src/gromacs/mdrun/legacymdrunoptions.cpp

   1 /*
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   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  37 /*! \internal \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  */
  48 #include "gmxpre.h"
  49
  50 #include "legacymdrunoptions.h"
  51
  52 #include "config.h"
  53
  54 #include <cstring>
  55
  56 #include "gromacs/gmxlib/network.h"
  57 #include "gromacs/math/functions.h"
  58 #include "gromacs/mdrunutility/handlerestart.h"
  59 #include "gromacs/mdrunutility/multisim.h"
  60 #include "gromacs/mdtypes/commrec.h"
  61 #include "gromacs/utility/arraysize.h"
  62 #include "gromacs/utility/fatalerror.h"
  63
  64 namespace gmx
  65 {
  66
  67 /*! \brief Return whether the command-line parameter that
  68  *  will trigger a multi-simulation is set */
  69 static bool is_multisim_option_set(int argc, const char *const argv[])
  70 {
  71     for (int i = 0; i < argc; ++i)
  72     {
  73         if (strcmp(argv[i], "-multidir") == 0)
  74         {
  75             return true;
  76         }
  77     }
  78     return false;
  79 }
  80
  81 int LegacyMdrunOptions::updateFromCommandLine(int argc, char **argv, ArrayRef<const char *> desc)
  82 {
  83     unsigned long     PCA_Flags = PCA_CAN_SET_DEFFNM;
  84     // With -multidir, the working directory still needs to be
  85     // changed, so we can't check for the existence of files during
  86     // parsing.  It isn't useful to do any completion based on file
  87     // system contents, either.
  88     if (is_multisim_option_set(argc, argv))
  89     {
  90         PCA_Flags |= PCA_DISABLE_INPUT_FILE_CHECKING;
  91     }
  92
  93     if (!parse_common_args(&argc, argv, PCA_Flags,
  94                            ssize(filenames), filenames.data(), asize(pa), pa,
  95                            ssize(desc), desc.data(), 0, nullptr, &oenv))
  96     {
  97         return 0;
  98     }
  99
 100     // Handle the options that permits the user to either declare
 101     // which compatible GPUs are availble for use, or to select a GPU
 102     // task assignment. Either could be in an environment variable (so
 103     // that there is a way to customize it, when using MPI in
 104     // heterogeneous contexts).
 105     {
 106         // TODO Argument parsing can't handle std::string. We should
 107         // fix that by changing the parsing, once more of the roles of
 108         // handling, validating and implementing defaults for user
 109         // command-line options have been seperated.
 110         hw_opt.gpuIdsAvailable       = gpuIdsAvailable;
 111         hw_opt.userGpuTaskAssignment = userGpuTaskAssignment;
 112
 113         const char *env = getenv("GMX_GPU_ID");
 114         if (env != nullptr)
 115         {
 116             if (!hw_opt.gpuIdsAvailable.empty())
 117             {
 118                 gmx_fatal(FARGS, "GMX_GPU_ID and -gpu_id can not be used at the same time");
 119             }
 120             hw_opt.gpuIdsAvailable = env;
 121         }
 122
 123         env = getenv("GMX_GPUTASKS");
 124         if (env != nullptr)
 125         {
 126             if (!hw_opt.userGpuTaskAssignment.empty())
 127             {
 128                 gmx_fatal(FARGS, "GMX_GPUTASKS and -gputasks can not be used at the same time");
 129             }
 130             hw_opt.userGpuTaskAssignment = env;
 131         }
 132
 133         if (!hw_opt.gpuIdsAvailable.empty() && !hw_opt.userGpuTaskAssignment.empty())
 134         {
 135             gmx_fatal(FARGS, "-gpu_id and -gputasks cannot be used at the same time");
 136         }
 137     }
 138
 139     hw_opt.threadAffinity = static_cast<ThreadAffinity>(nenum(thread_aff_opt_choices));
 140
 141     // now check for a multi-simulation
 142     ArrayRef<const std::string> multidir = opt2fnsIfOptionSet("-multidir",
 143                                                               ssize(filenames),
 144                                                               filenames.data());
 145     if (!multidir.empty())
 146     {
 147         ms = std::make_unique<gmx_multisim_t>(MPI_COMM_WORLD, multidir);
 148     }
 149
 150     /* Prepare the intra-simulation communication */
 151     // TODO consolidate this with init_commrec, after changing the
 152     // relative ordering of init_commrec and ms initialization.
 153     if (ms != nullptr)
 154     {
 155 #if GMX_MPI
 156         cr->nnodes = cr->nnodes / ms->nsim;
 157         MPI_Comm_split(MPI_COMM_WORLD, ms->sim, cr->sim_nodeid, &cr->mpi_comm_mysim);
 158         cr->mpi_comm_mygroup = cr->mpi_comm_mysim;
 159         MPI_Comm_rank(cr->mpi_comm_mysim, &cr->sim_nodeid);
 160         MPI_Comm_rank(cr->mpi_comm_mygroup, &cr->nodeid);
 161 #endif
 162     }
 163
 164     if (!opt2parg_bSet("-append", asize(pa), pa))
 165     {
 166         mdrunOptions.appendingBehavior = AppendingBehavior::Auto;
 167     }
 168     else
 169     {
 170         if (opt2parg_bool("-append", asize(pa), pa))
 171         {
 172             mdrunOptions.appendingBehavior = AppendingBehavior::Appending;
 173         }
 174         else
 175         {
 176             mdrunOptions.appendingBehavior = AppendingBehavior::NoAppending;
 177         }
 178     }
 179
 180     mdrunOptions.rerun            = opt2bSet("-rerun",
 181                                              ssize(filenames),
 182                                              filenames.data());
 183     mdrunOptions.ntompOptionIsSet = opt2parg_bSet("-ntomp", asize(pa), pa);
 184
 185     domdecOptions.rankOrder    = static_cast<DdRankOrder>(nenum(ddrank_opt_choices));
 186     domdecOptions.dlbOption    = static_cast<DlbOption>(nenum(dddlb_opt_choices));
 187     domdecOptions.numCells[XX] = roundToInt(realddxyz[XX]);
 188     domdecOptions.numCells[YY] = roundToInt(realddxyz[YY]);
 189     domdecOptions.numCells[ZZ] = roundToInt(realddxyz[ZZ]);
 190
 191     return 1;
 192 }
 193
 194 LegacyMdrunOptions::~LegacyMdrunOptions()
 195 {
 196     output_env_done(oenv);
 197 }
 198
 199 } // namespace gmx