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Gromacs
2020.4
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Gromacs
2020.4
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#include "gmxpre.h"#include "runner.h"#include "config.h"#include <cassert>#include <cinttypes>#include <csignal>#include <cstdlib>#include <cstring>#include <algorithm>#include <memory>#include "gromacs/commandline/filenm.h"#include "gromacs/domdec/builder.h"#include "gromacs/domdec/domdec.h"#include "gromacs/domdec/domdec_struct.h"#include "gromacs/domdec/gpuhaloexchange.h"#include "gromacs/domdec/localatomsetmanager.h"#include "gromacs/domdec/partition.h"#include "gromacs/ewald/ewald_utils.h"#include "gromacs/ewald/pme.h"#include "gromacs/ewald/pme_gpu_program.h"#include "gromacs/ewald/pme_pp_comm_gpu.h"#include "gromacs/fileio/checkpoint.h"#include "gromacs/fileio/gmxfio.h"#include "gromacs/fileio/oenv.h"#include "gromacs/fileio/tpxio.h"#include "gromacs/gmxlib/network.h"#include "gromacs/gmxlib/nrnb.h"#include "gromacs/gpu_utils/gpu_utils.h"#include "gromacs/hardware/cpuinfo.h"#include "gromacs/hardware/detecthardware.h"#include "gromacs/hardware/printhardware.h"#include "gromacs/imd/imd.h"#include "gromacs/listed_forces/disre.h"#include "gromacs/listed_forces/gpubonded.h"#include "gromacs/listed_forces/orires.h"#include "gromacs/math/functions.h"#include "gromacs/math/utilities.h"#include "gromacs/math/vec.h"#include "gromacs/mdlib/boxdeformation.h"#include "gromacs/mdlib/broadcaststructs.h"#include "gromacs/mdlib/calc_verletbuf.h"#include "gromacs/mdlib/dispersioncorrection.h"#include "gromacs/mdlib/enerdata_utils.h"#include "gromacs/mdlib/force.h"#include "gromacs/mdlib/forcerec.h"#include "gromacs/mdlib/gmx_omp_nthreads.h"#include "gromacs/mdlib/makeconstraints.h"#include "gromacs/mdlib/md_support.h"#include "gromacs/mdlib/mdatoms.h"#include "gromacs/mdlib/membed.h"#include "gromacs/mdlib/qmmm.h"#include "gromacs/mdlib/sighandler.h"#include "gromacs/mdlib/stophandler.h"#include "gromacs/mdlib/updategroups.h"#include "gromacs/mdrun/mdmodules.h"#include "gromacs/mdrun/simulationcontext.h"#include "gromacs/mdrunutility/handlerestart.h"#include "gromacs/mdrunutility/logging.h"#include "gromacs/mdrunutility/multisim.h"#include "gromacs/mdrunutility/printtime.h"#include "gromacs/mdrunutility/threadaffinity.h"#include "gromacs/mdtypes/commrec.h"#include "gromacs/mdtypes/enerdata.h"#include "gromacs/mdtypes/fcdata.h"#include "gromacs/mdtypes/group.h"#include "gromacs/mdtypes/inputrec.h"#include "gromacs/mdtypes/md_enums.h"#include "gromacs/mdtypes/mdrunoptions.h"#include "gromacs/mdtypes/observableshistory.h"#include "gromacs/mdtypes/simulation_workload.h"#include "gromacs/mdtypes/state.h"#include "gromacs/mdtypes/state_propagator_data_gpu.h"#include "gromacs/nbnxm/gpu_data_mgmt.h"#include "gromacs/nbnxm/nbnxm.h"#include "gromacs/nbnxm/pairlist_tuning.h"#include "gromacs/pbcutil/pbc.h"#include "gromacs/pulling/output.h"#include "gromacs/pulling/pull.h"#include "gromacs/pulling/pull_rotation.h"#include "gromacs/restraint/manager.h"#include "gromacs/restraint/restraintmdmodule.h"#include "gromacs/restraint/restraintpotential.h"#include "gromacs/swap/swapcoords.h"#include "gromacs/taskassignment/decidegpuusage.h"#include "gromacs/taskassignment/decidesimulationworkload.h"#include "gromacs/taskassignment/resourcedivision.h"#include "gromacs/taskassignment/taskassignment.h"#include "gromacs/taskassignment/usergpuids.h"#include "gromacs/timing/gpu_timing.h"#include "gromacs/timing/wallcycle.h"#include "gromacs/timing/wallcyclereporting.h"#include "gromacs/topology/mtop_util.h"#include "gromacs/trajectory/trajectoryframe.h"#include "gromacs/utility/basenetwork.h"#include "gromacs/utility/cstringutil.h"#include "gromacs/utility/exceptions.h"#include "gromacs/utility/fatalerror.h"#include "gromacs/utility/filestream.h"#include "gromacs/utility/gmxassert.h"#include "gromacs/utility/gmxmpi.h"#include "gromacs/utility/keyvaluetree.h"#include "gromacs/utility/logger.h"#include "gromacs/utility/loggerbuilder.h"#include "gromacs/utility/mdmodulenotification.h"#include "gromacs/utility/physicalnodecommunicator.h"#include "gromacs/utility/pleasecite.h"#include "gromacs/utility/programcontext.h"#include "gromacs/utility/smalloc.h"#include "gromacs/utility/stringutil.h"#include "isimulator.h"#include "replicaexchange.h"#include "simulatorbuilder.h"Implements the MD runner routine calling all integrators.
Functions | |
| static DevelopmentFeatureFlags | gmx::manageDevelopmentFeatures (const gmx::MDLogger &mdlog, const bool useGpuForNonbonded, const PmeRunMode pmeRunMode) |
| Manage any development feature flag variables encountered. More... | |
| static void | gmx::threadMpiMdrunnerAccessBarrier () |
| Barrier for safe simultaneous thread access to mdrunner data. More... | |
| static void | gmx::mdrunner_start_fn (const void *arg) |
| The callback used for running on spawned threads. More... | |
| static void | prepare_verlet_scheme (FILE *fplog, t_commrec *cr, t_inputrec *ir, int nstlist_cmdline, const gmx_mtop_t *mtop, const matrix box, bool makeGpuPairList, const gmx::CpuInfo &cpuinfo) |
| Initialize variables for Verlet scheme simulation. | |
| static void | override_nsteps_cmdline (const gmx::MDLogger &mdlog, int64_t nsteps_cmdline, t_inputrec *ir) |
| Override the nslist value in inputrec. More... | |
| static bool | gmx::gpuAccelerationOfNonbondedIsUseful (const MDLogger &mdlog, const t_inputrec &ir, bool issueWarning) |
| Return whether GPU acceleration of nonbondeds is supported with the given settings. More... | |
| static gmx::LoggerOwner | gmx::buildLogger (FILE *fplog, const bool isSimulationMasterRank) |
| Initializes the logger for mdrun. | |
| static TaskTarget | gmx::findTaskTarget (const char *optionString) |
| Make a TaskTarget from an mdrun argument string. | |
| static void | gmx::finish_run (FILE *fplog, const gmx::MDLogger &mdlog, const t_commrec *cr, const t_inputrec *inputrec, t_nrnb nrnb[], gmx_wallcycle_t wcycle, gmx_walltime_accounting_t walltime_accounting, nonbonded_verlet_t *nbv, const gmx_pme_t *pme, gmx_bool bWriteStat) |
| Finish run, aggregate data to print performance info. | |
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static |
Override the nslist value in inputrec.
with value passed on the command line (if any)
1.8.5