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39 * \brief This file declares helper functionality for legacy option handling for mdrun
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>
46 * \ingroup module_mdrun
50 #include "legacymdrunoptions.h"
56 #include "gromacs/gmxlib/network.h"
57 #include "gromacs/math/functions.h"
58 #include "gromacs/mdrun/multisim.h"
59 #include "gromacs/mdrunutility/handlerestart.h"
60 #include "gromacs/mdtypes/commrec.h"
61 #include "gromacs/utility/arraysize.h"
62 #include "gromacs/utility/fatalerror.h"
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[])
71 for (int i = 0; i < argc; ++i)
73 if (strcmp(argv[i], "-multidir") == 0)
81 int LegacyMdrunOptions::updateFromCommandLine(int argc, char **argv, ArrayRef<const char *> desc)
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))
90 PCA_Flags |= PCA_DISABLE_INPUT_FILE_CHECKING;
93 if (!parse_common_args(&argc, argv, PCA_Flags,
94 static_cast<int>(filenames.size()), filenames.data(), asize(pa), pa,
95 static_cast<int>(desc.size()), desc.data(), 0, nullptr, &oenv))
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).
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;
113 const char *env = getenv("GMX_GPU_ID");
116 if (!hw_opt.gpuIdsAvailable.empty())
118 gmx_fatal(FARGS, "GMX_GPU_ID and -gpu_id can not be used at the same time");
120 hw_opt.gpuIdsAvailable = env;
123 env = getenv("GMX_GPUTASKS");
126 if (!hw_opt.userGpuTaskAssignment.empty())
128 gmx_fatal(FARGS, "GMX_GPUTASKS and -gputasks can not be used at the same time");
130 hw_opt.userGpuTaskAssignment = env;
133 if (!hw_opt.gpuIdsAvailable.empty() && !hw_opt.userGpuTaskAssignment.empty())
135 gmx_fatal(FARGS, "-gpu_id and -gputasks cannot be used at the same time");
139 hw_opt.thread_affinity = nenum(thread_aff_opt_choices);
141 // now check for a multi-simulation
142 ArrayRef<const std::string> multidir = opt2fnsIfOptionSet("-multidir",
143 static_cast<int>(filenames.size()),
146 if (replExParams.exchangeInterval != 0 && multidir.size() < 2)
148 gmx_fatal(FARGS, "Need at least two replicas for replica exchange (use option -multidir)");
151 if (replExParams.numExchanges < 0)
153 gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
156 ms = init_multisystem(MPI_COMM_WORLD, multidir);
158 /* Prepare the intra-simulation communication */
159 // TODO consolidate this with init_commrec, after changing the
160 // relative ordering of init_commrec and init_multisystem
164 cr->nnodes = cr->nnodes / ms->nsim;
165 MPI_Comm_split(MPI_COMM_WORLD, ms->sim, cr->sim_nodeid, &cr->mpi_comm_mysim);
166 cr->mpi_comm_mygroup = cr->mpi_comm_mysim;
167 MPI_Comm_rank(cr->mpi_comm_mysim, &cr->sim_nodeid);
168 MPI_Comm_rank(cr->mpi_comm_mygroup, &cr->nodeid);
172 if (!opt2bSet("-cpi",
173 static_cast<int>(filenames.size()), filenames.data()))
175 // If we are not starting from a checkpoint we never allow files to be appended
176 // to, since that has caused a ton of strange behaviour and bugs in the past.
177 if (opt2parg_bSet("-append", asize(pa), pa))
179 // If the user explicitly used the -append option, explain that it is not possible.
180 gmx_fatal(FARGS, "GROMACS can only append to files when restarting from a checkpoint.");
184 // If the user did not say anything explicit, just disable appending.
185 bTryToAppendFiles = FALSE;
189 ContinuationOptions &continuationOptions = mdrunOptions.continuationOptions;
191 continuationOptions.appendFilesOptionSet = opt2parg_bSet("-append", asize(pa), pa);
193 handleRestart(cr, ms, bTryToAppendFiles,
194 static_cast<int>(filenames.size()),
196 &continuationOptions.appendFiles,
197 &continuationOptions.startedFromCheckpoint);
199 mdrunOptions.rerun = opt2bSet("-rerun",
200 static_cast<int>(filenames.size()),
202 mdrunOptions.ntompOptionIsSet = opt2parg_bSet("-ntomp", asize(pa), pa);
204 domdecOptions.rankOrder = static_cast<DdRankOrder>(nenum(ddrank_opt_choices));
205 domdecOptions.dlbOption = static_cast<DlbOption>(nenum(dddlb_opt_choices));
206 domdecOptions.numCells[XX] = roundToInt(realddxyz[XX]);
207 domdecOptions.numCells[YY] = roundToInt(realddxyz[YY]);
208 domdecOptions.numCells[ZZ] = roundToInt(realddxyz[ZZ]);
213 LegacyMdrunOptions::~LegacyMdrunOptions()
219 output_env_done(oenv);