/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fprintf(stdout,
"Test system '%s' cannot run with %d ranks.\n"
"The supported numbers are: %s\n",
- simulationName.c_str(), numRanksAvailable,
+ simulationName.c_str(),
+ numRanksAvailable,
reportNumbersOfPpRanksSupported(simulationName).c_str());
return;
}
EXPECT_EQ(0, runner->callGrompp(caller));
}
+ const std::string splitPoint = std::to_string(std::stoi(mdpFieldValues.at("nsteps")) / 2);
+
// prepare the .tpr file for the first part of the two-part run
{
// TODO evolve grompp to report the number of warnings issued, so
caller.addOption("-maxwarn", maxWarningsTolerated);
runner->useTopGroAndNdxFromDatabase(simulationName);
auto firstPartMdpFieldValues = mdpFieldValues;
- firstPartMdpFieldValues["nsteps"] = "8";
+ firstPartMdpFieldValues["nsteps"] = splitPoint;
runner->useStringAsMdpFile(prepareMdpFileContents(firstPartMdpFieldValues));
runner->tprFileName_ = firstPartRunTprFileName;
EXPECT_EQ(0, runner->callGrompp(caller));
runner->edrFileName_ = fullRunEdrFileName;
CommandLine fullRunCaller;
fullRunCaller.append("mdrun");
+ /* Force neighborlist update at the beginning of the second half of the trajectory.
+ * Doing so through CLI options prevents pairlist tuning from changing it. */
+ fullRunCaller.addOption("-nstlist", splitPoint);
ASSERT_EQ(0, runner->callMdrun(fullRunCaller));
}
// Build the functor that will compare energy frames on the chosen
// energy terms.
- EnergyComparison energyComparison(energyTermsToCompare);
+ EnergyComparison energyComparison(energyTermsToCompare, MaxNumFrames::compareAllFrames());
// Build the manager that will present matching pairs of frames to compare.
//
* \todo Add FEP case. */
class MdrunNoAppendContinuationIsExact :
public MdrunTestFixture,
- public ::testing::WithParamInterface<std::tuple<std::string, std::string, std::string, std::string>>
+ public ::testing::WithParamInterface<std::tuple<std::string, std::string, std::string, std::string, MdpParameterDatabase>>
{
public:
//! Constructor
TEST_P(MdrunNoAppendContinuationIsExact, WithinTolerances)
{
- auto params = GetParam();
- auto simulationName = std::get<0>(params);
- auto integrator = std::get<1>(params);
- auto temperatureCoupling = std::get<2>(params);
- auto pressureCoupling = std::get<3>(params);
+ auto params = GetParam();
+ auto simulationName = std::get<0>(params);
+ auto integrator = std::get<1>(params);
+ auto temperatureCoupling = std::get<2>(params);
+ auto pressureCoupling = std::get<3>(params);
+ auto additionalMdpParameters = std::get<4>(params);
+
+ // Check for unimplemented functionality
+ // TODO: Update this as modular simulator gains functionality
+ const bool isModularSimulatorExplicitlyDisabled = (getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
+ const bool isTCouplingCompatibleWithModularSimulator =
+ (temperatureCoupling == "no" || temperatureCoupling == "v-rescale"
+ || temperatureCoupling == "berendsen");
+ // GPU update is not compatible with modular simulator
+ const bool isGpuUpdateRequested = (getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") != nullptr);
+ if (integrator == "md-vv" && pressureCoupling == "parrinello-rahman"
+ && (isModularSimulatorExplicitlyDisabled || !isTCouplingCompatibleWithModularSimulator
+ || isGpuUpdateRequested))
+ {
+ // Under md-vv, Parrinello-Rahman is only implemented for the modular simulator
+ return;
+ }
+ if (integrator == "md-vv" && temperatureCoupling == "nose-hoover"
+ && pressureCoupling == "berendsen")
+ {
+ // This combination is not implemented in either legacy or modular simulator
+ return;
+ }
+
SCOPED_TRACE(
formatString("Comparing normal and two-part run of simulation '%s' "
"with integrator '%s'",
- simulationName.c_str(), integrator.c_str()));
-
- auto mdpFieldValues = prepareMdpFieldValues(simulationName.c_str(), integrator.c_str(),
- temperatureCoupling.c_str(), pressureCoupling.c_str());
+ simulationName.c_str(),
+ integrator.c_str()));
+
+ auto mdpFieldValues = prepareMdpFieldValues(simulationName.c_str(),
+ integrator.c_str(),
+ temperatureCoupling.c_str(),
+ pressureCoupling.c_str(),
+ additionalMdpParameters);
// The exact lambda state choice is unimportant, so long as there
// is one when using an FEP input.
- mdpFieldValues["other"] += formatString("\ninit-lambda-state = %d", 3);
+ mdpFieldValues["init-lambda-state"] = "3";
+ mdpFieldValues["nsteps"] = "16";
- // Forces on GPUs are generally not reproducible enough for a tight
- // tolerance. Similarly, the propagation of sd and bd are not as
+ // Forces and update on GPUs are generally not reproducible enough for a tight
+ // tolerance. Similarly, the propagation of bd is not as
// reproducible as the others. So we use several ULP tolerance
// in all cases. This is looser than needed e.g. for md and md-vv
// with forces on CPUs, but there is no real risk of a bug with
// those propagators that would only be caught with a tighter
// tolerance in this particular test.
- int ulpToleranceInMixed = 32;
+ int ulpToleranceInMixed = 128;
int ulpToleranceInDouble = 64;
if (integrator == "bd")
{
// Somehow, the bd integrator has never been as reproducible
// as the others, either in continuations or reruns.
- ulpToleranceInMixed = 128;
+ ulpToleranceInMixed = 200;
+ }
+ EnergyTermsToCompare energyTermsToCompare{
+ { { interaction_function[F_EPOT].longname,
+ relativeToleranceAsPrecisionDependentUlp(10.0, ulpToleranceInMixed, ulpToleranceInDouble) },
+ { interaction_function[F_EKIN].longname,
+ relativeToleranceAsPrecisionDependentUlp(10.0, ulpToleranceInMixed, ulpToleranceInDouble) } }
+ };
+
+ if (temperatureCoupling != "no" || pressureCoupling != "no")
+ {
+ if (simulationName == "alanine_vacuo")
+ {
+ // This is slightly less reproducible
+ energyTermsToCompare.insert({ interaction_function[F_ECONSERVED].longname,
+ relativeToleranceAsPrecisionDependentUlp(
+ 10.0, ulpToleranceInMixed * 2, ulpToleranceInDouble) });
+ }
+ else
+ {
+ energyTermsToCompare.insert({ interaction_function[F_ECONSERVED].longname,
+ relativeToleranceAsPrecisionDependentUlp(
+ 10.0, ulpToleranceInMixed, ulpToleranceInDouble) });
+ }
+ }
+
+ if (pressureCoupling == "parrinello-rahman")
+ {
+ energyTermsToCompare.insert({ "Box-Vel-XX",
+ relativeToleranceAsPrecisionDependentUlp(
+ 1e-12, ulpToleranceInMixed, ulpToleranceInDouble) });
+ energyTermsToCompare.insert({ "Box-Vel-YY",
+ relativeToleranceAsPrecisionDependentUlp(
+ 1e-12, ulpToleranceInMixed, ulpToleranceInDouble) });
+ energyTermsToCompare.insert({ "Box-Vel-ZZ",
+ relativeToleranceAsPrecisionDependentUlp(
+ 1e-12, ulpToleranceInMixed, ulpToleranceInDouble) });
}
- EnergyTermsToCompare energyTermsToCompare{ {
- { interaction_function[F_EPOT].longname,
- relativeToleranceAsPrecisionDependentUlp(10.0, ulpToleranceInMixed, ulpToleranceInDouble) },
- } };
int numWarningsToTolerate = 1;
- runTest(&fileManager_, &runner_, simulationName, numWarningsToTolerate, mdpFieldValues,
- energyTermsToCompare);
+ runTest(&fileManager_, &runner_, simulationName, numWarningsToTolerate, mdpFieldValues, energyTermsToCompare);
}
// TODO The time for OpenCL kernel compilation means these tests time
// out. Once that compilation is cached for the whole process, these
// tests can run in such configurations.
-#if GMX_GPU != GMX_GPU_OPENCL
+#if !GMX_GPU_OPENCL
-INSTANTIATE_TEST_CASE_P(
+INSTANTIATE_TEST_SUITE_P(
NormalIntegrators,
MdrunNoAppendContinuationIsExact,
::testing::Combine(::testing::Values("argon12", "spc2", "alanine_vsite_vacuo"),
::testing::Values("md", "md-vv", "bd", "sd"),
::testing::Values("no"),
- ::testing::Values("no")));
-
-INSTANTIATE_TEST_CASE_P(NormalIntegratorsWithFEP,
- MdrunNoAppendContinuationIsExact,
- ::testing::Combine(::testing::Values("nonanol_vacuo"),
- ::testing::Values("md", "md-vv", "bd", "sd"),
- ::testing::Values("no"),
- ::testing::Values("no")));
-
-INSTANTIATE_TEST_CASE_P(
- NormalNVT,
+ ::testing::Values("no"),
+ ::testing::Values(MdpParameterDatabase::Default)));
+
+INSTANTIATE_TEST_SUITE_P(NormalIntegratorsWithFEP,
+ MdrunNoAppendContinuationIsExact,
+ ::testing::Combine(::testing::Values("nonanol_vacuo"),
+ ::testing::Values("md", "md-vv", "bd", "sd"),
+ ::testing::Values("no"),
+ ::testing::Values("no"),
+ ::testing::Values(MdpParameterDatabase::Default)));
+
+INSTANTIATE_TEST_SUITE_P(
+ NVT,
MdrunNoAppendContinuationIsExact,
::testing::Combine(::testing::Values("argon12"),
::testing::Values("md", "md-vv"),
::testing::Values("berendsen", "v-rescale", "nose-hoover"),
- ::testing::Values("no")));
+ ::testing::Values("no"),
+ ::testing::Values(MdpParameterDatabase::Default)));
-INSTANTIATE_TEST_CASE_P(LeapfrogNPH,
- MdrunNoAppendContinuationIsExact,
- ::testing::Combine(::testing::Values("argon12"),
- ::testing::Values("md"),
- ::testing::Values("no"),
- ::testing::Values("berendsen", "parrinello-rahman")));
+INSTANTIATE_TEST_SUITE_P(
+ NPH,
+ MdrunNoAppendContinuationIsExact,
+ ::testing::Combine(::testing::Values("argon12"),
+ ::testing::Values("md", "md-vv"),
+ ::testing::Values("no"),
+ ::testing::Values("berendsen", "parrinello-rahman", "C-rescale"),
+ ::testing::Values(MdpParameterDatabase::Default)));
-INSTANTIATE_TEST_CASE_P(
- LeapfrogNPT,
+INSTANTIATE_TEST_SUITE_P(
+ NPT,
MdrunNoAppendContinuationIsExact,
::testing::Combine(::testing::Values("argon12"),
- ::testing::Values("md"),
+ ::testing::Values("md", "md-vv"),
::testing::Values("berendsen", "v-rescale", "nose-hoover"),
- ::testing::Values("berendsen", "parrinello-rahman")));
-
-INSTANTIATE_TEST_CASE_P(VelocityVerletNPH,
- MdrunNoAppendContinuationIsExact,
- ::testing::Combine(::testing::Values("argon12"),
- ::testing::Values("md-vv"),
- ::testing::Values("no"),
- ::testing::Values("berendsen")));
-
-INSTANTIATE_TEST_CASE_P(VelocityVerletNPT,
- MdrunNoAppendContinuationIsExact,
- ::testing::Combine(::testing::Values("argon12"),
- ::testing::Values("md-vv"),
- ::testing::Values("v-rescale"),
- ::testing::Values("berendsen")));
-
-INSTANTIATE_TEST_CASE_P(MTTK,
- MdrunNoAppendContinuationIsExact,
- ::testing::Combine(::testing::Values("argon12"),
- ::testing::Values("md-vv"),
- ::testing::Values("nose-hoover"),
- ::testing::Values("mttk")));
-
+ ::testing::Values("berendsen", "parrinello-rahman", "C-rescale"),
+ ::testing::Values(MdpParameterDatabase::Default)));
+
+INSTANTIATE_TEST_SUITE_P(MTTK,
+ MdrunNoAppendContinuationIsExact,
+ ::testing::Combine(::testing::Values("argon12"),
+ ::testing::Values("md-vv"),
+ ::testing::Values("nose-hoover"),
+ ::testing::Values("mttk"),
+ ::testing::Values(MdpParameterDatabase::Default)));
+
+INSTANTIATE_TEST_SUITE_P(Pull,
+ MdrunNoAppendContinuationIsExact,
+ ::testing::Combine(::testing::Values("spc2"),
+ ::testing::Values("md", "md-vv"),
+ ::testing::Values("no"),
+ ::testing::Values("no"),
+ ::testing::Values(MdpParameterDatabase::Pull)));
+
+INSTANTIATE_TEST_SUITE_P(Awh,
+ MdrunNoAppendContinuationIsExact,
+ ::testing::Combine(::testing::Values("alanine_vacuo"),
+ ::testing::Values("md", "md-vv"),
+ ::testing::Values("v-rescale"),
+ ::testing::Values("no"),
+ ::testing::Values(MdpParameterDatabase::Awh)));
+
+#else
+GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(MdrunNoAppendContinuationIsExact);
#endif
} // namespace
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff