Add dynamic pair-list pruning framework

[alexxy/gromacs.git] / src / programs / mdrun / runner.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
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 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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/*! \internal \file
 *
 * \brief Implements the MD runner routine calling all integrators.
 *
 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
 * \ingroup module_mdlib
 */
#include "gmxpre.h"

#include "runner.h"

#include "config.h"

#include <assert.h>
#include <signal.h>
#include <stdlib.h>
#include <string.h>

#include <algorithm>

#include "gromacs/commandline/filenm.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/fileio/checkpoint.h"
#include "gromacs/fileio/oenv.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/hardware/cpuinfo.h"
#include "gromacs/hardware/detecthardware.h"
#include "gromacs/hardware/hardwareassign.h"
#include "gromacs/hardware/printhardware.h"
#include "gromacs/listed-forces/disre.h"
#include "gromacs/listed-forces/orires.h"
#include "gromacs/math/calculate-ewald-splitting-coefficient.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/calc_verletbuf.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/integrator.h"
#include "gromacs/mdlib/main.h"
#include "gromacs/mdlib/md_support.h"
#include "gromacs/mdlib/mdatoms.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/minimize.h"
#include "gromacs/mdlib/nbnxn_search.h"
#include "gromacs/mdlib/qmmm.h"
#include "gromacs/mdlib/sighandler.h"
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdlib/tpi.h"
#include "gromacs/mdrunutility/mdmodules.h"
#include "gromacs/mdrunutility/threadaffinity.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/edsamhistory.h"
#include "gromacs/mdtypes/energyhistory.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/observableshistory.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/mdtypes/swaphistory.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/pulling/pull_rotation.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/trajectory/trajectoryframe.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/logger.h"
#include "gromacs/utility/loggerbuilder.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"

#include "deform.h"
#include "md.h"
#include "membed.h"
#include "repl_ex.h"
#include "resource-division.h"

#ifdef GMX_FAHCORE
#include "corewrap.h"
#endif

//! First step used in pressure scaling
gmx_int64_t         deform_init_init_step_tpx;
//! Initial box for pressure scaling
matrix              deform_init_box_tpx;
//! MPI variable for use in pressure scaling
tMPI_Thread_mutex_t deform_init_box_mutex = TMPI_THREAD_MUTEX_INITIALIZER;

#if GMX_THREAD_MPI
/* The minimum number of atoms per tMPI thread. With fewer atoms than this,
 * the number of threads will get lowered.
 */
#define MIN_ATOMS_PER_MPI_THREAD    90
#define MIN_ATOMS_PER_GPU           900

namespace gmx
{

void Mdrunner::reinitializeOnSpawnedThread()
{
    // TODO This duplication is formally necessary if any thread might
    // modify any memory in fnm or the pointers it contains. If the
    // contents are ever provably const, then we can remove this
    // allocation (and memory leak).
    // TODO This should probably become part of a copy constructor for
    // Mdrunner.
    fnm = dup_tfn(nfile, fnm);

    cr  = reinitialize_commrec_for_this_thread(cr);

    if (!MASTER(cr))
    {
        // Only the master rank writes to the log files
        fplog = nullptr;
    }
}

/*! \brief The callback used for running on spawned threads.
 *
 * Obtains the pointer to the master mdrunner object from the one
 * argument permitted to the thread-launch API call, copies it to make
 * a new runner for this thread, reinitializes necessary data, and
 * proceeds to the simulation. */
static void mdrunner_start_fn(void *arg)
{
    try
    {
        auto masterMdrunner = reinterpret_cast<const gmx::Mdrunner *>(arg);
        /* copy the arg list to make sure that it's thread-local. This
           doesn't copy pointed-to items, of course, but those are all
           const. */
        gmx::Mdrunner mdrunner = *masterMdrunner;
        mdrunner.reinitializeOnSpawnedThread();
        mdrunner.mdrunner();
    }
    GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}


/*! \brief Start thread-MPI threads.
 *
 * Called by mdrunner() to start a specific number of threads
 * (including the main thread) for thread-parallel runs. This in turn
 * calls mdrunner() for each thread. All options are the same as for
 * mdrunner(). */
t_commrec *Mdrunner::spawnThreads(int numThreadsToLaunch)
{

    /* first check whether we even need to start tMPI */
    if (numThreadsToLaunch < 2)
    {
        return cr;
    }

    gmx::Mdrunner spawnedMdrunner = *this;
    // TODO This duplication is formally necessary if any thread might
    // modify any memory in fnm or the pointers it contains. If the
    // contents are ever provably const, then we can remove this
    // allocation (and memory leak).
    // TODO This should probably become part of a copy constructor for
    // Mdrunner.
    spawnedMdrunner.fnm = dup_tfn(this->nfile, fnm);

    /* now spawn new threads that start mdrunner_start_fn(), while
       the main thread returns, we set thread affinity later */
    if (tMPI_Init_fn(TRUE, numThreadsToLaunch, TMPI_AFFINITY_NONE,
                     mdrunner_start_fn, static_cast<void*>(&spawnedMdrunner)) != TMPI_SUCCESS)
    {
        GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
    }

    return reinitialize_commrec_for_this_thread(cr);
}

}      // namespace

#endif /* GMX_THREAD_MPI */


/*! \brief Cost of non-bonded kernels
 *
 * We determine the extra cost of the non-bonded kernels compared to
 * a reference nstlist value of 10 (which is the default in grompp).
 */
static const int    nbnxnReferenceNstlist = 10;
//! The values to try when switching
const int           nstlist_try[] = { 20, 25, 40 };
//! Number of elements in the neighborsearch list trials.
#define NNSTL  sizeof(nstlist_try)/sizeof(nstlist_try[0])
/* Increase nstlist until the non-bonded cost increases more than listfac_ok,
 * but never more than listfac_max.
 * A standard (protein+)water system at 300K with PME ewald_rtol=1e-5
 * needs 1.28 at rcoulomb=0.9 and 1.24 at rcoulomb=1.0 to get to nstlist=40.
 * Note that both CPU and GPU factors are conservative. Performance should
 * not go down due to this tuning, except with a relatively slow GPU.
 * On the other hand, at medium/high parallelization or with fast GPUs
 * nstlist will not be increased enough to reach optimal performance.
 */
/* CPU: pair-search is about a factor 1.5 slower than the non-bonded kernel */
//! Max OK performance ratio beween force calc and neighbor searching
static const float  nbnxn_cpu_listfac_ok    = 1.05;
//! Too high performance ratio beween force calc and neighbor searching
static const float  nbnxn_cpu_listfac_max   = 1.09;
/* CPU: pair-search is about a factor 2-3 slower than the non-bonded kernel */
//! Max OK performance ratio beween force calc and neighbor searching
static const float  nbnxn_knl_listfac_ok    = 1.22;
//! Too high performance ratio beween force calc and neighbor searching
static const float  nbnxn_knl_listfac_max   = 1.3;
/* GPU: pair-search is a factor 1.5-3 slower than the non-bonded kernel */
//! Max OK performance ratio beween force calc and neighbor searching
static const float  nbnxn_gpu_listfac_ok    = 1.20;
//! Too high performance ratio beween force calc and neighbor searching
static const float  nbnxn_gpu_listfac_max   = 1.30;

/*! \brief Try to increase nstlist when using the Verlet cut-off scheme */
static void increase_nstlist(FILE *fp, t_commrec *cr,
                             t_inputrec *ir, int nstlist_cmdline,
                             const gmx_mtop_t *mtop, matrix box,
                             bool makeGpuPairList, const gmx::CpuInfo &cpuinfo)
{
    float                  listfac_ok, listfac_max;
    int                    nstlist_orig, nstlist_prev;
    verletbuf_list_setup_t ls;
    real                   rlistWithReferenceNstlist, rlist_inc, rlist_ok, rlist_max;
    real                   rlist_new, rlist_prev;
    size_t                 nstlist_ind = 0;
    gmx_bool               bBox, bDD, bCont;
    const char            *nstl_gpu = "\nFor optimal performance with a GPU nstlist (now %d) should be larger.\nThe optimum depends on your CPU and GPU resources.\nYou might want to try several nstlist values.\n";
    const char            *nve_err  = "Can not increase nstlist because an NVE ensemble is used";
    const char            *vbd_err  = "Can not increase nstlist because verlet-buffer-tolerance is not set or used";
    const char            *box_err  = "Can not increase nstlist because the box is too small";
    const char            *dd_err   = "Can not increase nstlist because of domain decomposition limitations";
    char                   buf[STRLEN];

    if (nstlist_cmdline <= 0)
    {
        if (ir->nstlist == 1)
        {
            /* The user probably set nstlist=1 for a reason,
             * don't mess with the settings.
             */
            return;
        }

        if (fp != nullptr && makeGpuPairList && ir->nstlist < nstlist_try[0])
        {
            fprintf(fp, nstl_gpu, ir->nstlist);
        }
        nstlist_ind = 0;
        while (nstlist_ind < NNSTL && ir->nstlist >= nstlist_try[nstlist_ind])
        {
            nstlist_ind++;
        }
        if (nstlist_ind == NNSTL)
        {
            /* There are no larger nstlist value to try */
            return;
        }
    }

    if (EI_MD(ir->eI) && ir->etc == etcNO)
    {
        if (MASTER(cr))
        {
            fprintf(stderr, "%s\n", nve_err);
        }
        if (fp != nullptr)
        {
            fprintf(fp, "%s\n", nve_err);
        }

        return;
    }

    if (ir->verletbuf_tol == 0 && makeGpuPairList)
    {
        gmx_fatal(FARGS, "You are using an old tpr file with a GPU, please generate a new tpr file with an up to date version of grompp");
    }

    if (ir->verletbuf_tol < 0)
    {
        if (MASTER(cr))
        {
            fprintf(stderr, "%s\n", vbd_err);
        }
        if (fp != nullptr)
        {
            fprintf(fp, "%s\n", vbd_err);
        }

        return;
    }

    if (makeGpuPairList)
    {
        listfac_ok  = nbnxn_gpu_listfac_ok;
        listfac_max = nbnxn_gpu_listfac_max;
    }
    else if (cpuinfo.feature(gmx::CpuInfo::Feature::X86_Avx512ER))
    {
        listfac_ok  = nbnxn_knl_listfac_ok;
        listfac_max = nbnxn_knl_listfac_max;
    }
    else
    {
        listfac_ok  = nbnxn_cpu_listfac_ok;
        listfac_max = nbnxn_cpu_listfac_max;
    }

    nstlist_orig = ir->nstlist;
    if (nstlist_cmdline > 0)
    {
        if (fp)
        {
            sprintf(buf, "Getting nstlist=%d from command line option",
                    nstlist_cmdline);
        }
        ir->nstlist = nstlist_cmdline;
    }

    verletbuf_get_list_setup(true, makeGpuPairList, &ls);

    /* Allow rlist to make the list a given factor larger than the list
     * would be with the reference value for nstlist (10).
     */
    nstlist_prev = ir->nstlist;
    ir->nstlist  = nbnxnReferenceNstlist;
    calc_verlet_buffer_size(mtop, det(box), ir, ir->nstlist, ir->nstlist - 1,
                            -1, &ls, nullptr, &rlistWithReferenceNstlist);
    ir->nstlist  = nstlist_prev;

    /* Determine the pair list size increase due to zero interactions */
    rlist_inc = nbnxn_get_rlist_effective_inc(ls.cluster_size_j,
                                              mtop->natoms/det(box));
    rlist_ok  = (rlistWithReferenceNstlist + rlist_inc)*std::cbrt(listfac_ok) - rlist_inc;
    rlist_max = (rlistWithReferenceNstlist + rlist_inc)*std::cbrt(listfac_max) - rlist_inc;
    if (debug)
    {
        fprintf(debug, "nstlist tuning: rlist_inc %.3f rlist_ok %.3f rlist_max %.3f\n",
                rlist_inc, rlist_ok, rlist_max);
    }

    nstlist_prev = nstlist_orig;
    rlist_prev   = ir->rlist;
    do
    {
        if (nstlist_cmdline <= 0)
        {
            ir->nstlist = nstlist_try[nstlist_ind];
        }

        /* Set the pair-list buffer size in ir */
        calc_verlet_buffer_size(mtop, det(box), ir, ir->nstlist, ir->nstlist - 1, -1, &ls, nullptr, &rlist_new);

        /* Does rlist fit in the box? */
        bBox = (gmx::square(rlist_new) < max_cutoff2(ir->ePBC, box));
        bDD  = TRUE;
        if (bBox && DOMAINDECOMP(cr))
        {
            /* Check if rlist fits in the domain decomposition */
            if (inputrec2nboundeddim(ir) < DIM)
            {
                gmx_incons("Changing nstlist with domain decomposition and unbounded dimensions is not implemented yet");
            }
            t_state state_tmp;
            copy_mat(box, state_tmp.box);
            bDD = change_dd_cutoff(cr, &state_tmp, ir, rlist_new);
        }

        if (debug)
        {
            fprintf(debug, "nstlist %d rlist %.3f bBox %d bDD %d\n",
                    ir->nstlist, rlist_new, bBox, bDD);
        }

        bCont = FALSE;

        if (nstlist_cmdline <= 0)
        {
            if (bBox && bDD && rlist_new <= rlist_max)
            {
                /* Increase nstlist */
                nstlist_prev = ir->nstlist;
                rlist_prev   = rlist_new;
                bCont        = (nstlist_ind+1 < NNSTL && rlist_new < rlist_ok);
            }
            else
            {
                /* Stick with the previous nstlist */
                ir->nstlist = nstlist_prev;
                rlist_new   = rlist_prev;
                bBox        = TRUE;
                bDD         = TRUE;
            }
        }

        nstlist_ind++;
    }
    while (bCont);

    if (!bBox || !bDD)
    {
        gmx_warning(!bBox ? box_err : dd_err);
        if (fp != nullptr)
        {
            fprintf(fp, "\n%s\n", bBox ? box_err : dd_err);
        }
        ir->nstlist = nstlist_orig;
    }
    else if (ir->nstlist != nstlist_orig || rlist_new != ir->rlist)
    {
        sprintf(buf, "Changing nstlist from %d to %d, rlist from %g to %g",
                nstlist_orig, ir->nstlist,
                ir->rlist, rlist_new);
        if (MASTER(cr))
        {
            fprintf(stderr, "%s\n\n", buf);
        }
        if (fp != nullptr)
        {
            fprintf(fp, "%s\n\n", buf);
        }
        ir->rlist     = rlist_new;
    }
}

/*! \brief Initialize variables for Verlet scheme simulation */
static void prepare_verlet_scheme(FILE                           *fplog,
                                  t_commrec                      *cr,
                                  t_inputrec                     *ir,
                                  int                             nstlist_cmdline,
                                  const gmx_mtop_t               *mtop,
                                  matrix                          box,
                                  bool                            makeGpuPairList,
                                  const gmx::CpuInfo             &cpuinfo)
{
    /* For NVE simulations, we will retain the initial list buffer */
    if (EI_DYNAMICS(ir->eI) &&
        ir->verletbuf_tol > 0 &&
        !(EI_MD(ir->eI) && ir->etc == etcNO))
    {
        /* Update the Verlet buffer size for the current run setup */
        verletbuf_list_setup_t ls;
        real                   rlist_new;

        /* Here we assume SIMD-enabled kernels are being used. But as currently
         * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
         * and 4x2 gives a larger buffer than 4x4, this is ok.
         */
        verletbuf_get_list_setup(true, makeGpuPairList, &ls);

        calc_verlet_buffer_size(mtop, det(box), ir, ir->nstlist, ir->nstlist - 1, -1, &ls, nullptr, &rlist_new);

        if (rlist_new != ir->rlist)
        {
            if (fplog != nullptr)
            {
                fprintf(fplog, "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
                        ir->rlist, rlist_new,
                        ls.cluster_size_i, ls.cluster_size_j);
            }
            ir->rlist     = rlist_new;
        }
    }

    if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
    {
        gmx_fatal(FARGS, "Can not set nstlist without %s",
                  !EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
    }

    if (EI_DYNAMICS(ir->eI))
    {
        /* Set or try nstlist values */
        increase_nstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, makeGpuPairList, cpuinfo);
    }
}

/*! \brief Override the nslist value in inputrec
 *
 * with value passed on the command line (if any)
 */
static void override_nsteps_cmdline(const gmx::MDLogger &mdlog,
                                    gmx_int64_t          nsteps_cmdline,
                                    t_inputrec          *ir)
{
    assert(ir);

    /* override with anything else than the default -2 */
    if (nsteps_cmdline > -2)
    {
        char sbuf_steps[STEPSTRSIZE];
        char sbuf_msg[STRLEN];

        ir->nsteps = nsteps_cmdline;
        if (EI_DYNAMICS(ir->eI) && nsteps_cmdline != -1)
        {
            sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
                    gmx_step_str(nsteps_cmdline, sbuf_steps),
                    fabs(nsteps_cmdline*ir->delta_t));
        }
        else
        {
            sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps",
                    gmx_step_str(nsteps_cmdline, sbuf_steps));
        }

        GMX_LOG(mdlog.warning).asParagraph().appendText(sbuf_msg);
    }
    else if (nsteps_cmdline < -2)
    {
        gmx_fatal(FARGS, "Invalid nsteps value passed on the command line: %d",
                  nsteps_cmdline);
    }
    /* Do nothing if nsteps_cmdline == -2 */
}

namespace gmx
{

//! Halt the run if there are inconsistences between user choices to run with GPUs and/or hardware detection.
static void exitIfCannotForceGpuRun(bool requirePhysicalGpu,
                                    bool emulateGpu,
                                    bool useVerletScheme,
                                    bool compatibleGpusFound)
{
    /* Was GPU acceleration either explicitly (-nb gpu) or implicitly
     * (gpu ID passed) requested? */
    if (!requirePhysicalGpu)
    {
        return;
    }

    if (GMX_GPU == GMX_GPU_NONE)
    {
        gmx_fatal(FARGS, "GPU acceleration requested, but %s was compiled without GPU support!",
                  gmx::getProgramContext().displayName());
    }

    if (emulateGpu)
    {
        gmx_fatal(FARGS, "GPU emulation cannot be requested together with GPU acceleration!");
    }

    if (!useVerletScheme)
    {
        gmx_fatal(FARGS, "GPU acceleration requested, but can't be used without cutoff-scheme=Verlet");
    }

    if (!compatibleGpusFound)
    {
        gmx_fatal(FARGS, "GPU acceleration requested, but no compatible GPUs were detected.");
    }
}

/*! \brief Return whether GPU acceleration is useful with the given settings.
 *
 * If not, logs a message about falling back to CPU code. */
static bool gpuAccelerationIsUseful(const MDLogger   &mdlog,
                                    const t_inputrec *ir,
                                    bool              doRerun)
{
    if (doRerun && ir->opts.ngener > 1)
    {
        /* Rerun execution time is dominated by I/O and pair search,
         * so GPUs are not very useful, plus they do not support more
         * than one energy group. If the user requested GPUs
         * explicitly, a fatal error is given later.  With non-reruns,
         * we fall back to a single whole-of system energy group
         * (which runs much faster than a multiple-energy-groups
         * implementation would), and issue a note in the .log
         * file. Users can re-run if they want the information. */
        GMX_LOG(mdlog.warning).asParagraph().appendText("Multiple energy groups is not implemented for GPUs, so is not useful for this rerun, so falling back to the CPU");
        return false;
    }

    return true;
}

//! \brief Return the correct integrator function.
static integrator_t *my_integrator(unsigned int ei)
{
    switch (ei)
    {
        case eiMD:
        case eiBD:
        case eiSD1:
        case eiVV:
        case eiVVAK:
            if (!EI_DYNAMICS(ei))
            {
                GMX_THROW(APIError("do_md integrator would be called for a non-dynamical integrator"));
            }
            return do_md;
        case eiSteep:
            return do_steep;
        case eiCG:
            return do_cg;
        case eiNM:
            return do_nm;
        case eiLBFGS:
            return do_lbfgs;
        case eiTPI:
        case eiTPIC:
            if (!EI_TPI(ei))
            {
                GMX_THROW(APIError("do_tpi integrator would be called for a non-TPI integrator"));
            }
            return do_tpi;
        case eiSD2_REMOVED:
            GMX_THROW(NotImplementedError("SD2 integrator has been removed"));
        default:
            GMX_THROW(APIError("Non existing integrator selected"));
    }
}

//! Initializes the logger for mdrun.
static gmx::LoggerOwner buildLogger(FILE *fplog, const t_commrec *cr)
{
    gmx::LoggerBuilder builder;
    if (fplog != nullptr)
    {
        builder.addTargetFile(gmx::MDLogger::LogLevel::Info, fplog);
    }
    if (cr == nullptr || SIMMASTER(cr))
    {
        builder.addTargetStream(gmx::MDLogger::LogLevel::Warning,
                                &gmx::TextOutputFile::standardError());
    }
    return builder.build();
}

int Mdrunner::mdrunner()
{
    matrix                    box;
    gmx_ddbox_t               ddbox = {0};
    int                       npme_major, npme_minor;
    t_nrnb                   *nrnb;
    gmx_mtop_t               *mtop          = nullptr;
    t_mdatoms                *mdatoms       = nullptr;
    t_forcerec               *fr            = nullptr;
    t_fcdata                 *fcd           = nullptr;
    real                      ewaldcoeff_q  = 0;
    real                      ewaldcoeff_lj = 0;
    struct gmx_pme_t        **pmedata       = nullptr;
    gmx_vsite_t              *vsite         = nullptr;
    gmx_constr_t              constr;
    int                       nChargePerturbed = -1, nTypePerturbed = 0, status;
    gmx_wallcycle_t           wcycle;
    gmx_walltime_accounting_t walltime_accounting = nullptr;
    int                       rc;
    gmx_int64_t               reset_counters;
    int                       nthreads_pme = 1;
    gmx_membed_t *            membed       = nullptr;
    gmx_hw_info_t            *hwinfo       = nullptr;

    /* CAUTION: threads may be started later on in this function, so
       cr doesn't reflect the final parallel state right now */
    gmx::MDModules mdModules;
    t_inputrec     inputrecInstance;
    t_inputrec    *inputrec = &inputrecInstance;
    snew(mtop, 1);

    if (Flags & MD_APPENDFILES)
    {
        fplog = nullptr;
    }

    bool doMembed = opt2bSet("-membed", nfile, fnm);
    bool doRerun  = (Flags & MD_RERUN);

    /* Handle GPU-related user options. Later, we check consistency
     * with things like whether support is compiled, or tMPI thread
     * count. */
    bool emulateGpu            = getenv("GMX_EMULATE_GPU") != nullptr;
    bool forceUseCpu           = (strncmp(nbpu_opt, "cpu", 3) == 0);
    if (!hw_opt.gpuIdTaskAssignment.empty() && forceUseCpu)
    {
        gmx_fatal(FARGS, "GPU IDs were specified, and short-ranged interactions were assigned to the CPU. Make no more than one of these choices.");
    }
    bool forceUsePhysicalGpu = (strncmp(nbpu_opt, "gpu", 3) == 0) || !hw_opt.gpuIdTaskAssignment.empty();
    bool tryUsePhysicalGpu   = (strncmp(nbpu_opt, "auto", 4) == 0) && !emulateGpu && (GMX_GPU != GMX_GPU_NONE);

    // Here we assume that SIMMASTER(cr) does not change even after the
    // threads are started.
    gmx::LoggerOwner logOwner(buildLogger(fplog, cr));
    gmx::MDLogger    mdlog(logOwner.logger());

    /* Detect hardware, gather information. This is an operation that is
     * global for this process (MPI rank). */
    bool detectGpus = forceUsePhysicalGpu || tryUsePhysicalGpu;
    hwinfo = gmx_detect_hardware(mdlog, cr, detectGpus);

    gmx_print_detected_hardware(fplog, cr, mdlog, hwinfo);

    if (fplog != nullptr)
    {
        /* Print references after all software/hardware printing */
        please_cite(fplog, "Abraham2015");
        please_cite(fplog, "Pall2015");
        please_cite(fplog, "Pronk2013");
        please_cite(fplog, "Hess2008b");
        please_cite(fplog, "Spoel2005a");
        please_cite(fplog, "Lindahl2001a");
        please_cite(fplog, "Berendsen95a");
    }

    std::unique_ptr<t_state> stateInstance = std::unique_ptr<t_state>(new t_state);
    t_state *                state         = stateInstance.get();

    if (SIMMASTER(cr))
    {
        /* Read (nearly) all data required for the simulation */
        read_tpx_state(ftp2fn(efTPR, nfile, fnm), inputrec, state, mtop);

        exitIfCannotForceGpuRun(forceUsePhysicalGpu,
                                emulateGpu,
                                inputrec->cutoff_scheme == ecutsVERLET,
                                compatibleGpusFound(hwinfo->gpu_info));

        if (inputrec->cutoff_scheme == ecutsVERLET)
        {
            /* TODO This logic could run later, e.g. before -npme -1
               is handled. If inputrec has already been communicated,
               then the resulting tryUsePhysicalGpu does not need to
               be communicated. */
            if ((tryUsePhysicalGpu || forceUsePhysicalGpu) &&
                !gpuAccelerationIsUseful(mdlog, inputrec, doRerun))
            {
                /* Fallback message printed by nbnxn_acceleration_supported */
                if (forceUsePhysicalGpu)
                {
                    gmx_fatal(FARGS, "GPU acceleration requested, but not supported with the given input settings");
                }
                tryUsePhysicalGpu = false;
            }
            /* TODO This logic could run later, e.g. after inputrec,
               mtop, and state have been communicated, but before DD
               is initialized. In particular, -ntmpi 0 only needs to
               know whether the Verlet scheme is active in order to
               choose the number of ranks (because GPUs might be
               usable).*/
            bool makeGpuPairList = (forceUsePhysicalGpu ||
                                    tryUsePhysicalGpu ||
                                    emulateGpu);
            prepare_verlet_scheme(fplog, cr,
                                  inputrec, nstlist_cmdline, mtop, state->box,
                                  makeGpuPairList, *hwinfo->cpuInfo);
        }
        else
        {
            if (nstlist_cmdline > 0)
            {
                gmx_fatal(FARGS, "Can not set nstlist with the group cut-off scheme");
            }

            if (compatibleGpusFound(hwinfo->gpu_info))
            {
                GMX_LOG(mdlog.warning).asParagraph().appendText(
                        "NOTE: GPU(s) found, but the current simulation can not use GPUs\n"
                        "      To use a GPU, set the mdp option: cutoff-scheme = Verlet");
                tryUsePhysicalGpu = false;
            }

#if GMX_TARGET_BGQ
            md_print_warn(cr, fplog,
                          "NOTE: There is no SIMD implementation of the group scheme kernels on\n"
                          "      BlueGene/Q. You will observe better performance from using the\n"
                          "      Verlet cut-off scheme.\n");
#endif
        }
    }

    /* Check and update the hardware options for internal consistency */
    check_and_update_hw_opt_1(&hw_opt, cr, npme);

    /* Early check for externally set process affinity. */
    gmx_check_thread_affinity_set(mdlog, cr,
                                  &hw_opt, hwinfo->nthreads_hw_avail, FALSE);

#if GMX_THREAD_MPI
    if (SIMMASTER(cr))
    {
        if (npme > 0 && hw_opt.nthreads_tmpi <= 0)
        {
            gmx_fatal(FARGS, "You need to explicitly specify the number of MPI threads (-ntmpi) when using separate PME ranks");
        }

        /* Since the master knows the cut-off scheme, update hw_opt for this.
         * This is done later for normal MPI and also once more with tMPI
         * for all tMPI ranks.
         */
        check_and_update_hw_opt_2(&hw_opt, inputrec->cutoff_scheme);

        // Determine how many thread-MPI ranks to start.
        hw_opt.nthreads_tmpi = get_nthreads_mpi(hwinfo,
                                                &hw_opt,
                                                inputrec, mtop,
                                                mdlog,
                                                doMembed);

        // Now start the threads for thread MPI.
        cr = spawnThreads(hw_opt.nthreads_tmpi);
        /* The main thread continues here with a new cr. We don't deallocate
           the old cr because other threads may still be reading it. */
        // TODO Both master and spawned threads call dup_tfn and
        // reinitialize_commrec_for_this_thread. Find a way to express
        // this better.
    }
#endif
    /* END OF CAUTION: cr is now reliable */

    if (PAR(cr))
    {
        /* now broadcast everything to the non-master nodes/threads: */
        init_parallel(cr, inputrec, mtop);

        gmx_bcast_sim(sizeof(tryUsePhysicalGpu), &tryUsePhysicalGpu, cr);
    }
    // TODO: Error handling
    mdModules.assignOptionsToModules(*inputrec->params, nullptr);

    if (fplog != nullptr)
    {
        pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
        fprintf(fplog, "\n");
    }

    /* now make sure the state is initialized and propagated */
    set_state_entries(state, inputrec);

    /* A parallel command line option consistency check that we can
       only do after any threads have started. */
    if (!PAR(cr) &&
        (ddxyz[XX] > 1 || ddxyz[YY] > 1 || ddxyz[ZZ] > 1 || npme > 0))
    {
        gmx_fatal(FARGS,
                  "The -dd or -npme option request a parallel simulation, "
#if !GMX_MPI
                  "but %s was compiled without threads or MPI enabled"
#else
#if GMX_THREAD_MPI
                  "but the number of MPI-threads (option -ntmpi) is not set or is 1"
#else
                  "but %s was not started through mpirun/mpiexec or only one rank was requested through mpirun/mpiexec"
#endif
#endif
                  , output_env_get_program_display_name(oenv)
                  );
    }

    if (doRerun &&
        (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
    {
        gmx_fatal(FARGS, "The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun");
    }

    if (can_use_allvsall(inputrec, TRUE, cr, fplog) && DOMAINDECOMP(cr))
    {
        gmx_fatal(FARGS, "All-vs-all loops do not work with domain decomposition, use a single MPI rank");
    }

    if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
    {
        if (npme > 0)
        {
            gmx_fatal_collective(FARGS, cr->mpi_comm_mysim, MASTER(cr),
                                 "PME-only ranks are requested, but the system does not use PME for electrostatics or LJ");
        }

        npme = 0;
    }

    if ((tryUsePhysicalGpu || forceUsePhysicalGpu) && npme < 0)
    {
        /* With GPUs we don't automatically use PME-only ranks. PME ranks can
         * improve performance with many threads per GPU, since our OpenMP
         * scaling is bad, but it's difficult to automate the setup.
         */
        npme = 0;
    }

#ifdef GMX_FAHCORE
    if (MASTER(cr))
    {
        fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
    }
#endif

    /* NMR restraints must be initialized before load_checkpoint,
     * since with time averaging the history is added to t_state.
     * For proper consistency check we therefore need to extend
     * t_state here.
     * So the PME-only nodes (if present) will also initialize
     * the distance restraints.
     */
    snew(fcd, 1);

    /* This needs to be called before read_checkpoint to extend the state */
    init_disres(fplog, mtop, inputrec, cr, fcd, state, replExParams.exchangeInterval > 0);

    init_orires(fplog, mtop, as_rvec_array(state->x.data()), inputrec, cr, &(fcd->orires),
                state);

    if (inputrecDeform(inputrec))
    {
        /* Store the deform reference box before reading the checkpoint */
        if (SIMMASTER(cr))
        {
            copy_mat(state->box, box);
        }
        if (PAR(cr))
        {
            gmx_bcast(sizeof(box), box, cr);
        }
        /* Because we do not have the update struct available yet
         * in which the reference values should be stored,
         * we store them temporarily in static variables.
         * This should be thread safe, since they are only written once
         * and with identical values.
         */
        tMPI_Thread_mutex_lock(&deform_init_box_mutex);
        deform_init_init_step_tpx = inputrec->init_step;
        copy_mat(box, deform_init_box_tpx);
        tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
    }

    ObservablesHistory observablesHistory = {};

    if (Flags & MD_STARTFROMCPT)
    {
        /* Check if checkpoint file exists before doing continuation.
         * This way we can use identical input options for the first and subsequent runs...
         */
        gmx_bool bReadEkin;

        load_checkpoint(opt2fn_master("-cpi", nfile, fnm, cr), &fplog,
                        cr, ddxyz, &npme,
                        inputrec, state, &bReadEkin, &observablesHistory,
                        (Flags & MD_APPENDFILES),
                        (Flags & MD_APPENDFILESSET),
                        (Flags & MD_REPRODUCIBLE));

        if (bReadEkin)
        {
            Flags |= MD_READ_EKIN;
        }
    }

    if (SIMMASTER(cr) && (Flags & MD_APPENDFILES))
    {
        gmx_log_open(ftp2fn(efLOG, nfile, fnm), cr,
                     Flags, &fplog);
        logOwner = buildLogger(fplog, nullptr);
        mdlog    = logOwner.logger();
    }

    /* override nsteps with value from cmdline */
    override_nsteps_cmdline(mdlog, nsteps_cmdline, inputrec);

    if (SIMMASTER(cr))
    {
        copy_mat(state->box, box);
    }

    if (PAR(cr))
    {
        gmx_bcast(sizeof(box), box, cr);
    }

    if (PAR(cr) && !(EI_TPI(inputrec->eI) ||
                     inputrec->eI == eiNM))
    {
        cr->dd = init_domain_decomposition(fplog, cr, Flags, ddxyz, npme,
                                           dd_rank_order,
                                           rdd, rconstr,
                                           dddlb_opt, dlb_scale,
                                           ddcsx, ddcsy, ddcsz,
                                           mtop, inputrec,
                                           box, as_rvec_array(state->x.data()),
                                           &ddbox, &npme_major, &npme_minor);
    }
    else
    {
        /* PME, if used, is done on all nodes with 1D decomposition */
        cr->npmenodes = 0;
        cr->duty      = (DUTY_PP | DUTY_PME);
        npme_major    = 1;
        npme_minor    = 1;

        if (inputrec->ePBC == epbcSCREW)
        {
            gmx_fatal(FARGS,
                      "pbc=%s is only implemented with domain decomposition",
                      epbc_names[inputrec->ePBC]);
        }
    }

    if (PAR(cr))
    {
        /* After possible communicator splitting in make_dd_communicators.
         * we can set up the intra/inter node communication.
         */
        gmx_setup_nodecomm(fplog, cr);
    }

    /* Initialize per-physical-node MPI process/thread ID and counters. */
    gmx_init_intranode_counters(cr);
#if GMX_MPI
    if (MULTISIM(cr))
    {
        GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
                "This is simulation %d out of %d running as a composite GROMACS\n"
                "multi-simulation job. Setup for this simulation:\n",
                cr->ms->sim, cr->ms->nsim);
    }
    GMX_LOG(mdlog.warning).appendTextFormatted(
            "Using %d MPI %s\n",
            cr->nnodes,
#if GMX_THREAD_MPI
            cr->nnodes == 1 ? "thread" : "threads"
#else
            cr->nnodes == 1 ? "process" : "processes"
#endif
            );
    fflush(stderr);
#endif

    /* Check and update hw_opt for the cut-off scheme */
    check_and_update_hw_opt_2(&hw_opt, inputrec->cutoff_scheme);

    /* Check and update hw_opt for the number of MPI ranks */
    check_and_update_hw_opt_3(&hw_opt);

    gmx_omp_nthreads_init(mdlog, cr,
                          hwinfo->nthreads_hw_avail,
                          hw_opt.nthreads_omp,
                          hw_opt.nthreads_omp_pme,
                          (cr->duty & DUTY_PP) == 0,
                          inputrec->cutoff_scheme == ecutsVERLET);

#ifndef NDEBUG
    if (EI_TPI(inputrec->eI) &&
        inputrec->cutoff_scheme == ecutsVERLET)
    {
        gmx_feenableexcept();
    }
#endif

    // Contains the ID of the GPU used by each PP rank on this node,
    // indexed by that rank. Empty if no GPUs are selected for use on
    // this node.
    std::vector<int> gpuTaskAssignment;
    if (tryUsePhysicalGpu || forceUsePhysicalGpu)
    {
        /* Currently the DD code assigns duty to ranks that can
         * include PP work that currently can be executed on a single
         * GPU, if present and compatible.  This has to be coordinated
         * across PP ranks on a node, with possible multiple devices
         * or sharing devices on a node, either from the user
         * selection, or automatically. */
        bool rankCanUseGpu = cr->duty & DUTY_PP;
        gpuTaskAssignment = mapPpRanksToGpus(rankCanUseGpu, cr, hwinfo->gpu_info, hw_opt);
    }

    reportGpuUsage(mdlog, hwinfo->gpu_info, !hw_opt.gpuIdTaskAssignment.empty(),
                   gpuTaskAssignment, cr->nrank_pp_intranode, cr->nnodes > 1);

    /* check consistency across ranks of things like SIMD
     * support and number of GPUs selected */
    gmx_check_hw_runconf_consistency(mdlog, hwinfo, cr, hw_opt, !hw_opt.gpuIdTaskAssignment.empty(), gpuTaskAssignment);

    /* Prevent other ranks from continuing after an inconsistency was found.
     *
     * TODO This function implements a barrier so that MPI runtimes
     * can organize an orderly shutdown if one of the ranks has had to
     * issue a fatal error in various code already run. When we have
     * MPI-aware error handling and reporting, this should be
     * improved. */
#if GMX_MPI
    if (PAR(cr))
    {
        MPI_Barrier(cr->mpi_comm_mysim);
    }
#endif

    /* Now that we know the setup is consistent, check for efficiency */
    check_resource_division_efficiency(hwinfo, hw_opt.nthreads_tot, !gpuTaskAssignment.empty(), Flags & MD_NTOMPSET,
                                       cr, mdlog);

    gmx_device_info_t *shortRangedDeviceInfo = nullptr;
    int                shortRangedDeviceId   = -1;
    if (cr->duty & DUTY_PP)
    {
        if (!gpuTaskAssignment.empty())
        {
            shortRangedDeviceId   = gpuTaskAssignment[cr->rank_pp_intranode];
            shortRangedDeviceInfo = getDeviceInfo(hwinfo->gpu_info, shortRangedDeviceId);
        }
    }

    if (DOMAINDECOMP(cr))
    {
        /* When we share GPUs over ranks, we need to know this for the DLB */
        dd_setup_dlb_resource_sharing(cr, shortRangedDeviceId);
    }

    /* getting number of PP/PME threads
       PME: env variable should be read only on one node to make sure it is
       identical everywhere;
     */
    nthreads_pme = gmx_omp_nthreads_get(emntPME);

    wcycle = wallcycle_init(fplog, resetstep, cr);

    if (PAR(cr))
    {
        /* Master synchronizes its value of reset_counters with all nodes
         * including PME only nodes */
        reset_counters = wcycle_get_reset_counters(wcycle);
        gmx_bcast_sim(sizeof(reset_counters), &reset_counters, cr);
        wcycle_set_reset_counters(wcycle, reset_counters);
    }

    // Membrane embedding must be initialized before we call init_forcerec()
    if (doMembed)
    {
        if (MASTER(cr))
        {
            fprintf(stderr, "Initializing membed");
        }
        /* Note that membed cannot work in parallel because mtop is
         * changed here. Fix this if we ever want to make it run with
         * multiple ranks. */
        membed = init_membed(fplog, nfile, fnm, mtop, inputrec, state, cr, &cpt_period);
    }

    snew(nrnb, 1);
    if (cr->duty & DUTY_PP)
    {
        bcast_state(cr, state);

        /* Initiate forcerecord */
        fr                 = mk_forcerec();
        fr->forceProviders = mdModules.initForceProviders();
        init_forcerec(fplog, mdlog, fr, fcd,
                      inputrec, mtop, cr, box,
                      opt2fn("-table", nfile, fnm),
                      opt2fn("-tablep", nfile, fnm),
                      getFilenm("-tableb", nfile, fnm),
                      nbpu_opt,
                      shortRangedDeviceInfo,
                      FALSE,
                      pforce);

        /* Initialize QM-MM */
        if (fr->bQMMM)
        {
            init_QMMMrec(cr, mtop, inputrec, fr);
        }

        /* Initialize the mdatoms structure.
         * mdatoms is not filled with atom data,
         * as this can not be done now with domain decomposition.
         */
        mdatoms = init_mdatoms(fplog, mtop, inputrec->efep != efepNO);

        /* Initialize the virtual site communication */
        vsite = init_vsite(mtop, cr, FALSE);

        calc_shifts(box, fr->shift_vec);

        /* With periodic molecules the charge groups should be whole at start up
         * and the virtual sites should not be far from their proper positions.
         */
        if (!inputrec->bContinuation && MASTER(cr) &&
            !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
        {
            /* Make molecules whole at start of run */
            if (fr->ePBC != epbcNONE)
            {
                do_pbc_first_mtop(fplog, inputrec->ePBC, box, mtop, as_rvec_array(state->x.data()));
            }
            if (vsite)
            {
                /* Correct initial vsite positions are required
                 * for the initial distribution in the domain decomposition
                 * and for the initial shell prediction.
                 */
                construct_vsites_mtop(vsite, mtop, as_rvec_array(state->x.data()));
            }
        }

        if (EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype))
        {
            ewaldcoeff_q  = fr->ewaldcoeff_q;
            ewaldcoeff_lj = fr->ewaldcoeff_lj;
            pmedata       = &fr->pmedata;
        }
        else
        {
            pmedata = nullptr;
        }
    }
    else
    {
        /* This is a PME only node */

        /* We don't need the state */
        stateInstance.reset();
        state         = nullptr;

        ewaldcoeff_q  = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
        ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
        snew(pmedata, 1);
    }

    if (hw_opt.thread_affinity != threadaffOFF)
    {
        /* Before setting affinity, check whether the affinity has changed
         * - which indicates that probably the OpenMP library has changed it
         * since we first checked).
         */
        gmx_check_thread_affinity_set(mdlog, cr,
                                      &hw_opt, hwinfo->nthreads_hw_avail, TRUE);

        int nthread_local;
        /* threads on this MPI process or TMPI thread */
        if (cr->duty & DUTY_PP)
        {
            nthread_local = gmx_omp_nthreads_get(emntNonbonded);
        }
        else
        {
            nthread_local = gmx_omp_nthreads_get(emntPME);
        }

        /* Set the CPU affinity */
        gmx_set_thread_affinity(mdlog, cr, &hw_opt, *hwinfo->hardwareTopology,
                                nthread_local, nullptr);
    }

    /* Initiate PME if necessary,
     * either on all nodes or on dedicated PME nodes only. */
    if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
    {
        if (mdatoms)
        {
            nChargePerturbed = mdatoms->nChargePerturbed;
            if (EVDW_PME(inputrec->vdwtype))
            {
                nTypePerturbed   = mdatoms->nTypePerturbed;
            }
        }
        if (cr->npmenodes > 0)
        {
            /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
            gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
            gmx_bcast_sim(sizeof(nTypePerturbed), &nTypePerturbed, cr);
        }

        if (cr->duty & DUTY_PME)
        {
            try
            {
                status = gmx_pme_init(pmedata, cr, npme_major, npme_minor, inputrec,
                                      mtop ? mtop->natoms : 0, nChargePerturbed, nTypePerturbed,
                                      (Flags & MD_REPRODUCIBLE),
                                      ewaldcoeff_q, ewaldcoeff_lj,
                                      nthreads_pme);
            }
            GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
            if (status != 0)
            {
                gmx_fatal(FARGS, "Error %d initializing PME", status);
            }
        }
    }


    if (EI_DYNAMICS(inputrec->eI))
    {
        /* Turn on signal handling on all nodes */
        /*
         * (A user signal from the PME nodes (if any)
         * is communicated to the PP nodes.
         */
        signal_handler_install();
    }

    if (cr->duty & DUTY_PP)
    {
        /* Assumes uniform use of the number of OpenMP threads */
        walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));

        if (inputrec->bPull)
        {
            /* Initialize pull code */
            inputrec->pull_work =
                init_pull(fplog, inputrec->pull, inputrec, nfile, fnm,
                          mtop, cr, oenv, inputrec->fepvals->init_lambda,
                          EI_DYNAMICS(inputrec->eI) && MASTER(cr), Flags);
        }

        if (inputrec->bRot)
        {
            /* Initialize enforced rotation code */
            init_rot(fplog, inputrec, nfile, fnm, cr, as_rvec_array(state->x.data()), state->box, mtop, oenv,
                     bVerbose, Flags);
        }

        /* Let init_constraints know whether we have essential dynamics constraints.
         * TODO: inputrec should tell us whether we use an algorithm, not a file option or the checkpoint
         */
        bool doEdsam = (opt2fn_null("-ei", nfile, fnm) != nullptr || observablesHistory.edsamHistory);

        constr = init_constraints(fplog, mtop, inputrec, doEdsam, cr);

        if (DOMAINDECOMP(cr))
        {
            GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
            /* This call is not included in init_domain_decomposition mainly
             * because fr->cginfo_mb is set later.
             */
            dd_init_bondeds(fplog, cr->dd, mtop, vsite, inputrec,
                            Flags & MD_DDBONDCHECK, fr->cginfo_mb);
        }

        /* Now do whatever the user wants us to do (how flexible...) */
        my_integrator(inputrec->eI) (fplog, cr, mdlog, nfile, fnm,
                                     oenv, bVerbose,
                                     nstglobalcomm,
                                     vsite, constr,
                                     nstepout, mdModules.outputProvider(),
                                     inputrec, mtop,
                                     fcd, state, &observablesHistory,
                                     mdatoms, nrnb, wcycle, fr,
                                     replExParams,
                                     membed,
                                     cpt_period, max_hours,
                                     imdport,
                                     Flags,
                                     walltime_accounting);

        if (inputrec->bRot)
        {
            finish_rot(inputrec->rot);
        }

        if (inputrec->bPull)
        {
            finish_pull(inputrec->pull_work);
        }

    }
    else
    {
        GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
        /* do PME only */
        walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
        gmx_pmeonly(*pmedata, cr, nrnb, wcycle, walltime_accounting, ewaldcoeff_q, ewaldcoeff_lj, inputrec);
    }

    wallcycle_stop(wcycle, ewcRUN);

    /* Finish up, write some stuff
     * if rerunMD, don't write last frame again
     */
    finish_run(fplog, mdlog, cr,
               inputrec, nrnb, wcycle, walltime_accounting,
               fr ? fr->nbv : nullptr,
               EI_DYNAMICS(inputrec->eI) && !MULTISIM(cr));

    // Free PME data
    if (pmedata)
    {
        gmx_pme_destroy(*pmedata); // TODO: pmedata is always a single element list, refactor
        pmedata = nullptr;
    }

    /* Free GPU memory and context */
    free_gpu_resources(fr, cr, shortRangedDeviceInfo);

    if (doMembed)
    {
        free_membed(membed);
    }

    gmx_hardware_info_free(hwinfo);

    /* Does what it says */
    print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
    walltime_accounting_destroy(walltime_accounting);

    /* Close logfile already here if we were appending to it */
    if (MASTER(cr) && (Flags & MD_APPENDFILES))
    {
        gmx_log_close(fplog);
    }

    rc = (int)gmx_get_stop_condition();

#if GMX_THREAD_MPI
    /* we need to join all threads. The sub-threads join when they
       exit this function, but the master thread needs to be told to
       wait for that. */
    if (PAR(cr) && MASTER(cr))
    {
        tMPI_Finalize();
    }
#endif

    return rc;
}

} // namespace gmx