${testname}
${exename}
# files with code for tests
+ multisim.cpp
+ multisimtest.cpp
replicaexchange.cpp
# files with code for test fixtures
moduletest.cpp
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2013,2014,2015, 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 for the mdrun multi-simulation functionality
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_mdrun
+ */
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include <gtest/gtest.h>
+
+#include "multisimtest.h"
+
+namespace gmx
+{
+namespace test
+{
+
+/* This test ensures mdrun can run multi-simulations. It runs one
+ * simulation per MPI rank.
+ *
+ * TODO Preferably, we could test that mdrun correctly refuses to run
+ * multi-simulation unless compiled with real MPI with more than one
+ * rank available. However, if we just call mdrun blindly, those cases
+ * trigger an error that is currently fatal to mdrun and also to the
+ * test binary. So, in the meantime we must not test those cases. If
+ * there is no MPI, we disable the test, so that there is a reminder
+ * that it is disabled. There's no elegant way to conditionally
+ * disable a test at run time, so currently there is no feedback if
+ * only one rank is available. However, the test harness knows to run
+ * this test with more than one rank.
+ *
+ * Strictly, this test does not need to be parameterized, but
+ * conditionally disabling it with respect to GMX_LIB_MPI is easier if
+ * it is parameterized. */
+TEST_P(MultiSimTest, ExitsNormally)
+{
+ if (size_ <= 1)
+ {
+ /* Can't test multi-sim without multiple ranks. */
+ return;
+ }
+
+ const char *pcoupl = GetParam();
+ organizeMdpFile(pcoupl);
+ /* Call grompp on every rank - the standard callGrompp() only runs
+ grompp on rank 0. */
+ EXPECT_EQ(0, runner_.callGromppOnThisRank());
+
+ // mdrun names the files without the rank suffix
+ runner_.tprFileName_ = mdrunTprFileName_;
+ ASSERT_EQ(0, runner_.callMdrun(*mdrunCaller_));
+}
+
+/* Note, not all preprocessor implementations nest macro expansions
+ the same way / at all, if we would try to duplicate less code. */
+#ifdef GMX_LIB_MPI
+INSTANTIATE_TEST_CASE_P(InNvt, MultiSimTest,
+ ::testing::Values("pcoupl = no"));
+#else
+// Test needs real MPI to run
+INSTANTIATE_TEST_CASE_P(DISABLED_InNvt, MultiSimTest,
+ ::testing::Values("pcoupl = no"));
+#endif
+
+} // namespace
+} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2013,2014,2015, 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 for the mdrun multi-simulation functionality
+ *
+ * \todo Test mdrun -multidir also
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_mdrun
+ */
+#include "gmxpre.h"
+
+#include "multisimtest.h"
+
+#include <cmath>
+
+#include <algorithm>
+#include <string>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/real.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/cmdlinetest.h"
+
+#include "moduletest.h"
+
+namespace gmx
+{
+namespace test
+{
+
+MultiSimTest::MultiSimTest() : size_(gmx_node_num()),
+ rank_(gmx_node_rank()),
+ mdrunCaller_(new CommandLine)
+{
+ runner_.mdpInputFileName_ = fileManager_.getTemporaryFilePath(formatString("input%d.mdp", rank_));
+ runner_.mdpOutputFileName_ = fileManager_.getTemporaryFilePath(formatString("output%d.mdp", rank_));
+
+ /* grompp needs to name the .tpr file so that when mdrun appends
+ the MPI rank, it will find the right file. If we just used
+ "%d.tpr" then \c TestFileManager prefixes that with an
+ underscore. Then, there is no way for mdrun to be told the
+ right name, because if you add the underscore manually, you get
+ a second one from \c TestFileManager. However, it's easy to
+ just start the suffix with "topol" in both cases. */
+ runner_.tprFileName_ = fileManager_.getTemporaryFilePath(formatString("topol%d.tpr", rank_));
+ mdrunTprFileName_ = fileManager_.getTemporaryFilePath("topol.tpr");
+
+ runner_.useTopGroAndNdxFromDatabase("spc2");
+
+ mdrunCaller_->append("mdrun_mpi");
+ mdrunCaller_->addOption("-multi", size_);
+}
+
+void MultiSimTest::organizeMdpFile(const char *controlVariable)
+{
+ const real baseTemperature = 298;
+ const real basePressure = 1;
+ std::string mdpFileContents =
+ formatString("nsteps = 2\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"
+ "ref-p = %f\n"
+ "compressibility = 4.5e-5\n"
+ // velocity generation
+ "gen-vel = yes\n"
+ "gen-temp = %f\n"
+ // control variable specification
+ "%s\n",
+ 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);
+ runner_.useStringAsMdpFile(mdpFileContents);
+}
+
+} // namespace
+} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2013,2014,2015, 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.
+ */
+#ifndef GMX_MDRUN_TESTS_MULTISIMTEST_H
+#define GMX_MDRUN_TESTS_MULTISIMTEST_H
+
+/*! \internal \file
+ * \brief
+ * Declares test fixture for the mdrun multi-simulation functionality
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_mdrun
+ */
+
+#include <string>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/utility/uniqueptr.h"
+
+#include "testutils/cmdlinetest.h"
+
+#include "moduletest.h"
+
+namespace gmx
+{
+namespace test
+{
+
+//! Convenience typedef
+typedef gmx_unique_ptr<CommandLine>::type CommandLinePointer;
+
+class MultiSimTest : public gmx::test::ParameterizedMdrunTestFixture
+{
+ public:
+ //! Constructor
+ MultiSimTest();
+
+ /*! \brief Organize the .mdp file for this rank
+ *
+ * For testing multi-simulation, this .mdp file is more
+ * complicated than it needs to be, but it does little harm,
+ * and doing it this way allows this function to be re-used
+ * for testing replica-exchange.
+ *
+ * \param controlVariable Allows parameterization to work with
+ * T, P or (later) lambda as the control variable, by passing a
+ * string with "mdp-param = value" such that different paths
+ * in init_replica_exchange() are followed.
+ */
+ void organizeMdpFile(const char *controlVariable);
+
+ //! Number of MPI ranks
+ int size_;
+ //! MPI rank of this process
+ int rank_;
+ //! Object for building the mdrun command line
+ CommandLinePointer mdrunCaller_;
+ //! Name of .tpr file to be used by mdrun
+ std::string mdrunTprFileName_;
+};
+
+} // namespace
+} // namespace
+
+#endif
/*! \internal \file
* \brief
- * Tests for the mdrun replica exchange functionality
+ * Tests for the mdrun replica-exchange functionality
*
* \author Mark Abraham <mark.j.abraham@gmail.com>
* \ingroup module_mdrun
#include "config.h"
-#include <math.h>
-
-#include <algorithm>
-#include <iostream>
-
#include <gtest/gtest.h>
-#include "gromacs/utility/basenetwork.h"
-#include "gromacs/utility/path.h"
-#include "gromacs/utility/real.h"
-#include "gromacs/utility/stringutil.h"
-#include "programs/mdrun/mdrun_main.h"
-
-#include "testutils/cmdlinetest.h"
+#include "multisimtest.h"
-#include "moduletest.h"
-
-namespace
+namespace gmx
{
-
-/*! \brief
- * Test fixture for replica exchange
- */
-class ReplicaExchangeTest : public gmx::test::ParameterizedMdrunTestFixture
+namespace test
{
- public:
- //! Constructor
- ReplicaExchangeTest() : size_(gmx_node_num()),
- rank_(gmx_node_rank())
- {
- mdrunCaller_.append("mdrun_mpi");
- }
-
- /*! \brief Organize the .mdp file for this rank
- *
- * \param controlVariable Allows parameterization to work with
- * T, P or (later) lamda as the control variable, by passing a
- * string with "mdp-param = value" such that different paths
- * in init_replica_exchange() are followed.
- */
- void organizeMdpFile(const char *controlVariable)
- {
- const real baseTemperature = 298;
- const real basePressure = 1;
- std::string mdpFileContents =
- gmx::formatString
- ("nsteps = 2\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"
- "ref-p = %f\n"
- "compressibility = 4.5e-5\n"
- // velocity generation
- "gen-vel = yes\n"
- "gen-temp = %f\n"
- // control variable specification
- "%s\n",
- baseTemperature + 0.0001*rank_,
- basePressure * 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);
- runner_.useStringAsMdpFile(mdpFileContents);
- }
- //! Number of MPI ranks
- int size_;
- //! MPI rank of this process
- int rank_;
- //! Object for building the mdrun command line
- gmx::test::CommandLine mdrunCaller_;
-};
+//! Convenience typedef
+typedef MultiSimTest ReplicaExchangeTest;
/* This test ensures mdrun can run NVT REMD under the supported
* conditions. It runs one replica per MPI rank.
*
- * TODO Preferably, we could test that mdrun correctly refuses to run
- * replica exchange unless under real MPI with more than one rank
- * available. However, if we just call mdrun blindly, those cases
- * trigger an error that is currently fatal to mdrun and also to the
- * test binary. So, in the meantime we must not test those cases. If
- * there is no MPI, we disable the test, so that there is a reminder
- * that it is disabled. There's no elegant way to conditionally
- * disable a test at run time, so currently there is no feedback if
- * only one rank is available. However, the test harness knows
- * to run this test with more than one rank. */
+ * See also comments about MultiSimTest */
TEST_P(ReplicaExchangeTest, ExitsNormally)
{
if (size_ <= 1)
return;
}
- runner_.mdpInputFileName_ = fileManager_.getTemporaryFilePath(gmx::formatString("input%d.mdp", rank_));
- runner_.mdpOutputFileName_ = fileManager_.getTemporaryFilePath(gmx::formatString("output%d.mdp", rank_));
-
- /* grompp needs to name the .tpr file so that when mdrun appends
- the MPI rank, it will find the right file. If we just used
- "%d.tpr" then \c TestFileManager prefixes that with an
- underscore. Then, there is no way for mdrun to be told the
- right name, because if you add the underscore manually, you get
- a second one from \c TestFileManager. However, it's easy to
- just start the suffix with "topol" in both cases. */
- runner_.tprFileName_ = fileManager_.getTemporaryFilePath(gmx::formatString("topol%d.tpr", rank_));
-
const char *pcoupl = GetParam();
organizeMdpFile(pcoupl);
- runner_.useTopGroAndNdxFromDatabase("spc2");
/* Call grompp on every rank - the standard callGrompp() only runs
grompp on rank 0. */
EXPECT_EQ(0, runner_.callGromppOnThisRank());
- runner_.tprFileName_ = fileManager_.getTemporaryFilePath("topol.tpr");
- mdrunCaller_.addOption("-multi", size_);
- mdrunCaller_.addOption("-replex", 1);
- ASSERT_EQ(0, runner_.callMdrun(mdrunCaller_));
+ // mdrun names the files without the rank suffix
+ runner_.tprFileName_ = mdrunTprFileName_;
+ mdrunCaller_->addOption("-replex", 1);
+ ASSERT_EQ(0, runner_.callMdrun(*mdrunCaller_));
}
+/* Note, not all preprocessor implementations nest macro expansions
+ the same way / at all, if we would try to duplicate less code. */
#ifdef GMX_LIB_MPI
INSTANTIATE_TEST_CASE_P(WithDifferentControlVariables, ReplicaExchangeTest,
::testing::Values("pcoupl = no", "pcoupl = Berendsen"));
#endif
} // namespace
+} // namespace
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff