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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/mdlib/stophandler.h"
58 #include "gromacs/mdrunutility/logging.h"
59 #include "gromacs/mdrunutility/multisim.h"
60 #include "gromacs/mdrun/runner.h"
61 #include "gromacs/mdrunutility/handlerestart.h"
62 #include "gromacs/utility/arraysize.h"
63 #include "gromacs/utility/fatalerror.h"
64 #include "gromacs/utility/smalloc.h"
66 #include "gmxapi/exceptions.h"
67 #include "gmxapi/session.h"
68 #include "gmxapi/status.h"
69 #include "gmxapi/version.h"
71 #include "context_impl.h"
72 #include "createsession.h"
73 #include "session_impl.h"
79 ContextImpl::ContextImpl()
81 GMX_ASSERT(session_
.expired(),
82 "This implementation assumes an expired weak_ptr at initialization.");
85 std::shared_ptr
<gmxapi::ContextImpl
> ContextImpl::create()
87 std::shared_ptr
<ContextImpl
> impl
= std::make_shared
<ContextImpl
>();
91 std::shared_ptr
<Session
> ContextImpl::launch(const Workflow
& work
)
94 // Much of this implementation is not easily testable: we need tools to inspect simulation
95 // results and to modify simulation inputs.
97 std::shared_ptr
<Session
> launchedSession
= nullptr;
99 // This implementation can only run one workflow at a time.
100 // Check whether we are already aware of an active session.
101 if (session_
.expired())
103 // Check workflow spec, build graph for current context, launch and return new session.
104 // \todo This is specific to the session implementation...
105 auto mdNode
= work
.getNode("MD");
106 std::string filename
{};
107 if (mdNode
!= nullptr)
109 filename
= mdNode
->params();
112 /* As default behavior, automatically extend trajectories from the checkpoint file.
113 * In the future, our API for objects used to initialize a simulation needs to address the fact that currently a
114 * microstate requires data from both the TPR and checkpoint file to be fully specified. Put another way,
116 * GROMACS simulations can take a "configuration" as input that does not constitute a complete microstate in
117 * terms of hidden degrees of freedom (integrator/thermostat/barostat/PRNG state), but we want a clear notion of
118 * a microstate for gmxapi interfaces.
121 // Set input TPR name
122 mdArgs_
.emplace_back("-s");
123 mdArgs_
.emplace_back(filename
);
125 // Set checkpoint file name
126 mdArgs_
.emplace_back("-cpi");
127 mdArgs_
.emplace_back("state.cpt");
128 /* Note: we normalize the checkpoint file name, but not its full path.
129 * Through version 0.0.8, gmxapi clients change working directory
130 * for each session, so relative path(s) below are appropriate.
131 * A future gmxapi version should avoid changing directories once the
132 * process starts and instead manage files (paths) in an absolute and
133 * immutable way, with abstraction provided through the Context chain-of-responsibility.
134 * TODO: API abstractions for initializing simulations that may be new or partially
135 * complete. Reference gmxapi milestone 13 at https://gitlab.com/gromacs/gromacs/-/issues/2585
138 // Create a mock argv. Note that argv[0] is expected to hold the program name.
139 const int offset
= 1;
140 const auto argc
= static_cast<size_t>(mdArgs_
.size() + offset
);
141 auto argv
= std::vector
<char*>(argc
, nullptr);
142 // argv[0] is ignored, but should be a valid string (e.g. null terminated array of char)
143 argv
[0] = new char[1];
145 for (size_t argvIndex
= offset
; argvIndex
< argc
; ++argvIndex
)
147 const auto& mdArg
= mdArgs_
[argvIndex
- offset
];
148 argv
[argvIndex
] = new char[mdArg
.length() + 1];
149 strcpy(argv
[argvIndex
], mdArg
.c_str());
152 auto mdModules
= std::make_unique
<MDModules
>();
154 const char* desc
[] = { "gmxapi placeholder text" };
155 if (options_
.updateFromCommandLine(argc
, argv
.data(), desc
) == 0)
160 ArrayRef
<const std::string
> multiSimDirectoryNames
=
161 opt2fnsIfOptionSet("-multidir", ssize(options_
.filenames
), options_
.filenames
.data());
162 // Set up the communicator, where possible (see docs for
163 // SimulationContext).
164 MPI_Comm communicator
= GMX_LIB_MPI
? MPI_COMM_WORLD
: MPI_COMM_NULL
;
165 // The SimulationContext is necessary with gmxapi so that
166 // resources owned by the client code can have suitable
167 // lifetime. The gmx wrapper binary uses the same infrastructure,
168 // but the lifetime is now trivially that of the invocation of the
170 SimulationContext
simulationContext(communicator
, multiSimDirectoryNames
);
173 StartingBehavior startingBehavior
= StartingBehavior::NewSimulation
;
174 LogFilePtr logFileGuard
= nullptr;
175 gmx_multisim_t
* ms
= simulationContext
.multiSimulation_
.get();
176 std::tie(startingBehavior
, logFileGuard
) =
177 handleRestart(findIsSimulationMasterRank(ms
, communicator
), communicator
, ms
,
178 options_
.mdrunOptions
.appendingBehavior
, ssize(options_
.filenames
),
179 options_
.filenames
.data());
181 auto builder
= MdrunnerBuilder(std::move(mdModules
),
182 compat::not_null
<SimulationContext
*>(&simulationContext
));
183 builder
.addSimulationMethod(options_
.mdrunOptions
, options_
.pforce
, startingBehavior
);
184 builder
.addDomainDecomposition(options_
.domdecOptions
);
185 // \todo pass by value
186 builder
.addNonBonded(options_
.nbpu_opt_choices
[0]);
187 // \todo pass by value
188 builder
.addElectrostatics(options_
.pme_opt_choices
[0], options_
.pme_fft_opt_choices
[0]);
189 builder
.addBondedTaskAssignment(options_
.bonded_opt_choices
[0]);
190 builder
.addUpdateTaskAssignment(options_
.update_opt_choices
[0]);
191 builder
.addNeighborList(options_
.nstlist_cmdline
);
192 builder
.addReplicaExchange(options_
.replExParams
);
193 // Need to establish run-time values from various inputs to provide a resource handle to Mdrunner
194 builder
.addHardwareOptions(options_
.hw_opt
);
195 // \todo File names are parameters that should be managed modularly through further factoring.
196 builder
.addFilenames(options_
.filenames
);
197 // Note: The gmx_output_env_t life time is not managed after the call to parse_common_args.
198 // \todo Implement lifetime management for gmx_output_env_t.
199 // \todo Output environment should be configured outside of Mdrunner and provided as a resource.
200 builder
.addOutputEnvironment(options_
.oenv
);
201 builder
.addLogFile(logFileGuard
.get());
203 // Note, creation is not mature enough to be exposed in the external API yet.
204 launchedSession
= createSession(shared_from_this(), std::move(builder
),
205 std::move(simulationContext
), std::move(logFileGuard
));
207 // Clean up argv once builder is no longer in use
208 for (auto&& string
: argv
)
210 if (string
!= nullptr)
219 throw gmxapi::ProtocolError("Tried to launch a session while a session is still active.");
222 if (launchedSession
!= nullptr)
224 // Update weak reference.
225 session_
= launchedSession
;
227 return launchedSession
;
230 // As of gmxapi 0.0.3 there is only one Context type
231 Context::Context() : Context
{ ContextImpl::create() }
233 GMX_ASSERT(impl_
, "Context requires a non-null implementation member.");
236 std::shared_ptr
<Session
> Context::launch(const Workflow
& work
)
238 return impl_
->launch(work
);
241 Context::Context(std::shared_ptr
<ContextImpl
> impl
) : impl_
{ std::move(impl
) }
243 GMX_ASSERT(impl_
, "Context requires a non-null implementation member.");
246 void Context::setMDArgs(const MDArgs
& mdArgs
)
248 impl_
->mdArgs_
= mdArgs
;
251 Context::~Context() = default;
253 } // end namespace gmxapi