--- /dev/null
+/*
+ * 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) 2013,2014,2015,2016,2017,2018, 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.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief This file defines integrators for energy minimization
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \author Erik Lindahl <erik@kth.se>
+ * \ingroup module_mdrun
+ */
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include <cmath>
+#include <cstring>
+#include <ctime>
+
+#include <algorithm>
+#include <vector>
+
+#include "gromacs/commandline/filenm.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/ewald/pme.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/mtxio.h"
+#include "gromacs/gmxlib/network.h"
+#include "gromacs/gmxlib/nrnb.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/listed-forces/manage-threading.h"
+#include "gromacs/math/functions.h"
+#include "gromacs/math/vec.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/md_support.h"
+#include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/mdebin.h"
+#include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdlib/mdsetup.h"
+#include "gromacs/mdlib/ns.h"
+#include "gromacs/mdlib/shellfc.h"
+#include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdlib/tgroup.h"
+#include "gromacs/mdlib/trajectory_writing.h"
+#include "gromacs/mdlib/update.h"
+#include "gromacs/mdlib/vsite.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/logger.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "integrator.h"
+
+//! Utility structure for manipulating states during EM
+typedef struct {
+ //! Copy of the global state
+ t_state s;
+ //! Force array
+ PaddedRVecVector f;
+ //! Potential energy
+ real epot;
+ //! Norm of the force
+ real fnorm;
+ //! Maximum force
+ real fmax;
+ //! Direction
+ int a_fmax;
+} em_state_t;
+
+//! Print the EM starting conditions
+static void print_em_start(FILE *fplog,
+ const t_commrec *cr,
+ gmx_walltime_accounting_t walltime_accounting,
+ gmx_wallcycle_t wcycle,
+ const char *name)
+{
+ walltime_accounting_start(walltime_accounting);
+ wallcycle_start(wcycle, ewcRUN);
+ print_start(fplog, cr, walltime_accounting, name);
+}
+
+//! Stop counting time for EM
+static void em_time_end(gmx_walltime_accounting_t walltime_accounting,
+ gmx_wallcycle_t wcycle)
+{
+ wallcycle_stop(wcycle, ewcRUN);
+
+ walltime_accounting_end(walltime_accounting);
+}
+
+//! Printing a log file and console header
+static void sp_header(FILE *out, const char *minimizer, real ftol, int nsteps)
+{
+ fprintf(out, "\n");
+ fprintf(out, "%s:\n", minimizer);
+ fprintf(out, " Tolerance (Fmax) = %12.5e\n", ftol);
+ fprintf(out, " Number of steps = %12d\n", nsteps);
+}
+
+//! Print warning message
+static void warn_step(FILE *fp,
+ real ftol,
+ real fmax,
+ gmx_bool bLastStep,
+ gmx_bool bConstrain)
+{
+ constexpr bool realIsDouble = GMX_DOUBLE;
+ char buffer[2048];
+
+ if (!std::isfinite(fmax))
+ {
+ sprintf(buffer,
+ "\nEnergy minimization has stopped because the force "
+ "on at least one atom is not finite. This usually means "
+ "atoms are overlapping. Modify the input coordinates to "
+ "remove atom overlap or use soft-core potentials with "
+ "the free energy code to avoid infinite forces.\n%s",
+ !realIsDouble ?
+ "You could also be lucky that switching to double precision "
+ "is sufficient to obtain finite forces.\n" :
+ "");
+ }
+ else if (bLastStep)
+ {
+ sprintf(buffer,
+ "\nEnergy minimization reached the maximum number "
+ "of steps before the forces reached the requested "
+ "precision Fmax < %g.\n", ftol);
+ }
+ else
+ {
+ sprintf(buffer,
+ "\nEnergy minimization has stopped, but the forces have "
+ "not converged to the requested precision Fmax < %g (which "
+ "may not be possible for your system). It stopped "
+ "because the algorithm tried to make a new step whose size "
+ "was too small, or there was no change in the energy since "
+ "last step. Either way, we regard the minimization as "
+ "converged to within the available machine precision, "
+ "given your starting configuration and EM parameters.\n%s%s",
+ ftol,
+ !realIsDouble ?
+ "\nDouble precision normally gives you higher accuracy, but "
+ "this is often not needed for preparing to run molecular "
+ "dynamics.\n" :
+ "",
+ bConstrain ?
+ "You might need to increase your constraint accuracy, or turn\n"
+ "off constraints altogether (set constraints = none in mdp file)\n" :
+ "");
+ }
+
+ fputs(wrap_lines(buffer, 78, 0, FALSE), stderr);
+ fputs(wrap_lines(buffer, 78, 0, FALSE), fp);
+}
+
+//! Print message about convergence of the EM
+static void print_converged(FILE *fp, const char *alg, real ftol,
+ gmx_int64_t count, gmx_bool bDone, gmx_int64_t nsteps,
+ const em_state_t *ems, double sqrtNumAtoms)
+{
+ char buf[STEPSTRSIZE];
+
+ if (bDone)
+ {
+ fprintf(fp, "\n%s converged to Fmax < %g in %s steps\n",
+ alg, ftol, gmx_step_str(count, buf));
+ }
+ else if (count < nsteps)
+ {
+ fprintf(fp, "\n%s converged to machine precision in %s steps,\n"
+ "but did not reach the requested Fmax < %g.\n",
+ alg, gmx_step_str(count, buf), ftol);
+ }
+ else
+ {
+ fprintf(fp, "\n%s did not converge to Fmax < %g in %s steps.\n",
+ alg, ftol, gmx_step_str(count, buf));
+ }
+
+#if GMX_DOUBLE
+ fprintf(fp, "Potential Energy = %21.14e\n", ems->epot);
+ fprintf(fp, "Maximum force = %21.14e on atom %d\n", ems->fmax, ems->a_fmax + 1);
+ fprintf(fp, "Norm of force = %21.14e\n", ems->fnorm/sqrtNumAtoms);
+#else
+ fprintf(fp, "Potential Energy = %14.7e\n", ems->epot);
+ fprintf(fp, "Maximum force = %14.7e on atom %d\n", ems->fmax, ems->a_fmax + 1);
+ fprintf(fp, "Norm of force = %14.7e\n", ems->fnorm/sqrtNumAtoms);
+#endif
+}
+
+//! Compute the norm and max of the force array in parallel
+static void get_f_norm_max(const t_commrec *cr,
+ t_grpopts *opts, t_mdatoms *mdatoms, const rvec *f,
+ real *fnorm, real *fmax, int *a_fmax)
+{
+ double fnorm2, *sum;
+ real fmax2, fam;
+ int la_max, a_max, start, end, i, m, gf;
+
+ /* This routine finds the largest force and returns it.
+ * On parallel machines the global max is taken.
+ */
+ fnorm2 = 0;
+ fmax2 = 0;
+ la_max = -1;
+ start = 0;
+ end = mdatoms->homenr;
+ if (mdatoms->cFREEZE)
+ {
+ for (i = start; i < end; i++)
+ {
+ gf = mdatoms->cFREEZE[i];
+ fam = 0;
+ for (m = 0; m < DIM; m++)
+ {
+ if (!opts->nFreeze[gf][m])
+ {
+ fam += gmx::square(f[i][m]);
+ }
+ }
+ fnorm2 += fam;
+ if (fam > fmax2)
+ {
+ fmax2 = fam;
+ la_max = i;
+ }
+ }
+ }
+ else
+ {
+ for (i = start; i < end; i++)
+ {
+ fam = norm2(f[i]);
+ fnorm2 += fam;
+ if (fam > fmax2)
+ {
+ fmax2 = fam;
+ la_max = i;
+ }
+ }
+ }
+
+ if (la_max >= 0 && DOMAINDECOMP(cr))
+ {
+ a_max = cr->dd->globalAtomIndices[la_max];
+ }
+ else
+ {
+ a_max = la_max;
+ }
+ if (PAR(cr))
+ {
+ snew(sum, 2*cr->nnodes+1);
+ sum[2*cr->nodeid] = fmax2;
+ sum[2*cr->nodeid+1] = a_max;
+ sum[2*cr->nnodes] = fnorm2;
+ gmx_sumd(2*cr->nnodes+1, sum, cr);
+ fnorm2 = sum[2*cr->nnodes];
+ /* Determine the global maximum */
+ for (i = 0; i < cr->nnodes; i++)
+ {
+ if (sum[2*i] > fmax2)
+ {
+ fmax2 = sum[2*i];
+ a_max = (int)(sum[2*i+1] + 0.5);
+ }
+ }
+ sfree(sum);
+ }
+
+ if (fnorm)
+ {
+ *fnorm = sqrt(fnorm2);
+ }
+ if (fmax)
+ {
+ *fmax = sqrt(fmax2);
+ }
+ if (a_fmax)
+ {
+ *a_fmax = a_max;
+ }
+}
+
+//! Compute the norm of the force
+static void get_state_f_norm_max(const t_commrec *cr,
+ t_grpopts *opts, t_mdatoms *mdatoms,
+ em_state_t *ems)
+{
+ get_f_norm_max(cr, opts, mdatoms, as_rvec_array(ems->f.data()),
+ &ems->fnorm, &ems->fmax, &ems->a_fmax);
+}
+
+//! Initialize the energy minimization
+static void init_em(FILE *fplog, const char *title,
+ const t_commrec *cr,
+ const gmx_multisim_t *ms,
+ gmx::IMDOutputProvider *outputProvider,
+ t_inputrec *ir,
+ const MdrunOptions &mdrunOptions,
+ t_state *state_global, gmx_mtop_t *top_global,
+ em_state_t *ems, gmx_localtop_t **top,
+ t_nrnb *nrnb, rvec mu_tot,
+ t_forcerec *fr, gmx_enerdata_t **enerd,
+ t_graph **graph, gmx::MDAtoms *mdAtoms, gmx_global_stat_t *gstat,
+ gmx_vsite_t *vsite, gmx::Constraints *constr, gmx_shellfc_t **shellfc,
+ int nfile, const t_filenm fnm[],
+ gmx_mdoutf_t *outf, t_mdebin **mdebin,
+ gmx_wallcycle_t wcycle)
+{
+ real dvdl_constr;
+
+ if (fplog)
+ {
+ fprintf(fplog, "Initiating %s\n", title);
+ }
+
+ if (MASTER(cr))
+ {
+ state_global->ngtc = 0;
+
+ /* Initialize lambda variables */
+ initialize_lambdas(fplog, ir, &(state_global->fep_state), state_global->lambda, nullptr);
+ }
+
+ init_nrnb(nrnb);
+
+ /* Interactive molecular dynamics */
+ init_IMD(ir, cr, ms, top_global, fplog, 1,
+ MASTER(cr) ? as_rvec_array(state_global->x.data()) : nullptr,
+ nfile, fnm, nullptr, mdrunOptions);
+
+ if (ir->eI == eiNM)
+ {
+ GMX_ASSERT(shellfc != nullptr, "With NM we always support shells");
+
+ *shellfc = init_shell_flexcon(stdout,
+ top_global,
+ constr ? constr->numFlexibleConstraints() : 0,
+ ir->nstcalcenergy,
+ DOMAINDECOMP(cr));
+ }
+ else
+ {
+ GMX_ASSERT(EI_ENERGY_MINIMIZATION(ir->eI), "This else currently only handles energy minimizers, consider if your algorithm needs shell/flexible-constraint support");
+
+ /* With energy minimization, shells and flexible constraints are
+ * automatically minimized when treated like normal DOFS.
+ */
+ if (shellfc != nullptr)
+ {
+ *shellfc = nullptr;
+ }
+ }
+
+ auto mdatoms = mdAtoms->mdatoms();
+ if (DOMAINDECOMP(cr))
+ {
+ *top = dd_init_local_top(top_global);
+
+ dd_init_local_state(cr->dd, state_global, &ems->s);
+
+ /* Distribute the charge groups over the nodes from the master node */
+ dd_partition_system(fplog, ir->init_step, cr, TRUE, 1,
+ state_global, top_global, ir,
+ &ems->s, &ems->f, mdAtoms, *top,
+ fr, vsite, constr,
+ nrnb, nullptr, FALSE);
+ dd_store_state(cr->dd, &ems->s);
+
+ *graph = nullptr;
+ }
+ else
+ {
+ state_change_natoms(state_global, state_global->natoms);
+ /* Just copy the state */
+ ems->s = *state_global;
+ state_change_natoms(&ems->s, ems->s.natoms);
+ /* We need to allocate one element extra, since we might use
+ * (unaligned) 4-wide SIMD loads to access rvec entries.
+ */
+ ems->f.resize(gmx::paddedRVecVectorSize(ems->s.natoms));
+
+ snew(*top, 1);
+ mdAlgorithmsSetupAtomData(cr, ir, top_global, *top, fr,
+ graph, mdAtoms,
+ constr, vsite, shellfc ? *shellfc : nullptr);
+
+ if (vsite)
+ {
+ set_vsite_top(vsite, *top, mdatoms);
+ }
+ }
+
+ update_mdatoms(mdAtoms->mdatoms(), ems->s.lambda[efptMASS]);
+
+ if (constr)
+ {
+ // TODO how should this cross-module support dependency be managed?
+ if (ir->eConstrAlg == econtSHAKE &&
+ gmx_mtop_ftype_count(top_global, F_CONSTR) > 0)
+ {
+ gmx_fatal(FARGS, "Can not do energy minimization with %s, use %s\n",
+ econstr_names[econtSHAKE], econstr_names[econtLINCS]);
+ }
+
+ if (!ir->bContinuation)
+ {
+ /* Constrain the starting coordinates */
+ dvdl_constr = 0;
+ constr->apply(TRUE, TRUE,
+ -1, 0, 1.0,
+ as_rvec_array(ems->s.x.data()),
+ as_rvec_array(ems->s.x.data()),
+ nullptr,
+ ems->s.box,
+ ems->s.lambda[efptFEP], &dvdl_constr,
+ nullptr, nullptr, gmx::ConstraintVariable::Positions);
+ }
+ }
+
+ if (PAR(cr))
+ {
+ *gstat = global_stat_init(ir);
+ }
+ else
+ {
+ *gstat = nullptr;
+ }
+
+ *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, nullptr, wcycle);
+
+ snew(*enerd, 1);
+ init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
+ *enerd);
+
+ if (mdebin != nullptr)
+ {
+ /* Init bin for energy stuff */
+ *mdebin = init_mdebin(mdoutf_get_fp_ene(*outf), top_global, ir, nullptr);
+ }
+
+ clear_rvec(mu_tot);
+ calc_shifts(ems->s.box, fr->shift_vec);
+}
+
+//! Finalize the minimization
+static void finish_em(const t_commrec *cr, gmx_mdoutf_t outf,
+ gmx_walltime_accounting_t walltime_accounting,
+ gmx_wallcycle_t wcycle)
+{
+ if (!thisRankHasDuty(cr, DUTY_PME))
+ {
+ /* Tell the PME only node to finish */
+ gmx_pme_send_finish(cr);
+ }
+
+ done_mdoutf(outf);
+
+ em_time_end(walltime_accounting, wcycle);
+}
+
+//! Swap two different EM states during minimization
+static void swap_em_state(em_state_t **ems1, em_state_t **ems2)
+{
+ em_state_t *tmp;
+
+ tmp = *ems1;
+ *ems1 = *ems2;
+ *ems2 = tmp;
+}
+
+//! Save the EM trajectory
+static void write_em_traj(FILE *fplog, const t_commrec *cr,
+ gmx_mdoutf_t outf,
+ gmx_bool bX, gmx_bool bF, const char *confout,
+ gmx_mtop_t *top_global,
+ t_inputrec *ir, gmx_int64_t step,
+ em_state_t *state,
+ t_state *state_global,
+ ObservablesHistory *observablesHistory)
+{
+ int mdof_flags = 0;
+
+ if (bX)
+ {
+ mdof_flags |= MDOF_X;
+ }
+ if (bF)
+ {
+ mdof_flags |= MDOF_F;
+ }
+
+ /* If we want IMD output, set appropriate MDOF flag */
+ if (ir->bIMD)
+ {
+ mdof_flags |= MDOF_IMD;
+ }
+
+ mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
+ top_global, step, (double)step,
+ &state->s, state_global, observablesHistory,
+ state->f);
+
+ if (confout != nullptr && MASTER(cr))
+ {
+ GMX_RELEASE_ASSERT(bX, "The code below assumes that (with domain decomposition), x is collected to state_global in the call above.");
+ /* With domain decomposition the call above collected the state->s.x
+ * into state_global->x. Without DD we copy the local state pointer.
+ */
+ if (!DOMAINDECOMP(cr))
+ {
+ state_global = &state->s;
+ }
+
+ if (ir->ePBC != epbcNONE && !ir->bPeriodicMols && DOMAINDECOMP(cr))
+ {
+ /* Make molecules whole only for confout writing */
+ do_pbc_mtop(fplog, ir->ePBC, state->s.box, top_global,
+ as_rvec_array(state_global->x.data()));
+ }
+
+ write_sto_conf_mtop(confout,
+ *top_global->name, top_global,
+ as_rvec_array(state_global->x.data()), nullptr, ir->ePBC, state->s.box);
+ }
+}
+
+//! \brief Do one minimization step
+//
+// \returns true when the step succeeded, false when a constraint error occurred
+static bool do_em_step(const t_commrec *cr,
+ t_inputrec *ir, t_mdatoms *md,
+ em_state_t *ems1, real a, const PaddedRVecVector *force,
+ em_state_t *ems2,
+ gmx::Constraints *constr,
+ gmx_int64_t count)
+
+{
+ t_state *s1, *s2;
+ int start, end;
+ real dvdl_constr;
+ int nthreads gmx_unused;
+
+ bool validStep = true;
+
+ s1 = &ems1->s;
+ s2 = &ems2->s;
+
+ if (DOMAINDECOMP(cr) && s1->ddp_count != cr->dd->ddp_count)
+ {
+ gmx_incons("state mismatch in do_em_step");
+ }
+
+ s2->flags = s1->flags;
+
+ if (s2->natoms != s1->natoms)
+ {
+ state_change_natoms(s2, s1->natoms);
+ /* We need to allocate one element extra, since we might use
+ * (unaligned) 4-wide SIMD loads to access rvec entries.
+ */
+ ems2->f.resize(gmx::paddedRVecVectorSize(s2->natoms));
+ }
+ if (DOMAINDECOMP(cr) && s2->cg_gl.size() != s1->cg_gl.size())
+ {
+ s2->cg_gl.resize(s1->cg_gl.size());
+ }
+
+ copy_mat(s1->box, s2->box);
+ /* Copy free energy state */
+ s2->lambda = s1->lambda;
+ copy_mat(s1->box, s2->box);
+
+ start = 0;
+ end = md->homenr;
+
+ // cppcheck-suppress unreadVariable
+ nthreads = gmx_omp_nthreads_get(emntUpdate);
+#pragma omp parallel num_threads(nthreads)
+ {
+ const rvec *x1 = as_rvec_array(s1->x.data());
+ rvec *x2 = as_rvec_array(s2->x.data());
+ const rvec *f = as_rvec_array(force->data());
+
+ int gf = 0;
+#pragma omp for schedule(static) nowait
+ for (int i = start; i < end; i++)
+ {
+ try
+ {
+ if (md->cFREEZE)
+ {
+ gf = md->cFREEZE[i];
+ }
+ for (int m = 0; m < DIM; m++)
+ {
+ if (ir->opts.nFreeze[gf][m])
+ {
+ x2[i][m] = x1[i][m];
+ }
+ else
+ {
+ x2[i][m] = x1[i][m] + a*f[i][m];
+ }
+ }
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ }
+
+ if (s2->flags & (1<<estCGP))
+ {
+ /* Copy the CG p vector */
+ const rvec *p1 = as_rvec_array(s1->cg_p.data());
+ rvec *p2 = as_rvec_array(s2->cg_p.data());
+#pragma omp for schedule(static) nowait
+ for (int i = start; i < end; i++)
+ {
+ // Trivial OpenMP block that does not throw
+ copy_rvec(p1[i], p2[i]);
+ }
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ s2->ddp_count = s1->ddp_count;
+
+ /* OpenMP does not supported unsigned loop variables */
+#pragma omp for schedule(static) nowait
+ for (int i = 0; i < static_cast<int>(s2->cg_gl.size()); i++)
+ {
+ s2->cg_gl[i] = s1->cg_gl[i];
+ }
+ s2->ddp_count_cg_gl = s1->ddp_count_cg_gl;
+ }
+ }
+
+ if (constr)
+ {
+ dvdl_constr = 0;
+ validStep =
+ constr->apply(TRUE, TRUE,
+ count, 0, 1.0,
+ as_rvec_array(s1->x.data()), as_rvec_array(s2->x.data()),
+ nullptr, s2->box,
+ s2->lambda[efptBONDED], &dvdl_constr,
+ nullptr, nullptr, gmx::ConstraintVariable::Positions);
+
++ if (cr->nnodes > 1)
++ {
++ /* This global reduction will affect performance at high
++ * parallelization, but we can not really avoid it.
++ * But usually EM is not run at high parallelization.
++ */
++ int reductionBuffer = !validStep;
++ gmx_sumi(1, &reductionBuffer, cr);
++ validStep = (reductionBuffer == 0);
++ }
++
+ // We should move this check to the different minimizers
+ if (!validStep && ir->eI != eiSteep)
+ {
+ gmx_fatal(FARGS, "The coordinates could not be constrained. Minimizer '%s' can not handle constraint failures, use minimizer '%s' before using '%s'.",
+ EI(ir->eI), EI(eiSteep), EI(ir->eI));
+ }
+ }
+
+ return validStep;
+}
+
+//! Prepare EM for using domain decomposition parallellization
+static void em_dd_partition_system(FILE *fplog, int step, const t_commrec *cr,
+ gmx_mtop_t *top_global, t_inputrec *ir,
+ em_state_t *ems, gmx_localtop_t *top,
+ gmx::MDAtoms *mdAtoms, t_forcerec *fr,
+ gmx_vsite_t *vsite, gmx::Constraints *constr,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle)
+{
+ /* Repartition the domain decomposition */
+ dd_partition_system(fplog, step, cr, FALSE, 1,
+ nullptr, top_global, ir,
+ &ems->s, &ems->f,
+ mdAtoms, top, fr, vsite, constr,
+ nrnb, wcycle, FALSE);
+ dd_store_state(cr->dd, &ems->s);
+}
+
+namespace
+{
+
+/*! \brief Class to handle the work of setting and doing an energy evaluation.
+ *
+ * This class is a mere aggregate of parameters to pass to evaluate an
+ * energy, so that future changes to names and types of them consume
+ * less time when refactoring other code.
+ *
+ * Aggregate initialization is used, for which the chief risk is that
+ * if a member is added at the end and not all initializer lists are
+ * updated, then the member will be value initialized, which will
+ * typically mean initialization to zero.
+ *
+ * We only want to construct one of these with an initializer list, so
+ * we explicitly delete the default constructor. */
+class EnergyEvaluator
+{
+ public:
+ //! We only intend to construct such objects with an initializer list.
+#if __GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 9)
+ // Aspects of the C++11 spec changed after GCC 4.8.5, and
+ // compilation of the initializer list construction in
+ // runner.cpp fails in GCC 4.8.5.
+ EnergyEvaluator() = delete;
+#endif
+ /*! \brief Evaluates an energy on the state in \c ems.
+ *
+ * \todo In practice, the same objects mu_tot, vir, and pres
+ * are always passed to this function, so we would rather have
+ * them as data members. However, their C-array types are
+ * unsuited for aggregate initialization. When the types
+ * improve, the call signature of this method can be reduced.
+ */
+ void run(em_state_t *ems, rvec mu_tot,
+ tensor vir, tensor pres,
+ gmx_int64_t count, gmx_bool bFirst);
+ //! Handles logging.
+ FILE *fplog;
+ //! Handles communication.
+ const t_commrec *cr;
+ //! Coordinates multi-simulations.
+ const gmx_multisim_t *ms;
+ //! Holds the simulation topology.
+ gmx_mtop_t *top_global;
+ //! Holds the domain topology.
+ gmx_localtop_t *top;
+ //! User input options.
+ t_inputrec *inputrec;
+ //! Manages flop accounting.
+ t_nrnb *nrnb;
+ //! Manages wall cycle accounting.
+ gmx_wallcycle_t wcycle;
+ //! Coordinates global reduction.
+ gmx_global_stat_t gstat;
+ //! Handles virtual sites.
+ gmx_vsite_t *vsite;
+ //! Handles constraints.
+ gmx::Constraints *constr;
+ //! Handles strange things.
+ t_fcdata *fcd;
+ //! Molecular graph for SHAKE.
+ t_graph *graph;
+ //! Per-atom data for this domain.
+ gmx::MDAtoms *mdAtoms;
+ //! Handles how to calculate the forces.
+ t_forcerec *fr;
+ //! Stores the computed energies.
+ gmx_enerdata_t *enerd;
+};
+
+void
+EnergyEvaluator::run(em_state_t *ems, rvec mu_tot,
+ tensor vir, tensor pres,
+ gmx_int64_t count, gmx_bool bFirst)
+{
+ real t;
+ gmx_bool bNS;
+ tensor force_vir, shake_vir, ekin;
+ real dvdl_constr, prescorr, enercorr, dvdlcorr;
+ real terminate = 0;
+
+ /* Set the time to the initial time, the time does not change during EM */
+ t = inputrec->init_t;
+
+ if (bFirst ||
+ (DOMAINDECOMP(cr) && ems->s.ddp_count < cr->dd->ddp_count))
+ {
+ /* This is the first state or an old state used before the last ns */
+ bNS = TRUE;
+ }
+ else
+ {
+ bNS = FALSE;
+ if (inputrec->nstlist > 0)
+ {
+ bNS = TRUE;
+ }
+ }
+
+ if (vsite)
+ {
+ construct_vsites(vsite, as_rvec_array(ems->s.x.data()), 1, nullptr,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, cr, ems->s.box);
+ }
+
+ if (DOMAINDECOMP(cr) && bNS)
+ {
+ /* Repartition the domain decomposition */
+ em_dd_partition_system(fplog, count, cr, top_global, inputrec,
+ ems, top, mdAtoms, fr, vsite, constr,
+ nrnb, wcycle);
+ }
+
+ /* Calc force & energy on new trial position */
+ /* do_force always puts the charge groups in the box and shifts again
+ * We do not unshift, so molecules are always whole in congrad.c
+ */
+ do_force(fplog, cr, ms, inputrec, nullptr,
+ count, nrnb, wcycle, top, &top_global->groups,
+ ems->s.box, ems->s.x, &ems->s.hist,
+ ems->f, force_vir, mdAtoms->mdatoms(), enerd, fcd,
+ ems->s.lambda, graph, fr, vsite, mu_tot, t, nullptr,
+ GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES |
+ GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY |
+ (bNS ? GMX_FORCE_NS : 0),
+ DOMAINDECOMP(cr) ?
+ DdOpenBalanceRegionBeforeForceComputation::yes :
+ DdOpenBalanceRegionBeforeForceComputation::no,
+ DOMAINDECOMP(cr) ?
+ DdCloseBalanceRegionAfterForceComputation::yes :
+ DdCloseBalanceRegionAfterForceComputation::no);
+
+ /* Clear the unused shake virial and pressure */
+ clear_mat(shake_vir);
+ clear_mat(pres);
+
+ /* Communicate stuff when parallel */
+ if (PAR(cr) && inputrec->eI != eiNM)
+ {
+ wallcycle_start(wcycle, ewcMoveE);
+
+ global_stat(gstat, cr, enerd, force_vir, shake_vir, mu_tot,
+ inputrec, nullptr, nullptr, nullptr, 1, &terminate,
+ nullptr, FALSE,
+ CGLO_ENERGY |
+ CGLO_PRESSURE |
+ CGLO_CONSTRAINT);
+
+ wallcycle_stop(wcycle, ewcMoveE);
+ }
+
+ /* Calculate long range corrections to pressure and energy */
+ calc_dispcorr(inputrec, fr, ems->s.box, ems->s.lambda[efptVDW],
+ pres, force_vir, &prescorr, &enercorr, &dvdlcorr);
+ enerd->term[F_DISPCORR] = enercorr;
+ enerd->term[F_EPOT] += enercorr;
+ enerd->term[F_PRES] += prescorr;
+ enerd->term[F_DVDL] += dvdlcorr;
+
+ ems->epot = enerd->term[F_EPOT];
+
+ if (constr)
+ {
+ /* Project out the constraint components of the force */
+ dvdl_constr = 0;
+ rvec *f_rvec = as_rvec_array(ems->f.data());
+ constr->apply(FALSE, FALSE,
+ count, 0, 1.0,
+ as_rvec_array(ems->s.x.data()), f_rvec, f_rvec,
+ ems->s.box,
+ ems->s.lambda[efptBONDED], &dvdl_constr,
+ nullptr, &shake_vir, gmx::ConstraintVariable::ForceDispl);
+ enerd->term[F_DVDL_CONSTR] += dvdl_constr;
+ m_add(force_vir, shake_vir, vir);
+ }
+ else
+ {
+ copy_mat(force_vir, vir);
+ }
+
+ clear_mat(ekin);
+ enerd->term[F_PRES] =
+ calc_pres(fr->ePBC, inputrec->nwall, ems->s.box, ekin, vir, pres);
+
+ sum_dhdl(enerd, ems->s.lambda, inputrec->fepvals);
+
+ if (EI_ENERGY_MINIMIZATION(inputrec->eI))
+ {
+ get_state_f_norm_max(cr, &(inputrec->opts), mdAtoms->mdatoms(), ems);
+ }
+}
+
+} // namespace
+
+//! Parallel utility summing energies and forces
+static double reorder_partsum(const t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms,
+ gmx_mtop_t *top_global,
+ em_state_t *s_min, em_state_t *s_b)
+{
+ t_block *cgs_gl;
+ int ncg, *cg_gl, *index, c, cg, i, a0, a1, a, gf, m;
+ double partsum;
+ unsigned char *grpnrFREEZE;
+
+ if (debug)
+ {
+ fprintf(debug, "Doing reorder_partsum\n");
+ }
+
+ const rvec *fm = as_rvec_array(s_min->f.data());
+ const rvec *fb = as_rvec_array(s_b->f.data());
+
+ cgs_gl = dd_charge_groups_global(cr->dd);
+ index = cgs_gl->index;
+
+ /* Collect fm in a global vector fmg.
+ * This conflicts with the spirit of domain decomposition,
+ * but to fully optimize this a much more complicated algorithm is required.
+ */
+ rvec *fmg;
+ snew(fmg, top_global->natoms);
+
+ ncg = s_min->s.cg_gl.size();
+ cg_gl = s_min->s.cg_gl.data();
+ i = 0;
+ for (c = 0; c < ncg; c++)
+ {
+ cg = cg_gl[c];
+ a0 = index[cg];
+ a1 = index[cg+1];
+ for (a = a0; a < a1; a++)
+ {
+ copy_rvec(fm[i], fmg[a]);
+ i++;
+ }
+ }
+ gmx_sum(top_global->natoms*3, fmg[0], cr);
+
+ /* Now we will determine the part of the sum for the cgs in state s_b */
+ ncg = s_b->s.cg_gl.size();
+ cg_gl = s_b->s.cg_gl.data();
+ partsum = 0;
+ i = 0;
+ gf = 0;
+ grpnrFREEZE = top_global->groups.grpnr[egcFREEZE];
+ for (c = 0; c < ncg; c++)
+ {
+ cg = cg_gl[c];
+ a0 = index[cg];
+ a1 = index[cg+1];
+ for (a = a0; a < a1; a++)
+ {
+ if (mdatoms->cFREEZE && grpnrFREEZE)
+ {
+ gf = grpnrFREEZE[i];
+ }
+ for (m = 0; m < DIM; m++)
+ {
+ if (!opts->nFreeze[gf][m])
+ {
+ partsum += (fb[i][m] - fmg[a][m])*fb[i][m];
+ }
+ }
+ i++;
+ }
+ }
+
+ sfree(fmg);
+
+ return partsum;
+}
+
+//! Print some stuff, like beta, whatever that means.
+static real pr_beta(const t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms,
+ gmx_mtop_t *top_global,
+ em_state_t *s_min, em_state_t *s_b)
+{
+ double sum;
+
+ /* This is just the classical Polak-Ribiere calculation of beta;
+ * it looks a bit complicated since we take freeze groups into account,
+ * and might have to sum it in parallel runs.
+ */
+
+ if (!DOMAINDECOMP(cr) ||
+ (s_min->s.ddp_count == cr->dd->ddp_count &&
+ s_b->s.ddp_count == cr->dd->ddp_count))
+ {
+ const rvec *fm = as_rvec_array(s_min->f.data());
+ const rvec *fb = as_rvec_array(s_b->f.data());
+ sum = 0;
+ int gf = 0;
+ /* This part of code can be incorrect with DD,
+ * since the atom ordering in s_b and s_min might differ.
+ */
+ for (int i = 0; i < mdatoms->homenr; i++)
+ {
+ if (mdatoms->cFREEZE)
+ {
+ gf = mdatoms->cFREEZE[i];
+ }
+ for (int m = 0; m < DIM; m++)
+ {
+ if (!opts->nFreeze[gf][m])
+ {
+ sum += (fb[i][m] - fm[i][m])*fb[i][m];
+ }
+ }
+ }
+ }
+ else
+ {
+ /* We need to reorder cgs while summing */
+ sum = reorder_partsum(cr, opts, mdatoms, top_global, s_min, s_b);
+ }
+ if (PAR(cr))
+ {
+ gmx_sumd(1, &sum, cr);
+ }
+
+ return sum/gmx::square(s_min->fnorm);
+}
+
+namespace gmx
+{
+
+void
+Integrator::do_cg()
+{
+ const char *CG = "Polak-Ribiere Conjugate Gradients";
+
+ gmx_localtop_t *top;
+ gmx_enerdata_t *enerd;
+ gmx_global_stat_t gstat;
+ t_graph *graph;
+ double tmp, minstep;
+ real stepsize;
+ real a, b, c, beta = 0.0;
+ real epot_repl = 0;
+ real pnorm;
+ t_mdebin *mdebin;
+ gmx_bool converged, foundlower;
+ rvec mu_tot;
+ gmx_bool do_log = FALSE, do_ene = FALSE, do_x, do_f;
+ tensor vir, pres;
+ int number_steps, neval = 0, nstcg = inputrec->nstcgsteep;
+ gmx_mdoutf_t outf;
+ int m, step, nminstep;
+ auto mdatoms = mdAtoms->mdatoms();
+
+ step = 0;
+
+ // Ensure the extra per-atom state array gets allocated
+ state_global->flags |= (1<<estCGP);
+
+ /* Create 4 states on the stack and extract pointers that we will swap */
+ em_state_t s0 {}, s1 {}, s2 {}, s3 {};
+ em_state_t *s_min = &s0;
+ em_state_t *s_a = &s1;
+ em_state_t *s_b = &s2;
+ em_state_t *s_c = &s3;
+
+ /* Init em and store the local state in s_min */
+ init_em(fplog, CG, cr, ms, outputProvider, inputrec, mdrunOptions,
+ state_global, top_global, s_min, &top,
+ nrnb, mu_tot, fr, &enerd, &graph, mdAtoms, &gstat,
+ vsite, constr, nullptr,
+ nfile, fnm, &outf, &mdebin, wcycle);
+
+ /* Print to log file */
+ print_em_start(fplog, cr, walltime_accounting, wcycle, CG);
+
+ /* Max number of steps */
+ number_steps = inputrec->nsteps;
+
+ if (MASTER(cr))
+ {
+ sp_header(stderr, CG, inputrec->em_tol, number_steps);
+ }
+ if (fplog)
+ {
+ sp_header(fplog, CG, inputrec->em_tol, number_steps);
+ }
+
+ EnergyEvaluator energyEvaluator {
+ fplog, cr, ms,
+ top_global, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph,
+ mdAtoms, fr, enerd
+ };
+ /* Call the force routine and some auxiliary (neighboursearching etc.) */
+ /* do_force always puts the charge groups in the box and shifts again
+ * We do not unshift, so molecules are always whole in congrad.c
+ */
+ energyEvaluator.run(s_min, mu_tot, vir, pres, -1, TRUE);
+
+ if (MASTER(cr))
+ {
+ /* Copy stuff to the energy bin for easy printing etc. */
+ upd_mdebin(mdebin, FALSE, FALSE, (double)step,
+ mdatoms->tmass, enerd, &s_min->s, inputrec->fepvals, inputrec->expandedvals, s_min->s.box,
+ nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
+
+ print_ebin_header(fplog, step, step);
+ print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
+ mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
+ }
+
+ /* Estimate/guess the initial stepsize */
+ stepsize = inputrec->em_stepsize/s_min->fnorm;
+
+ if (MASTER(cr))
+ {
+ double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
+ fprintf(stderr, " F-max = %12.5e on atom %d\n",
+ s_min->fmax, s_min->a_fmax+1);
+ fprintf(stderr, " F-Norm = %12.5e\n",
+ s_min->fnorm/sqrtNumAtoms);
+ fprintf(stderr, "\n");
+ /* and copy to the log file too... */
+ fprintf(fplog, " F-max = %12.5e on atom %d\n",
+ s_min->fmax, s_min->a_fmax+1);
+ fprintf(fplog, " F-Norm = %12.5e\n",
+ s_min->fnorm/sqrtNumAtoms);
+ fprintf(fplog, "\n");
+ }
+ /* Start the loop over CG steps.
+ * Each successful step is counted, and we continue until
+ * we either converge or reach the max number of steps.
+ */
+ converged = FALSE;
+ for (step = 0; (number_steps < 0 || step <= number_steps) && !converged; step++)
+ {
+
+ /* start taking steps in a new direction
+ * First time we enter the routine, beta=0, and the direction is
+ * simply the negative gradient.
+ */
+
+ /* Calculate the new direction in p, and the gradient in this direction, gpa */
+ rvec *pm = as_rvec_array(s_min->s.cg_p.data());
+ const rvec *sfm = as_rvec_array(s_min->f.data());
+ double gpa = 0;
+ int gf = 0;
+ for (int i = 0; i < mdatoms->homenr; i++)
+ {
+ if (mdatoms->cFREEZE)
+ {
+ gf = mdatoms->cFREEZE[i];
+ }
+ for (m = 0; m < DIM; m++)
+ {
+ if (!inputrec->opts.nFreeze[gf][m])
+ {
+ pm[i][m] = sfm[i][m] + beta*pm[i][m];
+ gpa -= pm[i][m]*sfm[i][m];
+ /* f is negative gradient, thus the sign */
+ }
+ else
+ {
+ pm[i][m] = 0;
+ }
+ }
+ }
+
+ /* Sum the gradient along the line across CPUs */
+ if (PAR(cr))
+ {
+ gmx_sumd(1, &gpa, cr);
+ }
+
+ /* Calculate the norm of the search vector */
+ get_f_norm_max(cr, &(inputrec->opts), mdatoms, pm, &pnorm, nullptr, nullptr);
+
+ /* Just in case stepsize reaches zero due to numerical precision... */
+ if (stepsize <= 0)
+ {
+ stepsize = inputrec->em_stepsize/pnorm;
+ }
+
+ /*
+ * Double check the value of the derivative in the search direction.
+ * If it is positive it must be due to the old information in the
+ * CG formula, so just remove that and start over with beta=0.
+ * This corresponds to a steepest descent step.
+ */
+ if (gpa > 0)
+ {
+ beta = 0;
+ step--; /* Don't count this step since we are restarting */
+ continue; /* Go back to the beginning of the big for-loop */
+ }
+
+ /* Calculate minimum allowed stepsize, before the average (norm)
+ * relative change in coordinate is smaller than precision
+ */
+ minstep = 0;
+ for (int i = 0; i < mdatoms->homenr; i++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ tmp = fabs(s_min->s.x[i][m]);
+ if (tmp < 1.0)
+ {
+ tmp = 1.0;
+ }
+ tmp = pm[i][m]/tmp;
+ minstep += tmp*tmp;
+ }
+ }
+ /* Add up from all CPUs */
+ if (PAR(cr))
+ {
+ gmx_sumd(1, &minstep, cr);
+ }
+
+ minstep = GMX_REAL_EPS/sqrt(minstep/(3*state_global->natoms));
+
+ if (stepsize < minstep)
+ {
+ converged = TRUE;
+ break;
+ }
+
+ /* Write coordinates if necessary */
+ do_x = do_per_step(step, inputrec->nstxout);
+ do_f = do_per_step(step, inputrec->nstfout);
+
+ write_em_traj(fplog, cr, outf, do_x, do_f, nullptr,
+ top_global, inputrec, step,
+ s_min, state_global, observablesHistory);
+
+ /* Take a step downhill.
+ * In theory, we should minimize the function along this direction.
+ * That is quite possible, but it turns out to take 5-10 function evaluations
+ * for each line. However, we dont really need to find the exact minimum -
+ * it is much better to start a new CG step in a modified direction as soon
+ * as we are close to it. This will save a lot of energy evaluations.
+ *
+ * In practice, we just try to take a single step.
+ * If it worked (i.e. lowered the energy), we increase the stepsize but
+ * the continue straight to the next CG step without trying to find any minimum.
+ * If it didn't work (higher energy), there must be a minimum somewhere between
+ * the old position and the new one.
+ *
+ * Due to the finite numerical accuracy, it turns out that it is a good idea
+ * to even accept a SMALL increase in energy, if the derivative is still downhill.
+ * This leads to lower final energies in the tests I've done. / Erik
+ */
+ s_a->epot = s_min->epot;
+ a = 0.0;
+ c = a + stepsize; /* reference position along line is zero */
+
+ if (DOMAINDECOMP(cr) && s_min->s.ddp_count < cr->dd->ddp_count)
+ {
+ em_dd_partition_system(fplog, step, cr, top_global, inputrec,
+ s_min, top, mdAtoms, fr, vsite, constr,
+ nrnb, wcycle);
+ }
+
+ /* Take a trial step (new coords in s_c) */
+ do_em_step(cr, inputrec, mdatoms, s_min, c, &s_min->s.cg_p, s_c,
+ constr, -1);
+
+ neval++;
+ /* Calculate energy for the trial step */
+ energyEvaluator.run(s_c, mu_tot, vir, pres, -1, FALSE);
+
+ /* Calc derivative along line */
+ const rvec *pc = as_rvec_array(s_c->s.cg_p.data());
+ const rvec *sfc = as_rvec_array(s_c->f.data());
+ double gpc = 0;
+ for (int i = 0; i < mdatoms->homenr; i++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ gpc -= pc[i][m]*sfc[i][m]; /* f is negative gradient, thus the sign */
+ }
+ }
+ /* Sum the gradient along the line across CPUs */
+ if (PAR(cr))
+ {
+ gmx_sumd(1, &gpc, cr);
+ }
+
+ /* This is the max amount of increase in energy we tolerate */
+ tmp = std::sqrt(GMX_REAL_EPS)*fabs(s_a->epot);
+
+ /* Accept the step if the energy is lower, or if it is not significantly higher
+ * and the line derivative is still negative.
+ */
+ if (s_c->epot < s_a->epot || (gpc < 0 && s_c->epot < (s_a->epot + tmp)))
+ {
+ foundlower = TRUE;
+ /* Great, we found a better energy. Increase step for next iteration
+ * if we are still going down, decrease it otherwise
+ */
+ if (gpc < 0)
+ {
+ stepsize *= 1.618034; /* The golden section */
+ }
+ else
+ {
+ stepsize *= 0.618034; /* 1/golden section */
+ }
+ }
+ else
+ {
+ /* New energy is the same or higher. We will have to do some work
+ * to find a smaller value in the interval. Take smaller step next time!
+ */
+ foundlower = FALSE;
+ stepsize *= 0.618034;
+ }
+
+
+
+
+ /* OK, if we didn't find a lower value we will have to locate one now - there must
+ * be one in the interval [a=0,c].
+ * The same thing is valid here, though: Don't spend dozens of iterations to find
+ * the line minimum. We try to interpolate based on the derivative at the endpoints,
+ * and only continue until we find a lower value. In most cases this means 1-2 iterations.
+ *
+ * I also have a safeguard for potentially really pathological functions so we never
+ * take more than 20 steps before we give up ...
+ *
+ * If we already found a lower value we just skip this step and continue to the update.
+ */
+ double gpb;
+ if (!foundlower)
+ {
+ nminstep = 0;
+
+ do
+ {
+ /* Select a new trial point.
+ * If the derivatives at points a & c have different sign we interpolate to zero,
+ * otherwise just do a bisection.
+ */
+ if (gpa < 0 && gpc > 0)
+ {
+ b = a + gpa*(a-c)/(gpc-gpa);
+ }
+ else
+ {
+ b = 0.5*(a+c);
+ }
+
+ /* safeguard if interpolation close to machine accuracy causes errors:
+ * never go outside the interval
+ */
+ if (b <= a || b >= c)
+ {
+ b = 0.5*(a+c);
+ }
+
+ if (DOMAINDECOMP(cr) && s_min->s.ddp_count != cr->dd->ddp_count)
+ {
+ /* Reload the old state */
+ em_dd_partition_system(fplog, -1, cr, top_global, inputrec,
+ s_min, top, mdAtoms, fr, vsite, constr,
+ nrnb, wcycle);
+ }
+
+ /* Take a trial step to this new point - new coords in s_b */
+ do_em_step(cr, inputrec, mdatoms, s_min, b, &s_min->s.cg_p, s_b,
+ constr, -1);
+
+ neval++;
+ /* Calculate energy for the trial step */
+ energyEvaluator.run(s_b, mu_tot, vir, pres, -1, FALSE);
+
+ /* p does not change within a step, but since the domain decomposition
+ * might change, we have to use cg_p of s_b here.
+ */
+ const rvec *pb = as_rvec_array(s_b->s.cg_p.data());
+ const rvec *sfb = as_rvec_array(s_b->f.data());
+ gpb = 0;
+ for (int i = 0; i < mdatoms->homenr; i++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ gpb -= pb[i][m]*sfb[i][m]; /* f is negative gradient, thus the sign */
+ }
+ }
+ /* Sum the gradient along the line across CPUs */
+ if (PAR(cr))
+ {
+ gmx_sumd(1, &gpb, cr);
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "CGE: EpotA %f EpotB %f EpotC %f gpb %f\n",
+ s_a->epot, s_b->epot, s_c->epot, gpb);
+ }
+
+ epot_repl = s_b->epot;
+
+ /* Keep one of the intervals based on the value of the derivative at the new point */
+ if (gpb > 0)
+ {
+ /* Replace c endpoint with b */
+ swap_em_state(&s_b, &s_c);
+ c = b;
+ gpc = gpb;
+ }
+ else
+ {
+ /* Replace a endpoint with b */
+ swap_em_state(&s_b, &s_a);
+ a = b;
+ gpa = gpb;
+ }
+
+ /*
+ * Stop search as soon as we find a value smaller than the endpoints.
+ * Never run more than 20 steps, no matter what.
+ */
+ nminstep++;
+ }
+ while ((epot_repl > s_a->epot || epot_repl > s_c->epot) &&
+ (nminstep < 20));
+
+ if (std::fabs(epot_repl - s_min->epot) < fabs(s_min->epot)*GMX_REAL_EPS ||
+ nminstep >= 20)
+ {
+ /* OK. We couldn't find a significantly lower energy.
+ * If beta==0 this was steepest descent, and then we give up.
+ * If not, set beta=0 and restart with steepest descent before quitting.
+ */
+ if (beta == 0.0)
+ {
+ /* Converged */
+ converged = TRUE;
+ break;
+ }
+ else
+ {
+ /* Reset memory before giving up */
+ beta = 0.0;
+ continue;
+ }
+ }
+
+ /* Select min energy state of A & C, put the best in B.
+ */
+ if (s_c->epot < s_a->epot)
+ {
+ if (debug)
+ {
+ fprintf(debug, "CGE: C (%f) is lower than A (%f), moving C to B\n",
+ s_c->epot, s_a->epot);
+ }
+ swap_em_state(&s_b, &s_c);
+ gpb = gpc;
+ }
+ else
+ {
+ if (debug)
+ {
+ fprintf(debug, "CGE: A (%f) is lower than C (%f), moving A to B\n",
+ s_a->epot, s_c->epot);
+ }
+ swap_em_state(&s_b, &s_a);
+ gpb = gpa;
+ }
+
+ }
+ else
+ {
+ if (debug)
+ {
+ fprintf(debug, "CGE: Found a lower energy %f, moving C to B\n",
+ s_c->epot);
+ }
+ swap_em_state(&s_b, &s_c);
+ gpb = gpc;
+ }
+
+ /* new search direction */
+ /* beta = 0 means forget all memory and restart with steepest descents. */
+ if (nstcg && ((step % nstcg) == 0))
+ {
+ beta = 0.0;
+ }
+ else
+ {
+ /* s_min->fnorm cannot be zero, because then we would have converged
+ * and broken out.
+ */
+
+ /* Polak-Ribiere update.
+ * Change to fnorm2/fnorm2_old for Fletcher-Reeves
+ */
+ beta = pr_beta(cr, &inputrec->opts, mdatoms, top_global, s_min, s_b);
+ }
+ /* Limit beta to prevent oscillations */
+ if (fabs(beta) > 5.0)
+ {
+ beta = 0.0;
+ }
+
+
+ /* update positions */
+ swap_em_state(&s_min, &s_b);
+ gpa = gpb;
+
+ /* Print it if necessary */
+ if (MASTER(cr))
+ {
+ if (mdrunOptions.verbose)
+ {
+ double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
+ fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
+ step, s_min->epot, s_min->fnorm/sqrtNumAtoms,
+ s_min->fmax, s_min->a_fmax+1);
+ fflush(stderr);
+ }
+ /* Store the new (lower) energies */
+ upd_mdebin(mdebin, FALSE, FALSE, (double)step,
+ mdatoms->tmass, enerd, &s_min->s, inputrec->fepvals, inputrec->expandedvals, s_min->s.box,
+ nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
+
+ do_log = do_per_step(step, inputrec->nstlog);
+ do_ene = do_per_step(step, inputrec->nstenergy);
+
+ /* Prepare IMD energy record, if bIMD is TRUE. */
+ IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, step, TRUE);
+
+ if (do_log)
+ {
+ print_ebin_header(fplog, step, step);
+ }
+ print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
+ do_log ? fplog : nullptr, step, step, eprNORMAL,
+ mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
+ }
+
+ /* Send energies and positions to the IMD client if bIMD is TRUE. */
+ if (do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, as_rvec_array(state_global->x.data()), inputrec, 0, wcycle) && MASTER(cr))
+ {
+ IMD_send_positions(inputrec->imd);
+ }
+
+ /* Stop when the maximum force lies below tolerance.
+ * If we have reached machine precision, converged is already set to true.
+ */
+ converged = converged || (s_min->fmax < inputrec->em_tol);
+
+ } /* End of the loop */
+
+ /* IMD cleanup, if bIMD is TRUE. */
+ IMD_finalize(inputrec->bIMD, inputrec->imd);
+
+ if (converged)
+ {
+ step--; /* we never took that last step in this case */
+
+ }
+ if (s_min->fmax > inputrec->em_tol)
+ {
+ if (MASTER(cr))
+ {
+ warn_step(fplog, inputrec->em_tol, s_min->fmax,
+ step-1 == number_steps, FALSE);
+ }
+ converged = FALSE;
+ }
+
+ if (MASTER(cr))
+ {
+ /* If we printed energy and/or logfile last step (which was the last step)
+ * we don't have to do it again, but otherwise print the final values.
+ */
+ if (!do_log)
+ {
+ /* Write final value to log since we didn't do anything the last step */
+ print_ebin_header(fplog, step, step);
+ }
+ if (!do_ene || !do_log)
+ {
+ /* Write final energy file entries */
+ print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
+ !do_log ? fplog : nullptr, step, step, eprNORMAL,
+ mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
+ }
+ }
+
+ /* Print some stuff... */
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "\nwriting lowest energy coordinates.\n");
+ }
+
+ /* IMPORTANT!
+ * For accurate normal mode calculation it is imperative that we
+ * store the last conformation into the full precision binary trajectory.
+ *
+ * However, we should only do it if we did NOT already write this step
+ * above (which we did if do_x or do_f was true).
+ */
+ do_x = !do_per_step(step, inputrec->nstxout);
+ do_f = (inputrec->nstfout > 0 && !do_per_step(step, inputrec->nstfout));
+
+ write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm),
+ top_global, inputrec, step,
+ s_min, state_global, observablesHistory);
+
+
+ if (MASTER(cr))
+ {
+ double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
+ print_converged(stderr, CG, inputrec->em_tol, step, converged, number_steps,
+ s_min, sqrtNumAtoms);
+ print_converged(fplog, CG, inputrec->em_tol, step, converged, number_steps,
+ s_min, sqrtNumAtoms);
+
+ fprintf(fplog, "\nPerformed %d energy evaluations in total.\n", neval);
+ }
+
+ finish_em(cr, outf, walltime_accounting, wcycle);
+
+ /* To print the actual number of steps we needed somewhere */
+ walltime_accounting_set_nsteps_done(walltime_accounting, step);
+}
+
+
+void
+Integrator::do_lbfgs()
+{
+ static const char *LBFGS = "Low-Memory BFGS Minimizer";
+ em_state_t ems;
+ gmx_localtop_t *top;
+ gmx_enerdata_t *enerd;
+ gmx_global_stat_t gstat;
+ t_graph *graph;
+ int ncorr, nmaxcorr, point, cp, neval, nminstep;
+ double stepsize, step_taken, gpa, gpb, gpc, tmp, minstep;
+ real *rho, *alpha, *p, *s, **dx, **dg;
+ real a, b, c, maxdelta, delta;
+ real diag, Epot0;
+ real dgdx, dgdg, sq, yr, beta;
+ t_mdebin *mdebin;
+ gmx_bool converged;
+ rvec mu_tot;
+ gmx_bool do_log, do_ene, do_x, do_f, foundlower, *frozen;
+ tensor vir, pres;
+ int start, end, number_steps;
+ gmx_mdoutf_t outf;
+ int i, k, m, n, gf, step;
+ int mdof_flags;
+ auto mdatoms = mdAtoms->mdatoms();
+
+ if (PAR(cr))
+ {
+ gmx_fatal(FARGS, "Cannot do parallel L-BFGS Minimization - yet.\n");
+ }
+
+ if (nullptr != constr)
+ {
+ gmx_fatal(FARGS, "The combination of constraints and L-BFGS minimization is not implemented. Either do not use constraints, or use another minimizer (e.g. steepest descent).");
+ }
+
+ n = 3*state_global->natoms;
+ nmaxcorr = inputrec->nbfgscorr;
+
+ snew(frozen, n);
+
+ snew(p, n);
+ snew(rho, nmaxcorr);
+ snew(alpha, nmaxcorr);
+
+ snew(dx, nmaxcorr);
+ for (i = 0; i < nmaxcorr; i++)
+ {
+ snew(dx[i], n);
+ }
+
+ snew(dg, nmaxcorr);
+ for (i = 0; i < nmaxcorr; i++)
+ {
+ snew(dg[i], n);
+ }
+
+ step = 0;
+ neval = 0;
+
+ /* Init em */
+ init_em(fplog, LBFGS, cr, ms, outputProvider, inputrec, mdrunOptions,
+ state_global, top_global, &ems, &top,
+ nrnb, mu_tot, fr, &enerd, &graph, mdAtoms, &gstat,
+ vsite, constr, nullptr,
+ nfile, fnm, &outf, &mdebin, wcycle);
+
+ start = 0;
+ end = mdatoms->homenr;
+
+ /* We need 4 working states */
+ em_state_t s0 {}, s1 {}, s2 {}, s3 {};
+ em_state_t *sa = &s0;
+ em_state_t *sb = &s1;
+ em_state_t *sc = &s2;
+ em_state_t *last = &s3;
+ /* Initialize by copying the state from ems (we could skip x and f here) */
+ *sa = ems;
+ *sb = ems;
+ *sc = ems;
+
+ /* Print to log file */
+ print_em_start(fplog, cr, walltime_accounting, wcycle, LBFGS);
+
+ do_log = do_ene = do_x = do_f = TRUE;
+
+ /* Max number of steps */
+ number_steps = inputrec->nsteps;
+
+ /* Create a 3*natoms index to tell whether each degree of freedom is frozen */
+ gf = 0;
+ for (i = start; i < end; i++)
+ {
+ if (mdatoms->cFREEZE)
+ {
+ gf = mdatoms->cFREEZE[i];
+ }
+ for (m = 0; m < DIM; m++)
+ {
+ frozen[3*i+m] = inputrec->opts.nFreeze[gf][m];
+ }
+ }
+ if (MASTER(cr))
+ {
+ sp_header(stderr, LBFGS, inputrec->em_tol, number_steps);
+ }
+ if (fplog)
+ {
+ sp_header(fplog, LBFGS, inputrec->em_tol, number_steps);
+ }
+
+ if (vsite)
+ {
+ construct_vsites(vsite, as_rvec_array(state_global->x.data()), 1, nullptr,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, cr, state_global->box);
+ }
+
+ /* Call the force routine and some auxiliary (neighboursearching etc.) */
+ /* do_force always puts the charge groups in the box and shifts again
+ * We do not unshift, so molecules are always whole
+ */
+ neval++;
+ EnergyEvaluator energyEvaluator {
+ fplog, cr, ms,
+ top_global, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph,
+ mdAtoms, fr, enerd
+ };
+ energyEvaluator.run(&ems, mu_tot, vir, pres, -1, TRUE);
+
+ if (MASTER(cr))
+ {
+ /* Copy stuff to the energy bin for easy printing etc. */
+ upd_mdebin(mdebin, FALSE, FALSE, (double)step,
+ mdatoms->tmass, enerd, state_global, inputrec->fepvals, inputrec->expandedvals, state_global->box,
+ nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
+
+ print_ebin_header(fplog, step, step);
+ print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
+ mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
+ }
+
+ /* Set the initial step.
+ * since it will be multiplied by the non-normalized search direction
+ * vector (force vector the first time), we scale it by the
+ * norm of the force.
+ */
+
+ if (MASTER(cr))
+ {
+ double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
+ fprintf(stderr, "Using %d BFGS correction steps.\n\n", nmaxcorr);
+ fprintf(stderr, " F-max = %12.5e on atom %d\n", ems.fmax, ems.a_fmax + 1);
+ fprintf(stderr, " F-Norm = %12.5e\n", ems.fnorm/sqrtNumAtoms);
+ fprintf(stderr, "\n");
+ /* and copy to the log file too... */
+ fprintf(fplog, "Using %d BFGS correction steps.\n\n", nmaxcorr);
+ fprintf(fplog, " F-max = %12.5e on atom %d\n", ems.fmax, ems.a_fmax + 1);
+ fprintf(fplog, " F-Norm = %12.5e\n", ems.fnorm/sqrtNumAtoms);
+ fprintf(fplog, "\n");
+ }
+
+ // Point is an index to the memory of search directions, where 0 is the first one.
+ point = 0;
+
+ // Set initial search direction to the force (-gradient), or 0 for frozen particles.
+ real *fInit = static_cast<real *>(as_rvec_array(ems.f.data())[0]);
+ for (i = 0; i < n; i++)
+ {
+ if (!frozen[i])
+ {
+ dx[point][i] = fInit[i]; /* Initial search direction */
+ }
+ else
+ {
+ dx[point][i] = 0;
+ }
+ }
+
+ // Stepsize will be modified during the search, and actually it is not critical
+ // (the main efficiency in the algorithm comes from changing directions), but
+ // we still need an initial value, so estimate it as the inverse of the norm
+ // so we take small steps where the potential fluctuates a lot.
+ stepsize = 1.0/ems.fnorm;
+
+ /* Start the loop over BFGS steps.
+ * Each successful step is counted, and we continue until
+ * we either converge or reach the max number of steps.
+ */
+
+ ncorr = 0;
+
+ /* Set the gradient from the force */
+ converged = FALSE;
+ for (step = 0; (number_steps < 0 || step <= number_steps) && !converged; step++)
+ {
+
+ /* Write coordinates if necessary */
+ do_x = do_per_step(step, inputrec->nstxout);
+ do_f = do_per_step(step, inputrec->nstfout);
+
+ mdof_flags = 0;
+ if (do_x)
+ {
+ mdof_flags |= MDOF_X;
+ }
+
+ if (do_f)
+ {
+ mdof_flags |= MDOF_F;
+ }
+
+ if (inputrec->bIMD)
+ {
+ mdof_flags |= MDOF_IMD;
+ }
+
+ mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
+ top_global, step, (real)step, &ems.s, state_global, observablesHistory, ems.f);
+
+ /* Do the linesearching in the direction dx[point][0..(n-1)] */
+
+ /* make s a pointer to current search direction - point=0 first time we get here */
+ s = dx[point];
+
+ real *xx = static_cast<real *>(as_rvec_array(ems.s.x.data())[0]);
+ real *ff = static_cast<real *>(as_rvec_array(ems.f.data())[0]);
+
+ // calculate line gradient in position A
+ for (gpa = 0, i = 0; i < n; i++)
+ {
+ gpa -= s[i]*ff[i];
+ }
+
+ /* Calculate minimum allowed stepsize along the line, before the average (norm)
+ * relative change in coordinate is smaller than precision
+ */
+ for (minstep = 0, i = 0; i < n; i++)
+ {
+ tmp = fabs(xx[i]);
+ if (tmp < 1.0)
+ {
+ tmp = 1.0;
+ }
+ tmp = s[i]/tmp;
+ minstep += tmp*tmp;
+ }
+ minstep = GMX_REAL_EPS/sqrt(minstep/n);
+
+ if (stepsize < minstep)
+ {
+ converged = TRUE;
+ break;
+ }
+
+ // Before taking any steps along the line, store the old position
+ *last = ems;
+ real *lastx = static_cast<real *>(as_rvec_array(last->s.x.data())[0]);
+ real *lastf = static_cast<real *>(as_rvec_array(last->f.data())[0]);
+ Epot0 = ems.epot;
+
+ *sa = ems;
+
+ /* Take a step downhill.
+ * In theory, we should find the actual minimum of the function in this
+ * direction, somewhere along the line.
+ * That is quite possible, but it turns out to take 5-10 function evaluations
+ * for each line. However, we dont really need to find the exact minimum -
+ * it is much better to start a new BFGS step in a modified direction as soon
+ * as we are close to it. This will save a lot of energy evaluations.
+ *
+ * In practice, we just try to take a single step.
+ * If it worked (i.e. lowered the energy), we increase the stepsize but
+ * continue straight to the next BFGS step without trying to find any minimum,
+ * i.e. we change the search direction too. If the line was smooth, it is
+ * likely we are in a smooth region, and then it makes sense to take longer
+ * steps in the modified search direction too.
+ *
+ * If it didn't work (higher energy), there must be a minimum somewhere between
+ * the old position and the new one. Then we need to start by finding a lower
+ * value before we change search direction. Since the energy was apparently
+ * quite rough, we need to decrease the step size.
+ *
+ * Due to the finite numerical accuracy, it turns out that it is a good idea
+ * to accept a SMALL increase in energy, if the derivative is still downhill.
+ * This leads to lower final energies in the tests I've done. / Erik
+ */
+
+ // State "A" is the first position along the line.
+ // reference position along line is initially zero
+ a = 0.0;
+
+ // Check stepsize first. We do not allow displacements
+ // larger than emstep.
+ //
+ do
+ {
+ // Pick a new position C by adding stepsize to A.
+ c = a + stepsize;
+
+ // Calculate what the largest change in any individual coordinate
+ // would be (translation along line * gradient along line)
+ maxdelta = 0;
+ for (i = 0; i < n; i++)
+ {
+ delta = c*s[i];
+ if (delta > maxdelta)
+ {
+ maxdelta = delta;
+ }
+ }
+ // If any displacement is larger than the stepsize limit, reduce the step
+ if (maxdelta > inputrec->em_stepsize)
+ {
+ stepsize *= 0.1;
+ }
+ }
+ while (maxdelta > inputrec->em_stepsize);
+
+ // Take a trial step and move the coordinate array xc[] to position C
+ real *xc = static_cast<real *>(as_rvec_array(sc->s.x.data())[0]);
+ for (i = 0; i < n; i++)
+ {
+ xc[i] = lastx[i] + c*s[i];
+ }
+
+ neval++;
+ // Calculate energy for the trial step in position C
+ energyEvaluator.run(sc, mu_tot, vir, pres, step, FALSE);
+
+ // Calc line gradient in position C
+ real *fc = static_cast<real *>(as_rvec_array(sc->f.data())[0]);
+ for (gpc = 0, i = 0; i < n; i++)
+ {
+ gpc -= s[i]*fc[i]; /* f is negative gradient, thus the sign */
+ }
+ /* Sum the gradient along the line across CPUs */
+ if (PAR(cr))
+ {
+ gmx_sumd(1, &gpc, cr);
+ }
+
+ // This is the max amount of increase in energy we tolerate.
+ // By allowing VERY small changes (close to numerical precision) we
+ // frequently find even better (lower) final energies.
+ tmp = std::sqrt(GMX_REAL_EPS)*fabs(sa->epot);
+
+ // Accept the step if the energy is lower in the new position C (compared to A),
+ // or if it is not significantly higher and the line derivative is still negative.
+ if (sc->epot < sa->epot || (gpc < 0 && sc->epot < (sa->epot + tmp)))
+ {
+ // Great, we found a better energy. We no longer try to alter the
+ // stepsize, but simply accept this new better position. The we select a new
+ // search direction instead, which will be much more efficient than continuing
+ // to take smaller steps along a line. Set fnorm based on the new C position,
+ // which will be used to update the stepsize to 1/fnorm further down.
+ foundlower = TRUE;
+ }
+ else
+ {
+ // If we got here, the energy is NOT lower in point C, i.e. it will be the same
+ // or higher than in point A. In this case it is pointless to move to point C,
+ // so we will have to do more iterations along the same line to find a smaller
+ // value in the interval [A=0.0,C].
+ // Here, A is still 0.0, but that will change when we do a search in the interval
+ // [0.0,C] below. That search we will do by interpolation or bisection rather
+ // than with the stepsize, so no need to modify it. For the next search direction
+ // it will be reset to 1/fnorm anyway.
+ foundlower = FALSE;
+ }
+
+ if (!foundlower)
+ {
+ // OK, if we didn't find a lower value we will have to locate one now - there must
+ // be one in the interval [a,c].
+ // The same thing is valid here, though: Don't spend dozens of iterations to find
+ // the line minimum. We try to interpolate based on the derivative at the endpoints,
+ // and only continue until we find a lower value. In most cases this means 1-2 iterations.
+ // I also have a safeguard for potentially really pathological functions so we never
+ // take more than 20 steps before we give up.
+ // If we already found a lower value we just skip this step and continue to the update.
+ real fnorm = 0;
+ nminstep = 0;
+ do
+ {
+ // Select a new trial point B in the interval [A,C].
+ // If the derivatives at points a & c have different sign we interpolate to zero,
+ // otherwise just do a bisection since there might be multiple minima/maxima
+ // inside the interval.
+ if (gpa < 0 && gpc > 0)
+ {
+ b = a + gpa*(a-c)/(gpc-gpa);
+ }
+ else
+ {
+ b = 0.5*(a+c);
+ }
+
+ /* safeguard if interpolation close to machine accuracy causes errors:
+ * never go outside the interval
+ */
+ if (b <= a || b >= c)
+ {
+ b = 0.5*(a+c);
+ }
+
+ // Take a trial step to point B
+ real *xb = static_cast<real *>(as_rvec_array(sb->s.x.data())[0]);
+ for (i = 0; i < n; i++)
+ {
+ xb[i] = lastx[i] + b*s[i];
+ }
+
+ neval++;
+ // Calculate energy for the trial step in point B
+ energyEvaluator.run(sb, mu_tot, vir, pres, step, FALSE);
+ fnorm = sb->fnorm;
+
+ // Calculate gradient in point B
+ real *fb = static_cast<real *>(as_rvec_array(sb->f.data())[0]);
+ for (gpb = 0, i = 0; i < n; i++)
+ {
+ gpb -= s[i]*fb[i]; /* f is negative gradient, thus the sign */
+
+ }
+ /* Sum the gradient along the line across CPUs */
+ if (PAR(cr))
+ {
+ gmx_sumd(1, &gpb, cr);
+ }
+
+ // Keep one of the intervals [A,B] or [B,C] based on the value of the derivative
+ // at the new point B, and rename the endpoints of this new interval A and C.
+ if (gpb > 0)
+ {
+ /* Replace c endpoint with b */
+ c = b;
+ /* swap states b and c */
+ swap_em_state(&sb, &sc);
+ }
+ else
+ {
+ /* Replace a endpoint with b */
+ a = b;
+ /* swap states a and b */
+ swap_em_state(&sa, &sb);
+ }
+
+ /*
+ * Stop search as soon as we find a value smaller than the endpoints,
+ * or if the tolerance is below machine precision.
+ * Never run more than 20 steps, no matter what.
+ */
+ nminstep++;
+ }
+ while ((sb->epot > sa->epot || sb->epot > sc->epot) && (nminstep < 20));
+
+ if (std::fabs(sb->epot - Epot0) < GMX_REAL_EPS || nminstep >= 20)
+ {
+ /* OK. We couldn't find a significantly lower energy.
+ * If ncorr==0 this was steepest descent, and then we give up.
+ * If not, reset memory to restart as steepest descent before quitting.
+ */
+ if (ncorr == 0)
+ {
+ /* Converged */
+ converged = TRUE;
+ break;
+ }
+ else
+ {
+ /* Reset memory */
+ ncorr = 0;
+ /* Search in gradient direction */
+ for (i = 0; i < n; i++)
+ {
+ dx[point][i] = ff[i];
+ }
+ /* Reset stepsize */
+ stepsize = 1.0/fnorm;
+ continue;
+ }
+ }
+
+ /* Select min energy state of A & C, put the best in xx/ff/Epot
+ */
+ if (sc->epot < sa->epot)
+ {
+ /* Use state C */
+ ems = *sc;
+ step_taken = c;
+ }
+ else
+ {
+ /* Use state A */
+ ems = *sa;
+ step_taken = a;
+ }
+
+ }
+ else
+ {
+ /* found lower */
+ /* Use state C */
+ ems = *sc;
+ step_taken = c;
+ }
+
+ /* Update the memory information, and calculate a new
+ * approximation of the inverse hessian
+ */
+
+ /* Have new data in Epot, xx, ff */
+ if (ncorr < nmaxcorr)
+ {
+ ncorr++;
+ }
+
+ for (i = 0; i < n; i++)
+ {
+ dg[point][i] = lastf[i]-ff[i];
+ dx[point][i] *= step_taken;
+ }
+
+ dgdg = 0;
+ dgdx = 0;
+ for (i = 0; i < n; i++)
+ {
+ dgdg += dg[point][i]*dg[point][i];
+ dgdx += dg[point][i]*dx[point][i];
+ }
+
+ diag = dgdx/dgdg;
+
+ rho[point] = 1.0/dgdx;
+ point++;
+
+ if (point >= nmaxcorr)
+ {
+ point = 0;
+ }
+
+ /* Update */
+ for (i = 0; i < n; i++)
+ {
+ p[i] = ff[i];
+ }
+
+ cp = point;
+
+ /* Recursive update. First go back over the memory points */
+ for (k = 0; k < ncorr; k++)
+ {
+ cp--;
+ if (cp < 0)
+ {
+ cp = ncorr-1;
+ }
+
+ sq = 0;
+ for (i = 0; i < n; i++)
+ {
+ sq += dx[cp][i]*p[i];
+ }
+
+ alpha[cp] = rho[cp]*sq;
+
+ for (i = 0; i < n; i++)
+ {
+ p[i] -= alpha[cp]*dg[cp][i];
+ }
+ }
+
+ for (i = 0; i < n; i++)
+ {
+ p[i] *= diag;
+ }
+
+ /* And then go forward again */
+ for (k = 0; k < ncorr; k++)
+ {
+ yr = 0;
+ for (i = 0; i < n; i++)
+ {
+ yr += p[i]*dg[cp][i];
+ }
+
+ beta = rho[cp]*yr;
+ beta = alpha[cp]-beta;
+
+ for (i = 0; i < n; i++)
+ {
+ p[i] += beta*dx[cp][i];
+ }
+
+ cp++;
+ if (cp >= ncorr)
+ {
+ cp = 0;
+ }
+ }
+
+ for (i = 0; i < n; i++)
+ {
+ if (!frozen[i])
+ {
+ dx[point][i] = p[i];
+ }
+ else
+ {
+ dx[point][i] = 0;
+ }
+ }
+
+ /* Print it if necessary */
+ if (MASTER(cr))
+ {
+ if (mdrunOptions.verbose)
+ {
+ double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
+ fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
+ step, ems.epot, ems.fnorm/sqrtNumAtoms, ems.fmax, ems.a_fmax + 1);
+ fflush(stderr);
+ }
+ /* Store the new (lower) energies */
+ upd_mdebin(mdebin, FALSE, FALSE, (double)step,
+ mdatoms->tmass, enerd, state_global, inputrec->fepvals, inputrec->expandedvals, state_global->box,
+ nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
+ do_log = do_per_step(step, inputrec->nstlog);
+ do_ene = do_per_step(step, inputrec->nstenergy);
+ if (do_log)
+ {
+ print_ebin_header(fplog, step, step);
+ }
+ print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
+ do_log ? fplog : nullptr, step, step, eprNORMAL,
+ mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
+ }
+
+ /* Send x and E to IMD client, if bIMD is TRUE. */
+ if (do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, as_rvec_array(state_global->x.data()), inputrec, 0, wcycle) && MASTER(cr))
+ {
+ IMD_send_positions(inputrec->imd);
+ }
+
+ // Reset stepsize in we are doing more iterations
+ stepsize = 1.0/ems.fnorm;
+
+ /* Stop when the maximum force lies below tolerance.
+ * If we have reached machine precision, converged is already set to true.
+ */
+ converged = converged || (ems.fmax < inputrec->em_tol);
+
+ } /* End of the loop */
+
+ /* IMD cleanup, if bIMD is TRUE. */
+ IMD_finalize(inputrec->bIMD, inputrec->imd);
+
+ if (converged)
+ {
+ step--; /* we never took that last step in this case */
+
+ }
+ if (ems.fmax > inputrec->em_tol)
+ {
+ if (MASTER(cr))
+ {
+ warn_step(fplog, inputrec->em_tol, ems.fmax,
+ step-1 == number_steps, FALSE);
+ }
+ converged = FALSE;
+ }
+
+ /* If we printed energy and/or logfile last step (which was the last step)
+ * we don't have to do it again, but otherwise print the final values.
+ */
+ if (!do_log) /* Write final value to log since we didn't do anythin last step */
+ {
+ print_ebin_header(fplog, step, step);
+ }
+ if (!do_ene || !do_log) /* Write final energy file entries */
+ {
+ print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
+ !do_log ? fplog : nullptr, step, step, eprNORMAL,
+ mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
+ }
+
+ /* Print some stuff... */
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "\nwriting lowest energy coordinates.\n");
+ }
+
+ /* IMPORTANT!
+ * For accurate normal mode calculation it is imperative that we
+ * store the last conformation into the full precision binary trajectory.
+ *
+ * However, we should only do it if we did NOT already write this step
+ * above (which we did if do_x or do_f was true).
+ */
+ do_x = !do_per_step(step, inputrec->nstxout);
+ do_f = !do_per_step(step, inputrec->nstfout);
+ write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm),
+ top_global, inputrec, step,
+ &ems, state_global, observablesHistory);
+
+ if (MASTER(cr))
+ {
+ double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
+ print_converged(stderr, LBFGS, inputrec->em_tol, step, converged,
+ number_steps, &ems, sqrtNumAtoms);
+ print_converged(fplog, LBFGS, inputrec->em_tol, step, converged,
+ number_steps, &ems, sqrtNumAtoms);
+
+ fprintf(fplog, "\nPerformed %d energy evaluations in total.\n", neval);
+ }
+
+ finish_em(cr, outf, walltime_accounting, wcycle);
+
+ /* To print the actual number of steps we needed somewhere */
+ walltime_accounting_set_nsteps_done(walltime_accounting, step);
+}
+
+void
+Integrator::do_steep()
+{
+ const char *SD = "Steepest Descents";
+ gmx_localtop_t *top;
+ gmx_enerdata_t *enerd;
+ gmx_global_stat_t gstat;
+ t_graph *graph;
+ real stepsize;
+ real ustep;
+ gmx_mdoutf_t outf;
+ t_mdebin *mdebin;
+ gmx_bool bDone, bAbort, do_x, do_f;
+ tensor vir, pres;
+ rvec mu_tot;
+ int nsteps;
+ int count = 0;
+ int steps_accepted = 0;
+ auto mdatoms = mdAtoms->mdatoms();
+
+ /* Create 2 states on the stack and extract pointers that we will swap */
+ em_state_t s0 {}, s1 {};
+ em_state_t *s_min = &s0;
+ em_state_t *s_try = &s1;
+
+ /* Init em and store the local state in s_try */
+ init_em(fplog, SD, cr, ms, outputProvider, inputrec, mdrunOptions,
+ state_global, top_global, s_try, &top,
+ nrnb, mu_tot, fr, &enerd, &graph, mdAtoms, &gstat,
+ vsite, constr, nullptr,
+ nfile, fnm, &outf, &mdebin, wcycle);
+
+ /* Print to log file */
+ print_em_start(fplog, cr, walltime_accounting, wcycle, SD);
+
+ /* Set variables for stepsize (in nm). This is the largest
+ * step that we are going to make in any direction.
+ */
+ ustep = inputrec->em_stepsize;
+ stepsize = 0;
+
+ /* Max number of steps */
+ nsteps = inputrec->nsteps;
+
+ if (MASTER(cr))
+ {
+ /* Print to the screen */
+ sp_header(stderr, SD, inputrec->em_tol, nsteps);
+ }
+ if (fplog)
+ {
+ sp_header(fplog, SD, inputrec->em_tol, nsteps);
+ }
+ EnergyEvaluator energyEvaluator {
+ fplog, cr, ms,
+ top_global, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph,
+ mdAtoms, fr, enerd
+ };
+
+ /**** HERE STARTS THE LOOP ****
+ * count is the counter for the number of steps
+ * bDone will be TRUE when the minimization has converged
+ * bAbort will be TRUE when nsteps steps have been performed or when
+ * the stepsize becomes smaller than is reasonable for machine precision
+ */
+ count = 0;
+ bDone = FALSE;
+ bAbort = FALSE;
+ while (!bDone && !bAbort)
+ {
+ bAbort = (nsteps >= 0) && (count == nsteps);
+
+ /* set new coordinates, except for first step */
+ bool validStep = true;
+ if (count > 0)
+ {
+ validStep =
+ do_em_step(cr, inputrec, mdatoms,
+ s_min, stepsize, &s_min->f, s_try,
+ constr, count);
+ }
+
+ if (validStep)
+ {
+ energyEvaluator.run(s_try, mu_tot, vir, pres, count, count == 0);
+ }
+ else
+ {
+ // Signal constraint error during stepping with energy=inf
+ s_try->epot = std::numeric_limits<real>::infinity();
+ }
+
+ if (MASTER(cr))
+ {
+ print_ebin_header(fplog, count, count);
+ }
+
+ if (count == 0)
+ {
+ s_min->epot = s_try->epot;
+ }
+
+ /* Print it if necessary */
+ if (MASTER(cr))
+ {
+ if (mdrunOptions.verbose)
+ {
+ fprintf(stderr, "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
+ count, ustep, s_try->epot, s_try->fmax, s_try->a_fmax+1,
+ ( (count == 0) || (s_try->epot < s_min->epot) ) ? '\n' : '\r');
+ fflush(stderr);
+ }
+
+ if ( (count == 0) || (s_try->epot < s_min->epot) )
+ {
+ /* Store the new (lower) energies */
+ upd_mdebin(mdebin, FALSE, FALSE, (double)count,
+ mdatoms->tmass, enerd, &s_try->s, inputrec->fepvals, inputrec->expandedvals,
+ s_try->s.box, nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
+
+ /* Prepare IMD energy record, if bIMD is TRUE. */
+ IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, count, TRUE);
+
+ print_ebin(mdoutf_get_fp_ene(outf), TRUE,
+ do_per_step(steps_accepted, inputrec->nstdisreout),
+ do_per_step(steps_accepted, inputrec->nstorireout),
+ fplog, count, count, eprNORMAL,
+ mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
+ fflush(fplog);
+ }
+ }
+
+ /* Now if the new energy is smaller than the previous...
+ * or if this is the first step!
+ * or if we did random steps!
+ */
+
+ if ( (count == 0) || (s_try->epot < s_min->epot) )
+ {
+ steps_accepted++;
+
+ /* Test whether the convergence criterion is met... */
+ bDone = (s_try->fmax < inputrec->em_tol);
+
+ /* Copy the arrays for force, positions and energy */
+ /* The 'Min' array always holds the coords and forces of the minimal
+ sampled energy */
+ swap_em_state(&s_min, &s_try);
+ if (count > 0)
+ {
+ ustep *= 1.2;
+ }
+
+ /* Write to trn, if necessary */
+ do_x = do_per_step(steps_accepted, inputrec->nstxout);
+ do_f = do_per_step(steps_accepted, inputrec->nstfout);
+ write_em_traj(fplog, cr, outf, do_x, do_f, nullptr,
+ top_global, inputrec, count,
+ s_min, state_global, observablesHistory);
+ }
+ else
+ {
+ /* If energy is not smaller make the step smaller... */
+ ustep *= 0.5;
+
+ if (DOMAINDECOMP(cr) && s_min->s.ddp_count != cr->dd->ddp_count)
+ {
+ /* Reload the old state */
+ em_dd_partition_system(fplog, count, cr, top_global, inputrec,
+ s_min, top, mdAtoms, fr, vsite, constr,
+ nrnb, wcycle);
+ }
+ }
+
+ /* Determine new step */
+ stepsize = ustep/s_min->fmax;
+
+ /* Check if stepsize is too small, with 1 nm as a characteristic length */
+#if GMX_DOUBLE
+ if (count == nsteps || ustep < 1e-12)
+#else
+ if (count == nsteps || ustep < 1e-6)
+#endif
+ {
+ if (MASTER(cr))
+ {
+ warn_step(fplog, inputrec->em_tol, s_min->fmax,
+ count == nsteps, constr != nullptr);
+ }
+ bAbort = TRUE;
+ }
+
+ /* Send IMD energies and positions, if bIMD is TRUE. */
+ if (do_IMD(inputrec->bIMD, count, cr, TRUE, state_global->box,
+ MASTER(cr) ? as_rvec_array(state_global->x.data()) : nullptr,
+ inputrec, 0, wcycle) &&
+ MASTER(cr))
+ {
+ IMD_send_positions(inputrec->imd);
+ }
+
+ count++;
+ } /* End of the loop */
+
+ /* IMD cleanup, if bIMD is TRUE. */
+ IMD_finalize(inputrec->bIMD, inputrec->imd);
+
+ /* Print some data... */
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "\nwriting lowest energy coordinates.\n");
+ }
+ write_em_traj(fplog, cr, outf, TRUE, inputrec->nstfout, ftp2fn(efSTO, nfile, fnm),
+ top_global, inputrec, count,
+ s_min, state_global, observablesHistory);
+
+ if (MASTER(cr))
+ {
+ double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
+
+ print_converged(stderr, SD, inputrec->em_tol, count, bDone, nsteps,
+ s_min, sqrtNumAtoms);
+ print_converged(fplog, SD, inputrec->em_tol, count, bDone, nsteps,
+ s_min, sqrtNumAtoms);
+ }
+
+ finish_em(cr, outf, walltime_accounting, wcycle);
+
+ /* To print the actual number of steps we needed somewhere */
+ inputrec->nsteps = count;
+
+ walltime_accounting_set_nsteps_done(walltime_accounting, count);
+}
+
+void
+Integrator::do_nm()
+{
+ const char *NM = "Normal Mode Analysis";
+ gmx_mdoutf_t outf;
+ int nnodes, node;
+ gmx_localtop_t *top;
+ gmx_enerdata_t *enerd;
+ gmx_global_stat_t gstat;
+ t_graph *graph;
+ tensor vir, pres;
+ rvec mu_tot;
+ rvec *fneg, *dfdx;
+ gmx_bool bSparse; /* use sparse matrix storage format */
+ size_t sz;
+ gmx_sparsematrix_t * sparse_matrix = nullptr;
+ real * full_matrix = nullptr;
+
+ /* added with respect to mdrun */
+ int row, col;
+ real der_range = 10.0*std::sqrt(GMX_REAL_EPS);
+ real x_min;
+ bool bIsMaster = MASTER(cr);
+ auto mdatoms = mdAtoms->mdatoms();
+
+ if (constr != nullptr)
+ {
+ gmx_fatal(FARGS, "Constraints present with Normal Mode Analysis, this combination is not supported");
+ }
+
+ gmx_shellfc_t *shellfc;
+
+ em_state_t state_work {};
+
+ /* Init em and store the local state in state_minimum */
+ init_em(fplog, NM, cr, ms, outputProvider, inputrec, mdrunOptions,
+ state_global, top_global, &state_work, &top,
+ nrnb, mu_tot, fr, &enerd, &graph, mdAtoms, &gstat,
+ vsite, constr, &shellfc,
+ nfile, fnm, &outf, nullptr, wcycle);
+
+ std::vector<size_t> atom_index = get_atom_index(top_global);
+ snew(fneg, atom_index.size());
+ snew(dfdx, atom_index.size());
+
+#if !GMX_DOUBLE
+ if (bIsMaster)
+ {
+ fprintf(stderr,
+ "NOTE: This version of GROMACS has been compiled in single precision,\n"
+ " which MIGHT not be accurate enough for normal mode analysis.\n"
+ " GROMACS now uses sparse matrix storage, so the memory requirements\n"
+ " are fairly modest even if you recompile in double precision.\n\n");
+ }
+#endif
+
+ /* Check if we can/should use sparse storage format.
+ *
+ * Sparse format is only useful when the Hessian itself is sparse, which it
+ * will be when we use a cutoff.
+ * For small systems (n<1000) it is easier to always use full matrix format, though.
+ */
+ if (EEL_FULL(fr->ic->eeltype) || fr->rlist == 0.0)
+ {
+ GMX_LOG(mdlog.warning).appendText("Non-cutoff electrostatics used, forcing full Hessian format.");
+ bSparse = FALSE;
+ }
+ else if (atom_index.size() < 1000)
+ {
+ GMX_LOG(mdlog.warning).appendTextFormatted("Small system size (N=%d), using full Hessian format.",
+ atom_index.size());
+ bSparse = FALSE;
+ }
+ else
+ {
+ GMX_LOG(mdlog.warning).appendText("Using compressed symmetric sparse Hessian format.");
+ bSparse = TRUE;
+ }
+
+ /* Number of dimensions, based on real atoms, that is not vsites or shell */
+ sz = DIM*atom_index.size();
+
+ fprintf(stderr, "Allocating Hessian memory...\n\n");
+
+ if (bSparse)
+ {
+ sparse_matrix = gmx_sparsematrix_init(sz);
+ sparse_matrix->compressed_symmetric = TRUE;
+ }
+ else
+ {
+ snew(full_matrix, sz*sz);
+ }
+
+ init_nrnb(nrnb);
+
+
+ /* Write start time and temperature */
+ print_em_start(fplog, cr, walltime_accounting, wcycle, NM);
+
+ /* fudge nr of steps to nr of atoms */
+ inputrec->nsteps = atom_index.size()*2;
+
+ if (bIsMaster)
+ {
+ fprintf(stderr, "starting normal mode calculation '%s'\n%d steps.\n\n",
+ *(top_global->name), (int)inputrec->nsteps);
+ }
+
+ nnodes = cr->nnodes;
+
+ /* Make evaluate_energy do a single node force calculation */
+ cr->nnodes = 1;
+ EnergyEvaluator energyEvaluator {
+ fplog, cr, ms,
+ top_global, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph,
+ mdAtoms, fr, enerd
+ };
+ energyEvaluator.run(&state_work, mu_tot, vir, pres, -1, TRUE);
+ cr->nnodes = nnodes;
+
+ /* if forces are not small, warn user */
+ get_state_f_norm_max(cr, &(inputrec->opts), mdatoms, &state_work);
+
+ GMX_LOG(mdlog.warning).appendTextFormatted("Maximum force:%12.5e", state_work.fmax);
+ if (state_work.fmax > 1.0e-3)
+ {
+ GMX_LOG(mdlog.warning).appendText(
+ "The force is probably not small enough to "
+ "ensure that you are at a minimum.\n"
+ "Be aware that negative eigenvalues may occur\n"
+ "when the resulting matrix is diagonalized.");
+ }
+
+ /***********************************************************
+ *
+ * Loop over all pairs in matrix
+ *
+ * do_force called twice. Once with positive and
+ * once with negative displacement
+ *
+ ************************************************************/
+
+ /* Steps are divided one by one over the nodes */
+ bool bNS = true;
+ for (unsigned int aid = cr->nodeid; aid < atom_index.size(); aid += nnodes)
+ {
+ size_t atom = atom_index[aid];
+ for (size_t d = 0; d < DIM; d++)
+ {
+ gmx_int64_t step = 0;
+ int force_flags = GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES;
+ double t = 0;
+
+ x_min = state_work.s.x[atom][d];
+
+ for (unsigned int dx = 0; (dx < 2); dx++)
+ {
+ if (dx == 0)
+ {
+ state_work.s.x[atom][d] = x_min - der_range;
+ }
+ else
+ {
+ state_work.s.x[atom][d] = x_min + der_range;
+ }
+
+ /* Make evaluate_energy do a single node force calculation */
+ cr->nnodes = 1;
+ if (shellfc)
+ {
+ /* Now is the time to relax the shells */
+ relax_shell_flexcon(fplog,
+ cr,
+ ms,
+ mdrunOptions.verbose,
+ step,
+ inputrec,
+ bNS,
+ force_flags,
+ top,
+ constr,
+ enerd,
+ fcd,
+ &state_work.s,
+ state_work.f,
+ vir,
+ mdatoms,
+ nrnb,
+ wcycle,
+ graph,
+ &top_global->groups,
+ shellfc,
+ fr,
+ t,
+ mu_tot,
+ vsite,
+ DdOpenBalanceRegionBeforeForceComputation::no,
+ DdCloseBalanceRegionAfterForceComputation::no);
+ bNS = false;
+ step++;
+ }
+ else
+ {
+ energyEvaluator.run(&state_work, mu_tot, vir, pres, atom*2+dx, FALSE);
+ }
+
+ cr->nnodes = nnodes;
+
+ if (dx == 0)
+ {
+ for (size_t i = 0; i < atom_index.size(); i++)
+ {
+ copy_rvec(state_work.f[atom_index[i]], fneg[i]);
+ }
+ }
+ }
+
+ /* x is restored to original */
+ state_work.s.x[atom][d] = x_min;
+
+ for (size_t j = 0; j < atom_index.size(); j++)
+ {
+ for (size_t k = 0; (k < DIM); k++)
+ {
+ dfdx[j][k] =
+ -(state_work.f[atom_index[j]][k] - fneg[j][k])/(2*der_range);
+ }
+ }
+
+ if (!bIsMaster)
+ {
+#if GMX_MPI
+#define mpi_type GMX_MPI_REAL
+ MPI_Send(dfdx[0], atom_index.size()*DIM, mpi_type, MASTER(cr),
+ cr->nodeid, cr->mpi_comm_mygroup);
+#endif
+ }
+ else
+ {
+ for (node = 0; (node < nnodes && atom+node < atom_index.size()); node++)
+ {
+ if (node > 0)
+ {
+#if GMX_MPI
+ MPI_Status stat;
+ MPI_Recv(dfdx[0], atom_index.size()*DIM, mpi_type, node, node,
+ cr->mpi_comm_mygroup, &stat);
+#undef mpi_type
+#endif
+ }
+
+ row = (atom + node)*DIM + d;
+
+ for (size_t j = 0; j < atom_index.size(); j++)
+ {
+ for (size_t k = 0; k < DIM; k++)
+ {
+ col = j*DIM + k;
+
+ if (bSparse)
+ {
+ if (col >= row && dfdx[j][k] != 0.0)
+ {
+ gmx_sparsematrix_increment_value(sparse_matrix,
+ row, col, dfdx[j][k]);
+ }
+ }
+ else
+ {
+ full_matrix[row*sz+col] = dfdx[j][k];
+ }
+ }
+ }
+ }
+ }
+
+ if (mdrunOptions.verbose && fplog)
+ {
+ fflush(fplog);
+ }
+ }
+ /* write progress */
+ if (bIsMaster && mdrunOptions.verbose)
+ {
+ fprintf(stderr, "\rFinished step %d out of %d",
+ static_cast<int>(std::min(atom+nnodes, atom_index.size())),
+ static_cast<int>(atom_index.size()));
+ fflush(stderr);
+ }
+ }
+
+ if (bIsMaster)
+ {
+ fprintf(stderr, "\n\nWriting Hessian...\n");
+ gmx_mtxio_write(ftp2fn(efMTX, nfile, fnm), sz, sz, full_matrix, sparse_matrix);
+ }
+
+ finish_em(cr, outf, walltime_accounting, wcycle);
+
+ walltime_accounting_set_nsteps_done(walltime_accounting, atom_index.size()*2);
+}
+
+} // namespace gmx
--- /dev/null
- check_and_update_hw_opt_1(&hw_opt, cr, domdecOptions.numPmeRanks);
+/*
+ * 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) 2011,2012,2013,2014,2015,2016,2017,2018, 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.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief Implements the MD runner routine calling all integrators.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_mdrun
+ */
+#include "gmxpre.h"
+
+#include "runner.h"
+
+#include "config.h"
+
+#include <cassert>
+#include <csignal>
+#include <cstdlib>
+#include <cstring>
+
+#include <algorithm>
+
+#include "gromacs/commandline/filenm.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/ewald/ewald-utils.h"
+#include "gromacs/ewald/pme.h"
+#include "gromacs/ewald/pme-gpu-program.h"
+#include "gromacs/fileio/checkpoint.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/clfftinitializer.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/listed-forces/disre.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/calc_verletbuf.h"
+#include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
+#include "gromacs/mdlib/main.h"
+#include "gromacs/mdlib/makeconstraints.h"
+#include "gromacs/mdlib/md_support.h"
+#include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdlib/membed.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/mdlib/nbnxn_tuning.h"
+#include "gromacs/mdlib/qmmm.h"
+#include "gromacs/mdlib/repl_ex.h"
+#include "gromacs/mdlib/sighandler.h"
+#include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdrunutility/mdmodules.h"
+#include "gromacs/mdrunutility/threadaffinity.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/fcdata.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/observableshistory.h"
+#include "gromacs/mdtypes/state.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/pulling/pull_rotation.h"
+#include "gromacs/taskassignment/decidegpuusage.h"
+#include "gromacs/taskassignment/resourcedivision.h"
+#include "gromacs/taskassignment/taskassignment.h"
+#include "gromacs/taskassignment/usergpuids.h"
+#include "gromacs/timing/wallcycle.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/logger.h"
+#include "gromacs/utility/loggerbuilder.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 "integrator.h"
+
+#ifdef GMX_FAHCORE
+#include "corewrap.h"
+#endif
+
+namespace gmx
+{
+
+/*! \brief Barrier for safe simultaneous thread access to mdrunner data
+ *
+ * Used to ensure that the master thread does not modify mdrunner during copy
+ * on the spawned threads. */
+static void threadMpiMdrunnerAccessBarrier()
+{
+#if GMX_THREAD_MPI
+ MPI_Barrier(MPI_COMM_WORLD);
+#endif
+}
+
+void Mdrunner::reinitializeOnSpawnedThread()
+{
+ threadMpiMdrunnerAccessBarrier();
+
+ cr = reinitialize_commrec_for_this_thread(cr);
+
+ GMX_RELEASE_ASSERT(!MASTER(cr), "reinitializeOnSpawnedThread should only be called on spawned threads");
+
+ // Only the master rank writes to the log file
+ 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(const 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; fnm, cr and fplog
+ are reset in the call below, all others should be 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) const
+{
+
+ /* first check whether we even need to start tMPI */
+ if (numThreadsToLaunch < 2)
+ {
+ return cr;
+ }
+
+#if GMX_THREAD_MPI
+ /* 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<const void*>(this)) != TMPI_SUCCESS)
+ {
+ GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
+ }
+
+ threadMpiMdrunnerAccessBarrier();
+#else
+ GMX_UNUSED_VALUE(mdrunner_start_fn);
+#endif
+
+ return reinitialize_commrec_for_this_thread(cr);
+}
+
+} // namespace
+
+/*! \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,
+ const 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 */
+
+ /* 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.
+ */
+ ListSetupType listType = (makeGpuPairList ? ListSetupType::Gpu : ListSetupType::CpuSimdWhenSupported);
+ VerletbufListSetup listSetup = verletbufGetSafeListSetup(listType);
+
+ real rlist_new;
+ calc_verlet_buffer_size(mtop, det(box), ir, ir->nstlist, ir->nstlist - 1, -1, &listSetup, 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,
+ listSetup.cluster_size_i, listSetup.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 */
+ increaseNstlist(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
+{
+
+/*! \brief Return whether GPU acceleration of nonbondeds is supported with the given settings.
+ *
+ * If not, and if a warning may be issued, logs a warning about
+ * falling back to CPU code. With thread-MPI, only the first
+ * call to this function should have \c issueWarning true. */
+static bool gpuAccelerationOfNonbondedIsUseful(const MDLogger &mdlog,
+ const t_inputrec *ir,
+ bool issueWarning)
+{
+ if (ir->opts.ngener - ir->nwall > 1)
+ {
+ /* The GPU code does not support more than one energy group.
+ * If the user requested GPUs explicitly, a fatal error is given later.
+ */
+ if (issueWarning)
+ {
+ GMX_LOG(mdlog.warning).asParagraph()
+ .appendText("Multiple energy groups is not implemented for GPUs, falling back to the CPU. "
+ "For better performance, run on the GPU without energy groups and then do "
+ "gmx mdrun -rerun option on the trajectory with an energy group .tpr file.");
+ }
+ return false;
+ }
+ return true;
+}
+
+//! 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();
+}
+
+//! Make a TaskTarget from an mdrun argument string.
+static TaskTarget findTaskTarget(const char *optionString)
+{
+ TaskTarget returnValue = TaskTarget::Auto;
+
+ if (strncmp(optionString, "auto", 3) == 0)
+ {
+ returnValue = TaskTarget::Auto;
+ }
+ else if (strncmp(optionString, "cpu", 3) == 0)
+ {
+ returnValue = TaskTarget::Cpu;
+ }
+ else if (strncmp(optionString, "gpu", 3) == 0)
+ {
+ returnValue = TaskTarget::Gpu;
+ }
+ else
+ {
+ GMX_ASSERT(false, "Option string should have been checked for sanity already");
+ }
+
+ return returnValue;
+}
+
+int Mdrunner::mdrunner()
+{
+ matrix box;
+ t_nrnb *nrnb;
+ t_forcerec *fr = nullptr;
+ t_fcdata *fcd = nullptr;
+ real ewaldcoeff_q = 0;
+ real ewaldcoeff_lj = 0;
+ gmx_vsite_t *vsite = nullptr;
+ int nChargePerturbed = -1, nTypePerturbed = 0;
+ 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 */
+ std::unique_ptr<gmx::MDModules> mdModules(new gmx::MDModules);
+ t_inputrec inputrecInstance;
+ t_inputrec *inputrec = &inputrecInstance;
+ gmx_mtop_t mtop;
+
+ if (mdrunOptions.continuationOptions.appendFiles)
+ {
+ fplog = nullptr;
+ }
+
+ bool doMembed = opt2bSet("-membed", nfile, fnm);
+ bool doRerun = mdrunOptions.rerun;
+
+ // Handle task-assignment related user options.
+ EmulateGpuNonbonded emulateGpuNonbonded = (getenv("GMX_EMULATE_GPU") != nullptr ?
+ EmulateGpuNonbonded::Yes : EmulateGpuNonbonded::No);
+ std::vector<int> gpuIdsAvailable;
+ try
+ {
+ gpuIdsAvailable = parseUserGpuIds(hw_opt.gpuIdsAvailable);
+ // TODO We could put the GPU IDs into a std::map to find
+ // duplicates, but for the small numbers of IDs involved, this
+ // code is simple and fast.
+ for (size_t i = 0; i != gpuIdsAvailable.size(); ++i)
+ {
+ for (size_t j = i+1; j != gpuIdsAvailable.size(); ++j)
+ {
+ if (gpuIdsAvailable[i] == gpuIdsAvailable[j])
+ {
+ GMX_THROW(InvalidInputError(formatString("The string of available GPU device IDs '%s' may not contain duplicate device IDs", hw_opt.gpuIdsAvailable.c_str())));
+ }
+ }
+ }
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+
+ std::vector<int> userGpuTaskAssignment;
+ try
+ {
+ userGpuTaskAssignment = parseUserGpuIds(hw_opt.userGpuTaskAssignment);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ auto nonbondedTarget = findTaskTarget(nbpu_opt);
+ auto pmeTarget = findTaskTarget(pme_opt);
+ auto pmeFftTarget = findTaskTarget(pme_fft_opt);
+ PmeRunMode pmeRunMode = PmeRunMode::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());
+
+ // TODO The thread-MPI master rank makes a working
+ // PhysicalNodeCommunicator here, but it gets rebuilt by all ranks
+ // after the threads have been launched. This works because no use
+ // is made of that communicator until after the execution paths
+ // have rejoined. But it is likely that we can improve the way
+ // this is expressed, e.g. by expressly running detection only the
+ // master rank for thread-MPI, rather than relying on the mutex
+ // and reference count.
+ PhysicalNodeCommunicator physicalNodeComm(MPI_COMM_WORLD, gmx_physicalnode_id_hash());
+ hwinfo = gmx_detect_hardware(mdlog, physicalNodeComm);
+
+ gmx_print_detected_hardware(fplog, cr, ms, mdlog, hwinfo);
+
+ std::vector<int> gpuIdsToUse;
+ auto compatibleGpus = getCompatibleGpus(hwinfo->gpu_info);
+ if (gpuIdsAvailable.empty())
+ {
+ gpuIdsToUse = compatibleGpus;
+ }
+ else
+ {
+ for (const auto &availableGpuId : gpuIdsAvailable)
+ {
+ bool availableGpuIsCompatible = false;
+ for (const auto &compatibleGpuId : compatibleGpus)
+ {
+ if (availableGpuId == compatibleGpuId)
+ {
+ availableGpuIsCompatible = true;
+ break;
+ }
+ }
+ if (!availableGpuIsCompatible)
+ {
+ gmx_fatal(FARGS, "You limited the set of compatible GPUs to a set that included ID #%d, but that ID is not for a compatible GPU. List only compatible GPUs.", availableGpuId);
+ }
+ gpuIdsToUse.push_back(availableGpuId);
+ }
+ }
+
+ 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> globalState;
+
+ if (SIMMASTER(cr))
+ {
+ /* Only the master rank has the global state */
+ globalState = std::unique_ptr<t_state>(new t_state);
+
+ /* Read (nearly) all data required for the simulation */
+ read_tpx_state(ftp2fn(efTPR, nfile, fnm), inputrec, globalState.get(), &mtop);
+
+ if (inputrec->cutoff_scheme != ecutsVERLET)
+ {
+ if (nstlist_cmdline > 0)
+ {
+ gmx_fatal(FARGS, "Can not set nstlist with the group cut-off scheme");
+ }
+
+ if (!compatibleGpus.empty())
+ {
+ 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");
+ }
+ }
+ }
+
+ /* Check and update the hardware options for internal consistency */
++ check_and_update_hw_opt_1(mdlog, &hw_opt, cr, domdecOptions.numPmeRanks);
+
+ /* 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 && SIMMASTER(cr))
+ {
+ if (domdecOptions.numPmeRanks > 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);
+
+ bool useGpuForNonbonded = false;
+ bool useGpuForPme = false;
+ try
+ {
+ // If the user specified the number of ranks, then we must
+ // respect that, but in default mode, we need to allow for
+ // the number of GPUs to choose the number of ranks.
+
+ useGpuForNonbonded = decideWhetherToUseGpusForNonbondedWithThreadMpi
+ (nonbondedTarget, gpuIdsToUse, userGpuTaskAssignment, emulateGpuNonbonded,
+ inputrec->cutoff_scheme == ecutsVERLET,
+ gpuAccelerationOfNonbondedIsUseful(mdlog, inputrec, GMX_THREAD_MPI),
+ hw_opt.nthreads_tmpi);
+ auto canUseGpuForPme = pme_gpu_supports_build(nullptr) && pme_gpu_supports_input(inputrec, nullptr);
+ useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi
+ (useGpuForNonbonded, pmeTarget, gpuIdsToUse, userGpuTaskAssignment,
+ canUseGpuForPme, hw_opt.nthreads_tmpi, domdecOptions.numPmeRanks);
+
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+
+ /* Determine how many thread-MPI ranks to start.
+ *
+ * TODO Over-writing the user-supplied value here does
+ * prevent any possible subsequent checks from working
+ * correctly. */
+ hw_opt.nthreads_tmpi = get_nthreads_mpi(hwinfo,
+ &hw_opt,
+ gpuIdsToUse,
+ useGpuForNonbonded,
+ useGpuForPme,
+ 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.
+ physicalNodeComm = PhysicalNodeCommunicator(MPI_COMM_WORLD, gmx_physicalnode_id_hash());
+ }
+ // END OF CAUTION: cr and physicalNodeComm are now reliable
+
+ if (PAR(cr))
+ {
+ /* now broadcast everything to the non-master nodes/threads: */
+ init_parallel(cr, inputrec, &mtop);
+ }
+
+ // Now each rank knows the inputrec that SIMMASTER read and used,
+ // and (if applicable) cr->nnodes has been assigned the number of
+ // thread-MPI ranks that have been chosen. The ranks can now all
+ // run the task-deciding functions and will agree on the result
+ // without needing to communicate.
+ //
+ // TODO Should we do the communication in debug mode to support
+ // having an assertion?
+ //
+ // Note that these variables describe only their own node.
+ bool useGpuForNonbonded = false;
+ bool useGpuForPme = false;
+ try
+ {
+ // It's possible that there are different numbers of GPUs on
+ // different nodes, which is the user's responsibilty to
+ // handle. If unsuitable, we will notice that during task
+ // assignment.
+ bool gpusWereDetected = hwinfo->ngpu_compatible_tot > 0;
+ useGpuForNonbonded = decideWhetherToUseGpusForNonbonded(nonbondedTarget, userGpuTaskAssignment,
+ emulateGpuNonbonded, inputrec->cutoff_scheme == ecutsVERLET,
+ gpuAccelerationOfNonbondedIsUseful(mdlog, inputrec, !GMX_THREAD_MPI),
+ gpusWereDetected);
+ auto canUseGpuForPme = pme_gpu_supports_build(nullptr) && pme_gpu_supports_input(inputrec, nullptr);
+ useGpuForPme = decideWhetherToUseGpusForPme(useGpuForNonbonded, pmeTarget, userGpuTaskAssignment,
+ canUseGpuForPme, cr->nnodes, domdecOptions.numPmeRanks,
+ gpusWereDetected);
+
+ pmeRunMode = (useGpuForPme ? PmeRunMode::GPU : PmeRunMode::CPU);
+ if (pmeRunMode == PmeRunMode::GPU)
+ {
+ if (pmeFftTarget == TaskTarget::Cpu)
+ {
+ pmeRunMode = PmeRunMode::Mixed;
+ }
+ }
+ else if (pmeFftTarget == TaskTarget::Gpu)
+ {
+ gmx_fatal(FARGS, "Assigning FFTs to GPU requires PME to be assigned to GPU as well. With PME on CPU you should not be using -pmefft.");
+ }
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+
+ // TODO: Error handling
+ mdModules->assignOptionsToModules(*inputrec->params, nullptr);
+
+ if (fplog != nullptr)
+ {
+ pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
+ fprintf(fplog, "\n");
+ }
+
+ if (SIMMASTER(cr))
+ {
+ /* now make sure the state is initialized and propagated */
+ set_state_entries(globalState.get(), inputrec);
+ }
+
+ /* NM and TPI parallelize over force/energy calculations, not atoms,
+ * so we need to initialize and broadcast the global state.
+ */
+ if (inputrec->eI == eiNM || inputrec->eI == eiTPI)
+ {
+ if (!MASTER(cr))
+ {
+ globalState = std::unique_ptr<t_state>(new t_state);
+ }
+ broadcastStateWithoutDynamics(cr, globalState.get());
+ }
+
+ /* A parallel command line option consistency check that we can
+ only do after any threads have started. */
+ if (!PAR(cr) && (domdecOptions.numCells[XX] > 1 ||
+ domdecOptions.numCells[YY] > 1 ||
+ domdecOptions.numCells[ZZ] > 1 ||
+ domdecOptions.numPmeRanks > 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 (domdecOptions.numPmeRanks > 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");
+ }
+
+ domdecOptions.numPmeRanks = 0;
+ }
+
+ if (useGpuForNonbonded && domdecOptions.numPmeRanks < 0)
+ {
+ /* With NB GPUs we don't automatically use PME-only CPU 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.
+ */
+ domdecOptions.numPmeRanks = 0;
+ }
+ if (useGpuForPme)
+ {
+ if (domdecOptions.numPmeRanks < 0)
+ {
+ domdecOptions.numPmeRanks = 0;
+ // TODO possibly print a note that one can opt-in for a separate PME GPU rank?
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(domdecOptions.numPmeRanks <= 1, "PME GPU decomposition is not supported");
+ }
+ }
+
+#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, ms, fcd, globalState.get(), replExParams.exchangeInterval > 0);
+
+ init_orires(fplog, &mtop, inputrec, cr, ms, globalState.get(), &(fcd->orires));
+
+ auto deform = prepareBoxDeformation(globalState->box, cr, *inputrec);
+
+ ObservablesHistory observablesHistory = {};
+
+ ContinuationOptions &continuationOptions = mdrunOptions.continuationOptions;
+
+ if (continuationOptions.startedFromCheckpoint)
+ {
+ /* 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, domdecOptions.numCells,
+ inputrec, globalState.get(),
+ &bReadEkin, &observablesHistory,
+ continuationOptions.appendFiles,
+ continuationOptions.appendFilesOptionSet,
+ mdrunOptions.reproducible);
+
+ if (bReadEkin)
+ {
+ continuationOptions.haveReadEkin = true;
+ }
+ }
+
+ if (SIMMASTER(cr) && continuationOptions.appendFiles)
+ {
+ gmx_log_open(ftp2fn(efLOG, nfile, fnm), cr,
+ continuationOptions.appendFiles, &fplog);
+ logOwner = buildLogger(fplog, nullptr);
+ mdlog = logOwner.logger();
+ }
+
+ if (mdrunOptions.numStepsCommandline > -2)
+ {
+ GMX_LOG(mdlog.info).asParagraph().
+ appendText("The -nsteps functionality is deprecated, and may be removed in a future version. "
+ "Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp file field.");
+ }
+ /* override nsteps with value set on the commamdline */
+ override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec);
+
+ if (SIMMASTER(cr))
+ {
+ copy_mat(globalState->box, box);
+ }
+
+ if (PAR(cr))
+ {
+ gmx_bcast(sizeof(box), box, cr);
+ }
+
+ /* Update rlist and nstlist. */
+ if (inputrec->cutoff_scheme == ecutsVERLET)
+ {
+ prepare_verlet_scheme(fplog, cr, inputrec, nstlist_cmdline, &mtop, box,
+ useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes), *hwinfo->cpuInfo);
+ }
+
+ /* Initalize the domain decomposition */
+ if (PAR(cr) && !(EI_TPI(inputrec->eI) ||
+ inputrec->eI == eiNM))
+ {
+ cr->dd = init_domain_decomposition(fplog, cr, domdecOptions, mdrunOptions,
+ &mtop, inputrec,
+ box, positionsFromStatePointer(globalState.get()));
+ // Note that local state still does not exist yet.
+ }
+ else
+ {
+ /* PME, if used, is done on all nodes with 1D decomposition */
+ cr->npmenodes = 0;
+ cr->duty = (DUTY_PP | DUTY_PME);
+
+ 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);
+ }
+
+#if GMX_MPI
+ if (isMultiSim(ms))
+ {
+ 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",
+ ms->sim, 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 the number of OpenMP threads requested */
+ checkAndUpdateRequestedNumOpenmpThreads(&hw_opt, *hwinfo, cr, ms, physicalNodeComm.size_,
+ pmeRunMode, mtop);
+
+ gmx_omp_nthreads_init(mdlog, cr,
+ hwinfo->nthreads_hw_avail,
+ physicalNodeComm.size_,
+ hw_opt.nthreads_omp,
+ hw_opt.nthreads_omp_pme,
+ !thisRankHasDuty(cr, DUTY_PP),
+ inputrec->cutoff_scheme == ecutsVERLET);
+
+#ifndef NDEBUG
+ if (EI_TPI(inputrec->eI) &&
+ inputrec->cutoff_scheme == ecutsVERLET)
+ {
+ gmx_feenableexcept();
+ }
+#endif
+
+ // Build a data structure that expresses which kinds of non-bonded
+ // task are handled by this rank.
+ //
+ // TODO Later, this might become a loop over all registered modules
+ // relevant to the mdp inputs, to find those that have such tasks.
+ //
+ // TODO This could move before init_domain_decomposition() as part
+ // of refactoring that separates the responsibility for duty
+ // assignment from setup for communication between tasks, and
+ // setup for tasks handled with a domain (ie including short-ranged
+ // tasks, bonded tasks, etc.).
+ //
+ // Note that in general useGpuForNonbonded, etc. can have a value
+ // that is inconsistent with the presence of actual GPUs on any
+ // rank, and that is not known to be a problem until the
+ // duty of the ranks on a node become node.
+ //
+ // TODO Later we might need the concept of computeTasksOnThisRank,
+ // from which we construct gpuTasksOnThisRank.
+ //
+ // 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.
+ auto haveGpus = !gpuIdsToUse.empty();
+ std::vector<GpuTask> gpuTasksOnThisRank;
+ if (thisRankHasDuty(cr, DUTY_PP))
+ {
+ if (useGpuForNonbonded)
+ {
+ if (haveGpus)
+ {
+ gpuTasksOnThisRank.push_back(GpuTask::Nonbonded);
+ }
+ else if (nonbondedTarget == TaskTarget::Gpu)
+ {
+ gmx_fatal(FARGS, "Cannot run short-ranged nonbonded interactions on a GPU because there is none detected.");
+ }
+ }
+ }
+ // TODO cr->duty & DUTY_PME should imply that a PME algorithm is active, but currently does not.
+ if (EEL_PME(inputrec->coulombtype) && (thisRankHasDuty(cr, DUTY_PME)))
+ {
+ if (useGpuForPme)
+ {
+ if (haveGpus)
+ {
+ gpuTasksOnThisRank.push_back(GpuTask::Pme);
+ }
+ else if (pmeTarget == TaskTarget::Gpu)
+ {
+ gmx_fatal(FARGS, "Cannot run PME on a GPU because there is none detected.");
+ }
+ }
+ }
+
+ GpuTaskAssignment gpuTaskAssignment;
+ try
+ {
+ // Produce the task assignment for this rank.
+ gpuTaskAssignment = runTaskAssignment(gpuIdsToUse, userGpuTaskAssignment, *hwinfo,
+ mdlog, cr, ms, physicalNodeComm, gpuTasksOnThisRank);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+
+ /* Prevent other ranks from continuing after an issue was found
+ * and reported as a fatal error.
+ *
+ * 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);
+ }
+ if (isMultiSim(ms))
+ {
+ if (SIMMASTER(cr))
+ {
+ MPI_Barrier(ms->mpi_comm_masters);
+ }
+ /* We need another barrier to prevent non-master ranks from contiuing
+ * when an error occured in a different simulation.
+ */
+ MPI_Barrier(cr->mpi_comm_mysim);
+ }
+#endif
+
+ /* Now that we know the setup is consistent, check for efficiency */
+ check_resource_division_efficiency(hwinfo, !gpuTaskAssignment.empty(), mdrunOptions.ntompOptionIsSet,
+ cr, mdlog);
+
+ gmx_device_info_t *nonbondedDeviceInfo = nullptr;
+
+ if (thisRankHasDuty(cr, DUTY_PP))
+ {
+ // This works because only one task of each type is currently permitted.
+ auto nbGpuTaskMapping = std::find_if(gpuTaskAssignment.begin(), gpuTaskAssignment.end(),
+ hasTaskType<GpuTask::Nonbonded>);
+ if (nbGpuTaskMapping != gpuTaskAssignment.end())
+ {
+ int nonbondedDeviceId = nbGpuTaskMapping->deviceId_;
+ nonbondedDeviceInfo = getDeviceInfo(hwinfo->gpu_info, nonbondedDeviceId);
+ init_gpu(mdlog, nonbondedDeviceInfo);
+
+ if (DOMAINDECOMP(cr))
+ {
+ /* When we share GPUs over ranks, we need to know this for the DLB */
+ dd_setup_dlb_resource_sharing(cr, nonbondedDeviceId);
+ }
+
+ }
+ }
+
+ std::unique_ptr<ClfftInitializer> initializedClfftLibrary;
+
+ gmx_device_info_t *pmeDeviceInfo = nullptr;
+ // Later, this program could contain kernels that might be later
+ // re-used as auto-tuning progresses, or subsequent simulations
+ // are invoked.
+ PmeGpuProgramStorage pmeGpuProgram;
+ // This works because only one task of each type is currently permitted.
+ auto pmeGpuTaskMapping = std::find_if(gpuTaskAssignment.begin(), gpuTaskAssignment.end(), hasTaskType<GpuTask::Pme>);
+ const bool thisRankHasPmeGpuTask = (pmeGpuTaskMapping != gpuTaskAssignment.end());
+ if (thisRankHasPmeGpuTask)
+ {
+ pmeDeviceInfo = getDeviceInfo(hwinfo->gpu_info, pmeGpuTaskMapping->deviceId_);
+ init_gpu(mdlog, pmeDeviceInfo);
+ pmeGpuProgram = buildPmeGpuProgram(pmeDeviceInfo);
+ // TODO It would be nice to move this logic into the factory
+ // function. See Redmine #2535.
+ bool isMasterThread = !GMX_THREAD_MPI || MASTER(cr);
+ if (pmeRunMode == PmeRunMode::GPU && !initializedClfftLibrary && isMasterThread)
+ {
+ initializedClfftLibrary = initializeClfftLibrary();
+ }
+ }
+
+ /* 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);
+
+ int numThreadsOnThisRank;
+ /* threads on this MPI process or TMPI thread */
+ if (thisRankHasDuty(cr, DUTY_PP))
+ {
+ numThreadsOnThisRank = gmx_omp_nthreads_get(emntNonbonded);
+ }
+ else
+ {
+ numThreadsOnThisRank = nthreads_pme;
+ }
+
+ checkHardwareOversubscription(numThreadsOnThisRank, cr->nodeid,
+ *hwinfo->hardwareTopology,
+ physicalNodeComm, mdlog);
+
+ 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 numThreadsOnThisNode, intraNodeThreadOffset;
+ analyzeThreadsOnThisNode(physicalNodeComm, numThreadsOnThisRank, &numThreadsOnThisNode,
+ &intraNodeThreadOffset);
+
+ /* Set the CPU affinity */
+ gmx_set_thread_affinity(mdlog, cr, &hw_opt, *hwinfo->hardwareTopology,
+ numThreadsOnThisRank, numThreadsOnThisNode,
+ intraNodeThreadOffset, nullptr);
+ }
+
+ if (mdrunOptions.timingOptions.resetStep > -1)
+ {
+ GMX_LOG(mdlog.info).asParagraph().
+ appendText("The -resetstep functionality is deprecated, and may be removed in a future version.");
+ }
+ wcycle = wallcycle_init(fplog, mdrunOptions.timingOptions.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, globalState.get(), cr, &mdrunOptions.checkpointOptions.period);
+ }
+
+ std::unique_ptr<MDAtoms> mdAtoms;
+
+ snew(nrnb, 1);
+ if (thisRankHasDuty(cr, DUTY_PP))
+ {
+ /* 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),
+ opt2fns("-tableb", nfile, fnm),
+ *hwinfo, nonbondedDeviceInfo,
+ FALSE,
+ pforce);
+
+ /* Initialize QM-MM */
+ if (fr->bQMMM)
+ {
+ GMX_LOG(mdlog.info).asParagraph().
+ appendText("Large parts of the QM/MM support is deprecated, and may be removed in a future "
+ "version. Please get in touch with the developers if you find the support useful, "
+ "as help is needed if the functionality is to continue to be available.");
+ 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 = makeMDAtoms(fplog, mtop, *inputrec, thisRankHasPmeGpuTask);
+ if (globalState && thisRankHasPmeGpuTask)
+ {
+ // The pinning of coordinates in the global state object works, because we only use
+ // PME on GPU without DD or on a separate PME rank, and because the local state pointer
+ // points to the global state object without DD.
+ // FIXME: MD and EM separately set up the local state - this should happen in the same function,
+ // which should also perform the pinning.
+ changePinningPolicy(&globalState->x, pme_get_pinning_policy());
+ }
+
+ /* Initialize the virtual site communication */
+ vsite = initVsite(mtop, cr);
+
+ 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)
+ {
+ rvec *xGlobal = as_rvec_array(globalState->x.data());
+ do_pbc_first_mtop(fplog, inputrec->ePBC, box, &mtop, xGlobal);
+ }
+ if (vsite)
+ {
+ /* Correct initial vsite positions are required
+ * for the initial distribution in the domain decomposition
+ * and for the initial shell prediction.
+ */
+ constructVsitesGlobal(mtop, globalState->x);
+ }
+ }
+
+ if (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
+ {
+ ewaldcoeff_q = fr->ic->ewaldcoeff_q;
+ ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
+ }
+ }
+ else
+ {
+ /* This is a PME only node */
+
+ GMX_ASSERT(globalState == nullptr, "We don't need the state on a PME only rank and expect it to be unitialized");
+
+ ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
+ ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
+ }
+
+ gmx_pme_t *sepPmeData = nullptr;
+ // This reference hides the fact that PME data is owned by runner on PME-only ranks and by forcerec on other ranks
+ GMX_ASSERT(thisRankHasDuty(cr, DUTY_PP) == (fr != nullptr), "Double-checking that only PME-only ranks have no forcerec");
+ gmx_pme_t * &pmedata = fr ? fr->pmedata : sepPmeData;
+
+ /* 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 && mdAtoms->mdatoms())
+ {
+ nChargePerturbed = mdAtoms->mdatoms()->nChargePerturbed;
+ if (EVDW_PME(inputrec->vdwtype))
+ {
+ nTypePerturbed = mdAtoms->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 (thisRankHasDuty(cr, DUTY_PME))
+ {
+ try
+ {
+ pmedata = gmx_pme_init(cr,
+ getNumPmeDomains(cr->dd),
+ inputrec,
+ mtop.natoms, nChargePerturbed, nTypePerturbed,
+ mdrunOptions.reproducible,
+ ewaldcoeff_q, ewaldcoeff_lj,
+ nthreads_pme,
+ pmeRunMode, nullptr,
+ pmeDeviceInfo, pmeGpuProgram.get(), mdlog);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ }
+ }
+
+
+ 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 (thisRankHasDuty(cr, 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,
+ &mtop, cr, inputrec->fepvals->init_lambda);
+ if (EI_DYNAMICS(inputrec->eI) && MASTER(cr))
+ {
+ init_pull_output_files(inputrec->pull_work,
+ nfile, fnm, oenv,
+ continuationOptions);
+ }
+ }
+
+ if (inputrec->bRot)
+ {
+ /* Initialize enforced rotation code */
+ init_rot(fplog, inputrec, nfile, fnm, cr, globalState.get(), &mtop, oenv, mdrunOptions);
+ }
+
+ /* Let makeConstraints 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 doEssentialDynamics = (opt2fn_null("-ei", nfile, fnm) != nullptr || observablesHistory.edsamHistory);
+ auto constr = makeConstraints(mtop, *inputrec, doEssentialDynamics,
+ fplog, *mdAtoms->mdatoms(),
+ cr, *ms, nrnb, wcycle, fr->bMolPBC);
+
+ 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,
+ domdecOptions.checkBondedInteractions,
+ fr->cginfo_mb);
+ }
+
+ /* Now do whatever the user wants us to do (how flexible...) */
+ Integrator integrator {
+ fplog, cr, ms, mdlog, nfile, fnm,
+ oenv,
+ mdrunOptions,
+ vsite, constr.get(),
+ deform.get(),
+ mdModules->outputProvider(),
+ inputrec, &mtop,
+ fcd,
+ globalState.get(),
+ &observablesHistory,
+ mdAtoms.get(), nrnb, wcycle, fr,
+ replExParams,
+ membed,
+ walltime_accounting
+ };
+ integrator.run(inputrec->eI);
+ 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, inputrec, pmeRunMode);
+ }
+
+ 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,
+ pmedata,
+ EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
+
+ // Free PME data
+ if (pmedata)
+ {
+ gmx_pme_destroy(pmedata);
+ pmedata = nullptr;
+ }
+
+ // FIXME: this is only here to manually unpin mdAtoms->chargeA_ and state->x,
+ // before we destroy the GPU context(s) in free_gpu_resources().
+ // Pinned buffers are associated with contexts in CUDA.
+ // As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
+ mdAtoms.reset(nullptr);
+ globalState.reset(nullptr);
+ mdModules.reset(nullptr); // destruct force providers here as they might also use the GPU
+
+ /* Free GPU memory and set a physical node tMPI barrier (which should eventually go away) */
+ free_gpu_resources(fr, physicalNodeComm);
+ free_gpu(nonbondedDeviceInfo);
+ free_gpu(pmeDeviceInfo);
+ done_forcerec(fr, mtop.molblock.size(), mtop.groups.grps[egcENER].nr);
+ sfree(fcd);
+
+ if (doMembed)
+ {
+ free_membed(membed);
+ }
+
+ gmx_hardware_info_free();
+
+ /* Does what it says */
+ print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
+ walltime_accounting_destroy(walltime_accounting);
+ sfree(nrnb);
+
+ /* Close logfile already here if we were appending to it */
+ if (MASTER(cr) && continuationOptions.appendFiles)
+ {
+ gmx_log_close(fplog);
+ fplog = nullptr;
+ }
+
+ 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))
+ {
+ done_commrec(cr);
+ tMPI_Finalize();
+ }
+#endif
+
+ return rc;
+}
+
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff