* 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, by the GROMACS development team, led by
+ * 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.
#include <gtest/gtest.h>
+#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/path.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/stringutil.h"
#include "testutils/cmdlinetest.h"
+#include "testutils/mpitest.h"
#include "moduletest.h"
#include "terminationhelper.h"
MultiSimTest::MultiSimTest() :
size_(gmx_node_num()),
rank_(gmx_node_rank()),
+ numRanksPerSimulation_(std::get<0>(GetParam())),
+ simulationNumber_(rank_ / numRanksPerSimulation_),
mdrunCaller_(new CommandLine)
{
+ // Zero or less ranks doesn't make sense
+ GMX_RELEASE_ASSERT(numRanksPerSimulation_ > 0, "Invalid number of ranks per simulation.");
+
const char* directoryNameFormat = "sim_%d";
// Modify the file manager to have a temporary directory unique to
// constructed it.
std::string originalTempDirectory = fileManager_.getOutputTempDirectory();
std::string newTempDirectory =
- Path::join(originalTempDirectory, formatString(directoryNameFormat, rank_));
- Directory::create(newTempDirectory);
+ Path::join(originalTempDirectory, formatString(directoryNameFormat, simulationNumber_));
+ if (rank_ % numRanksPerSimulation_ == 0)
+ {
+ // Only one rank per simulation creates directory
+ Directory::create(newTempDirectory);
+ }
+#if GMX_LIB_MPI
+ // Make sure directories got created.
+ MPI_Barrier(MdrunTestFixtureBase::communicator_);
+#endif
fileManager_.setOutputTempDirectory(newTempDirectory);
mdrunCaller_->append("mdrun");
mdrunCaller_->addOption("-multidir");
- for (int i = 0; i != size_; ++i)
+ for (int i = 0; i < size_ / numRanksPerSimulation_; ++i)
{
mdrunCaller_->append(Path::join(originalTempDirectory, formatString(directoryNameFormat, i)));
}
}
-void MultiSimTest::organizeMdpFile(SimulationRunner* runner, const char* controlVariable, int numSteps)
+bool MultiSimTest::mpiSetupValid() const
+{
+ // Single simulation case is not implemented in multi-sim
+ const bool haveAtLeastTwoSimulations = ((size_ / numRanksPerSimulation_) >= 2);
+ // Mdrun will throw error if simulations don't have identical number of ranks
+ const bool simulationsHaveIdenticalRankNumber = ((size_ % numRanksPerSimulation_) == 0);
+
+ return (haveAtLeastTwoSimulations && simulationsHaveIdenticalRankNumber);
+}
+
+void MultiSimTest::organizeMdpFile(SimulationRunner* runner,
+ IntegrationAlgorithm integrator,
+ TemperatureCoupling tcoupl,
+ PressureCoupling pcoupl,
+ int numSteps,
+ bool doRegression) const
{
+ GMX_RELEASE_ASSERT(mpiSetupValid(), "Creating the mdp file without valid MPI setup is useless.");
const real baseTemperature = 298;
const real basePressure = 1;
std::string mdpFileContents = formatString(
+ "integrator = %s\n"
+ "tcoupl = %s\n"
+ "pcoupl = %s\n"
"nsteps = %d\n"
"nstlog = 1\n"
"nstcalcenergy = 1\n"
- "tcoupl = v-rescale\n"
"tc-grps = System\n"
"tau-t = 1\n"
"ref-t = %f\n"
// pressure coupling (if active)
- "tau-p = 1\n"
+ "tau-p = 2\n"
"ref-p = %f\n"
"compressibility = 4.5e-5\n"
// velocity generation
"gen-vel = yes\n"
"gen-temp = %f\n"
- // control variable specification
- "%s\n",
- numSteps, baseTemperature + 0.0001 * rank_, basePressure * std::pow(1.01, rank_),
+ "gen-seed = %d\n"
+ // v-rescale and c-rescale use ld-seed
+ "ld-seed = %d\n"
+ // Two systems are used: spc2 non-interacting also at cutoff 1nm
+ // tip3p5 has box length of 1.86
+ "rcoulomb = 0.7\n"
+ "rvdw = 0.7\n"
+ // Trajectory output if required
+ "nstxout = %d\n"
+ "nstvout = %d\n"
+ "nstfout = %d\n"
+ "nstenergy = %d\n",
+ enumValueToString(integrator),
+ enumValueToString(tcoupl),
+ enumValueToString(pcoupl),
+ numSteps,
+ baseTemperature + 0.0001 * rank_,
+ basePressure * std::pow(1.01, rank_),
/* Set things up so that the initial KE decreases with
increasing replica number, so that the (identical)
starting PE decreases on the first step more for the
replicas with higher number, which will tend to force
replica exchange to occur. */
- std::max(baseTemperature - 10 * rank_, real(0)), controlVariable);
+ std::max(baseTemperature - 10 * rank_, real(0)),
+ // If we do regression, we need reproducible velocity
+ // generation, which can be different per simulation
+ (doRegression ? 671324 + simulationNumber_ : -1),
+ // If we do regression, we need reproducible temperature and
+ // pressure coupling, which can be different per simulation
+ (doRegression ? 51203 + simulationNumber_ : -1),
+ // If we do regression, write one intermediate point
+ (doRegression ? int(numSteps / 2) : 0),
+ (doRegression ? int(numSteps / 2) : 0),
+ (doRegression ? int(numSteps / 2) : 0),
+ // If we do regression, print energies every step so
+ // we're sure to catch the replica exchange steps
+ (doRegression ? 1 : 1000));
runner->useStringAsMdpFile(mdpFileContents);
}
+void MultiSimTest::runGrompp(SimulationRunner* runner, int numSteps, bool doRegression, int maxWarnings) const
+{
+ // Call grompp once per simulation
+ if (rank_ % numRanksPerSimulation_ == 0)
+ {
+ const auto& simulator = std::get<1>(GetParam());
+ const auto& tcoupl = std::get<2>(GetParam());
+ const auto& pcoupl = std::get<3>(GetParam());
+ organizeMdpFile(runner, simulator, tcoupl, pcoupl, numSteps, doRegression);
+ CommandLine caller;
+ caller.addOption("-maxwarn", maxWarnings);
+ EXPECT_EQ(0, runner->callGromppOnThisRank(caller));
+ }
+
+#if GMX_LIB_MPI
+ // Make sure simulation masters have written the .tpr file before other ranks try to read it.
+ MPI_Barrier(MdrunTestFixtureBase::communicator_);
+#endif
+}
+
void MultiSimTest::runExitsNormallyTest()
{
- if (size_ <= 1)
+ if (!mpiSetupValid())
{
- /* Can't test multi-sim without multiple ranks. */
+ // Can't test multi-sim without multiple simulations
return;
}
SimulationRunner runner(&fileManager_);
runner.useTopGroAndNdxFromDatabase("spc2");
- const char* pcoupl = GetParam();
- organizeMdpFile(&runner, pcoupl);
- /* Call grompp on every rank - the standard callGrompp() only runs
- grompp on rank 0. */
- EXPECT_EQ(0, runner.callGromppOnThisRank());
+ runGrompp(&runner);
ASSERT_EQ(0, runner.callMdrun(*mdrunCaller_));
}
void MultiSimTest::runMaxhTest()
{
- if (size_ <= 1)
+ if (!mpiSetupValid())
{
- /* Can't test replica exchange without multiple ranks. */
+ // Can't test multi-sim without multiple simulations
return;
}
TerminationHelper helper(&fileManager_, mdrunCaller_.get(), &runner);
// Make sure -maxh has a chance to propagate
int numSteps = 100;
- organizeMdpFile(&runner, "pcoupl = no", numSteps);
- /* Call grompp on every rank - the standard callGrompp() only runs
- grompp on rank 0. */
- EXPECT_EQ(0, runner.callGromppOnThisRank());
+ runGrompp(&runner, numSteps);
helper.runFirstMdrun(runner.cptFileName_);
helper.runSecondMdrun();
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff