrunnerBuilder &operator=(MdrunnerBuilder &&builder) noexcept;
360 * \brief Get ownership of an initialized gmx::Mdrunner.
362 * After build() is called, the Builder object should not be used
363 * again. It is an error to call build without first calling all builder
364 * methods described as "required."
366 * \return A new Mdrunner.
368 * \throws APIError if a required component has not been added before calling build().
373 * \brief Set up non-bonded short-range force calculations.
375 * Required. Director code must provide valid options for the non-bonded
376 * interaction code. The builder does not apply any defaults.
378 * \param nbpu_opt Target short-range interactions for "cpu", "gpu", or "auto".
380 * Calling must guarantee that the pointed-to C string is valid through
384 * \todo Replace with string or enum that we can have sensible defaults for.
385 * \todo Either the Builder or modular Director code should provide sensible defaults.
387 MdrunnerBuilder &addNonBonded(const char* nbpu_opt);
390 * \brief Set up long-range electrostatics calculations.
392 * Required. Director code should provide valid options for PME electrostatics,
393 * whether or not PME electrostatics are used. The builder does not apply
394 * any defaults, so client code should be prepared to provide (e.g.) "auto"
395 * in the event no user input or logic provides an alternative argument.
397 * \param pme_opt Target long-range interactions for "cpu", "gpu", or "auto".
398 * \param pme_fft_opt Target long-range interactions FFT/solve stages for "cpu", "gpu", or "auto".
400 * Calling must guarantee that the pointed-to C strings are valid through
404 * The arguments are passed as references to elements of arrays of C strings.
405 * \todo Replace with modern strings or (better) enum classes.
406 * \todo Make optional and/or encapsulate into electrostatics module.
408 MdrunnerBuilder &addElectrostatics(const char* pme_opt,
409 const char* pme_fft_opt);
412 * \brief Assign responsibility for tasks for bonded interactions.
414 * Required. Director code should provide valid options for
415 * bonded interaction task assignment, whether or not such
416 * interactions are present. The builder does not apply any
417 * defaults, so client code should be prepared to provide
418 * (e.g.) "auto" in the event no user input or logic provides
419 * an alternative argument.
421 * \param bonded_opt Target bonded interactions for "cpu", "gpu", or "auto".
423 * Calling must guarantee that the pointed-to C strings are valid through
427 * The arguments are passed as references to elements of arrays of C strings.
428 * \todo Replace with modern strings or (better) enum classes.
429 * \todo Make optional and/or encapsulate into task assignment module.
431 MdrunnerBuilder &addBondedTaskAssignment(const char *bonded_opt);
434 * \brief Provide access to the multisim communicator to use.
436 * \param multisim borrowed handle to multisim record.
438 * Required. Client should create a `gmx_multisim_t` and pass its address.
439 * Client is responsible for calling done_multisim() on the handle after
442 * \internal Pointer is copied, but calling code retains ownership and
443 * responsibility for multisim. Mdrunner must not do anything that would
444 * invalidate the original copied-from pointer.
446 * \todo Clarify semantics of specifying optional multisim work
447 * \todo Clarify ownership and management of multisim resources.
449 MdrunnerBuilder &addMultiSim(gmx_multisim_t* multisim);
452 * \brief Provide a commrec for mdrun to use.
454 * This will come from the simulation context, but differently
455 * for command-line gmx and a gmxapi Context. */
456 MdrunnerBuilder &addCommunicationRecord(t_commrec *cr);
459 * \brief Set MD options not owned by some other module.
461 * Optional. Override simulation parameters
463 * \param options structure to copy
464 * \param forceWarningThreshold Print a warning if any force is larger than this (in kJ/mol nm) (default -1)
465 * \param startingBehavior Whether the simulation will start afresh, or restart with/without appending.
468 * \todo Map these parameters to more appropriate encapsulating types.
469 * Find a better way to indicate "unspecified" than a magic value of the parameter type.
471 MdrunnerBuilder &addSimulationMethod(const MdrunOptions &options,
472 real forceWarningThreshold,
473 StartingBehavior startingBehavior);
476 * \brief Set the domain decomposition module.
478 * Optional. Overrides default constructed DomdecOptions if provided.
480 * \param options options with which to construct domain decomposition.
483 * \todo revisit whether we should be passing this parameter struct or a higher-level handle of some sort.
485 MdrunnerBuilder &addDomainDecomposition(const DomdecOptions &options);
488 * \brief Set Verlet list manager.
490 * Optional. Neighbor list existence, type, and parameters are mostly determined
491 * by the simulation parameters loaded elsewhere. This is just an override.
493 * \param rebuildInterval override for the duration of a neighbor list with the Verlet scheme.
495 MdrunnerBuilder &addNeighborList(int rebuildInterval);
498 * \brief Set replica exchange manager.
500 * Optional. For guidance on preparing a valid ReplicaExchangeParameters
501 * value, refer to the details in mdrun.cpp, the `t_pargs pa[]` defined there,
502 * and the action of parse_common_args() with regards to that structure.
503 * If not provided by client, a default constructed ReplicaExchangeParameters
506 * \param params parameters with which to set up replica exchange.
509 * \todo revisit whether we should be passing this parameter struct or a higher-level handle of some sort.
511 MdrunnerBuilder &addReplicaExchange(const ReplicaExchangeParameters ¶ms);
514 * \brief Specify parameters determining hardware resource allocation.
516 * Optional. If not provided, default-constructed gmx_hw_opt_t will be used.
518 * \param hardwareOptions Parallelism-related user options.
520 MdrunnerBuilder &addHardwareOptions(const gmx_hw_opt_t &hardwareOptions);
523 * \brief Provide the filenames options structure with option values chosen
525 * Required. The object is assumed to have been updated by
526 * parse_common_args or equivalent.
528 * \param filenames Filenames and properties from command-line argument values or defaults.
531 * \todo Modules should manage their own filename options and defaults.
533 MdrunnerBuilder &addFilenames(ArrayRef<const t_filenm> filenames);
536 * \brief Provide parameters for setting up output environment.
538 * Required. Handle is assumed to have been produced by output_env_init
539 * as in parse_common_args.
541 * \param outputEnvironment Output context for writing text files.
544 * \todo Allow client code to set up output environment and provide as a resource.
545 * This parameter is used to set up resources that are dependent on the execution
546 * environment and API context. Such resources should be retrieved by the simulator
547 * from a client-provided resource, but currently the resources are only fully
548 * initialized in Mdrunner.
550 MdrunnerBuilder &addOutputEnvironment(gmx_output_env_t* outputEnvironment);
553 * \brief Provide the filehandle pointer to be used for the MD log.
555 * Required. Either nullptr if no log should be written, or
556 * valid and open reading for writing.
558 * \param logFileHandle Non-owning handle to file used for logging.
561 MdrunnerBuilder &addLogFile(t_fileio *logFileHandle);
564 * \brief Provide a StopHandlerBuilder for the MD stop signal handling.
566 * Optional. Defaults to empty.
568 * Client may provide additional (non-default) issuers of simulation stop
569 * signals by preconfiguring the StopHandlerBuilder used later when the
574 MdrunnerBuilder &addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
579 std::unique_ptr<Mdrunner::BuilderImplementation> impl_;
584 #endif // GMX_MDRUN_RUNNER_H