src/gromacs/mdrun/legacymdrunoptions.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 #ifndef GMX_MDRUN_LEGACYMDRUNOPTIONS_H
  50 #define GMX_MDRUN_LEGACYMDRUNOPTIONS_H
  51
  52 #include "gromacs/commandline/filenm.h"
  53 #include "gromacs/commandline/pargs.h"
  54 #include "gromacs/domdec/options.h"
  55 #include "gromacs/hardware/hw_info.h"
  56 #include "gromacs/mdtypes/mdrunoptions.h"
  57
  58 #include "replicaexchange.h"
  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  * \warning Instances provide lifetime scope for members that do not have
  72  *  effective lifetime management or which are frequently accessed unsafely.
  73  *  The caller is responsible for keeping a LegacyMdrunOptions object alive
  74  *  for as long as any consumers, direct or transitive.
  75  *
  76  * \todo Modules in mdrun should acquire proper option handling so
  77  *       that all of these declarations and defaults are local to the
  78  *       modules.
  79  *
  80  * \todo Contextual aspects, such as working directory
  81  *       and environment variable handling are more properly
  82  *       the role of SimulationContext, and should be moved there.
  83  */
  84 class LegacyMdrunOptions
  85 {
  86 public:
  87     //! Ongoing collection of mdrun options
  88     MdrunOptions mdrunOptions;
  89     //! Options for the domain decomposition.
  90     DomdecOptions domdecOptions;
  91     //! Parallelism-related user options.
  92     gmx_hw_opt_t hw_opt;
  93     //! Command-line override for the duration of a neighbor list with the Verlet scheme.
  94     int nstlist_cmdline = 0;
  95     //! Parameters for replica-exchange simulations.
  96     ReplicaExchangeParameters replExParams;
  97
  98     //! Filename options to fill from command-line argument values.
  99     std::vector<t_filenm> filenames = { { { efTPR, nullptr, nullptr, ffREAD },
 100                                           { efTRN, "-o", nullptr, ffWRITE },
 101                                           { efCOMPRESSED, "-x", nullptr, ffOPTWR },
 102                                           { efCPT, "-cpi", nullptr, ffOPTRD | ffALLOW_MISSING },
 103                                           { efCPT, "-cpo", nullptr, ffOPTWR },
 104                                           { efSTO, "-c", "confout", ffWRITE },
 105                                           { efEDR, "-e", "ener", ffWRITE },
 106                                           { efLOG, "-g", "md", ffWRITE },
 107                                           { efXVG, "-dhdl", "dhdl", ffOPTWR },
 108                                           { efXVG, "-field", "field", ffOPTWR },
 109                                           { efXVG, "-table", "table", ffOPTRD },
 110                                           { efXVG, "-tablep", "tablep", ffOPTRD },
 111                                           { efXVG, "-tableb", "table", ffOPTRDMULT },
 112                                           { efTRX, "-rerun", "rerun", ffOPTRD },
 113                                           { efXVG, "-tpi", "tpi", ffOPTWR },
 114                                           { efXVG, "-tpid", "tpidist", ffOPTWR },
 115                                           { efEDI, "-ei", "sam", ffOPTRD },
 116                                           { efXVG, "-eo", "edsam", ffOPTWR },
 117                                           { efXVG, "-px", "pullx", ffOPTWR },
 118                                           { efXVG, "-pf", "pullf", ffOPTWR },
 119                                           { efXVG, "-ro", "rotation", ffOPTWR },
 120                                           { efLOG, "-ra", "rotangles", ffOPTWR },
 121                                           { efLOG, "-rs", "rotslabs", ffOPTWR },
 122                                           { efLOG, "-rt", "rottorque", ffOPTWR },
 123                                           { efMTX, "-mtx", "nm", ffOPTWR },
 124                                           { efRND, "-multidir", nullptr, ffOPTRDMULT },
 125                                           { efXVG, "-awh", "awhinit", ffOPTRD },
 126                                           { efDAT, "-membed", "membed", ffOPTRD },
 127                                           { efTOP, "-mp", "membed", ffOPTRD },
 128                                           { efNDX, "-mn", "membed", ffOPTRD },
 129                                           { efXVG, "-if", "imdforces", ffOPTWR },
 130                                           { efXVG, "-swap", "swapions", ffOPTWR } } };
 131
 132     //! Print a warning if any force is larger than this (in kJ/mol nm).
 133     real pforce = -1;
 134
 135     //! The value of the -append option
 136     bool appendOption = true;
 137
 138     /*! \brief Output context for writing text files
 139      *
 140      * \todo Clarify initialization, ownership, and lifetime. */
 141     gmx_output_env_t* oenv = nullptr;
 142
 143     /*! \brief Command line options, defaults, docs and storage for them to fill. */
 144     /*! \{ */
 145     rvec        realddxyz                                                    = { 0, 0, 0 };
 146     const char* ddrank_opt_choices[static_cast<int>(DdRankOrder::Count) + 1] = {
 147         nullptr, "interleave", "pp_pme", "cartesian", nullptr
 148     };
 149     const char* dddlb_opt_choices[static_cast<int>(DlbOption::Count) + 1] = { nullptr, "auto", "no",
 150                                                                               "yes", nullptr };
 151     const char* thread_aff_opt_choices[static_cast<int>(ThreadAffinity::Count) + 1] = {
 152         nullptr, "auto", "on", "off", nullptr
 153     };
 154     const char* nbpu_opt_choices[5]    = { nullptr, "auto", "cpu", "gpu", nullptr };
 155     const char* pme_opt_choices[5]     = { nullptr, "auto", "cpu", "gpu", nullptr };
 156     const char* pme_fft_opt_choices[5] = { nullptr, "auto", "cpu", "gpu", nullptr };
 157     const char* bonded_opt_choices[5]  = { nullptr, "auto", "cpu", "gpu", nullptr };
 158     const char* update_opt_choices[5]  = { nullptr, "auto", "cpu", "gpu", nullptr };
 159     const char* gpuIdsAvailable        = "";
 160     const char* userGpuTaskAssignment  = "";
 161
 162
 163     ImdOptions& imdOptions = mdrunOptions.imdOptions;
 164
 165     t_pargs pa[48] = {
 166
 167         { "-dd", FALSE, etRVEC, { &realddxyz }, "Domain decomposition grid, 0 is optimize" },
 168         { "-ddorder", FALSE, etENUM, { ddrank_opt_choices }, "DD rank order" },
 169         { "-npme",
 170           FALSE,
 171           etINT,
 172           { &domdecOptions.numPmeRanks },
 173           "Number of separate ranks to be used for PME, -1 is guess" },
 174         { "-nt",
 175           FALSE,
 176           etINT,
 177           { &hw_opt.nthreads_tot },
 178           "Total number of threads to start (0 is guess)" },
 179         { "-ntmpi",
 180           FALSE,
 181           etINT,
 182           { &hw_opt.nthreads_tmpi },
 183           "Number of thread-MPI ranks to start (0 is guess)" },
 184         { "-ntomp",
 185           FALSE,
 186           etINT,
 187           { &hw_opt.nthreads_omp },
 188           "Number of OpenMP threads per MPI rank to start (0 is guess)" },
 189         { "-ntomp_pme",
 190           FALSE,
 191           etINT,
 192           { &hw_opt.nthreads_omp_pme },
 193           "Number of OpenMP threads per MPI rank to start (0 is -ntomp)" },
 194         { "-pin",
 195           FALSE,
 196           etENUM,
 197           { thread_aff_opt_choices },
 198           "Whether mdrun should try to set thread affinities" },
 199         { "-pinoffset",
 200           FALSE,
 201           etINT,
 202           { &hw_opt.core_pinning_offset },
 203           "The lowest logical core number to which mdrun should pin the first thread" },
 204         { "-pinstride",
 205           FALSE,
 206           etINT,
 207           { &hw_opt.core_pinning_stride },
 208           "Pinning distance in logical cores for threads, use 0 to minimize the number of threads "
 209           "per physical core" },
 210         { "-gpu_id",
 211           FALSE,
 212           etSTR,
 213           { &gpuIdsAvailable },
 214           "List of unique GPU device IDs available to use" },
 215         { "-gputasks",
 216           FALSE,
 217           etSTR,
 218           { &userGpuTaskAssignment },
 219           "List of GPU device IDs, mapping each PP task on each node to a device" },
 220         { "-ddcheck",
 221           FALSE,
 222           etBOOL,
 223           { &domdecOptions.checkBondedInteractions },
 224           "Check for all bonded interactions with DD" },
 225         { "-ddbondcomm",
 226           FALSE,
 227           etBOOL,
 228           { &domdecOptions.useBondedCommunication },
 229           "HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
 230         { "-rdd",
 231           FALSE,
 232           etREAL,
 233           { &domdecOptions.minimumCommunicationRange },
 234           "The maximum distance for bonded interactions with DD (nm), 0 is determine from initial "
 235           "coordinates" },
 236         { "-rcon",
 237           FALSE,
 238           etREAL,
 239           { &domdecOptions.constraintCommunicationRange },
 240           "Maximum distance for P-LINCS (nm), 0 is estimate" },
 241         { "-dlb", FALSE, etENUM, { dddlb_opt_choices }, "Dynamic load balancing (with DD)" },
 242         { "-dds",
 243           FALSE,
 244           etREAL,
 245           { &domdecOptions.dlbScaling },
 246           "Fraction in (0,1) by whose reciprocal the initial DD cell size will be increased in "
 247           "order to "
 248           "provide a margin in which dynamic load balancing can act while preserving the minimum "
 249           "cell size." },
 250         { "-ddcsx",
 251           FALSE,
 252           etSTR,
 253           { &domdecOptions.cellSizeX },
 254           "HIDDENA string containing a vector of the relative sizes in the x "
 255           "direction of the corresponding DD cells. Only effective with static "
 256           "load balancing." },
 257         { "-ddcsy",
 258           FALSE,
 259           etSTR,
 260           { &domdecOptions.cellSizeY },
 261           "HIDDENA string containing a vector of the relative sizes in the y "
 262           "direction of the corresponding DD cells. Only effective with static "
 263           "load balancing." },
 264         { "-ddcsz",
 265           FALSE,
 266           etSTR,
 267           { &domdecOptions.cellSizeZ },
 268           "HIDDENA string containing a vector of the relative sizes in the z "
 269           "direction of the corresponding DD cells. Only effective with static "
 270           "load balancing." },
 271         { "-nb", FALSE, etENUM, { nbpu_opt_choices }, "Calculate non-bonded interactions on" },
 272         { "-nstlist",
 273           FALSE,
 274           etINT,
 275           { &nstlist_cmdline },
 276           "Set nstlist when using a Verlet buffer tolerance (0 is guess)" },
 277         { "-tunepme",
 278           FALSE,
 279           etBOOL,
 280           { &mdrunOptions.tunePme },
 281           "Optimize PME load between PP/PME ranks or GPU/CPU" },
 282         { "-pme", FALSE, etENUM, { pme_opt_choices }, "Perform PME calculations on" },
 283         { "-pmefft", FALSE, etENUM, { pme_fft_opt_choices }, "Perform PME FFT calculations on" },
 284         { "-bonded", FALSE, etENUM, { bonded_opt_choices }, "Perform bonded calculations on" },
 285         { "-update", FALSE, etENUM, { update_opt_choices }, "Perform update and constraints on" },
 286         { "-v", FALSE, etBOOL, { &mdrunOptions.verbose }, "Be loud and noisy" },
 287         { "-pforce", FALSE, etREAL, { &pforce }, "Print all forces larger than this (kJ/mol nm)" },
 288         { "-reprod",
 289           FALSE,
 290           etBOOL,
 291           { &mdrunOptions.reproducible },
 292           "Try to avoid optimizations that affect binary reproducibility" },
 293         { "-cpt",
 294           FALSE,
 295           etREAL,
 296           { &mdrunOptions.checkpointOptions.period },
 297           "Checkpoint interval (minutes)" },
 298         { "-cpnum",
 299           FALSE,
 300           etBOOL,
 301           { &mdrunOptions.checkpointOptions.keepAndNumberCheckpointFiles },
 302           "Keep and number checkpoint files" },
 303         { "-append",
 304           FALSE,
 305           etBOOL,
 306           { &appendOption },
 307           "Append to previous output files when continuing from checkpoint instead of adding the "
 308           "simulation part number to all file names" },
 309         { "-nsteps",
 310           FALSE,
 311           etINT64,
 312           { &mdrunOptions.numStepsCommandline },
 313           "Run this number of steps (-1 means infinite, -2 means use mdp option, smaller is "
 314           "invalid)" },
 315         { "-maxh",
 316           FALSE,
 317           etREAL,
 318           { &mdrunOptions.maximumHoursToRun },
 319           "Terminate after 0.99 times this time (hours)" },
 320         { "-replex",
 321           FALSE,
 322           etINT,
 323           { &replExParams.exchangeInterval },
 324           "Attempt replica exchange periodically with this period (steps)" },
 325         { "-nex",
 326           FALSE,
 327           etINT,
 328           { &replExParams.numExchanges },
 329           "Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). "
 330           " -nex zero or not specified gives neighbor replica exchange." },
 331         { "-reseed",
 332           FALSE,
 333           etINT,
 334           { &replExParams.randomSeed },
 335           "Seed for replica exchange, -1 is generate a seed" },
 336         { "-imdport", FALSE, etINT, { &imdOptions.port }, "HIDDENIMD listening port" },
 337         { "-imdwait",
 338           FALSE,
 339           etBOOL,
 340           { &imdOptions.wait },
 341           "HIDDENPause the simulation while no IMD client is connected" },
 342         { "-imdterm",
 343           FALSE,
 344           etBOOL,
 345           { &imdOptions.terminatable },
 346           "HIDDENAllow termination of the simulation from IMD client" },
 347         { "-imdpull",
 348           FALSE,
 349           etBOOL,
 350           { &imdOptions.pull },
 351           "HIDDENAllow pulling in the simulation from IMD client" },
 352         { "-rerunvsite",
 353           FALSE,
 354           etBOOL,
 355           { &mdrunOptions.rerunConstructVsites },
 356           "HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
 357         { "-confout",
 358           FALSE,
 359           etBOOL,
 360           { &mdrunOptions.writeConfout },
 361           "HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last "
 362           "step" },
 363         { "-stepout",
 364           FALSE,
 365           etINT,
 366           { &mdrunOptions.verboseStepPrintInterval },
 367           "HIDDENFrequency of writing the remaining wall clock time for the run" },
 368         { "-resetstep",
 369           FALSE,
 370           etINT,
 371           { &mdrunOptions.timingOptions.resetStep },
 372           "HIDDENReset cycle counters after these many time steps" },
 373         { "-resethway",
 374           FALSE,
 375           etBOOL,
 376           { &mdrunOptions.timingOptions.resetHalfway },
 377           "HIDDENReset the cycle counters after half the number of steps or halfway "
 378           "[TT]-maxh[tt]" }
 379     };
 380     /*! \} */
 381
 382     //! Parses the command-line input and prepares to start mdrun.
 383     int updateFromCommandLine(int argc, char** argv, ArrayRef<const char*> desc);
 384
 385     ~LegacyMdrunOptions();
 386 };
 387
 388 } // end namespace gmx
 389
 390 #endif