src/programs/mdrun/tests/simulator.cpp

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  35
  36 /*! \internal \file
  37  * \brief
  38  * Tests to compare two simulators which are expected to be identical
  39  *
  40  * \author Mark Abraham <mark.j.abraham@gmail.com>
  41  * \author Pascal Merz <pascal.merz@me.com>
  42  * \ingroup module_mdrun_integration_tests
  43  */
  44 #include "gmxpre.h"
  45
  46 #include "config.h"
  47
  48 #include "gromacs/topology/ifunc.h"
  49 #include "gromacs/utility/stringutil.h"
  50
  51 #include "testutils/mpitest.h"
  52 #include "testutils/setenv.h"
  53 #include "testutils/simulationdatabase.h"
  54
  55 #include "moduletest.h"
  56 #include "simulatorcomparison.h"
  57
  58 namespace gmx
  59 {
  60 namespace test
  61 {
  62 namespace
  63 {
  64
  65 /*! \brief Test fixture base for two equivalent simulators
  66  *
  67  * This test ensures that two simulator code paths (called via different mdp
  68  * options and/or environment variables) yield identical coordinate, velocity,
  69  * box, force and energy trajectories, up to some (arbitrary) precision.
  70  *
  71  * These tests are useful to check that re-implementations of existing simulators
  72  * are correct, and that different code paths expected to yield identical results
  73  * are equivalent.
  74  */
  75 using SimulatorComparisonTestParams =
  76         std::tuple<std::tuple<std::string, std::string, std::string, std::string, MdpParameterDatabase>, std::string>;
  77 class SimulatorComparisonTest :
  78     public MdrunTestFixture,
  79     public ::testing::WithParamInterface<SimulatorComparisonTestParams>
  80 {
  81 };
  82
  83 TEST_P(SimulatorComparisonTest, WithinTolerances)
  84 {
  85     const auto& params              = GetParam();
  86     const auto& mdpParams           = std::get<0>(params);
  87     const auto& simulationName      = std::get<0>(mdpParams);
  88     const auto& integrator          = std::get<1>(mdpParams);
  89     const auto& tcoupling           = std::get<2>(mdpParams);
  90     const auto& pcoupling           = std::get<3>(mdpParams);
  91     const auto& additionalParameter = std::get<4>(mdpParams);
  92     const auto& environmentVariable = std::get<1>(params);
  93
  94     int maxNumWarnings = 0;
  95
  96     const bool isAndersen     = (tcoupling == "andersen-massive" || tcoupling == "andersen");
  97     const bool hasConstraints = (simulationName != "argon12");
  98
  99     // TODO At some point we should also test PME-only ranks.
 100     const int numRanksAvailable = getNumberOfTestMpiRanks();
 101     if (!isNumberOfPpRanksSupported(simulationName, numRanksAvailable))
 102     {
 103         fprintf(stdout,
 104                 "Test system '%s' cannot run with %d ranks.\n"
 105                 "The supported numbers are: %s\n",
 106                 simulationName.c_str(),
 107                 numRanksAvailable,
 108                 reportNumbersOfPpRanksSupported(simulationName).c_str());
 109         return;
 110     }
 111
 112     if (integrator == "md-vv" && pcoupling == "Parrinello-Rahman")
 113     {
 114         // do_md calls this MTTK, requires Nose-Hoover, and
 115         // does not work with constraints or anisotropically
 116         return;
 117     }
 118
 119     if (isAndersen && pcoupling == "berendsen")
 120     {
 121         // "Using Berendsen pressure coupling invalidates the true ensemble for the thermostat"
 122         maxNumWarnings++;
 123     }
 124     if (tcoupling == "andersen" && hasConstraints)
 125     {
 126         // Constraints are not allowed with non-massive Andersen
 127         return;
 128     }
 129
 130     if (tcoupling == "nose-hoover" && pcoupling == "berendsen")
 131     {
 132         if (integrator == "md-vv")
 133         {
 134             // Combination not allowed by legacy do_md.
 135             return;
 136         }
 137         else
 138         {
 139             // "Using Berendsen pressure coupling invalidates the true ensemble for the thermostat"
 140             maxNumWarnings++;
 141         }
 142     }
 143
 144     const bool systemHasConstraints = (simulationName != "argon12");
 145     if (pcoupling == "mttk" && (tcoupling != "nose-hoover" || systemHasConstraints))
 146     {
 147         // Legacy mttk works only with Nose-Hoover and without constraints
 148         return;
 149     }
 150
 151     const std::string envVariableModSimOn  = "GMX_USE_MODULAR_SIMULATOR";
 152     const std::string envVariableModSimOff = "GMX_DISABLE_MODULAR_SIMULATOR";
 153
 154     GMX_RELEASE_ASSERT(
 155             environmentVariable == envVariableModSimOn || environmentVariable == envVariableModSimOff,
 156             ("Expected tested environment variable to be " + envVariableModSimOn + " or " + envVariableModSimOff)
 157                     .c_str());
 158
 159     const auto hasConservedField = !(tcoupling == "no" && pcoupling == "no")
 160                                    && !(tcoupling == "andersen-massive" || tcoupling == "andersen");
 161
 162     SCOPED_TRACE(formatString(
 163             "Comparing two simulations of '%s' "
 164             "with integrator '%s', '%s' temperature coupling, and '%s' pressure coupling "
 165             "switching environment variable '%s'",
 166             simulationName.c_str(),
 167             integrator.c_str(),
 168             tcoupling.c_str(),
 169             pcoupling.c_str(),
 170             environmentVariable.c_str()));
 171
 172     auto mdpFieldValues = prepareMdpFieldValues(
 173             simulationName.c_str(), integrator.c_str(), tcoupling.c_str(), pcoupling.c_str(), additionalParameter);
 174     if (tcoupling == "andersen")
 175     {
 176         // Fixes error "nstcomm must be 1, not 4 for Andersen, as velocities of
 177         //              atoms in coupled groups are randomized every time step"
 178         mdpFieldValues["nstcomm"]       = "1";
 179         mdpFieldValues["nstcalcenergy"] = "1";
 180     }
 181     if (pcoupling == "mttk")
 182     {
 183         // Standard parameters use compressibility of 5e-5
 184         // Increasing compressibility makes this test significantly more sensitive
 185         mdpFieldValues["compressibility"] = "1";
 186     }
 187
 188     EnergyTermsToCompare energyTermsToCompare{ {
 189             { interaction_function[F_EPOT].longname, relativeToleranceAsPrecisionDependentUlp(60.0, 200, 160) },
 190             { interaction_function[F_EKIN].longname, relativeToleranceAsPrecisionDependentUlp(60.0, 200, 160) },
 191             { interaction_function[F_PRES].longname,
 192               relativeToleranceAsPrecisionDependentFloatingPoint(10.0, 0.01, 0.001) },
 193     } };
 194     if (hasConservedField)
 195     {
 196         energyTermsToCompare.emplace(interaction_function[F_ECONSERVED].longname,
 197                                      relativeToleranceAsPrecisionDependentUlp(50.0, 100, 80));
 198     }
 199
 200     if (simulationName == "argon12")
 201     {
 202         // Without constraints, we can be more strict
 203         energyTermsToCompare = { {
 204                 { interaction_function[F_EPOT].longname,
 205                   relativeToleranceAsPrecisionDependentUlp(10.0, 24, 80) },
 206                 { interaction_function[F_EKIN].longname,
 207                   relativeToleranceAsPrecisionDependentUlp(10.0, 24, 80) },
 208                 { interaction_function[F_PRES].longname,
 209                   relativeToleranceAsPrecisionDependentFloatingPoint(10.0, 0.001, 0.0001) },
 210         } };
 211         if (hasConservedField)
 212         {
 213             energyTermsToCompare.emplace(interaction_function[F_ECONSERVED].longname,
 214                                          relativeToleranceAsPrecisionDependentUlp(10.0, 24, 80));
 215         }
 216     }
 217
 218     // Specify how trajectory frame matching must work.
 219     const TrajectoryFrameMatchSettings trajectoryMatchSettings{ true,
 220                                                                 true,
 221                                                                 true,
 222                                                                 ComparisonConditions::MustCompare,
 223                                                                 ComparisonConditions::MustCompare,
 224                                                                 ComparisonConditions::MustCompare,
 225                                                                 MaxNumFrames::compareAllFrames() };
 226     TrajectoryTolerances trajectoryTolerances = TrajectoryComparison::s_defaultTrajectoryTolerances;
 227     if (simulationName != "argon12")
 228     {
 229         trajectoryTolerances.velocities = trajectoryTolerances.coordinates;
 230     }
 231
 232     // Build the functor that will compare reference and test
 233     // trajectory frames in the chosen way.
 234     const TrajectoryComparison trajectoryComparison{ trajectoryMatchSettings, trajectoryTolerances };
 235
 236     // Set file names
 237     const auto simulator1TrajectoryFileName = fileManager_.getTemporaryFilePath("sim1.trr");
 238     const auto simulator1EdrFileName        = fileManager_.getTemporaryFilePath("sim1.edr");
 239     const auto simulator2TrajectoryFileName = fileManager_.getTemporaryFilePath("sim2.trr");
 240     const auto simulator2EdrFileName        = fileManager_.getTemporaryFilePath("sim2.edr");
 241
 242     // Run grompp
 243     runner_.tprFileName_ = fileManager_.getTemporaryFilePath("sim.tpr");
 244     runner_.useTopGroAndNdxFromDatabase(simulationName);
 245     runner_.useStringAsMdpFile(prepareMdpFileContents(mdpFieldValues));
 246     runGrompp(&runner_, { SimulationOptionTuple("-maxwarn", std::to_string(maxNumWarnings)) });
 247
 248     // Backup current state of both environment variables and unset them
 249     const char* environmentVariableBackupOn  = getenv(envVariableModSimOn.c_str());
 250     const char* environmentVariableBackupOff = getenv(envVariableModSimOff.c_str());
 251     gmxUnsetenv(envVariableModSimOn.c_str());
 252     gmxUnsetenv(envVariableModSimOff.c_str());
 253
 254     // Do first mdrun
 255     runner_.fullPrecisionTrajectoryFileName_ = simulator1TrajectoryFileName;
 256     runner_.edrFileName_                     = simulator1EdrFileName;
 257     runMdrun(&runner_);
 258
 259     // Set tested environment variable
 260     const int overWriteEnvironmentVariable = 1;
 261     gmxSetenv(environmentVariable.c_str(), "ON", overWriteEnvironmentVariable);
 262
 263     // Do second mdrun
 264     runner_.fullPrecisionTrajectoryFileName_ = simulator2TrajectoryFileName;
 265     runner_.edrFileName_                     = simulator2EdrFileName;
 266     runMdrun(&runner_);
 267
 268     // Unset tested environment variable
 269     gmxUnsetenv(environmentVariable.c_str());
 270     // Reset both environment variables to leave further tests undisturbed
 271     if (environmentVariableBackupOn != nullptr)
 272     {
 273         gmxSetenv(environmentVariable.c_str(), environmentVariableBackupOn, overWriteEnvironmentVariable);
 274     }
 275     if (environmentVariableBackupOff != nullptr)
 276     {
 277         gmxSetenv(environmentVariable.c_str(), environmentVariableBackupOff, overWriteEnvironmentVariable);
 278     }
 279
 280     // Compare simulation results
 281     compareEnergies(simulator1EdrFileName, simulator2EdrFileName, energyTermsToCompare);
 282     compareTrajectories(simulator1TrajectoryFileName, simulator2TrajectoryFileName, trajectoryComparison);
 283 }
 284
 285 // TODO: The time for OpenCL kernel compilation means these tests time
 286 //       out. Once that compilation is cached for the whole process, these
 287 //       tests can run in such configurations.
 288 // These tests are very sensitive, so we only run them in double precision.
 289 // As we change call ordering, they might actually become too strict to be useful.
 290 #if !GMX_GPU_OPENCL && GMX_DOUBLE
 291 INSTANTIATE_TEST_SUITE_P(
 292         SimulatorsAreEquivalentDefaultModular,
 293         SimulatorComparisonTest,
 294         ::testing::Combine(
 295                 ::testing::Combine(::testing::Values("argon12", "tip3p5"),
 296                                    ::testing::Values("md-vv"),
 297                                    ::testing::Values("no",
 298                                                      "v-rescale",
 299                                                      "berendsen",
 300                                                      "nose-hoover",
 301                                                      "andersen-massive",
 302                                                      "andersen"),
 303                                    ::testing::Values("mttk", "no", "berendsen", "c-rescale", "mttk"),
 304                                    ::testing::Values(MdpParameterDatabase::Default)),
 305                 ::testing::Values("GMX_DISABLE_MODULAR_SIMULATOR")));
 306 INSTANTIATE_TEST_SUITE_P(
 307         SimulatorsAreEquivalentDefaultLegacy,
 308         SimulatorComparisonTest,
 309         ::testing::Combine(
 310                 ::testing::Combine(
 311                         ::testing::Values("argon12", "tip3p5"),
 312                         ::testing::Values("md"),
 313                         ::testing::Values("no", "v-rescale", "berendsen", "nose-hoover"),
 314                         ::testing::Values("no", "Parrinello-Rahman", "berendsen", "c-rescale"),
 315                         ::testing::Values(MdpParameterDatabase::Default)),
 316                 ::testing::Values("GMX_USE_MODULAR_SIMULATOR")));
 317 #else
 318 INSTANTIATE_TEST_SUITE_P(
 319         DISABLED_SimulatorsAreEquivalentDefaultModular,
 320         SimulatorComparisonTest,
 321         ::testing::Combine(
 322                 ::testing::Combine(::testing::Values("argon12", "tip3p5"),
 323                                    ::testing::Values("md-vv"),
 324                                    ::testing::Values("no",
 325                                                      "v-rescale",
 326                                                      "berendsen",
 327                                                      "andersen-massive",
 328                                                      "andersen",
 329                                                      "nose-hoover"),
 330                                    ::testing::Values("no", "berendsen", "c-rescale", "mttk"),
 331                                    ::testing::Values(MdpParameterDatabase::Default)),
 332                 ::testing::Values("GMX_DISABLE_MODULAR_SIMULATOR")));
 333 INSTANTIATE_TEST_SUITE_P(
 334         DISABLED_SimulatorsAreEquivalentDefaultLegacy,
 335         SimulatorComparisonTest,
 336         ::testing::Combine(
 337                 ::testing::Combine(
 338                         ::testing::Values("argon12", "tip3p5"),
 339                         ::testing::Values("md"),
 340                         ::testing::Values("no", "v-rescale", "berendsen", "nose-hoover"),
 341                         ::testing::Values("no", "Parrinello-Rahman", "berendsen", "c-rescale"),
 342                         ::testing::Values(MdpParameterDatabase::Default)),
 343                 ::testing::Values("GMX_USE_MODULAR_SIMULATOR")));
 344 #endif
 345
 346 } // namespace
 347 } // namespace test
 348 } // namespace gmx