1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
4 * This source code is part of
8 * GROningen MAchine for Chemical Simulations
11 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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34 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
53 #include "md_logging.h"
54 #include "md_support.h"
57 #include "pull_rotation.h"
70 #include "checkpoint.h"
71 #include "mtop_util.h"
72 #include "sighandler.h"
73 #include "gromacs/fileio/tpxio.h"
75 #include "gmx_detect_hardware.h"
76 #include "gmx_omp_nthreads.h"
77 #include "pull_rotation.h"
78 #include "calc_verletbuf.h"
79 #include "../mdlib/nbnxn_search.h"
80 #include "../mdlib/nbnxn_consts.h"
81 #include "gmx_fatal_collective.h"
85 #include "gmx_thread_affinity.h"
87 #include "gromacs/utility/gmxmpi.h"
93 #include "gpu_utils.h"
94 #include "nbnxn_cuda_data_mgmt.h"
97 gmx_integrator_t *func;
100 /* The array should match the eI array in include/types/enums.h */
101 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}};
103 gmx_large_int_t deform_init_init_step_tpx;
104 matrix deform_init_box_tpx;
105 #ifdef GMX_THREAD_MPI
106 tMPI_Thread_mutex_t deform_init_box_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
110 #ifdef GMX_THREAD_MPI
111 struct mdrunner_arglist
113 gmx_hw_opt_t *hw_opt;
126 const char *dddlb_opt;
131 const char *nbpu_opt;
132 gmx_large_int_t nsteps_cmdline;
142 const char *deviceOptions;
144 int ret; /* return value */
148 /* The function used for spawning threads. Extracts the mdrunner()
149 arguments from its one argument and calls mdrunner(), after making
151 static void mdrunner_start_fn(void *arg)
153 struct mdrunner_arglist *mda = (struct mdrunner_arglist*)arg;
154 struct mdrunner_arglist mc = *mda; /* copy the arg list to make sure
155 that it's thread-local. This doesn't
156 copy pointed-to items, of course,
157 but those are all const. */
158 t_commrec *cr; /* we need a local version of this */
162 fnm = dup_tfn(mc.nfile, mc.fnm);
164 cr = reinitialize_commrec_for_this_thread(mc.cr);
171 mda->ret = mdrunner(mc.hw_opt, fplog, cr, mc.nfile, fnm, mc.oenv,
172 mc.bVerbose, mc.bCompact, mc.nstglobalcomm,
173 mc.ddxyz, mc.dd_node_order, mc.rdd,
174 mc.rconstr, mc.dddlb_opt, mc.dlb_scale,
175 mc.ddcsx, mc.ddcsy, mc.ddcsz,
177 mc.nsteps_cmdline, mc.nstepout, mc.resetstep,
178 mc.nmultisim, mc.repl_ex_nst, mc.repl_ex_nex, mc.repl_ex_seed, mc.pforce,
179 mc.cpt_period, mc.max_hours, mc.deviceOptions, mc.Flags);
182 /* called by mdrunner() to start a specific number of threads (including
183 the main thread) for thread-parallel runs. This in turn calls mdrunner()
185 All options besides nthreads are the same as for mdrunner(). */
186 static t_commrec *mdrunner_start_threads(gmx_hw_opt_t *hw_opt,
187 FILE *fplog, t_commrec *cr, int nfile,
188 const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
189 gmx_bool bCompact, int nstglobalcomm,
190 ivec ddxyz, int dd_node_order, real rdd, real rconstr,
191 const char *dddlb_opt, real dlb_scale,
192 const char *ddcsx, const char *ddcsy, const char *ddcsz,
193 const char *nbpu_opt,
194 gmx_large_int_t nsteps_cmdline,
195 int nstepout, int resetstep,
196 int nmultisim, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
197 real pforce, real cpt_period, real max_hours,
198 const char *deviceOptions, unsigned long Flags)
201 struct mdrunner_arglist *mda;
202 t_commrec *crn; /* the new commrec */
205 /* first check whether we even need to start tMPI */
206 if (hw_opt->nthreads_tmpi < 2)
211 /* a few small, one-time, almost unavoidable memory leaks: */
213 fnmn = dup_tfn(nfile, fnm);
215 /* fill the data structure to pass as void pointer to thread start fn */
216 mda->hw_opt = hw_opt;
222 mda->bVerbose = bVerbose;
223 mda->bCompact = bCompact;
224 mda->nstglobalcomm = nstglobalcomm;
225 mda->ddxyz[XX] = ddxyz[XX];
226 mda->ddxyz[YY] = ddxyz[YY];
227 mda->ddxyz[ZZ] = ddxyz[ZZ];
228 mda->dd_node_order = dd_node_order;
230 mda->rconstr = rconstr;
231 mda->dddlb_opt = dddlb_opt;
232 mda->dlb_scale = dlb_scale;
236 mda->nbpu_opt = nbpu_opt;
237 mda->nsteps_cmdline = nsteps_cmdline;
238 mda->nstepout = nstepout;
239 mda->resetstep = resetstep;
240 mda->nmultisim = nmultisim;
241 mda->repl_ex_nst = repl_ex_nst;
242 mda->repl_ex_nex = repl_ex_nex;
243 mda->repl_ex_seed = repl_ex_seed;
244 mda->pforce = pforce;
245 mda->cpt_period = cpt_period;
246 mda->max_hours = max_hours;
247 mda->deviceOptions = deviceOptions;
250 /* now spawn new threads that start mdrunner_start_fn(), while
251 the main thread returns, we set thread affinity later */
252 ret = tMPI_Init_fn(TRUE, hw_opt->nthreads_tmpi, TMPI_AFFINITY_NONE,
253 mdrunner_start_fn, (void*)(mda) );
254 if (ret != TMPI_SUCCESS)
259 crn = reinitialize_commrec_for_this_thread(cr);
264 static int get_tmpi_omp_thread_division(const gmx_hw_info_t *hwinfo,
265 const gmx_hw_opt_t *hw_opt,
271 /* There are no separate PME nodes here, as we ensured in
272 * check_and_update_hw_opt that nthreads_tmpi>0 with PME nodes
273 * and a conditional ensures we would not have ended up here.
274 * Note that separate PME nodes might be switched on later.
278 nthreads_tmpi = ngpu;
279 if (nthreads_tot > 0 && nthreads_tot < nthreads_tmpi)
281 nthreads_tmpi = nthreads_tot;
284 else if (hw_opt->nthreads_omp > 0)
286 /* Here we could oversubscribe, when we do, we issue a warning later */
287 nthreads_tmpi = max(1, nthreads_tot/hw_opt->nthreads_omp);
291 /* TODO choose nthreads_omp based on hardware topology
292 when we have a hardware topology detection library */
293 /* In general, when running up to 4 threads, OpenMP should be faster.
294 * Note: on AMD Bulldozer we should avoid running OpenMP over two dies.
295 * On Intel>=Nehalem running OpenMP on a single CPU is always faster,
296 * even on two CPUs it's usually faster (but with many OpenMP threads
297 * it could be faster not to use HT, currently we always use HT).
298 * On Nehalem/Westmere we want to avoid running 16 threads over
299 * two CPUs with HT, so we need a limit<16; thus we use 12.
300 * A reasonable limit for Intel Sandy and Ivy bridge,
301 * not knowing the topology, is 16 threads.
303 const int nthreads_omp_always_faster = 4;
304 const int nthreads_omp_always_faster_Nehalem = 12;
305 const int nthreads_omp_always_faster_SandyBridge = 16;
306 const int first_model_Nehalem = 0x1A;
307 const int first_model_SandyBridge = 0x2A;
308 gmx_bool bIntel_Family6;
311 (gmx_cpuid_vendor(hwinfo->cpuid_info) == GMX_CPUID_VENDOR_INTEL &&
312 gmx_cpuid_family(hwinfo->cpuid_info) == 6);
314 if (nthreads_tot <= nthreads_omp_always_faster ||
316 ((gmx_cpuid_model(hwinfo->cpuid_info) >= nthreads_omp_always_faster_Nehalem && nthreads_tot <= nthreads_omp_always_faster_Nehalem) ||
317 (gmx_cpuid_model(hwinfo->cpuid_info) >= nthreads_omp_always_faster_SandyBridge && nthreads_tot <= nthreads_omp_always_faster_SandyBridge))))
319 /* Use pure OpenMP parallelization */
324 /* Don't use OpenMP parallelization */
325 nthreads_tmpi = nthreads_tot;
329 return nthreads_tmpi;
333 /* Get the number of threads to use for thread-MPI based on how many
334 * were requested, which algorithms we're using,
335 * and how many particles there are.
336 * At the point we have already called check_and_update_hw_opt.
337 * Thus all options should be internally consistent and consistent
338 * with the hardware, except that ntmpi could be larger than #GPU.
340 static int get_nthreads_mpi(const gmx_hw_info_t *hwinfo,
341 gmx_hw_opt_t *hw_opt,
342 t_inputrec *inputrec, gmx_mtop_t *mtop,
346 int nthreads_hw, nthreads_tot_max, nthreads_tmpi, nthreads_new, ngpu;
347 int min_atoms_per_mpi_thread;
352 if (hw_opt->nthreads_tmpi > 0)
354 /* Trivial, return right away */
355 return hw_opt->nthreads_tmpi;
358 nthreads_hw = hwinfo->nthreads_hw_avail;
360 /* How many total (#tMPI*#OpenMP) threads can we start? */
361 if (hw_opt->nthreads_tot > 0)
363 nthreads_tot_max = hw_opt->nthreads_tot;
367 nthreads_tot_max = nthreads_hw;
370 bCanUseGPU = (inputrec->cutoff_scheme == ecutsVERLET && hwinfo->bCanUseGPU);
373 ngpu = hwinfo->gpu_info.ncuda_dev_use;
381 get_tmpi_omp_thread_division(hwinfo, hw_opt, nthreads_tot_max, ngpu);
383 if (inputrec->eI == eiNM || EI_TPI(inputrec->eI))
385 /* Dims/steps are divided over the nodes iso splitting the atoms */
386 min_atoms_per_mpi_thread = 0;
392 min_atoms_per_mpi_thread = MIN_ATOMS_PER_GPU;
396 min_atoms_per_mpi_thread = MIN_ATOMS_PER_MPI_THREAD;
400 /* Check if an algorithm does not support parallel simulation. */
401 if (nthreads_tmpi != 1 &&
402 ( inputrec->eI == eiLBFGS ||
403 inputrec->coulombtype == eelEWALD ) )
407 md_print_warn(cr, fplog, "The integration or electrostatics algorithm doesn't support parallel runs. Using a single thread-MPI thread.\n");
408 if (hw_opt->nthreads_tmpi > nthreads_tmpi)
410 gmx_fatal(FARGS, "You asked for more than 1 thread-MPI thread, but an algorithm doesn't support that");
413 else if (mtop->natoms/nthreads_tmpi < min_atoms_per_mpi_thread)
415 /* the thread number was chosen automatically, but there are too many
416 threads (too few atoms per thread) */
417 nthreads_new = max(1, mtop->natoms/min_atoms_per_mpi_thread);
419 /* Avoid partial use of Hyper-Threading */
420 if (gmx_cpuid_x86_smt(hwinfo->cpuid_info) == GMX_CPUID_X86_SMT_ENABLED &&
421 nthreads_new > nthreads_hw/2 && nthreads_new < nthreads_hw)
423 nthreads_new = nthreads_hw/2;
426 /* Avoid large prime numbers in the thread count */
427 if (nthreads_new >= 6)
429 /* Use only 6,8,10 with additional factors of 2 */
433 while (3*fac*2 <= nthreads_new)
438 nthreads_new = (nthreads_new/fac)*fac;
443 if (nthreads_new == 5)
449 nthreads_tmpi = nthreads_new;
451 fprintf(stderr, "\n");
452 fprintf(stderr, "NOTE: Parallelization is limited by the small number of atoms,\n");
453 fprintf(stderr, " only starting %d thread-MPI threads.\n", nthreads_tmpi);
454 fprintf(stderr, " You can use the -nt and/or -ntmpi option to optimize the number of threads.\n\n");
457 return nthreads_tmpi;
459 #endif /* GMX_THREAD_MPI */
462 /* Environment variable for setting nstlist */
463 static const char* NSTLIST_ENVVAR = "GMX_NSTLIST";
464 /* Try to increase nstlist when using a GPU with nstlist less than this */
465 static const int NSTLIST_GPU_ENOUGH = 20;
466 /* Increase nstlist until the non-bonded cost increases more than this factor */
467 static const float NBNXN_GPU_LIST_OK_FAC = 1.20;
468 /* Don't increase nstlist beyond a non-bonded cost increases of this factor.
469 * A standard (protein+)water system at 300K with PME ewald_rtol=1e-5
470 * needs 1.28 at rcoulomb=0.9 and 1.24 at rcoulomb=1.0 to get to nstlist=40.
472 static const float NBNXN_GPU_LIST_MAX_FAC = 1.30;
474 /* Try to increase nstlist when running on a GPU */
475 static void increase_nstlist(FILE *fp, t_commrec *cr,
476 t_inputrec *ir, const gmx_mtop_t *mtop, matrix box)
479 int nstlist_orig, nstlist_prev;
480 verletbuf_list_setup_t ls;
481 real rlist_nstlist10, rlist_inc, rlist_ok, rlist_max;
482 real rlist_new, rlist_prev;
485 gmx_bool bBox, bDD, bCont;
486 const char *nstl_fmt = "\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";
487 const char *vbd_err = "Can not increase nstlist for GPU run because verlet-buffer-drift is not set or used";
488 const char *box_err = "Can not increase nstlist for GPU run because the box is too small";
489 const char *dd_err = "Can not increase nstlist for GPU run because of domain decomposition limitations";
492 /* Number of + nstlist alternative values to try when switching */
493 const int nstl[] = { 20, 25, 40 };
494 #define NNSTL sizeof(nstl)/sizeof(nstl[0])
496 env = getenv(NSTLIST_ENVVAR);
501 fprintf(fp, nstl_fmt, ir->nstlist);
505 if (ir->verletbuf_drift == 0)
507 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");
510 if (ir->verletbuf_drift < 0)
514 fprintf(stderr, "%s\n", vbd_err);
518 fprintf(fp, "%s\n", vbd_err);
524 nstlist_orig = ir->nstlist;
527 sprintf(buf, "Getting nstlist from environment variable GMX_NSTLIST=%s", env);
530 fprintf(stderr, "%s\n", buf);
534 fprintf(fp, "%s\n", buf);
536 sscanf(env, "%d", &ir->nstlist);
539 verletbuf_get_list_setup(TRUE, &ls);
541 /* Allow rlist to make the list a given factor larger than the list
542 * would be with nstlist=10.
544 nstlist_prev = ir->nstlist;
546 calc_verlet_buffer_size(mtop, det(box), ir, ir->verletbuf_drift, &ls,
547 NULL, &rlist_nstlist10);
548 ir->nstlist = nstlist_prev;
550 /* Determine the pair list size increase due to zero interactions */
551 rlist_inc = nbnxn_get_rlist_effective_inc(NBNXN_GPU_CLUSTER_SIZE, mtop->natoms/det(box));
552 rlist_ok = (rlist_nstlist10 + rlist_inc)*pow(NBNXN_GPU_LIST_OK_FAC, 1.0/3.0) - rlist_inc;
553 rlist_max = (rlist_nstlist10 + rlist_inc)*pow(NBNXN_GPU_LIST_MAX_FAC, 1.0/3.0) - rlist_inc;
556 fprintf(debug, "GPU nstlist tuning: rlist_inc %.3f rlist_max %.3f\n",
557 rlist_inc, rlist_max);
561 nstlist_prev = nstlist_orig;
562 rlist_prev = ir->rlist;
567 ir->nstlist = nstl[i];
570 /* Set the pair-list buffer size in ir */
571 calc_verlet_buffer_size(mtop, det(box), ir, ir->verletbuf_drift, &ls,
574 /* Does rlist fit in the box? */
575 bBox = (sqr(rlist_new) < max_cutoff2(ir->ePBC, box));
577 if (bBox && DOMAINDECOMP(cr))
579 /* Check if rlist fits in the domain decomposition */
580 if (inputrec2nboundeddim(ir) < DIM)
582 gmx_incons("Changing nstlist with domain decomposition and unbounded dimensions is not implemented yet");
584 copy_mat(box, state_tmp.box);
585 bDD = change_dd_cutoff(cr, &state_tmp, ir, rlist_new);
592 if (bBox && bDD && rlist_new <= rlist_max)
594 /* Increase nstlist */
595 nstlist_prev = ir->nstlist;
596 rlist_prev = rlist_new;
597 bCont = (i+1 < NNSTL && rlist_new < rlist_ok);
601 /* Stick with the previous nstlist */
602 ir->nstlist = nstlist_prev;
603 rlist_new = rlist_prev;
615 gmx_warning(!bBox ? box_err : dd_err);
618 fprintf(fp, "\n%s\n", bBox ? box_err : dd_err);
620 ir->nstlist = nstlist_orig;
622 else if (ir->nstlist != nstlist_orig || rlist_new != ir->rlist)
624 sprintf(buf, "Changing nstlist from %d to %d, rlist from %g to %g",
625 nstlist_orig, ir->nstlist,
626 ir->rlist, rlist_new);
629 fprintf(stderr, "%s\n\n", buf);
633 fprintf(fp, "%s\n\n", buf);
635 ir->rlist = rlist_new;
636 ir->rlistlong = rlist_new;
640 static void prepare_verlet_scheme(FILE *fplog,
641 const gmx_hw_info_t *hwinfo,
644 const gmx_mtop_t *mtop,
648 /* Here we only check for GPU usage on the MPI master process,
649 * as here we don't know how many GPUs we will use yet.
650 * We check for a GPU on all processes later.
652 *bUseGPU = hwinfo->bCanUseGPU || (getenv("GMX_EMULATE_GPU") != NULL);
654 if (ir->verletbuf_drift > 0)
656 /* Update the Verlet buffer size for the current run setup */
657 verletbuf_list_setup_t ls;
660 /* Here we assume CPU acceleration is on. But as currently
661 * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
662 * and 4x2 gives a larger buffer than 4x4, this is ok.
664 verletbuf_get_list_setup(*bUseGPU, &ls);
666 calc_verlet_buffer_size(mtop, det(box), ir,
667 ir->verletbuf_drift, &ls,
669 if (rlist_new != ir->rlist)
673 fprintf(fplog, "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
674 ir->rlist, rlist_new,
675 ls.cluster_size_i, ls.cluster_size_j);
677 ir->rlist = rlist_new;
678 ir->rlistlong = rlist_new;
682 /* With GPU or emulation we should check nstlist for performance */
683 if ((EI_DYNAMICS(ir->eI) &&
685 ir->nstlist < NSTLIST_GPU_ENOUGH) ||
686 getenv(NSTLIST_ENVVAR) != NULL)
688 /* Choose a better nstlist */
689 increase_nstlist(fplog, cr, ir, mtop, box);
693 static void convert_to_verlet_scheme(FILE *fplog,
695 gmx_mtop_t *mtop, real box_vol)
697 char *conv_mesg = "Converting input file with group cut-off scheme to the Verlet cut-off scheme";
699 md_print_warn(NULL, fplog, "%s\n", conv_mesg);
701 ir->cutoff_scheme = ecutsVERLET;
702 ir->verletbuf_drift = 0.005;
704 if (ir->rcoulomb != ir->rvdw)
706 gmx_fatal(FARGS, "The VdW and Coulomb cut-offs are different, whereas the Verlet scheme only supports equal cut-offs");
709 if (ir->vdwtype == evdwUSER || EEL_USER(ir->coulombtype))
711 gmx_fatal(FARGS, "User non-bonded potentials are not (yet) supported with the Verlet scheme");
713 else if (EVDW_SWITCHED(ir->vdwtype) || EEL_SWITCHED(ir->coulombtype))
715 md_print_warn(NULL, fplog, "Converting switched or shifted interactions to a shifted potential (without force shift), this will lead to slightly different interaction potentials");
717 if (EVDW_SWITCHED(ir->vdwtype))
719 ir->vdwtype = evdwCUT;
721 if (EEL_SWITCHED(ir->coulombtype))
723 if (EEL_FULL(ir->coulombtype))
725 /* With full electrostatic only PME can be switched */
726 ir->coulombtype = eelPME;
730 md_print_warn(NULL, fplog, "NOTE: Replacing %s electrostatics with reaction-field with epsilon-rf=inf\n", eel_names[ir->coulombtype]);
731 ir->coulombtype = eelRF;
732 ir->epsilon_rf = 0.0;
736 /* We set the target energy drift to a small number.
737 * Note that this is only for testing. For production the user
738 * should think about this and set the mdp options.
740 ir->verletbuf_drift = 1e-4;
743 if (inputrec2nboundeddim(ir) != 3)
745 gmx_fatal(FARGS, "Can only convert old tpr files to the Verlet cut-off scheme with 3D pbc");
748 if (ir->efep != efepNO || ir->implicit_solvent != eisNO)
750 gmx_fatal(FARGS, "Will not convert old tpr files to the Verlet cut-off scheme with free-energy calculations or implicit solvent");
753 if (EI_DYNAMICS(ir->eI) && !(EI_MD(ir->eI) && ir->etc == etcNO))
755 verletbuf_list_setup_t ls;
757 verletbuf_get_list_setup(FALSE, &ls);
758 calc_verlet_buffer_size(mtop, box_vol, ir, ir->verletbuf_drift, &ls,
763 ir->verletbuf_drift = -1;
764 ir->rlist = 1.05*max(ir->rvdw, ir->rcoulomb);
767 gmx_mtop_remove_chargegroups(mtop);
770 static void check_and_update_hw_opt(gmx_hw_opt_t *hw_opt,
772 gmx_bool bIsSimMaster)
774 gmx_omp_nthreads_read_env(&hw_opt->nthreads_omp, bIsSimMaster);
776 #ifndef GMX_THREAD_MPI
777 if (hw_opt->nthreads_tot > 0)
779 gmx_fatal(FARGS, "Setting the total number of threads is only supported with thread-MPI and Gromacs was compiled without thread-MPI");
781 if (hw_opt->nthreads_tmpi > 0)
783 gmx_fatal(FARGS, "Setting the number of thread-MPI threads is only supported with thread-MPI and Gromacs was compiled without thread-MPI");
788 if (hw_opt->nthreads_omp > 1)
790 gmx_fatal(FARGS, "More than 1 OpenMP thread requested, but Gromacs was compiled without OpenMP support");
792 hw_opt->nthreads_omp = 1;
795 if (hw_opt->nthreads_tot > 0 && hw_opt->nthreads_omp_pme <= 0)
797 /* We have the same number of OpenMP threads for PP and PME processes,
798 * thus we can perform several consistency checks.
800 if (hw_opt->nthreads_tmpi > 0 &&
801 hw_opt->nthreads_omp > 0 &&
802 hw_opt->nthreads_tot != hw_opt->nthreads_tmpi*hw_opt->nthreads_omp)
804 gmx_fatal(FARGS, "The total number of threads requested (%d) does not match the thread-MPI threads (%d) times the OpenMP threads (%d) requested",
805 hw_opt->nthreads_tot, hw_opt->nthreads_tmpi, hw_opt->nthreads_omp);
808 if (hw_opt->nthreads_tmpi > 0 &&
809 hw_opt->nthreads_tot % hw_opt->nthreads_tmpi != 0)
811 gmx_fatal(FARGS, "The total number of threads requested (%d) is not divisible by the number of thread-MPI threads requested (%d)",
812 hw_opt->nthreads_tot, hw_opt->nthreads_tmpi);
815 if (hw_opt->nthreads_omp > 0 &&
816 hw_opt->nthreads_tot % hw_opt->nthreads_omp != 0)
818 gmx_fatal(FARGS, "The total number of threads requested (%d) is not divisible by the number of OpenMP threads requested (%d)",
819 hw_opt->nthreads_tot, hw_opt->nthreads_omp);
822 if (hw_opt->nthreads_tmpi > 0 &&
823 hw_opt->nthreads_omp <= 0)
825 hw_opt->nthreads_omp = hw_opt->nthreads_tot/hw_opt->nthreads_tmpi;
830 if (hw_opt->nthreads_omp > 1)
832 gmx_fatal(FARGS, "OpenMP threads are requested, but Gromacs was compiled without OpenMP support");
836 if (cutoff_scheme == ecutsGROUP)
838 /* We only have OpenMP support for PME only nodes */
839 if (hw_opt->nthreads_omp > 1)
841 gmx_fatal(FARGS, "OpenMP threads have been requested with cut-off scheme %s, but these are only supported with cut-off scheme %s",
842 ecutscheme_names[cutoff_scheme],
843 ecutscheme_names[ecutsVERLET]);
845 hw_opt->nthreads_omp = 1;
848 if (hw_opt->nthreads_omp_pme > 0 && hw_opt->nthreads_omp <= 0)
850 gmx_fatal(FARGS, "You need to specify -ntomp in addition to -ntomp_pme");
853 if (hw_opt->nthreads_tot == 1)
855 hw_opt->nthreads_tmpi = 1;
857 if (hw_opt->nthreads_omp > 1)
859 gmx_fatal(FARGS, "You requested %d OpenMP threads with %d total threads",
860 hw_opt->nthreads_tmpi, hw_opt->nthreads_tot);
862 hw_opt->nthreads_omp = 1;
865 if (hw_opt->nthreads_omp_pme <= 0 && hw_opt->nthreads_omp > 0)
867 hw_opt->nthreads_omp_pme = hw_opt->nthreads_omp;
872 fprintf(debug, "hw_opt: nt %d ntmpi %d ntomp %d ntomp_pme %d gpu_id '%s'\n",
873 hw_opt->nthreads_tot,
874 hw_opt->nthreads_tmpi,
875 hw_opt->nthreads_omp,
876 hw_opt->nthreads_omp_pme,
877 hw_opt->gpu_id != NULL ? hw_opt->gpu_id : "");
883 /* Override the value in inputrec with value passed on the command line (if any) */
884 static void override_nsteps_cmdline(FILE *fplog,
885 gmx_large_int_t nsteps_cmdline,
889 char sbuf[STEPSTRSIZE];
894 /* override with anything else than the default -2 */
895 if (nsteps_cmdline > -2)
899 ir->nsteps = nsteps_cmdline;
900 if (EI_DYNAMICS(ir->eI))
902 sprintf(stmp, "Overriding nsteps with value passed on the command line: %s steps, %.3f ps",
903 gmx_step_str(nsteps_cmdline, sbuf),
904 nsteps_cmdline*ir->delta_t);
908 sprintf(stmp, "Overriding nsteps with value passed on the command line: %s steps",
909 gmx_step_str(nsteps_cmdline, sbuf));
912 md_print_warn(cr, fplog, "%s\n", stmp);
916 /* Data structure set by SIMMASTER which needs to be passed to all nodes
917 * before the other nodes have read the tpx file and called gmx_detect_hardware.
920 int cutoff_scheme; /* The cutoff scheme from inputrec_t */
921 gmx_bool bUseGPU; /* Use GPU or GPU emulation */
924 int mdrunner(gmx_hw_opt_t *hw_opt,
925 FILE *fplog, t_commrec *cr, int nfile,
926 const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
927 gmx_bool bCompact, int nstglobalcomm,
928 ivec ddxyz, int dd_node_order, real rdd, real rconstr,
929 const char *dddlb_opt, real dlb_scale,
930 const char *ddcsx, const char *ddcsy, const char *ddcsz,
931 const char *nbpu_opt,
932 gmx_large_int_t nsteps_cmdline, int nstepout, int resetstep,
933 int nmultisim, int repl_ex_nst, int repl_ex_nex,
934 int repl_ex_seed, real pforce, real cpt_period, real max_hours,
935 const char *deviceOptions, unsigned long Flags)
937 gmx_bool bForceUseGPU, bTryUseGPU;
938 double nodetime = 0, realtime;
939 t_inputrec *inputrec;
940 t_state *state = NULL;
942 gmx_ddbox_t ddbox = {0};
943 int npme_major, npme_minor;
946 gmx_mtop_t *mtop = NULL;
947 t_mdatoms *mdatoms = NULL;
948 t_forcerec *fr = NULL;
949 t_fcdata *fcd = NULL;
951 gmx_pme_t *pmedata = NULL;
952 gmx_vsite_t *vsite = NULL;
954 int i, m, nChargePerturbed = -1, status, nalloc;
956 gmx_wallcycle_t wcycle;
957 gmx_bool bReadRNG, bReadEkin;
959 gmx_walltime_accounting_t walltime_accounting = NULL;
961 gmx_large_int_t reset_counters;
962 gmx_edsam_t ed = NULL;
963 t_commrec *cr_old = cr;
964 int nthreads_pme = 1;
966 gmx_membed_t membed = NULL;
967 gmx_hw_info_t *hwinfo = NULL;
968 master_inf_t minf = {-1, FALSE};
970 /* CAUTION: threads may be started later on in this function, so
971 cr doesn't reflect the final parallel state right now */
975 if (Flags & MD_APPENDFILES)
980 bForceUseGPU = (strncmp(nbpu_opt, "gpu", 3) == 0);
981 bTryUseGPU = (strncmp(nbpu_opt, "auto", 4) == 0) || bForceUseGPU;
983 /* Detect hardware, gather information. This is an operation that is
984 * global for this process (MPI rank). */
985 hwinfo = gmx_detect_hardware(fplog, cr,
986 bForceUseGPU, bTryUseGPU, hw_opt->gpu_id);
992 /* Read (nearly) all data required for the simulation */
993 read_tpx_state(ftp2fn(efTPX, nfile, fnm), inputrec, state, NULL, mtop);
995 if (inputrec->cutoff_scheme != ecutsVERLET &&
996 ((Flags & MD_TESTVERLET) || getenv("GMX_VERLET_SCHEME") != NULL))
998 convert_to_verlet_scheme(fplog, inputrec, mtop, det(state->box));
1002 minf.cutoff_scheme = inputrec->cutoff_scheme;
1003 minf.bUseGPU = FALSE;
1005 if (inputrec->cutoff_scheme == ecutsVERLET)
1007 prepare_verlet_scheme(fplog, hwinfo, cr,
1008 inputrec, mtop, state->box,
1011 else if (hwinfo->bCanUseGPU)
1013 md_print_warn(cr, fplog,
1014 "NOTE: GPU(s) found, but the current simulation can not use GPUs\n"
1015 " To use a GPU, set the mdp option: cutoff-scheme = Verlet\n"
1016 " (for quick performance testing you can use the -testverlet option)\n");
1020 gmx_fatal(FARGS, "GPU requested, but can't be used without cutoff-scheme=Verlet");
1026 md_print_warn(cr, fplog,
1027 "NOTE: There is no SIMD implementation of the group scheme kernels on\n"
1028 " BlueGene/Q. You will observe better performance from using the\n"
1029 " Verlet cut-off scheme.\n");
1033 #ifndef GMX_THREAD_MPI
1036 gmx_bcast_sim(sizeof(minf), &minf, cr);
1039 if (minf.bUseGPU && cr->npmenodes == -1)
1041 /* Don't automatically use PME-only nodes with GPUs */
1045 /* Check for externally set OpenMP affinity and turn off internal
1046 * pinning if any is found. We need to do this check early to tell
1047 * thread-MPI whether it should do pinning when spawning threads.
1048 * TODO: the above no longer holds, we should move these checks down
1050 gmx_omp_check_thread_affinity(fplog, cr, hw_opt);
1052 #ifdef GMX_THREAD_MPI
1053 /* With thread-MPI inputrec is only set here on the master thread */
1057 check_and_update_hw_opt(hw_opt, minf.cutoff_scheme, SIMMASTER(cr));
1059 #ifdef GMX_THREAD_MPI
1060 /* Early check for externally set process affinity. Can't do over all
1061 * MPI processes because hwinfo is not available everywhere, but with
1062 * thread-MPI it's needed as pinning might get turned off which needs
1063 * to be known before starting thread-MPI. */
1064 gmx_check_thread_affinity_set(fplog,
1066 hw_opt, hwinfo->nthreads_hw_avail, FALSE);
1069 #ifdef GMX_THREAD_MPI
1070 if (cr->npmenodes > 0 && hw_opt->nthreads_tmpi <= 0)
1072 gmx_fatal(FARGS, "You need to explicitly specify the number of MPI threads (-ntmpi) when using separate PME nodes");
1076 if (hw_opt->nthreads_omp_pme != hw_opt->nthreads_omp &&
1079 gmx_fatal(FARGS, "You need to explicitly specify the number of PME nodes (-npme) when using different number of OpenMP threads for PP and PME nodes");
1083 #ifdef GMX_THREAD_MPI
1086 /* NOW the threads will be started: */
1087 hw_opt->nthreads_tmpi = get_nthreads_mpi(hwinfo,
1091 if (hw_opt->nthreads_tot > 0 && hw_opt->nthreads_omp <= 0)
1093 hw_opt->nthreads_omp = hw_opt->nthreads_tot/hw_opt->nthreads_tmpi;
1096 if (hw_opt->nthreads_tmpi > 1)
1098 /* now start the threads. */
1099 cr = mdrunner_start_threads(hw_opt, fplog, cr_old, nfile, fnm,
1100 oenv, bVerbose, bCompact, nstglobalcomm,
1101 ddxyz, dd_node_order, rdd, rconstr,
1102 dddlb_opt, dlb_scale, ddcsx, ddcsy, ddcsz,
1104 nsteps_cmdline, nstepout, resetstep, nmultisim,
1105 repl_ex_nst, repl_ex_nex, repl_ex_seed, pforce,
1106 cpt_period, max_hours, deviceOptions,
1108 /* the main thread continues here with a new cr. We don't deallocate
1109 the old cr because other threads may still be reading it. */
1112 gmx_comm("Failed to spawn threads");
1117 /* END OF CAUTION: cr is now reliable */
1119 /* g_membed initialisation *
1120 * Because we change the mtop, init_membed is called before the init_parallel *
1121 * (in case we ever want to make it run in parallel) */
1122 if (opt2bSet("-membed", nfile, fnm))
1126 fprintf(stderr, "Initializing membed");
1128 membed = init_membed(fplog, nfile, fnm, mtop, inputrec, state, cr, &cpt_period);
1133 /* now broadcast everything to the non-master nodes/threads: */
1134 init_parallel(cr, inputrec, mtop);
1136 /* This check needs to happen after get_nthreads_mpi() */
1137 if (inputrec->cutoff_scheme == ecutsVERLET && (Flags & MD_PARTDEC))
1139 gmx_fatal_collective(FARGS, cr, NULL,
1140 "The Verlet cut-off scheme is not supported with particle decomposition.\n"
1141 "You can achieve the same effect as particle decomposition by running in parallel using only OpenMP threads.");
1146 pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
1149 /* now make sure the state is initialized and propagated */
1150 set_state_entries(state, inputrec, cr->nnodes);
1152 /* A parallel command line option consistency check that we can
1153 only do after any threads have started. */
1155 (ddxyz[XX] > 1 || ddxyz[YY] > 1 || ddxyz[ZZ] > 1 || cr->npmenodes > 0))
1158 "The -dd or -npme option request a parallel simulation, "
1160 "but %s was compiled without threads or MPI enabled"
1162 #ifdef GMX_THREAD_MPI
1163 "but the number of threads (option -nt) is 1"
1165 "but %s was not started through mpirun/mpiexec or only one process was requested through mpirun/mpiexec"
1172 if ((Flags & MD_RERUN) &&
1173 (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
1175 gmx_fatal(FARGS, "The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun");
1178 if (can_use_allvsall(inputrec, TRUE, cr, fplog) && PAR(cr))
1180 /* Simple neighbour searching and (also?) all-vs-all loops
1181 * do not work with domain decomposition. */
1182 Flags |= MD_PARTDEC;
1185 if (!EEL_PME(inputrec->coulombtype) || (Flags & MD_PARTDEC))
1187 if (cr->npmenodes > 0)
1189 if (!EEL_PME(inputrec->coulombtype))
1191 gmx_fatal_collective(FARGS, cr, NULL,
1192 "PME nodes are requested, but the system does not use PME electrostatics");
1194 if (Flags & MD_PARTDEC)
1196 gmx_fatal_collective(FARGS, cr, NULL,
1197 "PME nodes are requested, but particle decomposition does not support separate PME nodes");
1205 fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
1208 /* NMR restraints must be initialized before load_checkpoint,
1209 * since with time averaging the history is added to t_state.
1210 * For proper consistency check we therefore need to extend
1212 * So the PME-only nodes (if present) will also initialize
1213 * the distance restraints.
1217 /* This needs to be called before read_checkpoint to extend the state */
1218 init_disres(fplog, mtop, inputrec, cr, Flags & MD_PARTDEC, fcd, state, repl_ex_nst > 0);
1220 if (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0)
1222 if (PAR(cr) && !(Flags & MD_PARTDEC))
1224 gmx_fatal(FARGS, "Orientation restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd)");
1226 /* Orientation restraints */
1229 init_orires(fplog, mtop, state->x, inputrec, cr->ms, &(fcd->orires),
1234 if (DEFORM(*inputrec))
1236 /* Store the deform reference box before reading the checkpoint */
1239 copy_mat(state->box, box);
1243 gmx_bcast(sizeof(box), box, cr);
1245 /* Because we do not have the update struct available yet
1246 * in which the reference values should be stored,
1247 * we store them temporarily in static variables.
1248 * This should be thread safe, since they are only written once
1249 * and with identical values.
1251 #ifdef GMX_THREAD_MPI
1252 tMPI_Thread_mutex_lock(&deform_init_box_mutex);
1254 deform_init_init_step_tpx = inputrec->init_step;
1255 copy_mat(box, deform_init_box_tpx);
1256 #ifdef GMX_THREAD_MPI
1257 tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
1261 if (opt2bSet("-cpi", nfile, fnm))
1263 /* Check if checkpoint file exists before doing continuation.
1264 * This way we can use identical input options for the first and subsequent runs...
1266 if (gmx_fexist_master(opt2fn_master("-cpi", nfile, fnm, cr), cr) )
1268 load_checkpoint(opt2fn_master("-cpi", nfile, fnm, cr), &fplog,
1269 cr, Flags & MD_PARTDEC, ddxyz,
1270 inputrec, state, &bReadRNG, &bReadEkin,
1271 (Flags & MD_APPENDFILES),
1272 (Flags & MD_APPENDFILESSET));
1276 Flags |= MD_READ_RNG;
1280 Flags |= MD_READ_EKIN;
1285 if (((MASTER(cr) || (Flags & MD_SEPPOT)) && (Flags & MD_APPENDFILES))
1286 #ifdef GMX_THREAD_MPI
1287 /* With thread MPI only the master node/thread exists in mdrun.c,
1288 * therefore non-master nodes need to open the "seppot" log file here.
1290 || (!MASTER(cr) && (Flags & MD_SEPPOT))
1294 gmx_log_open(ftp2fn(efLOG, nfile, fnm), cr, !(Flags & MD_SEPPOT),
1298 /* override nsteps with value from cmdline */
1299 override_nsteps_cmdline(fplog, nsteps_cmdline, inputrec, cr);
1303 copy_mat(state->box, box);
1308 gmx_bcast(sizeof(box), box, cr);
1311 /* Essential dynamics */
1312 if (opt2bSet("-ei", nfile, fnm))
1314 /* Open input and output files, allocate space for ED data structure */
1315 ed = ed_open(mtop->natoms, &state->edsamstate, nfile, fnm, Flags, oenv, cr);
1318 if (PAR(cr) && !((Flags & MD_PARTDEC) ||
1319 EI_TPI(inputrec->eI) ||
1320 inputrec->eI == eiNM))
1322 cr->dd = init_domain_decomposition(fplog, cr, Flags, ddxyz, rdd, rconstr,
1323 dddlb_opt, dlb_scale,
1324 ddcsx, ddcsy, ddcsz,
1327 &ddbox, &npme_major, &npme_minor);
1329 make_dd_communicators(fplog, cr, dd_node_order);
1331 /* Set overallocation to avoid frequent reallocation of arrays */
1332 set_over_alloc_dd(TRUE);
1336 /* PME, if used, is done on all nodes with 1D decomposition */
1338 cr->duty = (DUTY_PP | DUTY_PME);
1341 /* NM and TPI perform single node energy calculations in parallel */
1342 if (!(inputrec->eI == eiNM || EI_TPI(inputrec->eI)))
1344 npme_major = cr->nnodes;
1347 if (inputrec->ePBC == epbcSCREW)
1350 "pbc=%s is only implemented with domain decomposition",
1351 epbc_names[inputrec->ePBC]);
1357 /* After possible communicator splitting in make_dd_communicators.
1358 * we can set up the intra/inter node communication.
1360 gmx_setup_nodecomm(fplog, cr);
1363 /* Initialize per-physical-node MPI process/thread ID and counters. */
1364 gmx_init_intranode_counters(cr);
1367 md_print_info(cr, fplog, "Using %d MPI %s\n",
1369 #ifdef GMX_THREAD_MPI
1370 cr->nnodes == 1 ? "thread" : "threads"
1372 cr->nnodes == 1 ? "process" : "processes"
1378 gmx_omp_nthreads_init(fplog, cr,
1379 hwinfo->nthreads_hw_avail,
1380 hw_opt->nthreads_omp,
1381 hw_opt->nthreads_omp_pme,
1382 (cr->duty & DUTY_PP) == 0,
1383 inputrec->cutoff_scheme == ecutsVERLET);
1385 /* check consistency and decide on the number of gpus to use. */
1386 gmx_check_hw_runconf_consistency(fplog, hwinfo, cr, hw_opt->nthreads_tmpi,
1389 /* getting number of PP/PME threads
1390 PME: env variable should be read only on one node to make sure it is
1391 identical everywhere;
1393 /* TODO nthreads_pp is only used for pinning threads.
1394 * This is a temporary solution until we have a hw topology library.
1396 nthreads_pp = gmx_omp_nthreads_get(emntNonbonded);
1397 nthreads_pme = gmx_omp_nthreads_get(emntPME);
1399 wcycle = wallcycle_init(fplog, resetstep, cr, nthreads_pp, nthreads_pme);
1403 /* Master synchronizes its value of reset_counters with all nodes
1404 * including PME only nodes */
1405 reset_counters = wcycle_get_reset_counters(wcycle);
1406 gmx_bcast_sim(sizeof(reset_counters), &reset_counters, cr);
1407 wcycle_set_reset_counters(wcycle, reset_counters);
1411 if (cr->duty & DUTY_PP)
1413 /* For domain decomposition we allocate dynamically
1414 * in dd_partition_system.
1416 if (DOMAINDECOMP(cr))
1418 bcast_state_setup(cr, state);
1424 bcast_state(cr, state, TRUE);
1428 /* Initiate forcerecord */
1430 fr->hwinfo = hwinfo;
1431 init_forcerec(fplog, oenv, fr, fcd, inputrec, mtop, cr, box,
1432 opt2fn("-table", nfile, fnm),
1433 opt2fn("-tabletf", nfile, fnm),
1434 opt2fn("-tablep", nfile, fnm),
1435 opt2fn("-tableb", nfile, fnm),
1439 /* version for PCA_NOT_READ_NODE (see md.c) */
1440 /*init_forcerec(fplog,fr,fcd,inputrec,mtop,cr,box,FALSE,
1441 "nofile","nofile","nofile","nofile",FALSE,pforce);
1443 fr->bSepDVDL = ((Flags & MD_SEPPOT) == MD_SEPPOT);
1445 /* Initialize QM-MM */
1448 init_QMMMrec(cr, mtop, inputrec, fr);
1451 /* Initialize the mdatoms structure.
1452 * mdatoms is not filled with atom data,
1453 * as this can not be done now with domain decomposition.
1455 mdatoms = init_mdatoms(fplog, mtop, inputrec->efep != efepNO);
1457 if (mdatoms->nPerturbed > 0 && inputrec->cutoff_scheme == ecutsVERLET)
1459 gmx_fatal(FARGS, "The Verlet cut-off scheme does not (yet) support free-energy calculations with perturbed atoms, only perturbed interactions. This will be implemented soon. Use the group scheme for now.");
1462 /* Initialize the virtual site communication */
1463 vsite = init_vsite(mtop, cr, FALSE);
1465 calc_shifts(box, fr->shift_vec);
1467 /* With periodic molecules the charge groups should be whole at start up
1468 * and the virtual sites should not be far from their proper positions.
1470 if (!inputrec->bContinuation && MASTER(cr) &&
1471 !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
1473 /* Make molecules whole at start of run */
1474 if (fr->ePBC != epbcNONE)
1476 do_pbc_first_mtop(fplog, inputrec->ePBC, box, mtop, state->x);
1480 /* Correct initial vsite positions are required
1481 * for the initial distribution in the domain decomposition
1482 * and for the initial shell prediction.
1484 construct_vsites_mtop(vsite, mtop, state->x);
1488 if (EEL_PME(fr->eeltype))
1490 ewaldcoeff = fr->ewaldcoeff;
1491 pmedata = &fr->pmedata;
1500 /* This is a PME only node */
1502 /* We don't need the state */
1505 ewaldcoeff = calc_ewaldcoeff(inputrec->rcoulomb, inputrec->ewald_rtol);
1509 if (hw_opt->thread_affinity != threadaffOFF)
1511 /* Before setting affinity, check whether the affinity has changed
1512 * - which indicates that probably the OpenMP library has changed it
1513 * since we first checked).
1515 gmx_check_thread_affinity_set(fplog, cr,
1516 hw_opt, hwinfo->nthreads_hw_avail, TRUE);
1518 /* Set the CPU affinity */
1519 gmx_set_thread_affinity(fplog, cr, hw_opt, hwinfo);
1522 /* Initiate PME if necessary,
1523 * either on all nodes or on dedicated PME nodes only. */
1524 if (EEL_PME(inputrec->coulombtype))
1528 nChargePerturbed = mdatoms->nChargePerturbed;
1530 if (cr->npmenodes > 0)
1532 /* The PME only nodes need to know nChargePerturbed */
1533 gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
1536 if (cr->duty & DUTY_PME)
1538 status = gmx_pme_init(pmedata, cr, npme_major, npme_minor, inputrec,
1539 mtop ? mtop->natoms : 0, nChargePerturbed,
1540 (Flags & MD_REPRODUCIBLE), nthreads_pme);
1543 gmx_fatal(FARGS, "Error %d initializing PME", status);
1549 if (integrator[inputrec->eI].func == do_md)
1551 /* Turn on signal handling on all nodes */
1553 * (A user signal from the PME nodes (if any)
1554 * is communicated to the PP nodes.
1556 signal_handler_install();
1559 if (cr->duty & DUTY_PP)
1561 /* Assumes uniform use of the number of OpenMP threads */
1562 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
1564 if (inputrec->ePull != epullNO)
1566 /* Initialize pull code */
1567 init_pull(fplog, inputrec, nfile, fnm, mtop, cr, oenv, inputrec->fepvals->init_lambda,
1568 EI_DYNAMICS(inputrec->eI) && MASTER(cr), Flags);
1573 /* Initialize enforced rotation code */
1574 init_rot(fplog, inputrec, nfile, fnm, cr, state->x, box, mtop, oenv,
1578 constr = init_constraints(fplog, mtop, inputrec, ed, state, cr);
1580 if (DOMAINDECOMP(cr))
1582 dd_init_bondeds(fplog, cr->dd, mtop, vsite, inputrec,
1583 Flags & MD_DDBONDCHECK, fr->cginfo_mb);
1585 set_dd_parameters(fplog, cr->dd, dlb_scale, inputrec, &ddbox);
1587 setup_dd_grid(fplog, cr->dd);
1590 /* Now do whatever the user wants us to do (how flexible...) */
1591 integrator[inputrec->eI].func(fplog, cr, nfile, fnm,
1592 oenv, bVerbose, bCompact,
1595 nstepout, inputrec, mtop,
1597 mdatoms, nrnb, wcycle, ed, fr,
1598 repl_ex_nst, repl_ex_nex, repl_ex_seed,
1600 cpt_period, max_hours,
1603 walltime_accounting);
1605 if (inputrec->ePull != epullNO)
1607 finish_pull(inputrec->pull);
1612 finish_rot(inputrec->rot);
1619 walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
1620 gmx_pmeonly(*pmedata, cr, nrnb, wcycle, walltime_accounting, ewaldcoeff, inputrec);
1623 wallcycle_stop(wcycle, ewcRUN);
1625 /* Finish up, write some stuff
1626 * if rerunMD, don't write last frame again
1628 finish_run(fplog, cr,
1629 inputrec, nrnb, wcycle, walltime_accounting,
1630 fr != NULL && fr->nbv != NULL && fr->nbv->bUseGPU ?
1631 nbnxn_cuda_get_timings(fr->nbv->cu_nbv) : NULL,
1632 EI_DYNAMICS(inputrec->eI) && !MULTISIM(cr));
1634 if ((cr->duty & DUTY_PP) && fr->nbv != NULL && fr->nbv->bUseGPU)
1636 char gpu_err_str[STRLEN];
1638 /* free GPU memory and uninitialize GPU (by destroying the context) */
1639 nbnxn_cuda_free(fplog, fr->nbv->cu_nbv);
1641 if (!free_gpu(gpu_err_str))
1643 gmx_warning("On node %d failed to free GPU #%d: %s",
1644 cr->nodeid, get_current_gpu_device_id(), gpu_err_str);
1648 if (opt2bSet("-membed", nfile, fnm))
1653 gmx_hardware_info_free(hwinfo);
1655 /* Does what it says */
1656 print_date_and_time(fplog, cr->nodeid, "Finished mdrun", walltime_accounting);
1657 walltime_accounting_destroy(walltime_accounting);
1659 /* Close logfile already here if we were appending to it */
1660 if (MASTER(cr) && (Flags & MD_APPENDFILES))
1662 gmx_log_close(fplog);
1665 rc = (int)gmx_get_stop_condition();
1667 #ifdef GMX_THREAD_MPI
1668 /* we need to join all threads. The sub-threads join when they
1669 exit this function, but the master thread needs to be told to
1671 if (PAR(cr) && MASTER(cr))