From 40b9519718d52b4cdb329dde25bb52a4bca46de9 Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Fri, 22 Apr 2016 14:52:29 +0200
Subject: [PATCH] gromacs 5.1.2 patch:
fix a problem when md.log was appended
plumed was trying to write on it after
md.log was already closed
---
.../src/programs/mdrun/mdrun.cpp | 6 -
.../src/programs/mdrun/runner.cpp | 1363 +++++++++++++++++
.../src/programs/mdrun/runner.cpp.preplumed | 1351 ++++++++++++++++
3 files changed, 2714 insertions(+), 6 deletions(-)
create mode 100644 patches/gromacs-5.1.2.diff/src/programs/mdrun/runner.cpp
create mode 100644 patches/gromacs-5.1.2.diff/src/programs/mdrun/runner.cpp.preplumed
diff --git a/patches/gromacs-5.1.2.diff/src/programs/mdrun/mdrun.cpp b/patches/gromacs-5.1.2.diff/src/programs/mdrun/mdrun.cpp
index 626a3c002..d91e40b12 100644
--- a/patches/gromacs-5.1.2.diff/src/programs/mdrun/mdrun.cpp
+++ b/patches/gromacs-5.1.2.diff/src/programs/mdrun/mdrun.cpp
@@ -575,12 +575,6 @@ int gmx_mdrun(int argc, char *argv[])
nmultisim, repl_ex_nst, repl_ex_nex, repl_ex_seed,
pforce, cpt_period, max_hours, imdport, Flags);
- /* PLUMED */
- if(plumedswitch){
- plumed_finalize(plumedmain);
- }
- /* END PLUMED */
-
/* Log file has to be closed in mdrunner if we are appending to it
(fplog not set here) */
if (MASTER(cr) && !bDoAppendFiles)
diff --git a/patches/gromacs-5.1.2.diff/src/programs/mdrun/runner.cpp b/patches/gromacs-5.1.2.diff/src/programs/mdrun/runner.cpp
new file mode 100644
index 000000000..398697eb4
--- /dev/null
+++ b/patches/gromacs-5.1.2.diff/src/programs/mdrun/runner.cpp
@@ -0,0 +1,1363 @@
+/*
+ * 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, 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.
+ */
+
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include <assert.h>
+#include <signal.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include <algorithm>
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/ewald/pme.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/gmx_detect_hardware.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/gmx_thread_affinity.h"
+#include "gromacs/legacyheaders/inputrec.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/sighandler.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/calculate-ewald-splitting-coefficient.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/calc_verletbuf.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/pulling/pull_rotation.h"
+#include "gromacs/swap/swapcoords.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "deform.h"
+#include "membed.h"
+#include "repl_ex.h"
+#include "resource-division.h"
+
+/* PLUMED */
+#include "../../../Plumed.h"
+extern int plumedswitch;
+extern plumed plumedmain;
+/* END PLUMED */
+
+#ifdef GMX_FAHCORE
+#include "corewrap.h"
+#endif
+
+typedef struct {
+ gmx_integrator_t *func;
+} gmx_intp_t;
+
+/* The array should match the eI array in include/types/enums.h */
+const gmx_intp_t integrator[eiNR] = { {do_md}, {do_steep}, {do_cg}, {do_md}, {do_md}, {do_nm}, {do_lbfgs}, {do_tpi}, {do_tpi}, {do_md}, {do_md}, {do_md}};
+
+gmx_int64_t deform_init_init_step_tpx;
+matrix deform_init_box_tpx;
+tMPI_Thread_mutex_t deform_init_box_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+
+
+#ifdef GMX_THREAD_MPI
+/* The minimum number of atoms per tMPI thread. With fewer atoms than this,
+ * the number of threads will get lowered.
+ */
+#define MIN_ATOMS_PER_MPI_THREAD 90
+#define MIN_ATOMS_PER_GPU 900
+
+struct mdrunner_arglist
+{
+ gmx_hw_opt_t hw_opt;
+ FILE *fplog;
+ t_commrec *cr;
+ int nfile;
+ const t_filenm *fnm;
+ output_env_t oenv;
+ gmx_bool bVerbose;
+ gmx_bool bCompact;
+ int nstglobalcomm;
+ ivec ddxyz;
+ int dd_node_order;
+ real rdd;
+ real rconstr;
+ const char *dddlb_opt;
+ real dlb_scale;
+ const char *ddcsx;
+ const char *ddcsy;
+ const char *ddcsz;
+ const char *nbpu_opt;
+ int nstlist_cmdline;
+ gmx_int64_t nsteps_cmdline;
+ int nstepout;
+ int resetstep;
+ int nmultisim;
+ int repl_ex_nst;
+ int repl_ex_nex;
+ int repl_ex_seed;
+ real pforce;
+ real cpt_period;
+ real max_hours;
+ int imdport;
+ unsigned long Flags;
+};
+
+
+/* The function used for spawning threads. Extracts the mdrunner()
+ arguments from its one argument and calls mdrunner(), after making
+ a commrec. */
+static void mdrunner_start_fn(void *arg)
+{
+ struct mdrunner_arglist *mda = (struct mdrunner_arglist*)arg;
+ struct mdrunner_arglist mc = *mda; /* copy the arg list to make sure
+ that it's thread-local. This doesn't
+ copy pointed-to items, of course,
+ but those are all const. */
+ t_commrec *cr; /* we need a local version of this */
+ FILE *fplog = NULL;
+ t_filenm *fnm;
+
+ fnm = dup_tfn(mc.nfile, mc.fnm);
+
+ cr = reinitialize_commrec_for_this_thread(mc.cr);
+
+ if (MASTER(cr))
+ {
+ fplog = mc.fplog;
+ }
+
+ mdrunner(&mc.hw_opt, fplog, cr, mc.nfile, fnm, mc.oenv,
+ mc.bVerbose, mc.bCompact, mc.nstglobalcomm,
+ mc.ddxyz, mc.dd_node_order, mc.rdd,
+ mc.rconstr, mc.dddlb_opt, mc.dlb_scale,
+ mc.ddcsx, mc.ddcsy, mc.ddcsz,
+ mc.nbpu_opt, mc.nstlist_cmdline,
+ mc.nsteps_cmdline, mc.nstepout, mc.resetstep,
+ mc.nmultisim, mc.repl_ex_nst, mc.repl_ex_nex, mc.repl_ex_seed, mc.pforce,
+ mc.cpt_period, mc.max_hours, mc.imdport, mc.Flags);
+}
+
+/* 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 besides nthreads are the same as for mdrunner(). */
+static t_commrec *mdrunner_start_threads(gmx_hw_opt_t *hw_opt,
+ FILE *fplog, t_commrec *cr, int nfile,
+ const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
+ gmx_bool bCompact, int nstglobalcomm,
+ ivec ddxyz, int dd_node_order, real rdd, real rconstr,
+ const char *dddlb_opt, real dlb_scale,
+ const char *ddcsx, const char *ddcsy, const char *ddcsz,
+ const char *nbpu_opt, int nstlist_cmdline,
+ gmx_int64_t nsteps_cmdline,
+ int nstepout, int resetstep,
+ int nmultisim, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
+ real pforce, real cpt_period, real max_hours,
+ unsigned long Flags)
+{
+ int ret;
+ struct mdrunner_arglist *mda;
+ t_commrec *crn; /* the new commrec */
+ t_filenm *fnmn;
+
+ /* first check whether we even need to start tMPI */
+ if (hw_opt->nthreads_tmpi < 2)
+ {
+ return cr;
+ }
+
+ /* a few small, one-time, almost unavoidable memory leaks: */
+ snew(mda, 1);
+ fnmn = dup_tfn(nfile, fnm);
+
+ /* fill the data structure to pass as void pointer to thread start fn */
+ /* hw_opt contains pointers, which should all be NULL at this stage */
+ mda->hw_opt = *hw_opt;
+ mda->fplog = fplog;
+ mda->cr = cr;
+ mda->nfile = nfile;
+ mda->fnm = fnmn;
+ mda->oenv = oenv;
+ mda->bVerbose = bVerbose;
+ mda->bCompact = bCompact;
+ mda->nstglobalcomm = nstglobalcomm;
+ mda->ddxyz[XX] = ddxyz[XX];
+ mda->ddxyz[YY] = ddxyz[YY];
+ mda->ddxyz[ZZ] = ddxyz[ZZ];
+ mda->dd_node_order = dd_node_order;
+ mda->rdd = rdd;
+ mda->rconstr = rconstr;
+ mda->dddlb_opt = dddlb_opt;
+ mda->dlb_scale = dlb_scale;
+ mda->ddcsx = ddcsx;
+ mda->ddcsy = ddcsy;
+ mda->ddcsz = ddcsz;
+ mda->nbpu_opt = nbpu_opt;
+ mda->nstlist_cmdline = nstlist_cmdline;
+ mda->nsteps_cmdline = nsteps_cmdline;
+ mda->nstepout = nstepout;
+ mda->resetstep = resetstep;
+ mda->nmultisim = nmultisim;
+ mda->repl_ex_nst = repl_ex_nst;
+ mda->repl_ex_nex = repl_ex_nex;
+ mda->repl_ex_seed = repl_ex_seed;
+ mda->pforce = pforce;
+ mda->cpt_period = cpt_period;
+ mda->max_hours = max_hours;
+ mda->Flags = Flags;
+
+ /* now spawn new threads that start mdrunner_start_fn(), while
+ the main thread returns, we set thread affinity later */
+ ret = tMPI_Init_fn(TRUE, hw_opt->nthreads_tmpi, TMPI_AFFINITY_NONE,
+ mdrunner_start_fn, (void*)(mda) );
+ if (ret != TMPI_SUCCESS)
+ {
+ return NULL;
+ }
+
+ crn = reinitialize_commrec_for_this_thread(cr);
+ return crn;
+}
+
+#endif /* GMX_THREAD_MPI */
+
+
+/* We determine the extra cost of the non-bonded kernels compared to
+ * a reference nstlist value of 10 (which is the default in grompp).
+ */
+static const int nbnxnReferenceNstlist = 10;
+/* The values to try when switching */
+const int nstlist_try[] = { 20, 25, 40 };
+#define NNSTL sizeof(nstlist_try)/sizeof(nstlist_try[0])
+/* Increase nstlist until the non-bonded cost increases more than listfac_ok,
+ * but never more than listfac_max.
+ * A standard (protein+)water system at 300K with PME ewald_rtol=1e-5
+ * needs 1.28 at rcoulomb=0.9 and 1.24 at rcoulomb=1.0 to get to nstlist=40.
+ * Note that both CPU and GPU factors are conservative. Performance should
+ * not go down due to this tuning, except with a relatively slow GPU.
+ * On the other hand, at medium/high parallelization or with fast GPUs
+ * nstlist will not be increased enough to reach optimal performance.
+ */
+/* CPU: pair-search is about a factor 1.5 slower than the non-bonded kernel */
+static const float nbnxn_cpu_listfac_ok = 1.05;
+static const float nbnxn_cpu_listfac_max = 1.09;
+/* GPU: pair-search is a factor 1.5-3 slower than the non-bonded kernel */
+static const float nbnxn_gpu_listfac_ok = 1.20;
+static const float nbnxn_gpu_listfac_max = 1.30;
+
+/* Try to increase nstlist when using the Verlet cut-off scheme */
+static void increase_nstlist(FILE *fp, t_commrec *cr,
+ t_inputrec *ir, int nstlist_cmdline,
+ const gmx_mtop_t *mtop, matrix box,
+ gmx_bool bGPU)
+{
+ float listfac_ok, listfac_max;
+ int nstlist_orig, nstlist_prev;
+ verletbuf_list_setup_t ls;
+ real rlistWithReferenceNstlist, rlist_inc, rlist_ok, rlist_max;
+ real rlist_new, rlist_prev;
+ size_t nstlist_ind = 0;
+ t_state state_tmp;
+ gmx_bool bBox, bDD, bCont;
+ const char *nstl_gpu = "\nFor optimal performance with a GPU nstlist (now %d) should be larger.\nThe optimum depends on your CPU and GPU resources.\nYou might want to try several nstlist values.\n";
+ const char *nve_err = "Can not increase nstlist because an NVE ensemble is used";
+ const char *vbd_err = "Can not increase nstlist because verlet-buffer-tolerance is not set or used";
+ const char *box_err = "Can not increase nstlist because the box is too small";
+ const char *dd_err = "Can not increase nstlist because of domain decomposition limitations";
+ char buf[STRLEN];
+ const float oneThird = 1.0f / 3.0f;
+
+ if (nstlist_cmdline <= 0)
+ {
+ if (ir->nstlist == 1)
+ {
+ /* The user probably set nstlist=1 for a reason,
+ * don't mess with the settings.
+ */
+ return;
+ }
+
+ if (fp != NULL && bGPU && ir->nstlist < nstlist_try[0])
+ {
+ fprintf(fp, nstl_gpu, ir->nstlist);
+ }
+ nstlist_ind = 0;
+ while (nstlist_ind < NNSTL && ir->nstlist >= nstlist_try[nstlist_ind])
+ {
+ nstlist_ind++;
+ }
+ if (nstlist_ind == NNSTL)
+ {
+ /* There are no larger nstlist value to try */
+ return;
+ }
+ }
+
+ if (EI_MD(ir->eI) && ir->etc == etcNO)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "%s\n", nve_err);
+ }
+ if (fp != NULL)
+ {
+ fprintf(fp, "%s\n", nve_err);
+ }
+
+ return;
+ }
+
+ if (ir->verletbuf_tol == 0 && bGPU)
+ {
+ gmx_fatal(FARGS, "You are using an old tpr file with a GPU, please generate a new tpr file with an up to date version of grompp");
+ }
+
+ if (ir->verletbuf_tol < 0)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "%s\n", vbd_err);
+ }
+ if (fp != NULL)
+ {
+ fprintf(fp, "%s\n", vbd_err);
+ }
+
+ return;
+ }
+
+ if (bGPU)
+ {
+ listfac_ok = nbnxn_gpu_listfac_ok;
+ listfac_max = nbnxn_gpu_listfac_max;
+ }
+ else
+ {
+ listfac_ok = nbnxn_cpu_listfac_ok;
+ listfac_max = nbnxn_cpu_listfac_max;
+ }
+
+ nstlist_orig = ir->nstlist;
+ if (nstlist_cmdline > 0)
+ {
+ if (fp)
+ {
+ sprintf(buf, "Getting nstlist=%d from command line option",
+ nstlist_cmdline);
+ }
+ ir->nstlist = nstlist_cmdline;
+ }
+
+ verletbuf_get_list_setup(TRUE, bGPU, &ls);
+
+ /* Allow rlist to make the list a given factor larger than the list
+ * would be with the reference value for nstlist (10).
+ */
+ nstlist_prev = ir->nstlist;
+ ir->nstlist = nbnxnReferenceNstlist;
+ calc_verlet_buffer_size(mtop, det(box), ir, -1, &ls, NULL,
+ &rlistWithReferenceNstlist);
+ ir->nstlist = nstlist_prev;
+
+ /* Determine the pair list size increase due to zero interactions */
+ rlist_inc = nbnxn_get_rlist_effective_inc(ls.cluster_size_j,
+ mtop->natoms/det(box));
+ rlist_ok = (rlistWithReferenceNstlist + rlist_inc)*pow(listfac_ok, oneThird) - rlist_inc;
+ rlist_max = (rlistWithReferenceNstlist + rlist_inc)*pow(listfac_max, oneThird) - rlist_inc;
+ if (debug)
+ {
+ fprintf(debug, "nstlist tuning: rlist_inc %.3f rlist_ok %.3f rlist_max %.3f\n",
+ rlist_inc, rlist_ok, rlist_max);
+ }
+
+ nstlist_prev = nstlist_orig;
+ rlist_prev = ir->rlist;
+ do
+ {
+ if (nstlist_cmdline <= 0)
+ {
+ ir->nstlist = nstlist_try[nstlist_ind];
+ }
+
+ /* Set the pair-list buffer size in ir */
+ calc_verlet_buffer_size(mtop, det(box), ir, -1, &ls, NULL, &rlist_new);
+
+ /* Does rlist fit in the box? */
+ bBox = (sqr(rlist_new) < max_cutoff2(ir->ePBC, box));
+ bDD = TRUE;
+ if (bBox && DOMAINDECOMP(cr))
+ {
+ /* Check if rlist fits in the domain decomposition */
+ if (inputrec2nboundeddim(ir) < DIM)
+ {
+ gmx_incons("Changing nstlist with domain decomposition and unbounded dimensions is not implemented yet");
+ }
+ copy_mat(box, state_tmp.box);
+ bDD = change_dd_cutoff(cr, &state_tmp, ir, rlist_new);
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "nstlist %d rlist %.3f bBox %d bDD %d\n",
+ ir->nstlist, rlist_new, bBox, bDD);
+ }
+
+ bCont = FALSE;
+
+ if (nstlist_cmdline <= 0)
+ {
+ if (bBox && bDD && rlist_new <= rlist_max)
+ {
+ /* Increase nstlist */
+ nstlist_prev = ir->nstlist;
+ rlist_prev = rlist_new;
+ bCont = (nstlist_ind+1 < NNSTL && rlist_new < rlist_ok);
+ }
+ else
+ {
+ /* Stick with the previous nstlist */
+ ir->nstlist = nstlist_prev;
+ rlist_new = rlist_prev;
+ bBox = TRUE;
+ bDD = TRUE;
+ }
+ }
+
+ nstlist_ind++;
+ }
+ while (bCont);
+
+ if (!bBox || !bDD)
+ {
+ gmx_warning(!bBox ? box_err : dd_err);
+ if (fp != NULL)
+ {
+ fprintf(fp, "\n%s\n", bBox ? box_err : dd_err);
+ }
+ ir->nstlist = nstlist_orig;
+ }
+ else if (ir->nstlist != nstlist_orig || rlist_new != ir->rlist)
+ {
+ sprintf(buf, "Changing nstlist from %d to %d, rlist from %g to %g",
+ nstlist_orig, ir->nstlist,
+ ir->rlist, rlist_new);
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "%s\n\n", buf);
+ }
+ if (fp != NULL)
+ {
+ fprintf(fp, "%s\n\n", buf);
+ }
+ ir->rlist = rlist_new;
+ ir->rlistlong = rlist_new;
+ }
+}
+
+static void prepare_verlet_scheme(FILE *fplog,
+ t_commrec *cr,
+ t_inputrec *ir,
+ int nstlist_cmdline,
+ const gmx_mtop_t *mtop,
+ matrix box,
+ gmx_bool bUseGPU)
+{
+ /* For NVE simulations, we will retain the initial list buffer */
+ if (EI_DYNAMICS(ir->eI) &&
+ ir->verletbuf_tol > 0 &&
+ !(EI_MD(ir->eI) && ir->etc == etcNO))
+ {
+ /* Update the Verlet buffer size for the current run setup */
+ verletbuf_list_setup_t ls;
+ real rlist_new;
+
+ /* Here we assume SIMD-enabled kernels are being used. But as currently
+ * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
+ * and 4x2 gives a larger buffer than 4x4, this is ok.
+ */
+ verletbuf_get_list_setup(TRUE, bUseGPU, &ls);
+
+ calc_verlet_buffer_size(mtop, det(box), ir, -1, &ls, NULL, &rlist_new);
+
+ if (rlist_new != ir->rlist)
+ {
+ if (fplog != NULL)
+ {
+ fprintf(fplog, "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
+ ir->rlist, rlist_new,
+ ls.cluster_size_i, ls.cluster_size_j);
+ }
+ ir->rlist = rlist_new;
+ ir->rlistlong = rlist_new;
+ }
+ }
+
+ if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
+ {
+ gmx_fatal(FARGS, "Can not set nstlist without %s",
+ !EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
+ }
+
+ if (EI_DYNAMICS(ir->eI))
+ {
+ /* Set or try nstlist values */
+ increase_nstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, bUseGPU);
+ }
+}
+
+/* Override the value in inputrec with value passed on the command line (if any) */
+static void override_nsteps_cmdline(FILE *fplog,
+ gmx_int64_t nsteps_cmdline,
+ t_inputrec *ir,
+ const t_commrec *cr)
+{
+ assert(ir);
+ assert(cr);
+
+ /* 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));
+ }
+
+ md_print_warn(cr, fplog, "%s\n", 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 */
+}
+
+int mdrunner(gmx_hw_opt_t *hw_opt,
+ FILE *fplog, t_commrec *cr, int nfile,
+ const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
+ gmx_bool bCompact, int nstglobalcomm,
+ ivec ddxyz, int dd_node_order, real rdd, real rconstr,
+ const char *dddlb_opt, real dlb_scale,
+ const char *ddcsx, const char *ddcsy, const char *ddcsz,
+ const char *nbpu_opt, int nstlist_cmdline,
+ gmx_int64_t nsteps_cmdline, int nstepout, int resetstep,
+ int gmx_unused nmultisim, int repl_ex_nst, int repl_ex_nex,
+ int repl_ex_seed, real pforce, real cpt_period, real max_hours,
+ int imdport, unsigned long Flags)
+{
+ gmx_bool bForceUseGPU, bTryUseGPU, bRerunMD;
+ t_inputrec *inputrec;
+ t_state *state = NULL;
+ matrix box;
+ gmx_ddbox_t ddbox = {0};
+ int npme_major, npme_minor;
+ t_nrnb *nrnb;
+ gmx_mtop_t *mtop = NULL;
+ t_mdatoms *mdatoms = NULL;
+ t_forcerec *fr = NULL;
+ t_fcdata *fcd = NULL;
+ real ewaldcoeff_q = 0;
+ real ewaldcoeff_lj = 0;
+ struct gmx_pme_t **pmedata = NULL;
+ gmx_vsite_t *vsite = NULL;
+ gmx_constr_t constr;
+ int nChargePerturbed = -1, nTypePerturbed = 0, status;
+ gmx_wallcycle_t wcycle;
+ gmx_bool bReadEkin;
+ gmx_walltime_accounting_t walltime_accounting = NULL;
+ int rc;
+ gmx_int64_t reset_counters;
+ gmx_edsam_t ed = NULL;
+ int nthreads_pme = 1;
+ int nthreads_pp = 1;
+ gmx_membed_t membed = NULL;
+ gmx_hw_info_t *hwinfo = NULL;
+ /* The master rank decides early on bUseGPU and broadcasts this later */
+ gmx_bool bUseGPU = FALSE;
+
+ /* CAUTION: threads may be started later on in this function, so
+ cr doesn't reflect the final parallel state right now */
+ snew(inputrec, 1);
+ snew(mtop, 1);
+
+ if (Flags & MD_APPENDFILES)
+ {
+ fplog = NULL;
+ }
+
+ bRerunMD = (Flags & MD_RERUN);
+ bForceUseGPU = (strncmp(nbpu_opt, "gpu", 3) == 0);
+ bTryUseGPU = (strncmp(nbpu_opt, "auto", 4) == 0) || bForceUseGPU;
+
+ /* Detect hardware, gather information. This is an operation that is
+ * global for this process (MPI rank). */
+ hwinfo = gmx_detect_hardware(fplog, cr, bTryUseGPU);
+
+ gmx_print_detected_hardware(fplog, cr, hwinfo);
+
+ if (fplog != NULL)
+ {
+ /* 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");
+ }
+
+ snew(state, 1);
+ if (SIMMASTER(cr))
+ {
+ /* Read (nearly) all data required for the simulation */
+ read_tpx_state(ftp2fn(efTPR, nfile, fnm), inputrec, state, NULL, mtop);
+
+ if (inputrec->cutoff_scheme == ecutsVERLET)
+ {
+ /* Here the master rank decides if all ranks will use GPUs */
+ bUseGPU = (hwinfo->gpu_info.n_dev_compatible > 0 ||
+ getenv("GMX_EMULATE_GPU") != NULL);
+
+ /* TODO add GPU kernels for this and replace this check by:
+ * (bUseGPU && (ir->vdwtype == evdwPME &&
+ * ir->ljpme_combination_rule == eljpmeLB))
+ * update the message text and the content of nbnxn_acceleration_supported.
+ */
+ if (bUseGPU &&
+ !nbnxn_gpu_acceleration_supported(fplog, cr, inputrec, bRerunMD))
+ {
+ /* Fallback message printed by nbnxn_acceleration_supported */
+ if (bForceUseGPU)
+ {
+ gmx_fatal(FARGS, "GPU acceleration requested, but not supported with the given input settings");
+ }
+ bUseGPU = FALSE;
+ }
+
+ prepare_verlet_scheme(fplog, cr,
+ inputrec, nstlist_cmdline, mtop, state->box,
+ bUseGPU);
+ }
+ else
+ {
+ if (nstlist_cmdline > 0)
+ {
+ gmx_fatal(FARGS, "Can not set nstlist with the group cut-off scheme");
+ }
+
+ if (hwinfo->gpu_info.n_dev_compatible > 0)
+ {
+ md_print_warn(cr, fplog,
+ "NOTE: GPU(s) found, but the current simulation can not use GPUs\n"
+ " To use a GPU, set the mdp option: cutoff-scheme = Verlet\n");
+ }
+
+ if (bForceUseGPU)
+ {
+ gmx_fatal(FARGS, "GPU requested, but can't be used without cutoff-scheme=Verlet");
+ }
+
+#ifdef GMX_TARGET_BGQ
+ md_print_warn(cr, fplog,
+ "NOTE: There is no SIMD implementation of the group scheme kernels on\n"
+ " BlueGene/Q. You will observe better performance from using the\n"
+ " Verlet cut-off scheme.\n");
+#endif
+ }
+
+ if (inputrec->eI == eiSD2)
+ {
+ md_print_warn(cr, fplog, "The stochastic dynamics integrator %s is deprecated, since\n"
+ "it is slower than integrator %s and is slightly less accurate\n"
+ "with constraints. Use the %s integrator.",
+ ei_names[inputrec->eI], ei_names[eiSD1], ei_names[eiSD1]);
+ }
+ }
+
+ /* Check and update the hardware options for internal consistency */
+ check_and_update_hw_opt_1(hw_opt, cr);
+
+ /* Early check for externally set process affinity. */
+ gmx_check_thread_affinity_set(fplog, cr,
+ hw_opt, hwinfo->nthreads_hw_avail, FALSE);
+
+#ifdef GMX_THREAD_MPI
+ if (SIMMASTER(cr))
+ {
+ if (cr->npmenodes > 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);
+
+ /* NOW the threads will be started: */
+ hw_opt->nthreads_tmpi = get_nthreads_mpi(hwinfo,
+ hw_opt,
+ inputrec, mtop,
+ cr, fplog, bUseGPU);
+
+ if (hw_opt->nthreads_tmpi > 1)
+ {
+ t_commrec *cr_old = cr;
+ /* now start the threads. */
+ cr = mdrunner_start_threads(hw_opt, fplog, cr_old, nfile, fnm,
+ oenv, bVerbose, bCompact, nstglobalcomm,
+ ddxyz, dd_node_order, rdd, rconstr,
+ dddlb_opt, dlb_scale, ddcsx, ddcsy, ddcsz,
+ nbpu_opt, nstlist_cmdline,
+ nsteps_cmdline, nstepout, resetstep, nmultisim,
+ repl_ex_nst, repl_ex_nex, repl_ex_seed, pforce,
+ cpt_period, max_hours,
+ Flags);
+ /* the main thread continues here with a new cr. We don't deallocate
+ the old cr because other threads may still be reading it. */
+ if (cr == NULL)
+ {
+ gmx_comm("Failed to spawn threads");
+ }
+ }
+ }
+#endif
+ /* END OF CAUTION: cr is now reliable */
+
+ /* g_membed initialisation *
+ * Because we change the mtop, init_membed is called before the init_parallel *
+ * (in case we ever want to make it run in parallel) */
+ if (opt2bSet("-membed", nfile, fnm))
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "Initializing membed");
+ }
+ membed = init_membed(fplog, nfile, fnm, mtop, inputrec, state, cr, &cpt_period);
+ }
+
+ if (PAR(cr))
+ {
+ /* now broadcast everything to the non-master nodes/threads: */
+ init_parallel(cr, inputrec, mtop);
+
+ /* The master rank decided on the use of GPUs,
+ * broadcast this information to all ranks.
+ */
+ gmx_bcast_sim(sizeof(bUseGPU), &bUseGPU, cr);
+ }
+
+ if (fplog != NULL)
+ {
+ pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
+ fprintf(fplog, "\n");
+ }
+
+ /* now make sure the state is initialized and propagated */
+ set_state_entries(state, inputrec);
+
+ /* A parallel command line option consistency check that we can
+ only do after any threads have started. */
+ if (!PAR(cr) &&
+ (ddxyz[XX] > 1 || ddxyz[YY] > 1 || ddxyz[ZZ] > 1 || cr->npmenodes > 0))
+ {
+ gmx_fatal(FARGS,
+ "The -dd or -npme option request a parallel simulation, "
+#ifndef GMX_MPI
+ "but %s was compiled without threads or MPI enabled"
+#else
+#ifdef GMX_THREAD_MPI
+ "but the number of threads (option -nt) 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 (bRerunMD &&
+ (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 (cr->npmenodes > 0)
+ {
+ gmx_fatal_collective(FARGS, cr, NULL,
+ "PME-only ranks are requested, but the system does not use PME for electrostatics or LJ");
+ }
+
+ cr->npmenodes = 0;
+ }
+
+ if (bUseGPU && cr->npmenodes < 0)
+ {
+ /* With GPUs we don't automatically use PME-only ranks. PME ranks can
+ * improve performance with many threads per GPU, since our OpenMP
+ * scaling is bad, but it's difficult to automate the setup.
+ */
+ cr->npmenodes = 0;
+ }
+
+#ifdef GMX_FAHCORE
+ if (MASTER(cr))
+ {
+ fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
+ }
+#endif
+
+ /* NMR restraints must be initialized before load_checkpoint,
+ * since with time averaging the history is added to t_state.
+ * For proper consistency check we therefore need to extend
+ * t_state here.
+ * So the PME-only nodes (if present) will also initialize
+ * the distance restraints.
+ */
+ snew(fcd, 1);
+
+ /* This needs to be called before read_checkpoint to extend the state */
+ init_disres(fplog, mtop, inputrec, cr, fcd, state, repl_ex_nst > 0);
+
+ init_orires(fplog, mtop, state->x, inputrec, cr, &(fcd->orires),
+ state);
+
+ if (DEFORM(*inputrec))
+ {
+ /* Store the deform reference box before reading the checkpoint */
+ if (SIMMASTER(cr))
+ {
+ copy_mat(state->box, box);
+ }
+ if (PAR(cr))
+ {
+ gmx_bcast(sizeof(box), box, cr);
+ }
+ /* Because we do not have the update struct available yet
+ * in which the reference values should be stored,
+ * we store them temporarily in static variables.
+ * This should be thread safe, since they are only written once
+ * and with identical values.
+ */
+ tMPI_Thread_mutex_lock(&deform_init_box_mutex);
+ deform_init_init_step_tpx = inputrec->init_step;
+ copy_mat(box, deform_init_box_tpx);
+ tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
+ }
+
+ if (opt2bSet("-cpi", nfile, fnm))
+ {
+ /* Check if checkpoint file exists before doing continuation.
+ * This way we can use identical input options for the first and subsequent runs...
+ */
+ if (gmx_fexist_master(opt2fn_master("-cpi", nfile, fnm, cr), cr) )
+ {
+ load_checkpoint(opt2fn_master("-cpi", nfile, fnm, cr), &fplog,
+ cr, ddxyz,
+ inputrec, state, &bReadEkin,
+ (Flags & MD_APPENDFILES),
+ (Flags & MD_APPENDFILESSET));
+
+ if (bReadEkin)
+ {
+ Flags |= MD_READ_EKIN;
+ }
+ }
+ }
+
+ if (MASTER(cr) && (Flags & MD_APPENDFILES))
+ {
+ gmx_log_open(ftp2fn(efLOG, nfile, fnm), cr,
+ Flags, &fplog);
+ }
+
+ /* override nsteps with value from cmdline */
+ override_nsteps_cmdline(fplog, nsteps_cmdline, inputrec, cr);
+
+ if (SIMMASTER(cr))
+ {
+ copy_mat(state->box, box);
+ }
+
+ if (PAR(cr))
+ {
+ gmx_bcast(sizeof(box), box, cr);
+ }
+
+ /* Essential dynamics */
+ if (opt2bSet("-ei", nfile, fnm))
+ {
+ /* Open input and output files, allocate space for ED data structure */
+ ed = ed_open(mtop->natoms, &state->edsamstate, nfile, fnm, Flags, oenv, cr);
+ }
+
+ if (PAR(cr) && !(EI_TPI(inputrec->eI) ||
+ inputrec->eI == eiNM))
+ {
+ cr->dd = init_domain_decomposition(fplog, cr, Flags, ddxyz, rdd, rconstr,
+ dddlb_opt, dlb_scale,
+ ddcsx, ddcsy, ddcsz,
+ mtop, inputrec,
+ box, state->x,
+ &ddbox, &npme_major, &npme_minor);
+
+ make_dd_communicators(fplog, cr, dd_node_order);
+
+ /* Set overallocation to avoid frequent reallocation of arrays */
+ set_over_alloc_dd(TRUE);
+ }
+ else
+ {
+ /* PME, if used, is done on all nodes with 1D decomposition */
+ cr->npmenodes = 0;
+ cr->duty = (DUTY_PP | DUTY_PME);
+ npme_major = 1;
+ npme_minor = 1;
+
+ if (inputrec->ePBC == epbcSCREW)
+ {
+ gmx_fatal(FARGS,
+ "pbc=%s is only implemented with domain decomposition",
+ epbc_names[inputrec->ePBC]);
+ }
+ }
+
+ if (PAR(cr))
+ {
+ /* After possible communicator splitting in make_dd_communicators.
+ * we can set up the intra/inter node communication.
+ */
+ gmx_setup_nodecomm(fplog, cr);
+ }
+
+ /* Initialize per-physical-node MPI process/thread ID and counters. */
+ gmx_init_intranode_counters(cr);
+#ifdef GMX_MPI
+ if (MULTISIM(cr))
+ {
+ md_print_info(cr, fplog,
+ "This is simulation %d out of %d running as a composite GROMACS\n"
+ "multi-simulation job. Setup for this simulation:\n\n",
+ cr->ms->sim, cr->ms->nsim);
+ }
+ md_print_info(cr, fplog, "Using %d MPI %s\n",
+ cr->nnodes,
+#ifdef GMX_THREAD_MPI
+ cr->nnodes == 1 ? "thread" : "threads"
+#else
+ cr->nnodes == 1 ? "process" : "processes"
+#endif
+ );
+ fflush(stderr);
+#endif
+
+ /* Check and update hw_opt for the cut-off scheme */
+ check_and_update_hw_opt_2(hw_opt, inputrec->cutoff_scheme);
+
+ /* Check and update hw_opt for the number of MPI ranks */
+ check_and_update_hw_opt_3(hw_opt);
+
+ gmx_omp_nthreads_init(fplog, cr,
+ hwinfo->nthreads_hw_avail,
+ hw_opt->nthreads_omp,
+ hw_opt->nthreads_omp_pme,
+ (cr->duty & DUTY_PP) == 0,
+ inputrec->cutoff_scheme == ecutsVERLET);
+
+#ifndef NDEBUG
+ if (integrator[inputrec->eI].func != do_tpi &&
+ inputrec->cutoff_scheme == ecutsVERLET)
+ {
+ gmx_feenableexcept();
+ }
+#endif
+
+ if (bUseGPU)
+ {
+ /* Select GPU id's to use */
+ gmx_select_gpu_ids(fplog, cr, &hwinfo->gpu_info, bForceUseGPU,
+ &hw_opt->gpu_opt);
+ }
+ else
+ {
+ /* Ignore (potentially) manually selected GPUs */
+ hw_opt->gpu_opt.n_dev_use = 0;
+ }
+
+ /* check consistency across ranks of things like SIMD
+ * support and number of GPUs selected */
+ gmx_check_hw_runconf_consistency(fplog, hwinfo, cr, hw_opt, bUseGPU);
+
+ /* Now that we know the setup is consistent, check for efficiency */
+ check_resource_division_efficiency(hwinfo, hw_opt, Flags & MD_NTOMPSET,
+ cr, fplog);
+
+ if (DOMAINDECOMP(cr))
+ {
+ /* When we share GPUs over ranks, we need to know this for the DLB */
+ dd_setup_dlb_resource_sharing(cr, hwinfo, hw_opt);
+ }
+
+ /* getting number of PP/PME threads
+ PME: env variable should be read only on one node to make sure it is
+ identical everywhere;
+ */
+ /* TODO nthreads_pp is only used for pinning threads.
+ * This is a temporary solution until we have a hw topology library.
+ */
+ nthreads_pp = gmx_omp_nthreads_get(emntNonbonded);
+ nthreads_pme = gmx_omp_nthreads_get(emntPME);
+
+ wcycle = wallcycle_init(fplog, resetstep, cr, nthreads_pp, nthreads_pme);
+
+ 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);
+ }
+
+ snew(nrnb, 1);
+ if (cr->duty & DUTY_PP)
+ {
+ bcast_state(cr, state);
+
+ /* Initiate forcerecord */
+ fr = mk_forcerec();
+ fr->hwinfo = hwinfo;
+ fr->gpu_opt = &hw_opt->gpu_opt;
+ init_forcerec(fplog, oenv, fr, fcd, inputrec, mtop, cr, box,
+ opt2fn("-table", nfile, fnm),
+ opt2fn("-tabletf", nfile, fnm),
+ opt2fn("-tablep", nfile, fnm),
+ opt2fn("-tableb", nfile, fnm),
+ nbpu_opt,
+ FALSE,
+ pforce);
+
+ /* version for PCA_NOT_READ_NODE (see md.c) */
+ /*init_forcerec(fplog,fr,fcd,inputrec,mtop,cr,box,FALSE,
+ "nofile","nofile","nofile","nofile",FALSE,pforce);
+ */
+
+ /* Initialize QM-MM */
+ if (fr->bQMMM)
+ {
+ init_QMMMrec(cr, mtop, inputrec, fr);
+ }
+
+ /* Initialize the mdatoms structure.
+ * mdatoms is not filled with atom data,
+ * as this can not be done now with domain decomposition.
+ */
+ mdatoms = init_mdatoms(fplog, mtop, inputrec->efep != efepNO);
+
+ /* Initialize the virtual site communication */
+ vsite = init_vsite(mtop, cr, FALSE);
+
+ calc_shifts(box, fr->shift_vec);
+
+ /* With periodic molecules the charge groups should be whole at start up
+ * and the virtual sites should not be far from their proper positions.
+ */
+ if (!inputrec->bContinuation && MASTER(cr) &&
+ !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
+ {
+ /* Make molecules whole at start of run */
+ if (fr->ePBC != epbcNONE)
+ {
+ do_pbc_first_mtop(fplog, inputrec->ePBC, box, mtop, state->x);
+ }
+ if (vsite)
+ {
+ /* Correct initial vsite positions are required
+ * for the initial distribution in the domain decomposition
+ * and for the initial shell prediction.
+ */
+ construct_vsites_mtop(vsite, mtop, state->x);
+ }
+ }
+
+ if (EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype))
+ {
+ ewaldcoeff_q = fr->ewaldcoeff_q;
+ ewaldcoeff_lj = fr->ewaldcoeff_lj;
+ pmedata = &fr->pmedata;
+ }
+ else
+ {
+ pmedata = NULL;
+ }
+ }
+ else
+ {
+ /* This is a PME only node */
+
+ /* We don't need the state */
+ done_state(state);
+
+ ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
+ ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
+ snew(pmedata, 1);
+ }
+
+ if (hw_opt->thread_affinity != threadaffOFF)
+ {
+ /* Before setting affinity, check whether the affinity has changed
+ * - which indicates that probably the OpenMP library has changed it
+ * since we first checked).
+ */
+ gmx_check_thread_affinity_set(fplog, cr,
+ hw_opt, hwinfo->nthreads_hw_avail, TRUE);
+
+ /* Set the CPU affinity */
+ gmx_set_thread_affinity(fplog, cr, hw_opt, hwinfo);
+ }
+
+ /* Initiate PME if necessary,
+ * either on all nodes or on dedicated PME nodes only. */
+ if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
+ {
+ if (mdatoms)
+ {
+ nChargePerturbed = mdatoms->nChargePerturbed;
+ if (EVDW_PME(inputrec->vdwtype))
+ {
+ nTypePerturbed = mdatoms->nTypePerturbed;
+ }
+ }
+ if (cr->npmenodes > 0)
+ {
+ /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
+ gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
+ gmx_bcast_sim(sizeof(nTypePerturbed), &nTypePerturbed, cr);
+ }
+
+ if (cr->duty & DUTY_PME)
+ {
+ status = gmx_pme_init(pmedata, cr, npme_major, npme_minor, inputrec,
+ mtop ? mtop->natoms : 0, nChargePerturbed, nTypePerturbed,
+ (Flags & MD_REPRODUCIBLE), nthreads_pme);
+ if (status != 0)
+ {
+ gmx_fatal(FARGS, "Error %d initializing PME", status);
+ }
+ }
+ }
+
+
+ if (integrator[inputrec->eI].func == do_md)
+ {
+ /* Turn on signal handling on all nodes */
+ /*
+ * (A user signal from the PME nodes (if any)
+ * is communicated to the PP nodes.
+ */
+ signal_handler_install();
+ }
+
+ if (cr->duty & DUTY_PP)
+ {
+ /* Assumes uniform use of the number of OpenMP threads */
+ walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
+
+ if (inputrec->bPull)
+ {
+ /* Initialize pull code */
+ inputrec->pull_work =
+ init_pull(fplog, inputrec->pull, inputrec, nfile, fnm,
+ mtop, cr, oenv, inputrec->fepvals->init_lambda,
+ EI_DYNAMICS(inputrec->eI) && MASTER(cr), Flags);
+ }
+
+ if (inputrec->bRot)
+ {
+ /* Initialize enforced rotation code */
+ init_rot(fplog, inputrec, nfile, fnm, cr, state->x, box, mtop, oenv,
+ bVerbose, Flags);
+ }
+
+ if (inputrec->eSwapCoords != eswapNO)
+ {
+ /* Initialize ion swapping code */
+ init_swapcoords(fplog, bVerbose, inputrec, opt2fn_master("-swap", nfile, fnm, cr),
+ mtop, state->x, state->box, &state->swapstate, cr, oenv, Flags);
+ }
+
+ constr = init_constraints(fplog, mtop, inputrec, ed, state, cr);
+
+ if (DOMAINDECOMP(cr))
+ {
+ GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
+ dd_init_bondeds(fplog, cr->dd, mtop, vsite, inputrec,
+ Flags & MD_DDBONDCHECK, fr->cginfo_mb);
+
+ set_dd_parameters(fplog, cr->dd, dlb_scale, inputrec, &ddbox);
+
+ setup_dd_grid(fplog, cr->dd);
+ }
+
+ /* Now do whatever the user wants us to do (how flexible...) */
+ integrator[inputrec->eI].func(fplog, cr, nfile, fnm,
+ oenv, bVerbose, bCompact,
+ nstglobalcomm,
+ vsite, constr,
+ nstepout, inputrec, mtop,
+ fcd, state,
+ mdatoms, nrnb, wcycle, ed, fr,
+ repl_ex_nst, repl_ex_nex, repl_ex_seed,
+ membed,
+ cpt_period, max_hours,
+ imdport,
+ Flags,
+ walltime_accounting);
+
+ if (inputrec->bPull)
+ {
+ finish_pull(inputrec->pull_work);
+ }
+
+ if (inputrec->bRot)
+ {
+ finish_rot(inputrec->rot);
+ }
+
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
+ /* do PME only */
+ walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
+ gmx_pmeonly(*pmedata, cr, nrnb, wcycle, walltime_accounting, ewaldcoeff_q, ewaldcoeff_lj, inputrec);
+ }
+
+ wallcycle_stop(wcycle, ewcRUN);
+
+ /* Finish up, write some stuff
+ * if rerunMD, don't write last frame again
+ */
+ finish_run(fplog, cr,
+ inputrec, nrnb, wcycle, walltime_accounting,
+ fr ? fr->nbv : NULL,
+ EI_DYNAMICS(inputrec->eI) && !MULTISIM(cr));
+
+
+ /* Free GPU memory and context */
+ free_gpu_resources(fr, cr, &hwinfo->gpu_info, fr ? fr->gpu_opt : NULL);
+
+ if (opt2bSet("-membed", nfile, fnm))
+ {
+ sfree(membed);
+ }
+
+ gmx_hardware_info_free(hwinfo);
+
+ /* Does what it says */
+ print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
+ walltime_accounting_destroy(walltime_accounting);
+
+ /* PLUMED */
+ if(plumedswitch){
+ plumed_finalize(plumedmain);
+ }
+ /* END PLUMED */
+
+ /* Close logfile already here if we were appending to it */
+ if (MASTER(cr) && (Flags & MD_APPENDFILES))
+ {
+ gmx_log_close(fplog);
+ }
+
+ rc = (int)gmx_get_stop_condition();
+
+ done_ed(&ed);
+
+#ifdef GMX_THREAD_MPI
+ /* we need to join all threads. The sub-threads join when they
+ exit this function, but the master thread needs to be told to
+ wait for that. */
+ if (PAR(cr) && MASTER(cr))
+ {
+ tMPI_Finalize();
+ }
+#endif
+
+ return rc;
+}
diff --git a/patches/gromacs-5.1.2.diff/src/programs/mdrun/runner.cpp.preplumed b/patches/gromacs-5.1.2.diff/src/programs/mdrun/runner.cpp.preplumed
new file mode 100644
index 000000000..f436a0188
--- /dev/null
+++ b/patches/gromacs-5.1.2.diff/src/programs/mdrun/runner.cpp.preplumed
@@ -0,0 +1,1351 @@
+/*
+ * 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, 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.
+ */
+
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include <assert.h>
+#include <signal.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include <algorithm>
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/ewald/pme.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/gmx_detect_hardware.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/gmx_thread_affinity.h"
+#include "gromacs/legacyheaders/inputrec.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/sighandler.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/calculate-ewald-splitting-coefficient.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/calc_verletbuf.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/pulling/pull_rotation.h"
+#include "gromacs/swap/swapcoords.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "deform.h"
+#include "membed.h"
+#include "repl_ex.h"
+#include "resource-division.h"
+
+#ifdef GMX_FAHCORE
+#include "corewrap.h"
+#endif
+
+typedef struct {
+ gmx_integrator_t *func;
+} gmx_intp_t;
+
+/* The array should match the eI array in include/types/enums.h */
+const gmx_intp_t integrator[eiNR] = { {do_md}, {do_steep}, {do_cg}, {do_md}, {do_md}, {do_nm}, {do_lbfgs}, {do_tpi}, {do_tpi}, {do_md}, {do_md}, {do_md}};
+
+gmx_int64_t deform_init_init_step_tpx;
+matrix deform_init_box_tpx;
+tMPI_Thread_mutex_t deform_init_box_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+
+
+#ifdef GMX_THREAD_MPI
+/* The minimum number of atoms per tMPI thread. With fewer atoms than this,
+ * the number of threads will get lowered.
+ */
+#define MIN_ATOMS_PER_MPI_THREAD 90
+#define MIN_ATOMS_PER_GPU 900
+
+struct mdrunner_arglist
+{
+ gmx_hw_opt_t hw_opt;
+ FILE *fplog;
+ t_commrec *cr;
+ int nfile;
+ const t_filenm *fnm;
+ output_env_t oenv;
+ gmx_bool bVerbose;
+ gmx_bool bCompact;
+ int nstglobalcomm;
+ ivec ddxyz;
+ int dd_node_order;
+ real rdd;
+ real rconstr;
+ const char *dddlb_opt;
+ real dlb_scale;
+ const char *ddcsx;
+ const char *ddcsy;
+ const char *ddcsz;
+ const char *nbpu_opt;
+ int nstlist_cmdline;
+ gmx_int64_t nsteps_cmdline;
+ int nstepout;
+ int resetstep;
+ int nmultisim;
+ int repl_ex_nst;
+ int repl_ex_nex;
+ int repl_ex_seed;
+ real pforce;
+ real cpt_period;
+ real max_hours;
+ int imdport;
+ unsigned long Flags;
+};
+
+
+/* The function used for spawning threads. Extracts the mdrunner()
+ arguments from its one argument and calls mdrunner(), after making
+ a commrec. */
+static void mdrunner_start_fn(void *arg)
+{
+ struct mdrunner_arglist *mda = (struct mdrunner_arglist*)arg;
+ struct mdrunner_arglist mc = *mda; /* copy the arg list to make sure
+ that it's thread-local. This doesn't
+ copy pointed-to items, of course,
+ but those are all const. */
+ t_commrec *cr; /* we need a local version of this */
+ FILE *fplog = NULL;
+ t_filenm *fnm;
+
+ fnm = dup_tfn(mc.nfile, mc.fnm);
+
+ cr = reinitialize_commrec_for_this_thread(mc.cr);
+
+ if (MASTER(cr))
+ {
+ fplog = mc.fplog;
+ }
+
+ mdrunner(&mc.hw_opt, fplog, cr, mc.nfile, fnm, mc.oenv,
+ mc.bVerbose, mc.bCompact, mc.nstglobalcomm,
+ mc.ddxyz, mc.dd_node_order, mc.rdd,
+ mc.rconstr, mc.dddlb_opt, mc.dlb_scale,
+ mc.ddcsx, mc.ddcsy, mc.ddcsz,
+ mc.nbpu_opt, mc.nstlist_cmdline,
+ mc.nsteps_cmdline, mc.nstepout, mc.resetstep,
+ mc.nmultisim, mc.repl_ex_nst, mc.repl_ex_nex, mc.repl_ex_seed, mc.pforce,
+ mc.cpt_period, mc.max_hours, mc.imdport, mc.Flags);
+}
+
+/* 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 besides nthreads are the same as for mdrunner(). */
+static t_commrec *mdrunner_start_threads(gmx_hw_opt_t *hw_opt,
+ FILE *fplog, t_commrec *cr, int nfile,
+ const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
+ gmx_bool bCompact, int nstglobalcomm,
+ ivec ddxyz, int dd_node_order, real rdd, real rconstr,
+ const char *dddlb_opt, real dlb_scale,
+ const char *ddcsx, const char *ddcsy, const char *ddcsz,
+ const char *nbpu_opt, int nstlist_cmdline,
+ gmx_int64_t nsteps_cmdline,
+ int nstepout, int resetstep,
+ int nmultisim, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
+ real pforce, real cpt_period, real max_hours,
+ unsigned long Flags)
+{
+ int ret;
+ struct mdrunner_arglist *mda;
+ t_commrec *crn; /* the new commrec */
+ t_filenm *fnmn;
+
+ /* first check whether we even need to start tMPI */
+ if (hw_opt->nthreads_tmpi < 2)
+ {
+ return cr;
+ }
+
+ /* a few small, one-time, almost unavoidable memory leaks: */
+ snew(mda, 1);
+ fnmn = dup_tfn(nfile, fnm);
+
+ /* fill the data structure to pass as void pointer to thread start fn */
+ /* hw_opt contains pointers, which should all be NULL at this stage */
+ mda->hw_opt = *hw_opt;
+ mda->fplog = fplog;
+ mda->cr = cr;
+ mda->nfile = nfile;
+ mda->fnm = fnmn;
+ mda->oenv = oenv;
+ mda->bVerbose = bVerbose;
+ mda->bCompact = bCompact;
+ mda->nstglobalcomm = nstglobalcomm;
+ mda->ddxyz[XX] = ddxyz[XX];
+ mda->ddxyz[YY] = ddxyz[YY];
+ mda->ddxyz[ZZ] = ddxyz[ZZ];
+ mda->dd_node_order = dd_node_order;
+ mda->rdd = rdd;
+ mda->rconstr = rconstr;
+ mda->dddlb_opt = dddlb_opt;
+ mda->dlb_scale = dlb_scale;
+ mda->ddcsx = ddcsx;
+ mda->ddcsy = ddcsy;
+ mda->ddcsz = ddcsz;
+ mda->nbpu_opt = nbpu_opt;
+ mda->nstlist_cmdline = nstlist_cmdline;
+ mda->nsteps_cmdline = nsteps_cmdline;
+ mda->nstepout = nstepout;
+ mda->resetstep = resetstep;
+ mda->nmultisim = nmultisim;
+ mda->repl_ex_nst = repl_ex_nst;
+ mda->repl_ex_nex = repl_ex_nex;
+ mda->repl_ex_seed = repl_ex_seed;
+ mda->pforce = pforce;
+ mda->cpt_period = cpt_period;
+ mda->max_hours = max_hours;
+ mda->Flags = Flags;
+
+ /* now spawn new threads that start mdrunner_start_fn(), while
+ the main thread returns, we set thread affinity later */
+ ret = tMPI_Init_fn(TRUE, hw_opt->nthreads_tmpi, TMPI_AFFINITY_NONE,
+ mdrunner_start_fn, (void*)(mda) );
+ if (ret != TMPI_SUCCESS)
+ {
+ return NULL;
+ }
+
+ crn = reinitialize_commrec_for_this_thread(cr);
+ return crn;
+}
+
+#endif /* GMX_THREAD_MPI */
+
+
+/* We determine the extra cost of the non-bonded kernels compared to
+ * a reference nstlist value of 10 (which is the default in grompp).
+ */
+static const int nbnxnReferenceNstlist = 10;
+/* The values to try when switching */
+const int nstlist_try[] = { 20, 25, 40 };
+#define NNSTL sizeof(nstlist_try)/sizeof(nstlist_try[0])
+/* Increase nstlist until the non-bonded cost increases more than listfac_ok,
+ * but never more than listfac_max.
+ * A standard (protein+)water system at 300K with PME ewald_rtol=1e-5
+ * needs 1.28 at rcoulomb=0.9 and 1.24 at rcoulomb=1.0 to get to nstlist=40.
+ * Note that both CPU and GPU factors are conservative. Performance should
+ * not go down due to this tuning, except with a relatively slow GPU.
+ * On the other hand, at medium/high parallelization or with fast GPUs
+ * nstlist will not be increased enough to reach optimal performance.
+ */
+/* CPU: pair-search is about a factor 1.5 slower than the non-bonded kernel */
+static const float nbnxn_cpu_listfac_ok = 1.05;
+static const float nbnxn_cpu_listfac_max = 1.09;
+/* GPU: pair-search is a factor 1.5-3 slower than the non-bonded kernel */
+static const float nbnxn_gpu_listfac_ok = 1.20;
+static const float nbnxn_gpu_listfac_max = 1.30;
+
+/* Try to increase nstlist when using the Verlet cut-off scheme */
+static void increase_nstlist(FILE *fp, t_commrec *cr,
+ t_inputrec *ir, int nstlist_cmdline,
+ const gmx_mtop_t *mtop, matrix box,
+ gmx_bool bGPU)
+{
+ float listfac_ok, listfac_max;
+ int nstlist_orig, nstlist_prev;
+ verletbuf_list_setup_t ls;
+ real rlistWithReferenceNstlist, rlist_inc, rlist_ok, rlist_max;
+ real rlist_new, rlist_prev;
+ size_t nstlist_ind = 0;
+ t_state state_tmp;
+ gmx_bool bBox, bDD, bCont;
+ const char *nstl_gpu = "\nFor optimal performance with a GPU nstlist (now %d) should be larger.\nThe optimum depends on your CPU and GPU resources.\nYou might want to try several nstlist values.\n";
+ const char *nve_err = "Can not increase nstlist because an NVE ensemble is used";
+ const char *vbd_err = "Can not increase nstlist because verlet-buffer-tolerance is not set or used";
+ const char *box_err = "Can not increase nstlist because the box is too small";
+ const char *dd_err = "Can not increase nstlist because of domain decomposition limitations";
+ char buf[STRLEN];
+ const float oneThird = 1.0f / 3.0f;
+
+ if (nstlist_cmdline <= 0)
+ {
+ if (ir->nstlist == 1)
+ {
+ /* The user probably set nstlist=1 for a reason,
+ * don't mess with the settings.
+ */
+ return;
+ }
+
+ if (fp != NULL && bGPU && ir->nstlist < nstlist_try[0])
+ {
+ fprintf(fp, nstl_gpu, ir->nstlist);
+ }
+ nstlist_ind = 0;
+ while (nstlist_ind < NNSTL && ir->nstlist >= nstlist_try[nstlist_ind])
+ {
+ nstlist_ind++;
+ }
+ if (nstlist_ind == NNSTL)
+ {
+ /* There are no larger nstlist value to try */
+ return;
+ }
+ }
+
+ if (EI_MD(ir->eI) && ir->etc == etcNO)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "%s\n", nve_err);
+ }
+ if (fp != NULL)
+ {
+ fprintf(fp, "%s\n", nve_err);
+ }
+
+ return;
+ }
+
+ if (ir->verletbuf_tol == 0 && bGPU)
+ {
+ gmx_fatal(FARGS, "You are using an old tpr file with a GPU, please generate a new tpr file with an up to date version of grompp");
+ }
+
+ if (ir->verletbuf_tol < 0)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "%s\n", vbd_err);
+ }
+ if (fp != NULL)
+ {
+ fprintf(fp, "%s\n", vbd_err);
+ }
+
+ return;
+ }
+
+ if (bGPU)
+ {
+ listfac_ok = nbnxn_gpu_listfac_ok;
+ listfac_max = nbnxn_gpu_listfac_max;
+ }
+ else
+ {
+ listfac_ok = nbnxn_cpu_listfac_ok;
+ listfac_max = nbnxn_cpu_listfac_max;
+ }
+
+ nstlist_orig = ir->nstlist;
+ if (nstlist_cmdline > 0)
+ {
+ if (fp)
+ {
+ sprintf(buf, "Getting nstlist=%d from command line option",
+ nstlist_cmdline);
+ }
+ ir->nstlist = nstlist_cmdline;
+ }
+
+ verletbuf_get_list_setup(TRUE, bGPU, &ls);
+
+ /* Allow rlist to make the list a given factor larger than the list
+ * would be with the reference value for nstlist (10).
+ */
+ nstlist_prev = ir->nstlist;
+ ir->nstlist = nbnxnReferenceNstlist;
+ calc_verlet_buffer_size(mtop, det(box), ir, -1, &ls, NULL,
+ &rlistWithReferenceNstlist);
+ ir->nstlist = nstlist_prev;
+
+ /* Determine the pair list size increase due to zero interactions */
+ rlist_inc = nbnxn_get_rlist_effective_inc(ls.cluster_size_j,
+ mtop->natoms/det(box));
+ rlist_ok = (rlistWithReferenceNstlist + rlist_inc)*pow(listfac_ok, oneThird) - rlist_inc;
+ rlist_max = (rlistWithReferenceNstlist + rlist_inc)*pow(listfac_max, oneThird) - rlist_inc;
+ if (debug)
+ {
+ fprintf(debug, "nstlist tuning: rlist_inc %.3f rlist_ok %.3f rlist_max %.3f\n",
+ rlist_inc, rlist_ok, rlist_max);
+ }
+
+ nstlist_prev = nstlist_orig;
+ rlist_prev = ir->rlist;
+ do
+ {
+ if (nstlist_cmdline <= 0)
+ {
+ ir->nstlist = nstlist_try[nstlist_ind];
+ }
+
+ /* Set the pair-list buffer size in ir */
+ calc_verlet_buffer_size(mtop, det(box), ir, -1, &ls, NULL, &rlist_new);
+
+ /* Does rlist fit in the box? */
+ bBox = (sqr(rlist_new) < max_cutoff2(ir->ePBC, box));
+ bDD = TRUE;
+ if (bBox && DOMAINDECOMP(cr))
+ {
+ /* Check if rlist fits in the domain decomposition */
+ if (inputrec2nboundeddim(ir) < DIM)
+ {
+ gmx_incons("Changing nstlist with domain decomposition and unbounded dimensions is not implemented yet");
+ }
+ copy_mat(box, state_tmp.box);
+ bDD = change_dd_cutoff(cr, &state_tmp, ir, rlist_new);
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "nstlist %d rlist %.3f bBox %d bDD %d\n",
+ ir->nstlist, rlist_new, bBox, bDD);
+ }
+
+ bCont = FALSE;
+
+ if (nstlist_cmdline <= 0)
+ {
+ if (bBox && bDD && rlist_new <= rlist_max)
+ {
+ /* Increase nstlist */
+ nstlist_prev = ir->nstlist;
+ rlist_prev = rlist_new;
+ bCont = (nstlist_ind+1 < NNSTL && rlist_new < rlist_ok);
+ }
+ else
+ {
+ /* Stick with the previous nstlist */
+ ir->nstlist = nstlist_prev;
+ rlist_new = rlist_prev;
+ bBox = TRUE;
+ bDD = TRUE;
+ }
+ }
+
+ nstlist_ind++;
+ }
+ while (bCont);
+
+ if (!bBox || !bDD)
+ {
+ gmx_warning(!bBox ? box_err : dd_err);
+ if (fp != NULL)
+ {
+ fprintf(fp, "\n%s\n", bBox ? box_err : dd_err);
+ }
+ ir->nstlist = nstlist_orig;
+ }
+ else if (ir->nstlist != nstlist_orig || rlist_new != ir->rlist)
+ {
+ sprintf(buf, "Changing nstlist from %d to %d, rlist from %g to %g",
+ nstlist_orig, ir->nstlist,
+ ir->rlist, rlist_new);
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "%s\n\n", buf);
+ }
+ if (fp != NULL)
+ {
+ fprintf(fp, "%s\n\n", buf);
+ }
+ ir->rlist = rlist_new;
+ ir->rlistlong = rlist_new;
+ }
+}
+
+static void prepare_verlet_scheme(FILE *fplog,
+ t_commrec *cr,
+ t_inputrec *ir,
+ int nstlist_cmdline,
+ const gmx_mtop_t *mtop,
+ matrix box,
+ gmx_bool bUseGPU)
+{
+ /* For NVE simulations, we will retain the initial list buffer */
+ if (EI_DYNAMICS(ir->eI) &&
+ ir->verletbuf_tol > 0 &&
+ !(EI_MD(ir->eI) && ir->etc == etcNO))
+ {
+ /* Update the Verlet buffer size for the current run setup */
+ verletbuf_list_setup_t ls;
+ real rlist_new;
+
+ /* Here we assume SIMD-enabled kernels are being used. But as currently
+ * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
+ * and 4x2 gives a larger buffer than 4x4, this is ok.
+ */
+ verletbuf_get_list_setup(TRUE, bUseGPU, &ls);
+
+ calc_verlet_buffer_size(mtop, det(box), ir, -1, &ls, NULL, &rlist_new);
+
+ if (rlist_new != ir->rlist)
+ {
+ if (fplog != NULL)
+ {
+ fprintf(fplog, "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
+ ir->rlist, rlist_new,
+ ls.cluster_size_i, ls.cluster_size_j);
+ }
+ ir->rlist = rlist_new;
+ ir->rlistlong = rlist_new;
+ }
+ }
+
+ if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
+ {
+ gmx_fatal(FARGS, "Can not set nstlist without %s",
+ !EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
+ }
+
+ if (EI_DYNAMICS(ir->eI))
+ {
+ /* Set or try nstlist values */
+ increase_nstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, bUseGPU);
+ }
+}
+
+/* Override the value in inputrec with value passed on the command line (if any) */
+static void override_nsteps_cmdline(FILE *fplog,
+ gmx_int64_t nsteps_cmdline,
+ t_inputrec *ir,
+ const t_commrec *cr)
+{
+ assert(ir);
+ assert(cr);
+
+ /* 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));
+ }
+
+ md_print_warn(cr, fplog, "%s\n", 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 */
+}
+
+int mdrunner(gmx_hw_opt_t *hw_opt,
+ FILE *fplog, t_commrec *cr, int nfile,
+ const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
+ gmx_bool bCompact, int nstglobalcomm,
+ ivec ddxyz, int dd_node_order, real rdd, real rconstr,
+ const char *dddlb_opt, real dlb_scale,
+ const char *ddcsx, const char *ddcsy, const char *ddcsz,
+ const char *nbpu_opt, int nstlist_cmdline,
+ gmx_int64_t nsteps_cmdline, int nstepout, int resetstep,
+ int gmx_unused nmultisim, int repl_ex_nst, int repl_ex_nex,
+ int repl_ex_seed, real pforce, real cpt_period, real max_hours,
+ int imdport, unsigned long Flags)
+{
+ gmx_bool bForceUseGPU, bTryUseGPU, bRerunMD;
+ t_inputrec *inputrec;
+ t_state *state = NULL;
+ matrix box;
+ gmx_ddbox_t ddbox = {0};
+ int npme_major, npme_minor;
+ t_nrnb *nrnb;
+ gmx_mtop_t *mtop = NULL;
+ t_mdatoms *mdatoms = NULL;
+ t_forcerec *fr = NULL;
+ t_fcdata *fcd = NULL;
+ real ewaldcoeff_q = 0;
+ real ewaldcoeff_lj = 0;
+ struct gmx_pme_t **pmedata = NULL;
+ gmx_vsite_t *vsite = NULL;
+ gmx_constr_t constr;
+ int nChargePerturbed = -1, nTypePerturbed = 0, status;
+ gmx_wallcycle_t wcycle;
+ gmx_bool bReadEkin;
+ gmx_walltime_accounting_t walltime_accounting = NULL;
+ int rc;
+ gmx_int64_t reset_counters;
+ gmx_edsam_t ed = NULL;
+ int nthreads_pme = 1;
+ int nthreads_pp = 1;
+ gmx_membed_t membed = NULL;
+ gmx_hw_info_t *hwinfo = NULL;
+ /* The master rank decides early on bUseGPU and broadcasts this later */
+ gmx_bool bUseGPU = FALSE;
+
+ /* CAUTION: threads may be started later on in this function, so
+ cr doesn't reflect the final parallel state right now */
+ snew(inputrec, 1);
+ snew(mtop, 1);
+
+ if (Flags & MD_APPENDFILES)
+ {
+ fplog = NULL;
+ }
+
+ bRerunMD = (Flags & MD_RERUN);
+ bForceUseGPU = (strncmp(nbpu_opt, "gpu", 3) == 0);
+ bTryUseGPU = (strncmp(nbpu_opt, "auto", 4) == 0) || bForceUseGPU;
+
+ /* Detect hardware, gather information. This is an operation that is
+ * global for this process (MPI rank). */
+ hwinfo = gmx_detect_hardware(fplog, cr, bTryUseGPU);
+
+ gmx_print_detected_hardware(fplog, cr, hwinfo);
+
+ if (fplog != NULL)
+ {
+ /* 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");
+ }
+
+ snew(state, 1);
+ if (SIMMASTER(cr))
+ {
+ /* Read (nearly) all data required for the simulation */
+ read_tpx_state(ftp2fn(efTPR, nfile, fnm), inputrec, state, NULL, mtop);
+
+ if (inputrec->cutoff_scheme == ecutsVERLET)
+ {
+ /* Here the master rank decides if all ranks will use GPUs */
+ bUseGPU = (hwinfo->gpu_info.n_dev_compatible > 0 ||
+ getenv("GMX_EMULATE_GPU") != NULL);
+
+ /* TODO add GPU kernels for this and replace this check by:
+ * (bUseGPU && (ir->vdwtype == evdwPME &&
+ * ir->ljpme_combination_rule == eljpmeLB))
+ * update the message text and the content of nbnxn_acceleration_supported.
+ */
+ if (bUseGPU &&
+ !nbnxn_gpu_acceleration_supported(fplog, cr, inputrec, bRerunMD))
+ {
+ /* Fallback message printed by nbnxn_acceleration_supported */
+ if (bForceUseGPU)
+ {
+ gmx_fatal(FARGS, "GPU acceleration requested, but not supported with the given input settings");
+ }
+ bUseGPU = FALSE;
+ }
+
+ prepare_verlet_scheme(fplog, cr,
+ inputrec, nstlist_cmdline, mtop, state->box,
+ bUseGPU);
+ }
+ else
+ {
+ if (nstlist_cmdline > 0)
+ {
+ gmx_fatal(FARGS, "Can not set nstlist with the group cut-off scheme");
+ }
+
+ if (hwinfo->gpu_info.n_dev_compatible > 0)
+ {
+ md_print_warn(cr, fplog,
+ "NOTE: GPU(s) found, but the current simulation can not use GPUs\n"
+ " To use a GPU, set the mdp option: cutoff-scheme = Verlet\n");
+ }
+
+ if (bForceUseGPU)
+ {
+ gmx_fatal(FARGS, "GPU requested, but can't be used without cutoff-scheme=Verlet");
+ }
+
+#ifdef GMX_TARGET_BGQ
+ md_print_warn(cr, fplog,
+ "NOTE: There is no SIMD implementation of the group scheme kernels on\n"
+ " BlueGene/Q. You will observe better performance from using the\n"
+ " Verlet cut-off scheme.\n");
+#endif
+ }
+
+ if (inputrec->eI == eiSD2)
+ {
+ md_print_warn(cr, fplog, "The stochastic dynamics integrator %s is deprecated, since\n"
+ "it is slower than integrator %s and is slightly less accurate\n"
+ "with constraints. Use the %s integrator.",
+ ei_names[inputrec->eI], ei_names[eiSD1], ei_names[eiSD1]);
+ }
+ }
+
+ /* Check and update the hardware options for internal consistency */
+ check_and_update_hw_opt_1(hw_opt, cr);
+
+ /* Early check for externally set process affinity. */
+ gmx_check_thread_affinity_set(fplog, cr,
+ hw_opt, hwinfo->nthreads_hw_avail, FALSE);
+
+#ifdef GMX_THREAD_MPI
+ if (SIMMASTER(cr))
+ {
+ if (cr->npmenodes > 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);
+
+ /* NOW the threads will be started: */
+ hw_opt->nthreads_tmpi = get_nthreads_mpi(hwinfo,
+ hw_opt,
+ inputrec, mtop,
+ cr, fplog, bUseGPU);
+
+ if (hw_opt->nthreads_tmpi > 1)
+ {
+ t_commrec *cr_old = cr;
+ /* now start the threads. */
+ cr = mdrunner_start_threads(hw_opt, fplog, cr_old, nfile, fnm,
+ oenv, bVerbose, bCompact, nstglobalcomm,
+ ddxyz, dd_node_order, rdd, rconstr,
+ dddlb_opt, dlb_scale, ddcsx, ddcsy, ddcsz,
+ nbpu_opt, nstlist_cmdline,
+ nsteps_cmdline, nstepout, resetstep, nmultisim,
+ repl_ex_nst, repl_ex_nex, repl_ex_seed, pforce,
+ cpt_period, max_hours,
+ Flags);
+ /* the main thread continues here with a new cr. We don't deallocate
+ the old cr because other threads may still be reading it. */
+ if (cr == NULL)
+ {
+ gmx_comm("Failed to spawn threads");
+ }
+ }
+ }
+#endif
+ /* END OF CAUTION: cr is now reliable */
+
+ /* g_membed initialisation *
+ * Because we change the mtop, init_membed is called before the init_parallel *
+ * (in case we ever want to make it run in parallel) */
+ if (opt2bSet("-membed", nfile, fnm))
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "Initializing membed");
+ }
+ membed = init_membed(fplog, nfile, fnm, mtop, inputrec, state, cr, &cpt_period);
+ }
+
+ if (PAR(cr))
+ {
+ /* now broadcast everything to the non-master nodes/threads: */
+ init_parallel(cr, inputrec, mtop);
+
+ /* The master rank decided on the use of GPUs,
+ * broadcast this information to all ranks.
+ */
+ gmx_bcast_sim(sizeof(bUseGPU), &bUseGPU, cr);
+ }
+
+ if (fplog != NULL)
+ {
+ pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
+ fprintf(fplog, "\n");
+ }
+
+ /* now make sure the state is initialized and propagated */
+ set_state_entries(state, inputrec);
+
+ /* A parallel command line option consistency check that we can
+ only do after any threads have started. */
+ if (!PAR(cr) &&
+ (ddxyz[XX] > 1 || ddxyz[YY] > 1 || ddxyz[ZZ] > 1 || cr->npmenodes > 0))
+ {
+ gmx_fatal(FARGS,
+ "The -dd or -npme option request a parallel simulation, "
+#ifndef GMX_MPI
+ "but %s was compiled without threads or MPI enabled"
+#else
+#ifdef GMX_THREAD_MPI
+ "but the number of threads (option -nt) 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 (bRerunMD &&
+ (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 (cr->npmenodes > 0)
+ {
+ gmx_fatal_collective(FARGS, cr, NULL,
+ "PME-only ranks are requested, but the system does not use PME for electrostatics or LJ");
+ }
+
+ cr->npmenodes = 0;
+ }
+
+ if (bUseGPU && cr->npmenodes < 0)
+ {
+ /* With GPUs we don't automatically use PME-only ranks. PME ranks can
+ * improve performance with many threads per GPU, since our OpenMP
+ * scaling is bad, but it's difficult to automate the setup.
+ */
+ cr->npmenodes = 0;
+ }
+
+#ifdef GMX_FAHCORE
+ if (MASTER(cr))
+ {
+ fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
+ }
+#endif
+
+ /* NMR restraints must be initialized before load_checkpoint,
+ * since with time averaging the history is added to t_state.
+ * For proper consistency check we therefore need to extend
+ * t_state here.
+ * So the PME-only nodes (if present) will also initialize
+ * the distance restraints.
+ */
+ snew(fcd, 1);
+
+ /* This needs to be called before read_checkpoint to extend the state */
+ init_disres(fplog, mtop, inputrec, cr, fcd, state, repl_ex_nst > 0);
+
+ init_orires(fplog, mtop, state->x, inputrec, cr, &(fcd->orires),
+ state);
+
+ if (DEFORM(*inputrec))
+ {
+ /* Store the deform reference box before reading the checkpoint */
+ if (SIMMASTER(cr))
+ {
+ copy_mat(state->box, box);
+ }
+ if (PAR(cr))
+ {
+ gmx_bcast(sizeof(box), box, cr);
+ }
+ /* Because we do not have the update struct available yet
+ * in which the reference values should be stored,
+ * we store them temporarily in static variables.
+ * This should be thread safe, since they are only written once
+ * and with identical values.
+ */
+ tMPI_Thread_mutex_lock(&deform_init_box_mutex);
+ deform_init_init_step_tpx = inputrec->init_step;
+ copy_mat(box, deform_init_box_tpx);
+ tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
+ }
+
+ if (opt2bSet("-cpi", nfile, fnm))
+ {
+ /* Check if checkpoint file exists before doing continuation.
+ * This way we can use identical input options for the first and subsequent runs...
+ */
+ if (gmx_fexist_master(opt2fn_master("-cpi", nfile, fnm, cr), cr) )
+ {
+ load_checkpoint(opt2fn_master("-cpi", nfile, fnm, cr), &fplog,
+ cr, ddxyz,
+ inputrec, state, &bReadEkin,
+ (Flags & MD_APPENDFILES),
+ (Flags & MD_APPENDFILESSET));
+
+ if (bReadEkin)
+ {
+ Flags |= MD_READ_EKIN;
+ }
+ }
+ }
+
+ if (MASTER(cr) && (Flags & MD_APPENDFILES))
+ {
+ gmx_log_open(ftp2fn(efLOG, nfile, fnm), cr,
+ Flags, &fplog);
+ }
+
+ /* override nsteps with value from cmdline */
+ override_nsteps_cmdline(fplog, nsteps_cmdline, inputrec, cr);
+
+ if (SIMMASTER(cr))
+ {
+ copy_mat(state->box, box);
+ }
+
+ if (PAR(cr))
+ {
+ gmx_bcast(sizeof(box), box, cr);
+ }
+
+ /* Essential dynamics */
+ if (opt2bSet("-ei", nfile, fnm))
+ {
+ /* Open input and output files, allocate space for ED data structure */
+ ed = ed_open(mtop->natoms, &state->edsamstate, nfile, fnm, Flags, oenv, cr);
+ }
+
+ if (PAR(cr) && !(EI_TPI(inputrec->eI) ||
+ inputrec->eI == eiNM))
+ {
+ cr->dd = init_domain_decomposition(fplog, cr, Flags, ddxyz, rdd, rconstr,
+ dddlb_opt, dlb_scale,
+ ddcsx, ddcsy, ddcsz,
+ mtop, inputrec,
+ box, state->x,
+ &ddbox, &npme_major, &npme_minor);
+
+ make_dd_communicators(fplog, cr, dd_node_order);
+
+ /* Set overallocation to avoid frequent reallocation of arrays */
+ set_over_alloc_dd(TRUE);
+ }
+ else
+ {
+ /* PME, if used, is done on all nodes with 1D decomposition */
+ cr->npmenodes = 0;
+ cr->duty = (DUTY_PP | DUTY_PME);
+ npme_major = 1;
+ npme_minor = 1;
+
+ if (inputrec->ePBC == epbcSCREW)
+ {
+ gmx_fatal(FARGS,
+ "pbc=%s is only implemented with domain decomposition",
+ epbc_names[inputrec->ePBC]);
+ }
+ }
+
+ if (PAR(cr))
+ {
+ /* After possible communicator splitting in make_dd_communicators.
+ * we can set up the intra/inter node communication.
+ */
+ gmx_setup_nodecomm(fplog, cr);
+ }
+
+ /* Initialize per-physical-node MPI process/thread ID and counters. */
+ gmx_init_intranode_counters(cr);
+#ifdef GMX_MPI
+ if (MULTISIM(cr))
+ {
+ md_print_info(cr, fplog,
+ "This is simulation %d out of %d running as a composite GROMACS\n"
+ "multi-simulation job. Setup for this simulation:\n\n",
+ cr->ms->sim, cr->ms->nsim);
+ }
+ md_print_info(cr, fplog, "Using %d MPI %s\n",
+ cr->nnodes,
+#ifdef GMX_THREAD_MPI
+ cr->nnodes == 1 ? "thread" : "threads"
+#else
+ cr->nnodes == 1 ? "process" : "processes"
+#endif
+ );
+ fflush(stderr);
+#endif
+
+ /* Check and update hw_opt for the cut-off scheme */
+ check_and_update_hw_opt_2(hw_opt, inputrec->cutoff_scheme);
+
+ /* Check and update hw_opt for the number of MPI ranks */
+ check_and_update_hw_opt_3(hw_opt);
+
+ gmx_omp_nthreads_init(fplog, cr,
+ hwinfo->nthreads_hw_avail,
+ hw_opt->nthreads_omp,
+ hw_opt->nthreads_omp_pme,
+ (cr->duty & DUTY_PP) == 0,
+ inputrec->cutoff_scheme == ecutsVERLET);
+
+#ifndef NDEBUG
+ if (integrator[inputrec->eI].func != do_tpi &&
+ inputrec->cutoff_scheme == ecutsVERLET)
+ {
+ gmx_feenableexcept();
+ }
+#endif
+
+ if (bUseGPU)
+ {
+ /* Select GPU id's to use */
+ gmx_select_gpu_ids(fplog, cr, &hwinfo->gpu_info, bForceUseGPU,
+ &hw_opt->gpu_opt);
+ }
+ else
+ {
+ /* Ignore (potentially) manually selected GPUs */
+ hw_opt->gpu_opt.n_dev_use = 0;
+ }
+
+ /* check consistency across ranks of things like SIMD
+ * support and number of GPUs selected */
+ gmx_check_hw_runconf_consistency(fplog, hwinfo, cr, hw_opt, bUseGPU);
+
+ /* Now that we know the setup is consistent, check for efficiency */
+ check_resource_division_efficiency(hwinfo, hw_opt, Flags & MD_NTOMPSET,
+ cr, fplog);
+
+ if (DOMAINDECOMP(cr))
+ {
+ /* When we share GPUs over ranks, we need to know this for the DLB */
+ dd_setup_dlb_resource_sharing(cr, hwinfo, hw_opt);
+ }
+
+ /* getting number of PP/PME threads
+ PME: env variable should be read only on one node to make sure it is
+ identical everywhere;
+ */
+ /* TODO nthreads_pp is only used for pinning threads.
+ * This is a temporary solution until we have a hw topology library.
+ */
+ nthreads_pp = gmx_omp_nthreads_get(emntNonbonded);
+ nthreads_pme = gmx_omp_nthreads_get(emntPME);
+
+ wcycle = wallcycle_init(fplog, resetstep, cr, nthreads_pp, nthreads_pme);
+
+ 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);
+ }
+
+ snew(nrnb, 1);
+ if (cr->duty & DUTY_PP)
+ {
+ bcast_state(cr, state);
+
+ /* Initiate forcerecord */
+ fr = mk_forcerec();
+ fr->hwinfo = hwinfo;
+ fr->gpu_opt = &hw_opt->gpu_opt;
+ init_forcerec(fplog, oenv, fr, fcd, inputrec, mtop, cr, box,
+ opt2fn("-table", nfile, fnm),
+ opt2fn("-tabletf", nfile, fnm),
+ opt2fn("-tablep", nfile, fnm),
+ opt2fn("-tableb", nfile, fnm),
+ nbpu_opt,
+ FALSE,
+ pforce);
+
+ /* version for PCA_NOT_READ_NODE (see md.c) */
+ /*init_forcerec(fplog,fr,fcd,inputrec,mtop,cr,box,FALSE,
+ "nofile","nofile","nofile","nofile",FALSE,pforce);
+ */
+
+ /* Initialize QM-MM */
+ if (fr->bQMMM)
+ {
+ init_QMMMrec(cr, mtop, inputrec, fr);
+ }
+
+ /* Initialize the mdatoms structure.
+ * mdatoms is not filled with atom data,
+ * as this can not be done now with domain decomposition.
+ */
+ mdatoms = init_mdatoms(fplog, mtop, inputrec->efep != efepNO);
+
+ /* Initialize the virtual site communication */
+ vsite = init_vsite(mtop, cr, FALSE);
+
+ calc_shifts(box, fr->shift_vec);
+
+ /* With periodic molecules the charge groups should be whole at start up
+ * and the virtual sites should not be far from their proper positions.
+ */
+ if (!inputrec->bContinuation && MASTER(cr) &&
+ !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
+ {
+ /* Make molecules whole at start of run */
+ if (fr->ePBC != epbcNONE)
+ {
+ do_pbc_first_mtop(fplog, inputrec->ePBC, box, mtop, state->x);
+ }
+ if (vsite)
+ {
+ /* Correct initial vsite positions are required
+ * for the initial distribution in the domain decomposition
+ * and for the initial shell prediction.
+ */
+ construct_vsites_mtop(vsite, mtop, state->x);
+ }
+ }
+
+ if (EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype))
+ {
+ ewaldcoeff_q = fr->ewaldcoeff_q;
+ ewaldcoeff_lj = fr->ewaldcoeff_lj;
+ pmedata = &fr->pmedata;
+ }
+ else
+ {
+ pmedata = NULL;
+ }
+ }
+ else
+ {
+ /* This is a PME only node */
+
+ /* We don't need the state */
+ done_state(state);
+
+ ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
+ ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
+ snew(pmedata, 1);
+ }
+
+ if (hw_opt->thread_affinity != threadaffOFF)
+ {
+ /* Before setting affinity, check whether the affinity has changed
+ * - which indicates that probably the OpenMP library has changed it
+ * since we first checked).
+ */
+ gmx_check_thread_affinity_set(fplog, cr,
+ hw_opt, hwinfo->nthreads_hw_avail, TRUE);
+
+ /* Set the CPU affinity */
+ gmx_set_thread_affinity(fplog, cr, hw_opt, hwinfo);
+ }
+
+ /* Initiate PME if necessary,
+ * either on all nodes or on dedicated PME nodes only. */
+ if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
+ {
+ if (mdatoms)
+ {
+ nChargePerturbed = mdatoms->nChargePerturbed;
+ if (EVDW_PME(inputrec->vdwtype))
+ {
+ nTypePerturbed = mdatoms->nTypePerturbed;
+ }
+ }
+ if (cr->npmenodes > 0)
+ {
+ /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
+ gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
+ gmx_bcast_sim(sizeof(nTypePerturbed), &nTypePerturbed, cr);
+ }
+
+ if (cr->duty & DUTY_PME)
+ {
+ status = gmx_pme_init(pmedata, cr, npme_major, npme_minor, inputrec,
+ mtop ? mtop->natoms : 0, nChargePerturbed, nTypePerturbed,
+ (Flags & MD_REPRODUCIBLE), nthreads_pme);
+ if (status != 0)
+ {
+ gmx_fatal(FARGS, "Error %d initializing PME", status);
+ }
+ }
+ }
+
+
+ if (integrator[inputrec->eI].func == do_md)
+ {
+ /* Turn on signal handling on all nodes */
+ /*
+ * (A user signal from the PME nodes (if any)
+ * is communicated to the PP nodes.
+ */
+ signal_handler_install();
+ }
+
+ if (cr->duty & DUTY_PP)
+ {
+ /* Assumes uniform use of the number of OpenMP threads */
+ walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
+
+ if (inputrec->bPull)
+ {
+ /* Initialize pull code */
+ inputrec->pull_work =
+ init_pull(fplog, inputrec->pull, inputrec, nfile, fnm,
+ mtop, cr, oenv, inputrec->fepvals->init_lambda,
+ EI_DYNAMICS(inputrec->eI) && MASTER(cr), Flags);
+ }
+
+ if (inputrec->bRot)
+ {
+ /* Initialize enforced rotation code */
+ init_rot(fplog, inputrec, nfile, fnm, cr, state->x, box, mtop, oenv,
+ bVerbose, Flags);
+ }
+
+ if (inputrec->eSwapCoords != eswapNO)
+ {
+ /* Initialize ion swapping code */
+ init_swapcoords(fplog, bVerbose, inputrec, opt2fn_master("-swap", nfile, fnm, cr),
+ mtop, state->x, state->box, &state->swapstate, cr, oenv, Flags);
+ }
+
+ constr = init_constraints(fplog, mtop, inputrec, ed, state, cr);
+
+ if (DOMAINDECOMP(cr))
+ {
+ GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
+ dd_init_bondeds(fplog, cr->dd, mtop, vsite, inputrec,
+ Flags & MD_DDBONDCHECK, fr->cginfo_mb);
+
+ set_dd_parameters(fplog, cr->dd, dlb_scale, inputrec, &ddbox);
+
+ setup_dd_grid(fplog, cr->dd);
+ }
+
+ /* Now do whatever the user wants us to do (how flexible...) */
+ integrator[inputrec->eI].func(fplog, cr, nfile, fnm,
+ oenv, bVerbose, bCompact,
+ nstglobalcomm,
+ vsite, constr,
+ nstepout, inputrec, mtop,
+ fcd, state,
+ mdatoms, nrnb, wcycle, ed, fr,
+ repl_ex_nst, repl_ex_nex, repl_ex_seed,
+ membed,
+ cpt_period, max_hours,
+ imdport,
+ Flags,
+ walltime_accounting);
+
+ if (inputrec->bPull)
+ {
+ finish_pull(inputrec->pull_work);
+ }
+
+ if (inputrec->bRot)
+ {
+ finish_rot(inputrec->rot);
+ }
+
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
+ /* do PME only */
+ walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
+ gmx_pmeonly(*pmedata, cr, nrnb, wcycle, walltime_accounting, ewaldcoeff_q, ewaldcoeff_lj, inputrec);
+ }
+
+ wallcycle_stop(wcycle, ewcRUN);
+
+ /* Finish up, write some stuff
+ * if rerunMD, don't write last frame again
+ */
+ finish_run(fplog, cr,
+ inputrec, nrnb, wcycle, walltime_accounting,
+ fr ? fr->nbv : NULL,
+ EI_DYNAMICS(inputrec->eI) && !MULTISIM(cr));
+
+
+ /* Free GPU memory and context */
+ free_gpu_resources(fr, cr, &hwinfo->gpu_info, fr ? fr->gpu_opt : NULL);
+
+ if (opt2bSet("-membed", nfile, fnm))
+ {
+ sfree(membed);
+ }
+
+ gmx_hardware_info_free(hwinfo);
+
+ /* Does what it says */
+ print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
+ walltime_accounting_destroy(walltime_accounting);
+
+ /* Close logfile already here if we were appending to it */
+ if (MASTER(cr) && (Flags & MD_APPENDFILES))
+ {
+ gmx_log_close(fplog);
+ }
+
+ rc = (int)gmx_get_stop_condition();
+
+ done_ed(&ed);
+
+#ifdef GMX_THREAD_MPI
+ /* we need to join all threads. The sub-threads join when they
+ exit this function, but the master thread needs to be told to
+ wait for that. */
+ if (PAR(cr) && MASTER(cr))
+ {
+ tMPI_Finalize();
+ }
+#endif
+
+ return rc;
+}
--
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