multisim.cpp
multisimtest.cpp
replicaexchange.cpp
+ domain_decomposition.cpp
# files with code for test fixtures
moduletest.cpp
# pseudo-library for code for mdrun
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 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 special cases in domain decomposition
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_mdrun_integration_tests
+ */
+#include "gmxpre.h"
+
+#include <string>
+
+#include <gtest/gtest.h>
+
+#include "testutils/cmdlinetest.h"
+
+#include "moduletest.h"
+
+namespace
+{
+
+//! Test fixture for domain decomposition special cases
+class DomainDecompositionSpecialCasesTest : public gmx::test::MdrunTestFixture
+{
+};
+
+//! When run with 2+ domains, ensures an empty cell, to make sure that zero-sized things work
+TEST_F(DomainDecompositionSpecialCasesTest, AnEmptyDomainWorks)
+{
+ runner_.useStringAsMdpFile("cutoff-scheme = Verlet\n");
+ runner_.useTopGroAndNdxFromDatabase("spc2");
+ /* Over-ride the use of spc2.gro with one with both waters close
+ * together.
+ *
+ * TODO Maybe refactor to avoid over-writing the .gro filename set
+ * above. */
+ runner_.useGroFromDatabase("spc2_and_vacuum");
+ ASSERT_EQ(0, runner_.callGrompp());
+
+ ASSERT_EQ(0, runner_.callMdrun());
+}
+
+} // namespace
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/file.h"
+#include "gromacs/utility/gmxmpi.h"
#include "programs/mdrun/mdrun_main.h"
#include "testutils/cmdlinetest.h"
void
SimulationRunner::useEmptyMdpFile()
{
+ // TODO When removing the group scheme, update actual and potential users of useEmptyMdpFile
useStringAsMdpFile("cutoff-scheme = Group\n");
}
ndxFileName_ = fixture_->fileManager_.getInputFilePath((std::string(name) + ".ndx").c_str());
}
+void
+SimulationRunner::useGroFromDatabase(const char *name)
+{
+ groFileName_ = fixture_->fileManager_.getInputFilePath((std::string(name) + ".gro").c_str());
+}
+
int
SimulationRunner::callGromppOnThisRank()
{
int
SimulationRunner::callGrompp()
{
+ int returnValue = 0;
#ifdef GMX_LIB_MPI
- // When compiled with external MPI, only call one instance of the
- // grompp function
- if (0 != gmx_node_rank())
+ // When compiled with external MPI, we're trying to run mdrun with
+ // MPI, but we need to make sure that we only do grompp on one
+ // rank
+ if (0 == gmx_node_rank())
+#endif
{
- return 0;
+ returnValue = callGromppOnThisRank();
}
+#ifdef GMX_LIB_MPI
+ // Make sure rank zero has written the .tpr file before other
+ // ranks try to read it. Thread-MPI and serial do this just fine
+ // on their own.
+ MPI_Barrier(MPI_COMM_WORLD);
#endif
- return callGromppOnThisRank();
+ return returnValue;
}
int
to this function. Passing a non-const reference might make it
easier to write code that incorrectly re-uses callerRef after
the call to this function. */
+
CommandLine caller(callerRef);
caller.addOption("-s", tprFileName_);
caller.addOption("-nsteps", nsteps_);
}
+#ifdef GMX_MPI
+# ifdef GMX_GPU
+# ifdef GMX_THREAD_MPI
+ int numGpusNeeded = g_numThreads;
+# else /* Must be real MPI */
+ int numGpusNeeded = gmx_node_num();
+# endif
+ std::string gpuIdString(numGpusNeeded, '0');
+ caller.addOption("-gpu_id", gpuIdString.c_str());
+# endif
+#endif
+
#ifdef GMX_THREAD_MPI
caller.addOption("-nt", g_numThreads);
#endif
+
#ifdef GMX_OPENMP
caller.addOption("-ntomp", g_numOpenMPThreads);
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * 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.
void useStringAsNdxFile(const char *ndxString);
//! Use a standard .top and .gro file as input to grompp
void useTopGroAndNdxFromDatabase(const char *name);
+ //! Use a standard .gro file as input to grompp
+ void useGroFromDatabase(const char *name);
//! Calls grompp (on rank 0) to prepare for the mdrun test
int callGrompp();
//! Calls grompp (on this rank) to prepare for the mdrun test
--- /dev/null
+Two nearby SPC waters, and a bunch of empty vacuum
+ 6
+ 1SOL OW 1 .230 .628 .113
+ 1SOL HW1 2 .137 .626 .150
+ 1SOL HW2 3 .231 .589 .021
+ 2SOL OW 4 .225 .275 -.866
+ 2SOL HW1 5 .260 .258 -.774
+ 2SOL HW2 6 .137 .230 -.878
+ 3.01000 3.01000 3.01000
# that ctest can run the test binary over a range of numbers of MPI
# ranks.
function (gmx_register_mpi_integration_test NAME EXENAME NUMPROC)
- if (GMX_BUILD_UNITTESTS AND BUILD_TESTING AND GMX_MPI)
- foreach(VARNAME MPIEXEC MPIEXEC_NUMPROC_FLAG MPIEXEC_PREFLAGS MPIEXEC_POSTFLAGS)
- # These variables need a valid value for the test to run
- # and pass, but conceivably any of them might be valid
- # with arbitrary (including empty) content. They can't be
- # valid if they've been populated with the CMake
- # find_package magic suffix/value "NOTFOUND", though.
- if (${VARNAME} MATCHES ".*NOTFOUND")
- message(STATUS "CMake variable ${VARNAME} was not detected to be a valid value. To test GROMACS correctly, check the advice in the install guide.")
+ if (GMX_BUILD_UNITTESTS AND BUILD_TESTING)
+ if (GMX_MPI)
+ foreach(VARNAME MPIEXEC MPIEXEC_NUMPROC_FLAG MPIEXEC_PREFLAGS MPIEXEC_POSTFLAGS)
+ # These variables need a valid value for the test to run
+ # and pass, but conceivably any of them might be valid
+ # with arbitrary (including empty) content. They can't be
+ # valid if they've been populated with the CMake
+ # find_package magic suffix/value "NOTFOUND", though.
+ if (${VARNAME} MATCHES ".*NOTFOUND")
+ message(STATUS "CMake variable ${VARNAME} was not detected to be a valid value. To test GROMACS correctly, check the advice in the install guide.")
+ set(_cannot_run_mpi_tests 1)
+ endif()
+ if (NOT VARNAME STREQUAL MPIEXEC AND ${VARNAME})
+ set(_an_mpi_variable_had_content 1)
+ endif()
+ endforeach()
+ if(_an_mpi_variable_had_content AND NOT MPIEXEC)
+ message(STATUS "CMake variable MPIEXEC must have a valid value if one of the other related MPIEXEC variables does. To test GROMACS correctly, check the advice in the install guide.")
set(_cannot_run_mpi_tests 1)
endif()
- if (NOT VARNAME STREQUAL MPIEXEC AND ${VARNAME})
- set(_an_mpi_variable_had_content 1)
+ if(NOT _cannot_run_mpi_tests)
+ add_test(NAME ${NAME}
+ COMMAND
+ ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${NUMPROC}
+ ${MPIEXEC_PREFLAGS} $<TARGET_FILE:${EXENAME}> ${MPIEXEC_POSTFLAGS}
+ --gtest_output=xml:${CMAKE_BINARY_DIR}/Testing/Temporary/${NAME}.xml
+ )
+ set_tests_properties(${testname} PROPERTIES LABELS "MpiIntegrationTest")
+ add_dependencies(tests ${EXENAME})
endif()
- endforeach()
- if(_an_mpi_variable_had_content AND NOT MPIEXEC)
- message(STATUS "CMake variable MPIEXEC must have a valid value if one of the other related MPIEXEC variables does. To test GROMACS correctly, check the advice in the install guide.")
- set(_cannot_run_mpi_tests 1)
- endif()
- if(NOT _cannot_run_mpi_tests)
+
+ # GMX_EXTRA_LIBRARIES might be needed for mdrun integration tests at
+ # some point.
+ # target_link_libraries(${EXENAME} ${GMX_EXTRA_LIBRARIES})
+ elseif(GMX_THREAD_MPI)
add_test(NAME ${NAME}
COMMAND
- ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${NUMPROC}
- ${MPIEXEC_PREFLAGS} $<TARGET_FILE:${EXENAME}> ${MPIEXEC_POSTFLAGS}
+ $<TARGET_FILE:${EXENAME}> -nt ${NUMPROC}
--gtest_output=xml:${CMAKE_BINARY_DIR}/Testing/Temporary/${NAME}.xml
)
set_tests_properties(${testname} PROPERTIES LABELS "MpiIntegrationTest")
add_dependencies(tests ${EXENAME})
- endif()
- # GMX_EXTRA_LIBRARIES might be needed for mdrun integration tests at
- # some point.
- # target_link_libraries(${EXENAME} ${GMX_EXTRA_LIBRARIES})
+ # GMX_EXTRA_LIBRARIES might be needed for mdrun integration tests at
+ # some point.
+ # target_link_libraries(${EXENAME} ${GMX_EXTRA_LIBRARIES})
+ endif()
endif()
endfunction ()
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff