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37 * Implements classes in moduletest.h.
39 * \author Mark Abraham <mark.j.abraham@gmail.com>
40 * \ingroup module_mdrun_integration_tests
44 #include "moduletest.h"
48 #include "gromacs/gmxpreprocess/grompp.h"
49 #include "gromacs/options/basicoptions.h"
50 #include "gromacs/options/options.h"
51 #include "gromacs/utility/basedefinitions.h"
52 #include "gromacs/utility/basenetwork.h"
53 #include "gromacs/utility/file.h"
54 #include "gromacs/utility/gmxmpi.h"
55 #include "programs/mdrun/mdrun_main.h"
57 #include "testutils/cmdlinetest.h"
58 #include "testutils/integrationtests.h"
59 #include "testutils/testoptions.h"
66 /********************************************************************
73 #if defined(GMX_THREAD_MPI) || defined(DOXYGEN)
74 //! Number of tMPI threads for child mdrun call.
77 #if defined(GMX_OPENMP) || defined(DOXYGEN)
78 //! Number of OpenMP threads for child mdrun call.
79 int g_numOpenMPThreads = 1;
82 GMX_TEST_OPTIONS(MdrunTestOptions, options)
84 GMX_UNUSED_VALUE(options);
86 options->addOption(IntegerOption("nt").store(&g_numThreads)
87 .description("Number of thread-MPI threads/ranks for child mdrun calls"));
90 options->addOption(IntegerOption("nt_omp").store(&g_numOpenMPThreads)
91 .description("Number of OpenMP threads for child mdrun calls"));
98 SimulationRunner::SimulationRunner(IntegrationTestFixture *fixture) :
102 fullPrecisionTrajectoryFileName_(),
104 mdpInputFileName_(fixture_->fileManager_.getTemporaryFilePath("input.mdp")),
105 mdpOutputFileName_(fixture_->fileManager_.getTemporaryFilePath("output.mdp")),
106 tprFileName_(fixture_->fileManager_.getTemporaryFilePath(".tpr")),
107 logFileName_(fixture_->fileManager_.getTemporaryFilePath(".log")),
108 edrFileName_(fixture_->fileManager_.getTemporaryFilePath(".edr")),
112 GMX_RELEASE_ASSERT(gmx_mpi_initialized(), "MPI system not initialized for mdrun tests");
116 // TODO The combination of defaulting to Verlet cut-off scheme, NVE,
117 // and verlet-buffer-tolerance = -1 gives a grompp error. If we keep
118 // things that way, this function should be renamed. For now,
119 // force the use of the group scheme.
121 SimulationRunner::useEmptyMdpFile()
123 // TODO When removing the group scheme, update actual and potential users of useEmptyMdpFile
124 useStringAsMdpFile("cutoff-scheme = Group\n");
128 SimulationRunner::useStringAsMdpFile(const char *mdpString)
130 useStringAsMdpFile(std::string(mdpString));
134 SimulationRunner::useStringAsMdpFile(const std::string &mdpString)
136 gmx::File::writeFileFromString(mdpInputFileName_, mdpString);
140 SimulationRunner::useStringAsNdxFile(const char *ndxString)
142 gmx::File::writeFileFromString(ndxFileName_, ndxString);
146 SimulationRunner::useTopGroAndNdxFromDatabase(const char *name)
148 topFileName_ = fixture_->fileManager_.getInputFilePath((std::string(name) + ".top").c_str());
149 groFileName_ = fixture_->fileManager_.getInputFilePath((std::string(name) + ".gro").c_str());
150 ndxFileName_ = fixture_->fileManager_.getInputFilePath((std::string(name) + ".ndx").c_str());
154 SimulationRunner::useGroFromDatabase(const char *name)
156 groFileName_ = fixture_->fileManager_.getInputFilePath((std::string(name) + ".gro").c_str());
160 SimulationRunner::callGromppOnThisRank()
163 caller.append("grompp");
164 caller.addOption("-f", mdpInputFileName_);
165 caller.addOption("-n", ndxFileName_);
166 caller.addOption("-p", topFileName_);
167 caller.addOption("-c", groFileName_);
169 caller.addOption("-po", mdpOutputFileName_);
170 caller.addOption("-o", tprFileName_);
172 return gmx_grompp(caller.argc(), caller.argv());
176 SimulationRunner::callGrompp()
180 // When compiled with external MPI, we're trying to run mdrun with
181 // MPI, but we need to make sure that we only do grompp on one
183 if (0 == gmx_node_rank())
186 returnValue = callGromppOnThisRank();
189 // Make sure rank zero has written the .tpr file before other
190 // ranks try to read it. Thread-MPI and serial do this just fine
192 MPI_Barrier(MPI_COMM_WORLD);
198 SimulationRunner::callMdrun(const CommandLine &callerRef)
200 /* Conforming to style guide by not passing a non-const reference
201 to this function. Passing a non-const reference might make it
202 easier to write code that incorrectly re-uses callerRef after
203 the call to this function. */
205 CommandLine caller(callerRef);
206 caller.addOption("-s", tprFileName_);
208 caller.addOption("-g", logFileName_);
209 caller.addOption("-e", edrFileName_);
210 caller.addOption("-o", fullPrecisionTrajectoryFileName_);
211 caller.addOption("-x", reducedPrecisionTrajectoryFileName_);
213 caller.addOption("-deffnm", fixture_->fileManager_.getTemporaryFilePath("state"));
217 caller.addOption("-nsteps", nsteps_);
222 # ifdef GMX_THREAD_MPI
223 int numGpusNeeded = g_numThreads;
224 # else /* Must be real MPI */
225 int numGpusNeeded = gmx_node_num();
227 std::string gpuIdString(numGpusNeeded, '0');
228 caller.addOption("-gpu_id", gpuIdString.c_str());
232 #ifdef GMX_THREAD_MPI
233 caller.addOption("-nt", g_numThreads);
237 caller.addOption("-ntomp", g_numOpenMPThreads);
240 return gmx_mdrun(caller.argc(), caller.argv());
244 SimulationRunner::callMdrun()
247 caller.append("mdrun");
248 return callMdrun(caller);
253 MdrunTestFixtureBase::MdrunTestFixtureBase()
256 GMX_RELEASE_ASSERT(gmx_mpi_initialized(), "MPI system not initialized for mdrun tests");
260 MdrunTestFixtureBase::~MdrunTestFixtureBase()
266 MdrunTestFixture::MdrunTestFixture() : runner_(this)
270 MdrunTestFixture::~MdrunTestFixture()