src/gromacs/mdrun/legacyoptions.h

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  37 /*! \libinternal \file
  38  *
  39  * \brief This file declares helper functionality for legacy option handling for mdrun
  40  *
  41  * \author Berk Hess <hess@kth.se>
  42  * \author David van der Spoel <david.vanderspoel@icm.uu.se>
  43  * \author Erik Lindahl <erik@kth.se>
  44  * \author Mark Abraham <mark.j.abraham@gmail.com>
  45  *
  46  * \ingroup module_mdrun
  47  * \inlibraryapi
  48  */
  49 #include "gromacs/commandline/filenm.h"
  50 #include "gromacs/commandline/pargs.h"
  51 #include "gromacs/domdec/domdec.h"
  52 #include "gromacs/hardware/hw_info.h"
  53 #include "gromacs/mdlib/mdrun.h"
  54 #include "gromacs/mdrun/logging.h"
  55
  56 #include "replicaexchange.h"
  57
  58 struct gmx_multisim_t;
  59
  60 namespace gmx
  61 {
  62
  63 /*! \libinternal
  64  * \brief This class provides the same command-line option
  65  * functionality to both CLI and API sessions.
  66  *
  67  * This class should not exist, but is necessary now to introduce
  68  * support for the CLI and API without duplicating code. It should be
  69  * eliminated following the TODOs below.
  70  *
  71  * \todo Modules in mdrun should acquire proper option handling so
  72  * that all of these declarations and defaults are local to the
  73  * modules.
  74  *
  75  * \todo Contextual aspects, such as working directory, MPI
  76  * environment, and environment variable handling are more properly
  77  * the role of SimulationContext, and should be moved there */
  78 class LegacyMdrunOptions
  79 {
  80     public:
  81         //! Ongoing collection of mdrun options
  82         MdrunOptions                     mdrunOptions;
  83         //! Options for the domain decomposition.
  84         DomdecOptions                    domdecOptions;
  85         //! Parallelism-related user options.
  86         gmx_hw_opt_t                     hw_opt;
  87         //! Command-line override for the duration of a neighbor list with the Verlet scheme.
  88         int                              nstlist_cmdline = 0;
  89         //! Parameters for replica-exchange simulations.
  90         ReplicaExchangeParameters        replExParams;
  91
  92         //! Filename options to fill from command-line argument values.
  93         std::vector<t_filenm> filenames =
  94         {{{ efTPR, nullptr,     nullptr,     ffREAD },
  95           { efTRN, "-o",        nullptr,     ffWRITE },
  96           { efCOMPRESSED, "-x", nullptr,     ffOPTWR },
  97           { efCPT, "-cpi",      nullptr,     ffOPTRD | ffALLOW_MISSING },
  98           { efCPT, "-cpo",      nullptr,     ffOPTWR },
  99           { efSTO, "-c",        "confout",   ffWRITE },
 100           { efEDR, "-e",        "ener",      ffWRITE },
 101           { efLOG, "-g",        "md",        ffWRITE },
 102           { efXVG, "-dhdl",     "dhdl",      ffOPTWR },
 103           { efXVG, "-field",    "field",     ffOPTWR },
 104           { efXVG, "-table",    "table",     ffOPTRD },
 105           { efXVG, "-tablep",   "tablep",    ffOPTRD },
 106           { efXVG, "-tableb",   "table",     ffOPTRDMULT },
 107           { efTRX, "-rerun",    "rerun",     ffOPTRD },
 108           { efXVG, "-tpi",      "tpi",       ffOPTWR },
 109           { efXVG, "-tpid",     "tpidist",   ffOPTWR },
 110           { efEDI, "-ei",       "sam",       ffOPTRD },
 111           { efXVG, "-eo",       "edsam",     ffOPTWR },
 112           { efXVG, "-devout",   "deviatie",  ffOPTWR },
 113           { efXVG, "-runav",    "runaver",   ffOPTWR },
 114           { efXVG, "-px",       "pullx",     ffOPTWR },
 115           { efXVG, "-pf",       "pullf",     ffOPTWR },
 116           { efXVG, "-ro",       "rotation",  ffOPTWR },
 117           { efLOG, "-ra",       "rotangles", ffOPTWR },
 118           { efLOG, "-rs",       "rotslabs",  ffOPTWR },
 119           { efLOG, "-rt",       "rottorque", ffOPTWR },
 120           { efMTX, "-mtx",      "nm",        ffOPTWR },
 121           { efRND, "-multidir", nullptr,     ffOPTRDMULT},
 122           { efXVG, "-awh",      "awhinit",   ffOPTRD },
 123           { efDAT, "-membed",   "membed",    ffOPTRD },
 124           { efTOP, "-mp",       "membed",    ffOPTRD },
 125           { efNDX, "-mn",       "membed",    ffOPTRD },
 126           { efXVG, "-if",       "imdforces", ffOPTWR },
 127           { efXVG, "-swap",     "swapions",  ffOPTWR }}};
 128
 129         //! Print a warning if any force is larger than this (in kJ/mol nm).
 130         real                             pforce = -1;
 131
 132         /*! \brief Output context for writing text files
 133          *
 134          * \todo Clarify initialization, ownership, and lifetime. */
 135         gmx_output_env_t                *oenv = nullptr;
 136
 137         //! Handle to file used for logging.
 138         LogFilePtr logFileGuard = nullptr;
 139
 140         /*! \brief Command line options, defaults, docs and storage for them to fill. */
 141         /*! \{ */
 142         rvec              realddxyz                                               = {0, 0, 0};
 143         const char       *ddrank_opt_choices[static_cast<int>(DdRankOrder::nr)+1] =
 144         { nullptr, "interleave", "pp_pme", "cartesian", nullptr };
 145         const char       *dddlb_opt_choices[static_cast<int>(DlbOption::nr)+1] =
 146         { nullptr, "auto", "no", "yes", nullptr };
 147         const char       *thread_aff_opt_choices[threadaffNR+1] =
 148         { nullptr, "auto", "on", "off", nullptr };
 149         const char       *nbpu_opt_choices[5] =
 150         { nullptr, "auto", "cpu", "gpu", nullptr };
 151         const char       *pme_opt_choices[5] =
 152         { nullptr, "auto", "cpu", "gpu", nullptr };
 153         const char       *pme_fft_opt_choices[5] =
 154         { nullptr, "auto", "cpu", "gpu", nullptr };
 155         gmx_bool          bTryToAppendFiles     = TRUE;
 156         const char       *gpuIdsAvailable       = "";
 157         const char       *userGpuTaskAssignment = "";
 158
 159         ImdOptions       &imdOptions = mdrunOptions.imdOptions;
 160
 161         t_pargs           pa[47] = {
 162
 163             { "-dd",      FALSE, etRVEC, {&realddxyz},
 164               "Domain decomposition grid, 0 is optimize" },
 165             { "-ddorder", FALSE, etENUM, {ddrank_opt_choices},
 166               "DD rank order" },
 167             { "-npme",    FALSE, etINT, {&domdecOptions.numPmeRanks},
 168               "Number of separate ranks to be used for PME, -1 is guess" },
 169             { "-nt",      FALSE, etINT, {&hw_opt.nthreads_tot},
 170               "Total number of threads to start (0 is guess)" },
 171             { "-ntmpi",   FALSE, etINT, {&hw_opt.nthreads_tmpi},
 172               "Number of thread-MPI ranks to start (0 is guess)" },
 173             { "-ntomp",   FALSE, etINT, {&hw_opt.nthreads_omp},
 174               "Number of OpenMP threads per MPI rank to start (0 is guess)" },
 175             { "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
 176               "Number of OpenMP threads per MPI rank to start (0 is -ntomp)" },
 177             { "-pin",     FALSE, etENUM, {thread_aff_opt_choices},
 178               "Whether mdrun should try to set thread affinities" },
 179             { "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
 180               "The lowest logical core number to which mdrun should pin the first thread" },
 181             { "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
 182               "Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
 183             { "-gpu_id",  FALSE, etSTR, {&gpuIdsAvailable},
 184               "List of unique GPU device IDs available to use" },
 185             { "-gputasks",  FALSE, etSTR, {&userGpuTaskAssignment},
 186               "List of GPU device IDs, mapping each PP task on each node to a device" },
 187             { "-ddcheck", FALSE, etBOOL, {&domdecOptions.checkBondedInteractions},
 188               "Check for all bonded interactions with DD" },
 189             { "-ddbondcomm", FALSE, etBOOL, {&domdecOptions.useBondedCommunication},
 190               "HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
 191             { "-rdd",     FALSE, etREAL, {&domdecOptions.minimumCommunicationRange},
 192               "The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
 193             { "-rcon",    FALSE, etREAL, {&domdecOptions.constraintCommunicationRange},
 194               "Maximum distance for P-LINCS (nm), 0 is estimate" },
 195             { "-dlb",     FALSE, etENUM, {dddlb_opt_choices},
 196               "Dynamic load balancing (with DD)" },
 197             { "-dds",     FALSE, etREAL, {&domdecOptions.dlbScaling},
 198               "Fraction in (0,1) by whose reciprocal the initial DD cell size will be increased in order to "
 199               "provide a margin in which dynamic load balancing can act while preserving the minimum cell size." },
 200             { "-ddcsx",   FALSE, etSTR, {&domdecOptions.cellSizeX},
 201               "HIDDENA string containing a vector of the relative sizes in the x "
 202               "direction of the corresponding DD cells. Only effective with static "
 203               "load balancing." },
 204             { "-ddcsy",   FALSE, etSTR, {&domdecOptions.cellSizeY},
 205               "HIDDENA string containing a vector of the relative sizes in the y "
 206               "direction of the corresponding DD cells. Only effective with static "
 207               "load balancing." },
 208             { "-ddcsz",   FALSE, etSTR, {&domdecOptions.cellSizeZ},
 209               "HIDDENA string containing a vector of the relative sizes in the z "
 210               "direction of the corresponding DD cells. Only effective with static "
 211               "load balancing." },
 212             { "-gcom",    FALSE, etINT, {&mdrunOptions.globalCommunicationInterval},
 213               "Global communication frequency" },
 214             { "-nb",      FALSE, etENUM, {nbpu_opt_choices},
 215               "Calculate non-bonded interactions on" },
 216             { "-nstlist", FALSE, etINT, {&nstlist_cmdline},
 217               "Set nstlist when using a Verlet buffer tolerance (0 is guess)" },
 218             { "-tunepme", FALSE, etBOOL, {&mdrunOptions.tunePme},
 219               "Optimize PME load between PP/PME ranks or GPU/CPU (only with the Verlet cut-off scheme)" },
 220             { "-pme",     FALSE, etENUM, {pme_opt_choices},
 221               "Perform PME calculations on" },
 222             { "-pmefft", FALSE, etENUM, {pme_fft_opt_choices},
 223               "Perform PME FFT calculations on" },
 224             { "-v",       FALSE, etBOOL, {&mdrunOptions.verbose},
 225               "Be loud and noisy" },
 226             { "-pforce",  FALSE, etREAL, {&pforce},
 227               "Print all forces larger than this (kJ/mol nm)" },
 228             { "-reprod",  FALSE, etBOOL, {&mdrunOptions.reproducible},
 229               "Try to avoid optimizations that affect binary reproducibility" },
 230             { "-cpt",     FALSE, etREAL, {&mdrunOptions.checkpointOptions.period},
 231               "Checkpoint interval (minutes)" },
 232             { "-cpnum",   FALSE, etBOOL, {&mdrunOptions.checkpointOptions.keepAndNumberCheckpointFiles},
 233               "Keep and number checkpoint files" },
 234             { "-append",  FALSE, etBOOL, {&bTryToAppendFiles},
 235               "Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
 236             { "-nsteps",  FALSE, etINT64, {&mdrunOptions.numStepsCommandline},
 237               "Run this number of steps, overrides .mdp file option (-1 means infinite, -2 means use mdp option, smaller is invalid)" },
 238             { "-maxh",   FALSE, etREAL, {&mdrunOptions.maximumHoursToRun},
 239               "Terminate after 0.99 times this time (hours)" },
 240             { "-replex",  FALSE, etINT, {&replExParams.exchangeInterval},
 241               "Attempt replica exchange periodically with this period (steps)" },
 242             { "-nex",  FALSE, etINT, {&replExParams.numExchanges},
 243               "Number of random exchanges to carry out each exchange interval (N^3 is one suggestion).  -nex zero or not specified gives neighbor replica exchange." },
 244             { "-reseed",  FALSE, etINT, {&replExParams.randomSeed},
 245               "Seed for replica exchange, -1 is generate a seed" },
 246             { "-imdport",    FALSE, etINT, {&imdOptions.port},
 247               "HIDDENIMD listening port" },
 248             { "-imdwait",  FALSE, etBOOL, {&imdOptions.wait},
 249               "HIDDENPause the simulation while no IMD client is connected" },
 250             { "-imdterm",  FALSE, etBOOL, {&imdOptions.terminatable},
 251               "HIDDENAllow termination of the simulation from IMD client" },
 252             { "-imdpull",  FALSE, etBOOL, {&imdOptions.pull},
 253               "HIDDENAllow pulling in the simulation from IMD client" },
 254             { "-rerunvsite", FALSE, etBOOL, {&mdrunOptions.rerunConstructVsites},
 255               "HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
 256             { "-confout", FALSE, etBOOL, {&mdrunOptions.writeConfout},
 257               "HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
 258             { "-stepout", FALSE, etINT, {&mdrunOptions.verboseStepPrintInterval},
 259               "HIDDENFrequency of writing the remaining wall clock time for the run" },
 260             { "-resetstep", FALSE, etINT, {&mdrunOptions.timingOptions.resetStep},
 261               "HIDDENReset cycle counters after these many time steps" },
 262             { "-resethway", FALSE, etBOOL, {&mdrunOptions.timingOptions.resetHalfway},
 263               "HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
 264         };
 265         /*! \} */
 266
 267         //! Handle to communication object.
 268         t_commrec        *cr = nullptr;
 269         //! Multi-simulation object.
 270         gmx_multisim_t   *ms = nullptr;
 271
 272         //! Parses the command-line input and prepares to start mdrun.
 273         int updateFromCommandLine(int argc, char **argv, ArrayRef<const char *> desc);
 274
 275         ~LegacyMdrunOptions();
 276 };
 277
 278 } // end namespace gmx