[alexxy/gromacs.git] / api / gmxapi / cpp / context.cpp

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/*! \file
 * \brief Implementation details of gmxapi::Context
 *
 * \todo Share mdrun input handling implementation via modernized modular options framework.
 * Initial implementation of `launch` relies on borrowed code from the mdrun command
 * line input processing.
 *
 * \author M. Eric Irrgang <ericirrgang@gmail.com>
 * \ingroup gmxapi
 */

#include "gmxapi/context.h"

#include <cstring>

#include <memory>
#include <utility>
#include <vector>

#include "gromacs/commandline/pargs.h"
#include "gromacs/commandline/filenm.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/mdlib/stophandler.h"
#include "gromacs/mdrunutility/logging.h"
#include "gromacs/mdrunutility/multisim.h"
#include "gromacs/mdrun/runner.h"
#include "gromacs/mdrunutility/handlerestart.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/init.h"
#include "gromacs/utility/smalloc.h"

#include "gmxapi/mpi/multiprocessingresources.h"
#include "gmxapi/exceptions.h"
#include "gmxapi/session.h"
#include "gmxapi/status.h"
#include "gmxapi/version.h"

#include "context_impl.h"
#include "createsession.h"
#include "session_impl.h"
#include "workflow.h"

namespace gmxapi
{

MpiContextManager::MpiContextManager(MPI_Comm communicator) :
    communicator_(std::make_unique<MPI_Comm>(communicator))
{
    GMX_ASSERT(*communicator_ == MPI_COMM_NULL ? !GMX_LIB_MPI : GMX_LIB_MPI,
               "Invalid communicator value for this library configuration.");
    // Safely increments the GROMACS MPI initialization counter after checking
    // whether the MPI library is already initialized. After this call, MPI_Init
    // or MPI_Init_thread has been called exactly once.
    gmx::init(nullptr, nullptr);
    GMX_RELEASE_ASSERT(!GMX_LIB_MPI || gmx_mpi_initialized(),
                       "MPI should be initialized before reaching this point.");
    if (this->communicator() != MPI_COMM_NULL)
    {
        // Synchronise at the point of acquiring a MpiContextManager.
        gmx_barrier(this->communicator());
    }
};

MpiContextManager::~MpiContextManager()
{
    if (communicator_)
    {
        // This is always safe to call. It is a no-op if
        // thread-MPI, and if the constructor completed then the
        // MPI library is initialized with reference counting.
        gmx::finalize();
    }
}

MpiContextManager::MpiContextManager() :
    MpiContextManager(GMX_LIB_MPI ? MPI_COMM_WORLD : MPI_COMM_NULL)
{
}

MPI_Comm MpiContextManager::communicator() const
{
    if (!communicator_)
    {
        throw UsageError("Invalid MpiContextManager. Accessed after `move`?");
    }
    return *communicator_;
}

ContextImpl::~ContextImpl() = default;

Context createContext(const ResourceAssignment& resources)
{
    CommHandle handle;
    resources.applyCommunicator(&handle);
    if (handle.communicator == MPI_COMM_NULL)
    {
        throw UsageError("MPI-enabled Simulator contexts require a valid communicator.");
    }
    auto contextmanager = MpiContextManager(handle.communicator);
    auto impl           = ContextImpl::create(std::move(contextmanager));
    GMX_ASSERT(impl, "ContextImpl creation method should not be able to return null.");
    auto context = Context(impl);
    return context;
}

Context createContext()
{
    MpiContextManager contextmanager;
    auto              impl = ContextImpl::create(std::move(contextmanager));
    GMX_ASSERT(impl, "ContextImpl creation method should not be able to return null.");
    auto context = Context(impl);
    return context;
}

ContextImpl::ContextImpl(MpiContextManager&& mpi) noexcept(std::is_nothrow_constructible_v<gmx::LegacyMdrunOptions>) :
    mpi_(std::move(mpi))
{
    // Confirm our understanding of the MpiContextManager invariant.
    GMX_ASSERT(mpi_.communicator() == MPI_COMM_NULL ? !GMX_LIB_MPI : GMX_LIB_MPI,
               "Precondition is an appropriate communicator for the library environment.");
    // Make sure we didn't change the data members and overlook implementation details.
    GMX_ASSERT(session_.expired(),
               "This implementation assumes an expired weak_ptr at initialization.");
}

std::shared_ptr<ContextImpl> ContextImpl::create(MpiContextManager&& mpi)
{
    std::shared_ptr<ContextImpl> impl;
    impl.reset(new ContextImpl(std::move(mpi)));
    return impl;
}

std::shared_ptr<Session> ContextImpl::launch(const Workflow& work)
{
    using namespace gmx;
    // Much of this implementation is not easily testable: we need tools to inspect simulation
    // results and to modify simulation inputs.

    std::shared_ptr<Session> launchedSession = nullptr;

    // This implementation can only run one workflow at a time.
    // Check whether we are already aware of an active session.
    if (session_.expired())
    {
        // Check workflow spec, build graph for current context, launch and return new session.
        // \todo This is specific to the session implementation...
        auto        mdNode = work.getNode("MD");
        std::string filename{};
        if (mdNode != nullptr)
        {
            filename = mdNode->params();
        }

        /* Mock up the argv interface used by option processing infrastructure.
         *
         * As default behavior, automatically extend trajectories from the checkpoint file.
         * In the future, our API for objects used to initialize a simulation needs to address the fact that currently a
         * microstate requires data from both the TPR and checkpoint file to be fully specified. Put another way,
         * current
         * GROMACS simulations can take a "configuration" as input that does not constitute a complete microstate in
         * terms of hidden degrees of freedom (integrator/thermostat/barostat/PRNG state), but we want a clear notion of
         * a microstate for gmxapi interfaces.
         *
         * TODO: Remove `-s` and `-cpi` arguments.
         *       Ref: https://gitlab.com/gromacs/gromacs/-/issues/3652
         */

        // Set input TPR name
        mdArgs_.emplace_back("-s");
        mdArgs_.emplace_back(filename);

        // Set checkpoint file name
        mdArgs_.emplace_back("-cpi");
        mdArgs_.emplace_back("state.cpt");
        /* Note: we normalize the checkpoint file name, but not its full path.
         * Through version 0.0.8, gmxapi clients change working directory
         * for each session, so relative path(s) below are appropriate.
         * A future gmxapi version should avoid changing directories once the
         * process starts and instead manage files (paths) in an absolute and
         * immutable way, with abstraction provided through the Context chain-of-responsibility.
         * TODO: API abstractions for initializing simulations that may be new or partially
         * complete. Reference gmxapi milestone 13 at https://gitlab.com/gromacs/gromacs/-/issues/2585
         */

        // Create a mock argv. Note that argv[0] is expected to hold the program name.
        const int  offset = 1;
        const auto argc   = static_cast<size_t>(mdArgs_.size() + offset);
        auto       argv   = std::vector<char*>(argc, nullptr);
        // argv[0] is ignored, but should be a valid string (e.g. null terminated array of char)
        argv[0]  = new char[1];
        *argv[0] = '\0';
        for (size_t argvIndex = offset; argvIndex < argc; ++argvIndex)
        {
            const auto& mdArg = mdArgs_[argvIndex - offset];
            argv[argvIndex]   = new char[mdArg.length() + 1];
            strcpy(argv[argvIndex], mdArg.c_str());
        }

        auto mdModules = std::make_unique<MDModules>();

        const char* desc[] = { "gmxapi placeholder text" };
        if (options_.updateFromCommandLine(argc, argv.data(), desc) == 0)
        {
            return nullptr;
        }

        ArrayRef<const std::string> multiSimDirectoryNames =
                opt2fnsIfOptionSet("-multidir", ssize(options_.filenames), options_.filenames.data());

        // The SimulationContext is necessary with gmxapi so that
        // resources owned by the client code can have suitable
        // lifetime. The gmx wrapper binary uses the same infrastructure,
        // but the lifetime is now trivially that of the invocation of the
        // wrapper binary.
        auto communicator = mpi_.communicator();
        // Confirm the precondition for simulationContext().
        GMX_ASSERT(communicator == MPI_COMM_NULL ? !GMX_LIB_MPI : GMX_LIB_MPI,
                   "Context communicator does not have an appropriate value for the environment.");
        SimulationContext simulationContext(communicator, multiSimDirectoryNames);


        StartingBehavior startingBehavior = StartingBehavior::NewSimulation;
        LogFilePtr       logFileGuard     = nullptr;
        gmx_multisim_t*  ms               = simulationContext.multiSimulation_.get();
        std::tie(startingBehavior, logFileGuard) =
                handleRestart(findIsSimulationMasterRank(ms, simulationContext.simulationCommunicator_),
                              communicator, ms, options_.mdrunOptions.appendingBehavior,
                              ssize(options_.filenames), options_.filenames.data());

        auto builder = MdrunnerBuilder(std::move(mdModules),
                                       compat::not_null<SimulationContext*>(&simulationContext));
        builder.addSimulationMethod(options_.mdrunOptions, options_.pforce, startingBehavior);
        builder.addDomainDecomposition(options_.domdecOptions);
        // \todo pass by value
        builder.addNonBonded(options_.nbpu_opt_choices[0]);
        // \todo pass by value
        builder.addElectrostatics(options_.pme_opt_choices[0], options_.pme_fft_opt_choices[0]);
        builder.addBondedTaskAssignment(options_.bonded_opt_choices[0]);
        builder.addUpdateTaskAssignment(options_.update_opt_choices[0]);
        builder.addNeighborList(options_.nstlist_cmdline);
        builder.addReplicaExchange(options_.replExParams);
        // Need to establish run-time values from various inputs to provide a resource handle to Mdrunner
        builder.addHardwareOptions(options_.hw_opt);

        // \todo File names are parameters that should be managed modularly through further factoring.
        builder.addFilenames(options_.filenames);
        // TODO: Remove `s` and `-cpi` from LegacyMdrunOptions before launch(). #3652
        auto simulationInput = makeSimulationInput(options_);
        builder.addInput(simulationInput);

        // Note: The gmx_output_env_t life time is not managed after the call to parse_common_args.
        // \todo Implement lifetime management for gmx_output_env_t.
        // \todo Output environment should be configured outside of Mdrunner and provided as a resource.
        builder.addOutputEnvironment(options_.oenv);
        builder.addLogFile(logFileGuard.get());

        // Note, creation is not mature enough to be exposed in the external API yet.
        launchedSession = createSession(shared_from_this(), std::move(builder),
                                        std::move(simulationContext), std::move(logFileGuard));

        // Clean up argv once builder is no longer in use
        // TODO: Remove long-lived references to argv so this is no longer necessary.
        //       Ref https://gitlab.com/gromacs/gromacs/-/issues/2877
        for (auto&& string : argv)
        {
            if (string != nullptr)
            {
                delete[] string;
                string = nullptr;
            }
        }
    }
    else
    {
        throw gmxapi::ProtocolError("Tried to launch a session while a session is still active.");
    }

    if (launchedSession != nullptr)
    {
        // Update weak reference.
        session_ = launchedSession;
    }
    return launchedSession;
}

std::shared_ptr<Session> Context::launch(const Workflow& work)
{
    return impl_->launch(work);
}

Context::Context(std::shared_ptr<ContextImpl> impl) : impl_{ std::move(impl) }
{
    if (!impl_)
    {
        throw UsageError("Context requires a non-null implementation member.");
    }
}

void Context::setMDArgs(const MDArgs& mdArgs)
{
    impl_->mdArgs_ = mdArgs;
}

Context::~Context() = default;

} // end namespace gmxapi