src/programs/mdrun/runner.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
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   4  * Copyright (c) 2015,2017,2018, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  35 /*! \libinternal \file
  36  *
  37  * \brief Declares the routine running the inetgrators.
  38  *
  39  * \author David van der Spoel <david.vanderspoel@icm.uu.se>
  40  * \ingroup module_mdlib
  41  */
  42 #ifndef GMX_MDLIB_RUNNER_H
  43 #define GMX_MDLIB_RUNNER_H
  44
  45 #include <cstdio>
  46
  47 #include <array>
  48
  49 #include "gromacs/commandline/filenm.h"
  50 #include "gromacs/domdec/domdec.h"
  51 #include "gromacs/hardware/hw_info.h"
  52 #include "gromacs/math/vec.h"
  53 #include "gromacs/mdlib/mdrun.h"
  54 #include "gromacs/utility/basedefinitions.h"
  55 #include "gromacs/utility/real.h"
  56
  57 #include "repl_ex.h"
  58
  59 struct gmx_output_env_t;
  60 struct ReplicaExchangeParameters;
  61 struct t_commrec;
  62
  63 namespace gmx
  64 {
  65
  66 /*! \libinternal \brief Runner object for supporting setup and execution of mdrun.
  67  *
  68  * This class has responsibility for the lifetime of data structures
  69  * that exist for the life of the simulation, e.g. for logging and
  70  * communication.
  71  *
  72  * \todo Most of the attributes should be declared by specific modules
  73  * as command-line options. Accordingly, they do not conform to the
  74  * naming scheme, because that would make for a lot of noise in the
  75  * diff, only to have it change again when the options move to their
  76  * modules.
  77  *
  78  * \todo Preparing logging and MPI contexts could probably be a
  79  * higher-level responsibility, so that an Mdrunner would get made
  80  * without needing to re-initialize these components (as currently
  81  * happens always for the master rank, and differently for the spawned
  82  * ranks with thread-MPI).
  83  */
  84 class Mdrunner
  85 {
  86     private:
  87         //! Parallelism-related user options.
  88         gmx_hw_opt_t             hw_opt;
  89         //! Filenames and properties from command-line argument values.
  90         std::array<t_filenm, 34> filenames =
  91         {{{ efTPR, nullptr,     nullptr,     ffREAD },
  92           { efTRN, "-o",        nullptr,     ffWRITE },
  93           { efCOMPRESSED, "-x", nullptr,     ffOPTWR },
  94           { efCPT, "-cpi",      nullptr,     ffOPTRD | ffALLOW_MISSING },
  95           { efCPT, "-cpo",      nullptr,     ffOPTWR },
  96           { efSTO, "-c",        "confout",   ffWRITE },
  97           { efEDR, "-e",        "ener",      ffWRITE },
  98           { efLOG, "-g",        "md",        ffWRITE },
  99           { efXVG, "-dhdl",     "dhdl",      ffOPTWR },
 100           { efXVG, "-field",    "field",     ffOPTWR },
 101           { efXVG, "-table",    "table",     ffOPTRD },
 102           { efXVG, "-tablep",   "tablep",    ffOPTRD },
 103           { efXVG, "-tableb",   "table",     ffOPTRDMULT },
 104           { efTRX, "-rerun",    "rerun",     ffOPTRD },
 105           { efXVG, "-tpi",      "tpi",       ffOPTWR },
 106           { efXVG, "-tpid",     "tpidist",   ffOPTWR },
 107           { efEDI, "-ei",       "sam",       ffOPTRD },
 108           { efXVG, "-eo",       "edsam",     ffOPTWR },
 109           { efXVG, "-devout",   "deviatie",  ffOPTWR },
 110           { efXVG, "-runav",    "runaver",   ffOPTWR },
 111           { efXVG, "-px",       "pullx",     ffOPTWR },
 112           { efXVG, "-pf",       "pullf",     ffOPTWR },
 113           { efXVG, "-ro",       "rotation",  ffOPTWR },
 114           { efLOG, "-ra",       "rotangles", ffOPTWR },
 115           { efLOG, "-rs",       "rotslabs",  ffOPTWR },
 116           { efLOG, "-rt",       "rottorque", ffOPTWR },
 117           { efMTX, "-mtx",      "nm",        ffOPTWR },
 118           { efRND, "-multidir", nullptr,     ffOPTRDMULT},
 119           { efXVG, "-awh",      "awhinit",   ffOPTRD },
 120           { efDAT, "-membed",   "membed",    ffOPTRD },
 121           { efTOP, "-mp",       "membed",    ffOPTRD },
 122           { efNDX, "-mn",       "membed",    ffOPTRD },
 123           { efXVG, "-if",       "imdforces", ffOPTWR },
 124           { efXVG, "-swap",     "swapions",  ffOPTWR }}};
 125         /*! \brief Filename arguments.
 126          *
 127          * Provided for compatibility with old C-style code accessing
 128          * command-line arguments that are file names. */
 129         t_filenm *fnm = filenames.data();
 130         /*! \brief Number of filename argument values.
 131          *
 132          * Provided for compatibility with old C-style code accessing
 133          * command-line arguments that are file names. */
 134         int nfile = filenames.size();
 135         //! Output context for writing text files
 136         gmx_output_env_t                *oenv = nullptr;
 137         //! Ongoing collection of mdrun options
 138         MdrunOptions                     mdrunOptions;
 139         //! Options for the domain decomposition.
 140         DomdecOptions                    domdecOptions;
 141         //! Target short-range interations for "cpu", "gpu", or "auto". Default is "auto".
 142         const char                      *nbpu_opt = nullptr;
 143         //! Target long-range interactions for "cpu", "gpu", or "auto". Default is "auto".
 144         const char                      *pme_opt = nullptr;
 145         //! Target long-range interactions FFT/solve stages for "cpu", "gpu", or "auto". Default is "auto".
 146         const char                      *pme_fft_opt = nullptr;
 147         //! Command-line override for the duration of a neighbor list with the Verlet scheme.
 148         int                              nstlist_cmdline = 0;
 149         //! Parameters for replica-exchange simulations.
 150         ReplicaExchangeParameters        replExParams;
 151         //! Print a warning if any force is larger than this (in kJ/mol nm).
 152         real                             pforce = -1;
 153         //! Handle to file used for logging.
 154         FILE                            *fplog;
 155         //! Handle to communication data structure.
 156         t_commrec                       *cr;
 157         //! Handle to multi-simulation handler.
 158         gmx_multisim_t                  *ms;
 159
 160     public:
 161         /*! \brief Defaulted constructor.
 162          *
 163          * Note that when member variables are not present in the constructor
 164          * member initialization list (which is true for the default constructor),
 165          * then they are initialized with any default member initializer specified
 166          * when they were declared, or default initialized. */
 167         Mdrunner() = default;
 168         //! Start running mdrun by calling its C-style main function.
 169         int mainFunction(int argc, char *argv[]);
 170         /*! \brief Driver routine, that calls the different simulation methods. */
 171         int mdrunner();
 172         //! Called when thread-MPI spawns threads.
 173         t_commrec *spawnThreads(int numThreadsToLaunch) const;
 174         /*! \brief Re-initializes the object after threads spawn.
 175          *
 176          * \todo Can this be refactored so that the Mdrunner on a spawned thread is
 177          * constructed ready to use? */
 178         void reinitializeOnSpawnedThread();
 179 };
 180
 181 }      // namespace gmx
 182
 183 #endif // GMX_MDLIB_RUNNER_H