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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/compat/make_unique.h"
58 #include "gromacs/gmxlib/network.h"
59 #include "gromacs/mdlib/stophandler.h"
60 #include "gromacs/mdrun/logging.h"
61 #include "gromacs/mdrun/multisim.h"
62 #include "gromacs/mdrun/runner.h"
63 #include "gromacs/mdrunutility/handlerestart.h"
64 #include "gromacs/mdtypes/commrec.h"
65 #include "gromacs/utility/arraysize.h"
66 #include "gromacs/utility/fatalerror.h"
67 #include "gromacs/utility/smalloc.h"
69 #include "gmxapi/exceptions.h"
70 #include "gmxapi/session.h"
71 #include "gmxapi/status.h"
72 #include "gmxapi/version.h"
74 #include "context-impl.h"
75 #include "createsession.h"
76 #include "session-impl.h"
82 ContextImpl::ContextImpl()
84 GMX_ASSERT(session_.expired(), "This implementation assumes an expired weak_ptr at initialization.");
87 std::shared_ptr<gmxapi::ContextImpl> ContextImpl::create()
89 std::shared_ptr<ContextImpl> impl = std::make_shared<ContextImpl>();
93 std::shared_ptr<Session> ContextImpl::launch(const Workflow &work)
96 // Much of this implementation is not easily testable: we need tools to inspect simulation results and to modify
99 std::shared_ptr<Session> launchedSession = nullptr;
101 // This implementation can only run one workflow at a time.
102 // Check whether we are already aware of an active session.
103 if (session_.expired())
105 // Check workflow spec, build graph for current context, launch and return new session.
106 // \todo This is specific to the session implementation...
107 auto mdNode = work.getNode("MD");
108 std::string filename {};
109 if (mdNode != nullptr)
111 filename = mdNode->params();
114 /* As default behavior, automatically extend trajectories from the checkpoint file.
115 * In the future, our API for objects used to initialize a simulation needs to address the fact that currently a
116 * microstate requires data from both the TPR and checkpoint file to be fully specified. Put another way,
118 * GROMACS simulations can take a "configuration" as input that does not constitute a complete microstate in
119 * terms of hidden degrees of freedom (integrator/thermostat/barostat/PRNG state), but we want a clear notion of
120 * a microstate for gmxapi interfaces.
123 // Set input TPR name
124 mdArgs_.emplace_back("-s");
125 mdArgs_.emplace_back(filename);
127 // Set checkpoint file name
128 mdArgs_.emplace_back("-cpi");
129 mdArgs_.emplace_back("state.cpt");
130 /* Note: we normalize the checkpoint file name, but not its full path.
131 * Through version 0.0.8, gmxapi clients change working directory
132 * for each session, so relative path(s) below are appropriate.
133 * A future gmxapi version should avoid changing directories once the
134 * process starts and instead manage files (paths) in an absolute and
135 * immutable way, with abstraction provided through the Context chain-of-responsibility.
136 * TODO: API abstractions for initializing simulations that may be new or partially complete.
137 * Reference gmxapi milestone 13 at https://redmine.gromacs.org/issues/2585
140 // Create a mock argv. Note that argv[0] is expected to hold the program name.
141 const int offset = 1;
142 const auto argc = static_cast<size_t>(mdArgs_.size() + offset);
143 auto argv = std::vector<char *>(argc, nullptr);
144 // argv[0] is ignored, but should be a valid string (e.g. null terminated array of char)
145 argv[0] = new char[1];
147 for (size_t argvIndex = offset; argvIndex < argc; ++argvIndex)
149 const auto &mdArg = mdArgs_[argvIndex - offset];
150 argv[argvIndex] = new char[mdArg.length() + 1];
151 strcpy(argv[argvIndex], mdArg.c_str());
154 // pointer-to-t_commrec is the de facto handle type for communications record.
155 // Complete shared / borrowed ownership requires a reference to this stack variable
156 // (or pointer-to-pointer-to-t_commrec) since borrowing code may update the pointer.
157 // \todo Define the ownership and lifetime management semantics for a communication record, handle or value type.
159 // Note: this communications record initialization acts directly on
160 // MPI_COMM_WORLD and is incompatible with MPI environment sharing in
161 // gmxapi through 0.0.7, at least.
162 options_.cr = init_commrec();
164 const char *desc[] = {"gmxapi placeholder text"};
165 if (options_.updateFromCommandLine(argc, argv.data(), desc) == 0)
170 if (MASTER(options_.cr))
172 options_.logFileGuard = openLogFile(ftp2fn(efLOG,
173 options_.filenames.size(),
174 options_.filenames.data()),
175 options_.mdrunOptions.continuationOptions.appendFiles);
178 auto simulationContext = createSimulationContext(options_.cr);
180 auto builder = MdrunnerBuilder(compat::not_null<decltype( &simulationContext)>(&simulationContext));
181 builder.addSimulationMethod(options_.mdrunOptions, options_.pforce);
182 builder.addDomainDecomposition(options_.domdecOptions);
183 // \todo pass by value
184 builder.addNonBonded(options_.nbpu_opt_choices[0]);
185 // \todo pass by value
186 builder.addElectrostatics(options_.pme_opt_choices[0], options_.pme_fft_opt_choices[0]);
187 builder.addBondedTaskAssignment(options_.bonded_opt_choices[0]);
188 builder.addNeighborList(options_.nstlist_cmdline);
189 builder.addReplicaExchange(options_.replExParams);
190 // \todo take ownership of multisim resources (ms)
191 builder.addMultiSim(options_.ms);
192 // \todo Provide parallelism resources through SimulationContext.
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(options_.logFileGuard.get());
203 // Note, creation is not mature enough to be exposed in the external API yet.
204 launchedSession = createSession(shared_from_this(),
207 std::move(options_.logFileGuard),
210 // Clean up argv once builder is no longer in use
211 for (auto && string : argv)
213 if (string != nullptr)
223 throw gmxapi::ProtocolError("Tried to launch a session while a session is still active.");
226 if (launchedSession != nullptr)
228 // Update weak reference.
229 session_ = launchedSession;
231 return launchedSession;
234 // As of gmxapi 0.0.3 there is only one Context type
236 Context {ContextImpl::create()}
238 GMX_ASSERT(impl_, "Context requires a non-null implementation member.");
241 std::shared_ptr<Session> Context::launch(const Workflow &work)
243 return impl_->launch(work);
246 Context::Context(std::shared_ptr<ContextImpl> impl) :
247 impl_ {std::move(impl)}
249 GMX_ASSERT(impl_, "Context requires a non-null implementation member.");
252 void Context::setMDArgs(const MDArgs &mdArgs)
254 impl_->mdArgs_ = mdArgs;
257 Context::~Context() = default;
259 } // end namespace gmxapi