2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2018, by the GROMACS development team, led by
5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 * and including many others, as listed in the AUTHORS file in the
7 * top-level source directory and at http://www.gromacs.org.
9 * GROMACS is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public License
11 * as published by the Free Software Foundation; either version 2.1
12 * of the License, or (at your option) any later version.
14 * GROMACS is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 * Lesser General Public License for more details.
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
28 * derived work must not be called official GROMACS. Details are found
29 * in the README & COPYING files - if they are missing, get the
30 * official version at http://www.gromacs.org.
32 * To help us fund GROMACS development, we humbly ask that you cite
33 * the research papers on the package. Check out http://www.gromacs.org.
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/mdtypes/commrec.h"
64 #include "gromacs/utility/arraysize.h"
65 #include "gromacs/utility/fatalerror.h"
66 #include "gromacs/utility/smalloc.h"
68 #include "gmxapi/exceptions.h"
69 #include "gmxapi/session.h"
70 #include "gmxapi/status.h"
71 #include "gmxapi/version.h"
73 #include "context_impl.h"
74 #include "createsession.h"
75 #include "session_impl.h"
81 ContextImpl::ContextImpl()
83 GMX_ASSERT(session_.expired(), "This implementation assumes an expired weak_ptr at initialization.");
86 std::shared_ptr<gmxapi::ContextImpl> ContextImpl::create()
88 std::shared_ptr<ContextImpl> impl = std::make_shared<ContextImpl>();
92 std::shared_ptr<Session> ContextImpl::launch(const Workflow &work)
95 // Much of this implementation is not easily testable: we need tools to inspect simulation results and to modify
98 std::shared_ptr<Session> launchedSession = nullptr;
100 // This implementation can only run one workflow at a time.
101 // Check whether we are already aware of an active session.
102 if (session_.expired())
104 // Check workflow spec, build graph for current context, launch and return new session.
105 // \todo This is specific to the session implementation...
106 auto mdNode = work.getNode("MD");
107 std::string filename {};
108 if (mdNode != nullptr)
110 filename = mdNode->params();
113 /* As default behavior, automatically extend trajectories from the checkpoint file.
114 * In the future, our API for objects used to initialize a simulation needs to address the fact that currently a
115 * microstate requires data from both the TPR and checkpoint file to be fully specified. Put another way,
117 * GROMACS simulations can take a "configuration" as input that does not constitute a complete microstate in
118 * terms of hidden degrees of freedom (integrator/thermostat/barostat/PRNG state), but we want a clear notion of
119 * a microstate for gmxapi interfaces.
122 // Set input TPR name
123 mdArgs_.emplace_back("-s");
124 mdArgs_.emplace_back(filename);
126 // Set checkpoint file name
127 mdArgs_.emplace_back("-cpi");
128 mdArgs_.emplace_back("state.cpt");
129 /* Note: we normalize the checkpoint file name, but not its full path.
130 * Through version 0.0.8, gmxapi clients change working directory
131 * for each session, so relative path(s) below are appropriate.
132 * A future gmxapi version should avoid changing directories once the
133 * process starts and instead manage files (paths) in an absolute and
134 * immutable way, with abstraction provided through the Context chain-of-responsibility.
135 * TODO: API abstractions for initializing simulations that may be new or partially complete.
136 * Reference gmxapi milestone 13 at https://redmine.gromacs.org/issues/2585
139 // Create a mock argv. Note that argv[0] is expected to hold the program name.
140 const int offset = 1;
141 const auto argc = static_cast<size_t>(mdArgs_.size() + offset);
142 auto argv = std::vector<char *>(argc, nullptr);
143 // argv[0] is ignored, but should be a valid string (e.g. null terminated array of char)
144 argv[0] = new char[1];
146 for (size_t argvIndex = offset; argvIndex < argc; ++argvIndex)
148 const auto &mdArg = mdArgs_[argvIndex - offset];
149 argv[argvIndex] = new char[mdArg.length() + 1];
150 strcpy(argv[argvIndex], mdArg.c_str());
153 auto mdModules = std::make_unique<MDModules>();
155 // pointer-to-t_commrec is the de facto handle type for communications record.
156 // Complete shared / borrowed ownership requires a reference to this stack variable
157 // (or pointer-to-pointer-to-t_commrec) since borrowing code may update the pointer.
158 // \todo Define the ownership and lifetime management semantics for a communication record, handle or value type.
160 // Note: this communications record initialization acts directly on
161 // MPI_COMM_WORLD and is incompatible with MPI environment sharing in
162 // gmxapi through 0.0.7, at least.
163 options_.cr = init_commrec();
165 const char *desc[] = {"gmxapi placeholder text"};
166 if (options_.updateFromCommandLine(argc, argv.data(), desc) == 0)
171 if (MASTER(options_.cr))
173 options_.logFileGuard = openLogFile(ftp2fn(efLOG,
174 options_.filenames.size(),
175 options_.filenames.data()),
176 options_.mdrunOptions.continuationOptions.appendFiles);
179 auto simulationContext = createSimulationContext(options_.cr);
181 auto builder = MdrunnerBuilder(std::move(mdModules),
182 compat::not_null<decltype( &simulationContext)>(&simulationContext));
183 builder.addSimulationMethod(options_.mdrunOptions, options_.pforce);
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.addNeighborList(options_.nstlist_cmdline);
191 builder.addReplicaExchange(options_.replExParams);
192 // \todo take ownership of multisim resources (ms)
193 builder.addMultiSim(options_.ms);
194 // \todo Provide parallelism resources through SimulationContext.
195 // Need to establish run-time values from various inputs to provide a resource handle to Mdrunner
196 builder.addHardwareOptions(options_.hw_opt);
197 // \todo File names are parameters that should be managed modularly through further factoring.
198 builder.addFilenames(options_.filenames);
199 // Note: The gmx_output_env_t life time is not managed after the call to parse_common_args.
200 // \todo Implement lifetime management for gmx_output_env_t.
201 // \todo Output environment should be configured outside of Mdrunner and provided as a resource.
202 builder.addOutputEnvironment(options_.oenv);
203 builder.addLogFile(options_.logFileGuard.get());
205 // Note, creation is not mature enough to be exposed in the external API yet.
206 launchedSession = createSession(shared_from_this(),
209 std::move(options_.logFileGuard),
212 // Clean up argv once builder is no longer in use
213 for (auto && string : argv)
215 if (string != nullptr)
225 throw gmxapi::ProtocolError("Tried to launch a session while a session is still active.");
228 if (launchedSession != nullptr)
230 // Update weak reference.
231 session_ = launchedSession;
233 return launchedSession;
236 // As of gmxapi 0.0.3 there is only one Context type
238 Context {ContextImpl::create()}
240 GMX_ASSERT(impl_, "Context requires a non-null implementation member.");
243 std::shared_ptr<Session> Context::launch(const Workflow &work)
245 return impl_->launch(work);
248 Context::Context(std::shared_ptr<ContextImpl> impl) :
249 impl_ {std::move(impl)}
251 GMX_ASSERT(impl_, "Context requires a non-null implementation member.");
254 void Context::setMDArgs(const MDArgs &mdArgs)
256 impl_->mdArgs_ = mdArgs;
259 Context::~Context() = default;
261 } // end namespace gmxapi