energyreader.cpp
energycomparison.cpp
moduletest.cpp
+ simulatorcomparison.cpp
terminationhelper.cpp
trajectorycomparison.cpp
trajectoryreader.cpp
#include "config.h"
#include "gromacs/topology/ifunc.h"
-#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/stringutil.h"
+#include "testutils/mpitest.h"
+#include "testutils/simulationdatabase.h"
+
+#include "moduletest.h"
#include "simulatorcomparison.h"
namespace gmx
ComparisonConditions::MustCompare
};
+void executeRerunTest(TestFileManager* fileManager,
+ SimulationRunner* runner,
+ const std::string& simulationName,
+ int numWarningsToTolerate,
+ const MdpFieldValues& mdpFieldValues,
+ const EnergyTermsToCompare& energyTermsToCompare,
+ const TrajectoryComparison& trajectoryComparison)
+{
+ // TODO At some point we should also test PME-only ranks.
+ int numRanksAvailable = getNumberOfTestMpiRanks();
+ if (!isNumberOfPpRanksSupported(simulationName, numRanksAvailable))
+ {
+ fprintf(stdout,
+ "Test system '%s' cannot run with %d ranks.\n"
+ "The supported numbers are: %s\n",
+ simulationName.c_str(), numRanksAvailable,
+ reportNumbersOfPpRanksSupported(simulationName).c_str());
+ return;
+ }
+
+ // Set file names
+ auto simulator1TrajectoryFileName = fileManager->getTemporaryFilePath("sim1.trr");
+ auto simulator1EdrFileName = fileManager->getTemporaryFilePath("sim1.edr");
+ auto simulator2TrajectoryFileName = fileManager->getTemporaryFilePath("sim2.trr");
+ auto simulator2EdrFileName = fileManager->getTemporaryFilePath("sim2.edr");
+
+ // Run grompp
+ runner->tprFileName_ = fileManager->getTemporaryFilePath("sim.tpr");
+ runner->useTopGroAndNdxFromDatabase(simulationName);
+ runner->useStringAsMdpFile(prepareMdpFileContents(mdpFieldValues));
+ auto options = std::vector<SimulationOptionTuple>();
+ if (numWarningsToTolerate > 0)
+ {
+ options.emplace_back(SimulationOptionTuple("-maxwarn", std::to_string(numWarningsToTolerate)));
+ }
+ runGrompp(runner, options);
+
+ // Do first mdrun
+ runner->fullPrecisionTrajectoryFileName_ = simulator1TrajectoryFileName;
+ runner->edrFileName_ = simulator1EdrFileName;
+ runMdrun(runner);
+
+ // Do second mdrun
+ runner->fullPrecisionTrajectoryFileName_ = simulator2TrajectoryFileName;
+ runner->edrFileName_ = simulator2EdrFileName;
+ runMdrun(runner, { SimulationOptionTuple("-rerun", simulator1TrajectoryFileName) });
+
+ // Compare simulation results
+ compareEnergies(simulator1EdrFileName, simulator2EdrFileName, energyTermsToCompare);
+ compareTrajectories(simulator1TrajectoryFileName, simulator2TrajectoryFileName, trajectoryComparison);
+}
+
TEST_P(MdrunRerunTest, WithinTolerances)
{
auto params = GetParam();
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, 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.
#include "config.h"
#include "gromacs/topology/ifunc.h"
-#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/stringutil.h"
+#include "testutils/mpitest.h"
+#include "testutils/setenv.h"
+#include "testutils/simulationdatabase.h"
+
+#include "moduletest.h"
#include "simulatorcomparison.h"
namespace gmx
TEST_P(SimulatorComparisonTest, WithinTolerances)
{
- auto params = GetParam();
- auto mdpParams = std::get<0>(params);
- auto simulationName = std::get<0>(mdpParams);
- auto integrator = std::get<1>(mdpParams);
- auto tcoupling = std::get<2>(mdpParams);
- auto pcoupling = std::get<3>(mdpParams);
- auto envVariable = std::get<1>(params);
+ auto params = GetParam();
+ auto mdpParams = std::get<0>(params);
+ auto simulationName = std::get<0>(mdpParams);
+ auto integrator = std::get<1>(mdpParams);
+ auto tcoupling = std::get<2>(mdpParams);
+ auto pcoupling = std::get<3>(mdpParams);
+ auto environmentVariable = std::get<1>(params);
+
+ // TODO At some point we should also test PME-only ranks.
+ int numRanksAvailable = getNumberOfTestMpiRanks();
+ if (!isNumberOfPpRanksSupported(simulationName, numRanksAvailable))
+ {
+ fprintf(stdout,
+ "Test system '%s' cannot run with %d ranks.\n"
+ "The supported numbers are: %s\n",
+ simulationName.c_str(), numRanksAvailable,
+ reportNumbersOfPpRanksSupported(simulationName).c_str());
+ return;
+ }
if (integrator == "md-vv" && pcoupling == "Parrinello-Rahman")
{
"Comparing two simulations of '%s' "
"with integrator '%s' and '%s' temperature coupling, "
"switching environment variable '%s'",
- simulationName.c_str(), integrator.c_str(), tcoupling.c_str(), envVariable.c_str()));
+ simulationName.c_str(), integrator.c_str(), tcoupling.c_str(), environmentVariable.c_str()));
auto mdpFieldValues = prepareMdpFieldValues(simulationName.c_str(), integrator.c_str(),
tcoupling.c_str(), pcoupling.c_str());
// trajectory frames in the chosen way.
TrajectoryComparison trajectoryComparison{ trajectoryMatchSettings, trajectoryTolerances };
- int numWarningsToTolerate = 0;
- executeSimulatorComparisonTest(envVariable, &fileManager_, &runner_, simulationName,
- numWarningsToTolerate, mdpFieldValues, energyTermsToCompare,
- trajectoryComparison);
+ // Set file names
+ auto simulator1TrajectoryFileName = fileManager_.getTemporaryFilePath("sim1.trr");
+ auto simulator1EdrFileName = fileManager_.getTemporaryFilePath("sim1.edr");
+ auto simulator2TrajectoryFileName = fileManager_.getTemporaryFilePath("sim2.trr");
+ auto simulator2EdrFileName = fileManager_.getTemporaryFilePath("sim2.edr");
+
+ // Run grompp
+ runner_.tprFileName_ = fileManager_.getTemporaryFilePath("sim.tpr");
+ runner_.useTopGroAndNdxFromDatabase(simulationName);
+ runner_.useStringAsMdpFile(prepareMdpFileContents(mdpFieldValues));
+ runGrompp(&runner_);
+
+ // Backup current state of environment variable and unset it
+ char* environmentVariableBackup = getenv(environmentVariable.c_str());
+ gmxUnsetenv(environmentVariable.c_str());
+
+ // Do first mdrun
+ runner_.fullPrecisionTrajectoryFileName_ = simulator1TrajectoryFileName;
+ runner_.edrFileName_ = simulator1EdrFileName;
+ runMdrun(&runner_);
+
+ // Set environment variable
+ const int overWriteEnvironmentVariable = 1;
+ gmxSetenv(environmentVariable.c_str(), "ON", overWriteEnvironmentVariable);
+
+ // Do second mdrun
+ runner_.fullPrecisionTrajectoryFileName_ = simulator2TrajectoryFileName;
+ runner_.edrFileName_ = simulator2EdrFileName;
+ runMdrun(&runner_);
+
+ // Reset or unset environment variable to leave further tests undisturbed
+ if (environmentVariableBackup != nullptr)
+ {
+ // set environment variable
+ gmxSetenv(environmentVariable.c_str(), environmentVariableBackup, overWriteEnvironmentVariable);
+ }
+ else
+ {
+ // unset environment variable
+ gmxUnsetenv(environmentVariable.c_str());
+ }
+
+ // Compare simulation results
+ compareEnergies(simulator1EdrFileName, simulator2EdrFileName, energyTermsToCompare);
+ compareTrajectories(simulator1TrajectoryFileName, simulator2TrajectoryFileName, trajectoryComparison);
}
// TODO: The time for OpenCL kernel compilation means these tests time
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, 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.
*/
/*! \internal \file
* \brief
- * Helper classes for tests that compare the results of equivalent
+ * Helper functions for tests that compare the results of equivalent
* simulation runs. Currently used for the rerun and the simulator
* tests
*
*/
#include "gmxpre.h"
-#include "testutils/mpitest.h"
-#include "testutils/setenv.h"
-#include "testutils/simulationdatabase.h"
+#include "simulatorcomparison.h"
+
+#include "gromacs/trajectory/energyframe.h"
-#include "energycomparison.h"
#include "energyreader.h"
#include "mdruncomparison.h"
#include "moduletest.h"
-#include "trajectorycomparison.h"
#include "trajectoryreader.h"
namespace gmx
{
namespace test
{
-namespace
-{
-//! Run grompp and mdrun for both sets of mdp field values
-template<bool doEnvironmentVariable, bool doRerun>
-void executeSimulatorComparisonTestImpl(TestFileManager* fileManager,
- SimulationRunner* runner,
- const std::string& simulationName,
- int maxWarningsTolerated,
- const MdpFieldValues& mdpFieldValues,
- const EnergyTermsToCompare& energyTermsToCompare,
- const TrajectoryComparison& trajectoryComparison,
- const std::string& environmentVariable)
+void runGrompp(SimulationRunner* runner, const std::vector<SimulationOptionTuple>& options)
{
- // TODO At some point we should also test PME-only ranks.
- int numRanksAvailable = getNumberOfTestMpiRanks();
- if (!isNumberOfPpRanksSupported(simulationName, numRanksAvailable))
- {
- fprintf(stdout,
- "Test system '%s' cannot run with %d ranks.\n"
- "The supported numbers are: %s\n",
- simulationName.c_str(), numRanksAvailable,
- reportNumbersOfPpRanksSupported(simulationName).c_str());
- return;
- }
-
- auto simulator1TrajectoryFileName = fileManager->getTemporaryFilePath("sim1.trr");
- auto simulator1EdrFileName = fileManager->getTemporaryFilePath("sim1.edr");
- auto simulator2TrajectoryFileName = fileManager->getTemporaryFilePath("sim2.trr");
- auto simulator2EdrFileName = fileManager->getTemporaryFilePath("sim2.edr");
- auto simulatorTprFileName = fileManager->getTemporaryFilePath("sim.tpr");
+ CommandLine caller;
+ caller.append("grompp");
- // prepare the .tpr file
+ for (const std::tuple<std::string, std::string>& option : options)
{
- // TODO evolve grompp to report the number of warnings issued, so
- // tests always expect the right number.
- CommandLine caller;
- caller.append("grompp");
- caller.addOption("-maxwarn", maxWarningsTolerated);
- runner->tprFileName_ = simulatorTprFileName;
- runner->useTopGroAndNdxFromDatabase(simulationName);
- runner->useStringAsMdpFile(prepareMdpFileContents(mdpFieldValues));
- EXPECT_EQ(0, runner->callGrompp(caller));
+ caller.addOption(std::get<0>(option).c_str(), std::get<1>(option));
}
- char* environmentVariableBackup = nullptr;
- if (doEnvironmentVariable)
- {
- // save state of environment variable
- environmentVariableBackup = getenv(environmentVariable.c_str());
- }
+ EXPECT_EQ(0, runner->callGrompp(caller));
+}
- // do the first mdrun
- {
- runner->fullPrecisionTrajectoryFileName_ = simulator1TrajectoryFileName;
- runner->edrFileName_ = simulator1EdrFileName;
- runner->tprFileName_ = simulatorTprFileName;
- CommandLine simulator1Caller;
- simulator1Caller.append("mdrun");
- if (doEnvironmentVariable)
- {
- // unset environment variable
- gmxUnsetenv(environmentVariable.c_str());
- }
- ASSERT_EQ(0, runner->callMdrun(simulator1Caller));
- }
+void runMdrun(SimulationRunner* runner, const std::vector<SimulationOptionTuple>& options)
+{
+ CommandLine caller;
+ caller.append("mdrun");
- // do the second mdrun
+ for (const std::tuple<std::string, std::string>& option : options)
{
- runner->fullPrecisionTrajectoryFileName_ = simulator2TrajectoryFileName;
- runner->edrFileName_ = simulator2EdrFileName;
- runner->tprFileName_ = simulatorTprFileName;
- CommandLine simulator2Caller;
- simulator2Caller.append("mdrun");
- if (doEnvironmentVariable)
- {
- // set environment variable
- gmxSetenv(environmentVariable.c_str(), "ON", true);
- }
- if (doRerun)
- {
- simulator2Caller.addOption("-rerun", simulator1TrajectoryFileName);
- }
- ASSERT_EQ(0, runner->callMdrun(simulator2Caller));
+ caller.addOption(std::get<0>(option).c_str(), std::get<1>(option));
}
- if (doEnvironmentVariable)
- {
- if (environmentVariableBackup != nullptr)
- {
- // set environment variable
- gmxSetenv(environmentVariable.c_str(), environmentVariableBackup, true);
- }
- else
- {
- // unset environment variable
- gmxUnsetenv(environmentVariable.c_str());
- }
- }
+ EXPECT_EQ(0, runner->callMdrun(caller));
+}
+void compareEnergies(const std::string& edr1Name,
+ const std::string& edr2Name,
+ const EnergyTermsToCompare& energyTermsToCompare)
+{
// Build the functor that will compare energy frames on the chosen
// energy terms.
EnergyComparison energyComparison(energyTermsToCompare);
// names), for convenience. In the future, use a range.
auto namesOfEnergiesToMatch = energyComparison.getEnergyNames();
FramePairManager<EnergyFrameReader> energyManager(
- openEnergyFileToReadTerms(simulator1EdrFileName, namesOfEnergiesToMatch),
- openEnergyFileToReadTerms(simulator2EdrFileName, namesOfEnergiesToMatch));
+ openEnergyFileToReadTerms(edr1Name, namesOfEnergiesToMatch),
+ openEnergyFileToReadTerms(edr2Name, namesOfEnergiesToMatch));
// Compare the energy frames.
energyManager.compareAllFramePairs<EnergyFrame>(energyComparison);
+}
+void compareTrajectories(const std::string& trajectory1Name,
+ const std::string& trajectory2Name,
+ const TrajectoryComparison& trajectoryComparison)
+{
// Build the manager that will present matching pairs of frames to compare
FramePairManager<TrajectoryFrameReader> trajectoryManager(
- std::make_unique<TrajectoryFrameReader>(simulator1TrajectoryFileName),
- std::make_unique<TrajectoryFrameReader>(simulator2TrajectoryFileName));
+ std::make_unique<TrajectoryFrameReader>(trajectory1Name),
+ std::make_unique<TrajectoryFrameReader>(trajectory2Name));
// Compare the trajectory frames.
trajectoryManager.compareAllFramePairs<TrajectoryFrame>(trajectoryComparison);
}
-} // namespace
-
-template<typename... Args>
-void executeSimulatorComparisonTest(const std::string& environmentVariable, Args&&... args)
-{
- executeSimulatorComparisonTestImpl<true, false>(std::forward<Args>(args)..., environmentVariable);
-}
-
-template<typename... Args>
-void executeRerunTest(Args&&... args)
-{
- executeSimulatorComparisonTestImpl<false, true>(std::forward<Args>(args)..., "");
-}
} // namespace test
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, 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.
#include <string>
+#include "energycomparison.h"
+#include "trajectorycomparison.h"
+
namespace gmx
{
namespace test
{
-/*!
- * \brief Run and compare a simulator run with and without an environment variable
- *
- * Run grompp, and repeat mdrun with and without the environment variable set.
- * Compare energies (via EnergyComparator) and trajectories.
- */
-template<typename... Args>
-void executeSimulatorComparisonTest(const std::string& environmentVariable, Args&&... args);
+class SimulationRunner;
-/*!
- * \brief Run and compare a simulator run to its rerun
- *
- * Run grompp, run mdrun and rerun the resulting trajectory.
- * Compare energies (via EnergyComparator) and trajectories.
- */
-template<typename... Args>
-void executeRerunTest(Args&&... args);
+typedef std::tuple<std::string, std::string> SimulationOptionTuple;
+
+void runGrompp(SimulationRunner* runner,
+ const std::vector<SimulationOptionTuple>& options = std::vector<SimulationOptionTuple>());
+
+void runMdrun(SimulationRunner* runner,
+ const std::vector<SimulationOptionTuple>& options = std::vector<SimulationOptionTuple>());
+
+void compareEnergies(const std::string& edr1Name,
+ const std::string& edr2Name,
+ const EnergyTermsToCompare& energyTermsToCompare);
+
+void compareTrajectories(const std::string& trajectory1Name,
+ const std::string& trajectory2Name,
+ const TrajectoryComparison& trajectoryComparison);
} // namespace test
} // namespace gmx
-// Including this here avoid having to put everything in the header file,
-// or to explicitly declare the templates (which would render the parameter
-// pack useless)
-#include "simulatorcomparison.cpp"
-
#endif // GMX_PROGRAMS_MDRUN_TESTS_SIMULATORCOMPARISON_H
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff