Update clang-tidy to clang version 8

[alexxy/gromacs.git] / src / gromacs / mdrun / runner.h

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 2015,2017,2018,2019, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
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/*! \libinternal \file
 *
 * \brief Declares the routine running the inetgrators.
 *
 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
 * \ingroup module_mdrun
 */
#ifndef GMX_MDRUN_RUNNER_H
#define GMX_MDRUN_RUNNER_H

#include <cstdio>

#include <array>
#include <memory>

#include "gromacs/commandline/filenm.h"
#include "gromacs/compat/pointers.h"
#include "gromacs/domdec/options.h"
#include "gromacs/hardware/hw_info.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdrun/mdmodules.h"
#include "gromacs/mdrunutility/handlerestart.h"
#include "gromacs/mdtypes/mdrunoptions.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"

#include "replicaexchange.h"

struct gmx_output_env_t;
struct ReplicaExchangeParameters;
struct t_commrec;
struct t_fileio;

namespace gmx
{

// Todo: move to forward declaration headers...
class MDModules;
class IRestraintPotential; // defined in restraint/restraintpotential.h
class RestraintManager;
class SimulationContext;
class StopHandlerBuilder;

//! Work-around for GCC bug 58265
constexpr bool BUGFREE_NOEXCEPT_STRING = std::is_nothrow_move_assignable<std::string>::value;

/*! \libinternal \brief Runner object for supporting setup and execution of mdrun.
 *
 * This class has responsibility for the lifetime of data structures
 * that exist for the life of the simulation, e.g. for logging and
 * communication.
 *
 * It is also responsible for initializing data members that
 * e.g. correspond to values potentially set by commmand-line
 * options. Later these will be obtained directly from modules, and
 * the results of command-line option handling returned directly to
 * the modules, rather than propagated to them by data members of this
 * class.
 *
 * \todo Most of the attributes should be declared by specific modules
 * as command-line options. Accordingly, they do not conform to the
 * naming scheme, because that would make for a lot of noise in the
 * diff, only to have it change again when the options move to their
 * modules.
 *
 * \todo Preparing logging and MPI contexts could probably be a
 * higher-level responsibility, so that an Mdrunner would get made
 * without needing to re-initialize these components (as currently
 * happens always for the master rank, and differently for the spawned
 * ranks with thread-MPI).
 *
 * \ingroup module_mdrun
 */
class Mdrunner
{
    public:
        /*! \brief Builder class to manage object creation.
         *
         * This class is a member of gmx::Mdrunner so that it can initialize
         * private members of gmx::Mdrunner.
         *
         * It is non-trivial to establish an initialized gmx::Mdrunner invariant,
         * so objects can be obtained by clients using a Builder or a move.
         * Clients cannot default initialize or copy gmx::Mdrunner.
         */
        class BuilderImplementation;

        ~Mdrunner();

        /*!
         * \brief Copy not allowed.
         *
         * An Mdrunner has unique resources and it is not clear whether any of
         * one of those resources should be duplicated or shared unless the
         * specific use case is known. Either build a fresh runner or use a
         * helper function for clearly indicated behavior. API clarification may
         * allow unambiguous initialization by copy in future versions.
         *
         * \{
         */
        Mdrunner(const Mdrunner &)            = delete;
        Mdrunner &operator=(const Mdrunner &) = delete;
        /* \} */

        /*!
         * \brief Mdrunner objects can be passed by value via move semantics.
         *
         * \param handle runner instance to be moved from.
         * \{
         */
        Mdrunner(Mdrunner &&handle) noexcept;
        //NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265
        Mdrunner &operator=(Mdrunner &&handle) noexcept(BUGFREE_NOEXCEPT_STRING);
        /* \} */

        /*! \brief Driver routine, that calls the different simulation methods. */
        /*!
         * Currently, thread-MPI does not spawn threads until during mdrunner() and parallelism
         * is not initialized until some time during this call...
         */
        int mdrunner();

        /*!
         * \brief Add a potential to be evaluated during MD integration.
         *
         * \param restraint MD restraint potential to apply
         * \param name User-friendly plain-text name to uniquely identify the puller
         *
         * This implementation attaches an object providing the gmx::IRestraintPotential
         * interface.
         * \todo Mdrunner should fetch such resources from the SimulationContext
         * rather than offering this public interface.
         */
        void addPotential(std::shared_ptr<IRestraintPotential> restraint,
                          const std::string                   &name);

        //! Called when thread-MPI spawns threads.
        t_commrec *spawnThreads(int numThreadsToLaunch) const;

        /*! \brief Initializes a new Mdrunner from the master.
         *
         * Run this method in a new thread from a master runner to get additional
         * workers on spawned threads.
         *
         * \returns New Mdrunner instance suitable for thread-MPI work on new ranks.
         *
         * \internal
         * \todo clarify (multiple) invariants during MD runner start-up.
         * The runner state before and after launching threads is distinct enough that
         * it should be codified in the invariants of different classes. That would
         * mean that the object returned by this method would be of a different type
         * than the object held by the client up to the point of call, and its name
         * would be changed to "launchOnSpawnedThread" or something not including the
         * word "clone".
         */
        Mdrunner cloneOnSpawnedThread() const;

    private:
        /*! \brief Constructor. */
        explicit Mdrunner(std::unique_ptr<MDModules> mdModules);

        //! Parallelism-related user options.
        gmx_hw_opt_t             hw_opt;

        //! Filenames and properties from command-line argument values.
        ArrayRef<const t_filenm> filenames;

        /*! \brief Output context for writing text files
         *
         * \internal
         * \todo push this data member down when the information can be queried from an encapsulated resource.
         */
        gmx_output_env_t                       *oenv = nullptr;
        //! Ongoing collection of mdrun options
        MdrunOptions                            mdrunOptions;
        //! Options for the domain decomposition.
        DomdecOptions                           domdecOptions;

        /*! \brief Target short-range interations for "cpu", "gpu", or "auto". Default is "auto".
         *
         * \internal
         * \todo replace with string or enum class and initialize with sensible value.
         */
        const char                             *nbpu_opt = nullptr;

        /*! \brief Target long-range interactions for "cpu", "gpu", or "auto". Default is "auto".
         *
         * \internal
         * \todo replace with string or enum class and initialize with sensible value.
         */
        const char                             *pme_opt = nullptr;

        /*! \brief Target long-range interactions FFT/solve stages for "cpu", "gpu", or "auto". Default is "auto".
         *
         * \internal
         * \todo replace with string or enum class and initialize with sensible value.
         */
        const char                             *pme_fft_opt = nullptr;

        /*! \brief Target bonded interations for "cpu", "gpu", or "auto". Default is "auto".
         *
         * \internal
         * \todo replace with string or enum class and initialize with sensible value.
         */
        const char                             *bonded_opt = nullptr;

        //! Command-line override for the duration of a neighbor list with the Verlet scheme.
        int                                     nstlist_cmdline = 0;
        //! Parameters for replica-exchange simulations.
        ReplicaExchangeParameters               replExParams;
        //! Print a warning if any force is larger than this (in kJ/mol nm).
        real                                    pforce = -1;

        //! Handle to file used for logging.
        LogFilePtr logFileGuard = nullptr;
        //! \brief Non-owning handle to file used for logging.
        t_fileio                               *logFileHandle = nullptr;

        //! \brief Non-owning handle to communication data structure.
        t_commrec                              *cr = nullptr;

        //! \brief Non-owning handle to multi-simulation handler.
        gmx_multisim_t                         *ms = nullptr;

        //! Whether the simulation will start afresh, or restart with/without appending.
        StartingBehavior startingBehavior = StartingBehavior::NewSimulation;

        /*!
         * \brief Handle to restraints manager for the current process.
         *
         * \internal
         * Use opaque pointer for this implementation detail.
         */
        std::unique_ptr<RestraintManager>     restraintManager_;

        /*!
         * \brief Builder for stop signal handler
         *
         * Optionally provided through MdrunnerBuilder. Client may create a
         * StopHandlerBuilder and register any number of signal providers before
         * launching the Mdrunner.
         *
         * Default is an empty signal handler that will have local signal issuers
         * added after being passed into the integrator.
         *
         * \internal
         * We do not need a full type specification here, so we use an opaque pointer.
         */
        std::unique_ptr<StopHandlerBuilder>    stopHandlerBuilder_;
        //! The modules that comprise mdrun.
        std::unique_ptr<MDModules>             mdModules_;
};

/*! \libinternal
 * \brief Build a gmx::Mdrunner.
 *
 * Client code (such as `gmx mdrun`) uses this builder to get an initialized Mdrunner.
 *
 * A builder allows the library to ensure that client code cannot obtain an
 * uninitialized or partially initialized runner by refusing to build() if the
 * client has not provided sufficient or self-consistent direction. Director
 * code can be implemented for different user interfaces, encapsulating any
 * run-time functionality that does not belong in the library MD code, such
 * as command-line option processing or interfacing to external libraries.
 *
 * \ingroup module_mdrun
 *
 * \internal
 *
 * The initial Builder implementation is neither extensible at run time nor
 * at compile time. Future implementations should evolve to compose the runner,
 * rather than just consolidating the parameters for initialization, but there
 * is not yet a firm design for how flexibly module code will be coupled to
 * the builder and how much of the client interface will be in this Builder
 * versus Builders provided by the various modules.
 *
 * The named components for the initial builder implementation are descriptive
 * of the state of mdrun at the time, and are not intended to be prescriptive of
 * future design.
 * The probable course of GROMACS development is for the modular components that
 * support MD simulation to independently express their input parameters (required
 * and optional) and to provide some sort of help to the UI for input preparation.
 * If each module provides or aids the instantiation of a Director
 * for the client code, the Directors could be constructed with a handle to this
 * Builder and it would not need a public interface.
 *
 * As the modules are more clearly encapsulated, each module can provide its own
 * builder, user interface helpers, and/or composable Director code.
 * The runner and client code will also have to be updated as appropriate
 * default behavior is clarified for
 * (a) default behavior of client when user does not provide input,
 * (b) default behavior of builder when client does not provide input, and
 * (c) default behavior of runner when builder does not provide input.
 */
class MdrunnerBuilder final
{
    public:
        /*!
         * \brief Constructor requires a handle to a SimulationContext to share.
         *
         * \param mdModules  The handle to the set of modules active in mdrun
         * \param context    The handle to run-time resources and execution environment details.
         *
         * The calling code must guarantee that the
         * pointer remains valid for the lifetime of the builder, and that the
         * resources retrieved from the context remain valid for the lifetime of
         * the runner produced.
         *
         * \internal
         * \todo Find and implement appropriate abstraction layers for SimulationContext.
         * At some point this parameter should become a constant reference or value
         * instead of a pointer.
         * Ref e.g. https://redmine.gromacs.org/issues/2587
         */
        explicit MdrunnerBuilder(std::unique_ptr<MDModules>           mdModules,
                                 compat::not_null<SimulationContext*> context);

        //! \cond
        MdrunnerBuilder() = delete;
        MdrunnerBuilder(const MdrunnerBuilder&)             = delete;
        MdrunnerBuilder &operator=(const MdrunnerBuilder &) = delete;
        //! \endcond

        /*! \brief Allow transfer of ownership with move semantics.
         *
         * \param builder source object to transfer.
         *
         * \{
         */
        MdrunnerBuilder(MdrunnerBuilder && builder) noexcept;
        MdrunnerBuilder &operator=(MdrunnerBuilder &&builder) noexcept;
        //! \}

        /*!
         * \brief Get ownership of an initialized gmx::Mdrunner.
         *
         * After build() is called, the Builder object should not be used
         * again. It is an error to call build without first calling all builder
         * methods described as "required."
         *
         * \return A new Mdrunner.
         *
         * \throws APIError if a required component has not been added before calling build().
         */
        Mdrunner build();

        /*!
         * \brief Set up non-bonded short-range force calculations.
         *
         * Required. Director code must provide valid options for the non-bonded
         * interaction code. The builder does not apply any defaults.
         *
         * \param nbpu_opt Target short-range interactions for "cpu", "gpu", or "auto".
         *
         * Calling must guarantee that the pointed-to C string is valid through
         * simulation launch.
         *
         * \internal
         * \todo Replace with string or enum that we can have sensible defaults for.
         * \todo Either the Builder or modular Director code should provide sensible defaults.
         */
        MdrunnerBuilder &addNonBonded(const char* nbpu_opt);

        /*!
         * \brief Set up long-range electrostatics calculations.
         *
         * Required. Director code should provide valid options for PME electrostatics,
         * whether or not PME electrostatics are used. The builder does not apply
         * any defaults, so client code should be prepared to provide (e.g.) "auto"
         * in the event no user input or logic provides an alternative argument.
         *
         * \param pme_opt Target long-range interactions for "cpu", "gpu", or "auto".
         * \param pme_fft_opt Target long-range interactions FFT/solve stages for "cpu", "gpu", or "auto".
         *
         * Calling must guarantee that the pointed-to C strings are valid through
         * simulation launch.
         *
         * \internal
         * The arguments are passed as references to elements of arrays of C strings.
         * \todo Replace with modern strings or (better) enum classes.
         * \todo Make optional and/or encapsulate into electrostatics module.
         */
        MdrunnerBuilder &addElectrostatics(const char* pme_opt,
                                           const char* pme_fft_opt);

        /*!
         * \brief Assign responsibility for tasks for bonded interactions.
         *
         * Required. Director code should provide valid options for
         * bonded interaction task assignment, whether or not such
         * interactions are present. The builder does not apply any
         * defaults, so client code should be prepared to provide
         * (e.g.) "auto" in the event no user input or logic provides
         * an alternative argument.
         *
         * \param bonded_opt Target bonded interactions for "cpu", "gpu", or "auto".
         *
         * Calling must guarantee that the pointed-to C strings are valid through
         * simulation launch.
         *
         * \internal
         * The arguments are passed as references to elements of arrays of C strings.
         * \todo Replace with modern strings or (better) enum classes.
         * \todo Make optional and/or encapsulate into task assignment module.
         */
        MdrunnerBuilder &addBondedTaskAssignment(const char *bonded_opt);

        /*!
         * \brief Provide access to the multisim communicator to use.
         *
         * \param multisim borrowed handle to multisim record.
         *
         * Required. Client should get a `gmx_multisim_t*` value from init_multisystem().
         * Client is responsible for calling done_multisim() on the handle after
         * simulation.
         *
         * \internal Pointer is copied, but calling code retains ownership and
         * responsibility for multisim. Mdrunner must not do anything that would
         * invalidate the original copied-from pointer.
         *
         * \todo Clarify semantics of specifying optional multisim work
         * \todo Clarify ownership and management of multisim resources.
         */
        MdrunnerBuilder &addMultiSim(gmx_multisim_t* multisim);

        /*!
         * \brief Set MD options not owned by some other module.
         *
         * Optional. Override simulation parameters
         *
         * \param options structure to copy
         * \param forceWarningThreshold Print a warning if any force is larger than this (in kJ/mol nm) (default -1)
         * \param startingBehavior Whether the simulation will start afresh, or restart with/without appending.
         *
         * \internal
         * \todo Map these parameters to more appropriate encapsulating types.
         * Find a better way to indicate "unspecified" than a magic value of the parameter type.
         */
        MdrunnerBuilder &addSimulationMethod(const MdrunOptions &options,
                                             real                forceWarningThreshold,
                                             StartingBehavior    startingBehavior);

        /*!
         * \brief Set the domain decomposition module.
         *
         * Optional. Overrides default constructed DomdecOptions if provided.
         *
         * \param options options with which to construct domain decomposition.
         *
         * \internal
         * \todo revisit whether we should be passing this parameter struct or a higher-level handle of some sort.
         */
        MdrunnerBuilder &addDomainDecomposition(const DomdecOptions &options);

        /*!
         * \brief Set Verlet list manager.
         *
         * Optional. Neighbor list existence, type, and parameters are mostly determined
         * by the simulation parameters loaded elsewhere. This is just an override.
         *
         * \param rebuildInterval override for the duration of a neighbor list with the Verlet scheme.
         */
        MdrunnerBuilder &addNeighborList(int rebuildInterval);

        /*!
         * \brief Set replica exchange manager.
         *
         * Optional. For guidance on preparing a valid ReplicaExchangeParameters
         * value, refer to the details in mdrun.cpp, the `t_pargs pa[]` defined there,
         * and the action of parse_common_args() with regards to that structure.
         * If not provided by client, a default constructed ReplicaExchangeParameters
         * is used.
         *
         * \param params parameters with which to set up replica exchange.
         *
         * \internal
         * \todo revisit whether we should be passing this parameter struct or a higher-level handle of some sort.
         */
        MdrunnerBuilder &addReplicaExchange(const ReplicaExchangeParameters &params);

        /*!
         * \brief Specify parameters determining hardware resource allocation.
         *
         * Optional. If not provided, default-constructed gmx_hw_opt_t will be used.
         *
         * \param hardwareOptions Parallelism-related user options.
         */
        MdrunnerBuilder &addHardwareOptions(const gmx_hw_opt_t &hardwareOptions);

        /*!
         * \brief Provide the filenames options structure with option values chosen
         *
         * Required. The object is assumed to have been updated by
         * parse_common_args or equivalent.
         *
         * \param filenames Filenames and properties from command-line argument values or defaults.
         *
         * \internal
         * \todo Modules should manage their own filename options and defaults.
         */
        MdrunnerBuilder &addFilenames(ArrayRef<const t_filenm> filenames);

        /*!
         * \brief Provide parameters for setting up output environment.
         *
         * Required. Handle is assumed to have been produced by output_env_init
         * as in parse_common_args.
         *
         * \param outputEnvironment Output context for writing text files.
         *
         * \internal
         * \todo Allow client code to set up output environment and provide as a resource.
         * This parameter is used to set up resources that are dependent on the execution
         * environment and API context. Such resources should be retrieved by the simulator
         * from a client-provided resource, but currently the resources are only fully
         * initialized in Mdrunner.
         */
        MdrunnerBuilder &addOutputEnvironment(gmx_output_env_t* outputEnvironment);

        /*!
         * \brief Provide the filehandle pointer to be used for the MD log.
         *
         * Required. Either nullptr if no log should be written, or
         * valid and open reading for writing.
         *
         * \param logFileHandle Non-owning handle to file used for logging.
         * \internal
         */
        MdrunnerBuilder &addLogFile(t_fileio *logFileHandle);

        /*!
         * \brief Provide a StopHandlerBuilder for the MD stop signal handling.
         *
         * Optional. Defaults to empty.
         *
         * Client may provide additional (non-default) issuers of simulation stop
         * signals by preconfiguring the StopHandlerBuilder used later when the
         * simulation runs.
         *
         * \param builder
         */
        MdrunnerBuilder &addStopHandlerBuilder(std::unique_ptr<StopHandlerBuilder> builder);

        ~MdrunnerBuilder();

    private:
        std::unique_ptr<Mdrunner::BuilderImplementation> impl_;
};

}      // namespace gmx

#endif // GMX_MDRUN_RUNNER_H