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.
12 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
13 * Copyright (c) 2001-2004, The GROMACS development team,
14 * check out http://www.gromacs.org for more information.
16 * This program is free software; you can redistribute it and/or
17 * modify it under the terms of the GNU General Public License
18 * as published by the Free Software Foundation; either version 2
19 * of the License, or (at your option) any later version.
21 * If you want to redistribute modifications, please consider that
22 * scientific software is very special. Version control is crucial -
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24 * inclusion in the official distribution, but derived work must not
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29 * the papers on the package - you can find them in the top README file.
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34 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
39 #if defined(HAVE_SCHED_H) && (defined(HAVE_SCHED_GETAFFINITY) || defined(HAVE_SCHED_SETAFFINITY))
42 #include <sys/syscall.h>
54 #include "md_logging.h"
55 #include "md_support.h"
65 #include "mpelogging.h"
71 #include "checkpoint.h"
72 #include "mtop_util.h"
73 #include "sighandler.h"
76 #include "gmx_detect_hardware.h"
77 #include "gmx_omp_nthreads.h"
78 #include "pull_rotation.h"
79 #include "calc_verletbuf.h"
80 #include "../mdlib/nbnxn_search.h"
81 #include "../mdlib/nbnxn_consts.h"
82 #include "gmx_fatal_collective.h"
84 #include "md_openmm.h"
99 #include "md_openmm.h"
102 #include "gpu_utils.h"
103 #include "nbnxn_cuda_data_mgmt.h"
106 gmx_integrator_t *func;
109 /* The array should match the eI array in include/types/enums.h */
110 #ifdef GMX_OPENMM /* FIXME do_md_openmm needs fixing */
111 const gmx_intp_t integrator[eiNR] = { {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm},{do_md_openmm}};
113 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}};
116 gmx_large_int_t deform_init_init_step_tpx;
117 matrix deform_init_box_tpx;
118 #ifdef GMX_THREAD_MPI
119 tMPI_Thread_mutex_t deform_init_box_mutex=TMPI_THREAD_MUTEX_INITIALIZER;
123 #ifdef GMX_THREAD_MPI
124 struct mdrunner_arglist
126 gmx_hw_opt_t *hw_opt;
139 const char *dddlb_opt;
144 const char *nbpu_opt;
155 const char *deviceOptions;
157 int ret; /* return value */
161 /* The function used for spawning threads. Extracts the mdrunner()
162 arguments from its one argument and calls mdrunner(), after making
164 static void mdrunner_start_fn(void *arg)
166 struct mdrunner_arglist *mda=(struct mdrunner_arglist*)arg;
167 struct mdrunner_arglist mc=*mda; /* copy the arg list to make sure
168 that it's thread-local. This doesn't
169 copy pointed-to items, of course,
170 but those are all const. */
171 t_commrec *cr; /* we need a local version of this */
175 fnm = dup_tfn(mc.nfile, mc.fnm);
177 cr = init_par_threads(mc.cr);
184 mda->ret=mdrunner(mc.hw_opt, fplog, cr, mc.nfile, fnm, mc.oenv,
185 mc.bVerbose, mc.bCompact, mc.nstglobalcomm,
186 mc.ddxyz, mc.dd_node_order, mc.rdd,
187 mc.rconstr, mc.dddlb_opt, mc.dlb_scale,
188 mc.ddcsx, mc.ddcsy, mc.ddcsz,
190 mc.nsteps_cmdline, mc.nstepout, mc.resetstep,
191 mc.nmultisim, mc.repl_ex_nst, mc.repl_ex_nex, mc.repl_ex_seed, mc.pforce,
192 mc.cpt_period, mc.max_hours, mc.deviceOptions, mc.Flags);
195 /* called by mdrunner() to start a specific number of threads (including
196 the main thread) for thread-parallel runs. This in turn calls mdrunner()
198 All options besides nthreads are the same as for mdrunner(). */
199 static t_commrec *mdrunner_start_threads(gmx_hw_opt_t *hw_opt,
200 FILE *fplog,t_commrec *cr,int nfile,
201 const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
202 gmx_bool bCompact, int nstglobalcomm,
203 ivec ddxyz,int dd_node_order,real rdd,real rconstr,
204 const char *dddlb_opt,real dlb_scale,
205 const char *ddcsx,const char *ddcsy,const char *ddcsz,
206 const char *nbpu_opt,
207 int nsteps_cmdline, int nstepout,int resetstep,
208 int nmultisim,int repl_ex_nst,int repl_ex_nex, int repl_ex_seed,
209 real pforce,real cpt_period, real max_hours,
210 const char *deviceOptions, unsigned long Flags)
213 struct mdrunner_arglist *mda;
214 t_commrec *crn; /* the new commrec */
217 /* first check whether we even need to start tMPI */
218 if (hw_opt->nthreads_tmpi < 2)
223 /* a few small, one-time, almost unavoidable memory leaks: */
225 fnmn=dup_tfn(nfile, fnm);
227 /* fill the data structure to pass as void pointer to thread start fn */
234 mda->bVerbose=bVerbose;
235 mda->bCompact=bCompact;
236 mda->nstglobalcomm=nstglobalcomm;
237 mda->ddxyz[XX]=ddxyz[XX];
238 mda->ddxyz[YY]=ddxyz[YY];
239 mda->ddxyz[ZZ]=ddxyz[ZZ];
240 mda->dd_node_order=dd_node_order;
242 mda->rconstr=rconstr;
243 mda->dddlb_opt=dddlb_opt;
244 mda->dlb_scale=dlb_scale;
248 mda->nbpu_opt=nbpu_opt;
249 mda->nsteps_cmdline=nsteps_cmdline;
250 mda->nstepout=nstepout;
251 mda->resetstep=resetstep;
252 mda->nmultisim=nmultisim;
253 mda->repl_ex_nst=repl_ex_nst;
254 mda->repl_ex_nex=repl_ex_nex;
255 mda->repl_ex_seed=repl_ex_seed;
257 mda->cpt_period=cpt_period;
258 mda->max_hours=max_hours;
259 mda->deviceOptions=deviceOptions;
262 fprintf(stderr, "Starting %d tMPI threads\n",hw_opt->nthreads_tmpi);
264 /* now spawn new threads that start mdrunner_start_fn(), while
265 the main thread returns */
266 ret=tMPI_Init_fn(TRUE, hw_opt->nthreads_tmpi,
267 (hw_opt->bThreadPinning ? TMPI_AFFINITY_ALL_CORES : TMPI_AFFINITY_NONE),
268 mdrunner_start_fn, (void*)(mda) );
269 if (ret!=TMPI_SUCCESS)
272 /* make a new comm_rec to reflect the new situation */
273 crn=init_par_threads(cr);
278 static int get_tmpi_omp_thread_division(const gmx_hw_info_t *hwinfo,
279 const gmx_hw_opt_t *hw_opt,
285 /* There are no separate PME nodes here, as we ensured in
286 * check_and_update_hw_opt that nthreads_tmpi>0 with PME nodes
287 * and a conditional ensures we would not have ended up here.
288 * Note that separate PME nodes might be switched on later.
292 nthreads_tmpi = ngpu;
293 if (nthreads_tot > 0 && nthreads_tot < nthreads_tmpi)
295 nthreads_tmpi = nthreads_tot;
298 else if (hw_opt->nthreads_omp > 0)
300 /* Here we could oversubscribe, when we do, we issue a warning later */
301 nthreads_tmpi = max(1,nthreads_tot/hw_opt->nthreads_omp);
305 /* TODO choose nthreads_omp based on hardware topology
306 when we have a hardware topology detection library */
307 /* In general, when running up to 4 threads, OpenMP should be faster.
308 * Note: on AMD Bulldozer we should avoid running OpenMP over two dies.
309 * On Intel>=Nehalem running OpenMP on a single CPU is always faster,
310 * even on two CPUs it's usually faster (but with many OpenMP threads
311 * it could be faster not to use HT, currently we always use HT).
312 * On Nehalem/Westmere we want to avoid running 16 threads over
313 * two CPUs with HT, so we need a limit<16; thus we use 12.
314 * A reasonable limit for Intel Sandy and Ivy bridge,
315 * not knowing the topology, is 16 threads.
317 const int nthreads_omp_always_faster = 4;
318 const int nthreads_omp_always_faster_Nehalem = 12;
319 const int nthreads_omp_always_faster_SandyBridge = 16;
320 const int first_model_Nehalem = 0x1A;
321 const int first_model_SandyBridge = 0x2A;
322 gmx_bool bIntel_Family6;
325 (gmx_cpuid_vendor(hwinfo->cpuid_info) == GMX_CPUID_VENDOR_INTEL &&
326 gmx_cpuid_family(hwinfo->cpuid_info) == 6);
328 if (nthreads_tot <= nthreads_omp_always_faster ||
330 ((gmx_cpuid_model(hwinfo->cpuid_info) >= nthreads_omp_always_faster_Nehalem && nthreads_tot <= nthreads_omp_always_faster_Nehalem) ||
331 (gmx_cpuid_model(hwinfo->cpuid_info) >= nthreads_omp_always_faster_SandyBridge && nthreads_tot <= nthreads_omp_always_faster_SandyBridge))))
333 /* Use pure OpenMP parallelization */
338 /* Don't use OpenMP parallelization */
339 nthreads_tmpi = nthreads_tot;
343 return nthreads_tmpi;
347 /* Get the number of threads to use for thread-MPI based on how many
348 * were requested, which algorithms we're using,
349 * and how many particles there are.
350 * At the point we have already called check_and_update_hw_opt.
351 * Thus all options should be internally consistent and consistent
352 * with the hardware, except that ntmpi could be larger than #GPU.
354 static int get_nthreads_mpi(gmx_hw_info_t *hwinfo,
355 gmx_hw_opt_t *hw_opt,
356 t_inputrec *inputrec, gmx_mtop_t *mtop,
360 int nthreads_hw,nthreads_tot_max,nthreads_tmpi,nthreads_new,ngpu;
361 int min_atoms_per_mpi_thread;
366 if (hw_opt->nthreads_tmpi > 0)
368 /* Trivial, return right away */
369 return hw_opt->nthreads_tmpi;
372 nthreads_hw = hwinfo->nthreads_hw_avail;
374 /* How many total (#tMPI*#OpenMP) threads can we start? */
375 if (hw_opt->nthreads_tot > 0)
377 nthreads_tot_max = hw_opt->nthreads_tot;
381 nthreads_tot_max = nthreads_hw;
384 bCanUseGPU = (inputrec->cutoff_scheme == ecutsVERLET && hwinfo->bCanUseGPU);
387 ngpu = hwinfo->gpu_info.ncuda_dev_use;
395 get_tmpi_omp_thread_division(hwinfo,hw_opt,nthreads_tot_max,ngpu);
397 if (inputrec->eI == eiNM || EI_TPI(inputrec->eI))
399 /* Steps are divided over the nodes iso splitting the atoms */
400 min_atoms_per_mpi_thread = 0;
406 min_atoms_per_mpi_thread = MIN_ATOMS_PER_GPU;
410 min_atoms_per_mpi_thread = MIN_ATOMS_PER_MPI_THREAD;
414 /* Check if an algorithm does not support parallel simulation. */
415 if (nthreads_tmpi != 1 &&
416 ( inputrec->eI == eiLBFGS ||
417 inputrec->coulombtype == eelEWALD ) )
421 md_print_warn(cr,fplog,"The integration or electrostatics algorithm doesn't support parallel runs. Using a single thread-MPI thread.\n");
422 if (hw_opt->nthreads_tmpi > nthreads_tmpi)
424 gmx_fatal(FARGS,"You asked for more than 1 thread-MPI thread, but an algorithm doesn't support that");
427 else if (mtop->natoms/nthreads_tmpi < min_atoms_per_mpi_thread)
429 /* the thread number was chosen automatically, but there are too many
430 threads (too few atoms per thread) */
431 nthreads_new = max(1,mtop->natoms/min_atoms_per_mpi_thread);
433 /* Avoid partial use of Hyper-Threading */
434 if (gmx_cpuid_x86_smt(hwinfo->cpuid_info) == GMX_CPUID_X86_SMT_ENABLED &&
435 nthreads_new > nthreads_hw/2 && nthreads_new < nthreads_hw)
437 nthreads_new = nthreads_hw/2;
440 /* Avoid large prime numbers in the thread count */
441 if (nthreads_new >= 6)
443 /* Use only 6,8,10 with additional factors of 2 */
447 while (3*fac*2 <= nthreads_new)
452 nthreads_new = (nthreads_new/fac)*fac;
457 if (nthreads_new == 5)
463 nthreads_tmpi = nthreads_new;
465 fprintf(stderr,"\n");
466 fprintf(stderr,"NOTE: Parallelization is limited by the small number of atoms,\n");
467 fprintf(stderr," only starting %d thread-MPI threads.\n",nthreads_tmpi);
468 fprintf(stderr," You can use the -nt and/or -ntmpi option to optimize the number of threads.\n\n");
471 return nthreads_tmpi;
473 #endif /* GMX_THREAD_MPI */
476 /* Environment variable for setting nstlist */
477 static const char* NSTLIST_ENVVAR = "GMX_NSTLIST";
478 /* Try to increase nstlist when using a GPU with nstlist less than this */
479 static const int NSTLIST_GPU_ENOUGH = 20;
480 /* Increase nstlist until the non-bonded cost increases more than this factor */
481 static const float NBNXN_GPU_LIST_OK_FAC = 1.25;
482 /* Don't increase nstlist beyond a non-bonded cost increases of this factor */
483 static const float NBNXN_GPU_LIST_MAX_FAC = 1.40;
485 /* Try to increase nstlist when running on a GPU */
486 static void increase_nstlist(FILE *fp,t_commrec *cr,
487 t_inputrec *ir,const gmx_mtop_t *mtop,matrix box)
490 int nstlist_orig,nstlist_prev;
491 verletbuf_list_setup_t ls;
492 real rlist_inc,rlist_ok,rlist_max,rlist_new,rlist_prev;
495 gmx_bool bBox,bDD,bCont;
496 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";
497 const char *vbd_err="Can not increase nstlist for GPU run because verlet-buffer-drift is not set or used";
498 const char *box_err="Can not increase nstlist for GPU run because the box is too small";
499 const char *dd_err ="Can not increase nstlist for GPU run because of domain decomposition limitations";
502 /* Number of + nstlist alternative values to try when switching */
503 const int nstl[]={ 20, 25, 40, 50 };
504 #define NNSTL sizeof(nstl)/sizeof(nstl[0])
506 env = getenv(NSTLIST_ENVVAR);
511 fprintf(fp,nstl_fmt,ir->nstlist);
515 if (ir->verletbuf_drift == 0)
517 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");
520 if (ir->verletbuf_drift < 0)
524 fprintf(stderr,"%s\n",vbd_err);
528 fprintf(fp,"%s\n",vbd_err);
534 nstlist_orig = ir->nstlist;
537 sprintf(buf,"Getting nstlist from environment variable GMX_NSTLIST=%s",env);
540 fprintf(stderr,"%s\n",buf);
544 fprintf(fp,"%s\n",buf);
546 sscanf(env,"%d",&ir->nstlist);
549 verletbuf_get_list_setup(TRUE,&ls);
551 /* Allow rlist to make the list double the size of the cut-off sphere */
552 rlist_inc = nbnxn_get_rlist_effective_inc(NBNXN_GPU_CLUSTER_SIZE,mtop->natoms/det(box));
553 rlist_ok = (max(ir->rvdw,ir->rcoulomb) + rlist_inc)*pow(NBNXN_GPU_LIST_OK_FAC,1.0/3.0) - rlist_inc;
554 rlist_max = (max(ir->rvdw,ir->rcoulomb) + rlist_inc)*pow(NBNXN_GPU_LIST_MAX_FAC,1.0/3.0) - rlist_inc;
557 fprintf(debug,"GPU nstlist tuning: rlist_inc %.3f rlist_max %.3f\n",
558 rlist_inc,rlist_max);
562 nstlist_prev = nstlist_orig;
563 rlist_prev = ir->rlist;
568 ir->nstlist = nstl[i];
571 /* Set the pair-list buffer size in ir */
572 calc_verlet_buffer_size(mtop,det(box),ir,ir->verletbuf_drift,&ls,
575 /* Does rlist fit in the box? */
576 bBox = (sqr(rlist_new) < max_cutoff2(ir->ePBC,box));
578 if (bBox && DOMAINDECOMP(cr))
580 /* Check if rlist fits in the domain decomposition */
581 if (inputrec2nboundeddim(ir) < DIM)
583 gmx_incons("Changing nstlist with domain decomposition and unbounded dimensions is not implemented yet");
585 copy_mat(box,state_tmp.box);
586 bDD = change_dd_cutoff(cr,&state_tmp,ir,rlist_new);
593 if (bBox && bDD && rlist_new <= rlist_max)
595 /* Increase nstlist */
596 nstlist_prev = ir->nstlist;
597 rlist_prev = rlist_new;
598 bCont = (i+1 < NNSTL && rlist_new < rlist_ok);
602 /* Stick with the previous nstlist */
603 ir->nstlist = nstlist_prev;
604 rlist_new = rlist_prev;
616 gmx_warning(!bBox ? box_err : dd_err);
619 fprintf(fp,"\n%s\n",bBox ? box_err : dd_err);
621 ir->nstlist = nstlist_orig;
623 else if (ir->nstlist != nstlist_orig || rlist_new != ir->rlist)
625 sprintf(buf,"Changing nstlist from %d to %d, rlist from %g to %g",
626 nstlist_orig,ir->nstlist,
627 ir->rlist,rlist_new);
630 fprintf(stderr,"%s\n\n",buf);
634 fprintf(fp,"%s\n\n",buf);
636 ir->rlist = rlist_new;
637 ir->rlistlong = rlist_new;
641 static void prepare_verlet_scheme(FILE *fplog,
642 gmx_hw_info_t *hwinfo,
644 gmx_hw_opt_t *hw_opt,
645 const char *nbpu_opt,
647 const gmx_mtop_t *mtop,
651 /* Here we only check for GPU usage on the MPI master process,
652 * as here we don't know how many GPUs we will use yet.
653 * We check for a GPU on all processes later.
655 *bUseGPU = hwinfo->bCanUseGPU || (getenv("GMX_EMULATE_GPU") != NULL);
657 if (ir->verletbuf_drift > 0)
659 /* Update the Verlet buffer size for the current run setup */
660 verletbuf_list_setup_t ls;
663 /* Here we assume CPU acceleration is on. But as currently
664 * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
665 * and 4x2 gives a larger buffer than 4x4, this is ok.
667 verletbuf_get_list_setup(*bUseGPU,&ls);
669 calc_verlet_buffer_size(mtop,det(box),ir,
670 ir->verletbuf_drift,&ls,
672 if (rlist_new != ir->rlist)
676 fprintf(fplog,"\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
678 ls.cluster_size_i,ls.cluster_size_j);
680 ir->rlist = rlist_new;
681 ir->rlistlong = rlist_new;
685 /* With GPU or emulation we should check nstlist for performance */
686 if ((EI_DYNAMICS(ir->eI) &&
688 ir->nstlist < NSTLIST_GPU_ENOUGH) ||
689 getenv(NSTLIST_ENVVAR) != NULL)
691 /* Choose a better nstlist */
692 increase_nstlist(fplog,cr,ir,mtop,box);
696 static void convert_to_verlet_scheme(FILE *fplog,
698 gmx_mtop_t *mtop,real box_vol)
700 char *conv_mesg="Converting input file with group cut-off scheme to the Verlet cut-off scheme";
702 md_print_warn(NULL,fplog,"%s\n",conv_mesg);
704 ir->cutoff_scheme = ecutsVERLET;
705 ir->verletbuf_drift = 0.005;
707 if (ir->rcoulomb != ir->rvdw)
709 gmx_fatal(FARGS,"The VdW and Coulomb cut-offs are different, whereas the Verlet scheme only supports equal cut-offs");
712 if (ir->vdwtype == evdwUSER || EEL_USER(ir->coulombtype))
714 gmx_fatal(FARGS,"User non-bonded potentials are not (yet) supported with the Verlet scheme");
716 else if (EVDW_SWITCHED(ir->vdwtype) || EEL_SWITCHED(ir->coulombtype))
718 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");
720 if (EVDW_SWITCHED(ir->vdwtype))
722 ir->vdwtype = evdwCUT;
724 if (EEL_SWITCHED(ir->coulombtype))
726 if (EEL_FULL(ir->coulombtype))
728 /* With full electrostatic only PME can be switched */
729 ir->coulombtype = eelPME;
733 md_print_warn(NULL,fplog,"NOTE: Replacing %s electrostatics with reaction-field with epsilon-rf=inf\n",eel_names[ir->coulombtype]);
734 ir->coulombtype = eelRF;
735 ir->epsilon_rf = 0.0;
739 /* We set the target energy drift to a small number.
740 * Note that this is only for testing. For production the user
741 * should think about this and set the mdp options.
743 ir->verletbuf_drift = 1e-4;
746 if (inputrec2nboundeddim(ir) != 3)
748 gmx_fatal(FARGS,"Can only convert old tpr files to the Verlet cut-off scheme with 3D pbc");
751 if (ir->efep != efepNO || ir->implicit_solvent != eisNO)
753 gmx_fatal(FARGS,"Will not convert old tpr files to the Verlet cut-off scheme with free-energy calculations or implicit solvent");
756 if (EI_DYNAMICS(ir->eI) && !(EI_MD(ir->eI) && ir->etc == etcNO))
758 verletbuf_list_setup_t ls;
760 verletbuf_get_list_setup(FALSE,&ls);
761 calc_verlet_buffer_size(mtop,box_vol,ir,ir->verletbuf_drift,&ls,
766 ir->verletbuf_drift = -1;
767 ir->rlist = 1.05*max(ir->rvdw,ir->rcoulomb);
770 gmx_mtop_remove_chargegroups(mtop);
773 /* Check the process affinity mask and if it is found to be non-zero,
774 * will honor it and disable mdrun internal affinity setting.
775 * This function should be called first before the OpenMP library gets
776 * initialized with the last argument FALSE (which will detect affinity
777 * set by external tools like taskset), and later, after the OpenMP
778 * initialization, with the last argument TRUE to detect affinity changes
779 * made by the OpenMP library.
781 * Note that this will only work on Linux as we use a GNU feature. */
782 static void check_cpu_affinity_set(FILE *fplog, const t_commrec *cr,
783 gmx_hw_opt_t *hw_opt, int ncpus,
784 gmx_bool bAfterOpenmpInit)
786 #ifdef HAVE_SCHED_GETAFFINITY
787 cpu_set_t mask_current;
788 int i, ret, cpu_count, cpu_set;
792 if (!hw_opt->bThreadPinning)
794 /* internal affinity setting is off, don't bother checking process affinity */
798 CPU_ZERO(&mask_current);
799 if ((ret = sched_getaffinity(0, sizeof(cpu_set_t), &mask_current)) != 0)
801 /* failed to query affinity mask, will just return */
804 fprintf(debug, "Failed to query affinity mask (error %d)", ret);
809 /* Before proceeding with the actual check, make sure that the number of
810 * detected CPUs is >= the CPUs in the current set. */
811 if (ncpus < CPU_COUNT(&mask_current))
815 fprintf(debug, "%d CPUs detected, but %d was returned by CPU_COUNT",
816 ncpus, CPU_COUNT(&mask_current));
822 for (i = 0; (i < ncpus && i < CPU_SETSIZE); i++)
824 bAllSet = bAllSet && (CPU_ISSET(i, &mask_current) != 0);
829 if (!bAfterOpenmpInit)
831 md_print_warn(cr, fplog,
832 "Non-default process affinity set, disabling internal affinity");
836 md_print_warn(cr, fplog,
837 "Non-default process affinity set probably by the OpenMP library, "
838 "disabling internal affinity");
840 hw_opt->bThreadPinning = FALSE;
844 fprintf(debug, "Non-default affinity mask found\n");
851 fprintf(debug, "Default affinity mask found\n");
854 #endif /* HAVE_SCHED_GETAFFINITY */
857 /* Set CPU affinity. Can be important for performance.
858 On some systems (e.g. Cray) CPU Affinity is set by default.
859 But default assigning doesn't work (well) with only some ranks
860 having threads. This causes very low performance.
861 External tools have cumbersome syntax for setting affinity
862 in the case that only some ranks have threads.
863 Thus it is important that GROMACS sets the affinity internally
864 if only PME is using threads.
866 static void set_cpu_affinity(FILE *fplog,
868 gmx_hw_opt_t *hw_opt,
870 const gmx_hw_info_t *hwinfo,
871 const t_inputrec *inputrec)
873 #if defined GMX_THREAD_MPI
874 /* With the number of TMPI threads equal to the number of cores
875 * we already pinned in thread-MPI, so don't pin again here.
877 if (hw_opt->nthreads_tmpi == tMPI_Thread_get_hw_number())
883 #ifdef GMX_OPENMP /* TODO: actually we could do this even without OpenMP?! */
884 #ifdef HAVE_SCHED_SETAFFINITY
885 if (hw_opt->bThreadPinning)
887 int thread, nthread_local, nthread_node, nthread_hw_max, nphyscore;
891 /* threads on this MPI process or TMPI thread */
892 if (cr->duty & DUTY_PP)
894 nthread_local = gmx_omp_nthreads_get(emntNonbonded);
898 nthread_local = gmx_omp_nthreads_get(emntPME);
901 /* map the current process to cores */
903 nthread_node = nthread_local;
905 if (PAR(cr) || MULTISIM(cr))
907 /* We need to determine a scan of the thread counts in this
912 MPI_Comm_split(MPI_COMM_WORLD,gmx_hostname_num(),cr->nodeid_intra,
914 MPI_Scan(&nthread_local,&thread,1,MPI_INT,MPI_SUM,comm_intra);
915 /* MPI_Scan is inclusive, but here we need exclusive */
916 thread -= nthread_local;
917 /* Get the total number of threads on this physical node */
918 MPI_Allreduce(&nthread_local,&nthread_node,1,MPI_INT,MPI_SUM,comm_intra);
919 MPI_Comm_free(&comm_intra);
924 if (hw_opt->core_pinning_offset > 0)
926 offset = hw_opt->core_pinning_offset;
929 fprintf(stderr, "Applying core pinning offset %d\n", offset);
933 fprintf(fplog, "Applying core pinning offset %d\n", offset);
937 /* With Intel Hyper-Threading enabled, we want to pin consecutive
938 * threads to physical cores when using more threads than physical
939 * cores or when the user requests so.
941 nthread_hw_max = hwinfo->nthreads_hw_avail;
943 if (hw_opt->bPinHyperthreading ||
944 (gmx_cpuid_x86_smt(hwinfo->cpuid_info) == GMX_CPUID_X86_SMT_ENABLED &&
945 nthread_node > nthread_hw_max/2 && getenv("GMX_DISABLE_PINHT") == NULL))
947 if (gmx_cpuid_x86_smt(hwinfo->cpuid_info) != GMX_CPUID_X86_SMT_ENABLED)
949 /* We print to stderr on all processes, as we might have
950 * different settings on different physical nodes.
952 if (gmx_cpuid_vendor(hwinfo->cpuid_info) != GMX_CPUID_VENDOR_INTEL)
954 md_print_warn(NULL, fplog, "Pinning for Hyper-Threading layout requested, "
955 "but non-Intel CPU detected (vendor: %s)\n",
956 gmx_cpuid_vendor_string[gmx_cpuid_vendor(hwinfo->cpuid_info)]);
960 md_print_warn(NULL, fplog, "Pinning for Hyper-Threading layout requested, "
961 "but the CPU detected does not have Intel Hyper-Threading support "
962 "(or it is turned off)\n");
965 nphyscore = nthread_hw_max/2;
969 fprintf(stderr, "Pinning to Hyper-Threading cores with %d physical cores in a compute node\n",
974 fprintf(fplog, "Pinning to Hyper-Threading cores with %d physical cores in a compute node\n",
979 /* set the per-thread affinity */
980 #pragma omp parallel firstprivate(thread) num_threads(nthread_local)
986 thread += gmx_omp_get_thread_num();
989 core = offset + thread;
993 /* Lock pairs of threads to the same hyperthreaded core */
994 core = offset + thread/2 + (thread % 2)*nphyscore;
996 CPU_SET(core, &mask);
997 sched_setaffinity((pid_t) syscall (SYS_gettid), sizeof(cpu_set_t), &mask);
1000 #endif /* HAVE_SCHED_SETAFFINITY */
1001 #endif /* GMX_OPENMP */
1005 static void check_and_update_hw_opt(gmx_hw_opt_t *hw_opt,
1008 gmx_omp_nthreads_read_env(&hw_opt->nthreads_omp);
1010 #ifndef GMX_THREAD_MPI
1011 if (hw_opt->nthreads_tot > 0)
1013 gmx_fatal(FARGS,"Setting the total number of threads is only supported with thread-MPI and Gromacs was compiled without thread-MPI");
1015 if (hw_opt->nthreads_tmpi > 0)
1017 gmx_fatal(FARGS,"Setting the number of thread-MPI threads is only supported with thread-MPI and Gromacs was compiled without thread-MPI");
1021 if (hw_opt->nthreads_tot > 0 && hw_opt->nthreads_omp_pme <= 0)
1023 /* We have the same number of OpenMP threads for PP and PME processes,
1024 * thus we can perform several consistency checks.
1026 if (hw_opt->nthreads_tmpi > 0 &&
1027 hw_opt->nthreads_omp > 0 &&
1028 hw_opt->nthreads_tot != hw_opt->nthreads_tmpi*hw_opt->nthreads_omp)
1030 gmx_fatal(FARGS,"The total number of threads requested (%d) does not match the thread-MPI threads (%d) times the OpenMP threads (%d) requested",
1031 hw_opt->nthreads_tot,hw_opt->nthreads_tmpi,hw_opt->nthreads_omp);
1034 if (hw_opt->nthreads_tmpi > 0 &&
1035 hw_opt->nthreads_tot % hw_opt->nthreads_tmpi != 0)
1037 gmx_fatal(FARGS,"The total number of threads requested (%d) is not divisible by the number of thread-MPI threads requested (%d)",
1038 hw_opt->nthreads_tot,hw_opt->nthreads_tmpi);
1041 if (hw_opt->nthreads_omp > 0 &&
1042 hw_opt->nthreads_tot % hw_opt->nthreads_omp != 0)
1044 gmx_fatal(FARGS,"The total number of threads requested (%d) is not divisible by the number of OpenMP threads requested (%d)",
1045 hw_opt->nthreads_tot,hw_opt->nthreads_omp);
1048 if (hw_opt->nthreads_tmpi > 0 &&
1049 hw_opt->nthreads_omp <= 0)
1051 hw_opt->nthreads_omp = hw_opt->nthreads_tot/hw_opt->nthreads_tmpi;
1056 if (hw_opt->nthreads_omp > 1)
1058 gmx_fatal(FARGS,"OpenMP threads are requested, but Gromacs was compiled without OpenMP support");
1062 if (cutoff_scheme == ecutsGROUP)
1064 /* We only have OpenMP support for PME only nodes */
1065 if (hw_opt->nthreads_omp > 1)
1067 gmx_fatal(FARGS,"OpenMP threads have been requested with cut-off scheme %s, but these are only supported with cut-off scheme %s",
1068 ecutscheme_names[cutoff_scheme],
1069 ecutscheme_names[ecutsVERLET]);
1071 hw_opt->nthreads_omp = 1;
1074 if (hw_opt->nthreads_omp_pme > 0 && hw_opt->nthreads_omp <= 0)
1076 gmx_fatal(FARGS,"You need to specify -ntomp in addition to -ntomp_pme");
1079 if (hw_opt->nthreads_tot == 1)
1081 hw_opt->nthreads_tmpi = 1;
1083 if (hw_opt->nthreads_omp > 1)
1085 gmx_fatal(FARGS,"You requested %d OpenMP threads with %d total threads",
1086 hw_opt->nthreads_tmpi,hw_opt->nthreads_tot);
1088 hw_opt->nthreads_omp = 1;
1091 if (hw_opt->nthreads_omp_pme <= 0 && hw_opt->nthreads_omp > 0)
1093 hw_opt->nthreads_omp_pme = hw_opt->nthreads_omp;
1098 fprintf(debug,"hw_opt: nt %d ntmpi %d ntomp %d ntomp_pme %d gpu_id '%s'\n",
1099 hw_opt->nthreads_tot,
1100 hw_opt->nthreads_tmpi,
1101 hw_opt->nthreads_omp,
1102 hw_opt->nthreads_omp_pme,
1103 hw_opt->gpu_id!=NULL ? hw_opt->gpu_id : "");
1109 /* Override the value in inputrec with value passed on the command line (if any) */
1110 static void override_nsteps_cmdline(FILE *fplog,
1113 const t_commrec *cr)
1118 /* override with anything else than the default -2 */
1119 if (nsteps_cmdline > -2)
1123 ir->nsteps = nsteps_cmdline;
1124 if (EI_DYNAMICS(ir->eI))
1126 sprintf(stmp, "Overriding nsteps with value passed on the command line: %d steps, %.3f ps",
1127 nsteps_cmdline, nsteps_cmdline*ir->delta_t);
1131 sprintf(stmp, "Overriding nsteps with value passed on the command line: %d steps",
1135 md_print_warn(cr, fplog, "%s\n", stmp);
1139 /* Data structure set by SIMMASTER which needs to be passed to all nodes
1140 * before the other nodes have read the tpx file and called gmx_detect_hardware.
1143 int cutoff_scheme; /* The cutoff scheme from inputrec_t */
1144 gmx_bool bUseGPU; /* Use GPU or GPU emulation */
1147 int mdrunner(gmx_hw_opt_t *hw_opt,
1148 FILE *fplog,t_commrec *cr,int nfile,
1149 const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
1150 gmx_bool bCompact, int nstglobalcomm,
1151 ivec ddxyz,int dd_node_order,real rdd,real rconstr,
1152 const char *dddlb_opt,real dlb_scale,
1153 const char *ddcsx,const char *ddcsy,const char *ddcsz,
1154 const char *nbpu_opt,
1155 int nsteps_cmdline, int nstepout,int resetstep,
1156 int nmultisim,int repl_ex_nst,int repl_ex_nex,
1157 int repl_ex_seed, real pforce,real cpt_period,real max_hours,
1158 const char *deviceOptions, unsigned long Flags)
1160 gmx_bool bForceUseGPU,bTryUseGPU;
1161 double nodetime=0,realtime;
1162 t_inputrec *inputrec;
1163 t_state *state=NULL;
1165 gmx_ddbox_t ddbox={0};
1166 int npme_major,npme_minor;
1169 gmx_mtop_t *mtop=NULL;
1170 t_mdatoms *mdatoms=NULL;
1171 t_forcerec *fr=NULL;
1174 gmx_pme_t *pmedata=NULL;
1175 gmx_vsite_t *vsite=NULL;
1176 gmx_constr_t constr;
1177 int i,m,nChargePerturbed=-1,status,nalloc;
1179 gmx_wallcycle_t wcycle;
1180 gmx_bool bReadRNG,bReadEkin;
1182 gmx_runtime_t runtime;
1184 gmx_large_int_t reset_counters;
1185 gmx_edsam_t ed=NULL;
1186 t_commrec *cr_old=cr;
1189 gmx_membed_t membed=NULL;
1190 gmx_hw_info_t *hwinfo=NULL;
1191 master_inf_t minf={-1,FALSE};
1193 /* CAUTION: threads may be started later on in this function, so
1194 cr doesn't reflect the final parallel state right now */
1198 if (Flags & MD_APPENDFILES)
1203 bForceUseGPU = (strncmp(nbpu_opt, "gpu", 3) == 0);
1204 bTryUseGPU = (strncmp(nbpu_opt, "auto", 4) == 0) || bForceUseGPU;
1209 /* Read (nearly) all data required for the simulation */
1210 read_tpx_state(ftp2fn(efTPX,nfile,fnm),inputrec,state,NULL,mtop);
1212 if (inputrec->cutoff_scheme != ecutsVERLET &&
1213 ((Flags & MD_TESTVERLET) || getenv("GMX_VERLET_SCHEME") != NULL))
1215 convert_to_verlet_scheme(fplog,inputrec,mtop,det(state->box));
1218 /* Detect hardware, gather information. With tMPI only thread 0 does it
1219 * and after threads are started broadcasts hwinfo around. */
1221 gmx_detect_hardware(fplog, hwinfo, cr,
1222 bForceUseGPU, bTryUseGPU, hw_opt->gpu_id);
1224 minf.cutoff_scheme = inputrec->cutoff_scheme;
1225 minf.bUseGPU = FALSE;
1227 if (inputrec->cutoff_scheme == ecutsVERLET)
1229 prepare_verlet_scheme(fplog,hwinfo,cr,hw_opt,nbpu_opt,
1230 inputrec,mtop,state->box,
1233 else if (hwinfo->bCanUseGPU)
1235 md_print_warn(cr,fplog,
1236 "NOTE: GPU(s) found, but the current simulation can not use GPUs\n"
1237 " To use a GPU, set the mdp option: cutoff-scheme = Verlet\n"
1238 " (for quick performance testing you can use the -testverlet option)\n");
1242 gmx_fatal(FARGS,"GPU requested, but can't be used without cutoff-scheme=Verlet");
1246 #ifndef GMX_THREAD_MPI
1249 gmx_bcast_sim(sizeof(minf),&minf,cr);
1252 if (minf.bUseGPU && cr->npmenodes == -1)
1254 /* Don't automatically use PME-only nodes with GPUs */
1258 /* Check for externally set OpenMP affinity and turn off internal
1259 * pinning if any is found. We need to do this check early to tell
1260 * thread-MPI whether it should do pinning when spawning threads.
1262 gmx_omp_check_thread_affinity(fplog, cr, hw_opt);
1264 #ifdef GMX_THREAD_MPI
1265 /* With thread-MPI inputrec is only set here on the master thread */
1269 check_and_update_hw_opt(hw_opt,minf.cutoff_scheme);
1271 #ifdef GMX_THREAD_MPI
1272 /* Early check for externally set process affinity. Can't do over all
1273 * MPI processes because hwinfo is not available everywhere, but with
1274 * thread-MPI it's needed as pinning might get turned off which needs
1275 * to be known before starting thread-MPI. */
1276 check_cpu_affinity_set(fplog,
1278 hw_opt, hwinfo->nthreads_hw_avail, FALSE);
1281 #ifdef GMX_THREAD_MPI
1282 if (cr->npmenodes > 0 && hw_opt->nthreads_tmpi <= 0)
1284 gmx_fatal(FARGS,"You need to explicitly specify the number of MPI threads (-ntmpi) when using separate PME nodes");
1288 if (hw_opt->nthreads_omp_pme != hw_opt->nthreads_omp &&
1291 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");
1295 #ifdef GMX_THREAD_MPI
1298 /* NOW the threads will be started: */
1299 hw_opt->nthreads_tmpi = get_nthreads_mpi(hwinfo,
1303 if (hw_opt->nthreads_tot > 0 && hw_opt->nthreads_omp <= 0)
1305 hw_opt->nthreads_omp = hw_opt->nthreads_tot/hw_opt->nthreads_tmpi;
1308 if (hw_opt->nthreads_tmpi > 1)
1310 /* now start the threads. */
1311 cr=mdrunner_start_threads(hw_opt, fplog, cr_old, nfile, fnm,
1312 oenv, bVerbose, bCompact, nstglobalcomm,
1313 ddxyz, dd_node_order, rdd, rconstr,
1314 dddlb_opt, dlb_scale, ddcsx, ddcsy, ddcsz,
1316 nsteps_cmdline, nstepout, resetstep, nmultisim,
1317 repl_ex_nst, repl_ex_nex, repl_ex_seed, pforce,
1318 cpt_period, max_hours, deviceOptions,
1320 /* the main thread continues here with a new cr. We don't deallocate
1321 the old cr because other threads may still be reading it. */
1324 gmx_comm("Failed to spawn threads");
1329 /* END OF CAUTION: cr is now reliable */
1331 /* g_membed initialisation *
1332 * Because we change the mtop, init_membed is called before the init_parallel *
1333 * (in case we ever want to make it run in parallel) */
1334 if (opt2bSet("-membed",nfile,fnm))
1338 fprintf(stderr,"Initializing membed");
1340 membed = init_membed(fplog,nfile,fnm,mtop,inputrec,state,cr,&cpt_period);
1345 /* now broadcast everything to the non-master nodes/threads: */
1346 init_parallel(fplog, cr, inputrec, mtop);
1348 /* This check needs to happen after get_nthreads_mpi() */
1349 if (inputrec->cutoff_scheme == ecutsVERLET && (Flags & MD_PARTDEC))
1351 gmx_fatal_collective(FARGS,cr,NULL,
1352 "The Verlet cut-off scheme is not supported with particle decomposition.\n"
1353 "You can achieve the same effect as particle decomposition by running in parallel using only OpenMP threads.");
1358 pr_inputrec(fplog,0,"Input Parameters",inputrec,FALSE);
1361 #if defined GMX_THREAD_MPI
1362 /* With tMPI we detected on thread 0 and we'll just pass the hwinfo pointer
1363 * to the other threads -- slightly uncool, but works fine, just need to
1364 * make sure that the data doesn't get freed twice. */
1371 gmx_bcast(sizeof(&hwinfo), &hwinfo, cr);
1374 if (PAR(cr) && !SIMMASTER(cr))
1376 /* now we have inputrec on all nodes, can run the detection */
1377 /* TODO: perhaps it's better to propagate within a node instead? */
1379 gmx_detect_hardware(fplog, hwinfo, cr,
1380 bForceUseGPU, bTryUseGPU, hw_opt->gpu_id);
1383 /* Now do the affinity check with MPI/no-MPI (done earlier with thread-MPI). */
1384 check_cpu_affinity_set(fplog, cr,
1385 hw_opt, hwinfo->nthreads_hw_avail, FALSE);
1388 /* now make sure the state is initialized and propagated */
1389 set_state_entries(state,inputrec,cr->nnodes);
1391 /* remove when vv and rerun works correctly! */
1392 if (PAR(cr) && EI_VV(inputrec->eI) && ((Flags & MD_RERUN) || (Flags & MD_RERUN_VSITE)))
1395 "Currently can't do velocity verlet with rerun in parallel.");
1398 /* A parallel command line option consistency check that we can
1399 only do after any threads have started. */
1401 (ddxyz[XX] > 1 || ddxyz[YY] > 1 || ddxyz[ZZ] > 1 || cr->npmenodes > 0))
1404 "The -dd or -npme option request a parallel simulation, "
1406 "but %s was compiled without threads or MPI enabled"
1408 #ifdef GMX_THREAD_MPI
1409 "but the number of threads (option -nt) is 1"
1411 "but %s was not started through mpirun/mpiexec or only one process was requested through mpirun/mpiexec"
1418 if ((Flags & MD_RERUN) &&
1419 (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
1421 gmx_fatal(FARGS, "The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun");
1424 if (can_use_allvsall(inputrec,mtop,TRUE,cr,fplog) && PAR(cr))
1426 /* All-vs-all loops do not work with domain decomposition */
1427 Flags |= MD_PARTDEC;
1430 if (!EEL_PME(inputrec->coulombtype) || (Flags & MD_PARTDEC))
1432 if (cr->npmenodes > 0)
1434 if (!EEL_PME(inputrec->coulombtype))
1436 gmx_fatal_collective(FARGS,cr,NULL,
1437 "PME nodes are requested, but the system does not use PME electrostatics");
1439 if (Flags & MD_PARTDEC)
1441 gmx_fatal_collective(FARGS,cr,NULL,
1442 "PME nodes are requested, but particle decomposition does not support separate PME nodes");
1450 fcRegisterSteps(inputrec->nsteps,inputrec->init_step);
1453 /* NMR restraints must be initialized before load_checkpoint,
1454 * since with time averaging the history is added to t_state.
1455 * For proper consistency check we therefore need to extend
1457 * So the PME-only nodes (if present) will also initialize
1458 * the distance restraints.
1462 /* This needs to be called before read_checkpoint to extend the state */
1463 init_disres(fplog,mtop,inputrec,cr,Flags & MD_PARTDEC,fcd,state);
1465 if (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0)
1467 if (PAR(cr) && !(Flags & MD_PARTDEC))
1469 gmx_fatal(FARGS,"Orientation restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd)");
1471 /* Orientation restraints */
1474 init_orires(fplog,mtop,state->x,inputrec,cr->ms,&(fcd->orires),
1479 if (DEFORM(*inputrec))
1481 /* Store the deform reference box before reading the checkpoint */
1484 copy_mat(state->box,box);
1488 gmx_bcast(sizeof(box),box,cr);
1490 /* Because we do not have the update struct available yet
1491 * in which the reference values should be stored,
1492 * we store them temporarily in static variables.
1493 * This should be thread safe, since they are only written once
1494 * and with identical values.
1496 #ifdef GMX_THREAD_MPI
1497 tMPI_Thread_mutex_lock(&deform_init_box_mutex);
1499 deform_init_init_step_tpx = inputrec->init_step;
1500 copy_mat(box,deform_init_box_tpx);
1501 #ifdef GMX_THREAD_MPI
1502 tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
1506 if (opt2bSet("-cpi",nfile,fnm))
1508 /* Check if checkpoint file exists before doing continuation.
1509 * This way we can use identical input options for the first and subsequent runs...
1511 if( gmx_fexist_master(opt2fn_master("-cpi",nfile,fnm,cr),cr) )
1513 load_checkpoint(opt2fn_master("-cpi",nfile,fnm,cr),&fplog,
1514 cr,Flags & MD_PARTDEC,ddxyz,
1515 inputrec,state,&bReadRNG,&bReadEkin,
1516 (Flags & MD_APPENDFILES),
1517 (Flags & MD_APPENDFILESSET));
1521 Flags |= MD_READ_RNG;
1525 Flags |= MD_READ_EKIN;
1530 if (((MASTER(cr) || (Flags & MD_SEPPOT)) && (Flags & MD_APPENDFILES))
1531 #ifdef GMX_THREAD_MPI
1532 /* With thread MPI only the master node/thread exists in mdrun.c,
1533 * therefore non-master nodes need to open the "seppot" log file here.
1535 || (!MASTER(cr) && (Flags & MD_SEPPOT))
1539 gmx_log_open(ftp2fn(efLOG,nfile,fnm),cr,!(Flags & MD_SEPPOT),
1543 /* override nsteps with value from cmdline */
1544 override_nsteps_cmdline(fplog, nsteps_cmdline, inputrec, cr);
1548 copy_mat(state->box,box);
1553 gmx_bcast(sizeof(box),box,cr);
1556 /* Essential dynamics */
1557 if (opt2bSet("-ei",nfile,fnm))
1559 /* Open input and output files, allocate space for ED data structure */
1560 ed = ed_open(nfile,fnm,Flags,cr);
1563 if (PAR(cr) && !((Flags & MD_PARTDEC) ||
1564 EI_TPI(inputrec->eI) ||
1565 inputrec->eI == eiNM))
1567 cr->dd = init_domain_decomposition(fplog,cr,Flags,ddxyz,rdd,rconstr,
1568 dddlb_opt,dlb_scale,
1572 &ddbox,&npme_major,&npme_minor);
1574 make_dd_communicators(fplog,cr,dd_node_order);
1576 /* Set overallocation to avoid frequent reallocation of arrays */
1577 set_over_alloc_dd(TRUE);
1581 /* PME, if used, is done on all nodes with 1D decomposition */
1583 cr->duty = (DUTY_PP | DUTY_PME);
1586 if (!EI_TPI(inputrec->eI))
1588 npme_major = cr->nnodes;
1591 if (inputrec->ePBC == epbcSCREW)
1594 "pbc=%s is only implemented with domain decomposition",
1595 epbc_names[inputrec->ePBC]);
1601 /* After possible communicator splitting in make_dd_communicators.
1602 * we can set up the intra/inter node communication.
1604 gmx_setup_nodecomm(fplog,cr);
1607 /* Initialize per-node process ID and counters. */
1608 gmx_init_intra_counters(cr);
1611 md_print_info(cr,fplog,"Using %d MPI %s\n",
1613 #ifdef GMX_THREAD_MPI
1614 cr->nnodes==1 ? "thread" : "threads"
1616 cr->nnodes==1 ? "process" : "processes"
1621 gmx_omp_nthreads_init(fplog, cr,
1622 hwinfo->nthreads_hw_avail,
1623 hw_opt->nthreads_omp,
1624 hw_opt->nthreads_omp_pme,
1625 (cr->duty & DUTY_PP) == 0,
1626 inputrec->cutoff_scheme == ecutsVERLET);
1628 gmx_check_hw_runconf_consistency(fplog, hwinfo, cr, hw_opt->nthreads_tmpi, minf.bUseGPU);
1630 /* getting number of PP/PME threads
1631 PME: env variable should be read only on one node to make sure it is
1632 identical everywhere;
1634 /* TODO nthreads_pp is only used for pinning threads.
1635 * This is a temporary solution until we have a hw topology library.
1637 nthreads_pp = gmx_omp_nthreads_get(emntNonbonded);
1638 nthreads_pme = gmx_omp_nthreads_get(emntPME);
1640 wcycle = wallcycle_init(fplog,resetstep,cr,nthreads_pp,nthreads_pme);
1644 /* Master synchronizes its value of reset_counters with all nodes
1645 * including PME only nodes */
1646 reset_counters = wcycle_get_reset_counters(wcycle);
1647 gmx_bcast_sim(sizeof(reset_counters),&reset_counters,cr);
1648 wcycle_set_reset_counters(wcycle, reset_counters);
1652 if (cr->duty & DUTY_PP)
1654 /* For domain decomposition we allocate dynamically
1655 * in dd_partition_system.
1657 if (DOMAINDECOMP(cr))
1659 bcast_state_setup(cr,state);
1665 bcast_state(cr,state,TRUE);
1669 /* Initiate forcerecord */
1671 fr->hwinfo = hwinfo;
1672 init_forcerec(fplog,oenv,fr,fcd,inputrec,mtop,cr,box,FALSE,
1673 opt2fn("-table",nfile,fnm),
1674 opt2fn("-tabletf",nfile,fnm),
1675 opt2fn("-tablep",nfile,fnm),
1676 opt2fn("-tableb",nfile,fnm),
1680 /* version for PCA_NOT_READ_NODE (see md.c) */
1681 /*init_forcerec(fplog,fr,fcd,inputrec,mtop,cr,box,FALSE,
1682 "nofile","nofile","nofile","nofile",FALSE,pforce);
1684 fr->bSepDVDL = ((Flags & MD_SEPPOT) == MD_SEPPOT);
1686 /* Initialize QM-MM */
1689 init_QMMMrec(cr,box,mtop,inputrec,fr);
1692 /* Initialize the mdatoms structure.
1693 * mdatoms is not filled with atom data,
1694 * as this can not be done now with domain decomposition.
1696 mdatoms = init_mdatoms(fplog,mtop,inputrec->efep!=efepNO);
1698 /* Initialize the virtual site communication */
1699 vsite = init_vsite(mtop,cr,FALSE);
1701 calc_shifts(box,fr->shift_vec);
1703 /* With periodic molecules the charge groups should be whole at start up
1704 * and the virtual sites should not be far from their proper positions.
1706 if (!inputrec->bContinuation && MASTER(cr) &&
1707 !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
1709 /* Make molecules whole at start of run */
1710 if (fr->ePBC != epbcNONE)
1712 do_pbc_first_mtop(fplog,inputrec->ePBC,box,mtop,state->x);
1716 /* Correct initial vsite positions are required
1717 * for the initial distribution in the domain decomposition
1718 * and for the initial shell prediction.
1720 construct_vsites_mtop(fplog,vsite,mtop,state->x);
1724 if (EEL_PME(fr->eeltype))
1726 ewaldcoeff = fr->ewaldcoeff;
1727 pmedata = &fr->pmedata;
1736 /* This is a PME only node */
1738 /* We don't need the state */
1741 ewaldcoeff = calc_ewaldcoeff(inputrec->rcoulomb, inputrec->ewald_rtol);
1745 /* Before setting affinity, check whether the affinity has changed
1746 * - which indicates that probably the OpenMP library has changed it since
1747 * we first checked). */
1748 check_cpu_affinity_set(fplog, cr, hw_opt, hwinfo->nthreads_hw_avail, TRUE);
1750 /* Set the CPU affinity */
1751 set_cpu_affinity(fplog,cr,hw_opt,nthreads_pme,hwinfo,inputrec);
1753 /* Initiate PME if necessary,
1754 * either on all nodes or on dedicated PME nodes only. */
1755 if (EEL_PME(inputrec->coulombtype))
1759 nChargePerturbed = mdatoms->nChargePerturbed;
1761 if (cr->npmenodes > 0)
1763 /* The PME only nodes need to know nChargePerturbed */
1764 gmx_bcast_sim(sizeof(nChargePerturbed),&nChargePerturbed,cr);
1767 if (cr->duty & DUTY_PME)
1769 status = gmx_pme_init(pmedata,cr,npme_major,npme_minor,inputrec,
1770 mtop ? mtop->natoms : 0,nChargePerturbed,
1771 (Flags & MD_REPRODUCIBLE),nthreads_pme);
1774 gmx_fatal(FARGS,"Error %d initializing PME",status);
1780 if (integrator[inputrec->eI].func == do_md
1783 integrator[inputrec->eI].func == do_md_openmm
1787 /* Turn on signal handling on all nodes */
1789 * (A user signal from the PME nodes (if any)
1790 * is communicated to the PP nodes.
1792 signal_handler_install();
1795 if (cr->duty & DUTY_PP)
1797 if (inputrec->ePull != epullNO)
1799 /* Initialize pull code */
1800 init_pull(fplog,inputrec,nfile,fnm,mtop,cr,oenv, inputrec->fepvals->init_lambda,
1801 EI_DYNAMICS(inputrec->eI) && MASTER(cr),Flags);
1806 /* Initialize enforced rotation code */
1807 init_rot(fplog,inputrec,nfile,fnm,cr,state->x,box,mtop,oenv,
1811 constr = init_constraints(fplog,mtop,inputrec,ed,state,cr);
1813 if (DOMAINDECOMP(cr))
1815 dd_init_bondeds(fplog,cr->dd,mtop,vsite,constr,inputrec,
1816 Flags & MD_DDBONDCHECK,fr->cginfo_mb);
1818 set_dd_parameters(fplog,cr->dd,dlb_scale,inputrec,fr,&ddbox);
1820 setup_dd_grid(fplog,cr->dd);
1823 /* Now do whatever the user wants us to do (how flexible...) */
1824 integrator[inputrec->eI].func(fplog,cr,nfile,fnm,
1825 oenv,bVerbose,bCompact,
1828 nstepout,inputrec,mtop,
1830 mdatoms,nrnb,wcycle,ed,fr,
1831 repl_ex_nst,repl_ex_nex,repl_ex_seed,
1833 cpt_period,max_hours,
1838 if (inputrec->ePull != epullNO)
1840 finish_pull(fplog,inputrec->pull);
1845 finish_rot(fplog,inputrec->rot);
1852 gmx_pmeonly(*pmedata,cr,nrnb,wcycle,ewaldcoeff,FALSE,inputrec);
1855 if (EI_DYNAMICS(inputrec->eI) || EI_TPI(inputrec->eI))
1857 /* Some timing stats */
1860 if (runtime.proc == 0)
1862 runtime.proc = runtime.real;
1871 wallcycle_stop(wcycle,ewcRUN);
1873 /* Finish up, write some stuff
1874 * if rerunMD, don't write last frame again
1876 finish_run(fplog,cr,ftp2fn(efSTO,nfile,fnm),
1877 inputrec,nrnb,wcycle,&runtime,
1878 fr != NULL && fr->nbv != NULL && fr->nbv->bUseGPU ?
1879 nbnxn_cuda_get_timings(fr->nbv->cu_nbv) : NULL,
1881 EI_DYNAMICS(inputrec->eI) && !MULTISIM(cr));
1883 if ((cr->duty & DUTY_PP) && fr->nbv != NULL && fr->nbv->bUseGPU)
1885 char gpu_err_str[STRLEN];
1887 /* free GPU memory and uninitialize GPU (by destroying the context) */
1888 nbnxn_cuda_free(fplog, fr->nbv->cu_nbv);
1890 if (!free_gpu(gpu_err_str))
1892 gmx_warning("On node %d failed to free GPU #%d: %s",
1893 cr->nodeid, get_current_gpu_device_id(), gpu_err_str);
1897 if (opt2bSet("-membed",nfile,fnm))
1902 #ifdef GMX_THREAD_MPI
1903 if (PAR(cr) && SIMMASTER(cr))
1906 gmx_hardware_info_free(hwinfo);
1909 /* Does what it says */
1910 print_date_and_time(fplog,cr->nodeid,"Finished mdrun",&runtime);
1912 /* Close logfile already here if we were appending to it */
1913 if (MASTER(cr) && (Flags & MD_APPENDFILES))
1915 gmx_log_close(fplog);
1918 rc=(int)gmx_get_stop_condition();
1920 #ifdef GMX_THREAD_MPI
1921 /* we need to join all threads. The sub-threads join when they
1922 exit this function, but the master thread needs to be told to
1924 if (PAR(cr) && MASTER(cr))