# This list file provides the Gromacs::gmxapi cmake target.
target_sources(gmxapi PRIVATE
+ multiprocessingresources.cpp
context.cpp
exceptions.cpp
gmxapi.cpp
namespace gmxapi
{
-MpiContextManager::MpiContextManager() :
- communicator_(std::make_unique<MPI_Comm>(GMX_LIB_MPI ? MPI_COMM_WORLD : MPI_COMM_NULL))
+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.
}
}
+MpiContextManager::MpiContextManager() :
+ MpiContextManager(GMX_LIB_MPI ? MPI_COMM_WORLD : MPI_COMM_NULL)
+{
+}
+
MPI_Comm MpiContextManager::communicator() const
{
if (!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;
LogFilePtr logFileGuard = nullptr;
gmx_multisim_t* ms = simulationContext.multiSimulation_.get();
std::tie(startingBehavior, logFileGuard) =
- handleRestart(findIsSimulationMasterRank(ms, communicator), communicator, ms,
- options_.mdrunOptions.appendingBehavior, ssize(options_.filenames),
- options_.filenames.data());
+ 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));
return launchedSession;
}
-// As of gmxapi 0.0.3 there is only one Context type
-Context::Context() : Context{ ContextImpl::create(MpiContextManager()) }
-{
- GMX_ASSERT(impl_, "Context requires a non-null implementation member.");
-}
-
std::shared_ptr<Session> Context::launch(const Workflow& work)
{
return impl_->launch(work);
Context::Context(std::shared_ptr<ContextImpl> impl) : impl_{ std::move(impl) }
{
- GMX_ASSERT(impl_, "Context requires a non-null implementation member.");
+ if (!impl_)
+ {
+ throw UsageError("Context requires a non-null implementation member.");
+ }
}
void Context::setMDArgs(const MDArgs& mdArgs)
*/
MpiContextManager();
+ /*!
+ * \brief Borrow a communicator and ensure that MPI is initialized, if applicable.
+ *
+ * \param communicator Optional communicator representing a client-managed MPI environment.
+ *
+ *
+ *
+ * Note that the communicator must be MPI_COMM_NULL if and only if GROMACS was built without an
+ * external MPI library.
+ *
+ * \todo (#3650?) Decide whether to exclude this from tMPI environments or find a sensible invariant.
+ */
+ explicit MpiContextManager(MPI_Comm communicator);
+
~MpiContextManager();
/*!
--- /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 Provide a bridge to communication resources appropriate for the library.
+ *
+ * Define the helper functions that the library provides for to help the client
+ * implement the interfaces. (This is dependent on the library configuration.)
+ *
+ * \author "M. Eric Irrgang <ericirrgang@gmail.com"
+ */
+
+#include "gmxapi/mpi/multiprocessingresources.h"
+
+#include "config.h"
+
+#include "gromacs/utility/gmxmpi.h"
+
+#include "context_impl.h"
+
+namespace gmxapi
+{
+
+ResourceAssignment::~ResourceAssignment() = default;
+
+// Base implementation is only overridden by client-provided code in certain
+// combinations of library and client build configurations.
+void ResourceAssignment::applyCommunicator(CommHandle* dst) const
+{
+ dst->communicator = MPI_COMM_NULL;
+}
+
+#if GMX_LIB_MPI
+void offerComm(MPI_Comm src, CommHandle* dst)
+{
+ dst->communicator = src;
+}
+#endif
+
+} // end namespace gmxapi
/*!
* \brief Get a handle to a new default context object.
*/
- Context();
+ Context() = delete;
~Context();
/*!
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, 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.
}
PyContext::PyContext() :
- context_{ std::make_shared<gmxapi::Context>() },
+ context_{ std::make_shared<gmxapi::Context>(gmxapi::createContext()) },
workNodes_{ std::make_shared<gmxapi::MDWorkSpec>() }
{
assert(context_);
add_library(gmxapi-testsupport INTERFACE)
target_include_directories(gmxapi-testsupport INTERFACE ${CMAKE_CURRENT_SOURCE_DIR})
+# TODO: Test tMPI build in a MPI-enabled client context.
gmx_add_gtest_executable(gmxapi-test
CPP_SOURCE_FILES
restraint.cpp
if (GMX_MPI)
gmx_add_gtest_executable(gmxapi-mpi-test MPI
CPP_SOURCE_FILES
+ context.cpp
restraint.cpp
runner.cpp
status.cpp
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018,2019,2020, 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 Test gmxapi::Context
+ *
+ * Provides additional test coverage of template headers only used by client code.
+ */
+
+#include "config.h"
+
+#include <gtest/gtest.h>
+
+#include "gromacs/utility/gmxmpi.h"
+
+#include "gmxapi/context.h"
+#include "gmxapi/mpi/gmxapi_mpi.h"
+
+
+namespace gmxapi
+{
+
+namespace testing
+{
+
+namespace
+{
+
+TEST(GmxApiMpiTest, AllContext)
+{
+ // Default Implicit COMM_WORLD for MPI builds.
+ auto context = createContext();
+}
+
+#if GMX_LIB_MPI
+TEST(GmxApiMpiTest, NullContext)
+{
+ // Explicit COMM_NULL is not supported.
+ EXPECT_ANY_THROW(assignResource(MPI_COMM_NULL));
+}
+
+TEST(GmxApiMpiTest, MpiWorldContext)
+{
+ // Note that this test is only compiled when GMX_MPI is enabled for the
+ // build tree, so we cannot unit test the behavior of non-MPI GROMACS
+ // provided with MPI-enabled Context. For that, we defer to the Python
+ // package testing.
+ // Note also that the code should look the same for tMPI or regular MPI.
+
+ // Explicit COMM_WORLD.
+ auto resources = assignResource(MPI_COMM_WORLD);
+ EXPECT_TRUE(resources->size() != 0);
+
+ // Store the rank for debugging convenience.
+ [[maybe_unused]] auto rank = resources->rank();
+
+ auto context = createContext(*resources);
+}
+
+TEST(GmxApiMpiTest, MpiSplitContext)
+{
+ // Explicit sub-communicator.
+ MPI_Comm communicator = MPI_COMM_NULL;
+ int rank{ 0 };
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ // Run each rank as a separate ensemble member.
+ MPI_Comm_split(MPI_COMM_WORLD, rank, rank, &communicator);
+ auto context = createContext(*assignResource(communicator));
+}
+#endif
+
+} // end anonymous namespace
+
+} // end namespace testing
+
+} // end namespace gmxapi
auto system = gmxapi::fromTprFile(runner_.tprFileName_);
{
- auto context = std::make_shared<gmxapi::Context>();
+ auto context = std::make_shared<gmxapi::Context>(gmxapi::createContext());
gmxapi::MDArgs args = makeMdArgs();
context->setMDArgs(args);
auto system = gmxapi::fromTprFile(runner_.tprFileName_);
{
- auto context = std::make_shared<gmxapi::Context>();
+ auto context = std::make_shared<gmxapi::Context>(gmxapi::createContext());
gmxapi::MDArgs args = makeMdArgs();
// TODO the command line arguments should be set through the
// usual command line options settings for the tests
*/
TEST_F(GmxApiTest, RunnerReinitialize)
{
- auto context = std::make_shared<gmxapi::Context>();
+ auto context = std::make_shared<gmxapi::Context>(gmxapi::createContext());
gmxapi::MDArgs args = makeMdArgs();
makeTprFile(20);
auto system = gmxapi::fromTprFile(runner_.tprFileName_);
{
- auto context = std::make_shared<gmxapi::Context>();
+ auto context = std::make_shared<gmxapi::Context>(gmxapi::createContext());
{
EXPECT_TRUE(context != nullptr);
const int nsteps = 1;
makeTprFile(nsteps);
auto system = gmxapi::fromTprFile(runner_.tprFileName_);
- auto context = std::make_shared<gmxapi::Context>();
+ auto context = std::make_shared<gmxapi::Context>(gmxapi::createContext());
// Check assumptions about basic simulation behavior.
{
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff