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38 * Implements classes in moduletest.h.
40 * \author Mark Abraham <mark.j.abraham@gmail.com>
41 * \ingroup module_mdrun_integration_tests
45 #include "moduletest.h"
53 #include "gromacs/gmxana/gmx_ana.h"
54 #include "gromacs/gmxpreprocess/grompp.h"
55 #include "gromacs/hardware/detecthardware.h"
56 #include "gromacs/hardware/hw_info.h"
57 #include "gromacs/options/basicoptions.h"
58 #include "gromacs/options/ioptionscontainer.h"
59 #include "gromacs/tools/convert_tpr.h"
60 #include "gromacs/utility/basedefinitions.h"
61 #include "gromacs/utility/basenetwork.h"
62 #include "gromacs/utility/gmxmpi.h"
63 #include "gromacs/utility/physicalnodecommunicator.h"
64 #include "gromacs/utility/textwriter.h"
65 #include "programs/mdrun/mdrun_main.h"
67 #include "testutils/cmdlinetest.h"
68 #include "testutils/mpitest.h"
69 #include "testutils/testfilemanager.h"
70 #include "testutils/testoptions.h"
77 /********************************************************************
84 #if GMX_OPENMP || defined(DOXYGEN)
85 //! Number of OpenMP threads for child mdrun call.
86 int g_numOpenMPThreads = 1;
89 GMX_TEST_OPTIONS(MdrunTestOptions, options)
91 GMX_UNUSED_VALUE(options);
94 IntegerOption("ntomp").store(&g_numOpenMPThreads).description("Number of OpenMP threads for child mdrun calls"));
101 SimulationRunner::SimulationRunner(TestFileManager* fileManager) :
102 fullPrecisionTrajectoryFileName_(fileManager->getTemporaryFilePath(".trr")),
103 mdpOutputFileName_(fileManager->getTemporaryFilePath("output.mdp")),
104 tprFileName_(fileManager->getTemporaryFilePath(".tpr")),
105 logFileName_(fileManager->getTemporaryFilePath(".log")),
106 edrFileName_(fileManager->getTemporaryFilePath(".edr")),
107 mtxFileName_(fileManager->getTemporaryFilePath(".mtx")),
110 mdpSource_(SimulationRunnerMdpSource::Undefined),
111 fileManager_(*fileManager)
114 GMX_RELEASE_ASSERT(gmx_mpi_initialized(), "MPI system not initialized for mdrun tests");
116 // It would be better to also detect this in a thread-MPI build,
117 // but there is no way to do that currently, and it is also not a
118 // problem for such a build. Any code based on such an invalid
119 // test fixture will be found in CI testing, however.
120 GMX_RELEASE_ASSERT(MdrunTestFixtureBase::communicator_ != MPI_COMM_NULL,
121 "SimulationRunner may only be used from a test fixture that inherits from "
122 "MdrunTestFixtureBase");
126 // TODO The combination of defaulting to Verlet cut-off scheme, NVE,
127 // and verlet-buffer-tolerance = -1 gives a grompp error. If we keep
128 // things that way, this function should be renamed. For now,
129 // we use the Verlet scheme and hard-code a tolerance.
130 // TODO There is possible outstanding unexplained behaviour of mdp
131 // input parsing e.g. Issue #2074, so this particular set of mdp
132 // contents is also tested with GetIrTest in gmxpreprocess-test.
133 void SimulationRunner::useEmptyMdpFile()
135 useStringAsMdpFile("");
138 void SimulationRunner::useStringAsMdpFile(const char* mdpString)
140 useStringAsMdpFile(std::string(mdpString));
143 void SimulationRunner::useStringAsMdpFile(const std::string& mdpString)
145 GMX_RELEASE_ASSERT(mdpSource_ != SimulationRunnerMdpSource::File,
146 "Cannot mix .mdp file from database with options set via string.");
147 mdpSource_ = SimulationRunnerMdpSource::String;
148 mdpInputContents_ = mdpString;
151 void SimulationRunner::useStringAsNdxFile(const char* ndxString)
153 gmx::TextWriter::writeFileFromString(ndxFileName_, ndxString);
156 void SimulationRunner::useTopG96AndNdxFromDatabase(const std::string& name)
158 topFileName_ = gmx::test::TestFileManager::getInputFilePath(name + ".top");
159 groFileName_ = gmx::test::TestFileManager::getInputFilePath(name + ".g96");
160 ndxFileName_ = gmx::test::TestFileManager::getInputFilePath(name + ".ndx");
163 void SimulationRunner::useTopGroAndNdxFromDatabase(const std::string& name)
165 topFileName_ = gmx::test::TestFileManager::getInputFilePath(name + ".top");
166 groFileName_ = gmx::test::TestFileManager::getInputFilePath(name + ".gro");
167 ndxFileName_ = gmx::test::TestFileManager::getInputFilePath(name + ".ndx");
170 void SimulationRunner::useGroFromDatabase(const char* name)
172 groFileName_ = gmx::test::TestFileManager::getInputFilePath((std::string(name) + ".gro").c_str());
175 void SimulationRunner::useTopGroAndMdpFromFepTestDatabase(const std::string& name)
177 GMX_RELEASE_ASSERT(mdpSource_ != SimulationRunnerMdpSource::String,
178 "Cannot mix .mdp file from database with options set via string.");
179 mdpSource_ = SimulationRunnerMdpSource::File;
180 topFileName_ = gmx::test::TestFileManager::getInputFilePath("freeenergy/" + name + "/topol.top");
181 groFileName_ = gmx::test::TestFileManager::getInputFilePath("freeenergy/" + name + "/conf.gro");
183 gmx::test::TestFileManager::getInputFilePath("freeenergy/" + name + "/grompp.mdp");
186 int SimulationRunner::callGromppOnThisRank(const CommandLine& callerRef)
188 std::string mdpInputFileName;
189 if (mdpSource_ == SimulationRunnerMdpSource::File)
191 mdpInputFileName = mdpFileName_;
195 mdpInputFileName = fileManager_.getTemporaryFilePath("input.mdp");
196 gmx::TextWriter::writeFileFromString(mdpInputFileName, mdpInputContents_);
200 caller.append("grompp");
201 caller.merge(callerRef);
202 caller.addOption("-f", mdpInputFileName);
203 if (!ndxFileName_.empty())
205 caller.addOption("-n", ndxFileName_);
207 caller.addOption("-p", topFileName_);
208 caller.addOption("-c", groFileName_);
209 caller.addOption("-r", groFileName_);
211 caller.addOption("-po", mdpOutputFileName_);
212 caller.addOption("-o", tprFileName_);
214 return gmx_grompp(caller.argc(), caller.argv());
217 int SimulationRunner::callGromppOnThisRank()
219 return callGromppOnThisRank(CommandLine());
222 int SimulationRunner::callGrompp(const CommandLine& callerRef)
226 // When compiled with external MPI, we're trying to run mdrun with
227 // MPI, but we need to make sure that we only do grompp on one
229 if (0 == gmx_node_rank())
232 returnValue = callGromppOnThisRank(callerRef);
235 // Make sure rank zero has written the .tpr file before other
236 // ranks try to read it. Thread-MPI and serial do this just fine
238 MPI_Barrier(MdrunTestFixtureBase::communicator_);
243 int SimulationRunner::callGrompp()
245 return callGrompp(CommandLine());
248 int SimulationRunner::changeTprNsteps(int nsteps)
251 caller.append("convert-tpr");
252 caller.addOption("-nsteps", nsteps);
253 // Because the operation is to change the .tpr, we replace the
254 // file. TODO Do we need to delete an automatic backup?
255 caller.addOption("-s", tprFileName_);
256 caller.addOption("-o", tprFileName_);
258 return gmx::test::CommandLineTestHelper::runModuleFactory(&gmx::ConvertTprInfo::create, &caller);
261 int SimulationRunner::callNmeig()
263 /* Conforming to style guide by not passing a non-const reference
264 to this function. Passing a non-const reference might make it
265 easier to write code that incorrectly re-uses callerRef after
266 the call to this function. */
269 caller.append("nmeig");
270 caller.addOption("-s", tprFileName_);
271 caller.addOption("-f", mtxFileName_);
272 // Ignore the overall translation and rotation in the
273 // first six eigenvectors.
274 caller.addOption("-first", "7");
275 // No need to check more than a number of output values.
276 caller.addOption("-last", "50");
277 caller.addOption("-xvg", "none");
279 return gmx_nmeig(caller.argc(), caller.argv());
282 int SimulationRunner::callMdrun(const CommandLine& callerRef)
284 /* Conforming to style guide by not passing a non-const reference
285 to this function. Passing a non-const reference might make it
286 easier to write code that incorrectly re-uses callerRef after
287 the call to this function. */
290 caller.append("mdrun");
291 caller.merge(callerRef);
292 caller.addOption("-s", tprFileName_);
294 caller.addOption("-g", logFileName_);
295 caller.addOption("-e", edrFileName_);
296 caller.addOption("-mtx", mtxFileName_);
297 caller.addOption("-o", fullPrecisionTrajectoryFileName_);
298 caller.addOption("-x", reducedPrecisionTrajectoryFileName_);
299 if (!dhdlFileName_.empty())
301 caller.addOption("-dhdl", dhdlFileName_);
304 caller.addOption("-deffnm", fileManager_.getTemporaryFilePath("state"));
308 caller.addOption("-nsteps", nsteps_);
312 caller.addOption("-ntmpi", getNumberOfTestMpiRanks());
316 caller.addOption("-ntomp", g_numOpenMPThreads);
319 return gmx_mdrun(MdrunTestFixtureBase::communicator_,
320 *MdrunTestFixtureBase::hwinfo_,
325 int SimulationRunner::callMdrun()
327 return callMdrun(CommandLine());
333 MPI_Comm MdrunTestFixtureBase::communicator_ = MPI_COMM_NULL;
335 std::unique_ptr<gmx_hw_info_t> MdrunTestFixtureBase::hwinfo_;
338 void MdrunTestFixtureBase::SetUpTestCase()
340 communicator_ = MPI_COMM_WORLD;
342 gmx_detect_hardware(PhysicalNodeCommunicator{ communicator_, gmx_physicalnode_id_hash() });
343 std::swap(hwinfo_, newHwinfo);
347 void MdrunTestFixtureBase::TearDownTestCase()
349 hwinfo_.reset(nullptr);
352 MdrunTestFixtureBase::MdrunTestFixtureBase()
355 GMX_RELEASE_ASSERT(gmx_mpi_initialized(), "MPI system not initialized for mdrun tests");
359 MdrunTestFixtureBase::~MdrunTestFixtureBase() {}
363 MdrunTestFixture::MdrunTestFixture() : runner_(&fileManager_) {}
365 MdrunTestFixture::~MdrunTestFixture()
368 // fileManager_ should only clean up after all the ranks are done.
369 MPI_Barrier(MdrunTestFixtureBase::communicator_);