src/programs/mdrun/tests/moduletest.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 /*! \internal \file
  36  * \brief
  37  * Implements classes in moduletest.h.
  38  *
  39  * \author Mark Abraham <mark.j.abraham@gmail.com>
  40  * \ingroup module_mdrun_integration_tests
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "moduletest.h"
  45
  46 #include "config.h"
  47
  48 #include <cstdio>
  49
  50 #include "gromacs/gmxpreprocess/grompp.h"
  51 #include "gromacs/hardware/detecthardware.h"
  52 #include "gromacs/options/basicoptions.h"
  53 #include "gromacs/options/ioptionscontainer.h"
  54 #include "gromacs/utility/basedefinitions.h"
  55 #include "gromacs/utility/basenetwork.h"
  56 #include "gromacs/utility/gmxmpi.h"
  57 #include "gromacs/utility/textwriter.h"
  58 #include "programs/mdrun/mdrun_main.h"
  59
  60 #include "testutils/cmdlinetest.h"
  61 #include "testutils/mpitest.h"
  62 #include "testutils/testfilemanager.h"
  63 #include "testutils/testoptions.h"
  64
  65 namespace gmx
  66 {
  67 namespace test
  68 {
  69
  70 /********************************************************************
  71  * MdrunTestFixture
  72  */
  73
  74 namespace
  75 {
  76
  77 #if GMX_OPENMP || defined(DOXYGEN)
  78 //! Number of OpenMP threads for child mdrun call.
  79 int g_numOpenMPThreads = 1;
  80 #endif
  81 //! \cond
  82 GMX_TEST_OPTIONS(MdrunTestOptions, options)
  83 {
  84     GMX_UNUSED_VALUE(options);
  85 #if GMX_OPENMP
  86     options->addOption(IntegerOption("nt_omp").store(&g_numOpenMPThreads)
  87                            .description("Number of OpenMP threads for child mdrun calls"));
  88 #endif
  89 }
  90 //! \endcond
  91
  92 }
  93
  94 SimulationRunner::SimulationRunner(TestFileManager *fileManager) :
  95     topFileName_(),
  96     groFileName_(),
  97     fullPrecisionTrajectoryFileName_(),
  98     ndxFileName_(),
  99     mdpInputFileName_(fileManager->getTemporaryFilePath("input.mdp")),
 100     mdpOutputFileName_(fileManager->getTemporaryFilePath("output.mdp")),
 101     tprFileName_(fileManager->getTemporaryFilePath(".tpr")),
 102     logFileName_(fileManager->getTemporaryFilePath(".log")),
 103     edrFileName_(fileManager->getTemporaryFilePath(".edr")),
 104     nsteps_(-2),
 105     fileManager_(*fileManager)
 106 {
 107 #if GMX_LIB_MPI
 108     GMX_RELEASE_ASSERT(gmx_mpi_initialized(), "MPI system not initialized for mdrun tests");
 109 #endif
 110 }
 111
 112 // TODO The combination of defaulting to Verlet cut-off scheme, NVE,
 113 // and verlet-buffer-tolerance = -1 gives a grompp error. If we keep
 114 // things that way, this function should be renamed. For now,
 115 // force the use of the group scheme.
 116 // TODO There is possible outstanding unexplained behaviour of mdp
 117 // input parsing e.g. Redmine 2074, so this particular set of mdp
 118 // contents is also tested with GetIrTest in gmxpreprocess-test.
 119 void
 120 SimulationRunner::useEmptyMdpFile()
 121 {
 122     // TODO When removing the group scheme, update actual and potential users of useEmptyMdpFile
 123     useStringAsMdpFile("cutoff-scheme = Group\n");
 124 }
 125
 126 void
 127 SimulationRunner::useStringAsMdpFile(const char *mdpString)
 128 {
 129     useStringAsMdpFile(std::string(mdpString));
 130 }
 131
 132 void
 133 SimulationRunner::useStringAsMdpFile(const std::string &mdpString)
 134 {
 135     gmx::TextWriter::writeFileFromString(mdpInputFileName_, mdpString);
 136 }
 137
 138 void
 139 SimulationRunner::useStringAsNdxFile(const char *ndxString)
 140 {
 141     gmx::TextWriter::writeFileFromString(ndxFileName_, ndxString);
 142 }
 143
 144 void
 145 SimulationRunner::useTopGroAndNdxFromDatabase(const char *name)
 146 {
 147     topFileName_ = fileManager_.getInputFilePath((std::string(name) + ".top").c_str());
 148     groFileName_ = fileManager_.getInputFilePath((std::string(name) + ".gro").c_str());
 149     ndxFileName_ = fileManager_.getInputFilePath((std::string(name) + ".ndx").c_str());
 150 }
 151
 152 void
 153 SimulationRunner::useGroFromDatabase(const char *name)
 154 {
 155     groFileName_ = fileManager_.getInputFilePath((std::string(name) + ".gro").c_str());
 156 }
 157
 158 int
 159 SimulationRunner::callGromppOnThisRank(const CommandLine &callerRef)
 160 {
 161     CommandLine caller;
 162     caller.append("grompp");
 163     caller.merge(callerRef);
 164     caller.addOption("-f", mdpInputFileName_);
 165     caller.addOption("-n", ndxFileName_);
 166     caller.addOption("-p", topFileName_);
 167     caller.addOption("-c", groFileName_);
 168     caller.addOption("-r", groFileName_);
 169
 170     caller.addOption("-po", mdpOutputFileName_);
 171     caller.addOption("-o", tprFileName_);
 172
 173     return gmx_grompp(caller.argc(), caller.argv());
 174 }
 175
 176 int
 177 SimulationRunner::callGromppOnThisRank()
 178 {
 179     return callGromppOnThisRank(CommandLine());
 180 }
 181
 182 int
 183 SimulationRunner::callGrompp(const CommandLine &callerRef)
 184 {
 185     int returnValue = 0;
 186 #if GMX_LIB_MPI
 187     // When compiled with external MPI, we're trying to run mdrun with
 188     // MPI, but we need to make sure that we only do grompp on one
 189     // rank
 190     if (0 == gmx_node_rank())
 191 #endif
 192     {
 193         returnValue = callGromppOnThisRank(callerRef);
 194     }
 195 #if GMX_LIB_MPI
 196     // Make sure rank zero has written the .tpr file before other
 197     // ranks try to read it. Thread-MPI and serial do this just fine
 198     // on their own.
 199     MPI_Barrier(MPI_COMM_WORLD);
 200 #endif
 201     return returnValue;
 202 }
 203
 204 int
 205 SimulationRunner::callGrompp()
 206 {
 207     return callGrompp(CommandLine());
 208 }
 209
 210 int
 211 SimulationRunner::callMdrun(const CommandLine &callerRef)
 212 {
 213     /* Conforming to style guide by not passing a non-const reference
 214        to this function. Passing a non-const reference might make it
 215        easier to write code that incorrectly re-uses callerRef after
 216        the call to this function. */
 217
 218     CommandLine caller;
 219     caller.append("mdrun");
 220     caller.merge(callerRef);
 221     caller.addOption("-s", tprFileName_);
 222
 223     caller.addOption("-g", logFileName_);
 224     caller.addOption("-e", edrFileName_);
 225     caller.addOption("-o", fullPrecisionTrajectoryFileName_);
 226     caller.addOption("-x", reducedPrecisionTrajectoryFileName_);
 227
 228     caller.addOption("-deffnm", fileManager_.getTemporaryFilePath("state"));
 229
 230     if (nsteps_ > -2)
 231     {
 232         caller.addOption("-nsteps", nsteps_);
 233     }
 234
 235 #if GMX_THREAD_MPI
 236     caller.addOption("-ntmpi", getNumberOfTestMpiRanks());
 237 #endif
 238
 239 #if GMX_OPENMP
 240     caller.addOption("-ntomp", g_numOpenMPThreads);
 241 #endif
 242
 243     return gmx_mdrun(caller.argc(), caller.argv());
 244 }
 245
 246 int
 247 SimulationRunner::callMdrun()
 248 {
 249     return callMdrun(CommandLine());
 250 }
 251
 252 // ====
 253
 254 MdrunTestFixtureBase::MdrunTestFixtureBase()
 255 {
 256 #if GMX_LIB_MPI
 257     GMX_RELEASE_ASSERT(gmx_mpi_initialized(), "MPI system not initialized for mdrun tests");
 258 #endif
 259 }
 260
 261 MdrunTestFixtureBase::~MdrunTestFixtureBase()
 262 {
 263 }
 264
 265 // ====
 266
 267 MdrunTestFixture::MdrunTestFixture() : runner_(&fileManager_)
 268 {
 269 }
 270
 271 MdrunTestFixture::~MdrunTestFixture()
 272 {
 273 }
 274
 275 } // namespace test
 276 } // namespace gmx