src/programs/mdrun/tests/moduletest.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements classes in moduletest.h.
  38  *
  39  * \author Mark Abraham <mark.j.abraham@gmail.com>
  40  * \ingroup module_mdrun_integration_tests
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "moduletest.h"
  45
  46 #include "config.h"
  47
  48 #include <cstdio>
  49
  50 #include "gromacs/gmxana/gmx_ana.h"
  51 #include "gromacs/gmxpreprocess/grompp.h"
  52 #include "gromacs/hardware/detecthardware.h"
  53 #include "gromacs/options/basicoptions.h"
  54 #include "gromacs/options/ioptionscontainer.h"
  55 #include "gromacs/tools/convert_tpr.h"
  56 #include "gromacs/utility/basedefinitions.h"
  57 #include "gromacs/utility/basenetwork.h"
  58 #include "gromacs/utility/gmxmpi.h"
  59 #include "gromacs/utility/textwriter.h"
  60 #include "programs/mdrun/mdrun_main.h"
  61
  62 #include "testutils/cmdlinetest.h"
  63 #include "testutils/mpitest.h"
  64 #include "testutils/testfilemanager.h"
  65 #include "testutils/testoptions.h"
  66
  67 namespace gmx
  68 {
  69 namespace test
  70 {
  71
  72 /********************************************************************
  73  * MdrunTestFixture
  74  */
  75
  76 namespace
  77 {
  78
  79 #if GMX_OPENMP || defined(DOXYGEN)
  80 //! Number of OpenMP threads for child mdrun call.
  81 int g_numOpenMPThreads = 1;
  82 #endif
  83 //! \cond
  84 GMX_TEST_OPTIONS(MdrunTestOptions, options)
  85 {
  86     GMX_UNUSED_VALUE(options);
  87 #if GMX_OPENMP
  88     options->addOption(IntegerOption("ntomp").store(&g_numOpenMPThreads)
  89                            .description("Number of OpenMP threads for child mdrun calls"));
  90 #endif
  91 }
  92 //! \endcond
  93
  94 }       // namespace
  95
  96 SimulationRunner::SimulationRunner(TestFileManager *fileManager) :
  97     fullPrecisionTrajectoryFileName_(fileManager->getTemporaryFilePath(".trr")),
  98     mdpOutputFileName_(fileManager->getTemporaryFilePath("output.mdp")),
  99     tprFileName_(fileManager->getTemporaryFilePath(".tpr")),
 100     logFileName_(fileManager->getTemporaryFilePath(".log")),
 101     edrFileName_(fileManager->getTemporaryFilePath(".edr")),
 102     mtxFileName_(fileManager->getTemporaryFilePath(".mtx")),
 103
 104     nsteps_(-2),
 105     fileManager_(*fileManager)
 106 {
 107 #if GMX_LIB_MPI
 108     GMX_RELEASE_ASSERT(gmx_mpi_initialized(), "MPI system not initialized for mdrun tests");
 109 #endif
 110 }
 111
 112 // TODO The combination of defaulting to Verlet cut-off scheme, NVE,
 113 // and verlet-buffer-tolerance = -1 gives a grompp error. If we keep
 114 // things that way, this function should be renamed. For now,
 115 // we use the Verlet scheme and hard-code a tolerance.
 116 // TODO There is possible outstanding unexplained behaviour of mdp
 117 // input parsing e.g. Redmine 2074, so this particular set of mdp
 118 // contents is also tested with GetIrTest in gmxpreprocess-test.
 119 void
 120 SimulationRunner::useEmptyMdpFile()
 121 {
 122     useStringAsMdpFile("");
 123 }
 124
 125 void
 126 SimulationRunner::useStringAsMdpFile(const char *mdpString)
 127 {
 128     useStringAsMdpFile(std::string(mdpString));
 129 }
 130
 131 void
 132 SimulationRunner::useStringAsMdpFile(const std::string &mdpString)
 133 {
 134     mdpInputContents_ = mdpString;
 135 }
 136
 137 void
 138 SimulationRunner::useStringAsNdxFile(const char *ndxString)
 139 {
 140     gmx::TextWriter::writeFileFromString(ndxFileName_, ndxString);
 141 }
 142
 143 void
 144 SimulationRunner::useTopG96AndNdxFromDatabase(const std::string &name)
 145 {
 146     topFileName_ = gmx::test::TestFileManager::getInputFilePath(name + ".top");
 147     groFileName_ = gmx::test::TestFileManager::getInputFilePath(name + ".g96");
 148     ndxFileName_ = gmx::test::TestFileManager::getInputFilePath(name + ".ndx");
 149 }
 150
 151 void
 152 SimulationRunner::useTopGroAndNdxFromDatabase(const std::string &name)
 153 {
 154     topFileName_ = gmx::test::TestFileManager::getInputFilePath(name + ".top");
 155     groFileName_ = gmx::test::TestFileManager::getInputFilePath(name + ".gro");
 156     ndxFileName_ = gmx::test::TestFileManager::getInputFilePath(name + ".ndx");
 157 }
 158
 159 void
 160 SimulationRunner::useGroFromDatabase(const char *name)
 161 {
 162     groFileName_ = gmx::test::TestFileManager::getInputFilePath((std::string(name) + ".gro").c_str());
 163 }
 164
 165 int
 166 SimulationRunner::callGromppOnThisRank(const CommandLine &callerRef)
 167 {
 168     const std::string mdpInputFileName(fileManager_.getTemporaryFilePath("input.mdp"));
 169     gmx::TextWriter::writeFileFromString(mdpInputFileName, mdpInputContents_);
 170
 171     CommandLine caller;
 172     caller.append("grompp");
 173     caller.merge(callerRef);
 174     caller.addOption("-f", mdpInputFileName);
 175     if (!ndxFileName_.empty())
 176     {
 177         caller.addOption("-n", ndxFileName_);
 178     }
 179     caller.addOption("-p", topFileName_);
 180     caller.addOption("-c", groFileName_);
 181     caller.addOption("-r", groFileName_);
 182
 183     caller.addOption("-po", mdpOutputFileName_);
 184     caller.addOption("-o", tprFileName_);
 185
 186     return gmx_grompp(caller.argc(), caller.argv());
 187 }
 188
 189 int
 190 SimulationRunner::callGromppOnThisRank()
 191 {
 192     return callGromppOnThisRank(CommandLine());
 193 }
 194
 195 int
 196 SimulationRunner::callGrompp(const CommandLine &callerRef)
 197 {
 198     int returnValue = 0;
 199 #if GMX_LIB_MPI
 200     // When compiled with external MPI, we're trying to run mdrun with
 201     // MPI, but we need to make sure that we only do grompp on one
 202     // rank
 203     if (0 == gmx_node_rank())
 204 #endif
 205     {
 206         returnValue = callGromppOnThisRank(callerRef);
 207     }
 208 #if GMX_LIB_MPI
 209     // Make sure rank zero has written the .tpr file before other
 210     // ranks try to read it. Thread-MPI and serial do this just fine
 211     // on their own.
 212     MPI_Barrier(MPI_COMM_WORLD);
 213 #endif
 214     return returnValue;
 215 }
 216
 217 int
 218 SimulationRunner::callGrompp()
 219 {
 220     return callGrompp(CommandLine());
 221 }
 222
 223 int
 224 SimulationRunner::changeTprNsteps(int nsteps)
 225 {
 226     CommandLine caller;
 227     caller.append("convert-tpr");
 228     caller.addOption("-nsteps", nsteps);
 229     // Because the operation is to change the .tpr, we replace the
 230     // file. TODO Do we need to delete an automatic backup?
 231     caller.addOption("-s", tprFileName_);
 232     caller.addOption("-o", tprFileName_);
 233
 234     return gmx_convert_tpr(caller.argc(), caller.argv());
 235 }
 236
 237 int
 238 SimulationRunner::callNmeig()
 239 {
 240     /* Conforming to style guide by not passing a non-const reference
 241        to this function. Passing a non-const reference might make it
 242        easier to write code that incorrectly re-uses callerRef after
 243        the call to this function. */
 244
 245     CommandLine caller;
 246     caller.append("nmeig");
 247     caller.addOption("-s", tprFileName_);
 248     caller.addOption("-f", mtxFileName_);
 249     // Ignore the overall translation and rotation in the
 250     // first six eigenvectors.
 251     caller.addOption("-first", "7");
 252     // No need to check more than a number of output values.
 253     caller.addOption("-last", "50");
 254     caller.addOption("-xvg", "none");
 255
 256     return gmx_nmeig(caller.argc(), caller.argv());
 257 }
 258
 259 int
 260 SimulationRunner::callMdrun(const CommandLine &callerRef)
 261 {
 262     /* Conforming to style guide by not passing a non-const reference
 263        to this function. Passing a non-const reference might make it
 264        easier to write code that incorrectly re-uses callerRef after
 265        the call to this function. */
 266
 267     CommandLine caller;
 268     caller.append("mdrun");
 269     caller.merge(callerRef);
 270     caller.addOption("-s", tprFileName_);
 271
 272     caller.addOption("-g", logFileName_);
 273     caller.addOption("-e", edrFileName_);
 274     caller.addOption("-mtx", mtxFileName_);
 275     caller.addOption("-o", fullPrecisionTrajectoryFileName_);
 276     caller.addOption("-x", reducedPrecisionTrajectoryFileName_);
 277
 278     caller.addOption("-deffnm", fileManager_.getTemporaryFilePath("state"));
 279
 280     if (nsteps_ > -2)
 281     {
 282         caller.addOption("-nsteps", nsteps_);
 283     }
 284
 285 #if GMX_THREAD_MPI
 286     caller.addOption("-ntmpi", getNumberOfTestMpiRanks());
 287 #endif
 288
 289 #if GMX_OPENMP
 290     caller.addOption("-ntomp", g_numOpenMPThreads);
 291 #endif
 292
 293     return gmx_mdrun(caller.argc(), caller.argv());
 294 }
 295
 296 int
 297 SimulationRunner::callMdrun()
 298 {
 299     return callMdrun(CommandLine());
 300 }
 301
 302 // ====
 303
 304 MdrunTestFixtureBase::MdrunTestFixtureBase()
 305 {
 306 #if GMX_LIB_MPI
 307     GMX_RELEASE_ASSERT(gmx_mpi_initialized(), "MPI system not initialized for mdrun tests");
 308 #endif
 309 }
 310
 311 MdrunTestFixtureBase::~MdrunTestFixtureBase()
 312 {
 313 }
 314
 315 // ====
 316
 317 MdrunTestFixture::MdrunTestFixture() : runner_(&fileManager_)
 318 {
 319 }
 320
 321 MdrunTestFixture::~MdrunTestFixture()
 322 {
 323 #if GMX_LIB_MPI
 324     // fileManager_ should only clean up after all the ranks are done.
 325     MPI_Barrier(MPI_COMM_WORLD);
 326 #endif
 327 }
 328
 329 } // namespace test
 330 } // namespace gmx