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39 * \brief Implements the MD runner routine calling all integrators.
41 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
42 * \ingroup module_mdlib
57 #include "gromacs/commandline/filenm.h"
58 #include "gromacs/domdec/domdec.h"
59 #include "gromacs/domdec/domdec_struct.h"
60 #include "gromacs/ewald/pme.h"
61 #include "gromacs/fileio/checkpoint.h"
62 #include "gromacs/fileio/oenv.h"
63 #include "gromacs/fileio/tpxio.h"
64 #include "gromacs/gmxlib/network.h"
65 #include "gromacs/gpu_utils/gpu_utils.h"
66 #include "gromacs/hardware/cpuinfo.h"
67 #include "gromacs/hardware/detecthardware.h"
68 #include "gromacs/hardware/hardwareassign.h"
69 #include "gromacs/hardware/printhardware.h"
70 #include "gromacs/listed-forces/disre.h"
71 #include "gromacs/listed-forces/orires.h"
72 #include "gromacs/math/calculate-ewald-splitting-coefficient.h"
73 #include "gromacs/math/functions.h"
74 #include "gromacs/math/utilities.h"
75 #include "gromacs/math/vec.h"
76 #include "gromacs/mdlib/calc_verletbuf.h"
77 #include "gromacs/mdlib/constr.h"
78 #include "gromacs/mdlib/force.h"
79 #include "gromacs/mdlib/forcerec.h"
80 #include "gromacs/mdlib/gmx_omp_nthreads.h"
81 #include "gromacs/mdlib/integrator.h"
82 #include "gromacs/mdlib/main.h"
83 #include "gromacs/mdlib/md_support.h"
84 #include "gromacs/mdlib/mdatoms.h"
85 #include "gromacs/mdlib/mdrun.h"
86 #include "gromacs/mdlib/minimize.h"
87 #include "gromacs/mdlib/nbnxn_search.h"
88 #include "gromacs/mdlib/qmmm.h"
89 #include "gromacs/mdlib/sighandler.h"
90 #include "gromacs/mdlib/sim_util.h"
91 #include "gromacs/mdlib/tpi.h"
92 #include "gromacs/mdrunutility/mdmodules.h"
93 #include "gromacs/mdrunutility/threadaffinity.h"
94 #include "gromacs/mdtypes/commrec.h"
95 #include "gromacs/mdtypes/edsamhistory.h"
96 #include "gromacs/mdtypes/energyhistory.h"
97 #include "gromacs/mdtypes/inputrec.h"
98 #include "gromacs/mdtypes/md_enums.h"
99 #include "gromacs/mdtypes/observableshistory.h"
100 #include "gromacs/mdtypes/state.h"
101 #include "gromacs/mdtypes/swaphistory.h"
102 #include "gromacs/pbcutil/pbc.h"
103 #include "gromacs/pulling/pull.h"
104 #include "gromacs/pulling/pull_rotation.h"
105 #include "gromacs/timing/wallcycle.h"
106 #include "gromacs/topology/mtop_util.h"
107 #include "gromacs/trajectory/trajectoryframe.h"
108 #include "gromacs/utility/cstringutil.h"
109 #include "gromacs/utility/exceptions.h"
110 #include "gromacs/utility/fatalerror.h"
111 #include "gromacs/utility/filestream.h"
112 #include "gromacs/utility/gmxassert.h"
113 #include "gromacs/utility/gmxmpi.h"
114 #include "gromacs/utility/logger.h"
115 #include "gromacs/utility/loggerbuilder.h"
116 #include "gromacs/utility/pleasecite.h"
117 #include "gromacs/utility/programcontext.h"
118 #include "gromacs/utility/smalloc.h"
124 #include "resource-division.h"
127 #include "corewrap.h"
130 //! First step used in pressure scaling
131 gmx_int64_t deform_init_init_step_tpx
;
132 //! Initial box for pressure scaling
133 matrix deform_init_box_tpx
;
134 //! MPI variable for use in pressure scaling
135 tMPI_Thread_mutex_t deform_init_box_mutex
= TMPI_THREAD_MUTEX_INITIALIZER
;
138 /* The minimum number of atoms per tMPI thread. With fewer atoms than this,
139 * the number of threads will get lowered.
141 #define MIN_ATOMS_PER_MPI_THREAD 90
142 #define MIN_ATOMS_PER_GPU 900
147 void Mdrunner::reinitializeOnSpawnedThread()
149 // TODO This duplication is formally necessary if any thread might
150 // modify any memory in fnm or the pointers it contains. If the
151 // contents are ever provably const, then we can remove this
152 // allocation (and memory leak).
153 // TODO This should probably become part of a copy constructor for
155 fnm
= dup_tfn(nfile
, fnm
);
157 cr
= reinitialize_commrec_for_this_thread(cr
);
161 // Only the master rank writes to the log files
166 /*! \brief The callback used for running on spawned threads.
168 * Obtains the pointer to the master mdrunner object from the one
169 * argument permitted to the thread-launch API call, copies it to make
170 * a new runner for this thread, reinitializes necessary data, and
171 * proceeds to the simulation. */
172 static void mdrunner_start_fn(void *arg
)
176 auto masterMdrunner
= reinterpret_cast<const gmx::Mdrunner
*>(arg
);
177 /* copy the arg list to make sure that it's thread-local. This
178 doesn't copy pointed-to items, of course, but those are all
180 gmx::Mdrunner mdrunner
= *masterMdrunner
;
181 mdrunner
.reinitializeOnSpawnedThread();
184 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
;
188 /*! \brief Start thread-MPI threads.
190 * Called by mdrunner() to start a specific number of threads
191 * (including the main thread) for thread-parallel runs. This in turn
192 * calls mdrunner() for each thread. All options are the same as for
194 t_commrec
*Mdrunner::spawnThreads(int numThreadsToLaunch
)
197 /* first check whether we even need to start tMPI */
198 if (numThreadsToLaunch
< 2)
203 gmx::Mdrunner spawnedMdrunner
= *this;
204 // TODO This duplication is formally necessary if any thread might
205 // modify any memory in fnm or the pointers it contains. If the
206 // contents are ever provably const, then we can remove this
207 // allocation (and memory leak).
208 // TODO This should probably become part of a copy constructor for
210 spawnedMdrunner
.fnm
= dup_tfn(this->nfile
, fnm
);
212 /* now spawn new threads that start mdrunner_start_fn(), while
213 the main thread returns, we set thread affinity later */
214 if (tMPI_Init_fn(TRUE
, numThreadsToLaunch
, TMPI_AFFINITY_NONE
,
215 mdrunner_start_fn
, static_cast<void*>(&spawnedMdrunner
)) != TMPI_SUCCESS
)
217 GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
220 return reinitialize_commrec_for_this_thread(cr
);
225 #endif /* GMX_THREAD_MPI */
228 /*! \brief Cost of non-bonded kernels
230 * We determine the extra cost of the non-bonded kernels compared to
231 * a reference nstlist value of 10 (which is the default in grompp).
233 static const int nbnxnReferenceNstlist
= 10;
234 //! The values to try when switching
235 const int nstlist_try
[] = { 20, 25, 40 };
236 //! Number of elements in the neighborsearch list trials.
237 #define NNSTL sizeof(nstlist_try)/sizeof(nstlist_try[0])
238 /* Increase nstlist until the non-bonded cost increases more than listfac_ok,
239 * but never more than listfac_max.
240 * A standard (protein+)water system at 300K with PME ewald_rtol=1e-5
241 * needs 1.28 at rcoulomb=0.9 and 1.24 at rcoulomb=1.0 to get to nstlist=40.
242 * Note that both CPU and GPU factors are conservative. Performance should
243 * not go down due to this tuning, except with a relatively slow GPU.
244 * On the other hand, at medium/high parallelization or with fast GPUs
245 * nstlist will not be increased enough to reach optimal performance.
247 /* CPU: pair-search is about a factor 1.5 slower than the non-bonded kernel */
248 //! Max OK performance ratio beween force calc and neighbor searching
249 static const float nbnxn_cpu_listfac_ok
= 1.05;
250 //! Too high performance ratio beween force calc and neighbor searching
251 static const float nbnxn_cpu_listfac_max
= 1.09;
252 /* CPU: pair-search is about a factor 2-3 slower than the non-bonded kernel */
253 //! Max OK performance ratio beween force calc and neighbor searching
254 static const float nbnxn_knl_listfac_ok
= 1.22;
255 //! Too high performance ratio beween force calc and neighbor searching
256 static const float nbnxn_knl_listfac_max
= 1.3;
257 /* GPU: pair-search is a factor 1.5-3 slower than the non-bonded kernel */
258 //! Max OK performance ratio beween force calc and neighbor searching
259 static const float nbnxn_gpu_listfac_ok
= 1.20;
260 //! Too high performance ratio beween force calc and neighbor searching
261 static const float nbnxn_gpu_listfac_max
= 1.30;
263 /*! \brief Try to increase nstlist when using the Verlet cut-off scheme */
264 static void increase_nstlist(FILE *fp
, t_commrec
*cr
,
265 t_inputrec
*ir
, int nstlist_cmdline
,
266 const gmx_mtop_t
*mtop
, matrix box
,
267 bool makeGpuPairList
, const gmx::CpuInfo
&cpuinfo
)
269 float listfac_ok
, listfac_max
;
270 int nstlist_orig
, nstlist_prev
;
271 verletbuf_list_setup_t ls
;
272 real rlistWithReferenceNstlist
, rlist_inc
, rlist_ok
, rlist_max
;
273 real rlist_new
, rlist_prev
;
274 size_t nstlist_ind
= 0;
275 gmx_bool bBox
, bDD
, bCont
;
276 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";
277 const char *nve_err
= "Can not increase nstlist because an NVE ensemble is used";
278 const char *vbd_err
= "Can not increase nstlist because verlet-buffer-tolerance is not set or used";
279 const char *box_err
= "Can not increase nstlist because the box is too small";
280 const char *dd_err
= "Can not increase nstlist because of domain decomposition limitations";
283 if (nstlist_cmdline
<= 0)
285 if (ir
->nstlist
== 1)
287 /* The user probably set nstlist=1 for a reason,
288 * don't mess with the settings.
293 if (fp
!= nullptr && makeGpuPairList
&& ir
->nstlist
< nstlist_try
[0])
295 fprintf(fp
, nstl_gpu
, ir
->nstlist
);
298 while (nstlist_ind
< NNSTL
&& ir
->nstlist
>= nstlist_try
[nstlist_ind
])
302 if (nstlist_ind
== NNSTL
)
304 /* There are no larger nstlist value to try */
309 if (EI_MD(ir
->eI
) && ir
->etc
== etcNO
)
313 fprintf(stderr
, "%s\n", nve_err
);
317 fprintf(fp
, "%s\n", nve_err
);
323 if (ir
->verletbuf_tol
== 0 && makeGpuPairList
)
325 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");
328 if (ir
->verletbuf_tol
< 0)
332 fprintf(stderr
, "%s\n", vbd_err
);
336 fprintf(fp
, "%s\n", vbd_err
);
344 listfac_ok
= nbnxn_gpu_listfac_ok
;
345 listfac_max
= nbnxn_gpu_listfac_max
;
347 else if (cpuinfo
.feature(gmx::CpuInfo::Feature::X86_Avx512ER
))
349 listfac_ok
= nbnxn_knl_listfac_ok
;
350 listfac_max
= nbnxn_knl_listfac_max
;
354 listfac_ok
= nbnxn_cpu_listfac_ok
;
355 listfac_max
= nbnxn_cpu_listfac_max
;
358 nstlist_orig
= ir
->nstlist
;
359 if (nstlist_cmdline
> 0)
363 sprintf(buf
, "Getting nstlist=%d from command line option",
366 ir
->nstlist
= nstlist_cmdline
;
369 verletbuf_get_list_setup(true, makeGpuPairList
, &ls
);
371 /* Allow rlist to make the list a given factor larger than the list
372 * would be with the reference value for nstlist (10).
374 nstlist_prev
= ir
->nstlist
;
375 ir
->nstlist
= nbnxnReferenceNstlist
;
376 calc_verlet_buffer_size(mtop
, det(box
), ir
, -1, &ls
, nullptr,
377 &rlistWithReferenceNstlist
);
378 ir
->nstlist
= nstlist_prev
;
380 /* Determine the pair list size increase due to zero interactions */
381 rlist_inc
= nbnxn_get_rlist_effective_inc(ls
.cluster_size_j
,
382 mtop
->natoms
/det(box
));
383 rlist_ok
= (rlistWithReferenceNstlist
+ rlist_inc
)*std::cbrt(listfac_ok
) - rlist_inc
;
384 rlist_max
= (rlistWithReferenceNstlist
+ rlist_inc
)*std::cbrt(listfac_max
) - rlist_inc
;
387 fprintf(debug
, "nstlist tuning: rlist_inc %.3f rlist_ok %.3f rlist_max %.3f\n",
388 rlist_inc
, rlist_ok
, rlist_max
);
391 nstlist_prev
= nstlist_orig
;
392 rlist_prev
= ir
->rlist
;
395 if (nstlist_cmdline
<= 0)
397 ir
->nstlist
= nstlist_try
[nstlist_ind
];
400 /* Set the pair-list buffer size in ir */
401 calc_verlet_buffer_size(mtop
, det(box
), ir
, -1, &ls
, nullptr, &rlist_new
);
403 /* Does rlist fit in the box? */
404 bBox
= (gmx::square(rlist_new
) < max_cutoff2(ir
->ePBC
, box
));
406 if (bBox
&& DOMAINDECOMP(cr
))
408 /* Check if rlist fits in the domain decomposition */
409 if (inputrec2nboundeddim(ir
) < DIM
)
411 gmx_incons("Changing nstlist with domain decomposition and unbounded dimensions is not implemented yet");
414 copy_mat(box
, state_tmp
.box
);
415 bDD
= change_dd_cutoff(cr
, &state_tmp
, ir
, rlist_new
);
420 fprintf(debug
, "nstlist %d rlist %.3f bBox %d bDD %d\n",
421 ir
->nstlist
, rlist_new
, bBox
, bDD
);
426 if (nstlist_cmdline
<= 0)
428 if (bBox
&& bDD
&& rlist_new
<= rlist_max
)
430 /* Increase nstlist */
431 nstlist_prev
= ir
->nstlist
;
432 rlist_prev
= rlist_new
;
433 bCont
= (nstlist_ind
+1 < NNSTL
&& rlist_new
< rlist_ok
);
437 /* Stick with the previous nstlist */
438 ir
->nstlist
= nstlist_prev
;
439 rlist_new
= rlist_prev
;
451 gmx_warning(!bBox
? box_err
: dd_err
);
454 fprintf(fp
, "\n%s\n", bBox
? box_err
: dd_err
);
456 ir
->nstlist
= nstlist_orig
;
458 else if (ir
->nstlist
!= nstlist_orig
|| rlist_new
!= ir
->rlist
)
460 sprintf(buf
, "Changing nstlist from %d to %d, rlist from %g to %g",
461 nstlist_orig
, ir
->nstlist
,
462 ir
->rlist
, rlist_new
);
465 fprintf(stderr
, "%s\n\n", buf
);
469 fprintf(fp
, "%s\n\n", buf
);
471 ir
->rlist
= rlist_new
;
475 /*! \brief Initialize variables for Verlet scheme simulation */
476 static void prepare_verlet_scheme(FILE *fplog
,
480 const gmx_mtop_t
*mtop
,
482 bool makeGpuPairList
,
483 const gmx::CpuInfo
&cpuinfo
)
485 /* For NVE simulations, we will retain the initial list buffer */
486 if (EI_DYNAMICS(ir
->eI
) &&
487 ir
->verletbuf_tol
> 0 &&
488 !(EI_MD(ir
->eI
) && ir
->etc
== etcNO
))
490 /* Update the Verlet buffer size for the current run setup */
491 verletbuf_list_setup_t ls
;
494 /* Here we assume SIMD-enabled kernels are being used. But as currently
495 * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
496 * and 4x2 gives a larger buffer than 4x4, this is ok.
498 verletbuf_get_list_setup(true, makeGpuPairList
, &ls
);
500 calc_verlet_buffer_size(mtop
, det(box
), ir
, -1, &ls
, nullptr, &rlist_new
);
502 if (rlist_new
!= ir
->rlist
)
504 if (fplog
!= nullptr)
506 fprintf(fplog
, "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
507 ir
->rlist
, rlist_new
,
508 ls
.cluster_size_i
, ls
.cluster_size_j
);
510 ir
->rlist
= rlist_new
;
514 if (nstlist_cmdline
> 0 && (!EI_DYNAMICS(ir
->eI
) || ir
->verletbuf_tol
<= 0))
516 gmx_fatal(FARGS
, "Can not set nstlist without %s",
517 !EI_DYNAMICS(ir
->eI
) ? "dynamics" : "verlet-buffer-tolerance");
520 if (EI_DYNAMICS(ir
->eI
))
522 /* Set or try nstlist values */
523 increase_nstlist(fplog
, cr
, ir
, nstlist_cmdline
, mtop
, box
, makeGpuPairList
, cpuinfo
);
527 /*! \brief Override the nslist value in inputrec
529 * with value passed on the command line (if any)
531 static void override_nsteps_cmdline(const gmx::MDLogger
&mdlog
,
532 gmx_int64_t nsteps_cmdline
,
537 /* override with anything else than the default -2 */
538 if (nsteps_cmdline
> -2)
540 char sbuf_steps
[STEPSTRSIZE
];
541 char sbuf_msg
[STRLEN
];
543 ir
->nsteps
= nsteps_cmdline
;
544 if (EI_DYNAMICS(ir
->eI
) && nsteps_cmdline
!= -1)
546 sprintf(sbuf_msg
, "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
547 gmx_step_str(nsteps_cmdline
, sbuf_steps
),
548 fabs(nsteps_cmdline
*ir
->delta_t
));
552 sprintf(sbuf_msg
, "Overriding nsteps with value passed on the command line: %s steps",
553 gmx_step_str(nsteps_cmdline
, sbuf_steps
));
556 GMX_LOG(mdlog
.warning
).asParagraph().appendText(sbuf_msg
);
558 else if (nsteps_cmdline
< -2)
560 gmx_fatal(FARGS
, "Invalid nsteps value passed on the command line: %d",
563 /* Do nothing if nsteps_cmdline == -2 */
569 //! Halt the run if there are inconsistences between user choices to run with GPUs and/or hardware detection.
570 static void exitIfCannotForceGpuRun(bool requirePhysicalGpu
,
572 bool useVerletScheme
,
573 bool compatibleGpusFound
)
575 /* Was GPU acceleration either explicitly (-nb gpu) or implicitly
576 * (gpu ID passed) requested? */
577 if (!requirePhysicalGpu
)
582 if (GMX_GPU
== GMX_GPU_NONE
)
584 gmx_fatal(FARGS
, "GPU acceleration requested, but %s was compiled without GPU support!",
585 gmx::getProgramContext().displayName());
590 gmx_fatal(FARGS
, "GPU emulation cannot be requested together with GPU acceleration!");
593 if (!useVerletScheme
)
595 gmx_fatal(FARGS
, "GPU acceleration requested, but can't be used without cutoff-scheme=Verlet");
598 if (!compatibleGpusFound
)
600 gmx_fatal(FARGS
, "GPU acceleration requested, but no compatible GPUs were detected.");
604 /*! \brief Return whether GPU acceleration is useful with the given settings.
606 * If not, logs a message about falling back to CPU code. */
607 static bool gpuAccelerationIsUseful(const MDLogger
&mdlog
,
608 const t_inputrec
*ir
,
611 if (doRerun
&& ir
->opts
.ngener
> 1)
613 /* Rerun execution time is dominated by I/O and pair search,
614 * so GPUs are not very useful, plus they do not support more
615 * than one energy group. If the user requested GPUs
616 * explicitly, a fatal error is given later. With non-reruns,
617 * we fall back to a single whole-of system energy group
618 * (which runs much faster than a multiple-energy-groups
619 * implementation would), and issue a note in the .log
620 * file. Users can re-run if they want the information. */
621 GMX_LOG(mdlog
.warning
).asParagraph().appendText("Multiple energy groups is not implemented for GPUs, so is not useful for this rerun, so falling back to the CPU");
628 //! \brief Return the correct integrator function.
629 static integrator_t
*my_integrator(unsigned int ei
)
638 if (!EI_DYNAMICS(ei
))
640 GMX_THROW(APIError("do_md integrator would be called for a non-dynamical integrator"));
655 GMX_THROW(APIError("do_tpi integrator would be called for a non-TPI integrator"));
659 GMX_THROW(NotImplementedError("SD2 integrator has been removed"));
661 GMX_THROW(APIError("Non existing integrator selected"));
665 //! Initializes the logger for mdrun.
666 static gmx::LoggerOwner
buildLogger(FILE *fplog
, const t_commrec
*cr
)
668 gmx::LoggerBuilder builder
;
669 if (fplog
!= nullptr)
671 builder
.addTargetFile(gmx::MDLogger::LogLevel::Info
, fplog
);
673 if (cr
== nullptr || SIMMASTER(cr
))
675 builder
.addTargetStream(gmx::MDLogger::LogLevel::Warning
,
676 &gmx::TextOutputFile::standardError());
678 return builder
.build();
681 int Mdrunner::mdrunner()
684 gmx_ddbox_t ddbox
= {0};
685 int npme_major
, npme_minor
;
687 gmx_mtop_t
*mtop
= nullptr;
688 t_mdatoms
*mdatoms
= nullptr;
689 t_forcerec
*fr
= nullptr;
690 t_fcdata
*fcd
= nullptr;
691 real ewaldcoeff_q
= 0;
692 real ewaldcoeff_lj
= 0;
693 struct gmx_pme_t
**pmedata
= nullptr;
694 gmx_vsite_t
*vsite
= nullptr;
696 int nChargePerturbed
= -1, nTypePerturbed
= 0, status
;
697 gmx_wallcycle_t wcycle
;
698 gmx_walltime_accounting_t walltime_accounting
= nullptr;
700 gmx_int64_t reset_counters
;
701 int nthreads_pme
= 1;
702 gmx_membed_t
* membed
= nullptr;
703 gmx_hw_info_t
*hwinfo
= nullptr;
705 /* CAUTION: threads may be started later on in this function, so
706 cr doesn't reflect the final parallel state right now */
707 gmx::MDModules mdModules
;
708 t_inputrec inputrecInstance
;
709 t_inputrec
*inputrec
= &inputrecInstance
;
712 if (Flags
& MD_APPENDFILES
)
717 bool doMembed
= opt2bSet("-membed", nfile
, fnm
);
718 bool doRerun
= (Flags
& MD_RERUN
);
720 /* Handle GPU-related user options. Later, we check consistency
721 * with things like whether support is compiled, or tMPI thread
723 bool emulateGpu
= getenv("GMX_EMULATE_GPU") != nullptr;
724 auto userGpuTaskAssignment
= parseGpuTaskAssignment(hw_opt
.gpuIdTaskAssignment
);
725 bool forceUseCpu
= (strncmp(nbpu_opt
, "cpu", 3) == 0);
726 if (!userGpuTaskAssignment
.empty() && forceUseCpu
)
728 gmx_fatal(FARGS
, "GPU IDs were specified, and short-ranged interactions were assigned to the CPU. Make no more than one of these choices.");
730 bool forceUsePhysicalGpu
= (strncmp(nbpu_opt
, "gpu", 3) == 0) || !userGpuTaskAssignment
.empty();
731 bool tryUsePhysicalGpu
= (strncmp(nbpu_opt
, "auto", 4) == 0) && !emulateGpu
&& (GMX_GPU
!= GMX_GPU_NONE
);
733 // Here we assume that SIMMASTER(cr) does not change even after the
734 // threads are started.
735 gmx::LoggerOwner
logOwner(buildLogger(fplog
, cr
));
736 gmx::MDLogger
mdlog(logOwner
.logger());
738 /* Detect hardware, gather information. This is an operation that is
739 * global for this process (MPI rank). */
740 bool detectGpus
= forceUsePhysicalGpu
|| tryUsePhysicalGpu
;
741 hwinfo
= gmx_detect_hardware(mdlog
, cr
, detectGpus
);
743 gmx_print_detected_hardware(fplog
, cr
, mdlog
, hwinfo
);
745 if (fplog
!= nullptr)
747 /* Print references after all software/hardware printing */
748 please_cite(fplog
, "Abraham2015");
749 please_cite(fplog
, "Pall2015");
750 please_cite(fplog
, "Pronk2013");
751 please_cite(fplog
, "Hess2008b");
752 please_cite(fplog
, "Spoel2005a");
753 please_cite(fplog
, "Lindahl2001a");
754 please_cite(fplog
, "Berendsen95a");
757 std::unique_ptr
<t_state
> stateInstance
= std::unique_ptr
<t_state
>(new t_state
);
758 t_state
* state
= stateInstance
.get();
762 /* Read (nearly) all data required for the simulation */
763 read_tpx_state(ftp2fn(efTPR
, nfile
, fnm
), inputrec
, state
, mtop
);
765 exitIfCannotForceGpuRun(forceUsePhysicalGpu
,
767 inputrec
->cutoff_scheme
== ecutsVERLET
,
768 compatibleGpusFound(hwinfo
->gpu_info
));
770 if (inputrec
->cutoff_scheme
== ecutsVERLET
)
772 /* TODO This logic could run later, e.g. before -npme -1
773 is handled. If inputrec has already been communicated,
774 then the resulting tryUsePhysicalGpu does not need to
776 if ((tryUsePhysicalGpu
|| forceUsePhysicalGpu
) &&
777 !gpuAccelerationIsUseful(mdlog
, inputrec
, doRerun
))
779 /* Fallback message printed by nbnxn_acceleration_supported */
780 if (forceUsePhysicalGpu
)
782 gmx_fatal(FARGS
, "GPU acceleration requested, but not supported with the given input settings");
784 tryUsePhysicalGpu
= false;
786 /* TODO This logic could run later, e.g. after inputrec,
787 mtop, and state have been communicated, but before DD
788 is initialized. In particular, -ntmpi 0 only needs to
789 know whether the Verlet scheme is active in order to
790 choose the number of ranks (because GPUs might be
792 bool makeGpuPairList
= (forceUsePhysicalGpu
||
795 prepare_verlet_scheme(fplog
, cr
,
796 inputrec
, nstlist_cmdline
, mtop
, state
->box
,
797 makeGpuPairList
, *hwinfo
->cpuInfo
);
801 if (nstlist_cmdline
> 0)
803 gmx_fatal(FARGS
, "Can not set nstlist with the group cut-off scheme");
806 if (compatibleGpusFound(hwinfo
->gpu_info
))
808 GMX_LOG(mdlog
.warning
).asParagraph().appendText(
809 "NOTE: GPU(s) found, but the current simulation can not use GPUs\n"
810 " To use a GPU, set the mdp option: cutoff-scheme = Verlet");
811 tryUsePhysicalGpu
= false;
815 md_print_warn(cr
, fplog
,
816 "NOTE: There is no SIMD implementation of the group scheme kernels on\n"
817 " BlueGene/Q. You will observe better performance from using the\n"
818 " Verlet cut-off scheme.\n");
823 /* Check and update the hardware options for internal consistency */
824 check_and_update_hw_opt_1(&hw_opt
, cr
, npme
);
826 /* Early check for externally set process affinity. */
827 gmx_check_thread_affinity_set(mdlog
, cr
,
828 &hw_opt
, hwinfo
->nthreads_hw_avail
, FALSE
);
833 if (npme
> 0 && hw_opt
.nthreads_tmpi
<= 0)
835 gmx_fatal(FARGS
, "You need to explicitly specify the number of MPI threads (-ntmpi) when using separate PME ranks");
838 /* Since the master knows the cut-off scheme, update hw_opt for this.
839 * This is done later for normal MPI and also once more with tMPI
840 * for all tMPI ranks.
842 check_and_update_hw_opt_2(&hw_opt
, inputrec
->cutoff_scheme
);
844 // Determine how many thread-MPI ranks to start.
845 hw_opt
.nthreads_tmpi
= get_nthreads_mpi(hwinfo
,
847 userGpuTaskAssignment
,
852 // Now start the threads for thread MPI.
853 cr
= spawnThreads(hw_opt
.nthreads_tmpi
);
854 /* The main thread continues here with a new cr. We don't deallocate
855 the old cr because other threads may still be reading it. */
856 // TODO Both master and spawned threads call dup_tfn and
857 // reinitialize_commrec_for_this_thread. Find a way to express
861 /* END OF CAUTION: cr is now reliable */
865 /* now broadcast everything to the non-master nodes/threads: */
866 init_parallel(cr
, inputrec
, mtop
);
868 gmx_bcast_sim(sizeof(tryUsePhysicalGpu
), &tryUsePhysicalGpu
, cr
);
870 // TODO: Error handling
871 mdModules
.assignOptionsToModules(*inputrec
->params
, nullptr);
873 if (fplog
!= nullptr)
875 pr_inputrec(fplog
, 0, "Input Parameters", inputrec
, FALSE
);
876 fprintf(fplog
, "\n");
879 /* now make sure the state is initialized and propagated */
880 set_state_entries(state
, inputrec
);
882 /* A parallel command line option consistency check that we can
883 only do after any threads have started. */
885 (ddxyz
[XX
] > 1 || ddxyz
[YY
] > 1 || ddxyz
[ZZ
] > 1 || npme
> 0))
888 "The -dd or -npme option request a parallel simulation, "
890 "but %s was compiled without threads or MPI enabled"
893 "but the number of MPI-threads (option -ntmpi) is not set or is 1"
895 "but %s was not started through mpirun/mpiexec or only one rank was requested through mpirun/mpiexec"
898 , output_env_get_program_display_name(oenv
)
903 (EI_ENERGY_MINIMIZATION(inputrec
->eI
) || eiNM
== inputrec
->eI
))
905 gmx_fatal(FARGS
, "The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun");
908 if (can_use_allvsall(inputrec
, TRUE
, cr
, fplog
) && DOMAINDECOMP(cr
))
910 gmx_fatal(FARGS
, "All-vs-all loops do not work with domain decomposition, use a single MPI rank");
913 if (!(EEL_PME(inputrec
->coulombtype
) || EVDW_PME(inputrec
->vdwtype
)))
917 gmx_fatal_collective(FARGS
, cr
->mpi_comm_mysim
, MASTER(cr
),
918 "PME-only ranks are requested, but the system does not use PME for electrostatics or LJ");
924 if ((tryUsePhysicalGpu
|| forceUsePhysicalGpu
) && npme
< 0)
926 /* With GPUs we don't automatically use PME-only ranks. PME ranks can
927 * improve performance with many threads per GPU, since our OpenMP
928 * scaling is bad, but it's difficult to automate the setup.
936 fcRegisterSteps(inputrec
->nsteps
, inputrec
->init_step
);
940 /* NMR restraints must be initialized before load_checkpoint,
941 * since with time averaging the history is added to t_state.
942 * For proper consistency check we therefore need to extend
944 * So the PME-only nodes (if present) will also initialize
945 * the distance restraints.
949 /* This needs to be called before read_checkpoint to extend the state */
950 init_disres(fplog
, mtop
, inputrec
, cr
, fcd
, state
, replExParams
.exchangeInterval
> 0);
952 init_orires(fplog
, mtop
, as_rvec_array(state
->x
.data()), inputrec
, cr
, &(fcd
->orires
),
955 if (inputrecDeform(inputrec
))
957 /* Store the deform reference box before reading the checkpoint */
960 copy_mat(state
->box
, box
);
964 gmx_bcast(sizeof(box
), box
, cr
);
966 /* Because we do not have the update struct available yet
967 * in which the reference values should be stored,
968 * we store them temporarily in static variables.
969 * This should be thread safe, since they are only written once
970 * and with identical values.
972 tMPI_Thread_mutex_lock(&deform_init_box_mutex
);
973 deform_init_init_step_tpx
= inputrec
->init_step
;
974 copy_mat(box
, deform_init_box_tpx
);
975 tMPI_Thread_mutex_unlock(&deform_init_box_mutex
);
978 ObservablesHistory observablesHistory
= {};
980 if (Flags
& MD_STARTFROMCPT
)
982 /* Check if checkpoint file exists before doing continuation.
983 * This way we can use identical input options for the first and subsequent runs...
987 load_checkpoint(opt2fn_master("-cpi", nfile
, fnm
, cr
), &fplog
,
989 inputrec
, state
, &bReadEkin
, &observablesHistory
,
990 (Flags
& MD_APPENDFILES
),
991 (Flags
& MD_APPENDFILESSET
),
992 (Flags
& MD_REPRODUCIBLE
));
996 Flags
|= MD_READ_EKIN
;
1000 if (SIMMASTER(cr
) && (Flags
& MD_APPENDFILES
))
1002 gmx_log_open(ftp2fn(efLOG
, nfile
, fnm
), cr
,
1004 logOwner
= buildLogger(fplog
, nullptr);
1005 mdlog
= logOwner
.logger();
1008 /* override nsteps with value from cmdline */
1009 override_nsteps_cmdline(mdlog
, nsteps_cmdline
, inputrec
);
1013 copy_mat(state
->box
, box
);
1018 gmx_bcast(sizeof(box
), box
, cr
);
1021 if (PAR(cr
) && !(EI_TPI(inputrec
->eI
) ||
1022 inputrec
->eI
== eiNM
))
1024 cr
->dd
= init_domain_decomposition(fplog
, cr
, Flags
, ddxyz
, npme
,
1027 dddlb_opt
, dlb_scale
,
1028 ddcsx
, ddcsy
, ddcsz
,
1030 box
, as_rvec_array(state
->x
.data()),
1031 &ddbox
, &npme_major
, &npme_minor
);
1035 /* PME, if used, is done on all nodes with 1D decomposition */
1037 cr
->duty
= (DUTY_PP
| DUTY_PME
);
1041 if (inputrec
->ePBC
== epbcSCREW
)
1044 "pbc=%s is only implemented with domain decomposition",
1045 epbc_names
[inputrec
->ePBC
]);
1051 /* After possible communicator splitting in make_dd_communicators.
1052 * we can set up the intra/inter node communication.
1054 gmx_setup_nodecomm(fplog
, cr
);
1057 /* Initialize per-physical-node MPI process/thread ID and counters. */
1058 gmx_init_intranode_counters(cr
);
1062 GMX_LOG(mdlog
.warning
).asParagraph().appendTextFormatted(
1063 "This is simulation %d out of %d running as a composite GROMACS\n"
1064 "multi-simulation job. Setup for this simulation:\n",
1065 cr
->ms
->sim
, cr
->ms
->nsim
);
1067 GMX_LOG(mdlog
.warning
).appendTextFormatted(
1068 "Using %d MPI %s\n",
1071 cr
->nnodes
== 1 ? "thread" : "threads"
1073 cr
->nnodes
== 1 ? "process" : "processes"
1079 /* Check and update hw_opt for the cut-off scheme */
1080 check_and_update_hw_opt_2(&hw_opt
, inputrec
->cutoff_scheme
);
1082 /* Check and update hw_opt for the number of MPI ranks */
1083 check_and_update_hw_opt_3(&hw_opt
);
1085 gmx_omp_nthreads_init(mdlog
, cr
,
1086 hwinfo
->nthreads_hw_avail
,
1087 hw_opt
.nthreads_omp
,
1088 hw_opt
.nthreads_omp_pme
,
1089 (cr
->duty
& DUTY_PP
) == 0,
1090 inputrec
->cutoff_scheme
== ecutsVERLET
);
1093 if (EI_TPI(inputrec
->eI
) &&
1094 inputrec
->cutoff_scheme
== ecutsVERLET
)
1096 gmx_feenableexcept();
1100 // Contains the ID of the GPU used by each PP rank on this node,
1101 // indexed by that rank. Empty if no GPUs are selected for use on
1103 std::vector
<int> gpuTaskAssignment
;
1104 if (tryUsePhysicalGpu
|| forceUsePhysicalGpu
)
1106 /* Currently the DD code assigns duty to ranks that can
1107 * include PP work that currently can be executed on a single
1108 * GPU, if present and compatible. This has to be coordinated
1109 * across PP ranks on a node, with possible multiple devices
1110 * or sharing devices on a node, either from the user
1111 * selection, or automatically. */
1112 bool rankCanUseGpu
= cr
->duty
& DUTY_PP
;
1113 gpuTaskAssignment
= mapPpRanksToGpus(rankCanUseGpu
, cr
, hwinfo
->gpu_info
,
1114 userGpuTaskAssignment
);
1117 /* If we are using GPUs, report on this rank how they are being
1118 * used on this node. */
1119 if (!gpuTaskAssignment
.empty())
1121 auto gpuUsageReport
=
1122 makeGpuUsageReport(hwinfo
->gpu_info
, !userGpuTaskAssignment
.empty(),
1123 gpuTaskAssignment
, cr
->nrank_pp_intranode
,
1126 /* NOTE: this print is only for and on one physical node */
1127 GMX_LOG(mdlog
.warning
).appendText(gpuUsageReport
);
1130 /* check consistency across ranks of things like SIMD
1131 * support and number of GPUs selected */
1132 gmx_check_hw_runconf_consistency(mdlog
, hwinfo
, cr
, hw_opt
, !userGpuTaskAssignment
.empty(), gpuTaskAssignment
);
1133 /* From now on, the userGpuTaskAssignment should never be used */
1135 /* Prevent other ranks from continuing after an inconsistency was found.
1137 * TODO This function implements a barrier so that MPI runtimes
1138 * can organize an orderly shutdown if one of the ranks has had to
1139 * issue a fatal error in various code already run. When we have
1140 * MPI-aware error handling and reporting, this should be
1145 MPI_Barrier(cr
->mpi_comm_mysim
);
1149 /* Now that we know the setup is consistent, check for efficiency */
1150 check_resource_division_efficiency(hwinfo
, hw_opt
.nthreads_tot
, !gpuTaskAssignment
.empty(), Flags
& MD_NTOMPSET
,
1153 gmx_device_info_t
*shortRangedDeviceInfo
= nullptr;
1154 int shortRangedDeviceId
= -1;
1155 if (cr
->duty
& DUTY_PP
)
1157 if (!gpuTaskAssignment
.empty())
1159 shortRangedDeviceId
= gpuTaskAssignment
[cr
->rank_pp_intranode
];
1160 shortRangedDeviceInfo
= getDeviceInfo(hwinfo
->gpu_info
, shortRangedDeviceId
);
1164 if (DOMAINDECOMP(cr
))
1166 /* When we share GPUs over ranks, we need to know this for the DLB */
1167 dd_setup_dlb_resource_sharing(cr
, shortRangedDeviceId
);
1170 /* getting number of PP/PME threads
1171 PME: env variable should be read only on one node to make sure it is
1172 identical everywhere;
1174 nthreads_pme
= gmx_omp_nthreads_get(emntPME
);
1176 wcycle
= wallcycle_init(fplog
, resetstep
, cr
);
1180 /* Master synchronizes its value of reset_counters with all nodes
1181 * including PME only nodes */
1182 reset_counters
= wcycle_get_reset_counters(wcycle
);
1183 gmx_bcast_sim(sizeof(reset_counters
), &reset_counters
, cr
);
1184 wcycle_set_reset_counters(wcycle
, reset_counters
);
1187 // Membrane embedding must be initialized before we call init_forcerec()
1192 fprintf(stderr
, "Initializing membed");
1194 /* Note that membed cannot work in parallel because mtop is
1195 * changed here. Fix this if we ever want to make it run with
1196 * multiple ranks. */
1197 membed
= init_membed(fplog
, nfile
, fnm
, mtop
, inputrec
, state
, cr
, &cpt_period
);
1201 if (cr
->duty
& DUTY_PP
)
1203 bcast_state(cr
, state
);
1205 /* Initiate forcerecord */
1207 fr
->forceProviders
= mdModules
.initForceProviders();
1208 init_forcerec(fplog
, mdlog
, fr
, fcd
,
1209 inputrec
, mtop
, cr
, box
,
1210 opt2fn("-table", nfile
, fnm
),
1211 opt2fn("-tablep", nfile
, fnm
),
1212 getFilenm("-tableb", nfile
, fnm
),
1214 shortRangedDeviceInfo
,
1218 /* Initialize QM-MM */
1221 init_QMMMrec(cr
, mtop
, inputrec
, fr
);
1224 /* Initialize the mdatoms structure.
1225 * mdatoms is not filled with atom data,
1226 * as this can not be done now with domain decomposition.
1228 mdatoms
= init_mdatoms(fplog
, mtop
, inputrec
->efep
!= efepNO
);
1230 /* Initialize the virtual site communication */
1231 vsite
= init_vsite(mtop
, cr
, FALSE
);
1233 calc_shifts(box
, fr
->shift_vec
);
1235 /* With periodic molecules the charge groups should be whole at start up
1236 * and the virtual sites should not be far from their proper positions.
1238 if (!inputrec
->bContinuation
&& MASTER(cr
) &&
1239 !(inputrec
->ePBC
!= epbcNONE
&& inputrec
->bPeriodicMols
))
1241 /* Make molecules whole at start of run */
1242 if (fr
->ePBC
!= epbcNONE
)
1244 do_pbc_first_mtop(fplog
, inputrec
->ePBC
, box
, mtop
, as_rvec_array(state
->x
.data()));
1248 /* Correct initial vsite positions are required
1249 * for the initial distribution in the domain decomposition
1250 * and for the initial shell prediction.
1252 construct_vsites_mtop(vsite
, mtop
, as_rvec_array(state
->x
.data()));
1256 if (EEL_PME(fr
->eeltype
) || EVDW_PME(fr
->vdwtype
))
1258 ewaldcoeff_q
= fr
->ewaldcoeff_q
;
1259 ewaldcoeff_lj
= fr
->ewaldcoeff_lj
;
1260 pmedata
= &fr
->pmedata
;
1269 /* This is a PME only node */
1271 /* We don't need the state */
1272 stateInstance
.reset();
1275 ewaldcoeff_q
= calc_ewaldcoeff_q(inputrec
->rcoulomb
, inputrec
->ewald_rtol
);
1276 ewaldcoeff_lj
= calc_ewaldcoeff_lj(inputrec
->rvdw
, inputrec
->ewald_rtol_lj
);
1280 if (hw_opt
.thread_affinity
!= threadaffOFF
)
1282 /* Before setting affinity, check whether the affinity has changed
1283 * - which indicates that probably the OpenMP library has changed it
1284 * since we first checked).
1286 gmx_check_thread_affinity_set(mdlog
, cr
,
1287 &hw_opt
, hwinfo
->nthreads_hw_avail
, TRUE
);
1290 /* threads on this MPI process or TMPI thread */
1291 if (cr
->duty
& DUTY_PP
)
1293 nthread_local
= gmx_omp_nthreads_get(emntNonbonded
);
1297 nthread_local
= gmx_omp_nthreads_get(emntPME
);
1300 /* Set the CPU affinity */
1301 gmx_set_thread_affinity(mdlog
, cr
, &hw_opt
, *hwinfo
->hardwareTopology
,
1302 nthread_local
, nullptr);
1305 /* Initiate PME if necessary,
1306 * either on all nodes or on dedicated PME nodes only. */
1307 if (EEL_PME(inputrec
->coulombtype
) || EVDW_PME(inputrec
->vdwtype
))
1311 nChargePerturbed
= mdatoms
->nChargePerturbed
;
1312 if (EVDW_PME(inputrec
->vdwtype
))
1314 nTypePerturbed
= mdatoms
->nTypePerturbed
;
1317 if (cr
->npmenodes
> 0)
1319 /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
1320 gmx_bcast_sim(sizeof(nChargePerturbed
), &nChargePerturbed
, cr
);
1321 gmx_bcast_sim(sizeof(nTypePerturbed
), &nTypePerturbed
, cr
);
1324 if (cr
->duty
& DUTY_PME
)
1328 status
= gmx_pme_init(pmedata
, cr
, npme_major
, npme_minor
, inputrec
,
1329 mtop
? mtop
->natoms
: 0, nChargePerturbed
, nTypePerturbed
,
1330 (Flags
& MD_REPRODUCIBLE
),
1331 ewaldcoeff_q
, ewaldcoeff_lj
,
1334 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
;
1337 gmx_fatal(FARGS
, "Error %d initializing PME", status
);
1343 if (EI_DYNAMICS(inputrec
->eI
))
1345 /* Turn on signal handling on all nodes */
1347 * (A user signal from the PME nodes (if any)
1348 * is communicated to the PP nodes.
1350 signal_handler_install();
1353 if (cr
->duty
& DUTY_PP
)
1355 /* Assumes uniform use of the number of OpenMP threads */
1356 walltime_accounting
= walltime_accounting_init(gmx_omp_nthreads_get(emntDefault
));
1358 if (inputrec
->bPull
)
1360 /* Initialize pull code */
1361 inputrec
->pull_work
=
1362 init_pull(fplog
, inputrec
->pull
, inputrec
, nfile
, fnm
,
1363 mtop
, cr
, oenv
, inputrec
->fepvals
->init_lambda
,
1364 EI_DYNAMICS(inputrec
->eI
) && MASTER(cr
), Flags
);
1369 /* Initialize enforced rotation code */
1370 init_rot(fplog
, inputrec
, nfile
, fnm
, cr
, as_rvec_array(state
->x
.data()), state
->box
, mtop
, oenv
,
1374 /* Let init_constraints know whether we have essential dynamics constraints.
1375 * TODO: inputrec should tell us whether we use an algorithm, not a file option or the checkpoint
1377 bool doEdsam
= (opt2fn_null("-ei", nfile
, fnm
) != nullptr || observablesHistory
.edsamHistory
);
1379 constr
= init_constraints(fplog
, mtop
, inputrec
, doEdsam
, cr
);
1381 if (DOMAINDECOMP(cr
))
1383 GMX_RELEASE_ASSERT(fr
, "fr was NULL while cr->duty was DUTY_PP");
1384 /* This call is not included in init_domain_decomposition mainly
1385 * because fr->cginfo_mb is set later.
1387 dd_init_bondeds(fplog
, cr
->dd
, mtop
, vsite
, inputrec
,
1388 Flags
& MD_DDBONDCHECK
, fr
->cginfo_mb
);
1391 /* Now do whatever the user wants us to do (how flexible...) */
1392 my_integrator(inputrec
->eI
) (fplog
, cr
, mdlog
, nfile
, fnm
,
1396 nstepout
, mdModules
.outputProvider(),
1398 fcd
, state
, &observablesHistory
,
1399 mdatoms
, nrnb
, wcycle
, fr
,
1402 cpt_period
, max_hours
,
1405 walltime_accounting
);
1409 finish_rot(inputrec
->rot
);
1412 if (inputrec
->bPull
)
1414 finish_pull(inputrec
->pull_work
);
1420 GMX_RELEASE_ASSERT(pmedata
, "pmedata was NULL while cr->duty was not DUTY_PP");
1422 walltime_accounting
= walltime_accounting_init(gmx_omp_nthreads_get(emntPME
));
1423 gmx_pmeonly(*pmedata
, cr
, nrnb
, wcycle
, walltime_accounting
, ewaldcoeff_q
, ewaldcoeff_lj
, inputrec
);
1426 wallcycle_stop(wcycle
, ewcRUN
);
1428 /* Finish up, write some stuff
1429 * if rerunMD, don't write last frame again
1431 finish_run(fplog
, mdlog
, cr
,
1432 inputrec
, nrnb
, wcycle
, walltime_accounting
,
1433 fr
? fr
->nbv
: nullptr,
1434 EI_DYNAMICS(inputrec
->eI
) && !MULTISIM(cr
));
1439 gmx_pme_destroy(*pmedata
); // TODO: pmedata is always a single element list, refactor
1443 /* Free GPU memory and context */
1444 free_gpu_resources(fr
, cr
, shortRangedDeviceInfo
);
1448 free_membed(membed
);
1451 gmx_hardware_info_free(hwinfo
);
1453 /* Does what it says */
1454 print_date_and_time(fplog
, cr
->nodeid
, "Finished mdrun", gmx_gettime());
1455 walltime_accounting_destroy(walltime_accounting
);
1457 /* Close logfile already here if we were appending to it */
1458 if (MASTER(cr
) && (Flags
& MD_APPENDFILES
))
1460 gmx_log_close(fplog
);
1463 rc
= (int)gmx_get_stop_condition();
1466 /* we need to join all threads. The sub-threads join when they
1467 exit this function, but the master thread needs to be told to
1469 if (PAR(cr
) && MASTER(cr
))