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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/domdec.h"
53 #include "gromacs/hardware/hw_info.h"
54 #include "gromacs/math/vec.h"
55 #include "gromacs/mdtypes/mdrunoptions.h"
56 #include "gromacs/utility/basedefinitions.h"
57 #include "gromacs/utility/real.h"
59 #include "replicaexchange.h"
61 struct gmx_output_env_t;
62 struct ReplicaExchangeParameters;
69 // Todo: move to forward declaration headers...
71 class IRestraintPotential; // defined in restraint/restraintpotential.h
72 class RestraintManager;
73 class SimulationContext;
74 class StopHandlerBuilder;
76 //! Work-around for GCC bug 58265
77 constexpr bool BUGFREE_NOEXCEPT_STRING = std::is_nothrow_move_assignable<std::string>::value;
79 /*! \libinternal \brief Runner object for supporting setup and execution of mdrun.
81 * This class has responsibility for the lifetime of data structures
82 * that exist for the life of the simulation, e.g. for logging and
85 * It is also responsible for initializing data members that
86 * e.g. correspond to values potentially set by commmand-line
87 * options. Later these will be obtained directly from modules, and
88 * the results of command-line option handling returned directly to
89 * the modules, rather than propagated to them by data members of this
92 * \todo Most of the attributes should be declared by specific modules
93 * as command-line options. Accordingly, they do not conform to the
94 * naming scheme, because that would make for a lot of noise in the
95 * diff, only to have it change again when the options move to their
98 * \todo Preparing logging and MPI contexts could probably be a
99 * higher-level responsibility, so that an Mdrunner would get made
100 * without needing to re-initialize these components (as currently
101 * happens always for the master rank, and differently for the spawned
102 * ranks with thread-MPI).
104 * \ingroup module_mdrun
109 /*! \brief Builder class to manage object creation.
111 * This class is a member of gmx::Mdrunner so that it can initialize
112 * private members of gmx::Mdrunner.
114 * It is non-trivial to establish an initialized gmx::Mdrunner invariant,
115 * so objects can be obtained by clients using a Builder or a move.
116 * Clients cannot default initialize or copy gmx::Mdrunner.
118 class BuilderImplementation;
123 * \brief Copy not allowed.
125 * An Mdrunner has unique resources and it is not clear whether any of
126 * one of those resources should be duplicated or shared unless the
127 * specific use case is known. Either build a fresh runner or use a
128 * helper function for clearly indicated behavior. API clarification may
129 * allow unambiguous initialization by copy in future versions.
133 Mdrunner(const Mdrunner &) = delete;
134 Mdrunner &operator=(const Mdrunner &) = delete;
138 * \brief Mdrunner objects can be passed by value via move semantics.
140 * \param handle runner instance to be moved from.
143 Mdrunner(Mdrunner &&handle) noexcept;
144 //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265
145 Mdrunner &operator=(Mdrunner &&handle) noexcept(BUGFREE_NOEXCEPT_STRING);
148 /*! \brief Driver routine, that calls the different simulation methods. */
150 * Currently, thread-MPI does not spawn threads until during mdrunner() and parallelism
151 * is not initialized until some time during this call...
156 * \brief Add a potential to be evaluated during MD integration.
158 * \param restraint MD restraint potential to apply
159 * \param name User-friendly plain-text name to uniquely identify the puller
161 * This implementation attaches an object providing the gmx::IRestraintPotential
163 * \todo Mdrunner should fetch such resources from the SimulationContext
164 * rather than offering this public interface.
166 void addPotential(std::shared_ptr<IRestraintPotential> restraint,
169 //! Called when thread-MPI spawns threads.
170 t_commrec *spawnThreads(int numThreadsToLaunch) const;
172 /*! \brief Initializes a new Mdrunner from the master.
174 * Run this method in a new thread from a master runner to get additional
175 * workers on spawned threads.
177 * \returns New Mdrunner instance suitable for thread-MPI work on new ranks.
180 * \todo clarify (multiple) invariants during MD runner start-up.
181 * The runner state before and after launching threads is distinct enough that
182 * it should be codified in the invariants of different classes. That would
183 * mean that the object returned by this method would be of a different type
184 * than the object held by the client up to the point of call, and its name
185 * would be changed to "launchOnSpawnedThread" or something not including the
188 Mdrunner cloneOnSpawnedThread() const;
191 /*! \brief Constructor.
193 * Note that when member variables are not present in the constructor
194 * member initialization list (which is true for the default constructor),
195 * then they are initialized with any default member initializer specified
196 * when they were declared, or default initialized. */
197 Mdrunner() = default;
199 //! Parallelism-related user options.
202 //! Filenames and properties from command-line argument values.
203 ArrayRef<const t_filenm> filenames;
205 /*! \brief Output context for writing text files
208 * \todo push this data member down when the information can be queried from an encapsulated resource.
210 gmx_output_env_t *oenv = nullptr;
211 //! Ongoing collection of mdrun options
212 MdrunOptions mdrunOptions;
213 //! Options for the domain decomposition.
214 DomdecOptions domdecOptions;
216 /*! \brief Target short-range interations for "cpu", "gpu", or "auto". Default is "auto".
219 * \todo replace with string or enum class and initialize with sensible value.
221 const char *nbpu_opt = nullptr;
223 /*! \brief Target long-range interactions for "cpu", "gpu", or "auto". Default is "auto".
226 * \todo replace with string or enum class and initialize with sensible value.
228 const char *pme_opt = nullptr;
230 /*! \brief Target long-range interactions FFT/solve stages for "cpu", "gpu", or "auto". Default is "auto".
233 * \todo replace with string or enum class and initialize with sensible value.
235 const char *pme_fft_opt = nullptr;
237 /*! \brief Target bonded interations for "cpu", "gpu", or "auto". Default is "auto".
240 * \todo replace with string or enum class and initialize with sensible value.
242 const char *bonded_opt = nullptr;
244 //! Command-line override for the duration of a neighbor list with the Verlet scheme.
245 int nstlist_cmdline = 0;
246 //! Parameters for replica-exchange simulations.
247 ReplicaExchangeParameters replExParams;
248 //! Print a warning if any force is larger than this (in kJ/mol nm).
251 //! \brief Non-owning handle to file used for logging.
252 t_fileio *logFileHandle = nullptr;
254 //! \brief Non-owning handle to communication data structure.
255 t_commrec *cr = nullptr;
257 //! \brief Non-owning handle to multi-simulation handler.
258 gmx_multisim_t *ms = nullptr;
261 * \brief Handle to restraints manager for the current process.
264 * Use opaque pointer for this implementation detail.
266 std::unique_ptr<RestraintManager> restraintManager_;
269 * \brief Builder for stop signal handler
271 * Optionally provided through MdrunnerBuilder. Client may create a
272 * StopHandlerBuilder and register any number of signal providers before
273 * launching the Mdrunner.
275 * Default is an empty signal handler that will have local signal issuers
276 * added after being passed into the integrator.
279 * We do not need a full type specification here, so we use an opaque pointer.
281 std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_;
285 * \brief Build a gmx::Mdrunner.
287 * Client code (such as `gmx mdrun`) uses this builder to get an initialized Mdrunner.
289 * A builder allows the library to ensure that client code cannot obtain an
290 * uninitialized or partially initialized runner by refusing to build() if the
291 * client has not provided sufficient or self-consistent direction. Director
292 * code can be implemented for different user interfaces, encapsulating any
293 * run-time functionality that does not belong in the library MD code, such
294 * as command-line option processing or interfacing to external libraries.
296 * \ingroup module_mdrun
300 * The initial Builder implementation is neither extensible at run time nor
301 * at compile time. Future implementations should evolve to compose the runner,
302 * rather than just consolidating the parameters for initialization, but there
303 * is not yet a firm design for how flexibly module code will be coupled to
304 * the builder and how much of the client interface will be in this Builder
305 * versus Builders provided by the various modules.
307 * The named components for the initial builder implementation are descriptive
308 * of the state of mdrun at the time, and are not intended to be prescriptive of
310 * The probable course of GROMACS development is for the modular components that
311 * support MD simulation to independently express their input parameters (required
312 * and optional) and to provide some sort of help to the UI for input preparation.
313 * If each module provides or aids the instantiation of a Director
314 * for the client code, the Directors could be constructed with a handle to this
315 * Builder and it would not need a public interface.
317 * As the modules are more clearly encapsulated, each module can provide its own
318 * builder, user interface helpers, and/or composable Director code.
319 * The runner and client code will also have to be updated as appropriate
320 * default behavior is clarified for
321 * (a) default behavior of client when user does not provide input,
322 * (b) default behavior of builder when client does not provide input, and
323 * (c) default behavior of runner when builder does not provide input.
325 class MdrunnerBuilder final
329 * \brief Constructor requires a handle to a SimulationContext to share.
331 * \param context handle to run-time resources and execution environment details.
333 * The calling code must guarantee that the
334 * pointer remains valid for the lifetime of the builder, and that the
335 * resources retrieved from the context remain valid for the lifetime of
336 * the runner produced.
339 * \todo Find and implement appropriate abstraction layers for SimulationContext.
340 * At some point this parameter should become a constant reference or value
341 * instead of a pointer.
342 * Ref e.g. https://redmine.gromacs.org/issues/2587
344 explicit MdrunnerBuilder(compat::not_null<SimulationContext*> context);
347 MdrunnerBuilder() = delete;
348 MdrunnerBuilder(const MdrunnerBuilder&) = delete;
349 MdrunnerBuilder &operator=(const MdrunnerBuilder &) = delete;
352 /*! \brief Allow transfer of ownership with move semantics.
354 * \param builder source object to transfer.
358 MdrunnerBuilder(MdrunnerBuilder && builder) noexcept;
359 MdrunnerBuilder &operator=(MdrunnerBuilder &&builder) noexcept;
363 * \brief Get ownership of an initialized gmx::Mdrunner.
365 * After build() is called, the Builder object should not be used
366 * again. It is an error to call build without first calling all builder
367 * methods described as "required."
369 * \return A new Mdrunner.
371 * \throws APIError if a required component has not been added before calling build().
376 * \brief Set up non-bonded short-range force calculations.
378 * Required. Director code must provide valid options for the non-bonded
379 * interaction code. The builder does not apply any defaults.
381 * \param nbpu_opt Target short-range interactions for "cpu", "gpu", or "auto".
383 * Calling must guarantee that the pointed-to C string is valid through
387 * \todo Replace with string or enum that we can have sensible defaults for.
388 * \todo Either the Builder or modular Director code should provide sensible defaults.
390 MdrunnerBuilder &addNonBonded(const char* nbpu_opt);
393 * \brief Set up long-range electrostatics calculations.
395 * Required. Director code should provide valid options for PME electrostatics,
396 * whether or not PME electrostatics are used. The builder does not apply
397 * any defaults, so client code should be prepared to provide (e.g.) "auto"
398 * in the event no user input or logic provides an alternative argument.
400 * \param pme_opt Target long-range interactions for "cpu", "gpu", or "auto".
401 * \param pme_fft_opt Target long-range interactions FFT/solve stages for "cpu", "gpu", or "auto".
403 * Calling must guarantee that the pointed-to C strings are valid through
407 * The arguments are passed as references to elements of arrays of C strings.
408 * \todo Replace with modern strings or (better) enum classes.
409 * \todo Make optional and/or encapsulate into electrostatics module.
411 MdrunnerBuilder &addElectrostatics(const char* pme_opt,
412 const char* pme_fft_opt);
415 * \brief Assign responsibility for tasks for bonded interactions.
417 * Required. Director code should provide valid options for
418 * bonded interaction task assignment, whether or not such
419 * interactions are present. The builder does not apply any
420 * defaults, so client code should be prepared to provide
421 * (e.g.) "auto" in the event no user input or logic provides
422 * an alternative argument.
424 * \param bonded_opt Target bonded interactions for "cpu", "gpu", or "auto".
426 * Calling must guarantee that the pointed-to C strings are valid through
430 * The arguments are passed as references to elements of arrays of C strings.
431 * \todo Replace with modern strings or (better) enum classes.
432 * \todo Make optional and/or encapsulate into task assignment module.
434 MdrunnerBuilder &addBondedTaskAssignment(const char *bonded_opt);
437 * \brief Provide access to the multisim communicator to use.
439 * \param multisim borrowed handle to multisim record.
441 * Required. Client should get a `gmx_multisim_t*` value from init_multisystem().
442 * Client is responsible for calling done_multisim() on the handle after
445 * \internal Pointer is copied, but calling code retains ownership and
446 * responsibility for multisim. Mdrunner must not do anything that would
447 * invalidate the original copied-from pointer.
449 * \todo Clarify semantics of specifying optional multisim work
450 * \todo Clarify ownership and management of multisim resources.
452 MdrunnerBuilder &addMultiSim(gmx_multisim_t* multisim);
455 * \brief Set MD options not owned by some other module.
457 * Optional. Override simulation parameters
459 * \param options structure to copy
460 * \param forceWarningThreshold Print a warning if any force is larger than this (in kJ/mol nm) (default -1)
463 * \todo Map these parameters to more appropriate encapsulating types.
464 * Find a better way to indicate "unspecified" than a magic value of the parameter type.
466 MdrunnerBuilder &addSimulationMethod(const MdrunOptions &options,
467 real forceWarningThreshold);
470 * \brief Set the domain decomposition module.
472 * Optional. Overrides default constructed DomdecOptions if provided.
474 * \param options options with which to construct domain decomposition.
477 * \todo revisit whether we should be passing this parameter struct or a higher-level handle of some sort.
479 MdrunnerBuilder &addDomainDecomposition(const DomdecOptions &options);
482 * \brief Set Verlet list manager.
484 * Optional. Neighbor list existence, type, and parameters are mostly determined
485 * by the simulation parameters loaded elsewhere. This is just an override.
487 * \param rebuildInterval override for the duration of a neighbor list with the Verlet scheme.
489 MdrunnerBuilder &addNeighborList(int rebuildInterval);
492 * \brief Set replica exchange manager.
494 * Optional. For guidance on preparing a valid ReplicaExchangeParameters
495 * value, refer to the details in mdrun.cpp, the `t_pargs pa[]` defined there,
496 * and the action of parse_common_args() with regards to that structure.
497 * If not provided by client, a default constructed ReplicaExchangeParameters
500 * \param params parameters with which to set up replica exchange.
503 * \todo revisit whether we should be passing this parameter struct or a higher-level handle of some sort.
505 MdrunnerBuilder &addReplicaExchange(const ReplicaExchangeParameters ¶ms);
508 * \brief Specify parameters determining hardware resource allocation.
510 * Optional. If not provided, default-constructed gmx_hw_opt_t will be used.
512 * \param hardwareOptions Parallelism-related user options.
514 MdrunnerBuilder &addHardwareOptions(const gmx_hw_opt_t &hardwareOptions);
517 * \brief Provide the filenames options structure with option values chosen
519 * Required. The object is assumed to have been updated by
520 * parse_common_args or equivalent.
522 * \param filenames Filenames and properties from command-line argument values or defaults.
525 * \todo Modules should manage their own filename options and defaults.
527 MdrunnerBuilder &addFilenames(ArrayRef<const t_filenm> filenames);
530 * \brief Provide parameters for setting up output environment.
532 * Required. Handle is assumed to have been produced by output_env_init
533 * as in parse_common_args.
535 * \param outputEnvironment Output context for writing text files.
538 * \todo Allow client code to set up output environment and provide as a resource.
539 * This parameter is used to set up resources that are dependent on the execution
540 * environment and API context. Such resources should be retrieved by the simulator
541 * from a client-provided resource, but currently the resources are only fully
542 * initialized in Mdrunner.
544 MdrunnerBuilder &addOutputEnvironment(gmx_output_env_t* outputEnvironment);
547 * \brief Provide the filehandle pointer to be used for the MD log.
549 * Required. Either nullptr if no log should be written, or
550 * valid and open reading for writing.
552 * \param logFileHandle Non-owning handle to file used for logging.
555 MdrunnerBuilder &addLogFile(t_fileio *logFileHandle);
558 * \brief Provide a StopHandlerBuilder for the MD stop signal handling.
560 * Optional. Defaults to empty.
562 * Client may provide additional (non-default) issuers of simulation stop
563 * signals by preconfiguring the StopHandlerBuilder used later when the
568 MdrunnerBuilder &addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);
573 std::unique_ptr<Mdrunner::BuilderImplementation> impl_;
578 #endif // GMX_MDRUN_RUNNER_H