runner.cpp
shellfc.cpp
simulationcontext.cpp
+ simulationinput.cpp
+ simulationinpututility.cpp
simulatorbuilder.cpp
tpi.cpp
)
#include "isimulator.h"
#include "membedholder.h"
#include "replicaexchange.h"
+#include "simulationinput.h"
+#include "simulationinpututility.h"
#include "simulatorbuilder.h"
#if GMX_FAHCORE
// Print citation requests after all software/hardware printing
pleaseCiteGromacs(fplog);
+ // TODO: Use SimulationInputHolder member to access SimulationInput. Issue #3374.
+ const auto* const tprFilename = ftp2fn(efTPR, filenames.size(), filenames.data());
+ const auto* const cpiFilename = opt2fn("-cpi", filenames.size(), filenames.data());
+ // Note that, as of this change, there is no public API for simulationInput or its creation.
+ // TODO: (#3374) Public API for providing simulationInput from client.
+ auto simulationInput = detail::makeSimulationInput(tprFilename, cpiFilename);
+
// Note: legacy program logic relies on checking whether these pointers are assigned.
// Objects may or may not be allocated later.
std::unique_ptr<t_inputrec> inputrec;
/* Read (nearly) all data required for the simulation
* and keep the partly serialized tpr contents to send to other ranks later
*/
- *partialDeserializedTpr = read_tpx_state(ftp2fn(efTPR, filenames.size(), filenames.data()),
- inputrec.get(), globalState.get(), &mtop);
+ applyGlobalSimulationState(*simulationInput.object_, partialDeserializedTpr.get(),
+ globalState.get(), inputrec.get(), &mtop);
}
/* Check and update the hardware options for internal consistency */
inputrec->nsteps = -1;
}
- load_checkpoint(opt2fn_master("-cpi", filenames.size(), filenames.data(), cr),
- logFileHandle, cr, domdecOptions.numCells, inputrec.get(), globalState.get(),
- &observablesHistory, mdrunOptions.reproducible, mdModules_->notifier(),
+ // Finish applying initial simulation state information from external sources on all ranks.
+ // Reconcile checkpoint file data with Mdrunner state established up to this point.
+ applyLocalState(*simulationInput.object_, logFileHandle, cr, domdecOptions.numCells,
+ inputrec.get(), globalState.get(), &observablesHistory,
+ mdrunOptions.reproducible, mdModules_->notifier(),
modularSimulatorCheckpointData.get(), useModularSimulator);
+ // TODO: (#3652) Synchronize filesystem state, SimulationInput contents, and program
+ // invariants
+ // on all code paths.
+ // Write checkpoint or provide hook to update SimulationInput.
+ // If there was a checkpoint file, SimulationInput contains more information
+ // than if there wasn't. At this point, we have synchronized the in-memory
+ // state with the filesystem state only for restarted simulations. We should
+ // be calling applyLocalState unconditionally and expect that the completeness
+ // of SimulationInput is not dependent on its creation method.
if (startingBehavior == StartingBehavior::RestartWithAppending && logFileHandle)
{
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#include "gmxpre.h"
+
+#include "simulationinput.h"
+
+#include <utility>
+
+#include "simulationinput_impl.h"
+
+namespace gmx
+{
+
+struct MdModulesNotifier;
+
+SimulationInput::SimulationInput(const char* tprFilename, const char* cpiFilename) :
+ tprFilename_(tprFilename),
+ cpiFilename_(cpiFilename)
+{
+}
+
+SimulationInputHolder::SimulationInputHolder() = default;
+
+SimulationInputHolder::~SimulationInputHolder() = default;
+
+namespace detail
+{
+
+SimulationInputHolder makeSimulationInput(const char* tprFilename, const char* cpiFilename)
+{
+ // Note: it seems clear that we will want a SimulationInput to be linked to
+ // a communications context (whether the SimulationContext or something higher level)
+ // so that it can encapsulate the data locality details. Otherwise, we have
+ // to choose whether to read the files everywhere or just to store the
+ // filenames until a communications context is known.
+ auto simulationInput = std::make_unique<SimulationInput>(tprFilename, cpiFilename);
+
+ SimulationInputHolder holder;
+ holder.object_ = std::move(simulationInput);
+ return holder;
+}
+
+} // end namespace detail
+
+} // end namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief Public interface for SimulationInput facilities.
+ *
+ * \author M. Eric Irrgang <ericirrgang@gmail.com>
+ * \ingroup module_mdrun
+ */
+
+#ifndef GMX_MDRUN_SIMULATIONINPUT_H
+#define GMX_MDRUN_SIMULATIONINPUT_H
+
+#include <memory>
+
+namespace gmx
+{
+
+// Forward declarations for types from other modules that are opaque to the public API.
+class LegacyMdrunOptions;
+
+/*!
+ * \brief Prescription for molecular simulation.
+ *
+ * Represents the complete and unique information needed to generate a simulation
+ * trajectory segment. SimulationInput objects are opaque to the public API.
+ * Clients can acquire SimulationInput objects through makeSimulationInput().
+ *
+ * See also https://gitlab.com/gromacs/gromacs/-/issues/3379 for design and development road map.
+ */
+class SimulationInput;
+
+/*!
+ * \brief Owning handle to a SimulationInput object.
+ *
+ * SimulationInput has no public API. Acquire a SimulationInputHolder with makeSimulationInput().
+ * See https://gitlab.com/gromacs/gromacs/-/issues/3374
+ */
+class SimulationInputHolder
+{
+public:
+ SimulationInputHolder();
+ ~SimulationInputHolder();
+
+ SimulationInputHolder(SimulationInputHolder&&) noexcept = default;
+ SimulationInputHolder& operator=(SimulationInputHolder&&) noexcept = default;
+
+ std::unique_ptr<SimulationInput> object_;
+};
+
+namespace detail
+{
+
+/*! \brief Get a SimulationInput.
+ *
+ * \internal
+ * Design notes: SimulationInput creation will warrant a builder protocol, and
+ * this helper can evolve into a director to apply the contents of LegacyMdrunOptions,
+ * while such an operation is still relevant.
+ *
+ * Example:
+ * // After preparing a LegacyMdrunOptions and calling handleRestart()...
+ * SimulationInputBuilder builder;
+ * auto simulationInputHandle = makeSimulationInput(options, &builder);
+ *
+ * // In addition to MdrunnerBuilder::addFiles(),
+ * mdrunnerBuilder.addInput(simulationInputHandle.get());
+ *
+ */
+SimulationInputHolder makeSimulationInput(const char* tprFilename, const char* cpiFilename);
+
+} // end namespace detail
+
+} // end namespace gmx
+
+#endif // GMX_MDRUN_SIMULATIONINPUT_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GROMACS_SIMULATIONINPUT_IMPL_H
+#define GROMACS_SIMULATIONINPUT_IMPL_H
+
+/*! \libinternal \file
+ * \brief Library interface for SimulationInput.
+ *
+ * \ingroup module_mdrun
+ */
+
+#include <string>
+
+namespace gmx
+{
+
+struct MdModulesNotifier;
+
+/*
+ * \brief Prescription for molecular simulation.
+ *
+ * In the first implementation, this is a POD struct to allow removal of direct
+ * references to TPR and CPT files from Mdrunner. The interface for SimulationInput
+ * should be considered to be *completely unspecified* until resolution of
+ * https://gitlab.com/gromacs/gromacs/-/issues/3374
+ *
+ * Clients should use the utility functions defined in simulationinpututility.h
+ *
+ * Design note: It is probably sufficient for future versions to compose SimulationInput
+ * through a Builder rather than to subclass an Interface or base class. Outside of this
+ * translation unit, we should avoid coupling to the class definition until/unless we
+ * develop a much better understanding of simulation input portability.
+ */
+class SimulationInput
+{
+public:
+ SimulationInput(const char* tprFilename, const char* cpiFilename);
+
+ std::string tprFilename_;
+ std::string cpiFilename_;
+};
+
+} // end namespace gmx
+
+#endif // GROMACS_SIMULATIONINPUT_IMPL_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#include "gmxpre.h"
+
+#include "simulationinpututility.h"
+
+#include "gromacs/fileio/checkpoint.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/observableshistory.h"
+#include "gromacs/mdtypes/state.h"
+
+#include "simulationinput_impl.h"
+
+namespace gmx
+{
+
+void applyGlobalSimulationState(const SimulationInput& simulationInput,
+ PartialDeserializedTprFile* partialDeserializedTpr,
+ t_state* globalState,
+ t_inputrec* inputRecord,
+ gmx_mtop_t* molecularTopology)
+{
+ *partialDeserializedTpr = read_tpx_state(simulationInput.tprFilename_.c_str(), inputRecord,
+ globalState, molecularTopology);
+}
+
+void applyLocalState(const SimulationInput& simulationInput,
+ t_fileio* logfio,
+ const t_commrec* cr,
+ int* dd_nc,
+ t_inputrec* inputRecord,
+ t_state* state,
+ ObservablesHistory* observablesHistory,
+ bool reproducibilityRequested,
+ const MdModulesNotifier& mdModulesNotifier,
+ gmx::ReadCheckpointDataHolder* modularSimulatorCheckpointData,
+ const bool useModularSimulator)
+{
+ load_checkpoint(simulationInput.cpiFilename_.c_str(), logfio, cr, dd_nc, inputRecord, state,
+ observablesHistory, reproducibilityRequested, mdModulesNotifier,
+ modularSimulatorCheckpointData, useModularSimulator);
+}
+
+} // end namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, 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
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief Utilities for interacting with SimulationInput.
+ *
+ * \author M. Eric Irrgang <ericirrgang@gmail.com>
+ * \ingroup module_mdrun
+ */
+
+#ifndef GMX_MDRUN_SIMULATIONINPUTUTILITY_H
+#define GMX_MDRUN_SIMULATIONINPUTUTILITY_H
+
+#include <memory>
+
+#include "gromacs/mdtypes/checkpointdata.h"
+#include "gromacs/utility/mdmodulenotification.h"
+
+#include "simulationinput.h"
+
+// Forward declarations for types from other modules that are opaque to the public API.
+// TODO: Document the sources of these symbols or import a (self-documenting) fwd header.
+struct gmx_mtop_t;
+struct t_commrec;
+struct t_fileio;
+struct t_inputrec;
+class t_state;
+struct ObservablesHistory;
+struct PartialDeserializedTprFile;
+
+namespace gmx
+{
+
+/*! \brief Get the global simulation input.
+ *
+ * Acquire global simulation data structures from the SimulationInput handle.
+ * Note that global data is returned in the calling thread. In parallel
+ * computing contexts, the client is responsible for calling only where needed.
+ *
+ * Example:
+ * if (SIMMASTER(cr))
+ * {
+ * // Only the master rank has the global state
+ * globalState = globalSimulationState(simulationInput);
+ *
+ * // Read (nearly) all data required for the simulation
+ * applyGlobalInputRecord(simulationInput, inputrec);
+ * applyGlobalTopology(simulationInput, &mtop);
+ * }
+ *
+ * \todo Factor the logic for global/local and master-rank-checks.
+ * The SimulationInput utilities should behave properly for the various distributed data scenarios.
+ * Consider supplying data directly to the consumers rather than exposing the
+ * implementation details of the legacy aggregate types.
+ *
+ * \{
+ */
+// TODO: Remove this monolithic detail as member data can be separately cached and managed. (#3374)
+// Note that clients still need tpxio.h for PartialDeserializedTprFile.
+void applyGlobalSimulationState(const SimulationInput& simulationInput,
+ PartialDeserializedTprFile* partialDeserializedTpr,
+ t_state* globalState,
+ t_inputrec* inputrec,
+ gmx_mtop_t* globalTopology);
+// TODO: Implement the following, pending further discussion re #3374.
+std::unique_ptr<t_state> globalSimulationState(const SimulationInput&);
+void applyGlobalInputRecord(const SimulationInput&, t_inputrec*);
+void applyGlobalTopology(const SimulationInput&, gmx_mtop_t*);
+//! \}
+
+/*! \brief Initialize local stateful simulation data.
+ *
+ * Establish an invariant for the simulator at a trajectory point.
+ * Call on all ranks (after domain decomposition and task assignments).
+ *
+ * After this call, the simulator has all of the information it will
+ * receive in order to advance a trajectory from the current step.
+ * Checkpoint information has been applied, if applicable, and stateful
+ * data has been (re)initialized.
+ *
+ * \warning Mdrunner instances do not clearly distinguish between global and local
+ * versions of t_state.
+ *
+ * \todo Factor the distributed data aspects of simulation input data into the
+ * SimulationInput implementation.
+ *
+ * \todo Consider refactoring to decouple the checkpoint facility from its consumers
+ * (state, observablesHistory, mdModulesNotifier, and parts of ir).
+ *
+ * \warning It is the caller’s responsibility to make sure that
+ * preconditions are satisfied for the parameter objects.
+ *
+ * \see globalSimulationState()
+ * \see applyGlobalInputRecord()
+ * \see applyGlobalTopology()
+ */
+void applyLocalState(const SimulationInput& simulationInput,
+ t_fileio* logfio,
+ const t_commrec* cr,
+ int* dd_nc,
+ t_inputrec* ir,
+ t_state* state,
+ ObservablesHistory* observablesHistory,
+ bool reproducibilityRequested,
+ const MdModulesNotifier& notifier,
+ gmx::ReadCheckpointDataHolder* modularSimulatorCheckpointData,
+ bool useModularSimulator);
+
+} // end namespace gmx
+
+#endif // GMX_MDRUN_SIMULATIONINPUTUTILITY_H
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff