do_verbose = mdrunOptions.verbose
&& (step % mdrunOptions.verboseStepPrintInterval == 0 || bFirstStep || bLastStep);
- if (useGpuForUpdate && !bFirstStep && bNS)
+ // On search steps, when doing the update on the GPU, copy
+ // the coordinates and velocities to the host unless they are
+ // already there (ie on the first step and after replica
+ // exchange).
+ if (useGpuForUpdate && bNS && !bFirstStep && !bExchanged)
{
- // Copy velocities from the GPU on search steps to keep a copy on host (device buffers are reinitialized).
stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
- stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
- // Copy coordinate from the GPU when needed at the search step.
- // NOTE: The cases when coordinates needed on CPU for force evaluation are handled in sim_utils.
- // NOTE: If the coordinates are to be written into output file they are also copied separately before the output.
stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
+ stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
}
if (correct_box(fplog, step, state->box))
{
bMasterState = TRUE;
- // If update is offloaded, it should be informed about the box size change
- if (useGpuForUpdate)
- {
- integrator->setPbc(PbcType::Xyz, state->box);
- }
}
}
+ // If update is offloaded, and the box was changed either
+ // above or in a replica exchange on the previous step,
+ // the GPU Update object should be informed
+ if (useGpuForUpdate && (bMasterState || bExchanged))
+ {
+ integrator->setPbc(PbcType::Xyz, state->box);
+ }
if (haveDDAtomOrdering(*cr) && bMasterState)
{
dd_collect_state(cr->dd, state, state_global);
{
if (useGpuForUpdate)
{
- if (bNS && (bFirstStep || haveDDAtomOrdering(*cr)))
+ // On search steps, update handles to device vectors
+ if (bNS && (bFirstStep || haveDDAtomOrdering(*cr) || bExchanged))
{
integrator->set(stateGpu->getCoordinates(),
stateGpu->getVelocities(),
/* The velocity copy is redundant if we had Center-of-Mass motion removed on
* the previous step. We don't check that now. */
stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
- if (!runScheduleWork->stepWork.haveGpuPmeOnThisRank
- && !runScheduleWork->stepWork.useGpuXBufferOps)
+ if (bExchanged
+ || (!runScheduleWork->stepWork.haveGpuPmeOnThisRank
+ && !runScheduleWork->stepWork.useGpuXBufferOps))
{
stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
}
doParrinelloRahman,
ir->nstpcouple * ir->delta_t,
M);
-
- // Copy velocities D2H after update if:
- // - Globals are computed this step (includes the energy output steps).
- // - Temperature is needed for the next step.
- if (bGStat || needHalfStepKineticEnergy)
- {
- stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
- stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
- }
}
else
{
// and when algorithms require it.
const bool doInterSimSignal = (simulationsShareState && do_per_step(step, nstSignalComm));
- if (bGStat || needHalfStepKineticEnergy || doInterSimSignal)
+ if (useGpuForUpdate)
{
- // Copy coordinates when needed to stop the CM motion.
- if (useGpuForUpdate && (bDoReplEx || (!EI_VV(ir->eI) && bStopCM)))
+ const bool coordinatesRequiredForStopCM =
+ bStopCM && (bGStat || needHalfStepKineticEnergy || doInterSimSignal)
+ && !EI_VV(ir->eI);
+
+ // Copy coordinates when needed to stop the CM motion or for replica exchange
+ if (coordinatesRequiredForStopCM || bDoReplEx)
{
stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
}
+
+ // Copy velocities back to the host if:
+ // - Globals are computed this step (includes the energy output steps).
+ // - Temperature is needed for the next step.
+ // - This is a replica exchange step (even though we will only need
+ // the velocities if an exchange succeeds)
+ if (bGStat || needHalfStepKineticEnergy || bDoReplEx)
+ {
+ stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
+ stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
+ }
+ }
+
+ if (bGStat || needHalfStepKineticEnergy || doInterSimSignal)
+ {
// Since we're already communicating at this step, we
// can propagate intra-simulation signals. Note that
// check_nstglobalcomm has the responsibility for
accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
}
+ bool scaleCoordinates = !useGpuForUpdate || bDoReplEx;
update_pcouple_after_coordinates(fplog,
step,
ir,
state,
nrnb,
upd.deform(),
- !useGpuForUpdate);
+ scaleCoordinates);
const bool doBerendsenPressureCoupling = (inputrec->epc == PressureCoupling::Berendsen
&& do_per_step(step, inputrec->nstpcouple));
# files with code for tests
multisim.cpp
multisimtest.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
+ )
+target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
+gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 4 INTEGRATION_TEST IGNORE_LEAKS)
+
+set(testname "MdrunMultiSimReplexTests")
+set(exename "mdrun-multisim-replex-test")
+
+gmx_add_gtest_executable(${exename} MPI
+ CPP_SOURCE_FILES
+ # files with code for tests
+ multisimtest.cpp
replicaexchange.cpp
# pseudo-library for code for mdrun
$<TARGET_OBJECTS:mdrun_objlib>
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 4 INTEGRATION_TEST IGNORE_LEAKS)
+set(testname "MdrunMultiSimReplexEquivalenceTests")
+set(exename "mdrun-multisim-replex-equivalence-test")
+
+gmx_add_gtest_executable(${exename} MPI
+ CPP_SOURCE_FILES
+ # files with code for tests
+ multisimtest.cpp
+ replicaexchange_equivalence.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
+ )
+target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
+gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 4 INTEGRATION_TEST IGNORE_LEAKS)
+
# Tests that only make sense to run with multiple ranks and/or real
# MPI are implemented here. Special case for slow PME tests
set(testname "MdrunMpiPmeTests")
gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
# Slow-running tests that target testing multiple-rank coordination behaviors
-set(exename "mdrun-mpi-coordination-test")
+# These tests are extremely slow without optimization or OpenMP, so only run them for
+# build types like Release or RelWithDebInfo and if the build has been configured
+# with OpenMP enabled
+set(exename "mdrun-mpi-coordination-basic-test")
gmx_add_gtest_executable(${exename} MPI
CPP_SOURCE_FILES
# files with code for tests
periodicactions.cpp
+ periodicactions_basic.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
+ )
+target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
+
+if (CMAKE_BUILD_TYPE MATCHES "Rel" AND GMX_OPENMP)
+ set(testname "MdrunMpiCoordinationBasicTestsOneRank")
+ gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 1 SLOW_TEST IGNORE_LEAKS)
+ set(testname "MdrunMpiCoordinationBasicTestsTwoRanks")
+ gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 SLOW_TEST IGNORE_LEAKS)
+endif()
+
+set(exename "mdrun-mpi-coordination-coupling-test")
+gmx_add_gtest_executable(${exename} MPI
+ CPP_SOURCE_FILES
+ # files with code for tests
+ periodicactions.cpp
+ periodicactions_coupling.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
+ )
+target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
+
+if (CMAKE_BUILD_TYPE MATCHES "Rel" AND GMX_OPENMP)
+ set(testname "MdrunMpiCoordinationCouplingTestsOneRank")
+ gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 1 SLOW_TEST IGNORE_LEAKS)
+ set(testname "MdrunMpiCoordinationCouplingTestsTwoRanks")
+ gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 SLOW_TEST IGNORE_LEAKS)
+endif()
+
+set(exename "mdrun-mpi-coordination-constraints-test")
+gmx_add_gtest_executable(${exename} MPI
+ CPP_SOURCE_FILES
+ # files with code for tests
+ periodicactions.cpp
+ periodicactions_constraints.cpp
# pseudo-library for code for mdrun
$<TARGET_OBJECTS:mdrun_objlib>
)
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
-# These tests are extremely slow without optimization or OpenMP, so only run them for
-# build types like Release or RelWithDebInfo and if the build has been configured
-# with OpenMP enabled.
if (CMAKE_BUILD_TYPE MATCHES "Rel" AND GMX_OPENMP)
- set(testname "MdrunMpiCoordinationTestsOneRank")
+ set(testname "MdrunMpiCoordinationConstraintsTestsOneRank")
gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 1 SLOW_TEST IGNORE_LEAKS)
- set(testname "MdrunMpiCoordinationTestsTwoRanks")
+ set(testname "MdrunMpiCoordinationConstraintsTestsTwoRanks")
gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 SLOW_TEST IGNORE_LEAKS)
endif()
*/
/*! \internal \file
- * \brief Tests to verify that a simulator that only does some actions
+ * \brief Utility functions for tests to verify that a simulator that only does some actions
* periodically produces the expected results.
*
* \author Mark Abraham <mark.j.abraham@gmail.com>
#include "config.h"
-#include <tuple>
-
-#include "gromacs/trajectory/energyframe.h"
-#include "gromacs/utility/strconvert.h"
-#include "gromacs/utility/stringutil.h"
-
-#include "testutils/simulationdatabase.h"
-#include "testutils/testasserts.h"
-
-#include "energycomparison.h"
-#include "energyreader.h"
-#include "moduletest.h"
+#include "periodicactions.h"
namespace gmx
{
namespace test
{
-namespace
-{
/*! \brief Mdp parameters that determine the manner of simulation
* propagation. */
* not the simulation propagation. */
using PeriodicOutputParameters = MdpFieldValues;
-//! Helper type of output file names for the reference mdrun call
-struct ReferenceFileNames
-{
- //! Name of energy file
- std::string edrFileName_;
-};
-
//! Function type to produce sets of .mdp parameters for testing periodic output
using OutputParameterGeneratorFunction = std::vector<PeriodicOutputParameters> (*)();
-/*! \brief Test fixture base for comparing a simulator with one that
- * does everything every step
- *
- * This test ensures that two simulator code paths called via
- * different mdp options yield identical energy trajectories,
- * up to some (arbitrary) precision.
- *
- * These tests are useful to check that periodic actions implemented
- * in simulators are correct, and that different code paths expected
- * to yield identical results are equivalent.
- */
-class PeriodicActionsTest :
- public MdrunTestFixture,
- public ::testing::WithParamInterface<std::tuple<PropagationParameters, OutputParameterGeneratorFunction>>
-{
-public:
- // PeriodicActionsTest();
- //! Run mdrun with given output parameters
- void doMdrun(const PeriodicOutputParameters& output);
- //! Generate reference data from mdrun writing everything every step.
- void prepareReferenceData();
- //! Names for the output files from the reference mdrun call
- ReferenceFileNames referenceFileNames_ = { fileManager_.getTemporaryFilePath("reference.edr") };
- //! Functor for energy comparison
- EnergyComparison energyComparison_{ EnergyComparison::defaultEnergyTermsToCompare(),
- MaxNumFrames::compareAllFrames() };
- //! Names of energies compared by energyComparison_
- std::vector<std::string> namesOfEnergiesToMatch_ = energyComparison_.getEnergyNames();
-};
-
void PeriodicActionsTest::doMdrun(const PeriodicOutputParameters& output)
{
auto propagation = std::get<0>(GetParam());
/*! \brief Some common choices of periodic output mdp parameters to
* simplify defining values for the combinations under test */
-PeriodicOutputParameters g_basicPeriodicOutputParameters = {
+static PeriodicOutputParameters g_basicPeriodicOutputParameters = {
{ "nstenergy", "0" }, { "nstlog", "0" }, { "nstxout", "0" },
{ "nstvout", "0" }, { "nstfout", "0" }, { "nstxout-compressed", "0" },
{ "nstdhdl", "0" }, { "description", "unknown" }
};
-/*! \brief Return vector of mdp parameter sets to test
- *
- * These are constructed to observe the mdp parameter choices that
- * only affect when output is written agree with those that were
- * written from a reference run where output was done every step. The
- * numbers are chosen in the context of the defaults in
- * prepareDefaultMdpFieldValues().
- *
- * \todo Test nstlog, nstdhdl, nstxout-compressed */
+// \todo Test nstlog, nstdhdl, nstxout-compressed
std::vector<PeriodicOutputParameters> outputParameters()
{
std::vector<PeriodicOutputParameters> parameterSets;
return parameterSets;
}
-//! Returns sets of simple simulation propagators
std::vector<PropagationParameters> simplePropagationParameters()
{
return {
};
}
-/*! \brief Returns sets of simulation propagators including coupling
- *
- * These are chosen to cover the commonly used space of propagation
- * algorithms togther with the perdiods between their actions. The
- * periods tested are chosen to be mutually co-prime and distinct from
- * the pair search and user output period (4), so that over the
- * duration of a short simulation many kinds of simulation step
- * behavior are tested. */
std::vector<PropagationParameters> propagationParametersWithCoupling()
{
std::string nsttcouple = "2";
return parameterSets;
}
-/*! \brief Returns sets of simulation propagators including coupling
- *
- * These are chosen to cover the commonly used space of propagation
- * algorithms on systems with constraints. */
std::vector<PropagationParameters> propagationParametersWithConstraints()
{
std::string nsttcouple = "2";
return parameterSets;
}
-using ::testing::Combine;
-using ::testing::Values;
-using ::testing::ValuesIn;
-
-// 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_OPENCL
-INSTANTIATE_TEST_SUITE_P(BasicPropagators,
- PeriodicActionsTest,
- Combine(ValuesIn(simplePropagationParameters()), Values(outputParameters)));
-INSTANTIATE_TEST_SUITE_P(PropagatorsWithCoupling,
- PeriodicActionsTest,
- Combine(ValuesIn(propagationParametersWithCoupling()), Values(outputParameters)));
-INSTANTIATE_TEST_SUITE_P(PropagatorsWithConstraints,
- PeriodicActionsTest,
- Combine(ValuesIn(propagationParametersWithConstraints()),
- Values(outputParameters)));
-#else
-INSTANTIATE_TEST_SUITE_P(DISABLED_BasicPropagators,
- PeriodicActionsTest,
- Combine(ValuesIn(simplePropagationParameters()), Values(outputParameters)));
-INSTANTIATE_TEST_SUITE_P(DISABLED_PropagatorsWithCoupling,
- PeriodicActionsTest,
- Combine(ValuesIn(propagationParametersWithCoupling()), Values(outputParameters)));
-INSTANTIATE_TEST_SUITE_P(DISABLED_PropagatorsWithConstraints,
- PeriodicActionsTest,
- Combine(ValuesIn(propagationParametersWithConstraints()),
- Values(outputParameters)));
-#endif
-
-} // namespace
} // namespace test
} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief Interfaces of related classes for tests to verify that a simulator that only does some
+ * actions periodically produces the expected results.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_mdrun_integration_tests
+ */
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include <tuple>
+
+#include "gromacs/trajectory/energyframe.h"
+#include "gromacs/utility/strconvert.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/simulationdatabase.h"
+#include "testutils/testasserts.h"
+
+#include "energycomparison.h"
+#include "energyreader.h"
+#include "moduletest.h"
+
+namespace gmx
+{
+namespace test
+{
+
+/*! \brief Mdp parameters that determine the manner of simulation
+ * propagation. */
+using PropagationParameters = MdpFieldValues;
+
+/*! \brief Mdp parameters that should only affect the observations,
+ * not the simulation propagation. */
+using PeriodicOutputParameters = MdpFieldValues;
+
+//! Helper type of output file names for the reference mdrun call
+struct ReferenceFileNames
+{
+ //! Name of energy file
+ std::string edrFileName_;
+};
+
+//! Function type to produce sets of .mdp parameters for testing periodic output
+using OutputParameterGeneratorFunction = std::vector<PeriodicOutputParameters> (*)();
+
+/*! \brief Test fixture base for comparing a simulator with one that
+ * does everything every step
+ *
+ * This test ensures that two simulator code paths called via
+ * different mdp options yield identical energy trajectories,
+ * up to some (arbitrary) precision.
+ *
+ * These tests are useful to check that periodic actions implemented
+ * in simulators are correct, and that different code paths expected
+ * to yield identical results are equivalent.
+ */
+class PeriodicActionsTest :
+ public MdrunTestFixture,
+ public ::testing::WithParamInterface<std::tuple<PropagationParameters, OutputParameterGeneratorFunction>>
+{
+public:
+ // PeriodicActionsTest();
+ //! Run mdrun with given output parameters
+ void doMdrun(const PeriodicOutputParameters& output);
+ //! Generate reference data from mdrun writing everything every step.
+ void prepareReferenceData();
+ //! Names for the output files from the reference mdrun call
+ ReferenceFileNames referenceFileNames_ = { fileManager_.getTemporaryFilePath("reference.edr") };
+ //! Functor for energy comparison
+ EnergyComparison energyComparison_{ EnergyComparison::defaultEnergyTermsToCompare(),
+ MaxNumFrames::compareAllFrames() };
+ //! Names of energies compared by energyComparison_
+ std::vector<std::string> namesOfEnergiesToMatch_ = energyComparison_.getEnergyNames();
+};
+
+/*! \brief Return vector of mdp parameter sets to test
+ *
+ * These are constructed to observe the mdp parameter choices that
+ * only affect when output is written agree with those that were
+ * written from a reference run where output was done every step. The
+ * numbers are chosen in the context of the defaults in
+ * prepareDefaultMdpFieldValues().
+ *
+ * \todo Test nstlog, nstdhdl, nstxout-compressed */
+std::vector<PeriodicOutputParameters> outputParameters();
+
+//! Returns sets of simple simulation propagators
+std::vector<PropagationParameters> simplePropagationParameters();
+
+/*! \brief Returns sets of simulation propagators including coupling
+ *
+ * These are chosen to cover the commonly used space of propagation
+ * algorithms togther with the perdiods between their actions. The
+ * periods tested are chosen to be mutually co-prime and distinct from
+ * the pair search and user output period (4), so that over the
+ * duration of a short simulation many kinds of simulation step
+ * behavior are tested. */
+std::vector<PropagationParameters> propagationParametersWithCoupling();
+
+/*! \brief Returns sets of simulation propagators including coupling
+ *
+ * These are chosen to cover the commonly used space of propagation
+ * algorithms on systems with constraints. */
+std::vector<PropagationParameters> propagationParametersWithConstraints();
+
+} // namespace test
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief Tests to verify that a simulator that only does some actions
+ * periodically with basic propagators produces the expected results.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_mdrun_integration_tests
+ */
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include "periodicactions.h"
+
+namespace gmx
+{
+namespace test
+{
+
+using ::testing::Combine;
+using ::testing::Values;
+using ::testing::ValuesIn;
+
+// 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_OPENCL
+INSTANTIATE_TEST_SUITE_P(BasicPropagators,
+ PeriodicActionsTest,
+ Combine(ValuesIn(simplePropagationParameters()), Values(outputParameters)));
+#else
+INSTANTIATE_TEST_SUITE_P(DISABLED_BasicPropagators,
+ PeriodicActionsTest,
+ Combine(ValuesIn(simplePropagationParameters()), Values(outputParameters)));
+#endif
+
+} // namespace test
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief Tests to verify that a simulator that only does some actions
+ * periodically with propagators with constraints produces the expected results.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_mdrun_integration_tests
+ */
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include "periodicactions.h"
+
+namespace gmx
+{
+namespace test
+{
+
+using ::testing::Combine;
+using ::testing::Values;
+using ::testing::ValuesIn;
+
+// 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_OPENCL
+INSTANTIATE_TEST_SUITE_P(PropagatorsWithConstraints,
+ PeriodicActionsTest,
+ Combine(ValuesIn(propagationParametersWithConstraints()),
+ Values(outputParameters)));
+#else
+INSTANTIATE_TEST_SUITE_P(DISABLED_PropagatorsWithConstraints,
+ PeriodicActionsTest,
+ Combine(ValuesIn(propagationParametersWithConstraints()),
+ Values(outputParameters)));
+#endif
+
+} // namespace test
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief Tests to verify that a simulator that only does some actions
+ * periodically with propagators with coupling produces the expected results.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_mdrun_integration_tests
+ */
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include "periodicactions.h"
+
+namespace gmx
+{
+namespace test
+{
+
+using ::testing::Combine;
+using ::testing::Values;
+using ::testing::ValuesIn;
+
+// 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_OPENCL
+INSTANTIATE_TEST_SUITE_P(PropagatorsWithCoupling,
+ PeriodicActionsTest,
+ Combine(ValuesIn(propagationParametersWithCoupling()), Values(outputParameters)));
+#else
+INSTANTIATE_TEST_SUITE_P(DISABLED_PropagatorsWithCoupling,
+ PeriodicActionsTest,
+ Combine(ValuesIn(propagationParametersWithCoupling()), Values(outputParameters)));
+#endif
+
+} // namespace test
+} // namespace gmx
::testing::Values(TemperatureCoupling::VRescale),
::testing::Values(PressureCoupling::No)));
-/*! \brief Return replica exchange related output from logfile
- *
- * All replica exchange related output in log files start with 'Repl',
- * making extraction easy. This function also removes the printing of
- * energy differences, as the log files are compared exactly, and
- * energy differences will slightly vary between runs.
- *
- * \param logFileName Name of log file
- * \return Replica exchange related output in log file
- */
-static std::string getReplicaExchangeOutputFromLogFile(const std::string& logFileName)
-{
- TextInputFile logFile(logFileName);
- std::string replExOutput;
- std::string line;
- while (logFile.readLine(&line))
- {
- // All replica exchange output lines starts with "Repl"
- if (startsWith(line, "Repl"))
- {
- // This is an exact comparison, so we can't compare the energies which
- // are slightly different per run. Energies are tested later.
- const auto pos = line.find("dE_term");
- if (pos != std::string::npos)
- {
- line.replace(line.begin() + pos, line.end(), "[ not checked ]\n");
- }
- replExOutput.append(line);
- }
- }
- return replExOutput;
-}
-
-//! Convenience typedef
-typedef MultiSimTest ReplicaExchangeRegressionTest;
-
-/* Run replica exchange simulations, compare to reference data
- *
- * Reference data generated by
- *
- * GROMACS version: 2022-dev
- * Precision: single and double (separate reference data)
- * Memory model: 64 bit
- * MPI library: MPI
- * OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
- * GPU support: disabled
- * SIMD instructions: AVX2_256
- * FFT library: fftw-3.3.9-sse2-avx
- * RDTSCP usage: enabled
- * TNG support: enabled
- * Hwloc support: disabled
- * Tracing support: disabled
- * C compiler: /usr/local/bin/mpicc Clang 8.0.1
- * C++ compiler: /usr/local/bin/mpic++ Clang 8.0.1
- *
- */
-TEST_P(ReplicaExchangeRegressionTest, WithinTolerances)
-{
- if (!mpiSetupValid())
- {
- // Can't test multi-sim without multiple simulations
- return;
- }
-
- if (size_ != 4)
- {
- // Results are depending on number of ranks, and we can't have reference
- // data for all cases. Restricting the regression tests to runs with 4 ranks.
- // This allows testing 4 replicas with single rank, or 2 replicas with 2 ranks each.
- return;
- }
- const auto& tcoupl = std::get<2>(GetParam());
- const auto& pcoupl = std::get<3>(GetParam());
-
- const int numSteps = 16;
- const int exchangePeriod = 4;
- // grompp warns about generating velocities and using parrinello-rahman
- const int maxWarnings = (pcoupl == PressureCoupling::ParrinelloRahman ? 1 : 0);
-
- mdrunCaller_->addOption("-replex", exchangePeriod);
- // Seeds need to be reproducible for regression, but can be different per simulation
- mdrunCaller_->addOption("-reseed", 98713 + simulationNumber_);
-
- SimulationRunner runner(&fileManager_);
- runner.useTopGroAndNdxFromDatabase("tip3p5");
-
- runGrompp(&runner, numSteps, true, maxWarnings);
- ASSERT_EQ(0, runner.callMdrun(*mdrunCaller_));
-
-#if GMX_LIB_MPI
- // Make sure all simulations are finished before checking the results.
- MPI_Barrier(MdrunTestFixtureBase::communicator_);
-#endif
-
- // We only test simulation results on one rank to avoid problems with reference file access.
- if (rank_ == 0)
- {
- // Create reference data helper object
- TestReferenceData refData;
-
- // Specify how energy trajectory comparison must work
- const auto hasConservedField =
- !(tcoupl == TemperatureCoupling::No && pcoupl == PressureCoupling::No);
- // Tolerances copied from simulator tests
- EnergyTermsToCompare energyTermsToCompare{ {
- { interaction_function[F_EPOT].longname,
- relativeToleranceAsPrecisionDependentUlp(60.0, 200, 160) },
- { interaction_function[F_EKIN].longname,
- relativeToleranceAsPrecisionDependentUlp(60.0, 200, 160) },
- } };
- if (hasConservedField)
- {
- energyTermsToCompare.emplace(interaction_function[F_ECONSERVED].longname,
- relativeToleranceAsPrecisionDependentUlp(50.0, 100, 80));
- }
- if (pcoupl != PressureCoupling::No)
- {
- energyTermsToCompare.emplace("Volume",
- relativeToleranceAsPrecisionDependentUlp(10.0, 200, 160));
- }
-
- // Specify how trajectory frame matching must work.
- const TrajectoryFrameMatchSettings trajectoryMatchSettings{ true,
- true,
- true,
- ComparisonConditions::MustCompare,
- ComparisonConditions::MustCompare,
- ComparisonConditions::MustCompare,
- MaxNumFrames::compareAllFrames() };
- TrajectoryTolerances trajectoryTolerances = TrajectoryComparison::s_defaultTrajectoryTolerances;
- // By default, velocity tolerance is MUCH tighter than force tolerance
- trajectoryTolerances.velocities = trajectoryTolerances.forces;
- // Build the functor that will compare reference and test
- // trajectory frames in the chosen way.
- TrajectoryComparison trajectoryComparison{ trajectoryMatchSettings, trajectoryTolerances };
-
- // Loop over simulations
- for (int simulationNumber = 0; simulationNumber < (size_ / numRanksPerSimulation_);
- simulationNumber++)
- {
- TestReferenceChecker simulationChecker(refData.rootChecker().checkCompound(
- "Simulation", formatString("Replica %d", simulationNumber)));
-
- const auto logFileName =
- std::regex_replace(runner.logFileName_,
- std::regex(formatString("sim_%d", simulationNumber_)),
- formatString("sim_%d", simulationNumber));
- const auto energyFileName =
- std::regex_replace(runner.edrFileName_,
- std::regex(formatString("sim_%d", simulationNumber_)),
- formatString("sim_%d", simulationNumber));
- const auto trajectoryFileName =
- std::regex_replace(runner.fullPrecisionTrajectoryFileName_,
- std::regex(formatString("sim_%d", simulationNumber_)),
- formatString("sim_%d", simulationNumber));
-
- // Check log replica exchange related output (contains exchange statistics)
- auto replicaExchangeOutputChecker =
- simulationChecker.checkCompound("ReplExOutput", "Output");
- const auto replExOutput = getReplicaExchangeOutputFromLogFile(logFileName);
- replicaExchangeOutputChecker.checkTextBlock(replExOutput, "Replica Exchange Output");
-
- // Check that the energies agree with the refdata within tolerance.
- checkEnergiesAgainstReferenceData(energyFileName, energyTermsToCompare, &simulationChecker);
-
- // Check that the trajectories agree with the refdata within tolerance.
- checkTrajectoryAgainstReferenceData(trajectoryFileName, trajectoryComparison, &simulationChecker);
-
- } // end loop over simulations
- } // end testing simulations on one rank
-
-#if GMX_LIB_MPI
- // Make sure testing is complete before returning - ranks delete temporary files on exit
- MPI_Barrier(MdrunTestFixtureBase::communicator_);
-#endif
-}
-
-/*! \brief Helper struct printing custom test name
- *
- * Regression test results not only depend on the test parameters, but
- * also on the total number of ranks and the precision. Names must
- * reflect that to identify correct reference data.
- */
-struct PrintReplicaExchangeParametersToString
-{
- template<class ParamType>
- std::string operator()(const testing::TestParamInfo<ParamType>& parameter) const
- {
- auto testIdentifier =
- formatString("ReplExRegression_%s_%s_%s_%dRanks_%dRanksPerSimulation_%s",
- enumValueToString(std::get<1>(parameter.param)),
- enumValueToString(std::get<2>(parameter.param)),
- enumValueToString(std::get<3>(parameter.param)),
- gmx_node_num(),
- static_cast<int>(std::get<0>(parameter.param)),
- GMX_DOUBLE ? "d" : "s");
- // Valid GTest names cannot include hyphens
- testIdentifier.erase(std::remove(testIdentifier.begin(), testIdentifier.end(), '-'),
- testIdentifier.end());
- return testIdentifier;
- }
-};
-
-#if GMX_LIB_MPI
-INSTANTIATE_TEST_SUITE_P(
- ReplicaExchangeIsEquivalentToReferenceLeapFrog,
- ReplicaExchangeRegressionTest,
- ::testing::Combine(::testing::Values(NumRanksPerSimulation(1), NumRanksPerSimulation(2)),
- ::testing::Values(IntegrationAlgorithm::MD),
- ::testing::Values(TemperatureCoupling::VRescale, TemperatureCoupling::NoseHoover),
- ::testing::Values(PressureCoupling::CRescale, PressureCoupling::ParrinelloRahman)),
- PrintReplicaExchangeParametersToString());
-INSTANTIATE_TEST_SUITE_P(ReplicaExchangeIsEquivalentToReferenceVelocityVerlet,
- ReplicaExchangeRegressionTest,
- ::testing::Combine(::testing::Values(NumRanksPerSimulation(1),
- NumRanksPerSimulation(2)),
- ::testing::Values(IntegrationAlgorithm::VV),
- ::testing::Values(TemperatureCoupling::NoseHoover),
- ::testing::Values(PressureCoupling::No)),
- PrintReplicaExchangeParametersToString());
-#else
-INSTANTIATE_TEST_SUITE_P(
- DISABLED_ReplicaExchangeIsEquivalentToReferenceLeapFrog,
- ReplicaExchangeRegressionTest,
- ::testing::Combine(::testing::Values(NumRanksPerSimulation(1), NumRanksPerSimulation(2)),
- ::testing::Values(IntegrationAlgorithm::MD),
- ::testing::Values(TemperatureCoupling::VRescale, TemperatureCoupling::NoseHoover),
- ::testing::Values(PressureCoupling::CRescale, PressureCoupling::ParrinelloRahman)),
- PrintReplicaExchangeParametersToString());
-INSTANTIATE_TEST_SUITE_P(DISABLED_ReplicaExchangeIsEquivalentToReferenceVelocityVerlet,
- ReplicaExchangeRegressionTest,
- ::testing::Combine(::testing::Values(NumRanksPerSimulation(1),
- NumRanksPerSimulation(2)),
- ::testing::Values(IntegrationAlgorithm::VV),
- ::testing::Values(TemperatureCoupling::NoseHoover),
- ::testing::Values(PressureCoupling::No)),
- PrintReplicaExchangeParametersToString());
-#endif
} // namespace test
} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
+ * Copyright (c) 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief
+ * Equivalence tests for the mdrun replica-exchange functionality
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_mdrun_integration_tests
+ */
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include <regex>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/topology/ifunc.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/filestream.h"
+#include "gromacs/utility/path.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testfilemanager.h"
+
+#include "energycomparison.h"
+#include "multisimtest.h"
+#include "trajectorycomparison.h"
+
+namespace gmx
+{
+namespace test
+{
+
+/*! \brief Return replica exchange related output from logfile
+ *
+ * All replica exchange related output in log files start with 'Repl',
+ * making extraction easy. This function also removes the printing of
+ * energy differences, as the log files are compared exactly, and
+ * energy differences will slightly vary between runs.
+ *
+ * \param logFileName Name of log file
+ * \return Replica exchange related output in log file
+ */
+static std::string getReplicaExchangeOutputFromLogFile(const std::string& logFileName)
+{
+ TextInputFile logFile(logFileName);
+ std::string replExOutput;
+ std::string line;
+ while (logFile.readLine(&line))
+ {
+ // All replica exchange output lines starts with "Repl"
+ if (startsWith(line, "Repl"))
+ {
+ // This is an exact comparison, so we can't compare the energies which
+ // are slightly different per run. Energies are tested later.
+ const auto pos = line.find("dE_term");
+ if (pos != std::string::npos)
+ {
+ line.replace(line.begin() + pos, line.end(), "[ not checked ]\n");
+ }
+ replExOutput.append(line);
+ }
+ }
+ return replExOutput;
+}
+
+//! Convenience typedef
+typedef MultiSimTest ReplicaExchangeRegressionTest;
+
+/* Run replica exchange simulations, compare to reference data
+ *
+ * Reference data generated by
+ *
+ * GROMACS version: 2022-dev
+ * Precision: single and double (separate reference data)
+ * Memory model: 64 bit
+ * MPI library: MPI
+ * OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
+ * GPU support: disabled
+ * SIMD instructions: AVX2_256
+ * FFT library: fftw-3.3.9-sse2-avx
+ * RDTSCP usage: enabled
+ * TNG support: enabled
+ * Hwloc support: disabled
+ * Tracing support: disabled
+ * C compiler: /usr/local/bin/mpicc Clang 8.0.1
+ * C++ compiler: /usr/local/bin/mpic++ Clang 8.0.1
+ *
+ */
+TEST_P(ReplicaExchangeRegressionTest, WithinTolerances)
+{
+ if (!mpiSetupValid())
+ {
+ // Can't test multi-sim without multiple simulations
+ return;
+ }
+
+ if (size_ != 4)
+ {
+ // Results are depending on number of ranks, and we can't have reference
+ // data for all cases. Restricting the regression tests to runs with 4 ranks.
+ // This allows testing 4 replicas with single rank, or 2 replicas with 2 ranks each.
+ return;
+ }
+ const auto& tcoupl = std::get<2>(GetParam());
+ const auto& pcoupl = std::get<3>(GetParam());
+
+ const int numSteps = 16;
+ const int exchangePeriod = 4;
+ // grompp warns about generating velocities and using parrinello-rahman
+ const int maxWarnings = (pcoupl == PressureCoupling::ParrinelloRahman ? 1 : 0);
+
+ mdrunCaller_->addOption("-replex", exchangePeriod);
+ // Seeds need to be reproducible for regression, but can be different per simulation
+ mdrunCaller_->addOption("-reseed", 98713 + simulationNumber_);
+
+ SimulationRunner runner(&fileManager_);
+ runner.useTopGroAndNdxFromDatabase("tip3p5");
+
+ runGrompp(&runner, numSteps, true, maxWarnings);
+ ASSERT_EQ(0, runner.callMdrun(*mdrunCaller_));
+
+#if GMX_LIB_MPI
+ // Make sure all simulations are finished before checking the results.
+ MPI_Barrier(MdrunTestFixtureBase::communicator_);
+#endif
+
+ // We only test simulation results on one rank to avoid problems with reference file access.
+ if (rank_ == 0)
+ {
+ // Create reference data helper object
+ TestReferenceData refData;
+
+ // Specify how energy trajectory comparison must work
+ const auto hasConservedField =
+ !(tcoupl == TemperatureCoupling::No && pcoupl == PressureCoupling::No);
+ // Tolerances copied from simulator tests
+ EnergyTermsToCompare energyTermsToCompare{ {
+ { interaction_function[F_EPOT].longname,
+ relativeToleranceAsPrecisionDependentUlp(60.0, 200, 160) },
+ { interaction_function[F_EKIN].longname,
+ relativeToleranceAsPrecisionDependentUlp(60.0, 200, 160) },
+ } };
+ if (hasConservedField)
+ {
+ energyTermsToCompare.emplace(interaction_function[F_ECONSERVED].longname,
+ relativeToleranceAsPrecisionDependentUlp(50.0, 100, 80));
+ }
+ if (pcoupl != PressureCoupling::No)
+ {
+ energyTermsToCompare.emplace("Volume",
+ relativeToleranceAsPrecisionDependentUlp(10.0, 200, 160));
+ }
+
+ // Specify how trajectory frame matching must work.
+ const TrajectoryFrameMatchSettings trajectoryMatchSettings{ true,
+ true,
+ true,
+ ComparisonConditions::MustCompare,
+ ComparisonConditions::MustCompare,
+ ComparisonConditions::MustCompare,
+ MaxNumFrames::compareAllFrames() };
+ TrajectoryTolerances trajectoryTolerances = TrajectoryComparison::s_defaultTrajectoryTolerances;
+ // By default, velocity tolerance is MUCH tighter than force tolerance
+ trajectoryTolerances.velocities = trajectoryTolerances.forces;
+ // Build the functor that will compare reference and test
+ // trajectory frames in the chosen way.
+ TrajectoryComparison trajectoryComparison{ trajectoryMatchSettings, trajectoryTolerances };
+
+ // Loop over simulations
+ for (int simulationNumber = 0; simulationNumber < (size_ / numRanksPerSimulation_);
+ simulationNumber++)
+ {
+ TestReferenceChecker simulationChecker(refData.rootChecker().checkCompound(
+ "Simulation", formatString("Replica %d", simulationNumber)));
+
+ const auto logFileName =
+ std::regex_replace(runner.logFileName_,
+ std::regex(formatString("sim_%d", simulationNumber_)),
+ formatString("sim_%d", simulationNumber));
+ const auto energyFileName =
+ std::regex_replace(runner.edrFileName_,
+ std::regex(formatString("sim_%d", simulationNumber_)),
+ formatString("sim_%d", simulationNumber));
+ const auto trajectoryFileName =
+ std::regex_replace(runner.fullPrecisionTrajectoryFileName_,
+ std::regex(formatString("sim_%d", simulationNumber_)),
+ formatString("sim_%d", simulationNumber));
+
+ // Check log replica exchange related output (contains exchange statistics)
+ auto replicaExchangeOutputChecker =
+ simulationChecker.checkCompound("ReplExOutput", "Output");
+ const auto replExOutput = getReplicaExchangeOutputFromLogFile(logFileName);
+ replicaExchangeOutputChecker.checkTextBlock(replExOutput, "Replica Exchange Output");
+
+ // Check that the energies agree with the refdata within tolerance.
+ checkEnergiesAgainstReferenceData(energyFileName, energyTermsToCompare, &simulationChecker);
+
+ // Check that the trajectories agree with the refdata within tolerance.
+ checkTrajectoryAgainstReferenceData(trajectoryFileName, trajectoryComparison, &simulationChecker);
+
+ } // end loop over simulations
+ } // end testing simulations on one rank
+
+#if GMX_LIB_MPI
+ // Make sure testing is complete before returning - ranks delete temporary files on exit
+ MPI_Barrier(MdrunTestFixtureBase::communicator_);
+#endif
+}
+
+/*! \brief Helper struct printing custom test name
+ *
+ * Regression test results not only depend on the test parameters, but
+ * also on the total number of ranks and the precision. Names must
+ * reflect that to identify correct reference data.
+ */
+struct PrintReplicaExchangeParametersToString
+{
+ template<class ParamType>
+ std::string operator()(const testing::TestParamInfo<ParamType>& parameter) const
+ {
+ auto testIdentifier =
+ formatString("ReplExRegression_%s_%s_%s_%dRanks_%dRanksPerSimulation_%s",
+ enumValueToString(std::get<1>(parameter.param)),
+ enumValueToString(std::get<2>(parameter.param)),
+ enumValueToString(std::get<3>(parameter.param)),
+ gmx_node_num(),
+ static_cast<int>(std::get<0>(parameter.param)),
+ GMX_DOUBLE ? "d" : "s");
+ // Valid GTest names cannot include hyphens
+ testIdentifier.erase(std::remove(testIdentifier.begin(), testIdentifier.end(), '-'),
+ testIdentifier.end());
+ return testIdentifier;
+ }
+};
+
+#if GMX_LIB_MPI
+INSTANTIATE_TEST_SUITE_P(
+ ReplicaExchangeIsEquivalentToReferenceLeapFrog,
+ ReplicaExchangeRegressionTest,
+ ::testing::Combine(::testing::Values(NumRanksPerSimulation(1), NumRanksPerSimulation(2)),
+ ::testing::Values(IntegrationAlgorithm::MD),
+ ::testing::Values(TemperatureCoupling::VRescale, TemperatureCoupling::NoseHoover),
+ ::testing::Values(PressureCoupling::CRescale, PressureCoupling::ParrinelloRahman)),
+ PrintReplicaExchangeParametersToString());
+INSTANTIATE_TEST_SUITE_P(ReplicaExchangeIsEquivalentToReferenceVelocityVerlet,
+ ReplicaExchangeRegressionTest,
+ ::testing::Combine(::testing::Values(NumRanksPerSimulation(1),
+ NumRanksPerSimulation(2)),
+ ::testing::Values(IntegrationAlgorithm::VV),
+ ::testing::Values(TemperatureCoupling::NoseHoover),
+ ::testing::Values(PressureCoupling::No)),
+ PrintReplicaExchangeParametersToString());
+#else
+INSTANTIATE_TEST_SUITE_P(
+ DISABLED_ReplicaExchangeIsEquivalentToReferenceLeapFrog,
+ ReplicaExchangeRegressionTest,
+ ::testing::Combine(::testing::Values(NumRanksPerSimulation(1), NumRanksPerSimulation(2)),
+ ::testing::Values(IntegrationAlgorithm::MD),
+ ::testing::Values(TemperatureCoupling::VRescale, TemperatureCoupling::NoseHoover),
+ ::testing::Values(PressureCoupling::CRescale, PressureCoupling::ParrinelloRahman)),
+ PrintReplicaExchangeParametersToString());
+INSTANTIATE_TEST_SUITE_P(DISABLED_ReplicaExchangeIsEquivalentToReferenceVelocityVerlet,
+ ReplicaExchangeRegressionTest,
+ ::testing::Combine(::testing::Values(NumRanksPerSimulation(1),
+ NumRanksPerSimulation(2)),
+ ::testing::Values(IntegrationAlgorithm::VV),
+ ::testing::Values(TemperatureCoupling::NoseHoover),
+ ::testing::Values(PressureCoupling::No)),
+ PrintReplicaExchangeParametersToString());
+#endif
+} // namespace test
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff