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36 * \brief Implementation details of gmxapi::Context
38 * \todo Share mdrun input handling implementation via modernized modular options framework.
39 * Initial implementation of `launch` relies on borrowed code from the mdrun command
40 * line input processing.
42 * \author M. Eric Irrgang <ericirrgang@gmail.com>
46 #include "gmxapi/context.h"
54 #include "gromacs/commandline/pargs.h"
55 #include "gromacs/commandline/filenm.h"
56 #include "gromacs/commandline/pargs.h"
57 #include "gromacs/gmxlib/network.h"
58 #include "gromacs/mdlib/stophandler.h"
59 #include "gromacs/mdrunutility/logging.h"
60 #include "gromacs/mdrunutility/multisim.h"
61 #include "gromacs/mdrun/runner.h"
62 #include "gromacs/mdrunutility/handlerestart.h"
63 #include "gromacs/utility/arraysize.h"
64 #include "gromacs/utility/basenetwork.h"
65 #include "gromacs/utility/fatalerror.h"
66 #include "gromacs/utility/gmxmpi.h"
67 #include "gromacs/utility/init.h"
68 #include "gromacs/utility/smalloc.h"
70 #include "gmxapi/mpi/multiprocessingresources.h"
71 #include "gmxapi/exceptions.h"
72 #include "gmxapi/session.h"
73 #include "gmxapi/status.h"
74 #include "gmxapi/version.h"
76 #include "context_impl.h"
77 #include "createsession.h"
78 #include "session_impl.h"
84 // Support some tag dispatch. Warning: These are just aliases (not strong types).
86 * \brief Logical helper alias to convert preprocessor constant to type.
88 * \tparam Value Provide the GMX\_LIB\_MPI macro.
91 using hasLibraryMpi
= std::bool_constant
<Value
>;
92 using gmxThreadMpi
= hasLibraryMpi
<false>;
93 using gmxLibMpi
= hasLibraryMpi
<true>;
94 using MpiType
= std::conditional_t
<GMX_LIB_MPI
, gmxLibMpi
, gmxThreadMpi
>;
96 using MpiContextInitializationError
= BasicException
<struct MpiContextInitialization
>;
100 * \brief Helpers to evaluate the correct precondition for the library build.
102 * TODO: (#3650) Consider distinct MpiContextManager types for clearer definition of preconditions.
107 [[maybe_unused
]] MPI_Comm
validCommunicator(const MPI_Comm
& communicator
, const gmxThreadMpi
&)
109 if (communicator
!= MPI_COMM_NULL
)
111 throw MpiContextInitializationError(
112 "Provided communicator must be MPI_COMM_NULL for GROMACS built without MPI "
118 [[maybe_unused
]] MPI_Comm
validCommunicator(const MPI_Comm
& communicator
, const gmxLibMpi
&)
120 if (communicator
== MPI_COMM_NULL
)
122 throw MpiContextInitializationError("MPI-enabled GROMACS requires a valid communicator.");
128 * \brief Return the communicator if it is appropriate for the environment.
130 * \throws MpiContextInitializationError if communicator does not match the
131 * MpiContextManager precondition for the current library configuration.
133 MPI_Comm
validCommunicator(const MPI_Comm
& communicator
)
135 return validCommunicator(communicator
, MpiType());
138 //! \brief Provide a reasonable default value.
139 MPI_Comm
validCommunicator()
141 return GMX_LIB_MPI
? MPI_COMM_WORLD
: MPI_COMM_NULL
;
144 } // anonymous namespace
146 MpiContextManager::MpiContextManager(MPI_Comm communicator
) :
147 communicator_(std::make_unique
<MPI_Comm
>(validCommunicator(communicator
)))
149 // Safely increments the GROMACS MPI initialization counter after checking
150 // whether the MPI library is already initialized. After this call, MPI_Init
151 // or MPI_Init_thread has been called exactly once.
152 gmx::init(nullptr, nullptr);
153 GMX_RELEASE_ASSERT(!GMX_LIB_MPI
|| gmx_mpi_initialized(),
154 "MPI should be initialized before reaching this point.");
155 if (this->communicator() != MPI_COMM_NULL
)
157 // Synchronise at the point of acquiring a MpiContextManager.
158 gmx_barrier(this->communicator());
162 MpiContextManager::~MpiContextManager()
166 // This is always safe to call. It is a no-op if
167 // thread-MPI, and if the constructor completed then the
168 // MPI library is initialized with reference counting.
173 MpiContextManager::MpiContextManager() : MpiContextManager(validCommunicator()) {}
175 MPI_Comm
MpiContextManager::communicator() const
179 throw UsageError("Invalid MpiContextManager. Accessed after `move`?");
181 return *communicator_
;
184 ContextImpl::~ContextImpl() = default;
186 [[maybe_unused
]] static Context
createContext(const ResourceAssignment
& resources
, const gmxLibMpi
&)
189 resources
.applyCommunicator(&handle
);
190 if (handle
.communicator
== MPI_COMM_NULL
)
192 throw UsageError("MPI-enabled Simulator contexts require a valid communicator.");
194 auto contextmanager
= MpiContextManager(handle
.communicator
);
195 auto impl
= ContextImpl::create(std::move(contextmanager
));
196 GMX_ASSERT(impl
, "ContextImpl creation method should not be able to return null.");
197 auto context
= Context(impl
);
201 [[maybe_unused
]] static Context
createContext(const ResourceAssignment
& resources
, const gmxThreadMpi
&)
203 if (resources
.size() > 1)
205 throw UsageError("Only one thread-MPI Simulation per Context is supported.");
207 // Thread-MPI Context does not yet have a need for user-provided resources.
208 // However, see #3650.
209 return createContext();
212 Context
createContext(const ResourceAssignment
& resources
)
214 return createContext(resources
, hasLibraryMpi
<GMX_LIB_MPI
>());
217 Context
createContext()
219 MpiContextManager contextmanager
;
220 auto impl
= ContextImpl::create(std::move(contextmanager
));
221 GMX_ASSERT(impl
, "ContextImpl creation method should not be able to return null.");
222 auto context
= Context(impl
);
226 ContextImpl::ContextImpl(MpiContextManager
&& mpi
) noexcept(std::is_nothrow_constructible_v
<gmx::LegacyMdrunOptions
>) :
229 // Confirm our understanding of the MpiContextManager invariant.
230 GMX_ASSERT(mpi_
.communicator() == MPI_COMM_NULL
? !GMX_LIB_MPI
: GMX_LIB_MPI
,
231 "Precondition is an appropriate communicator for the library environment.");
232 // Make sure we didn't change the data members and overlook implementation details.
233 GMX_ASSERT(session_
.expired(),
234 "This implementation assumes an expired weak_ptr at initialization.");
237 std::shared_ptr
<ContextImpl
> ContextImpl::create(MpiContextManager
&& mpi
)
239 std::shared_ptr
<ContextImpl
> impl
;
240 impl
.reset(new ContextImpl(std::move(mpi
)));
244 std::shared_ptr
<Session
> ContextImpl::launch(const Workflow
& work
)
247 // Much of this implementation is not easily testable: we need tools to inspect simulation
248 // results and to modify simulation inputs.
250 std::shared_ptr
<Session
> launchedSession
= nullptr;
252 // This implementation can only run one workflow at a time.
253 // Check whether we are already aware of an active session.
254 if (session_
.expired())
256 // Check workflow spec, build graph for current context, launch and return new session.
257 // \todo This is specific to the session implementation...
258 auto mdNode
= work
.getNode("MD");
259 std::string filename
{};
260 if (mdNode
!= nullptr)
262 filename
= mdNode
->params();
265 /* Mock up the argv interface used by option processing infrastructure.
267 * As default behavior, automatically extend trajectories from the checkpoint file.
268 * In the future, our API for objects used to initialize a simulation needs to address the fact that currently a
269 * microstate requires data from both the TPR and checkpoint file to be fully specified. Put another way,
271 * GROMACS simulations can take a "configuration" as input that does not constitute a complete microstate in
272 * terms of hidden degrees of freedom (integrator/thermostat/barostat/PRNG state), but we want a clear notion of
273 * a microstate for gmxapi interfaces.
275 * TODO: Remove `-s` and `-cpi` arguments.
276 * Ref: https://gitlab.com/gromacs/gromacs/-/issues/3652
279 // Set input TPR name
280 mdArgs_
.emplace_back("-s");
281 mdArgs_
.emplace_back(filename
);
283 // Set checkpoint file name
284 mdArgs_
.emplace_back("-cpi");
285 mdArgs_
.emplace_back("state.cpt");
286 /* Note: we normalize the checkpoint file name, but not its full path.
287 * Through version 0.0.8, gmxapi clients change working directory
288 * for each session, so relative path(s) below are appropriate.
289 * A future gmxapi version should avoid changing directories once the
290 * process starts and instead manage files (paths) in an absolute and
291 * immutable way, with abstraction provided through the Context chain-of-responsibility.
292 * TODO: API abstractions for initializing simulations that may be new or partially
293 * complete. Reference gmxapi milestone 13 at https://gitlab.com/gromacs/gromacs/-/issues/2585
296 // Create a mock argv. Note that argv[0] is expected to hold the program name.
297 const int offset
= 1;
298 const auto argc
= static_cast<size_t>(mdArgs_
.size() + offset
);
299 auto argv
= std::vector
<char*>(argc
, nullptr);
300 // argv[0] is ignored, but should be a valid string (e.g. null terminated array of char)
301 argv
[0] = new char[1];
303 for (size_t argvIndex
= offset
; argvIndex
< argc
; ++argvIndex
)
305 const auto& mdArg
= mdArgs_
[argvIndex
- offset
];
306 argv
[argvIndex
] = new char[mdArg
.length() + 1];
307 strcpy(argv
[argvIndex
], mdArg
.c_str());
310 auto mdModules
= std::make_unique
<MDModules
>();
312 const char* desc
[] = { "gmxapi placeholder text" };
313 if (options_
.updateFromCommandLine(argc
, argv
.data(), desc
) == 0)
318 ArrayRef
<const std::string
> multiSimDirectoryNames
=
319 opt2fnsIfOptionSet("-multidir", ssize(options_
.filenames
), options_
.filenames
.data());
321 // The SimulationContext is necessary with gmxapi so that
322 // resources owned by the client code can have suitable
323 // lifetime. The gmx wrapper binary uses the same infrastructure,
324 // but the lifetime is now trivially that of the invocation of the
326 auto communicator
= mpi_
.communicator();
327 // Confirm the precondition for simulationContext().
328 GMX_ASSERT(communicator
== MPI_COMM_NULL
? !GMX_LIB_MPI
: GMX_LIB_MPI
,
329 "Context communicator does not have an appropriate value for the environment.");
330 SimulationContext
simulationContext(communicator
, multiSimDirectoryNames
);
333 StartingBehavior startingBehavior
= StartingBehavior::NewSimulation
;
334 LogFilePtr logFileGuard
= nullptr;
335 gmx_multisim_t
* ms
= simulationContext
.multiSimulation_
.get();
336 std::tie(startingBehavior
, logFileGuard
) =
337 handleRestart(findIsSimulationMasterRank(ms
, simulationContext
.simulationCommunicator_
),
338 communicator
, ms
, options_
.mdrunOptions
.appendingBehavior
,
339 ssize(options_
.filenames
), options_
.filenames
.data());
341 auto builder
= MdrunnerBuilder(std::move(mdModules
),
342 compat::not_null
<SimulationContext
*>(&simulationContext
));
343 builder
.addSimulationMethod(options_
.mdrunOptions
, options_
.pforce
, startingBehavior
);
344 builder
.addDomainDecomposition(options_
.domdecOptions
);
345 // \todo pass by value
346 builder
.addNonBonded(options_
.nbpu_opt_choices
[0]);
347 // \todo pass by value
348 builder
.addElectrostatics(options_
.pme_opt_choices
[0], options_
.pme_fft_opt_choices
[0]);
349 builder
.addBondedTaskAssignment(options_
.bonded_opt_choices
[0]);
350 builder
.addUpdateTaskAssignment(options_
.update_opt_choices
[0]);
351 builder
.addNeighborList(options_
.nstlist_cmdline
);
352 builder
.addReplicaExchange(options_
.replExParams
);
353 // Need to establish run-time values from various inputs to provide a resource handle to Mdrunner
354 builder
.addHardwareOptions(options_
.hw_opt
);
356 // \todo File names are parameters that should be managed modularly through further factoring.
357 builder
.addFilenames(options_
.filenames
);
358 // TODO: Remove `s` and `-cpi` from LegacyMdrunOptions before launch(). #3652
359 auto simulationInput
= makeSimulationInput(options_
);
360 builder
.addInput(simulationInput
);
362 // Note: The gmx_output_env_t life time is not managed after the call to parse_common_args.
363 // \todo Implement lifetime management for gmx_output_env_t.
364 // \todo Output environment should be configured outside of Mdrunner and provided as a resource.
365 builder
.addOutputEnvironment(options_
.oenv
);
366 builder
.addLogFile(logFileGuard
.get());
368 // Note, creation is not mature enough to be exposed in the external API yet.
369 launchedSession
= createSession(shared_from_this(), std::move(builder
),
370 std::move(simulationContext
), std::move(logFileGuard
));
372 // Clean up argv once builder is no longer in use
373 // TODO: Remove long-lived references to argv so this is no longer necessary.
374 // Ref https://gitlab.com/gromacs/gromacs/-/issues/2877
375 for (auto&& string
: argv
)
377 if (string
!= nullptr)
386 throw gmxapi::ProtocolError("Tried to launch a session while a session is still active.");
389 if (launchedSession
!= nullptr)
391 // Update weak reference.
392 session_
= launchedSession
;
394 return launchedSession
;
397 std::shared_ptr
<Session
> Context::launch(const Workflow
& work
)
399 return impl_
->launch(work
);
402 Context::Context(std::shared_ptr
<ContextImpl
> impl
) : impl_
{ std::move(impl
) }
406 throw UsageError("Context requires a non-null implementation member.");
410 void Context::setMDArgs(const MDArgs
& mdArgs
)
412 impl_
->mdArgs_
= mdArgs
;
415 Context::~Context() = default;
417 } // end namespace gmxapi